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Sample records for protein-ligand interactions obtained

  1. Statistical Estimation of the Protein-Ligand Binding Free Energy Based On Direct Protein-Ligand Interaction Obtained by Molecular Dynamics Simulation

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    Haruki Nakamura

    2012-09-01

    Full Text Available We have developed a method for estimating protein-ligand binding free energy (DG based on the direct protein-ligand interaction obtained by a molecular dynamics simulation. Using this method, we estimated the DG value statistically by the average values of the van der Waals and electrostatic interactions between each amino acid of the target protein and the ligand molecule. In addition, we introduced fluctuations in the accessible surface area (ASA and dihedral angles of the protein-ligand complex system as the entropy terms of the DG estimation. The present method included the fluctuation term of structural change of the protein and the effective dielectric constant. We applied this method to 34 protein-ligand complex structures. As a result, the correlation coefficient between the experimental and calculated DG values was 0.81, and the average error of DG was 1.2 kcal/mol with the use of the fixed parameters. These results were obtained from a 2 nsec molecular dynamics simulation.

  2. Exact and Effective Pair-Wise Potential for Protein-Ligand Interactions Obtained from a Semiempirical Energy Partition

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    André Melo

    2008-09-01

    Full Text Available In this work, the partition method introduced by Carvalho and Melo was used to study the complex between Cucurbita maxima trypsin inhibitor (CMTI-I and glycerol at the AM1 level. An effective potential, combining non-bonding and polarization plus charge transfer (PLCT terms, was introduced to evaluate the magnitude of the interaction between each amino acid and the ligand. In this case study, the nonbonding–PLCT noncompensation characterizes the stabilization energy of the association process in study. The main residues (Gly29, Cys3 and Arg5 with net attractive effects and Arg1 (with a net repulsive effect, responsible by the stability of protein-ligand complex, are associated with large nonbonding energies non-compensated by PLCT effects. The results obtained enable us to conclude that the present decomposition scheme can be used for understanding the cohesive phenomena in proteins.

  3. Quantitative analysis of protein-ligand interactions by NMR.

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    Furukawa, Ayako; Konuma, Tsuyoshi; Yanaka, Saeko; Sugase, Kenji

    2016-08-01

    Protein-ligand interactions have been commonly studied through static structures of the protein-ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein-ligand interactions both for fundamental understanding of the underlying mechanisms and for drug development. NMR is a versatile and powerful tool, especially because it provides site-specific quantitative information. NMR has widely been used to determine the dissociation constant (KD), in particular, for relatively weak interactions. The simplest NMR method is a chemical-shift titration experiment, in which the chemical-shift changes of a protein in response to ligand titration are measured. There are other quantitative NMR methods, but they mostly apply only to interactions in the fast-exchange regime. These methods derive the dissociation constant from population-averaged NMR quantities of the free and bound states of a protein or ligand. In contrast, the recent advent of new relaxation-based experiments, including R2 relaxation dispersion and ZZ-exchange, has enabled us to obtain kinetic information on protein-ligand interactions in the intermediate- and slow-exchange regimes. Based on R2 dispersion or ZZ-exchange, methods that can determine the association rate, kon, dissociation rate, koff, and KD have been developed. In these approaches, R2 dispersion or ZZ-exchange curves are measured for multiple samples with different protein and/or ligand concentration ratios, and the relaxation data are fitted to theoretical kinetic models. It is critical to choose an appropriate kinetic model, such as the two- or three-state exchange model, to derive the correct kinetic information. The R2 dispersion and ZZ-exchange methods are suitable for the analysis of protein-ligand interactions with a micromolar or sub-micromolar dissociation constant but not for very weak interactions, which are typical in very fast exchange. This contrasts with the NMR methods that are used

  4. Quantitative chemogenomics: machine-learning models of protein-ligand interaction.

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    Andersson, Claes R; Gustafsson, Mats G; Strömbergsson, Helena

    2011-01-01

    Chemogenomics is an emerging interdisciplinary field that lies in the interface of biology, chemistry, and informatics. Most of the currently used drugs are small molecules that interact with proteins. Understanding protein-ligand interaction is therefore central to drug discovery and design. In the subfield of chemogenomics known as proteochemometrics, protein-ligand-interaction models are induced from data matrices that consist of both protein and ligand information along with some experimentally measured variable. The two general aims of this quantitative multi-structure-property-relationship modeling (QMSPR) approach are to exploit sparse/incomplete information sources and to obtain more general models covering larger parts of the protein-ligand space, than traditional approaches that focuses mainly on specific targets or ligands. The data matrices, usually obtained from multiple sparse/incomplete sources, typically contain series of proteins and ligands together with quantitative information about their interactions. A useful model should ideally be easy to interpret and generalize well to new unseen protein-ligand combinations. Resolving this requires sophisticated machine-learning methods for model induction, combined with adequate validation. This review is intended to provide a guide to methods and data sources suitable for this kind of protein-ligand-interaction modeling. An overview of the modeling process is presented including data collection, protein and ligand descriptor computation, data preprocessing, machine-learning-model induction and validation. Concerns and issues specific for each step in this kind of data-driven modeling will be discussed. © 2011 Bentham Science Publishers

  5. Protein-Ligand Empirical Interaction Components for Virtual Screening.

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    Yan, Yuna; Wang, Weijun; Sun, Zhaoxi; Zhang, John Z H; Ji, Changge

    2017-08-28

    A major shortcoming of empirical scoring functions is that they often fail to predict binding affinity properly. Removing false positives of docking results is one of the most challenging works in structure-based virtual screening. Postdocking filters, making use of all kinds of experimental structure and activity information, may help in solving the issue. We describe a new method based on detailed protein-ligand interaction decomposition and machine learning. Protein-ligand empirical interaction components (PLEIC) are used as descriptors for support vector machine learning to develop a classification model (PLEIC-SVM) to discriminate false positives from true positives. Experimentally derived activity information is used for model training. An extensive benchmark study on 36 diverse data sets from the DUD-E database has been performed to evaluate the performance of the new method. The results show that the new method performs much better than standard empirical scoring functions in structure-based virtual screening. The trained PLEIC-SVM model is able to capture important interaction patterns between ligand and protein residues for one specific target, which is helpful in discarding false positives in postdocking filtering.

  6. THERMODYNAMICS OF PROTEIN-LIGAND INTERACTIONS AND THEIR ANALYSIS

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    Rummi Devi Saini

    2017-11-01

    Full Text Available Physiological processes are controlled mainly by intermolecular recognition mechanisms which involve protein–protein and protein–ligand interactions with a high specificity and affinity to form a specific complex. Proteins being an important class of macromolecules in biological systems, it is important to understand their actions through binding to other molecules of proteins or ligands. In fact, the binding of low molecular weight ligands to proteins plays a significant role in regulating biological processes such as cellular metabolism and signal transmission. Therefore knowledge of the protein–ligand interactions and the knowledge of the mechanisms involved in the protein-ligand recognition and binding are key in understanding biology at molecular level which will facilitate the discovery, design, and development of drugs. In this review, the mechanisms involved in protein–ligand binding, the binding kinetics, thermodynamic concepts and binding driving forces are discussed. Thermodynamic mechanisms involved in a few important protein-ligand binding are described. Various spectroscopic, non-spectroscopic and computational method for analysis of protein–ligand binding are also discussed.

  7. Physics-based scoring of protein-ligand interactions: explicit polarizability, quantum mechanics and free energies.

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    Bryce, Richard A

    2011-04-01

    The ability to accurately predict the interaction of a ligand with its receptor is a key limitation in computer-aided drug design approaches such as virtual screening and de novo design. In this article, we examine current strategies for a physics-based approach to scoring of protein-ligand affinity, as well as outlining recent developments in force fields and quantum chemical techniques. We also consider advances in the development and application of simulation-based free energy methods to study protein-ligand interactions. Fuelled by recent advances in computational algorithms and hardware, there is the opportunity for increased integration of physics-based scoring approaches at earlier stages in computationally guided drug discovery. Specifically, we envisage increased use of implicit solvent models and simulation-based scoring methods as tools for computing the affinities of large virtual ligand libraries. Approaches based on end point simulations and reference potentials allow the application of more advanced potential energy functions to prediction of protein-ligand binding affinities. Comprehensive evaluation of polarizable force fields and quantum mechanical (QM)/molecular mechanical and QM methods in scoring of protein-ligand interactions is required, particularly in their ability to address challenging targets such as metalloproteins and other proteins that make highly polar interactions. Finally, we anticipate increasingly quantitative free energy perturbation and thermodynamic integration methods that are practical for optimization of hits obtained from screened ligand libraries.

  8. Force spectroscopy studies on protein-ligand interactions: a single protein mechanics perspective.

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    Hu, Xiaotang; Li, Hongbin

    2014-10-01

    Protein-ligand interactions are ubiquitous and play important roles in almost every biological process. The direct elucidation of the thermodynamic, structural and functional consequences of protein-ligand interactions is thus of critical importance to decipher the mechanism underlying these biological processes. A toolbox containing a variety of powerful techniques has been developed to quantitatively study protein-ligand interactions in vitro as well as in living systems. The development of atomic force microscopy-based single molecule force spectroscopy techniques has expanded this toolbox and made it possible to directly probe the mechanical consequence of ligand binding on proteins. Many recent experiments have revealed how ligand binding affects the mechanical stability and mechanical unfolding dynamics of proteins, and provided mechanistic understanding on these effects. The enhancement effect of mechanical stability by ligand binding has been used to help tune the mechanical stability of proteins in a rational manner and develop novel functional binding assays for protein-ligand interactions. Single molecule force spectroscopy studies have started to shed new lights on the structural and functional consequence of ligand binding on proteins that bear force under their biological settings. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  9. Intuitive Density Functional Theory-Based Energy Decomposition Analysis for Protein-Ligand Interactions.

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    Phipps, M J S; Fox, T; Tautermann, C S; Skylaris, C-K

    2017-04-11

    First-principles quantum mechanical calculations with methods such as density functional theory (DFT) allow the accurate calculation of interaction energies between molecules. These interaction energies can be dissected into chemically relevant components such as electrostatics, polarization, and charge transfer using energy decomposition analysis (EDA) approaches. Typically EDA has been used to study interactions between small molecules; however, it has great potential to be applied to large biomolecular assemblies such as protein-protein and protein-ligand interactions. We present an application of EDA calculations to the study of ligands that bind to the thrombin protein, using the ONETEP program for linear-scaling DFT calculations. Our approach goes beyond simply providing the components of the interaction energy; we are also able to provide visual representations of the changes in density that happen as a result of polarization and charge transfer, thus pinpointing the functional groups between the ligand and protein that participate in each kind of interaction. We also demonstrate with this approach that we can focus on studying parts (fragments) of ligands. The method is relatively insensitive to the protocol that is used to prepare the structures, and the results obtained are therefore robust. This is an application to a real protein drug target of a whole new capability where accurate DFT calculations can produce both energetic and visual descriptors of interactions. These descriptors can be used to provide insights for tailoring interactions, as needed for example in drug design.

  10. iview: an interactive WebGL visualizer for protein-ligand complex.

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    Li, Hongjian; Leung, Kwong-Sak; Nakane, Takanori; Wong, Man-Hon

    2014-02-25

    Visualization of protein-ligand complex plays an important role in elaborating protein-ligand interactions and aiding novel drug design. Most existing web visualizers either rely on slow software rendering, or lack virtual reality support. The vital feature of macromolecular surface construction is also unavailable. We have developed iview, an easy-to-use interactive WebGL visualizer of protein-ligand complex. It exploits hardware acceleration rather than software rendering. It features three special effects in virtual reality settings, namely anaglyph, parallax barrier and oculus rift, resulting in visually appealing identification of intermolecular interactions. It supports four surface representations including Van der Waals surface, solvent excluded surface, solvent accessible surface and molecular surface. Moreover, based on the feature-rich version of iview, we have also developed a neat and tailor-made version specifically for our istar web platform for protein-ligand docking purpose. This demonstrates the excellent portability of iview. Using innovative 3D techniques, we provide a user friendly visualizer that is not intended to compete with professional visualizers, but to enable easy accessibility and platform independence.

  11. NMR Studies of Protein Hydration and Protein-Ligand Interactions

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    Chong, Yuan

    Water on the surface of a protein is called hydration water. Hydration water is known to play a crucial role in a variety of biological processes including protein folding, enzymatic activation, and drug binding. Although the significance of hydration water has been recognized, the underlying mechanism remains far from being understood. This dissertation employs a unique in-situ nuclear magnetic resonance (NMR) technique to study the mechanism of protein hydration and the role of hydration in alcohol-protein interactions. Water isotherms in proteins are measured at different temperatures via the in-situ NMR technique. Water is found to interact differently with hydrophilic and hydrophobic groups on the protein. Water adsorption on hydrophilic groups is hardly affected by the temperature, while water adsorption on hydrophobic groups strongly depends on the temperature around 10 C, below which the adsorption is substantially reduced. This effect is induced by the dramatic decrease in the protein flexibility below 10 C. Furthermore, nanosecond to microsecond protein dynamics and the free energy, enthalpy, and entropy of protein hydration are studied as a function of hydration level and temperature. A crossover at 10 C in protein dynamics and thermodynamics is revealed. The effect of water at hydrophilic groups on protein dynamics and thermodynamics shows little temperature dependence, whereas water at hydrophobic groups has stronger effect above 10 C. In addition, I investigate the role of water in alcohol binding to the protein using the in-situ NMR detection. The isotherms of alcohols are first measured on dry proteins, then on proteins with a series of controlled hydration levels. The free energy, enthalpy, and entropy of alcohol binding are also determined. Two distinct types of alcohol binding are identified. On the one hand, alcohols can directly bind to a few specific sites on the protein. This type of binding is independent of temperature and can be

  12. Simple knowledge-based descriptors to predict protein-ligand interactions. Methodology and validation

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    Nissink, J. Willem M.; Verdonk, Marcel L.; Klebe, Gerhard

    2000-11-01

    A new type of shape descriptor is proposed to describe the spatial orientation for non-covalent interactions. It is built from simple, anisotropic Gaussian contributions that are parameterised by 10 adjustable values. The descriptors have been used to fit propensity distributions derived from scatter data stored in the IsoStar database. This database holds composite pictures of possible interaction geometries between a common central group and various interacting moieties, as extracted from small-molecule crystal structures. These distributions can be related to probabilities for the occurrence of certain interaction geometries among different functional groups. A fitting procedure is described that generates the descriptors in a fully automated way. For this purpose, we apply a similarity index that is tailored to the problem, the Split Hodgkin Index. It accounts for the similarity in regions of either high or low propensity in a separate way. Although dependent on the division into these two subregions, the index is robust and performs better than the regular Hodgkin index. The reliability and coverage of the fitted descriptors was assessed using SuperStar. SuperStar usually operates on the raw IsoStar data to calculate propensity distributions, e.g., for a binding site in a protein. For our purpose we modified the code to have it operate on our descriptors instead. This resulted in a substantial reduction in calculation time (factor of five to eight) compared to the original implementation. A validation procedure was performed on a set of 130 protein-ligand complexes, using four representative interacting probes to map the properties of the various binding sites: ammonium nitrogen, alcohol oxygen, carbonyl oxygen, and methyl carbon. The predicted `hot spots' for the binding of these probes were compared to the actual arrangement of ligand atoms in experimentally determined protein-ligand complexes. Results indicate that the version of SuperStar that applies to

  13. Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein-Ligand Binding Free Energy.

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    Duan, Lili; Liu, Xiao; Zhang, John Z H

    2016-05-04

    Efficient and reliable calculation of protein-ligand binding free energy is a grand challenge in computational biology and is of critical importance in drug design and many other molecular recognition problems. The main challenge lies in the calculation of entropic contribution to protein-ligand binding or interaction systems. In this report, we present a new interaction entropy method which is theoretically rigorous, computationally efficient, and numerically reliable for calculating entropic contribution to free energy in protein-ligand binding and other interaction processes. Drastically different from the widely employed but extremely expensive normal mode method for calculating entropy change in protein-ligand binding, the new method calculates the entropic component (interaction entropy or -TΔS) of the binding free energy directly from molecular dynamics simulation without any extra computational cost. Extensive study of over a dozen randomly selected protein-ligand binding systems demonstrated that this interaction entropy method is both computationally efficient and numerically reliable and is vastly superior to the standard normal mode approach. This interaction entropy paradigm introduces a novel and intuitive conceptual understanding of the entropic effect in protein-ligand binding and other general interaction systems as well as a practical method for highly efficient calculation of this effect.

  14. Forging the Basis for Developing Protein-Ligand Interaction Scoring Functions.

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    Liu, Zhihai; Su, Minyi; Han, Li; Liu, Jie; Yang, Qifan; Li, Yan; Wang, Renxiao

    2017-02-21

    In structure-based drug design, scoring functions are widely used for fast evaluation of protein-ligand interactions. They are often applied in combination with molecular docking and de novo design methods. Since the early 1990s, a whole spectrum of protein-ligand interaction scoring functions have been developed. Regardless of their technical difference, scoring functions all need data sets combining protein-ligand complex structures and binding affinity data for parametrization and validation. However, data sets of this kind used to be rather limited in terms of size and quality. On the other hand, standard metrics for evaluating scoring function used to be ambiguous. Scoring functions are often tested in molecular docking or even virtual screening trials, which do not directly reflect the genuine quality of scoring functions. Collectively, these underlying obstacles have impeded the invention of more advanced scoring functions. In this Account, we describe our long-lasting efforts to overcome these obstacles, which involve two related projects. On the first project, we have created the PDBbind database. It is the first database that systematically annotates the protein-ligand complexes in the Protein Data Bank (PDB) with experimental binding data. This database has been updated annually since its first public release in 2004. The latest release (version 2016) provides binding data for 16 179 biomolecular complexes in PDB. Data sets provided by PDBbind have been applied to many computational and statistical studies on protein-ligand interaction and various subjects. In particular, it has become a major data resource for scoring function development. On the second project, we have established the Comparative Assessment of Scoring Functions (CASF) benchmark for scoring function evaluation. Our key idea is to decouple the "scoring" process from the "sampling" process, so scoring functions can be tested in a relatively pure context to reflect their quality. In our

  15. Descriptor Data Bank (DDB): A Cloud Platform for Multiperspective Modeling of Protein-Ligand Interactions.

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    Ashtawy, Hossam M; Mahapatra, Nihar R

    2018-01-22

    Protein-ligand (PL) interactions play a key role in many life processes such as molecular recognition, molecular binding, signal transmission, and cell metabolism. Examples of interaction forces include hydrogen bonding, hydrophobic effects, steric clashes, electrostatic contacts, and van der Waals attractions. Currently, a large number of hypotheses and perspectives to model these interaction forces are scattered throughout the literature and largely forgotten. Instead, had they been assembled and utilized collectively, they would have substantially improved the accuracy of predicting binding affinity of protein-ligand complexes. In this work, we present Descriptor Data Bank (DDB), a data-driven platform on the cloud for facilitating multiperspective modeling of PL interactions. DDB is an open-access hub for depositing, hosting, executing, and sharing descriptor extraction tools and data for a large number of interaction modeling hypotheses. The platform also implements a machine-learning (ML) toolbox for automatic descriptor filtering and analysis and scoring function (SF) fitting and prediction. The descriptor filtering module is used to filter out irrelevant and/or noisy descriptors and to produce a compact subset from all available features. We seed DDB with 16 diverse descriptor extraction tools developed in-house and collected from the literature. The tools altogether generate over 2700 descriptors that characterize (i) proteins, (ii) ligands, and (iii) protein-ligand complexes. The in-house descriptors we extract are protein-specific which are based on pairwise primary and tertiary alignment of protein structures followed by clustering and trilateration. We built and used DDB's ML library to fit SFs to the in-house descriptors and those collected from the literature. We then evaluated them on several data sets that were constructed to reflect real-world drug screening scenarios. We found that multiperspective SFs that were constructed using a large number

  16. Recent Progress in Treating Protein-Ligand Interactions with Quantum-Mechanical Methods.

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    Yilmazer, Nusret Duygu; Korth, Martin

    2016-05-16

    We review the first successes and failures of a "new wave" of quantum chemistry-based approaches to the treatment of protein/ligand interactions. These approaches share the use of "enhanced", dispersion (D), and/or hydrogen-bond (H) corrected density functional theory (DFT) or semi-empirical quantum mechanical (SQM) methods, in combination with ensemble weighting techniques of some form to capture entropic effects. Benchmark and model system calculations in comparison to high-level theoretical as well as experimental references have shown that both DFT-D (dispersion-corrected density functional theory) and SQM-DH (dispersion and hydrogen bond-corrected semi-empirical quantum mechanical) perform much more accurately than older DFT and SQM approaches and also standard docking methods. In addition, DFT-D might soon become and SQM-DH already is fast enough to compute a large number of binding modes of comparably large protein/ligand complexes, thus allowing for a more accurate assessment of entropic effects.

  17. A method for fast energy estimation and visualization of protein-ligand interaction

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    Tomioka, Nobuo; Itai, Akiko; Iitaka, Yoichi

    1987-10-01

    A new computational and graphical method for facilitating ligand-protein docking studies is developed on a three-dimensional computer graphics display. Various physical and chemical properties inside the ligand binding pocket of a receptor protein, whose structure is elucidated by X-ray crystal analysis, are calculated on three-dimensional grid points and are stored in advance. By utilizing those tabulated data, it is possible to estimate the non-bonded and electrostatic interaction energy and the number of possible hydrogen bonds between protein and ligand molecules in real time during an interactive docking operation. The method also provides a comprehensive visualization of the local environment inside the binding pocket. With this method, it becomes easier to find a roughly stable geometry of ligand molecules, and one can therefore make a rapid survey of the binding capability of many drug candidates. The method will be useful for drug design as well as for the examination of protein-ligand interactions.

  18. Accuracy and precision of protein-ligand interaction kinetics determined from chemical shift titrations

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    Markin, Craig J.; Spyracopoulos, Leo, E-mail: leo.spyracopoulos@ualberta.ca [University of Alberta, Department of Biochemistry (Canada)

    2012-12-15

    NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K{sub D}) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K{sub D} value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of {sup 1}H-{sup 15}N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k{sub off}). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k{sub off} {approx} 3,000 s{sup -1} in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k{sub off} from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k{sub off} values over a wide range, from 100 to 15,000 s{sup -1}. The validity of line shape analysis for k{sub off} values approaching intermediate exchange ({approx}100 s{sup -1}), may be facilitated by

  19. Accuracy and precision of protein-ligand interaction kinetics determined from chemical shift titrations.

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    Markin, Craig J; Spyracopoulos, Leo

    2012-12-01

    NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K ( D )) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K ( D ) value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of (1)H-(15)N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k ( off )). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k ( off ) ~ 3,000 s(-1) in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k ( off ) from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k ( off ) values over a wide range, from 100 to 15,000 s(-1). The validity of line shape analysis for k ( off ) values approaching intermediate exchange (~100 s(-1)), may be facilitated by more accurate K ( D ) measurements

  20. Protein-ligand interactions investigated by thermal shift assays (TSA) and dual polarization interferometry (DPI).

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    Grøftehauge, Morten K; Hajizadeh, Nelly R; Swann, Marcus J; Pohl, Ehmke

    2015-01-01

    Over the last decades, a wide range of biophysical techniques investigating protein-ligand interactions have become indispensable tools to complement high-resolution crystal structure determinations. Current approaches in solution range from high-throughput-capable methods such as thermal shift assays (TSA) to highly accurate techniques including microscale thermophoresis (MST) and isothermal titration calorimetry (ITC) that can provide a full thermodynamic description of binding events. Surface-based methods such as surface plasmon resonance (SPR) and dual polarization interferometry (DPI) allow real-time measurements and can provide kinetic parameters as well as binding constants. DPI provides additional spatial information about the binding event. Here, an account is presented of new developments and recent applications of TSA and DPI connected to crystallography.

  1. Structural analysis of protein-ligand interactions: the binding of endogenous compounds and of synthetic drugs.

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    Gallina, Anna M; Bork, Peer; Bordo, Domenico

    2014-02-01

    The large number of macromolecular structures deposited with the Protein Data Bank (PDB) describing complexes between proteins and either physiological compounds or synthetic drugs made it possible a systematic analysis of the interactions occurring between proteins and their ligands. In this work, the binding pockets of about 4000 PDB protein-ligand complexes were investigated and amino acid and interaction types were analyzed. The residues observed with lowest frequency in protein sequences, Trp, His, Met, Tyr, and Phe, turned out to be the most abundant in binding pockets. Significant differences between drug-like and physiological compounds were found. On average, physiological compounds establish with respect to drugs about twice as many hydrogen bonds with protein atoms, whereas drugs rely more on hydrophobic interactions to establish target selectivity. The large number of PDB structures describing homologous proteins in complex with the same ligand made it possible to analyze the conservation of binding pocket residues among homologous protein structures bound to the same ligand, showing that Gly, Glu, Arg, Asp, His, and Thr are more conserved than other amino acids. Also in the cases in which the same ligand is bound to unrelated proteins, the binding pockets showed significant conservation in the residue types. In this case, the probability of co-occurrence of the same amino acid type in the binding pockets could be up to thirteen times higher than that expected on a random basis. The trends identified in this study may provide an useful guideline in the process of drug design and lead optimization. Copyright © 2014 John Wiley & Sons, Ltd.

  2. PL-PatchSurfer: a novel molecular local surface-based method for exploring protein-ligand interactions.

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    Hu, Bingjie; Zhu, Xiaolei; Monroe, Lyman; Bures, Mark G; Kihara, Daisuke

    2014-08-27

    Structure-based computational methods have been widely used in exploring protein-ligand interactions, including predicting the binding ligands of a given protein based on their structural complementarity. Compared to other protein and ligand representations, the advantages of a surface representation include reduced sensitivity to subtle changes in the pocket and ligand conformation and fast search speed. Here we developed a novel method named PL-PatchSurfer (Protein-Ligand PatchSurfer). PL-PatchSurfer represents the protein binding pocket and the ligand molecular surface as a combination of segmented surface patches. Each patch is characterized by its geometrical shape and the electrostatic potential, which are represented using the 3D Zernike descriptor (3DZD). We first tested PL-PatchSurfer on binding ligand prediction and found it outperformed the pocket-similarity based ligand prediction program. We then optimized the search algorithm of PL-PatchSurfer using the PDBbind dataset. Finally, we explored the utility of applying PL-PatchSurfer to a larger and more diverse dataset and showed that PL-PatchSurfer was able to provide a high early enrichment for most of the targets. To the best of our knowledge, PL-PatchSurfer is the first surface patch-based method that treats ligand complementarity at protein binding sites. We believe that using a surface patch approach to better understand protein-ligand interactions has the potential to significantly enhance the design of new ligands for a wide array of drug-targets.

  3. Post hoc support vector machine learning for impedimetric biosensors based on weak protein-ligand interactions.

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    Rong, Y; Padron, A V; Hagerty, K J; Nelson, N; Chi, S; Keyhani, N O; Katz, J; Datta, S P A; Gomes, C; McLamore, E S

    2018-04-30

    Impedimetric biosensors for measuring small molecules based on weak/transient interactions between bioreceptors and target analytes are a challenge for detection electronics, particularly in field studies or in the analysis of complex matrices. Protein-ligand binding sensors have enormous potential for biosensing, but achieving accuracy in complex solutions is a major challenge. There is a need for simple post hoc analytical tools that are not computationally expensive, yet provide near real time feedback on data derived from impedance spectra. Here, we show the use of a simple, open source support vector machine learning algorithm for analyzing impedimetric data in lieu of using equivalent circuit analysis. We demonstrate two different protein-based biosensors to show that the tool can be used for various applications. We conclude with a mobile phone-based demonstration focused on the measurement of acetone, an important biomarker related to the onset of diabetic ketoacidosis. In all conditions tested, the open source classifier was capable of performing as well as, or better, than the equivalent circuit analysis for characterizing weak/transient interactions between a model ligand (acetone) and a small chemosensory protein derived from the tsetse fly. In addition, the tool has a low computational requirement, facilitating use for mobile acquisition systems such as mobile phones. The protocol is deployed through Jupyter notebook (an open source computing environment available for mobile phone, tablet or computer use) and the code was written in Python. For each of the applications, we provide step-by-step instructions in English, Spanish, Mandarin and Portuguese to facilitate widespread use. All codes were based on scikit-learn, an open source software machine learning library in the Python language, and were processed in Jupyter notebook, an open-source web application for Python. The tool can easily be integrated with the mobile biosensor equipment for rapid

  4. Protein-Ligand Informatics Force Field (PLIff): Toward a Fully Knowledge Driven "Force Field" for Biomolecular Interactions.

    Science.gov (United States)

    Verdonk, Marcel L; Ludlow, R Frederick; Giangreco, Ilenia; Rathi, Prakash Chandra

    2016-07-28

    The Protein Data Bank (PDB) contains a wealth of data on nonbonded biomolecular interactions. If this information could be distilled down to nonbonded interaction potentials, these would have some key advantages over standard force fields. However, there are some important outstanding issues to address in order to do this successfully. This paper introduces the protein-ligand informatics "force field", PLIff, which begins to address these key challenges ( https://bitbucket.org/AstexUK/pli ). As a result of their knowledge-based nature, the next-generation nonbonded potentials that make up PLIff automatically capture a wide range of interaction types, including special interactions that are often poorly described by standard force fields. We illustrate how PLIff may be used in structure-based design applications, including interaction fields, fragment mapping, and protein-ligand docking. PLIff performs at least as well as state-of-the art scoring functions in terms of pose predictions and ranking compounds in a virtual screening context.

  5. PL-PatchSurfer: A Novel Molecular Local Surface-Based Method for Exploring Protein-Ligand Interactions

    Directory of Open Access Journals (Sweden)

    Bingjie Hu

    2014-08-01

    Full Text Available Structure-based computational methods have been widely used in exploring protein-ligand interactions, including predicting the binding ligands of a given protein based on their structural complementarity. Compared to other protein and ligand representations, the advantages of a surface representation include reduced sensitivity to subtle changes in the pocket and ligand conformation and fast search speed. Here we developed a novel method named PL-PatchSurfer (Protein-Ligand PatchSurfer. PL-PatchSurfer represents the protein binding pocket and the ligand molecular surface as a combination of segmented surface patches. Each patch is characterized by its geometrical shape and the electrostatic potential, which are represented using the 3D Zernike descriptor (3DZD. We first tested PL-PatchSurfer on binding ligand prediction and found it outperformed the pocket-similarity based ligand prediction program. We then optimized the search algorithm of PL-PatchSurfer using the PDBbind dataset. Finally, we explored the utility of applying PL-PatchSurfer to a larger and more diverse dataset and showed that PL-PatchSurfer was able to provide a high early enrichment for most of the targets. To the best of our knowledge, PL-PatchSurfer is the first surface patch-based method that treats ligand complementarity at protein binding sites. We believe that using a surface patch approach to better understand protein-ligand interactions has the potential to significantly enhance the design of new ligands for a wide array of drug-targets.

  6. Enhance the performance of current scoring functions with the aid of 3D protein-ligand interaction fingerprints.

    Science.gov (United States)

    Liu, Jie; Su, Minyi; Liu, Zhihai; Li, Jie; Li, Yan; Wang, Renxiao

    2017-07-18

    In structure-based drug design, binding affinity prediction remains as a challenging goal for current scoring functions. Development of target-biased scoring functions provides a new possibility for tackling this problem, but this approach is also associated with certain technical difficulties. We previously reported the Knowledge-Guided Scoring (KGS) method as an alternative approach (BMC Bioinformatics, 2010, 11, 193-208). The key idea is to compute the binding affinity of a given protein-ligand complex based on the known binding data of an appropriate reference complex, so the error in binding affinity prediction can be reduced effectively. In this study, we have developed an upgraded version, i.e. KGS2, by employing 3D protein-ligand interaction fingerprints in reference selection. KGS2 was evaluated in combination with four scoring functions (X-Score, ChemPLP, ASP, and GoldScore) on five drug targets (HIV-1 protease, carbonic anhydrase 2, beta-secretase 1, beta-trypsin, and checkpoint kinase 1). In the in situ scoring test, considerable improvements were observed in most cases after application of KGS2. Besides, the performance of KGS2 was always better than KGS in all cases. In the more challenging molecular docking test, application of KGS2 also led to improved structure-activity relationship in some cases. KGS2 can be applied as a convenient "add-on" to current scoring functions without the need to re-engineer them, and its application is not limited to certain target proteins as customized scoring functions. As an interpolation method, its accuracy in principle can be improved further with the increasing knowledge of protein-ligand complex structures and binding affinity data. We expect that KGS2 will become a practical tool for enhancing the performance of current scoring functions in binding affinity prediction. The KGS2 software is available upon contacting the authors.

  7. Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study

    Directory of Open Access Journals (Sweden)

    A Santos Jose C

    2012-07-01

    Full Text Available Abstract Background There is a need for automated methods to learn general features of the interactions of a ligand class with its diverse set of protein receptors. An appropriate machine learning approach is Inductive Logic Programming (ILP, which automatically generates comprehensible rules in addition to prediction. The development of ILP systems which can learn rules of the complexity required for studies on protein structure remains a challenge. In this work we use a new ILP system, ProGolem, and demonstrate its performance on learning features of hexose-protein interactions. Results The rules induced by ProGolem detect interactions mediated by aromatics and by planar-polar residues, in addition to less common features such as the aromatic sandwich. The rules also reveal a previously unreported dependency for residues cys and leu. They also specify interactions involving aromatic and hydrogen bonding residues. This paper shows that Inductive Logic Programming implemented in ProGolem can derive rules giving structural features of protein/ligand interactions. Several of these rules are consistent with descriptions in the literature. Conclusions In addition to confirming literature results, ProGolem’s model has a 10-fold cross-validated predictive accuracy that is superior, at the 95% confidence level, to another ILP system previously used to study protein/hexose interactions and is comparable with state-of-the-art statistical learners.

  8. Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study.

    Science.gov (United States)

    A Santos, Jose C; Nassif, Houssam; Page, David; Muggleton, Stephen H; E Sternberg, Michael J

    2012-07-11

    There is a need for automated methods to learn general features of the interactions of a ligand class with its diverse set of protein receptors. An appropriate machine learning approach is Inductive Logic Programming (ILP), which automatically generates comprehensible rules in addition to prediction. The development of ILP systems which can learn rules of the complexity required for studies on protein structure remains a challenge. In this work we use a new ILP system, ProGolem, and demonstrate its performance on learning features of hexose-protein interactions. The rules induced by ProGolem detect interactions mediated by aromatics and by planar-polar residues, in addition to less common features such as the aromatic sandwich. The rules also reveal a previously unreported dependency for residues cys and leu. They also specify interactions involving aromatic and hydrogen bonding residues. This paper shows that Inductive Logic Programming implemented in ProGolem can derive rules giving structural features of protein/ligand interactions. Several of these rules are consistent with descriptions in the literature. In addition to confirming literature results, ProGolem's model has a 10-fold cross-validated predictive accuracy that is superior, at the 95% confidence level, to another ILP system previously used to study protein/hexose interactions and is comparable with state-of-the-art statistical learners.

  9. Alignment of SWNTs by protein-ligand interaction of functionalized magnetic particles under low magnetic fields.

    Science.gov (United States)

    Park, Tae Jung; Park, Jong Pil; Lee, Seok Jae; Jung, Dae-Hwan; Ko, Young Koan; Jung, Hee-Tae; Lee, Sang Yup

    2011-05-01

    Carbon nanotubes (CNTs) have attracted considerable attention for applications using their superior mechanical, thermal and electrical properties. A simple method to controllably align single-walled CNTs (SWNTs) by using magnetic particles embedded with superparamagnetic iron oxide as an accelerator under the magnetic field was developed. The functionalization of SWNTs using biotin, interacted with streptavidin-coupled magnetic particles (micro-to-nano in diameter), and layer-by-layer assembly were performed for the alignment of a particular direction onto the clean silicon and the gold substrate at very low magnetic forces (0.02-0.89 T) at room temperature. The successful alignment of the SWNTs with multi-layer film was observed by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). By changing the orientation and location of the substrates, crossed-networks of SWNTs-magnetic particle complex could easily be fabricated. We suggest that this approach, which consists of a combination of biological interaction among streptavidin-biotin and magnetite particles, should be useful for lateral orientation of individual SWNTs with controllable direction.

  10. IChem: A Versatile Toolkit for Detecting, Comparing, and Predicting Protein-Ligand Interactions.

    Science.gov (United States)

    Da Silva, Franck; Desaphy, Jeremy; Rognan, Didier

    2018-03-20

    Structure-based ligand design requires an exact description of the topology of molecular entities under scrutiny. IChem is a software package that reflects the many contributions of our research group in this area over the last decade. It facilitates and automates many tasks (e.g., ligand/cofactor atom typing, identification of key water molecules) usually left to the modeler's choice. It therefore permits the detection of molecular interactions between two molecules in a very precise and flexible manner. Moreover, IChem enables the conversion of intricate three-dimensional (3D) molecular objects into simple representations (fingerprints, graphs) that facilitate knowledge acquisition at very high throughput. The toolkit is an ideal companion for setting up and performing many structure-based design computations. © 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  11. High pressure as a tool for investigating protein-ligand interactions

    International Nuclear Information System (INIS)

    Marchal, S; Lange, R; Tortora, P; Balny, C

    2004-01-01

    In recent years, the application of pressure on biological systems has gained increasing interest. Pressure-induced destabilization of electrostatic and hydrophobic interactions is currently exploited to study conformational protein stability and macromolecular assemblies of proteins. Due to links between severe human pathologies and ordered protein oligomerization into aggregates, which have become apparent, a better knowledge of the molecular and structural determinants that ensure the packing efficiency and stability of such complexes has taken on special importance. Here, we report the effect of pressure on the property of human ataxin-3 of aggregation. The results indicate the importance of its polyglutamine chain length in the stability and the tendency of the protein to form spheroids. Partial unfolding of the protein leading to solvent exposure of hydrophobic domains appears to be a prerequisite in the aggregation process of ataxin-3

  12. Structural insights, protein-ligand interactions and spectroscopic characterization of isoformononetin

    Science.gov (United States)

    Srivastava, Anubha; Singh, Harshita; Mishra, Rashmi; Dev, Kapil; Tandon, Poonam; Maurya, Rakesh

    2017-04-01

    Isoformononetin, a methoxylated isoflavone present in medicinal plants, has non-estrogenic bone forming effect via differential mitogen-activated protein kinase (MAPK) signaling. Spectroscopic (FT-Raman, FT-IR, UV-vis and NMR spectra) and quantum chemical calculations using density functional theory (DFT) and 6-311++G(d,p) as a large basis set have been employed to study the structural and electronic properties of isoformononetin. A detailed conformational analysis is performed to determine the stability among conformers and the various possibilities of intramolecular hydrogen bonding formation. Molecular docking studies with different protein kinases were performed on isoformononetin and previously studied isoflavonoid, formononetin in order to understand their inhibitory nature and the effect of functional groups on osteogenic or osteoporosis associated proteins. It is found that the oxygen atoms of methoxy, hydroxyl groups attached to phenyl rings R1, R3 and carbonyl group attached to pyran ring R2, play a major role in binding with the protein kinases that is responsible for the osteoporosis; however, no hydrophobic interactions are observed between rings of ligand and protein. The electronic properties such as HOMO and LUMO energies were determined by time-dependent TD-DFT which predict that conformer II is a little bit more stable and chemically low reactive than conformer I of isoformononetin. To estimate the structure-activity relationship, the molecular electrostatic potential (MEP) surface map, and reactivity descriptors are calculated from the optimized geometry of the molecule. From these results, it is also found that isoformononetin is kinetically more stable, less toxic, weak electrophile and chemically less reactive than formononetin. The atoms in molecules and natural bond orbital analysis are applied for the detailed analysis of intra and intermolecular hydrogen bonding interactions.

  13. Ranking docking poses by graph matching of protein-ligand interactions: lessons learned from the D3R Grand Challenge 2

    Science.gov (United States)

    da Silva Figueiredo Celestino Gomes, Priscila; Da Silva, Franck; Bret, Guillaume; Rognan, Didier

    2018-01-01

    A novel docking challenge has been set by the Drug Design Data Resource (D3R) in order to predict the pose and affinity ranking of a set of Farnesoid X receptor (FXR) agonists, prior to the public release of their bound X-ray structures and potencies. In a first phase, 36 agonists were docked to 26 Protein Data Bank (PDB) structures of the FXR receptor, and next rescored using the in-house developed GRIM method. GRIM aligns protein-ligand interaction patterns of docked poses to those of available PDB templates for the target protein, and rescore poses by a graph matching method. In agreement with results obtained during the previous 2015 docking challenge, we clearly show that GRIM rescoring improves the overall quality of top-ranked poses by prioritizing interaction patterns already visited in the PDB. Importantly, this challenge enables us to refine the applicability domain of the method by better defining the conditions of its success. We notably show that rescoring apolar ligands in hydrophobic pockets leads to frequent GRIM failures. In the second phase, 102 FXR agonists were ranked by decreasing affinity according to the Gibbs free energy of the corresponding GRIM-selected poses, computed by the HYDE scoring function. Interestingly, this fast and simple rescoring scheme provided the third most accurate ranking method among 57 contributions. Although the obtained ranking is still unsuitable for hit to lead optimization, the GRIM-HYDE scoring scheme is accurate and fast enough to post-process virtual screening data.

  14. PLASS: Protein-ligand affinity statistical score a knowledge-based force-field model of interaction derived from the PDB

    Science.gov (United States)

    Ozrin, V. D.; Subbotin, M. V.; Nikitin, S. M.

    2004-04-01

    We have developed PLASS (Protein-Ligand Affinity Statistical Score), a pair-wise potential of mean-force for rapid estimation of the binding affinity of a ligand molecule to a protein active site. This scoring function is derived from the frequency of occurrence of atom-type pairs in crystallographic complexes taken from the Protein Data Bank (PDB). Statistical distributions are converted into distance-dependent contributions to the Gibbs free interaction energy for 10 atomic types using the Boltzmann hypothesis, with only one adjustable parameter. For a representative set of 72 protein-ligand structures, PLASS scores correlate well with the experimentally measured dissociation constants: a correlation coefficient R of 0.82 and RMS error of 2.0 kcal/mol. Such high accuracy results from our novel treatment of the volume correction term, which takes into account the inhomogeneous properties of the protein-ligand complexes. PLASS is able to rank reliably the affinity of complexes which have as much diversity as in the PDB.

  15. Molecular recognition in a diverse set of protein-ligand interactions studied with molecular dynamics simulations and end-point free energy calculations.

    Science.gov (United States)

    Wang, Bo; Li, Liwei; Hurley, Thomas D; Meroueh, Samy O

    2013-10-28

    End-point free energy calculations using MM-GBSA and MM-PBSA provide a detailed understanding of molecular recognition in protein-ligand interactions. The binding free energy can be used to rank-order protein-ligand structures in virtual screening for compound or target identification. Here, we carry out free energy calculations for a diverse set of 11 proteins bound to 14 small molecules using extensive explicit-solvent MD simulations. The structure of these complexes was previously solved by crystallography and their binding studied with isothermal titration calorimetry (ITC) data enabling direct comparison to the MM-GBSA and MM-PBSA calculations. Four MM-GBSA and three MM-PBSA calculations reproduced the ITC free energy within 1 kcal·mol(-1) highlighting the challenges in reproducing the absolute free energy from end-point free energy calculations. MM-GBSA exhibited better rank-ordering with a Spearman ρ of 0.68 compared to 0.40 for MM-PBSA with dielectric constant (ε = 1). An increase in ε resulted in significantly better rank-ordering for MM-PBSA (ρ = 0.91 for ε = 10), but larger ε significantly reduced the contributions of electrostatics, suggesting that the improvement is due to the nonpolar and entropy components, rather than a better representation of the electrostatics. The SVRKB scoring function applied to MD snapshots resulted in excellent rank-ordering (ρ = 0.81). Calculations of the configurational entropy using normal-mode analysis led to free energies that correlated significantly better to the ITC free energy than the MD-based quasi-harmonic approach, but the computed entropies showed no correlation with the ITC entropy. When the adaptation energy is taken into consideration by running separate simulations for complex, apo, and ligand (MM-PBSAADAPT), there is less agreement with the ITC data for the individual free energies, but remarkably good rank-ordering is observed (ρ = 0.89). Interestingly, filtering MD snapshots by prescoring

  16. Photo-cross-linked small-molecule microarrays as chemical genomic tools for dissecting protein-ligand interactions.

    Science.gov (United States)

    Kanoh, Naoki; Asami, Aya; Kawatani, Makoto; Honda, Kaori; Kumashiro, Saori; Takayama, Hiroshi; Simizu, Siro; Amemiya, Tomoyuki; Kondoh, Yasumitsu; Hatakeyama, Satoru; Tsuganezawa, Keiko; Utata, Rei; Tanaka, Akiko; Yokoyama, Shigeyuki; Tashiro, Hideo; Osada, Hiroyuki

    2006-12-18

    We have developed a unique photo-cross-linking approach for immobilizing a variety of small molecules in a functional-group-independent manner. Our approach depends on the reactivity of the carbene species generated from trifluoromethylaryldiazirine upon UV irradiation. It was demonstrated in model experiments that the photogenerated carbenes were able to react with every small molecule tested, and they produced multiple conjugates in most cases. It was also found in on-array immobilization experiments that various small molecules were immobilized, and the immobilized small molecules retained their ability to interact with their binding proteins. With this approach, photo-cross-linked microarrays of about 2000 natural products and drugs were constructed. This photo-cross-linked microarray format was found to be useful not merely for ligand screening but also to study the structure-activity relationship, that is, the relationship between the structural motif (or pharmacophore) found in small molecules and its binding affinity toward a protein, by taking advantage of the nonselective nature of the photo-cross-linking process.

  17. A rapid method for selecting suitable animal species for studying pathogen interactions with plasma protein ligands in vivo.

    Science.gov (United States)

    Naudin, Clément; Schumski, Ariane; Salo-Ahen, Outi M H; Herwald, Heiko; Smeds, Emanuel

    2017-05-01

    Species tropism constitutes a serious problem for developing relevant animal models of infection. Human pathogens can express virulence factors that show specific selectivity to human proteins, while their affinity for orthologs from other species can vary significantly. Suitable animal species must be used to analyse whether virulence factors are potential targets for drug development. We developed an assay that rapidly predicts applicable animal species for studying virulence factors binding plasma proteins. We used two well-characterized Staphylococcus aureus proteins, SSL7 and Efb, to develop an ELISA-based inhibition assay using plasma from different animal species. The interaction between SSL7 and human C5 and the binding of Efb to human fibrinogen and human C3 was studied. Affinity experiments and Western blot analyses were used to validate the assay. Human, monkey and cat plasma interfered with binding of SSL7 to human C5. Binding of Efb to human fibrinogen was blocked in human, monkey, gerbil and pig plasma, while human, monkey, gerbil, rabbit, cat and guinea pig plasma inhibited the binding of Efb to human C3. These results emphasize the importance of choosing correct animal models, and thus, our approach is a rapid and cost-effective method that can be used to prevent unnecessary animal experiments. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  18. Size versus polarizability in protein-ligand interactions: binding of noble gases within engineered cavities in phage T4 lysozyme.

    Science.gov (United States)

    Quillin, M L; Breyer, W A; Griswold, I J; Matthews, B W

    2000-09-29

    To investigate the relative importance of size and polarizability in ligand binding within proteins, we have determined the crystal structures of pseudo wild-type and cavity-containing mutant phage T4 lysozymes in the presence of argon, krypton, and xenon. These proteins provide a representative sample of predominantly apolar cavities of varying size and shape. Even though the volumes of these cavities range up to the equivalent of five xenon atoms, the noble gases bind preferentially at highly localized sites that appear to be defined by constrictions in the walls of the cavities, coupled with the relatively large radii of the noble gases. The cavities within pseudo wild-type and L121A lysozymes each bind only a single atom of noble gas, while the cavities within mutants L133A and F153A have two independent binding sites, and the L99A cavity has three interacting sites. The binding of noble gases within two double mutants was studied to characterize the additivity of binding at such sites. In general, when a cavity in a protein is created by a "large-to-small" substitution, the surrounding residues relax somewhat to reduce the volume of the cavity. The binding of xenon and, to a lesser degree, krypton and argon, tend to expand the volume of the cavity and to return it closer to what it would have been had no relaxation occurred. In nearly all cases, the extent of binding of the noble gases follows the trend xenon>krypton>argon. Pressure titrations of the L99A mutant have confirmed that the crystallographic occupancies accurately reflect fractional saturation of the binding sites. The trend in noble gas affinity can be understood in terms of the effects of size and polarizability on the intermolecular potential. The plasticity of the protein matrix permits repulsion due to increased ligand size to be more than compensated for by attraction due to increased ligand polarizability. These results have implications for the mechanism of general anesthesia, the migration

  19. Calculation of protein-ligand binding affinities.

    Science.gov (United States)

    Gilson, Michael K; Zhou, Huan-Xiang

    2007-01-01

    Accurate methods of computing the affinity of a small molecule with a protein are needed to speed the discovery of new medications and biological probes. This paper reviews physics-based models of binding, beginning with a summary of the changes in potential energy, solvation energy, and configurational entropy that influence affinity, and a theoretical overview to frame the discussion of specific computational approaches. Important advances are reported in modeling protein-ligand energetics, such as the incorporation of electronic polarization and the use of quantum mechanical methods. Recent calculations suggest that changes in configurational entropy strongly oppose binding and must be included if accurate affinities are to be obtained. The linear interaction energy (LIE) and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methods are analyzed, as are free energy pathway methods, which show promise and may be ready for more extensive testing. Ultimately, major improvements in modeling accuracy will likely require advances on multiple fronts, as well as continued validation against experiment.

  20. Evaluation of several two-step scoring functions based on linear interaction energy, effective ligand size, and empirical pair potentials for prediction of protein-ligand binding geometry and free energy.

    Science.gov (United States)

    Rahaman, Obaidur; Estrada, Trilce P; Doren, Douglas J; Taufer, Michela; Brooks, Charles L; Armen, Roger S

    2011-09-26

    The performances of several two-step scoring approaches for molecular docking were assessed for their ability to predict binding geometries and free energies. Two new scoring functions designed for "step 2 discrimination" were proposed and compared to our CHARMM implementation of the linear interaction energy (LIE) approach using the Generalized-Born with Molecular Volume (GBMV) implicit solvation model. A scoring function S1 was proposed by considering only "interacting" ligand atoms as the "effective size" of the ligand and extended to an empirical regression-based pair potential S2. The S1 and S2 scoring schemes were trained and 5-fold cross-validated on a diverse set of 259 protein-ligand complexes from the Ligand Protein Database (LPDB). The regression-based parameters for S1 and S2 also demonstrated reasonable transferability in the CSARdock 2010 benchmark using a new data set (NRC HiQ) of diverse protein-ligand complexes. The ability of the scoring functions to accurately predict ligand geometry was evaluated by calculating the discriminative power (DP) of the scoring functions to identify native poses. The parameters for the LIE scoring function with the optimal discriminative power (DP) for geometry (step 1 discrimination) were found to be very similar to the best-fit parameters for binding free energy over a large number of protein-ligand complexes (step 2 discrimination). Reasonable performance of the scoring functions in enrichment of active compounds in four different protein target classes established that the parameters for S1 and S2 provided reasonable accuracy and transferability. Additional analysis was performed to definitively separate scoring function performance from molecular weight effects. This analysis included the prediction of ligand binding efficiencies for a subset of the CSARdock NRC HiQ data set where the number of ligand heavy atoms ranged from 17 to 35. This range of ligand heavy atoms is where improved accuracy of predicted ligand

  1. Characterization of protein/ligand interactions by 1H/3H exchange: application to the hAsf1/ histone H3 complex

    International Nuclear Information System (INIS)

    Mousseau, G.

    2007-05-01

    In the first chapter will be exposed the main current methods of identification to high debit of the interactions protein-protein. Then the methods allowing to characterize the surfaces of interaction or to determine the structures of the complexes will be listed by discussing the main advantages and the inconveniences. Our approach of characterization of the zones of interaction protein-protein is a method of 'foot-printing' 1, based on the identification and radicals' quantification formed on the residues of proteins accessible to the water. The second chapter will so discuss the development of this method of radical identification using the atom of tritium as radioactive label. Our approach will finally be validated in the third chapter by applying it to the characterization of amino acids involved in the interaction enter the human protein anti silencing factor 1 (hAsf11-156) and a fragment of the histone H 3 . (N.C.)

  2. Functional structural motifs for protein-ligand, protein-protein, and protein-nucleic acid interactions and their connection to supersecondary structures.

    Science.gov (United States)

    Kinjo, Akira R; Nakamura, Haruki

    2013-01-01

    Protein functions are mediated by interactions between proteins and other molecules. One useful approach to analyze protein functions is to compare and classify the structures of interaction interfaces of proteins. Here, we describe the procedures for compiling a database of interface structures and efficiently comparing the interface structures. To do so requires a good understanding of the data structures of the Protein Data Bank (PDB). Therefore, we also provide a detailed account of the PDB exchange dictionary necessary for extracting data that are relevant for analyzing interaction interfaces and secondary structures. We identify recurring structural motifs by classifying similar interface structures, and we define a coarse-grained representation of supersecondary structures (SSS) which represents a sequence of two or three secondary structure elements including their relative orientations as a string of four to seven letters. By examining the correspondence between structural motifs and SSS strings, we show that no SSS string has particularly high propensity to be found interaction interfaces in general, indicating any SSS can be used as a binding interface. When individual structural motifs are examined, there are some SSS strings that have high propensity for particular groups of structural motifs. In addition, it is shown that while the SSS strings found in particular structural motifs for nonpolymer and protein interfaces are as abundant as in other structural motifs that belong to the same subunit, structural motifs for nucleic acid interfaces exhibit somewhat stronger preference for SSS strings. In regard to protein folds, many motif-specific SSS strings were found across many folds, suggesting that SSS may be a useful description to investigate the universality of ligand binding modes.

  3. AMMOS2: a web server for protein-ligand-water complexes refinement via molecular mechanics.

    Science.gov (United States)

    Labbé, Céline M; Pencheva, Tania; Jereva, Dessislava; Desvillechabrol, Dimitri; Becot, Jérôme; Villoutreix, Bruno O; Pajeva, Ilza; Miteva, Maria A

    2017-07-03

    AMMOS2 is an interactive web server for efficient computational refinement of protein-small organic molecule complexes. The AMMOS2 protocol employs atomic-level energy minimization of a large number of experimental or modeled protein-ligand complexes. The web server is based on the previously developed standalone software AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening). AMMOS utilizes the physics-based force field AMMP sp4 and performs optimization of protein-ligand interactions at five levels of flexibility of the protein receptor. The new version 2 of AMMOS implemented in the AMMOS2 web server allows the users to include explicit water molecules and individual metal ions in the protein-ligand complexes during minimization. The web server provides comprehensive analysis of computed energies and interactive visualization of refined protein-ligand complexes. The ligands are ranked by the minimized binding energies allowing the users to perform additional analysis for drug discovery or chemical biology projects. The web server has been extensively tested on 21 diverse protein-ligand complexes. AMMOS2 minimization shows consistent improvement over the initial complex structures in terms of minimized protein-ligand binding energies and water positions optimization. The AMMOS2 web server is freely available without any registration requirement at the URL: http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Impact of protein and ligand impurities on ITC-derived protein-ligand thermodynamics.

    Science.gov (United States)

    Grüner, Stefan; Neeb, Manuel; Barandun, Luzi Jakob; Sielaff, Frank; Hohn, Christoph; Kojima, Shun; Steinmetzer, Torsten; Diederich, François; Klebe, Gerhard

    2014-09-01

    The thermodynamic characterization of protein-ligand interactions by isothermal titration calorimetry (ITC) is a powerful tool in drug design, giving valuable insight into the interaction driving forces. ITC is thought to require protein and ligand solutions of high quality, meaning both the absence of contaminants as well as accurately determined concentrations. Ligands synthesized to deviating purity and protein of different pureness were titrated by ITC. Data curation was attempted also considering information from analytical techniques to correct stoichiometry. We used trypsin and tRNA-guanine transglycosylase (TGT), together with high affinity ligands to investigate the effect of errors in protein concentration as well as the impact of ligand impurities on the apparent thermodynamics. We found that errors in protein concentration did not change the thermodynamic properties obtained significantly. However, most ligand impurities led to pronounced changes in binding enthalpy. If protein binding of the respective impurity is not expected, the actual ligand concentration was corrected for and the thus revised data compared to thermodynamic properties obtained with the respective pure ligand. Even in these cases, we observed differences in binding enthalpy of about 4kJ⋅mol(-1), which is considered significant. Our results indicate that ligand purity is the critical parameter to monitor if accurate thermodynamic data of a protein-ligand complex are to be recorded. Furthermore, artificially changing fitting parameters to obtain a sound interaction stoichiometry in the presence of uncharacterized ligand impurities may lead to thermodynamic parameters significantly deviating from the accurate thermodynamic signature. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. Cloud computing for protein-ligand binding site comparison.

    Science.gov (United States)

    Hung, Che-Lun; Hua, Guan-Jie

    2013-01-01

    The proteome-wide analysis of protein-ligand binding sites and their interactions with ligands is important in structure-based drug design and in understanding ligand cross reactivity and toxicity. The well-known and commonly used software, SMAP, has been designed for 3D ligand binding site comparison and similarity searching of a structural proteome. SMAP can also predict drug side effects and reassign existing drugs to new indications. However, the computing scale of SMAP is limited. We have developed a high availability, high performance system that expands the comparison scale of SMAP. This cloud computing service, called Cloud-PLBS, combines the SMAP and Hadoop frameworks and is deployed on a virtual cloud computing platform. To handle the vast amount of experimental data on protein-ligand binding site pairs, Cloud-PLBS exploits the MapReduce paradigm as a management and parallelizing tool. Cloud-PLBS provides a web portal and scalability through which biologists can address a wide range of computer-intensive questions in biology and drug discovery.

  6. Characterization of protein/ligand interactions by {sup 1}H/{sup 3}H exchange: application to the hAsf{sup 1}/ histone H{sup 3} complex; Caracterisation des interactions proteine / ligand par echange {sup 1}H/{sup 3}H: application au complexe entre la proteine hAsf{sup 1} et l'histone H{sup 3}

    Energy Technology Data Exchange (ETDEWEB)

    Mousseau, G

    2007-05-15

    In the first chapter will be exposed the main current methods of identification to high debit of the interactions protein-protein. Then the methods allowing to characterize the surfaces of interaction or to determine the structures of the complexes will be listed by discussing the main advantages and the inconveniences. Our approach of characterization of the zones of interaction protein-protein is a method of 'foot-printing' 1, based on the identification and radicals' quantification formed on the residues of proteins accessible to the water. The second chapter will so discuss the development of this method of radical identification using the atom of tritium as radioactive label. Our approach will finally be validated in the third chapter by applying it to the characterization of amino acids involved in the interaction enter the human protein anti silencing factor 1 (hAsf11-156) and a fragment of the histone H{sup 3}. (N.C.)

  7. A sequence-based dynamic ensemble learning system for protein ligand-binding site prediction

    KAUST Repository

    Chen, Peng

    2015-12-03

    Background: Proteins have the fundamental ability to selectively bind to other molecules and perform specific functions through such interactions, such as protein-ligand binding. Accurate prediction of protein residues that physically bind to ligands is important for drug design and protein docking studies. Most of the successful protein-ligand binding predictions were based on known structures. However, structural information is not largely available in practice due to the huge gap between the number of known protein sequences and that of experimentally solved structures

  8. A sequence-based dynamic ensemble learning system for protein ligand-binding site prediction

    KAUST Repository

    Chen, Peng; Hu, ShanShan; Zhang, Jun; Gao, Xin; Li, Jinyan; Xia, Junfeng; Wang, Bing

    2015-01-01

    Background: Proteins have the fundamental ability to selectively bind to other molecules and perform specific functions through such interactions, such as protein-ligand binding. Accurate prediction of protein residues that physically bind to ligands is important for drug design and protein docking studies. Most of the successful protein-ligand binding predictions were based on known structures. However, structural information is not largely available in practice due to the huge gap between the number of known protein sequences and that of experimentally solved structures

  9. Models of protein-ligand crystal structures: trust, but verify.

    Science.gov (United States)

    Deller, Marc C; Rupp, Bernhard

    2015-09-01

    X-ray crystallography provides the most accurate models of protein-ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein-ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein-ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein-ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein-ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein-ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein-ligand models for their computational and biological studies, and we provide an overview of how this can be achieved.

  10. Effect of urea on protein-ligand association.

    Science.gov (United States)

    Stepanian, Lora; Son, Ikbae; Chalikian, Tigran V

    2017-12-01

    We combine experimental and theoretical approaches to investigate the influence of a cosolvent on a ligand-protein association event. We apply fluorescence measurements to determining the affinity of the inhibitor tri-N-acetylglucosamine [(GlcNAc) 3 ] for lysozyme at urea concentrations ranging from 0 to 8M. Notwithstanding that, at room temperature and neutral pH, lysozyme retains its native conformation up to the solubility limit of urea, the affinity of (GlcNAc) 3 for the protein steadily decreases as the concentration of urea increases. We analyze the urea dependence of the binding free energy within the framework of a simplified statistical thermodynamics-based model that accounts for the excluded volume effect and direct solute-solvent interactions. The analysis reveals that the detrimental action of urea on the inhibitor-lysozyme binding originates from competition between the free energy contributions of the excluded volume effect and direct solute-solvent interactions. The free energy contribution of direct urea-solute interactions narrowly overcomes the excluded volume contribution thereby resulting in urea weakening the protein-ligand association. More broadly, the successful application of the simple model employed in this work points to the possibility of its use in quantifying the stabilizing/destabilizing action of individual cosolvents on biochemical folding and binding reactions. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Nanoparticle-Based Receptors Mimic Protein-Ligand Recognition.

    Science.gov (United States)

    Riccardi, Laura; Gabrielli, Luca; Sun, Xiaohuan; De Biasi, Federico; Rastrelli, Federico; Mancin, Fabrizio; De Vivo, Marco

    2017-07-13

    The self-assembly of a monolayer of ligands on the surface of noble-metal nanoparticles dictates the fundamental nanoparticle's behavior and its functionality. In this combined computational-experimental study, we analyze the structure, organization, and dynamics of functionalized coating thiols in monolayer-protected gold nanoparticles (AuNPs). We explain how functionalized coating thiols self-organize through a delicate and somehow counterintuitive balance of interactions within the monolayer itself and with the solvent. We further describe how the nature and plasticity of these interactions modulate nanoparticle-based chemosensing. Importantly, we found that self-organization of coating thiols can induce the formation of binding pockets in AuNPs. These transient cavities can accommodate small molecules, mimicking protein-ligand recognition, which could explain the selectivity and sensitivity observed for different organic analytes in NMR chemosensing experiments. Thus, our findings advocate for the rational design of tailored coating groups to form specific recognition binding sites on monolayer-protected AuNPs.

  12. Identification of individual protein-ligand NOEs in the limit of intermediate exchange

    International Nuclear Information System (INIS)

    Reibarkh, Mikhail; Malia, Thomas J.; Hopkins, Brian T.; Wagner, Gerhard

    2006-01-01

    Interactions of proteins with small molecules or other macromolecules play key roles in many biological processes and in drug action, and NMR is an excellent tool for their structural characterization. Frequently, however, line broadening due to intermediate exchange completely eliminates the signals needed for measuring specific intermolecular NOEs. This limits the use of NMR for detailed structural studies in such kinetic situations. Here we show that an optimally chosen excess of ligand over protein can reduce the extent of line broadening for both the ligand and the protein. This makes observation of ligand resonances possible but reduces the size of the measurable NOEs due to the residual line broadening and the non-stoichiometric concentrations. Because the solubility of small molecule drug leads are often limited to high micromolar concentrations, protein concentrations are restricted to even lower values in the low micromolar range. At these non-stoichiometric concentrations and in the presence of significant residual line broadening, conventional NOESY experiments very often are not sensitive enough to observe intermolecular NOEs since the signals inverted by the NOESY preparation pulse sequence relax prior to significant NOE build up. Thus, we employ methods related to driven NOE spectroscopy to investigate protein-ligand interactions in the intermediate exchange regime. In this approach, individual protein resonances are selectively irradiated for up to five seconds to build up measurable NOEs at the ligand resonances. To enable saturation of individual protein resonances we prepare deuterated protein samples selectively protonated at a few sites so that the 1D 1 H spectrum of the protein is resolved well enough to permit irradiation of individual protein signals, which do not overlap with the ligand spectrum. This approach is suitable for measuring a sufficiently large number of protein-ligand NOEs that allow calculation of initial complex structures

  13. Evaluation of Docking Target Functions by the Comprehensive Investigation of Protein-Ligand Energy Minima.

    Science.gov (United States)

    Oferkin, Igor V; Katkova, Ekaterina V; Sulimov, Alexey V; Kutov, Danil C; Sobolev, Sergey I; Voevodin, Vladimir V; Sulimov, Vladimir B

    2015-01-01

    The adequate choice of the docking target function impacts the accuracy of the ligand positioning as well as the accuracy of the protein-ligand binding energy calculation. To evaluate a docking target function we compared positions of its minima with the experimentally known pose of the ligand in the protein active site. We evaluated five docking target functions based on either the MMFF94 force field or the PM7 quantum-chemical method with or without implicit solvent models: PCM, COSMO, and SGB. Each function was tested on the same set of 16 protein-ligand complexes. For exhaustive low-energy minima search the novel MPI parallelized docking program FLM and large supercomputer resources were used. Protein-ligand binding energies calculated using low-energy minima were compared with experimental values. It was demonstrated that the docking target function on the base of the MMFF94 force field in vacuo can be used for discovery of native or near native ligand positions by finding the low-energy local minima spectrum of the target function. The importance of solute-solvent interaction for the correct ligand positioning is demonstrated. It is shown that docking accuracy can be improved by replacement of the MMFF94 force field by the new semiempirical quantum-chemical PM7 method.

  14. Evaluation of Docking Target Functions by the Comprehensive Investigation of Protein-Ligand Energy Minima

    Directory of Open Access Journals (Sweden)

    Igor V. Oferkin

    2015-01-01

    Full Text Available The adequate choice of the docking target function impacts the accuracy of the ligand positioning as well as the accuracy of the protein-ligand binding energy calculation. To evaluate a docking target function we compared positions of its minima with the experimentally known pose of the ligand in the protein active site. We evaluated five docking target functions based on either the MMFF94 force field or the PM7 quantum-chemical method with or without implicit solvent models: PCM, COSMO, and SGB. Each function was tested on the same set of 16 protein-ligand complexes. For exhaustive low-energy minima search the novel MPI parallelized docking program FLM and large supercomputer resources were used. Protein-ligand binding energies calculated using low-energy minima were compared with experimental values. It was demonstrated that the docking target function on the base of the MMFF94 force field in vacuo can be used for discovery of native or near native ligand positions by finding the low-energy local minima spectrum of the target function. The importance of solute-solvent interaction for the correct ligand positioning is demonstrated. It is shown that docking accuracy can be improved by replacement of the MMFF94 force field by the new semiempirical quantum-chemical PM7 method.

  15. Increased precision for analysis of protein-ligand dissociation constants determined from chemical shift titrations

    Energy Technology Data Exchange (ETDEWEB)

    Markin, Craig J.; Spyracopoulos, Leo, E-mail: leo.spyracopoulos@ualberta.ca [University of Alberta, Department of Biochemistry (Canada)

    2012-06-15

    NMR is ideally suited for the analysis of protein-protein and protein ligand interactions with dissociation constants ranging from {approx}2 {mu}M to {approx}1 mM, and with kinetics in the fast exchange regime on the NMR timescale. For the determination of dissociation constants (K{sub D}) of 1:1 protein-protein or protein-ligand interactions using NMR, the protein and ligand concentrations must necessarily be similar in magnitude to the K{sub D}, and nonlinear least squares analysis of chemical shift changes as a function of ligand concentration is employed to determine estimates for the parameters K{sub D} and the maximum chemical shift change ({Delta}{delta}{sub max}). During a typical NMR titration, the initial protein concentration, [P{sub 0}], is held nearly constant. For this condition, to determine the most accurate parameters for K{sub D} and {Delta}{delta}{sub max} from nonlinear least squares analyses requires initial protein concentrations that are {approx}0.5 Multiplication-Sign K{sub D}, and a maximum concentration for the ligand, or titrant, of {approx}10 Multiplication-Sign [P{sub 0}]. From a practical standpoint, these requirements are often difficult to achieve. Using Monte Carlo simulations, we demonstrate that co-variation of the ligand and protein concentrations during a titration leads to an increase in the precision of the fitted K{sub D} and {Delta}{delta}{sub max} values when [P{sub 0}] > K{sub D}. Importantly, judicious choice of protein and ligand concentrations for a given NMR titration, combined with nonlinear least squares analyses using two independent variables (ligand and protein concentrations) and two parameters (K{sub D} and {Delta}{delta}{sub max}) is a straightforward approach to increasing the accuracy of measured dissociation constants for 1:1 protein-ligand interactions.

  16. Fast automated placement of polar hydrogen atoms in protein-ligand complexes

    Directory of Open Access Journals (Sweden)

    Lippert Tobias

    2009-08-01

    Full Text Available Abstract Background Hydrogen bonds play a major role in the stabilization of protein-ligand complexes. The ability of a functional group to form them depends on the position of its hydrogen atoms. An accurate knowledge of the positions of hydrogen atoms in proteins is therefore important to correctly identify hydrogen bonds and their properties. The high mobility of hydrogen atoms introduces several degrees of freedom: Tautomeric states, where a hydrogen atom alters its binding partner, torsional changes where the position of the hydrogen atom is rotated around the last heavy-atom bond in a residue, and protonation states, where the number of hydrogen atoms at a functional group may change. Also, side-chain flips in glutamine and asparagine and histidine residues, which are common crystallographic ambiguities must be identified before structure-based calculations can be conducted. Results We have implemented a method to determine the most probable hydrogen atom positions in a given protein-ligand complex. Optimality of hydrogen bond geometries is determined by an empirical scoring function which is used in molecular docking. This allows to evaluate protein-ligand interactions with an established model. Also, our method allows to resolve common crystallographic ambiguities such as as flipped amide groups and histidine residues. To ensure high speed, we make use of a dynamic programming approach. Conclusion Our results were checked against selected high-resolution structures from an external dataset, for which the positions of the hydrogen atoms have been validated manually. The quality of our results is comparable to that of other programs, with the advantage of being fast enough to be applied on-the-fly for interactive usage or during score evaluation.

  17. 2D MI-DRAGON: a new predictor for protein-ligands interactions and theoretic-experimental studies of US FDA drug-target network, oxoisoaporphine inhibitors for MAO-A and human parasite proteins.

    Science.gov (United States)

    Prado-Prado, Francisco; García-Mera, Xerardo; Escobar, Manuel; Sobarzo-Sánchez, Eduardo; Yañez, Matilde; Riera-Fernandez, Pablo; González-Díaz, Humberto

    2011-12-01

    There are many pairs of possible Drug-Proteins Interactions that may take place or not (DPIs/nDPIs) between drugs with high affinity/non-affinity for different proteins. This fact makes expensive in terms of time and resources, for instance, the determination of all possible ligands-protein interactions for a single drug. In this sense, we can use Quantitative Structure-Activity Relationships (QSAR) models to carry out rational DPIs prediction. Unfortunately, almost all QSAR models predict activity against only one target. To solve this problem we can develop multi-target QSAR (mt-QSAR) models. In this work, we introduce the technique 2D MI-DRAGON a new predictor for DPIs based on two different well-known software. We use the software MARCH-INSIDE (MI) to calculate 3D structural parameters for targets and the software DRAGON was used to calculated 2D molecular descriptors all drugs showing known DPIs present in the Drug Bank (US FDA benchmark dataset). Both classes of parameters were used as input of different Artificial Neural Network (ANN) algorithms to seek an accurate non-linear mt-QSAR predictor. The best ANN model found is a Multi-Layer Perceptron (MLP) with profile MLP 21:21-31-1:1. This MLP classifies correctly 303 out of 339 DPIs (Sensitivity = 89.38%) and 480 out of 510 nDPIs (Specificity = 94.12%), corresponding to training Accuracy = 92.23%. The validation of the model was carried out by means of external predicting series with Sensitivity = 92.18% (625/678 DPIs; Specificity = 90.12% (730/780 nDPIs) and Accuracy = 91.06%. 2D MI-DRAGON offers a good opportunity for fast-track calculation of all possible DPIs of one drug enabling us to re-construct large drug-target or DPIs Complex Networks (CNs). For instance, we reconstructed the CN of the US FDA benchmark dataset with 855 nodes 519 drugs+336 targets). We predicted CN with similar topology (observed and predicted values of average distance are equal to 6.7 vs. 6.6). These CNs can be used to explore

  18. Exploring the composition of protein-ligand binding sites on a large scale.

    Directory of Open Access Journals (Sweden)

    Nickolay A Khazanov

    Full Text Available The residue composition of a ligand binding site determines the interactions available for diffusion-mediated ligand binding, and understanding general composition of these sites is of great importance if we are to gain insight into the functional diversity of the proteome. Many structure-based drug design methods utilize such heuristic information for improving prediction or characterization of ligand-binding sites in proteins of unknown function. The Binding MOAD database if one of the largest curated sets of protein-ligand complexes, and provides a source of diverse, high-quality data for establishing general trends of residue composition from currently available protein structures. We present an analysis of 3,295 non-redundant proteins with 9,114 non-redundant binding sites to identify residues over-represented in binding regions versus the rest of the protein surface. The Binding MOAD database delineates biologically-relevant "valid" ligands from "invalid" small-molecule ligands bound to the protein. Invalids are present in the crystallization medium and serve no known biological function. Contacts are found to differ between these classes of ligands, indicating that residue composition of biologically relevant binding sites is distinct not only from the rest of the protein surface, but also from surface regions capable of opportunistic binding of non-functional small molecules. To confirm these trends, we perform a rigorous analysis of the variation of residue propensity with respect to the size of the dataset and the content bias inherent in structure sets obtained from a large protein structure database. The optimal size of the dataset for establishing general trends of residue propensities, as well as strategies for assessing the significance of such trends, are suggested for future studies of binding-site composition.

  19. A web server for analysis, comparison and prediction of protein ligand binding sites.

    Science.gov (United States)

    Singh, Harinder; Srivastava, Hemant Kumar; Raghava, Gajendra P S

    2016-03-25

    One of the major challenges in the field of system biology is to understand the interaction between a wide range of proteins and ligands. In the past, methods have been developed for predicting binding sites in a protein for a limited number of ligands. In order to address this problem, we developed a web server named 'LPIcom' to facilitate users in understanding protein-ligand interaction. Analysis, comparison and prediction modules are available in the "LPIcom' server to predict protein-ligand interacting residues for 824 ligands. Each ligand must have at least 30 protein binding sites in PDB. Analysis module of the server can identify residues preferred in interaction and binding motif for a given ligand; for example residues glycine, lysine and arginine are preferred in ATP binding sites. Comparison module of the server allows comparing protein-binding sites of multiple ligands to understand the similarity between ligands based on their binding site. This module indicates that ATP, ADP and GTP ligands are in the same cluster and thus their binding sites or interacting residues exhibit a high level of similarity. Propensity-based prediction module has been developed for predicting ligand-interacting residues in a protein for more than 800 ligands. In addition, a number of web-based tools have been integrated to facilitate users in creating web logo and two-sample between ligand interacting and non-interacting residues. In summary, this manuscript presents a web-server for analysis of ligand interacting residue. This server is available for public use from URL http://crdd.osdd.net/raghava/lpicom .

  20. Composition of Overlapping Protein-Protein and Protein-Ligand Interfaces.

    Directory of Open Access Journals (Sweden)

    Ruzianisra Mohamed

    Full Text Available Protein-protein interactions (PPIs play a major role in many biological processes and they represent an important class of targets for therapeutic intervention. However, targeting PPIs is challenging because often no convenient natural substrates are available as starting point for small-molecule design. Here, we explored the characteristics of protein interfaces in five non-redundant datasets of 174 protein-protein (PP complexes, and 161 protein-ligand (PL complexes from the ABC database, 436 PP complexes, and 196 PL complexes from the PIBASE database and a dataset of 89 PL complexes from the Timbal database. In all cases, the small molecule ligands must bind at the respective PP interface. We observed similar amino acid frequencies in all three datasets. Remarkably, also the characteristics of PP contacts and overlapping PL contacts are highly similar.

  1. Comparison of molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics-three-dimensional reference interaction site model (MM-3D-RISM) method to calculate the binding free energy of protein-ligand complexes: Effect of metal ion and advance statistical test

    Science.gov (United States)

    Pandey, Preeti; Srivastava, Rakesh; Bandyopadhyay, Pradipta

    2018-03-01

    The relative performance of MM-PBSA and MM-3D-RISM methods to estimate the binding free energy of protein-ligand complexes is investigated by applying these to three proteins (Dihydrofolate Reductase, Catechol-O-methyltransferase, and Stromelysin-1) differing in the number of metal ions they contain. None of the computational methods could distinguish all the ligands based on their calculated binding free energies (as compared to experimental values). The difference between the two comes from both polar and non-polar part of solvation. For charged ligand case, MM-PBSA and MM-3D-RISM give a qualitatively different result for the polar part of solvation.

  2. LiGRO: a graphical user interface for protein-ligand molecular dynamics.

    Science.gov (United States)

    Kagami, Luciano Porto; das Neves, Gustavo Machado; da Silva, Alan Wilter Sousa; Caceres, Rafael Andrade; Kawano, Daniel Fábio; Eifler-Lima, Vera Lucia

    2017-10-04

    To speed up the drug-discovery process, molecular dynamics (MD) calculations performed in GROMACS can be coupled to docking simulations for the post-screening analyses of large compound libraries. This requires generating the topology of the ligands in different software, some basic knowledge of Linux command lines, and a certain familiarity in handling the output files. LiGRO-the python-based graphical interface introduced here-was designed to overcome these protein-ligand parameterization challenges by allowing the graphical (non command line-based) control of GROMACS (MD and analysis), ACPYPE (ligand topology builder) and PLIP (protein-binder interactions monitor)-programs that can be used together to fully perform and analyze the outputs of complex MD simulations (including energy minimization and NVT/NPT equilibration). By allowing the calculation of linear interaction energies in a simple and quick fashion, LiGRO can be used in the drug-discovery pipeline to select compounds with a better protein-binding interaction profile. The design of LiGRO allows researchers to freely download and modify the software, with the source code being available under the terms of a GPLv3 license from http://www.ufrgs.br/lasomfarmacia/ligro/ .

  3. Locating binding poses in protein-ligand systems using reconnaissance metadynamics

    Science.gov (United States)

    Söderhjelm, Pär; Tribello, Gareth A.; Parrinello, Michele

    2012-01-01

    A molecular dynamics-based protocol is proposed for finding and scoring protein-ligand binding poses. This protocol uses the recently developed reconnaissance metadynamics method, which employs a self-learning algorithm to construct a bias that pushes the system away from the kinetic traps where it would otherwise remain. The exploration of phase space with this algorithm is shown to be roughly six to eight times faster than unbiased molecular dynamics and is only limited by the time taken to diffuse about the surface of the protein. We apply this method to the well-studied trypsin–benzamidine system and show that we are able to refind all the poses obtained from a reference EADock blind docking calculation. These poses can be scored based on the length of time the system remains trapped in the pose. Alternatively, one can perform dimensionality reduction on the output trajectory and obtain a map of phase space that can be used in more expensive free-energy calculations. PMID:22440749

  4. INTERACTIVE GLOBAL NETWORK FOR WEATHER DATA OBTAINING, EXCHANGE AND DISSEMINATION

    Directory of Open Access Journals (Sweden)

    Ю.А. Авер’янова

    2012-12-01

    Full Text Available  The possibility to enhance the weather information provision of relevant customers is considered. It is based on the use of the complex global system for weather information obtaining, exchange and dissemination. The structural diagram of the system is proposed. The structural diagram is completed with addition connections that allow to pay strong attention on the most dangerous meteorological phenomena at the critical moment of flight. The proposed approach gives possibility to aircraft crew to select and use specified operative information and increase the probability for proper decision taking. The aircraft are used as the dynamic elements for data obtaining and exchange in the frame of the global system for weather information obtaining, exchange and dissemination.

  5. Discovering protein-ligand chalcogen bonding in the protein data bank using endocyclic sulfur-containing heterocycles as ligand search subsets.

    Science.gov (United States)

    Mitchell, Miguel O

    2017-09-24

    The chalcogen bond, the noncovalent, electrostatic attraction between covalently bonded atoms in group 16 and Lewis bases, is present in protein-ligand interactions based on X-ray structures deposited in the Protein Data Bank (PDB). Discovering protein-ligand chalcogen bonding in the PDB employed a strategy that focused on searching the database for protein complexes of five-membered, heterocyclic ligands containing endocyclic sulfur with endo electron-withdrawing groups (isothiazoles; thiazoles; 1,2,3-, 1,2.4-, 1,2,5-, 1,3,4-thiadiazoles) and thiophenes with exo electron-withdrawing groups, e.g., 2-chloro, 2-bromo, 2-amino, 2-alkylthio. Out of 930 ligands investigated, 33 or 3.5% have protein-ligand S---O interactions of which 31 are chalcogen bonds and two appear to be S---HO hydrogen bonds. The bond angles for some of the chalcogen bonds found in the PDB are less than 90°, and an electrostatic model is proposed to explain this phenomenon.

  6. Associative self-anchoring interacts with obtainability of chosen objects

    Directory of Open Access Journals (Sweden)

    Dean eMobbs

    2016-01-01

    Full Text Available While there is evidence that implicit self-esteem transfers to chosen objects (associative self-anchoring, it is still unknown whether this phenomenon extends to explicit self-esteem. Moreover, whether the knowledge that these objects might belong to the self in the future or not affects the evaluation of these objects has yet to be tested. Here, we demonstrate that evaluations of chosen objects are further enhanced when they are obtainable as compared to when they are not in participants with high explicit self-esteem, whereas participants with low explicit self-esteem exhibit the opposite pattern. These findings extend previous results and shed new light on the role of self-esteem in altering preferences for chosen objects depending on their obtainability.

  7. Consistent two-dimensional visualization of protein-ligand complex series

    Directory of Open Access Journals (Sweden)

    Stierand Katrin

    2011-06-01

    Full Text Available Abstract Background The comparative two-dimensional graphical representation of protein-ligand complex series featuring different ligands bound to the same active site offers a quick insight in their binding mode differences. In comparison to arbitrary orientations of the residue molecules in the individual complex depictions a consistent placement improves the legibility and comparability within the series. The automatic generation of such consistent layouts offers the possibility to apply it to large data sets originating from computer-aided drug design methods. Results We developed a new approach, which automatically generates a consistent layout of interacting residues for a given series of complexes. Based on the structural three-dimensional input information, a global two-dimensional layout for all residues of the complex ensemble is computed. The algorithm incorporates the three-dimensional adjacencies of the active site residues in order to find an universally valid circular arrangement of the residues around the ligand. Subsequent to a two-dimensional ligand superimposition step, a global placement for each residue is derived from the set of already placed ligands. The method generates high-quality layouts, showing mostly overlap-free solutions with molecules which are displayed as structure diagrams providing interaction information in atomic detail. Application examples document an improved legibility compared to series of diagrams whose layouts are calculated independently from each other. Conclusions The presented method extends the field of complex series visualizations. A series of molecules binding to the same protein active site is drawn in a graphically consistent way. Compared to existing approaches these drawings substantially simplify the visual analysis of large compound series.

  8. Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding.

    Science.gov (United States)

    Katkova, E V; Onufriev, A V; Aguilar, B; Sulimov, V B

    2017-03-01

    In this study several commonly used implicit solvent models are compared with respect to their accuracy of estimating solvation energies of small molecules and proteins, as well as desolvation penalty in protein-ligand binding. The test set consists of 19 small proteins, 104 small molecules, and 15 protein-ligand complexes. We compared predicted hydration energies of small molecules with their experimental values; the results of the solvation and desolvation energy calculations for small molecules, proteins and protein-ligand complexes in water were also compared with Thermodynamic Integration calculations based on TIP3P water model and Amber12 force field. The following implicit solvent (water) models considered here are: PCM (Polarized Continuum Model implemented in DISOLV and MCBHSOLV programs), GB (Generalized Born method implemented in DISOLV program, S-GB, and GBNSR6 stand-alone version), COSMO (COnductor-like Screening Model implemented in the DISOLV program and the MOPAC package) and the Poisson-Boltzmann model (implemented in the APBS program). Different parameterizations of the molecules were examined: we compared MMFF94 force field, Amber12 force field and the quantum-chemical semi-empirical PM7 method implemented in the MOPAC package. For small molecules, all of the implicit solvent models tested here yield high correlation coefficients (0.87-0.93) between the calculated solvation energies and the experimental values of hydration energies. For small molecules high correlation (0.82-0.97) with the explicit solvent energies is seen as well. On the other hand, estimated protein solvation energies and protein-ligand binding desolvation energies show substantial discrepancy (up to 10kcal/mol) with the explicit solvent reference. The correlation of polar protein solvation energies and protein-ligand desolvation energies with the corresponding explicit solvent results is 0.65-0.99 and 0.76-0.96 respectively, though this difference in correlations is caused

  9. [Supercomputer investigation of the protein-ligand system low-energy minima].

    Science.gov (United States)

    Oferkin, I V; Sulimov, A V; Katkova, E V; Kutov, D K; Grigoriev, F V; Kondakova, O A; Sulimov, V B

    2015-01-01

    The accuracy of the protein-ligand binding energy calculations and ligand positioning is strongly influenced by the choice of the docking target function. This work demonstrates the evaluation of the five different target functions used in docking: functions based on MMFF94 force field and functions based on PM7 quantum-chemical method accounting or without accounting the implicit solvent model (PCM, COSMO or SGB). For these purposes the ligand positions corresponding to the minima of the target function and the experimentally known ligand positions in the protein active site (crystal ligand positions) were compared. Each function was examined on the same test-set of 16 protein-ligand complexes. The new parallelized docking program FLM based on Monte Carlo search algorithm was developed to perform the comprehensive low-energy minima search and to calculate the protein-ligand binding energy. This study demonstrates that the docking target function based on the MMFF94 force field can be used to detect the crystal or near crystal positions of the ligand by the finding the low-energy local minima spectrum of the target function. The importance of solvent accounting in the docking process for the accurate ligand positioning is also shown. The accuracy of the ligand positioning as well as the correlation between the calculated and experimentally determined protein-ligand binding energies are improved when the MMFF94 force field is substituted by the new PM7 method with implicit solvent accounting.

  10. Nanoparticle-based receptors mimic protein-ligand recognition

    OpenAIRE

    Riccardi, Laura; Gabrielli, Luca; Sun, Xiaohuan; Biasi, Federico De; Rastrelli, Federico; Mancin, Fabrizio; De Vivo, Marco

    2017-01-01

    Summary The self-assembly of a monolayer of ligands on the surface of noble-metal nanoparticles dictates the fundamental nanoparticle's behavior and its functionality. In this combined computational-experimental study, we analyze the structure, organization, and dynamics of functionalized coating thiols in monolayer-protected gold nanoparticles (AuNPs). We explain how functionalized coating thiols self-organize through a delicate and somehow counterintuitive balance of interactions within the...

  11. In Silico Generation of Peptides by Replica Exchange Monte Carlo: Docking-Based Optimization of Maltose-Binding-Protein Ligands.

    Directory of Open Access Journals (Sweden)

    Anna Russo

    Full Text Available Short peptides can be designed in silico and synthesized through automated techniques, making them advantageous and versatile protein binders. A number of docking-based algorithms allow for a computational screening of peptides as binders. Here we developed ex-novo peptides targeting the maltose site of the Maltose Binding Protein, the prototypical system for the study of protein ligand recognition. We used a Monte Carlo based protocol, to computationally evolve a set of octapeptides starting from a polialanine sequence. We screened in silico the candidate peptides and characterized their binding abilities by surface plasmon resonance, fluorescence and electrospray ionization mass spectrometry assays. These experiments showed the designed binders to recognize their target with micromolar affinity. We finally discuss the obtained results in the light of further improvement in the ex-novo optimization of peptide based binders.

  12. Computational Approaches to the Chemical Equilibrium Constant in Protein-ligand Binding.

    Science.gov (United States)

    Montalvo-Acosta, Joel José; Cecchini, Marco

    2016-12-01

    The physiological role played by protein-ligand recognition has motivated the development of several computational approaches to the ligand binding affinity. Some of them, termed rigorous, have a strong theoretical foundation but involve too much computation to be generally useful. Some others alleviate the computational burden by introducing strong approximations and/or empirical calibrations, which also limit their general use. Most importantly, there is no straightforward correlation between the predictive power and the level of approximation introduced. Here, we present a general framework for the quantitative interpretation of protein-ligand binding based on statistical mechanics. Within this framework, we re-derive self-consistently the fundamental equations of some popular approaches to the binding constant and pinpoint the inherent approximations. Our analysis represents a first step towards the development of variants with optimum accuracy/efficiency ratio for each stage of the drug discovery pipeline. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Strength and Character of Halogen Bonds in Protein-Ligand Complexes

    Czech Academy of Sciences Publication Activity Database

    Riley, Kevin Eugene; Hobza, Pavel

    2011-01-01

    Roč. 11, č. 10 (2011), s. 4272-4278 ISSN 1528-7483 R&D Projects: GA MŠk LC512 Grant - others:Research and Development for Innovations of European Social Fund(XE) CZ.1.05/2.1.00/03.0058 Institutional research plan: CEZ:AV0Z40550506 Keywords : halogen bond * protein-ligand complexes * calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.720, year: 2011

  14. Automatic generation of bioinformatics tools for predicting protein-ligand binding sites.

    Science.gov (United States)

    Komiyama, Yusuke; Banno, Masaki; Ueki, Kokoro; Saad, Gul; Shimizu, Kentaro

    2016-03-15

    Predictive tools that model protein-ligand binding on demand are needed to promote ligand research in an innovative drug-design environment. However, it takes considerable time and effort to develop predictive tools that can be applied to individual ligands. An automated production pipeline that can rapidly and efficiently develop user-friendly protein-ligand binding predictive tools would be useful. We developed a system for automatically generating protein-ligand binding predictions. Implementation of this system in a pipeline of Semantic Web technique-based web tools will allow users to specify a ligand and receive the tool within 0.5-1 day. We demonstrated high prediction accuracy for three machine learning algorithms and eight ligands. The source code and web application are freely available for download at http://utprot.net They are implemented in Python and supported on Linux. shimizu@bi.a.u-tokyo.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

  15. GalaxyDock BP2 score: a hybrid scoring function for accurate protein-ligand docking

    Science.gov (United States)

    Baek, Minkyung; Shin, Woong-Hee; Chung, Hwan Won; Seok, Chaok

    2017-07-01

    Protein-ligand docking is a useful tool for providing atomic-level understanding of protein functions in nature and design principles for artificial ligands or proteins with desired properties. The ability to identify the true binding pose of a ligand to a target protein among numerous possible candidate poses is an essential requirement for successful protein-ligand docking. Many previously developed docking scoring functions were trained to reproduce experimental binding affinities and were also used for scoring binding poses. However, in this study, we developed a new docking scoring function, called GalaxyDock BP2 Score, by directly training the scoring power of binding poses. This function is a hybrid of physics-based, empirical, and knowledge-based score terms that are balanced to strengthen the advantages of each component. The performance of the new scoring function exhibits significant improvement over existing scoring functions in decoy pose discrimination tests. In addition, when the score is used with the GalaxyDock2 protein-ligand docking program, it outperformed other state-of-the-art docking programs in docking tests on the Astex diverse set, the Cross2009 benchmark set, and the Astex non-native set. GalaxyDock BP2 Score and GalaxyDock2 with this score are freely available at http://galaxy.seoklab.org/softwares/galaxydock.html.

  16. PSOVina: The hybrid particle swarm optimization algorithm for protein-ligand docking.

    Science.gov (United States)

    Ng, Marcus C K; Fong, Simon; Siu, Shirley W I

    2015-06-01

    Protein-ligand docking is an essential step in modern drug discovery process. The challenge here is to accurately predict and efficiently optimize the position and orientation of ligands in the binding pocket of a target protein. In this paper, we present a new method called PSOVina which combined the particle swarm optimization (PSO) algorithm with the efficient Broyden-Fletcher-Goldfarb-Shannon (BFGS) local search method adopted in AutoDock Vina to tackle the conformational search problem in docking. Using a diverse data set of 201 protein-ligand complexes from the PDBbind database and a full set of ligands and decoys for four representative targets from the directory of useful decoys (DUD) virtual screening data set, we assessed the docking performance of PSOVina in comparison to the original Vina program. Our results showed that PSOVina achieves a remarkable execution time reduction of 51-60% without compromising the prediction accuracies in the docking and virtual screening experiments. This improvement in time efficiency makes PSOVina a better choice of a docking tool in large-scale protein-ligand docking applications. Our work lays the foundation for the future development of swarm-based algorithms in molecular docking programs. PSOVina is freely available to non-commercial users at http://cbbio.cis.umac.mo .

  17. High Throughput, Label-free Screening Small Molecule Compound Libraries for Protein-Ligands using Combination of Small Molecule Microarrays and a Special Ellipsometry-based Optical Scanner.

    Science.gov (United States)

    Landry, James P; Fei, Yiyan; Zhu, X D

    2011-12-01

    Small-molecule compounds remain the major source of therapeutic and preventative drugs. Developing new drugs against a protein target often requires screening large collections of compounds with diverse structures for ligands or ligand fragments that exhibit sufficiently affinity and desirable inhibition effect on the target before further optimization and development. Since the number of small molecule compounds is large, high-throughput screening (HTS) methods are needed. Small-molecule microarrays (SMM) on a solid support in combination with a suitable binding assay form a viable HTS platform. We demonstrate that by combining an oblique-incidence reflectivity difference optical scanner with SMM we can screen 10,000 small-molecule compounds on a single glass slide for protein ligands without fluorescence labeling. Furthermore using such a label-free assay platform we can simultaneously acquire binding curves of a solution-phase protein to over 10,000 immobilized compounds, thus enabling full characterization of protein-ligand interactions over a wide range of affinity constants.

  18. Limits on Interactions between Weakly Interacting Massive Particles and Nucleons Obtained with CsI(Tl) Crystal Detectors

    International Nuclear Information System (INIS)

    Lee, H. S.; Bhang, H. C.; Choi, J. H.; Kim, D. W.; Kim, S. C.; Kim, S. K.; Kwak, J. W.; Lee, J.; Lee, J. H.; Lee, M. J.; Lee, S. J.; Myung, S. S.; Ryu, S.; Dao, H.; Li, J.; Li, X.; Li, Y. J.; Yue, Q.; Zhu, J. J.; Hahn, I. S.

    2007-01-01

    The Korea Invisible Mass Search (KIMS) experiment presents new limits on the weakly interacting massive particle (WIMP)-nucleon cross section using data from an exposure of 3409 kg·d taken with low-background CsI(Tl) crystals at the Yangyang Underground Laboratory. The most stringent limit on the spin-dependent interaction for a pure proton case is obtained. The DAMA signal region for both spin-independent and spin-dependent interactions for the WIMP masses greater than 20 GeV/c 2 is excluded by the single experiment with crystal scintillators

  19. The role of interactive control systems in obtaining internal consistency in the management control system package

    DEFF Research Database (Denmark)

    Toldbod, Thomas; Israelsen, Poul

    2014-01-01

    Companies rely on multiple Management Control Systems to obtain their short and long term objectives. When applying a multifaceted perspective on Management Control System the concept of internal consistency has been found to be important in obtaining goal congruency in the company. However, to d...... management is aware of this shortcoming they use the cybernetic controls more interactively to overcome this shortcoming, whereby the cybernetic controls are also used as a learning platform and not just for performance control....

  20. Control of Anther Cell Differentiation by the Small Protein Ligand TPD1 and Its Receptor EMS1 in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Jian Huang

    2016-08-01

    Full Text Available A fundamental feature of sexual reproduction in plants and animals is the specification of reproductive cells that conduct meiosis to form gametes, and the associated somatic cells that provide nutrition and developmental cues to ensure successful gamete production. The anther, which is the male reproductive organ in seed plants, produces reproductive microsporocytes (pollen mother cells and surrounding somatic cells. The microsporocytes yield pollen via meiosis, and the somatic cells, particularly the tapetum, are required for the normal development of pollen. It is not known how the reproductive cells affect the differentiation of these somatic cells, and vice versa. Here, we use molecular genetics, cell biological, and biochemical approaches to demonstrate that TPD1 (TAPETUM DETERMINANT1 is a small secreted cysteine-rich protein ligand that interacts with the LRR (Leucine-Rich Repeat domain of the EMS1 (EXCESS MICROSPOROCYTES1 receptor kinase at two sites. Analyses of the expressions and localizations of TPD1 and EMS1, ectopic expression of TPD1, experimental missorting of TPD1, and ablation of microsporocytes yielded results suggesting that the precursors of microsporocyte/microsporocyte-derived TPD1 and pre-tapetal-cell-localized EMS1 initially promote the periclinal division of secondary parietal cells and then determine one of the two daughter cells as a functional tapetal cell. Our results also indicate that tapetal cells suppress microsporocyte proliferation. Collectively, our findings show that tapetal cell differentiation requires reproductive-cell-secreted TPD1, illuminating a novel mechanism whereby signals from reproductive cells determine somatic cell fate in plant sexual reproduction.

  1. A general approach for developing system-specific functions to score protein-ligand docked complexes using support vector inductive logic programming.

    Science.gov (United States)

    Amini, Ata; Shrimpton, Paul J; Muggleton, Stephen H; Sternberg, Michael J E

    2007-12-01

    Despite the increased recent use of protein-ligand and protein-protein docking in the drug discovery process due to the increases in computational power, the difficulty of accurately ranking the binding affinities of a series of ligands or a series of proteins docked to a protein receptor remains largely unsolved. This problem is of major concern in lead optimization procedures and has lead to the development of scoring functions tailored to rank the binding affinities of a series of ligands to a specific system. However, such methods can take a long time to develop and their transferability to other systems remains open to question. Here we demonstrate that given a suitable amount of background information a new approach using support vector inductive logic programming (SVILP) can be used to produce system-specific scoring functions. Inductive logic programming (ILP) learns logic-based rules for a given dataset that can be used to describe properties of each member of the set in a qualitative manner. By combining ILP with support vector machine regression, a quantitative set of rules can be obtained. SVILP has previously been used in a biological context to examine datasets containing a series of singular molecular structures and properties. Here we describe the use of SVILP to produce binding affinity predictions of a series of ligands to a particular protein. We also for the first time examine the applicability of SVILP techniques to datasets consisting of protein-ligand complexes. Our results show that SVILP performs comparably with other state-of-the-art methods on five protein-ligand systems as judged by similar cross-validated squares of their correlation coefficients. A McNemar test comparing SVILP to CoMFA and CoMSIA across the five systems indicates our method to be significantly better on one occasion. The ability to graphically display and understand the SVILP-produced rules is demonstrated and this feature of ILP can be used to derive hypothesis for

  2. istar: a web platform for large-scale protein-ligand docking.

    Directory of Open Access Journals (Sweden)

    Hongjian Li

    Full Text Available Protein-ligand docking is a key computational method in the design of starting points for the drug discovery process. We are motivated by the desire to automate large-scale docking using our popular docking engine idock and thus have developed a publicly-accessible web platform called istar. Without tedious software installation, users can submit jobs using our website. Our istar website supports 1 filtering ligands by desired molecular properties and previewing the number of ligands to dock, 2 monitoring job progress in real time, and 3 visualizing ligand conformations and outputting free energy and ligand efficiency predicted by idock, binding affinity predicted by RF-Score, putative hydrogen bonds, and supplier information for easy purchase, three useful features commonly lacked on other online docking platforms like DOCK Blaster or iScreen. We have collected 17,224,424 ligands from the All Clean subset of the ZINC database, and revamped our docking engine idock to version 2.0, further improving docking speed and accuracy, and integrating RF-Score as an alternative rescoring function. To compare idock 2.0 with the state-of-the-art AutoDock Vina 1.1.2, we have carried out a rescoring benchmark and a redocking benchmark on the 2,897 and 343 protein-ligand complexes of PDBbind v2012 refined set and CSAR NRC HiQ Set 24Sept2010 respectively, and an execution time benchmark on 12 diverse proteins and 3,000 ligands of different molecular weight. Results show that, under various scenarios, idock achieves comparable success rates while outperforming AutoDock Vina in terms of docking speed by at least 8.69 times and at most 37.51 times. When evaluated on the PDBbind v2012 core set, our istar platform combining with RF-Score manages to reproduce Pearson's correlation coefficient and Spearman's correlation coefficient of as high as 0.855 and 0.859 respectively between the experimental binding affinity and the predicted binding affinity of the docked

  3. istar: a web platform for large-scale protein-ligand docking.

    Science.gov (United States)

    Li, Hongjian; Leung, Kwong-Sak; Ballester, Pedro J; Wong, Man-Hon

    2014-01-01

    Protein-ligand docking is a key computational method in the design of starting points for the drug discovery process. We are motivated by the desire to automate large-scale docking using our popular docking engine idock and thus have developed a publicly-accessible web platform called istar. Without tedious software installation, users can submit jobs using our website. Our istar website supports 1) filtering ligands by desired molecular properties and previewing the number of ligands to dock, 2) monitoring job progress in real time, and 3) visualizing ligand conformations and outputting free energy and ligand efficiency predicted by idock, binding affinity predicted by RF-Score, putative hydrogen bonds, and supplier information for easy purchase, three useful features commonly lacked on other online docking platforms like DOCK Blaster or iScreen. We have collected 17,224,424 ligands from the All Clean subset of the ZINC database, and revamped our docking engine idock to version 2.0, further improving docking speed and accuracy, and integrating RF-Score as an alternative rescoring function. To compare idock 2.0 with the state-of-the-art AutoDock Vina 1.1.2, we have carried out a rescoring benchmark and a redocking benchmark on the 2,897 and 343 protein-ligand complexes of PDBbind v2012 refined set and CSAR NRC HiQ Set 24Sept2010 respectively, and an execution time benchmark on 12 diverse proteins and 3,000 ligands of different molecular weight. Results show that, under various scenarios, idock achieves comparable success rates while outperforming AutoDock Vina in terms of docking speed by at least 8.69 times and at most 37.51 times. When evaluated on the PDBbind v2012 core set, our istar platform combining with RF-Score manages to reproduce Pearson's correlation coefficient and Spearman's correlation coefficient of as high as 0.855 and 0.859 respectively between the experimental binding affinity and the predicted binding affinity of the docked conformation. istar

  4. Empirical scoring functions for advanced protein-ligand docking with PLANTS.

    Science.gov (United States)

    Korb, Oliver; Stützle, Thomas; Exner, Thomas E

    2009-01-01

    In this paper we present two empirical scoring functions, PLANTS(CHEMPLP) and PLANTS(PLP), designed for our docking algorithm PLANTS (Protein-Ligand ANT System), which is based on ant colony optimization (ACO). They are related, regarding their functional form, to parts of already published scoring functions and force fields. The parametrization procedure described here was able to identify several parameter settings showing an excellent performance for the task of pose prediction on two test sets comprising 298 complexes in total. Up to 87% of the complexes of the Astex diverse set and 77% of the CCDC/Astex clean listnc (noncovalently bound complexes of the clean list) could be reproduced with root-mean-square deviations of less than 2 A with respect to the experimentally determined structures. A comparison with the state-of-the-art docking tool GOLD clearly shows that this is, especially for the druglike Astex diverse set, an improvement in pose prediction performance. Additionally, optimized parameter settings for the search algorithm were identified, which can be used to balance pose prediction reliability and search speed.

  5. Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures.

    Science.gov (United States)

    Ahmed, Aqeel; Smith, Richard D; Clark, Jordan J; Dunbar, James B; Carlson, Heather A

    2015-01-01

    For over 10 years, Binding MOAD (Mother of All Databases; http://www.BindingMOAD.org) has been one of the largest resources for high-quality protein-ligand complexes and associated binding affinity data. Binding MOAD has grown at the rate of 1994 complexes per year, on average. Currently, it contains 23,269 complexes and 8156 binding affinities. Our annual updates curate the data using a semi-automated literature search of the references cited within the PDB file, and we have recently upgraded our website and added new features and functionalities to better serve Binding MOAD users. In order to eliminate the legacy application server of the old platform and to accommodate new changes, the website has been completely rewritten in the LAMP (Linux, Apache, MySQL and PHP) environment. The improved user interface incorporates current third-party plugins for better visualization of protein and ligand molecules, and it provides features like sorting, filtering and filtered downloads. In addition to the field-based searching, Binding MOAD now can be searched by structural queries based on the ligand. In order to remove redundancy, Binding MOAD records are clustered in different families based on 90% sequence identity. The new Binding MOAD, with the upgraded platform, features and functionalities, is now equipped to better serve its users. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. @TOME-2: a new pipeline for comparative modeling of protein-ligand complexes.

    Science.gov (United States)

    Pons, Jean-Luc; Labesse, Gilles

    2009-07-01

    @TOME 2.0 is new web pipeline dedicated to protein structure modeling and small ligand docking based on comparative analyses. @TOME 2.0 allows fold recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation. These tasks are routinely used in sequence analyses for structure prediction. In our pipeline the necessary software is efficiently interconnected in an original manner to accelerate all the processes. Furthermore, we have also connected comparative docking of small ligands that is performed using protein-protein superposition. The input is a simple protein sequence in one-letter code with no comment. The resulting 3D model, protein-ligand complexes and structural alignments can be visualized through dedicated Web interfaces or can be downloaded for further studies. These original features will aid in the functional annotation of proteins and the selection of templates for molecular modeling and virtual screening. Several examples are described to highlight some of the new functionalities provided by this pipeline. The server and its documentation are freely available at http://abcis.cbs.cnrs.fr/AT2/

  7. Entanglement in bipartite pure states of an interacting boson gas obtained by local projective measurements

    International Nuclear Information System (INIS)

    Paraan, Francis N. C.; Korepin, Vladimir E.; Molina-Vilaplana, Javier; Bose, Sougato

    2011-01-01

    We quantify the extractable entanglement of excited states of a Lieb-Liniger gas that are obtained from coarse-grained measurements on the ground state in which the boson number in one of two complementary contiguous partitions of the gas is determined. Numerically exact results obtained from the coordinate Bethe ansatz show that the von Neumann entropy of the resulting bipartite pure state increases monotonically with the strength of repulsive interactions and saturates to the impenetrable-boson limiting value. We also present evidence indicating that the largest amount of entanglement can be extracted from the most probable projected state having half the number of bosons in a given partition. Our study points to a fundamental difference between the nature of the entanglement in free-bosonic and free-fermionic systems, with the entanglement in the former being zero after projection, while that in the latter (corresponding to the impenetrable-boson limit) being nonzero.

  8. A scalable and accurate method for classifying protein-ligand binding geometries using a MapReduce approach.

    Science.gov (United States)

    Estrada, T; Zhang, B; Cicotti, P; Armen, R S; Taufer, M

    2012-07-01

    We present a scalable and accurate method for classifying protein-ligand binding geometries in molecular docking. Our method is a three-step process: the first step encodes the geometry of a three-dimensional (3D) ligand conformation into a single 3D point in the space; the second step builds an octree by assigning an octant identifier to every single point in the space under consideration; and the third step performs an octree-based clustering on the reduced conformation space and identifies the most dense octant. We adapt our method for MapReduce and implement it in Hadoop. The load-balancing, fault-tolerance, and scalability in MapReduce allow screening of very large conformation spaces not approachable with traditional clustering methods. We analyze results for docking trials for 23 protein-ligand complexes for HIV protease, 21 protein-ligand complexes for Trypsin, and 12 protein-ligand complexes for P38alpha kinase. We also analyze cross docking trials for 24 ligands, each docking into 24 protein conformations of the HIV protease, and receptor ensemble docking trials for 24 ligands, each docking in a pool of HIV protease receptors. Our method demonstrates significant improvement over energy-only scoring for the accurate identification of native ligand geometries in all these docking assessments. The advantages of our clustering approach make it attractive for complex applications in real-world drug design efforts. We demonstrate that our method is particularly useful for clustering docking results using a minimal ensemble of representative protein conformational states (receptor ensemble docking), which is now a common strategy to address protein flexibility in molecular docking. Copyright © 2012 Elsevier Ltd. All rights reserved.

  9. Severe Acute Respiratory Syndrome-Coronavirus Papain-Like Novel Protease Inhibitors: Design, Synthesis, Protein-Ligand X-ray Structure and Biological Evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Arun K.; Takayama, Jun; Rao, Kalapala Venkateswar; Ratia, Kiira; Chaudhuri, Rima; Mulhearn, Debbie C.; Lee, Hyun; Nichols, Daniel B.; Baliji, Surendranath; Baker, Susan C.; Johnson, Michael E.; Mesecar, Andrew D. (Purdue); (UC); (UIC)

    2012-02-21

    The design, synthesis, X-ray crystal structure, molecular modeling, and biological evaluation of a series of new generation SARS-CoV PLpro inhibitors are described. A new lead compound 3 (6577871) was identified via high-throughput screening of a diverse chemical library. Subsequently, we carried out lead optimization and structure-activity studies to provide a series of improved inhibitors that show potent PLpro inhibition and antiviral activity against SARS-CoV infected Vero E6 cells. Interestingly, the (S)-Me inhibitor 15h (enzyme IC{sub 50} = 0.56 {mu}M; antiviral EC{sub 50} = 9.1 {mu}M) and the corresponding (R)-Me 15g (IC{sub 50} = 0.32 {mu}M; antiviral EC{sub 50} = 9.1 {mu}M) are the most potent compounds in this series, with nearly equivalent enzymatic inhibition and antiviral activity. A protein-ligand X-ray structure of 15g-bound SARS-CoV PLpro and a corresponding model of 15h docked to PLpro provide intriguing molecular insight into the ligand-binding site interactions.

  10. Discovery of a new chemical series of BRD4(1) inhibitors using protein-ligand docking and structure-guided design.

    Science.gov (United States)

    Duffy, Bryan C; Liu, Shuang; Martin, Gregory S; Wang, Ruifang; Hsia, Ming Min; Zhao, He; Guo, Cheng; Ellis, Michael; Quinn, John F; Kharenko, Olesya A; Norek, Karen; Gesner, Emily M; Young, Peter R; McLure, Kevin G; Wagner, Gregory S; Lakshminarasimhan, Damodharan; White, Andre; Suto, Robert K; Hansen, Henrik C; Kitchen, Douglas B

    2015-07-15

    Bromodomains are key transcriptional regulators that are thought to be druggable epigenetic targets for cancer, inflammation, diabetes and cardiovascular therapeutics. Of particular importance is the first of two bromodomains in bromodomain containing 4 protein (BRD4(1)). Protein-ligand docking in BRD4(1) was used to purchase a small, focused screening set of compounds possessing a large variety of core structures. Within this set, a small number of weak hits each contained a dihydroquinoxalinone ring system. We purchased other analogs with this ring system and further validated the new hit series and obtained improvement in binding inhibition. Limited exploration by new analog synthesis showed that the binding inhibition in a FRET assay could be improved to the low μM level making this new core a potential hit-to-lead series. Additionally, the predicted geometries of the initial hit and an improved analog were confirmed by X-ray co-crystallography with BRD4(1). Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Molten fuel/coolant interaction studies: some results obtained with the Windscale small shock tube rig

    International Nuclear Information System (INIS)

    Higham, E.J.; Vaughan, G.J.

    1978-02-01

    Experiments are described in which water has been brought into contact with various molten metals in a shock tube, thus simulating the fall of coolant into molten uranium dioxide in a postulated reactor accident. Impact velocities of the water on to the molten material were in the range 5 to 7 m/s. Shock-pulse pressures in the water column after impact and particle size distributions of the dispersed resolidified material that was recovered were measured. The proportion of dispersed material and the size of the shock pulse (by comparison with that expected from water hammer alone) have been used as criteria for the occurrence of a molten fuel/coolant interaction and such interactions of varying degrees of violence have been found for water/aluminium, water/bismuth, water/tin, over a range of temperatures from 350 0 C to 950 0 C, for water/boric oxide, but not for water/magnesium. (author)

  12. An evaluation of diverse methods of obtaining effective Schroedinger interaction potentials for elastic scattering

    International Nuclear Information System (INIS)

    Amos, K.; Allen, L.J.; Steward, C.; Hodgson, P.E.; Sofianos, S.A.

    1995-01-01

    Direct solution of the Schroedinger equation and inversion methods of analysis of elastic scattering data are considered to evaluate the information that they can provide about the physical interaction between colliding nuclear particles. It was found that both optical model and inversion methods based upon inverse scattering theories are subject to ambiguities. Therefore, it is essential that elastic scattering data analyses are consistent with microscopic calculations of the potential. 25 refs

  13. An evaluation of diverse methods of obtaining effective Schroedinger interaction potentials for elastic scattering

    Energy Technology Data Exchange (ETDEWEB)

    Amos, K.; Allen, L.J.; Steward, C. [Melbourne Univ., Parkville, VIC (Australia). School of Physics; Hodgson, P.E. [Oxford Univ. (United Kingdom). Dept. of Physics; Sofianos, S.A. [University of South Africa (UNISA), Pretoria (South Africa). Dept. of Physics

    1995-10-01

    Direct solution of the Schroedinger equation and inversion methods of analysis of elastic scattering data are considered to evaluate the information that they can provide about the physical interaction between colliding nuclear particles. It was found that both optical model and inversion methods based upon inverse scattering theories are subject to ambiguities. Therefore, it is essential that elastic scattering data analyses are consistent with microscopic calculations of the potential. 25 refs.

  14. Use of total cross sections for obtaining the anisotropic interaction potential in atom--diatom system

    International Nuclear Information System (INIS)

    Eccles, J.; Secrest, D.

    1977-01-01

    A study is made of the ''conservation of the total cross section'' and the ''equivalence of the total cross section'' rules for scattering from H 2 . It is shown that these rules are a better approximation than the random phase approximation would indicate. Cross section formulas are given for scattering atoms from m/sub j/ state selected molecules and it is shown that total cross sections for state selected molecules depend on the anisotropic part of the interaction potential, while the spin-averaged total cross section often depends only on the spherically symmetric part of the interaction potential. The total spin-averaged cross section is thus independent of the initial rotation state of the molecule and depends only on the relative collision energy. It is further demonstrated that isotopic substitution, which shifts the center of mass changing the symmetric part of the interaction potential, has too small an effect on the total cross section to be useful as a means of determining the anisotropy of the potential

  15. Screening small-molecule compound microarrays for protein ligands without fluorescence labeling with a high-throughput scanning microscope.

    Science.gov (United States)

    Fei, Yiyan; Landry, James P; Sun, Yungshin; Zhu, Xiangdong; Wang, Xiaobing; Luo, Juntao; Wu, Chun-Yi; Lam, Kit S

    2010-01-01

    We describe a high-throughput scanning optical microscope for detecting small-molecule compound microarrays on functionalized glass slides. It is based on measurements of oblique-incidence reflectivity difference and employs a combination of a y-scan galvometer mirror and an x-scan translation stage with an effective field of view of 2 cm x 4 cm. Such a field of view can accommodate a printed small-molecule compound microarray with as many as 10,000 to 20,000 targets. The scanning microscope is capable of measuring kinetics as well as endpoints of protein-ligand reactions simultaneously. We present the experimental results on solution-phase protein reactions with small-molecule compound microarrays synthesized from one-bead, one-compound combinatorial chemistry and immobilized on a streptavidin-functionalized glass slide.

  16. A Critical Review of Validation, Blind Testing, and Real- World Use of Alchemical Protein-Ligand Binding Free Energy Calculations.

    Science.gov (United States)

    Abel, Robert; Wang, Lingle; Mobley, David L; Friesner, Richard A

    2017-01-01

    Protein-ligand binding is among the most fundamental phenomena underlying all molecular biology, and a greater ability to more accurately and robustly predict the binding free energy of a small molecule ligand for its cognate protein is expected to have vast consequences for improving the efficiency of pharmaceutical drug discovery. We briefly reviewed a number of scientific and technical advances that have enabled alchemical free energy calculations to recently emerge as a preferred approach, and critically considered proper validation and effective use of these techniques. In particular, we characterized a selection bias effect which may be important in prospective free energy calculations, and introduced a strategy to improve the accuracy of the free energy predictions. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  17. Measuring Binding Affinity of Protein-Ligand Interaction Using Spectrophotometry: Binding of Neutral Red to Riboflavin-Binding Protein

    Science.gov (United States)

    Chenprakhon, Pirom; Sucharitakul, Jeerus; Panijpan, Bhinyo; Chaiyen, Pimchai

    2010-01-01

    The dissociation constant, K[subscript d], of the binding of riboflavin-binding protein (RP) with neutral red (NR) can be determined by titrating RP to a fixed concentration of NR. Upon adding RP to the NR solution, the maximum absorption peak of NR shifts to 545 nm from 450 nm for the free NR. The change of the absorption can be used to determine…

  18. Computer program for Scatchard analysis of protein: Ligand interaction - use for determination of soluble and nuclear steroid receptor concentrations

    International Nuclear Information System (INIS)

    Leake, R.; Cowan, S.; Eason, R.

    1998-01-01

    Steroid receptor concentration may be determined routinely in biopsy samples of breast and endometrial cancer by the competition method. This method yields data for both the soluble and nuclear fractions of the tissue. The data are usually subject to Scatchard analysis. This Appendix describes a computer program written initially for a PDP-11. It has been modified for use with IBM, Apple Macintosh and BBC microcomputers. The nature of the correction for competition is described and examples of the printout are given. The program is flexible and its use for different receptors is explained. The program can be readily adapted to other assays in which Scatchard analysis is appropriate

  19. 3D-QSAR Study of Steroidal and Azaheterocyclic Human Aromatase Inhibitors using Quantitative Profile of Protein-Ligand Interactions

    Science.gov (United States)

    Aromatase is a member of the cytochrome P450 superfamily responsible for a key step in the biosynthesis of estrogens. As estrogens are involved in the control of important reproduction-related processes, including sexual differentiation and maturation, aromatase is a potential ta...

  20. The XChemExplorer graphical workflow tool for routine or large-scale protein-ligand structure determination.

    Science.gov (United States)

    Krojer, Tobias; Talon, Romain; Pearce, Nicholas; Collins, Patrick; Douangamath, Alice; Brandao-Neto, Jose; Dias, Alexandre; Marsden, Brian; von Delft, Frank

    2017-03-01

    XChemExplorer (XCE) is a data-management and workflow tool to support large-scale simultaneous analysis of protein-ligand complexes during structure-based ligand discovery (SBLD). The user interfaces of established crystallographic software packages such as CCP4 [Winn et al. (2011), Acta Cryst. D67, 235-242] or PHENIX [Adams et al. (2010), Acta Cryst. D66, 213-221] have entrenched the paradigm that a `project' is concerned with solving one structure. This does not hold for SBLD, where many almost identical structures need to be solved and analysed quickly in one batch of work. Functionality to track progress and annotate structures is essential. XCE provides an intuitive graphical user interface which guides the user from data processing, initial map calculation, ligand identification and refinement up until data dissemination. It provides multiple entry points depending on the need of each project, enables batch processing of multiple data sets and records metadata, progress and annotations in an SQLite database. XCE is freely available and works on any Linux and Mac OS X system, and the only dependency is to have the latest version of CCP4 installed. The design and usage of this tool are described here, and its usefulness is demonstrated in the context of fragment-screening campaigns at the Diamond Light Source. It is routinely used to analyse projects comprising 1000 data sets or more, and therefore scales well to even very large ligand-design projects.

  1. Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015.

    Science.gov (United States)

    Deng, Nanjie; Flynn, William F; Xia, Junchao; Vijayan, R S K; Zhang, Baofeng; He, Peng; Mentes, Ahmet; Gallicchio, Emilio; Levy, Ronald M

    2016-09-01

    We describe binding free energy calculations in the D3R Grand Challenge 2015 for blind prediction of the binding affinities of 180 ligands to Hsp90. The present D3R challenge was built around experimental datasets involving Heat shock protein (Hsp) 90, an ATP-dependent molecular chaperone which is an important anticancer drug target. The Hsp90 ATP binding site is known to be a challenging target for accurate calculations of ligand binding affinities because of the ligand-dependent conformational changes in the binding site, the presence of ordered waters and the broad chemical diversity of ligands that can bind at this site. Our primary focus here is to distinguish binders from nonbinders. Large scale absolute binding free energy calculations that cover over 3000 protein-ligand complexes were performed using the BEDAM method starting from docked structures generated by Glide docking. Although the ligand dataset in this study resembles an intermediate to late stage lead optimization project while the BEDAM method is mainly developed for early stage virtual screening of hit molecules, the BEDAM binding free energy scoring has resulted in a moderate enrichment of ligand screening against this challenging drug target. Results show that, using a statistical mechanics based free energy method like BEDAM starting from docked poses offers better enrichment than classical docking scoring functions and rescoring methods like Prime MM-GBSA for the Hsp90 data set in this blind challenge. Importantly, among the three methods tested here, only the mean value of the BEDAM binding free energy scores is able to separate the large group of binders from the small group of nonbinders with a gap of 2.4 kcal/mol. None of the three methods that we have tested provided accurate ranking of the affinities of the 147 active compounds. We discuss the possible sources of errors in the binding free energy calculations. The study suggests that BEDAM can be used strategically to discriminate

  2. Simple Ligand-Receptor Interaction Descriptor (SILIRID) for alignment-free binding site comparison.

    Science.gov (United States)

    Chupakhin, Vladimir; Marcou, Gilles; Gaspar, Helena; Varnek, Alexandre

    2014-06-01

    We describe SILIRID (Simple Ligand-Receptor Interaction Descriptor), a novel fixed size descriptor characterizing protein-ligand interactions. SILIRID can be obtained from the binary interaction fingerprints (IFPs) by summing up the bits corresponding to identical amino acids. This results in a vector of 168 integer numbers corresponding to the product of the number of entries (20 amino acids and one cofactor) and 8 interaction types per amino acid (hydrophobic, aromatic face to face, aromatic edge to face, H-bond donated by the protein, H-bond donated by the ligand, ionic bond with protein cation and protein anion, and interaction with metal ion). Efficiency of SILIRID to distinguish different protein binding sites has been examined in similarity search in sc-PDB database, a druggable portion of the Protein Data Bank, using various protein-ligand complexes as queries. The performance of retrieval of structurally and evolutionary related classes of proteins was comparable to that of state-of-the-art approaches (ROC AUC ≈ 0.91). SILIRID can efficiently be used to visualize chemogenomic space covered by sc-PDB using Generative Topographic Mapping (GTM): sc-PDB SILIRID data form clusters corresponding to different protein types.

  3. Acetylcholinesterase complexed with bivalent ligands related to huperzine a: experimental evidence for species-dependent protein-ligand complementarity.

    Science.gov (United States)

    Wong, Dawn M; Greenblatt, Harry M; Dvir, Hay; Carlier, Paul R; Han, Yi-Fan; Pang, Yuan-Ping; Silman, Israel; Sussman, Joel L

    2003-01-15

    active-site gorge explain the switch in inhibitory potency of (-)-2a and 2b and the larger dimer/(-)-HupA potency ratios observed for TcAChE relative to rat AChE. The results offer new insights into factors affecting protein-ligand complementarity within the gorge and should assist the further development of improved AChE inhibitors.

  4. Online size-exclusion high-performance liquid chromatography light scattering and differential refractometry methods to determine degree of polymer conjugation to proteins and protein-protein or protein-ligand association states.

    Science.gov (United States)

    Kendrick, B S; Kerwin, B A; Chang, B S; Philo, J S

    2001-12-15

    Characterizing the solution structure of protein-polymer conjugates and protein-ligand interactions is important in fields such as biotechnology and biochemistry. Size-exclusion high-performance liquid chromatography with online classical light scattering (LS), refractive index (RI), and UV detection offers a powerful tool in such characterization. Novel methods are presented utilizing LS, RI, and UV signals to rapidly determine the degree of conjugation and the molecular mass of the protein conjugate. Baseline resolution of the chromatographic peaks is not required; peaks need only be sufficiently separated to represent relatively pure fractions. An improved technique for determining the polypeptide-only mass of protein conjugates is also described. These techniques are applied to determining the degree of erythropoietin glycosylation, the degree of polyethylene glycol conjugation to RNase A and brain-derived neurotrophic factor, and the solution association states of these molecules. Calibration methods for the RI, UV, and LS detectors will also be addressed, as well as online methods to determine protein extinction coefficients and dn/dc values both unconjugated and conjugated protein molecules. (c)2001 Elsevier Science.

  5. Combined quantum mechanics/molecular mechanics (QM/MM) simulations for protein-ligand complexes: free energies of binding of water molecules in influenza neuraminidase.

    Science.gov (United States)

    Woods, Christopher J; Shaw, Katherine E; Mulholland, Adrian J

    2015-01-22

    The applicability of combined quantum mechanics/molecular mechanics (QM/MM) methods for the calculation of absolute binding free energies of conserved water molecules in protein/ligand complexes is demonstrated. Here, we apply QM/MM Monte Carlo simulations to investigate binding of water molecules to influenza neuraminidase. We investigate five different complexes, including those with the drugs oseltamivir and peramivir. We investigate water molecules in two different environments, one more hydrophobic and one hydrophilic. We calculate the free-energy change for perturbation of a QM to MM representation of the bound water molecule. The calculations are performed at the BLYP/aVDZ (QM) and TIP4P (MM) levels of theory, which we have previously demonstrated to be consistent with one another for QM/MM modeling. The results show that the QM to MM perturbation is significant in both environments (greater than 1 kcal mol(-1)) and larger in the more hydrophilic site. Comparison with the same perturbation in bulk water shows that this makes a contribution to binding. The results quantify how electronic polarization differences in different environments affect binding affinity and also demonstrate that extensive, converged QM/MM free-energy simulations, with good levels of QM theory, are now practical for protein/ligand complexes.

  6. Dimensional structure of the Social Interaction Anxiety Scale according to the analysis of data obtained with a German version.

    Science.gov (United States)

    Eidecker, Judith; Glöckner-Rist, Angelika; Gerlach, Alexander L

    2010-08-01

    The Social Interaction and Anxiety Scale (SIAS) is widely used to assess social interaction anxiety. Yet its dimensional structure is still not well-defined. Especially, the conceptual pertinence of three negatively keyed items has been challenged. In this study, dimensionality of the answers of a student sample to a German SIAS version was first analyzed exploratorily. Subsequently, we tested confirmatorily several measurement models specifying different SIAS dimensions, and investigated how these relate to extraversion. The most reasonable model was cross-validated relying on data from healthy controls and social phobia sufferers. All analyses involved methods suited for an adequate handling of ordinal data. The findings confirm that three negatively keyed items are dubious indicators of social interaction anxiety. Thus, only the remaining 17 items should be used for this purpose in future studies. Analyses of their psychometric properties show, in addition, that they apparently tap three different facets of social interaction anxiety. (c) 2010 Elsevier Ltd. All rights reserved.

  7. Predicting binding affinities of protein ligands from three-dimensional models: application to peptide binding to class I major histocompatibility proteins

    DEFF Research Database (Denmark)

    Rognan, D; Lauemoller, S L; Holm, A

    1999-01-01

    A simple and fast free energy scoring function (Fresno) has been developed to predict the binding free energy of peptides to class I major histocompatibility (MHC) proteins. It differs from existing scoring functions mainly by the explicit treatment of ligand desolvation and of unfavorable protein...... coordinates of the MHC-bound peptide have first been determined with an accuracy of about 1-1.5 A. Furthermore, it may be easily recalibrated for any protein-ligand complex.......) and of a series of 16 peptides to H-2K(k). Predictions were more accurate for HLA-A2-binding peptides as the training set had been built from experimentally determined structures. The average error in predicting the binding free energy of the test peptides was 3.1 kJ/mol. For the homology model-derived equation...

  8. Optimization of memory use of fragment extension-based protein-ligand docking with an original fast minimum cost flow algorithm.

    Science.gov (United States)

    Yanagisawa, Keisuke; Komine, Shunta; Kubota, Rikuto; Ohue, Masahito; Akiyama, Yutaka

    2018-03-16

    The need to accelerate large-scale protein-ligand docking in virtual screening against a huge compound database led researchers to propose a strategy that entails memorizing the evaluation result of the partial structure of a compound and reusing it to evaluate other compounds. However, the previous method required frequent disk accesses, resulting in insufficient acceleration. Thus, more efficient memory usage can be expected to lead to further acceleration, and optimal memory usage could be achieved by solving the minimum cost flow problem. In this research, we propose a fast algorithm for the minimum cost flow problem utilizing the characteristics of the graph generated for this problem as constraints. The proposed algorithm, which optimized memory usage, was approximately seven times faster compared to existing minimum cost flow algorithms. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

  9. Moessbauer spectroscopic characterisation of catalysts obtained by interaction between tetra-n-butyl-tin and silica or silica supported rhodium

    International Nuclear Information System (INIS)

    Millet, J.M.M.; Toyir, J.; Didillon, B.; Candy, J.P.; Nedez, C.; Basset, J.M.

    1997-01-01

    Moessbauer spectroscopy at 78 K was used to study the interaction between tetra-n-butyl-tin and the surfaces of silica or silica supported rhodium. At room temperature, the tetra-n-butyl-tin was physically adsorbed on the surfaces. After reaction under hydrogen at 373 K, the formation of grafted organometallic fragments on the Rh surface was confirmed whereas with pure silica, ≡SiO-Sn(n-C 4 H 9 ) 3 moieties were observed. After treatment at 523 K, the rhodium grafted organometallic species was completely decomposed and there was formation of a defined bimetallic RhSn compound

  10. Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2

    Science.gov (United States)

    Rifai, Eko Aditya; van Dijk, Marc; Vermeulen, Nico P. E.; Geerke, Daan P.

    2018-01-01

    Computational protein binding affinity prediction can play an important role in drug research but performing efficient and accurate binding free energy calculations is still challenging. In the context of phase 2 of the Drug Design Data Resource (D3R) Grand Challenge 2 we used our automated eTOX ALLIES approach to apply the (iterative) linear interaction energy (LIE) method and we evaluated its performance in predicting binding affinities for farnesoid X receptor (FXR) agonists. Efficiency was obtained by our pre-calibrated LIE models and molecular dynamics (MD) simulations at the nanosecond scale, while predictive accuracy was obtained for a small subset of compounds. Using our recently introduced reliability estimation metrics, we could classify predictions with higher confidence by featuring an applicability domain (AD) analysis in combination with protein-ligand interaction profiling. The outcomes of and agreement between our AD and interaction-profile analyses to distinguish and rationalize the performance of our predictions highlighted the relevance of sufficiently exploring protein-ligand interactions during training and it demonstrated the possibility to quantitatively and efficiently evaluate if this is achieved by using simulation data only.

  11. In Situ IR Characterization of CO Interacting with Rh Nanoparticles Obtained by Calcination and Reduction of Hydrotalcite-Type Precursors

    Directory of Open Access Journals (Sweden)

    F. Basile

    2011-01-01

    Full Text Available Supported Rh nanoparticles obtained by reduction in hydrogen of severely calcined Rh/Mg/Al hydrotalcite-type (HT phases have been characterized by FT-IR spectroscopy of adsorbed CO [both at room temperature (r.t. and nominal liquid nitrogen temperature] and Transmission Electron Microscopy (TEM. The effect of reducing temperature has been investigated, showing that Rh crystal size increases from 1.4 nm to 1.8 nm when the reduction temperature increases from 750°C to 950°C. The crystal growth favours the formation of bridged CO species and linear monocarbonyl species with respect to gem-dicarbonyl species; when CO adsorbs at r.t., CO disproportionation occurs on Rh and it accompanies the formation of RhI(CO2. The role of interlayer anions in the HT precursors to affect the properties of the final materials has been also investigated considering samples prepared from silicate-instead of carbonate-containing precursors. In this case, formation of RhI(CO2 and CO disproportionation do not occur, and this evidence is discussed in terms of support effect.

  12. Exploring the role of water in molecular recognition: predicting protein ligandability using a combinatorial search of surface hydration sites

    Science.gov (United States)

    Vukovic, Sinisa; Brennan, Paul E.; Huggins, David J.

    2016-09-01

    The interaction between any two biological molecules must compete with their interaction with water molecules. This makes water the most important molecule in medicine, as it controls the interactions of every therapeutic with its target. A small molecule binding to a protein is able to recognize a unique binding site on a protein by displacing bound water molecules from specific hydration sites. Quantifying the interactions of these water molecules allows us to estimate the potential of the protein to bind a small molecule. This is referred to as ligandability. In the study, we describe a method to predict ligandability by performing a search of all possible combinations of hydration sites on protein surfaces. We predict ligandability as the summed binding free energy for each of the constituent hydration sites, computed using inhomogeneous fluid solvation theory. We compared the predicted ligandability with the maximum observed binding affinity for 20 proteins in the human bromodomain family. Based on this comparison, it was determined that effective inhibitors have been developed for the majority of bromodomains, in the range from 10 to 100 nM. However, we predict that more potent inhibitors can be developed for the bromodomains BPTF and BRD7 with relative ease, but that further efforts to develop inhibitors for ATAD2 will be extremely challenging. We have also made predictions for the 14 bromodomains with no reported small molecule K d values by isothermal titration calorimetry. The calculations predict that PBRM1(1) will be a challenging target, while others such as TAF1L(2), PBRM1(4) and TAF1(2), should be highly ligandable. As an outcome of this work, we assembled a database of experimental maximal K d that can serve as a community resource assisting medicinal chemistry efforts focused on BRDs. Effective prediction of ligandability would be a very useful tool in the drug discovery process.

  13. Exploring the role of water in molecular recognition: predicting protein ligandability using a combinatorial search of surface hydration sites.

    Science.gov (United States)

    Vukovic, Sinisa; Brennan, Paul E; Huggins, David J

    2016-09-01

    The interaction between any two biological molecules must compete with their interaction with water molecules. This makes water the most important molecule in medicine, as it controls the interactions of every therapeutic with its target. A small molecule binding to a protein is able to recognize a unique binding site on a protein by displacing bound water molecules from specific hydration sites. Quantifying the interactions of these water molecules allows us to estimate the potential of the protein to bind a small molecule. This is referred to as ligandability. In the study, we describe a method to predict ligandability by performing a search of all possible combinations of hydration sites on protein surfaces. We predict ligandability as the summed binding free energy for each of the constituent hydration sites, computed using inhomogeneous fluid solvation theory. We compared the predicted ligandability with the maximum observed binding affinity for 20 proteins in the human bromodomain family. Based on this comparison, it was determined that effective inhibitors have been developed for the majority of bromodomains, in the range from 10 to 100 nM. However, we predict that more potent inhibitors can be developed for the bromodomains BPTF and BRD7 with relative ease, but that further efforts to develop inhibitors for ATAD2 will be extremely challenging. We have also made predictions for the 14 bromodomains with no reported small molecule K d values by isothermal titration calorimetry. The calculations predict that PBRM1(1) will be a challenging target, while others such as TAF1L(2), PBRM1(4) and TAF1(2), should be highly ligandable. As an outcome of this work, we assembled a database of experimental maximal K d that can serve as a community resource assisting medicinal chemistry efforts focused on BRDs. Effective prediction of ligandability would be a very useful tool in the drug discovery process.

  14. New insights into the mechanism of interaction between CO2 and polymers from thermodynamic parameters obtained by in situ ATR-FTIR spectroscopy.

    Science.gov (United States)

    Gabrienko, Anton A; Ewing, Andrew V; Chibiryaev, Andrey M; Agafontsev, Alexander M; Dubkov, Konstantin A; Kazarian, Sergei G

    2016-03-07

    This work reports new physical insights of the thermodynamic parameters and mechanisms of possible interactions occurring in polymers subjected to high-pressure CO2. ATR-FTIR spectroscopy has been used in situ to determine the thermodynamic parameters of the intermolecular interactions between CO2 and different functional groups of the polymers capable of specific interactions with sorbed CO2 molecules. Based on the measured ATR-FTIR spectra of the polymer samples subjected to high-pressure CO2 (30 bar) at different temperatures (300-340 K), it was possible to characterize polymer-polymer and CO2-polymer interactions. Particularly, the enthalpy and entropy of the formation of the specific non-covalent complexes between CO2 and the hydroxy (-OH), carbonyl (C[double bond, length as m-dash]O) and hydroxyimino ([double bond, length as m-dash]N-OH) functional groups of the polymer samples have been measured. Furthermore, the obtained spectroscopic results have provided an opportunity for the structure of these complexes to be proposed. An interesting phenomenon regarding the behavior of CO2/polymer systems has also been observed. It has been found that only for the polyketone, the value of enthalpy was negative indicating an exothermic process during the formation of the CO2-polymer non-covalent complexes. Conversely, for the polyoxime and polyalcohol samples there is a positive enthalpy determined. This is a result of the initial polymer-polymer interactions requiring more energy to break than is released during the formation of the CO2-polymer complex. The effect of increasing temperature to facilitate the breaking of the polymer-polymer interactions has also been observed. Hence, a mechanism for the formation of CO2-polymer complexes was suggested based on these results, which occurs via a two-step process: (1) the breaking of the existing polymer-polymer interactions followed by (2) the formation of new CO2-polymer non-covalent interactions.

  15. Analysis of the ionic interaction between the hydrophobin RodA and two cutinases of Aspergillus nidulans obtained via an Aspergillus oryzae expression system.

    Science.gov (United States)

    Tanaka, Takumi; Nakayama, Mayumi; Takahashi, Toru; Nanatani, Kei; Yamagata, Youhei; Abe, Keietsu

    2017-03-01

    Hydrophobins are amphipathic secretory proteins with eight conserved cysteine residues and are ubiquitous among filamentous fungi. In the fungus Aspergillus oryzae, the hydrophobin RolA and the polyesterase CutL1 are co-expressed when the sole available carbon source is the biodegradable polyester polybutylene succinate-co-adipate (PBSA). RolA promotes the degradation of PBSA by attaching to the particle surface, changing its structure and interacting with CutL1 to concentrate CutL1 on the PBSA surface. We previously reported that positively charged residues in RolA and negatively charged residues in CutL1 are cooperatively involved in the ionic interaction between RolA and CutL1. We also reported that hydrophobin RodA of the model fungus Aspergillus nidulans, which was obtained via an A. oryzae expression system, interacted via ionic interactions with CutL1. In the present study, phylogenetic and alignment analyses revealed that the N-terminal regions of several RolA orthologs contained positively charged residues and that the corresponding negatively charged residues on the surface of CutL1 that were essential for the RolA-CutL1 interaction were highly conserved in several CutL1 orthologs. A PBSA microparticle degradation assay, a pull-down assay using a dispersion of Teflon particles, and a kinetic analysis using a quartz crystal microbalance revealed that recombinant A. nidulans RodA interacted via ionic interactions with two recombinant A. nidulans cutinases. Together, these results imply that ionic interactions between hydrophobins and cutinases may be common among aspergilli and other filamentous fungi.

  16. How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.

    Science.gov (United States)

    Kaus, Joseph W; Harder, Edward; Lin, Teng; Abel, Robert; McCammon, J Andrew; Wang, Lingle

    2015-06-09

    Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the

  17. The Role of Protein-Ligand Contacts in Allosteric Regulation of the Escherichia coli Catabolite Activator Protein*

    Science.gov (United States)

    Townsend, Philip D.; Rodgers, Thomas L.; Glover, Laura C.; Korhonen, Heidi J.; Richards, Shane A.; Colwell, Lucy J.; Pohl, Ehmke; Wilson, Mark R.; Hodgson, David R. W.; McLeish, Tom C. B.; Cann, Martin J.

    2015-01-01

    Allostery is a fundamental process by which ligand binding to a protein alters its activity at a distant site. Both experimental and theoretical evidence demonstrate that allostery can be communicated through altered slow relaxation protein dynamics without conformational change. The catabolite activator protein (CAP) of Escherichia coli is an exemplar for the analysis of such entropically driven allostery. Negative allostery in CAP occurs between identical cAMP binding sites. Changes to the cAMP-binding pocket can therefore impact the allosteric properties of CAP. Here we demonstrate, through a combination of coarse-grained modeling, isothermal calorimetry, and structural analysis, that decreasing the affinity of CAP for cAMP enhances negative cooperativity through an entropic penalty for ligand binding. The use of variant cAMP ligands indicates the data are not explained by structural heterogeneity between protein mutants. We observe computationally that altered interaction strength between CAP and cAMP variously modifies the change in allosteric cooperativity due to second site CAP mutations. As the degree of correlated motion between the cAMP-contacting site and a second site on CAP increases, there is a tendency for computed double mutations at these sites to drive CAP toward noncooperativity. Naturally occurring pairs of covarying residues in CAP do not display this tendency, suggesting a selection pressure to fine tune allostery on changes to the CAP ligand-binding pocket without a drive to a noncooperative state. In general, we hypothesize an evolutionary selection pressure to retain slow relaxation dynamics-induced allostery in proteins in which evolution of the ligand-binding site is occurring. PMID:26187469

  18. The Role of Protein-Ligand Contacts in Allosteric Regulation of the Escherichia coli Catabolite Activator Protein.

    Science.gov (United States)

    Townsend, Philip D; Rodgers, Thomas L; Glover, Laura C; Korhonen, Heidi J; Richards, Shane A; Colwell, Lucy J; Pohl, Ehmke; Wilson, Mark R; Hodgson, David R W; McLeish, Tom C B; Cann, Martin J

    2015-09-04

    Allostery is a fundamental process by which ligand binding to a protein alters its activity at a distant site. Both experimental and theoretical evidence demonstrate that allostery can be communicated through altered slow relaxation protein dynamics without conformational change. The catabolite activator protein (CAP) of Escherichia coli is an exemplar for the analysis of such entropically driven allostery. Negative allostery in CAP occurs between identical cAMP binding sites. Changes to the cAMP-binding pocket can therefore impact the allosteric properties of CAP. Here we demonstrate, through a combination of coarse-grained modeling, isothermal calorimetry, and structural analysis, that decreasing the affinity of CAP for cAMP enhances negative cooperativity through an entropic penalty for ligand binding. The use of variant cAMP ligands indicates the data are not explained by structural heterogeneity between protein mutants. We observe computationally that altered interaction strength between CAP and cAMP variously modifies the change in allosteric cooperativity due to second site CAP mutations. As the degree of correlated motion between the cAMP-contacting site and a second site on CAP increases, there is a tendency for computed double mutations at these sites to drive CAP toward noncooperativity. Naturally occurring pairs of covarying residues in CAP do not display this tendency, suggesting a selection pressure to fine tune allostery on changes to the CAP ligand-binding pocket without a drive to a noncooperative state. In general, we hypothesize an evolutionary selection pressure to retain slow relaxation dynamics-induced allostery in proteins in which evolution of the ligand-binding site is occurring. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  19. ReFlexIn: a flexible receptor protein-ligand docking scheme evaluated on HIV-1 protease.

    Directory of Open Access Journals (Sweden)

    Simon Leis

    Full Text Available For many targets of pharmaceutical importance conformational changes of the receptor protein are relevant during the ligand binding process. A new docking approach, ReFlexIn (Receptor Flexibility by Interpolation, that combines receptor flexibility with the computationally efficient potential grid representation of receptor molecules has been evaluated on the retroviral HIV-1 (Human Immunodeficiency Virus 1 protease system. An approximate inclusion of receptor flexibility is achieved by using interpolation between grid representations of individual receptor conformations. For the retroviral protease the method was tested on an ensemble of protease structures crystallized in the presence of different ligands and on a set of structures obtained from morphing between the unbound and a ligand-bound protease structure. Docking was performed on ligands known to bind to the protease and several non-binders. For the binders the ReFlexIn method yielded in almost all cases ligand placements in similar or closer agreement with experiment than docking to any of the ensemble members without degrading the discrimination with respect to non-binders. The improved docking performance compared to docking to rigid receptors allows for systematic virtual screening applications at very small additional computational cost.

  20. The SQM/COSMO filter: reliable native pose identification based on the quantum-mechanical description of protein-ligand interactions and implicit COSMO solvation

    Czech Academy of Sciences Publication Activity Database

    Pecina, Adam; Meier, R.; Fanfrlík, Jindřich; Lepšík, Martin; Řezáč, Jan; Hobza, Pavel; Baldauf, C.

    2016-01-01

    Roč. 52, č. 16 (2016), s. 3312-3315 ISSN 1359-7345 R&D Projects: GA ČR GBP208/12/G016 Institutional support: RVO:61388963 Keywords : empirical scoring functions * density functional theory * binding affinity Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 6.319, year: 2016 http://pubs.rsc.org/en/content/articlepdf/2016/cc/c5cc09499b

  1. Predicting binding poses and affinities for protein - ligand complexes in the 2015 D3R Grand Challenge using a physical model with a statistical parameter estimation

    Science.gov (United States)

    Grudinin, Sergei; Kadukova, Maria; Eisenbarth, Andreas; Marillet, Simon; Cazals, Frédéric

    2016-09-01

    The 2015 D3R Grand Challenge provided an opportunity to test our new model for the binding free energy of small molecules, as well as to assess our protocol to predict binding poses for protein-ligand complexes. Our pose predictions were ranked 3-9 for the HSP90 dataset, depending on the assessment metric. For the MAP4K dataset the ranks are very dispersed and equal to 2-35, depending on the assessment metric, which does not provide any insight into the accuracy of the method. The main success of our pose prediction protocol was the re-scoring stage using the recently developed Convex-PL potential. We make a thorough analysis of our docking predictions made with AutoDock Vina and discuss the effect of the choice of rigid receptor templates, the number of flexible residues in the binding pocket, the binding pocket size, and the benefits of re-scoring. However, the main challenge was to predict experimentally determined binding affinities for two blind test sets. Our affinity prediction model consisted of two terms, a pairwise-additive enthalpy, and a non pairwise-additive entropy. We trained the free parameters of the model with a regularized regression using affinity and structural data from the PDBBind database. Our model performed very well on the training set, however, failed on the two test sets. We explain the drawback and pitfalls of our model, in particular in terms of relative coverage of the test set by the training set and missed dynamical properties from crystal structures, and discuss different routes to improve it.

  2. Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge.

    Science.gov (United States)

    Perryman, Alexander L; Santiago, Daniel N; Forli, Stefano; Martins, Diogo Santos; Olson, Arthur J

    2014-04-01

    To rigorously assess the tools and protocols that can be used to understand and predict macromolecular recognition, and to gain more structural insight into three newly discovered allosteric binding sites on a critical drug target involved in the treatment of HIV infections, the Olson and Levy labs collaborated on the SAMPL4 challenge. This computational blind challenge involved predicting protein-ligand binding against the three allosteric sites of HIV integrase (IN), a viral enzyme for which two drugs (that target the active site) have been approved by the FDA. Positive control cross-docking experiments were utilized to select 13 receptor models out of an initial ensemble of 41 different crystal structures of HIV IN. These 13 models of the targets were selected using our new "Rank Difference Ratio" metric. The first stage of SAMPL4 involved using virtual screens to identify 62 active, allosteric IN inhibitors out of a set of 321 compounds. The second stage involved predicting the binding site(s) and crystallographic binding mode(s) for 57 of these inhibitors. Our team submitted four entries for the first stage that utilized: (1) AutoDock Vina (AD Vina) plus visual inspection; (2) a new common pharmacophore engine; (3) BEDAM replica exchange free energy simulations, and a Consensus approach that combined the predictions of all three strategies. Even with the SAMPL4's very challenging compound library that displayed a significantly lower amount of structural diversity than most libraries that are conventionally employed in prospective virtual screens, these approaches produced hit rates of 24, 25, 34, and 27 %, respectively, on a set with 19 % declared binders. Our only entry for the second stage challenge was based on the results of AD Vina plus visual inspection, and it ranked third place overall according to several different metrics provided by the SAMPL4 organizers. The successful results displayed by these approaches highlight the utility of the computational

  3. Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge

    Science.gov (United States)

    Perryman, Alexander L.; Santiago, Daniel N.; Forli, Stefano; Santos-Martins, Diogo; Olson, Arthur J.

    2014-04-01

    To rigorously assess the tools and protocols that can be used to understand and predict macromolecular recognition, and to gain more structural insight into three newly discovered allosteric binding sites on a critical drug target involved in the treatment of HIV infections, the Olson and Levy labs collaborated on the SAMPL4 challenge. This computational blind challenge involved predicting protein-ligand binding against the three allosteric sites of HIV integrase (IN), a viral enzyme for which two drugs (that target the active site) have been approved by the FDA. Positive control cross-docking experiments were utilized to select 13 receptor models out of an initial ensemble of 41 different crystal structures of HIV IN. These 13 models of the targets were selected using our new "Rank Difference Ratio" metric. The first stage of SAMPL4 involved using virtual screens to identify 62 active, allosteric IN inhibitors out of a set of 321 compounds. The second stage involved predicting the binding site(s) and crystallographic binding mode(s) for 57 of these inhibitors. Our team submitted four entries for the first stage that utilized: (1) AutoDock Vina (AD Vina) plus visual inspection; (2) a new common pharmacophore engine; (3) BEDAM replica exchange free energy simulations, and a Consensus approach that combined the predictions of all three strategies. Even with the SAMPL4's very challenging compound library that displayed a significantly lower amount of structural diversity than most libraries that are conventionally employed in prospective virtual screens, these approaches produced hit rates of 24, 25, 34, and 27 %, respectively, on a set with 19 % declared binders. Our only entry for the second stage challenge was based on the results of AD Vina plus visual inspection, and it ranked third place overall according to several different metrics provided by the SAMPL4 organizers. The successful results displayed by these approaches highlight the utility of the computational

  4. Applying Computational Scoring Functions to Assess Biomolecular Interactions in Food Science: Applications to the Estrogen Receptors

    Directory of Open Access Journals (Sweden)

    Francesca Spyrakis

    2016-10-01

    Thus, key computational medicinal chemistry methods like molecular dynamics can be used to decipher protein flexibility and to obtain stable models for docking and scoring in food-related studies, and virtual screening is increasingly being applied to identify molecules with potential to act as endocrine disruptors, food mycotoxins, and new nutraceuticals [3,4,5]. All of these methods and simulations are based on protein-ligand interaction phenomena, and represent the basis for any subsequent modification of the targeted receptor's or enzyme's physiological activity. We describe here the energetics of binding of biological complexes, providing a survey of the most common and successful algorithms used in evaluating these energetics, and we report case studies in which computational techniques have been applied to food science issues. In particular, we explore a handful of studies involving the estrogen receptors for which we have a long-term interest.

  5. Different impressions of other agents obtained through social interaction uniquely modulate dorsal and ventral pathway activities in the social human brain.

    Science.gov (United States)

    Takahashi, Hideyuki; Terada, Kazunori; Morita, Tomoyo; Suzuki, Shinsuke; Haji, Tomoki; Kozima, Hideki; Yoshikawa, Masahiro; Matsumoto, Yoshio; Omori, Takashi; Asada, Minoru; Naito, Eiichi

    2014-09-01

    Internal (neuronal) representations in the brain are modified by our experiences, and this phenomenon is not unique to sensory and motor systems. Here, we show that different impressions obtained through social interaction with a variety of agents uniquely modulate activity of dorsal and ventral pathways of the brain network that mediates human social behavior. We scanned brain activity with functional magnetic resonance imaging (fMRI) in 16 healthy volunteers when they performed a simple matching-pennies game with a human, human-like android, mechanical robot, interactive robot, and a computer. Before playing this game in the scanner, participants experienced social interactions with each opponent separately and scored their initial impressions using two questionnaires. We found that the participants perceived opponents in two mental dimensions: one represented "mind-holderness" in which participants attributed anthropomorphic impressions to some of the opponents that had mental functions, while the other dimension represented "mind-readerness" in which participants characterized opponents as intelligent. Interestingly, this "mind-readerness" dimension correlated to participants frequently changing their game tactic to prevent opponents from envisioning their strategy, and this was corroborated by increased entropy during the game. We also found that the two factors separately modulated activity in distinct social brain regions. Specifically, mind-holderness modulated activity in the dorsal aspect of the temporoparietal junction (TPJ) and medial prefrontal and posterior paracingulate cortices, while mind-readerness modulated activity in the ventral aspect of TPJ and the temporal pole. These results clearly demonstrate that activity in social brain networks is modulated through pre-scanning experiences of social interaction with a variety of agents. Furthermore, our findings elucidated the existence of two distinct functional networks in the social human brain

  6. A novel interaction fingerprint derived from per atom score contributions: exhaustive evaluation of interaction fingerprint performance in docking based virtual screening.

    Science.gov (United States)

    Jasper, Julia B; Humbeck, Lina; Brinkjost, Tobias; Koch, Oliver

    2018-03-16

    Protein ligand interaction fingerprints are a powerful approach for the analysis and assessment of docking poses to improve docking performance in virtual screening. In this study, a novel interaction fingerprint approach (PADIF, protein per atom score contributions derived interaction fingerprint) is presented which was specifically designed for utilising the GOLD scoring functions' atom contributions together with a specific scoring scheme. This allows the incorporation of known protein-ligand complex structures for a target-specific scoring. Unlike many other methods, this approach uses weighting factors reflecting the relative frequency of a specific interaction in the references and penalizes destabilizing interactions. In addition, and for the first time, an exhaustive validation study was performed that assesses the performance of PADIF and two other interaction fingerprints in virtual screening. Here, PADIF shows superior results, and some rules of thumb for a successful use of interaction fingerprints could be identified.

  7. Characterising non-covalent interactions with the Cambridge Structural Database.

    Science.gov (United States)

    Lommerse, J P; Taylor, R

    1997-02-01

    This review describes how the CSD can be used to study non-covalent interactions. Several different types of information may be obtained. First, the relative frequencies of various interactions can be studied; for example, we have shown that the terminal oxygen atoms of phosphate groups accept hydrogen bonds far more often than the linkage oxygens. Secondly, information can be obtained about the geometries of nonbonded contacts; for example, hydrogen bonds to P-O groups rarely form along the extension of the P-O bond, whereas short contacts between oxygen and carbon-bound iodine show a strong preference for linear C-I ... O angles. Thirdly, the CSD can be searched for novel interactions which may be exploited in inhibitor design; for example, the I ... O contacts just mentioned, and N-H ... pi hydrogen bonds. Finally, the CSD can suggest synthetic targets for medicinal chemistry; for example, molecules containing delocalised electron deficient groups such as trimethylammonium, pyridinium, thaizolium and dinitrophenyl have a good chance of binding to an active-site tryptophan. Although the CSD contains small-molecule crystal structures, not protein-ligand complexes, there is considerable evidence that the contacts seen in the two types of structures are similar. We have illustrated this a number of times in the present review and additional evidence has been given previously by Klebe. The major advantages of the CSD are its size, diversity and experimental accuracy. For these reasons, it is a useful tool for modellers engaged in rational inhibitor design.

  8. Protein-ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes.

    Science.gov (United States)

    Raschka, Sebastian; Wolf, Alex J; Bemister-Buffington, Joseph; Kuhn, Leslie A

    2018-04-01

    Understanding how proteins encode ligand specificity is fascinating and similar in importance to deciphering the genetic code. For protein-ligand recognition, the combination of an almost infinite variety of interfacial shapes and patterns of chemical groups makes the problem especially challenging. Here we analyze data across non-homologous proteins in complex with small biological ligands to address observations made in our inhibitor discovery projects: that proteins favor donating H-bonds to ligands and avoid using groups with both H-bond donor and acceptor capacity. The resulting clear and significant chemical group matching preferences elucidate the code for protein-native ligand binding, similar to the dominant patterns found in nucleic acid base-pairing. On average, 90% of the keto and carboxylate oxygens occurring in the biological ligands formed direct H-bonds to the protein. A two-fold preference was found for protein atoms to act as H-bond donors and ligand atoms to act as acceptors, and 76% of all intermolecular H-bonds involved an amine donor. Together, the tight chemical and geometric constraints associated with satisfying donor groups generate a hydrogen-bonding lock that can be matched only by ligands bearing the right acceptor-rich key. Measuring an index of H-bond preference based on the observed chemical trends proved sufficient to predict other protein-ligand complexes and can be used to guide molecular design. The resulting Hbind and Protein Recognition Index software packages are being made available for rigorously defining intermolecular H-bonds and measuring the extent to which H-bonding patterns in a given complex match the preference key.

  9. Protein-ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes

    Science.gov (United States)

    Raschka, Sebastian; Wolf, Alex J.; Bemister-Buffington, Joseph; Kuhn, Leslie A.

    2018-02-01

    Understanding how proteins encode ligand specificity is fascinating and similar in importance to deciphering the genetic code. For protein-ligand recognition, the combination of an almost infinite variety of interfacial shapes and patterns of chemical groups makes the problem especially challenging. Here we analyze data across non-homologous proteins in complex with small biological ligands to address observations made in our inhibitor discovery projects: that proteins favor donating H-bonds to ligands and avoid using groups with both H-bond donor and acceptor capacity. The resulting clear and significant chemical group matching preferences elucidate the code for protein-native ligand binding, similar to the dominant patterns found in nucleic acid base-pairing. On average, 90% of the keto and carboxylate oxygens occurring in the biological ligands formed direct H-bonds to the protein. A two-fold preference was found for protein atoms to act as H-bond donors and ligand atoms to act as acceptors, and 76% of all intermolecular H-bonds involved an amine donor. Together, the tight chemical and geometric constraints associated with satisfying donor groups generate a hydrogen-bonding lock that can be matched only by ligands bearing the right acceptor-rich key. Measuring an index of H-bond preference based on the observed chemical trends proved sufficient to predict other protein-ligand complexes and can be used to guide molecular design. The resulting Hbind and Protein Recognition Index software packages are being made available for rigorously defining intermolecular H-bonds and measuring the extent to which H-bonding patterns in a given complex match the preference key.

  10. In Vitro Evaluation of the Type of Interaction Obtained by the Combination of Terbinafine and Itraconazole, Voriconazole, or Amphotericin B against Dematiaceous Molds▿

    Science.gov (United States)

    Biancalana, Fernanda Simas Corrêa; Lyra, Luzia; Schreiber, Angélica Zaninelli

    2011-01-01

    In vitro associations using the checkerboard microdilution method indicated lower MIC ranges and MIC median values for each drug (terbinafine, itraconazole, voriconazole, and amphotericin B) in association than those obtained for each single drug. Fractional inhibitory concentration index (FIC) results showed 100% synergism in the association of terbinafine with voriconazole, 96.5% in the association of terbinafine with amphotericin B, and 75.9% in the association of terbinafine with itraconazole. Drug combinations may be useful for treatment of dematiaceous mold infections as an alternative treatment to enhance the effectiveness of each drug. PMID:21690288

  11. The Interaction between Environmental Preservation throuout Sustainability as an Agrarian Law Principle: Hermeneutics Transcending Borders in Order to Obtain a New Paradigm

    Directory of Open Access Journals (Sweden)

    Luciana Ramos Jordão

    2016-10-01

    Full Text Available This paper discusses environmental preservation as a principle of Agrarian Law and hermeneutics. It aims to comprehend connection between both concepts from refounding Agroecology and Sustainability as a major precept in order to obtain agrarian development and environmental preservation. By using the deductive method, it analyses the fact that environment (and studying Law cannot be seen in separate ways, otherwise, it would risk having high complexity environmental and agrarian damage. Therefore, consciousness of how dependent human is from environment as an issue of fundamentality and materiality of mere formal rights nowadays.

  12. Improving the iterative Linear Interaction Energy approach using automated recognition of configurational transitions.

    Science.gov (United States)

    Vosmeer, C Ruben; Kooi, Derk P; Capoferri, Luigi; Terpstra, Margreet M; Vermeulen, Nico P E; Geerke, Daan P

    2016-01-01

    Recently an iterative method was proposed to enhance the accuracy and efficiency of ligand-protein binding affinity prediction through linear interaction energy (LIE) theory. For ligand binding to flexible Cytochrome P450s (CYPs), this method was shown to decrease the root-mean-square error and standard deviation of error prediction by combining interaction energies of simulations starting from different conformations. Thereby, different parts of protein-ligand conformational space are sampled in parallel simulations. The iterative LIE framework relies on the assumption that separate simulations explore different local parts of phase space, and do not show transitions to other parts of configurational space that are already covered in parallel simulations. In this work, a method is proposed to (automatically) detect such transitions during the simulations that are performed to construct LIE models and to predict binding affinities. Using noise-canceling techniques and splines to fit time series of the raw data for the interaction energies, transitions during simulation between different parts of phase space are identified. Boolean selection criteria are then applied to determine which parts of the interaction energy trajectories are to be used as input for the LIE calculations. Here we show that this filtering approach benefits the predictive quality of our previous CYP 2D6-aryloxypropanolamine LIE model. In addition, an analysis is performed of the gain in computational efficiency that can be obtained from monitoring simulations using the proposed filtering method and by prematurely terminating simulations accordingly.

  13. Interaction of albumins and heparinoids investigated by affinity capillary electrophoresis and free flow electrophoresis.

    Science.gov (United States)

    Mozafari, Mona; El Deeb, Sami; Krull, Friederike; Wildgruber, Robert; Weber, Gerhard; Reiter, Christian G; Wätzig, Hermann

    2018-02-01

    A fast and precise affinity capillary electrophoresis (ACE) method has been applied to investigate the interactions between two serum albumins (HSA and BSA) and heparinoids. Furthermore, different free flow electrophoresis methods were developed to separate the species which appears owing to interaction of albumins with pentosan polysulfate sodium (PPS) under different experimental conditions. For ACE experiments, the normalized mobility ratios (∆R/R f ), which provided information about the binding strength and the overall charge of the protein-ligand complex, were used to evaluate the binding affinities. ACE experiments were performed at two different temperatures (23 and 37°C). Both BSA and HSA interact more strongly with PPS than with unfractionated and low molecular weight heparins. For PPS, the interactions can already be observed at low mg/L concentrations (3 mg/L), and saturation is already obtained at approximately 20 mg/L. Unfractionated heparin showed almost no interactions with BSA at 23°C, but weak interactions at 37°C at higher heparin concentrations. The additional signals also appeared at higher concentrations at 37°C. Nevertheless, in most cases the binding data were similar at both temperatures. Furthermore, HSA showed a characteristic splitting in two peaks especially after interacting with PPS, which is probably attributable to the formation of two species or conformational change of HSA after interacting with PPS. The free flow electrophoresis methods have confirmed and completed the ACE experiments. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. INTERACT

    DEFF Research Database (Denmark)

    Jochum, Elizabeth; Borggreen, Gunhild; Murphey, TD

    This paper considers the impact of visual art and performance on robotics and human-computer interaction and outlines a research project that combines puppetry and live performance with robotics. Kinesics—communication through movement—is the foundation of many theatre and performance traditions ...

  15. Synthesizing Novel Anthraquinone Natural Product-Like Compounds to Investigate Protein-Ligand Interactions in Both an in Vitro and in Vivo Assay: An Integrated Research-Based Third-Year Chemical Biology Laboratory Course

    Science.gov (United States)

    McKenzie, Nancy; McNulty, James; McLeod, David; McFadden, Meghan; Balachandran, Naresh

    2012-01-01

    A new undergraduate program in chemical biology was launched in 2008 to provide a unique learning experience for those students interested in this interdisciplinary science. An innovative undergraduate chemical biology laboratory course at the third-year level was developed as a key component of the curriculum. The laboratory course introduces…

  16. Combining combinatorial chemistry and affinity chromatography protocols for systematically probing protein-ligand interactions: application to the development of highly selective phosphinic inhibitors of human bataine: homocysteine S-methyltransferase

    Czech Academy of Sciences Publication Activity Database

    Collinsová, Michaela; Garrow, T. A.; Castro, C.; Dive, V.; Yiotakis, A.; Jiráček, Jiří

    2002-01-01

    Roč. 8, - (2002), s. S221 ISSN 1075-2617. [European Peptide Symposium /27./. 31.08.2002-06.09.2002, Sorrento] Institutional research plan: CEZ:AV0Z4055905 Keywords : homocysteine S-methyltransferase Subject RIV: CE - Biochemistry

  17. Obtaining of inulin acetate

    OpenAIRE

    Khusenov, Arslonnazar; Rakhmanberdiev, Gappar; Rakhimov, Dilshod; Khalikov, Muzaffar

    2014-01-01

    In the article first obtained inulin ester inulin acetate, by etherification of inulin with acetic anhydride has been exposed. Obtained product has been studied using elementary analysis and IR spectroscopy.

  18. In silico modeling and experimental evidence of coagulant protein interaction with precursors for nanoparticle functionalization.

    Science.gov (United States)

    Okoli, Chuka; Sengottaiyan, Selvaraj; Arul Murugan, N; Pavankumar, Asalapuram R; Agren, Hans; Kuttuva Rajarao, Gunaratna

    2013-10-01

    The design of novel protein-nanoparticle hybrid systems has applications in many fields of science ranging from biomedicine, catalysis, water treatment, etc. The main barrier in devising such tool is lack of adequate information or poor understanding of protein-ligand chemistry. Here, we establish a new strategy based on computational modeling for protein and precursor linkers that can decorate the nanoparticles. Moringa oleifera (MO2.1) seed protein that has coagulation and antimicrobial properties was used. Superparamagnetic nanoparticles (SPION) with precursor ligands were used for the protein-ligand interaction studies. The molecular docking studies reveal that there are two binding sites, one is located at the core binding site; tetraethoxysilane (TEOS) or 3-aminopropyl trimethoxysilane (APTES) binds to this site while the other one is located at the side chain residues where trisodium citrate (TSC) or Si60 binds to this site. The protein-ligand distance profile analysis explains the differences in functional activity of the decorated SPION. Experimentally, TSC-coated nanoparticles showed higher coagulation activity as compared to TEOS- and APTES-coated SPION. To our knowledge, this is the first report on in vitro experimental data, which endorses the computational modeling studies as a powerful tool to design novel precursors for functionalization of nanomaterials; and develop interface hybrid systems for various applications.

  19. Probing the role of backbone hydrogen bonds in protein-peptide interactions by amide-to-ester mutations

    DEFF Research Database (Denmark)

    Eildal, Jonas N N; Hultqvist, Greta; Balle, Thomas

    2013-01-01

    -protein interactions, those of the PDZ domain family involve formation of intermolecular hydrogen bonds: C-termini or internal linear motifs of proteins bind as β-strands to form an extended antiparallel β-sheet with the PDZ domain. Whereas extensive work has focused on the importance of the amino acid side chains...... of the protein ligand, the role of the backbone hydrogen bonds in the binding reaction is not known. Using amide-to-ester substitutions to perturb the backbone hydrogen-bonding pattern, we have systematically probed putative backbone hydrogen bonds between four different PDZ domains and peptides corresponding...... to natural protein ligands. Amide-to-ester mutations of the three C-terminal amides of the peptide ligand severely affected the affinity with the PDZ domain, demonstrating that hydrogen bonds contribute significantly to ligand binding (apparent changes in binding energy, ΔΔG = 1.3 to >3.8 kcal mol(-1...

  20. Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes

    Directory of Open Access Journals (Sweden)

    Uchikoga Nobuyuki

    2010-05-01

    Full Text Available Abstract Background Protein-protein docking for proteins with large conformational changes was analyzed by using interaction fingerprints, one of the scales for measuring similarities among complex structures, utilized especially for searching near-native protein-ligand or protein-protein complex structures. Here, we have proposed a combined method for analyzing protein-protein docking by taking large conformational changes into consideration. This combined method consists of ensemble soft docking with multiple protein structures, refinement of complexes, and cluster analysis using interaction fingerprints and energy profiles. Results To test for the applicability of this combined method, various CaM-ligand complexes were reconstructed from the NMR structures of unbound CaM. For the purpose of reconstruction, we used three known CaM-ligands, namely, the CaM-binding peptides of cyclic nucleotide gateway (CNG, CaM kinase kinase (CaMKK and the plasma membrane Ca2+ ATPase pump (PMCA, and thirty-one structurally diverse CaM conformations. For each ligand, 62000 CaM-ligand complexes were generated in the docking step and the relationship between their energy profiles and structural similarities to the native complex were analyzed using interaction fingerprint and RMSD. Near-native clusters were obtained in the case of CNG and CaMKK. Conclusions The interaction fingerprint method discriminated near-native structures better than the RMSD method in cluster analysis. We showed that a combined method that includes the interaction fingerprint is very useful for protein-protein docking analysis of certain cases.

  1. (S)Pinning down protein interactions by NMR

    DEFF Research Database (Denmark)

    Teilum, Kaare; Kunze, Micha Ben Achim; Erlendsson, Simon

    2017-01-01

    Protein molecules are highly diverse communication platforms and their interaction repertoire stretches from atoms over small molecules such as sugars and lipids to macromolecules. An important route to understanding molecular communication is to quantitatively describe their interactions...... all types of protein reactions, which can span orders of magnitudes in affinities, reaction rates and lifetimes of states. As the more versatile technique, solution NMR spectroscopy offers a remarkable catalogue of methods that can be successfully applied to the quantitative as well as qualitative...... descriptions of protein interactions. In this review we provide an easy-access approach to NMR for the non-NMR specialist and describe how and when solution state NMR spectroscopy is the method of choice for addressing protein ligand interaction. We describe very briefly the theoretical background...

  2. An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method

    Science.gov (United States)

    Asada, Naoya; Fedorov, Dmitri G.; Kitaura, Kazuo; Nakanishi, Isao; Merz, Kenneth M.

    2012-01-01

    We propose an approach based on the overlapping multicenter ONIOM to evaluate intermolecular interaction energies in large systems and demonstrate its accuracy on several representative systems in the complete basis set limit at the MP2 and CCSD(T) level of theory. In the application to the intermolecular interaction energy between insulin dimer and 4′-hydroxyacetanilide at the MP2/CBS level, we use the fragment molecular orbital method for the calculation of the entire complex assigned to the lowest layer in three-layer ONIOM. The developed method is shown to be efficient and accurate in the evaluation of the protein-ligand interaction energies. PMID:23050059

  3. Raman Spectroscopic Signature Markers of Dopamine-Human Dopamine Transporter Interaction in Living Cells.

    Science.gov (United States)

    Silwal, Achut P; Yadav, Rajeev; Sprague, Jon E; Lu, H Peter

    2017-07-19

    Dopamine (DA) controls many psychological and behavioral activities in the central nervous system (CNS) through interactions with the human dopamine transporter (hDAT) and dopamine receptors. The roles of DA in the function of the CNS are affected by the targeted binding of drugs to hDAT; thus, hDAT plays a critical role in neurophysiology and neuropathophysiology. An effective experimental method is necessary to study the DA-hDAT interaction and effects of variety of drugs like psychostimulants and antidepressants that are dependent on this interaction. In searching for obtaining and identifying the Raman spectral signatures, we have used surface enhanced Raman scattering (SERS) spectroscopy to record SERS spectra from DA, human embryonic kidney 293 cells (HEK293), hDAT-HEK293, DA-HEK293, and DA-hDAT-HEK293. We have demonstrated a specific 2D-distribution SERS spectral analytical approach to analyze DA-hDAT interaction. Our study shows that the Raman modes at 807, 839, 1076, 1090, 1538, and 1665 cm -1 are related to DA-hDAT interaction, where Raman shifts at 807 and 1076 cm -1 are the signature markers for the bound state of DA to probe DA-hDAT interaction. On the basis of density function theory (DFT) calculation, Raman shift of the bound state of DA at 807 cm -1 is related to combination of bending modes α(C3-O10-H21), α(C2-O11-H22), α(C7-C8-H18), α(C6-C4-H13), α(C7-C8-H19), and α(C7-C8-N9), and Raman shift at 1076 cm -1 is related to combination of bending modes α(H19-N9-C8), γ(N9-H19), γ(C8-H19), γ(N9-H20), γ(C8-H18), and α(C7-C8-H18). These findings demonstrate that protein-ligand interactions can be confirmed by probing change in Raman shift of ligand molecules, which could be crucial to understanding molecular interactions between neurotransmitters and their receptors or transporters.

  4. Accounting for Intraligand Interactions in Flexible Ligand Docking with a PMF-Based Scoring Function.

    Science.gov (United States)

    Lizunov, A Y; Gonchar, A L; Zaitseva, N I; Zosimov, V V

    2015-10-26

    We analyzed the frequency with which intraligand contacts occurred in a set of 1300 protein-ligand complexes [ Plewczynski et al. J. Comput. Chem. 2011 , 32 , 742 - 755 .]. Our analysis showed that flexible ligands often form intraligand hydrophobic contacts, while intraligand hydrogen bonds are rare. The test set was also thoroughly investigated and classified. We suggest a universal method for enhancement of a scoring function based on a potential of mean force (PMF-based score) by adding a term accounting for intraligand interactions. The method was implemented via in-house developed program, utilizing an Algo_score scoring function [ Ramensky et al. Proteins: Struct., Funct., Genet. 2007 , 69 , 349 - 357 .] based on the Tarasov-Muryshev PMF [ Muryshev et al. J. Comput.-Aided Mol. Des. 2003 , 17 , 597 - 605 .]. The enhancement of the scoring function was shown to significantly improve the docking and scoring quality for flexible ligands in the test set of 1300 protein-ligand complexes [ Plewczynski et al. J. Comput. Chem. 2011 , 32 , 742 - 755 .]. We then investigated the correlation of the docking results with two parameters of intraligand interactions estimation. These parameters are the weight of intraligand interactions and the minimum number of bonds between the ligand atoms required to take their interaction into account.

  5. Combination of multi-scale and multi-edge X-ray spectroscopy for investigating the products obtained from the interaction between kaolinite and metallic iron in anoxic conditions at 90 °C

    Science.gov (United States)

    Rivard, Camille; Montargès-Pelletier, Emmanuelle; Vantelon, Delphine; Pelletier, Manuel; Karunakaran, Chithra; Michot, Laurent J.; Villieras, Frédéric; Michau, Nicolas

    2013-02-01

    In the context of radioactive waste repository in geological formation, kaolinite-metallic iron interaction in chlorine solution was conducted in batch experiments, under anoxic conditions at 90 °C during 9 months. After a mineralogical characterization at a global scale, products were analyzed at the micrometer and nanometer scales by X-ray absorption spectroscopic techniques (XAS and STXM). Absorption at Al, Si and Fe edges was investigated to have a complete overview of the distribution and status of constituting elements. Whereas Si K-edge results do not evidence significant evolution of silicon status, investigations at Al K-edge and Fe L-edges demonstrate variations at aggregate and particle scales of IVAl:VIAl and Fe2+:Fe3+ ratios. Spectroscopic data evidence the systematic crystallization of Fe-serpentines onto the remaining particles of kaolinite and the absence of pure species (kaolinite or Fe-serpentines). Combination of spatially resolved spectroscopic analyses and TEM-EDXS elemental distribution aims to calculate unit cell formulae of Fe-serpentines layers and abundance of each species in mixed particles. For most of the investigated particles, results reveal that the variations of particles composition are directly linked to the relative contributions of kaolinite and Fe-berthierine in mixed particles. However, for some particles, microscale investigations evidence crystallization of two other Fe-serpentines species, devoid of aluminum, cronstedtite and greenalite.

  6. Understanding the Selectivity Mechanism of the Human Asialoglycoprotein Receptor (ASGP-R toward Gal- and Man- type Ligands for Predicting Interactions with Exogenous Sugars

    Directory of Open Access Journals (Sweden)

    Emo Chiellini

    2007-01-01

    Full Text Available A practical approach for addressing the computer simulation of protein-carbohydrate interactions is described here. An articulated computational protocol was setup and validated by checking its ability to predict experimental data, available in theliterature, and concerning the selectivity shown by the Carbohydrate Recognition Domain(CRD of the human asialoglycoprotein receptor (ASGP-R toward Gal-type ligands. Somerequired features responsible for the interactions were identified. Subsequently the sameprotocol was applied to monomer sugar molecules that constitute the building blocks foralginates and ulvans. Such sugar polymers may supply a low-cost source of rare sugars witha potential impact on several industrial applications, from pharmaceutical to fine chemicalindustry. An example of their applicative exploitation could be given by their use indeveloping biomaterial with adhesion properties toward hepatocytes, through interactionwith the ASGP-R. Such a receptor has been already proposed as a target for exogenousmolecules, specifically in the case of hepatocytes, for diagnostic and therapeutic purposes.The DOCK5.2 program was used to search optimal locations of the above ligands of interestinto CRD binding site and to roughly estimate interaction energies. Finally, the binding ∆G oftheoretical protein-ligand complexes was estimated by using the DelPhi program in which thesolvation free energy is accounted for with a continuum solvent model, by solving the Poisson-Boltzmann equation. The structure analysis of the obtained complexes and their ∆G values suggest that one of the sugar monomers of interest shows the desired characteristics.

  7. Experiments for obtaining field influence mass particles.

    CERN Document Server

    Yahalomi, E

    2010-01-01

    Analyzing time dilation experiments the existence of a universal field interacting with moving mass particles is obtained. It is found that mass particle changes its properties depend on its velocity relative to this universal scalar field and not on its velocity relative to the laboratory. High energy proton momentum, energy and mass were calculated obtaining new results. Experiments in high energy accelerators are suggested as additional proofs for the existence of this universal field. This universal field may explain some results of other high energy experiments.

  8. Ligand-receptor Interactions by NMR Spectroscopy

    Directory of Open Access Journals (Sweden)

    Novak. P.

    2008-04-01

    Full Text Available Today NMR spectroscopy is a method of choice for elucidation of interactions between biomolecules and the potential ligands. Knowledge on these interactions is an essential prerequisite for the rational drug design. The most important contribution of NMR to drug design a few years ago was the 3D structure determination of proteins. Besides delivering the 3D structures of the free proteins as a raw material for the modeling studies on ligand binding, NMR can directly yield valuable experimental data on the biologically important protein-ligand complexes. In addition to X-ray diffraction, NMR spectroscopy can provide information on the internal protein dynamics ordynamics of intermolecular interactions. Changes in NMR parameters allow us to detect ("SAR by NMR" and quantitatively determine binding affinities (titration, diffusion NMR experiments, etc. of potential ligands. Also, it is possible to determine the binding site and conformations of ligands, receptors and receptor-ligand complexes with the help of NMR methods such as tr-NOESY. Epitopes or functional groups responsible for binding of ligands to the receptor can be identified by employing STD or WaterLOGSY experiments. In this review are described some of the most frequent NMR methods for the characterization of the interactions between biomolecules and ligands, together with their advantages and disadvantages.

  9. IsoStar: A library of information about nonbonded interactions

    Science.gov (United States)

    Bruno, Ian J.; Cole, Jason C.; Lommerse, Jos P. M.; Rowland, R. Scott; Taylor, Robin; Verdonk, Marcel L.

    1997-11-01

    Crystallographic and theoretical (ab initio) data on intermolecular nonbondedinteractions have been gathered together in a computerised library('IsoStar`). The library contains information about the nonbonded contactsformed by some 250 chemical groupings. The data can be displayed visually andused to aid protein-ligand docking or the identification of bioisostericreplacements. Data from the library show that there is great variability inthe geometrical preferences of different types of hydrogen bonds, although ingeneral there is a tendency for H-bonds to form along lone-pair directions.The H-bond acceptor abilities of oxygen and sulphur atoms are highly dependenton intramolecular environments. The nonbonded contacts formed by manyhydrophobic groups show surprisingly strong directional preferences. Manyunusual nonbonded interactions are to be found in the library and are ofpotential value for designing novel biologically active molecules.

  10. Prediction of sensitivity to gefitinib/erlotinib for EGFR mutations in NSCLC based on structural interaction fingerprints and multilinear principal component analysis.

    Science.gov (United States)

    Zou, Bin; Lee, Victor H F; Yan, Hong

    2018-03-07

    Non-small cell lung cancer (NSCLC) with activating EGFR mutations, especially exon 19 deletions and the L858R point mutation, is particularly responsive to gefitinib and erlotinib. However, the sensitivity varies for less common and rare EGFR mutations. There are various explanations for the low sensitivity of EGFR exon 20 insertions and the exon 20 T790 M point mutation to gefitinib/erlotinib. However, few studies discuss, from a structural perspective, why less common mutations, like G719X and L861Q, have moderate sensitivity to gefitinib/erlotinib. To decode the drug sensitivity/selectivity of EGFR mutants, it is important to analyze the interaction between EGFR mutants and EGFR inhibitors. In this paper, the 30 most common EGFR mutants were selected and the technique of protein-ligand interaction fingerprint (IFP) was applied to analyze and compare the binding modes of EGFR mutant-gefitinib/erlotinib complexes. Molecular dynamics simulations were employed to obtain the dynamic trajectory and a matrix of IFPs for each EGFR mutant-inhibitor complex. Multilinear Principal Component Analysis (MPCA) was applied for dimensionality reduction and feature selection. The selected features were further analyzed for use as a drug sensitivity predictor. The results showed that the accuracy of prediction of drug sensitivity was very high for both gefitinib and erlotinib. Targeted Projection Pursuit (TPP) was used to show that the data points can be easily separated based on their sensitivities to gefetinib/erlotinib. We can conclude that the IFP features of EGFR mutant-TKI complexes and the MPCA-based tensor object feature extraction are useful to predict the drug sensitivity of EGFR mutants. The findings provide new insights for studying and predicting drug resistance/sensitivity of EGFR mutations in NSCLC and can be beneficial to the design of future targeted therapies and innovative drug discovery.

  11. Proposal for novel curcumin derivatives as potent inhibitors against Alzheimer's disease: Ab initio molecular simulations on the specific interactions between amyloid-beta peptide and curcumin

    Science.gov (United States)

    Ota, Shintaro; Fujimori, Mitsuki; Ishimura, Hiromi; Shulga, Sergiy; Kurita, Noriyuki

    2017-10-01

    Accumulation of amyloid-β (Aβ) peptides in a brain is closely related with the pathogenesis of Alzheimer's disease. To suppress the production of Aβ peptides, we propose novel curcumin derivatives and investigate their binding properties with the amyloid precursor protein (APP), using protein-ligand docking as well as ab initio molecular simulations. Our proposed derivative (curcumin XIV) is found to have a large binding energy with APP and interacts strongly with the cleavage site Ala19 by secretase. It is thus expected that curcumin XIV can protect APP from the secretase attack and be a potent inhibitor against the production of Aβ peptides.

  12. Recent Progress in Treating Protein–Ligand Interactions with Quantum-Mechanical Methods

    Directory of Open Access Journals (Sweden)

    Nusret Duygu Yilmazer

    2016-05-01

    Full Text Available We review the first successes and failures of a “new wave” of quantum chemistry-based approaches to the treatment of protein/ligand interactions. These approaches share the use of “enhanced”, dispersion (D, and/or hydrogen-bond (H corrected density functional theory (DFT or semi-empirical quantum mechanical (SQM methods, in combination with ensemble weighting techniques of some form to capture entropic effects. Benchmark and model system calculations in comparison to high-level theoretical as well as experimental references have shown that both DFT-D (dispersion-corrected density functional theory and SQM-DH (dispersion and hydrogen bond-corrected semi-empirical quantum mechanical perform much more accurately than older DFT and SQM approaches and also standard docking methods. In addition, DFT-D might soon become and SQM-DH already is fast enough to compute a large number of binding modes of comparably large protein/ligand complexes, thus allowing for a more accurate assessment of entropic effects.

  13. Towards Automated Binding Affinity Prediction Using an Iterative Linear Interaction Energy Approach

    Directory of Open Access Journals (Sweden)

    C. Ruben Vosmeer

    2014-01-01

    Full Text Available Binding affinity prediction of potential drugs to target and off-target proteins is an essential asset in drug development. These predictions require the calculation of binding free energies. In such calculations, it is a major challenge to properly account for both the dynamic nature of the protein and the possible variety of ligand-binding orientations, while keeping computational costs tractable. Recently, an iterative Linear Interaction Energy (LIE approach was introduced, in which results from multiple simulations of a protein-ligand complex are combined into a single binding free energy using a Boltzmann weighting-based scheme. This method was shown to reach experimental accuracy for flexible proteins while retaining the computational efficiency of the general LIE approach. Here, we show that the iterative LIE approach can be used to predict binding affinities in an automated way. A workflow was designed using preselected protein conformations, automated ligand docking and clustering, and a (semi-automated molecular dynamics simulation setup. We show that using this workflow, binding affinities of aryloxypropanolamines to the malleable Cytochrome P450 2D6 enzyme can be predicted without a priori knowledge of dominant protein-ligand conformations. In addition, we provide an outlook for an approach to assess the quality of the LIE predictions, based on simulation outcomes only.

  14. Computational multiscale modeling in protein--ligand docking.

    Science.gov (United States)

    Taufer, Michela; Armen, Roger; Chen, Jianhan; Teller, Patricia; Brooks, Charles

    2009-01-01

    In biological systems, the binding of small molecule ligands to proteins is a crucial process for almost every aspect of biochemistry and molecular biology. Enzymes are proteins that function by catalyzing specific biochemical reactions that convert reactants into products. Complex organisms are typically composed of cells in which thousands of enzymes participate in complex and interconnected biochemical pathways. Some enzymes serve as sequential steps in specific pathways (such as energy metabolism), while others function to regulate entire pathways and cellular functions [1]. Small molecule ligands can be designed to bind to a specific enzyme and inhibit the biochemical reaction. Inhibiting the activity of key enzymes may result in the entire biochemical pathways being turned on or off [2], [3]. Many small molecule drugs marketed today function in this generic way as enzyme inhibitors. If research identifies a specific enzyme as being crucial to the progress of disease, then this enzyme may be targeted with an inhibitor, which may slow down or reverse the progress of disease. In this way, enzymes are targeted from specific pathogens (e.g., virus, bacteria, fungi) for infectious diseases [4], [5], and human enzymes are targeted for noninfectious diseases such as cardiovascular disease, cancer, diabetes, and neurodegenerative diseases [6].

  15. Experimental results obtained at GANIL

    International Nuclear Information System (INIS)

    Borrel, V.

    1993-01-01

    A review of experimental results obtained at GANIL on the study of nuclear structure and nuclear reactions with secondary radioactive beams is presented. Mass measurements by means of the GANIL cyclotrons are described. The possibilities of GANIL/LISE3 for the production and separation of radioactive beams are illustrated through a large variety of experiments. (author). 19 refs., 8 figs

  16. Geopolymer obtained from coal ash

    International Nuclear Information System (INIS)

    Conte, V.; Bissari, E.S.; Uggioni, E.; Bernardin, A.M.

    2011-01-01

    Geopolymers are three-dimensional alumino silicates that can be rapidly formed at low temperature from naturally occurring aluminosilicates with a structure similar to zeolites. In this work coal ash (Tractebel Energy) was used as source of aluminosilicate according a full factorial design in eight formulations with three factors (hydroxide type and concentration and temperature) and two-levels. The ash was dried and hydroxide was added according type and concentration. The geopolymer was poured into cylindrical molds, cured (14 days) and subjected to compression test. The coal ash from power plants belongs to the Si-Al system and thus can easily form geopolymers. The compression tests showed that it is possible to obtain samples with strength comparable to conventional Portland cement. As a result, temperature and molarity are the main factors affecting the compressive strength of the obtained geopolymer. (author)

  17. Truncated States Obtained by Iteration

    International Nuclear Information System (INIS)

    Cardoso, W. B.; Almeida, N. G. de

    2008-01-01

    We introduce the concept of truncated states obtained via iterative processes (TSI) and study its statistical features, making an analogy with dynamical systems theory (DST). As a specific example, we have studied TSI for the doubling and the logistic functions, which are standard functions in studying chaos. TSI for both the doubling and logistic functions exhibit certain similar patterns when their statistical features are compared from the point of view of DST

  18. Obtaining zircaloy powder through hydriding

    International Nuclear Information System (INIS)

    Dupim, Ivaldete da Silva; Moreira, Joao M.L.

    2009-01-01

    Zirconium alloys are good options for the metal matrix in dispersion fuels for power reactors due to their low thermal neutron absorption cross-section, good corrosion resistance, good mechanical strength and high thermal conductivity. A necessary step for obtaining such fuels is producing Zr alloy powder for the metal matrix composite material. This article presents results from the Zircaloy-4 hydrogenation tests with the purpose to embrittle the alloy as a first step for comminuting. Several hydrogenation tests were performed and studied through thermogravimetric analysis. They included H 2 pressures of 25 and 50 kPa and temperatures ranging between from 20 to 670 deg C. X-ray diffraction analysis showed in the hydrogenated samples the predominant presence of ZrH 2 and some ZrO 2 . Some kinetics parameters for the Zircaloy-4 hydrogenation reaction were obtained: the time required to reach the equilibrium state at the dwell temperature was about 100 minutes; the hydrogenation rate during the heating process from 20 to 670 deg C was about 21 mg/h, and at constant temperature of 670 deg C, the hydride rate was about 1.15 mg/h. The hydrogenation rate is largest during the heating process and most of it occurs during this period. After hydrogenated, the samples could easily be comminuted indicating that this is a possible technology to obtain Zircaloy powder. The results show that only few minutes of hydrogenation are necessary to reach the hydride levels required for comminuting the Zircaloy. The final hydride stoichiometry was between 2.7 and 2.8 H for each Zr atom in the sample (author)

  19. Drugs obtained by biotechnology processing

    Directory of Open Access Journals (Sweden)

    Hugo Almeida

    2011-06-01

    Full Text Available In recent years, the number of drugs of biotechnological origin available for many different diseases has increased exponentially, including different types of cancer, diabetes mellitus, infectious diseases (e.g. AIDS Virus / HIV as well as cardiovascular, neurological, respiratory, and autoimmune diseases, among others. The pharmaceutical industry has used different technologies to obtain new and promising active ingredients, as exemplified by the fermentation technique, recombinant DNA technique and the hybridoma technique. The expiry of the patents of the first drugs of biotechnological origin and the consequent emergence of biosimilar products, have posed various questions to health authorities worldwide regarding the definition, framework, and requirements for authorization to market such products.Nos últimos anos, tem aumentado exponencialmente o número de fármacos de origem biotecnológica ao dispor das mais diversas patologias, entre elas destacam-se, os diferentes tipos de cancêr, as doenças infecciosas (ex. vírus AIDS/HIV, as doenças autoimunes, as doenças cardiovasculares, a Diabetes Mellitus, as doenças neurológicas, as doenças respiratórias, entre outras. A indústria farmacêutica tem recorrido a diferentes tecnologias para a obtenção de novos e promissores princípios ativos, como são exemplo a fermentação, a técnica de DNA Recombinante, a técnica de hidridoma, entre outras. A queda das patentes dos primeiros fármacos de origem biotecnológica e o consequente aparecimento dos produtos biossimilares têm colocado diferentes questões às autoridades de saúde mundiais, sobre a definição, enquadramento e exigências para a autorização de entrada no mercado deste tipo de produtos.

  20. Analysis of protein stability and ligand interactions by thermal shift assay.

    Science.gov (United States)

    Huynh, Kathy; Partch, Carrie L

    2015-02-02

    Purification of recombinant proteins for biochemical assays and structural studies is time-consuming and presents inherent difficulties that depend on the optimization of protein stability. The use of dyes to monitor thermal denaturation of proteins with sensitive fluorescence detection enables rapid and inexpensive determination of protein stability using real-time PCR instruments. By screening a wide range of solution conditions and additives in a 96-well format, the thermal shift assay easily identifies conditions that significantly enhance the stability of recombinant proteins. The same approach can be used as an initial low-cost screen to discover new protein-ligand interactions by capitalizing on increases in protein stability that typically occur upon ligand binding. This unit presents a methodological workflow for small-scale, high-throughput thermal denaturation of recombinant proteins in the presence of SYPRO Orange dye. Copyright © 2015 John Wiley & Sons, Inc.

  1. Power transformations improve interpolation of grids for molecular mechanics interaction energies.

    Science.gov (United States)

    Minh, David D L

    2018-02-18

    A common strategy for speeding up molecular docking calculations is to precompute nonbonded interaction energies between a receptor molecule and a set of three-dimensional grids. The grids are then interpolated to compute energies for ligand atoms in many different binding poses. Here, I evaluate a smoothing strategy of taking a power transformation of grid point energies and inverse transformation of the result from trilinear interpolation. For molecular docking poses from 85 protein-ligand complexes, this smoothing procedure leads to significant accuracy improvements, including an approximately twofold reduction in the root mean square error at a grid spacing of 0.4 Å and retaining the ability to rank docking poses even at a grid spacing of 0.7 Å. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

  2. Linear Interaction Energy Based Prediction of Cytochrome P450 1A2 Binding Affinities with Reliability Estimation.

    Directory of Open Access Journals (Sweden)

    Luigi Capoferri

    Full Text Available Prediction of human Cytochrome P450 (CYP binding affinities of small ligands, i.e., substrates and inhibitors, represents an important task for predicting drug-drug interactions. A quantitative assessment of the ligand binding affinity towards different CYPs can provide an estimate of inhibitory activity or an indication of isoforms prone to interact with the substrate of inhibitors. However, the accuracy of global quantitative models for CYP substrate binding or inhibition based on traditional molecular descriptors can be limited, because of the lack of information on the structure and flexibility of the catalytic site of CYPs. Here we describe the application of a method that combines protein-ligand docking, Molecular Dynamics (MD simulations and Linear Interaction Energy (LIE theory, to allow for quantitative CYP affinity prediction. Using this combined approach, a LIE model for human CYP 1A2 was developed and evaluated, based on a structurally diverse dataset for which the estimated experimental uncertainty was 3.3 kJ mol-1. For the computed CYP 1A2 binding affinities, the model showed a root mean square error (RMSE of 4.1 kJ mol-1 and a standard error in prediction (SDEP in cross-validation of 4.3 kJ mol-1. A novel approach that includes information on both structural ligand description and protein-ligand interaction was developed for estimating the reliability of predictions, and was able to identify compounds from an external test set with a SDEP for the predicted affinities of 4.6 kJ mol-1 (corresponding to 0.8 pKi units.

  3. Effect of protein-surfactant interactions on aggregation of β-lactoglobulin.

    Science.gov (United States)

    Hansted, Jon G; Wejse, Peter L; Bertelsen, Hans; Otzen, Daniel E

    2011-05-01

    The milk protein β-lactoglobulin (βLG) dominates the properties of whey aggregates in food products. Here we use spectroscopic and calorimetric techniques to elucidate how anionic, cationic and non-ionic surfactants interact with bovine βLG and modulate its heat-induced aggregation. Alkyl trimethyl ammonium chlorides (xTAC) strongly promote aggregation, while sodium alkyl sulfates (SxS) and alkyl maltopyranosides (xM) reduce aggregation. Sodium dodecyl sulfate (SDS) binds to non-aggregated βLG in several steps, but reduction of aggregation was associated with the first binding step, which occurs far below the critical micelle concentration. In contrast, micellar concentrations of xMs are required to reduce aggregation. The ranking order for reduction of aggregation (normalized to their tendency to self-associate) was C10-C12>C8>C14 for SxS and C8>C10>C12>C14>C16 for xM. xTAC promote aggregation in the same ranking order as xM reduce it. We conclude that SxS reduce aggregation by stabilizing the protein's ligand-bound state (the melting temperature t(m) increases by up to 10°C) and altering its charge potential. xM monomers also stabilize the protein's ligand-bound state (increasing t(m) up to 6°C) but in the absence of charged head groups this is not sufficient by itself to prevent aggregation. Although micelles of both anionic and non-ionic surfactants destabilize βLG, they also solubilize unfolded protein monomers, leaving them unavailable for protein-protein association and thus inhibiting aggregation. Cationic surfactants promote aggregation by a combination of destabilization and charge neutralization. The food compatible surfactant sodium dodecanoate also inhibited aggregation well below the cmc, suggesting that surfactants may be a practical way to modulate whey protein properties. Copyright © 2011 Elsevier B.V. All rights reserved.

  4. Electrostatic similarities between protein and small molecule ligands facilitate the design of protein-protein interaction inhibitors.

    Directory of Open Access Journals (Sweden)

    Arnout Voet

    Full Text Available One of the underlying principles in drug discovery is that a biologically active compound is complimentary in shape and molecular recognition features to its receptor. This principle infers that molecules binding to the same receptor may share some common features. Here, we have investigated whether the electrostatic similarity can be used for the discovery of small molecule protein-protein interaction inhibitors (SMPPIIs. We have developed a method that can be used to evaluate the similarity of electrostatic potentials between small molecules and known protein ligands. This method was implemented in a software called EleKit. Analyses of all available (at the time of research SMPPII structures indicate that SMPPIIs bear some similarities of electrostatic potential with the ligand proteins of the same receptor. This is especially true for the more polar SMPPIIs. Retrospective analysis of several successful SMPPIIs has shown the applicability of EleKit in the design of new SMPPIIs.

  5. Combined molecular docking and multi-spectroscopic investigation on the interaction between Eosin B and human serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Yang Qing; Zhou Ximin [National Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000 (China); Department of Chemistry, Lanzhou University, Lanzhou 730000 (China); Chen Xingguo, E-mail: chenxg@lzu.edu.c [National Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000 (China); Department of Chemistry, Lanzhou University, Lanzhou 730000 (China)

    2011-04-15

    The binding of Eosin B to human serum albumin (HSA) was studied using molecular docking, fluorescence, UV-vis, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy. The mechanism of interaction between Eosin B and HSA in terms of the binding parameters, the thermodynamic functions and the effect of Eosin B on the conformation of HSA were investigated. Protein-ligand docking study indicated that Eosin B bound to residues located in the subdomain IIA of HSA and Eosin B-HSA complex was stabilized by hydrophobic force and hydrogen bonding. In addition, fluorescence data revealed that Eosin B strongly quenched the intrinsic fluorescence of HSA through a static quenching procedure. Furthermore, alteration of the secondary structure of HSA in the presence of the dye was conformed by UV-vis, FT-IR and CD spectroscopy.

  6. Combined molecular docking and multi-spectroscopic investigation on the interaction between Eosin B and human serum albumin

    International Nuclear Information System (INIS)

    Yang Qing; Zhou Ximin; Chen Xingguo

    2011-01-01

    The binding of Eosin B to human serum albumin (HSA) was studied using molecular docking, fluorescence, UV-vis, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy. The mechanism of interaction between Eosin B and HSA in terms of the binding parameters, the thermodynamic functions and the effect of Eosin B on the conformation of HSA were investigated. Protein-ligand docking study indicated that Eosin B bound to residues located in the subdomain IIA of HSA and Eosin B-HSA complex was stabilized by hydrophobic force and hydrogen bonding. In addition, fluorescence data revealed that Eosin B strongly quenched the intrinsic fluorescence of HSA through a static quenching procedure. Furthermore, alteration of the secondary structure of HSA in the presence of the dye was conformed by UV-vis, FT-IR and CD spectroscopy.

  7. Obtaining shale oil suitable for lighting

    Energy Technology Data Exchange (ETDEWEB)

    Giraudel, M

    1851-11-12

    Treats with sulphuric acid and then with soda, obtaining 57 per cent of products suitable for lighting in place of the usual 35 to 40 per cent as obtained by present processes. The product has a less disagreeable odor.

  8. Energetics of the protein-DNA-water interaction

    Directory of Open Access Journals (Sweden)

    Marabotti Anna

    2007-01-01

    Full Text Available Abstract Background To understand the energetics of the interaction between protein and DNA we analyzed 39 crystallographically characterized complexes with the HINT (Hydropathic INTeractions computational model. HINT is an empirical free energy force field based on solvent partitioning of small molecules between water and 1-octanol. Our previous studies on protein-ligand complexes demonstrated that free energy predictions were significantly improved by taking into account the energetic contribution of water molecules that form at least one hydrogen bond with each interacting species. Results An initial correlation between the calculated HINT scores and the experimentally determined binding free energies in the protein-DNA system exhibited a relatively poor r2 of 0.21 and standard error of ± 1.71 kcal mol-1. However, the inclusion of 261 waters that bridge protein and DNA improved the HINT score-free energy correlation to an r2 of 0.56 and standard error of ± 1.28 kcal mol-1. Analysis of the water role and energy contributions indicate that 46% of the bridging waters act as linkers between amino acids and nucleotide bases at the protein-DNA interface, while the remaining 54% are largely involved in screening unfavorable electrostatic contacts. Conclusion This study quantifies the key energetic role of bridging waters in protein-DNA associations. In addition, the relevant role of hydrophobic interactions and entropy in driving protein-DNA association is indicated by analyses of interaction character showing that, together, the favorable polar and unfavorable polar/hydrophobic-polar interactions (i.e., desolvation mostly cancel.

  9. Overview of galactic results obtained by MAGIC

    Energy Technology Data Exchange (ETDEWEB)

    Zanin, Roberta

    2013-06-15

    MAGIC is a system of two atmospheric Cherenkov telescopes which explores the very-high-energy sky, from some tens of GeV up to tens of TeV. Located in the Canary island of La Palma, MAGIC has the lowest energy threshold among the instruments of its kind, well suited to study the still poorly explored energy band below 100 GeV. Although the space-borne gamma-ray telescope Fermi/LAT is sensitive up to 300 GeV, gamma-ray rates drop fast with increasing energy, so γ-ray collection areas larger than 10{sup 4}m{sup 2}, as those provided by grounds-based instruments, are crucial above a few GeV. The combination of MAGIC and Fermi/LAT observations have provided the first astrophysical spectra sampled in the inverse Compton peak region, resulting in a complete coverage from MeV up to TeV energies, as well as the discovery of a pulsed emission in the very-high-energy band. This paper focuses on the latest results on Galactic sources obtained by MAGIC which are highlighted by the detection of the pulsed gamma-ray emission from the Crab pulsar up to 400 GeV. In addition, we will present the morphological study on the W51 complex which allowed to pinpoint the location of the majority of the emission around the interaction point between the supernova remnant W51C and the star forming region W51B, but also to find a possible contribution from the associated pulsar wind nebula. Other important scientific achievements involve the Crab Nebula with an unprecedented spectrum covering three decades in energy starting from 50 GeV and a morphological study of the unidentified source HESS J1857+026 which supports the pulsar wind nebula scenario. Finally we will report on the searches of very-high-energy signals from gamma-ray binaries, mainly LS I 303+ and HESS J0632+057.

  10. Interacting boson model with surface delta interaction between nucleons

    International Nuclear Information System (INIS)

    Druce, C.; Moszkowski, S.A.

    1984-01-01

    The surface delta interaction is used as an effective nucleon-nucleon interaction to investigate the structure and interaction of the bosons in the interacting boson model. The authors have obtained analytical expressions for the coefficients of a multipole expansion of the neutron-boson proton-boson interaction for the case of degenerate orbits

  11. Obtaining of potassium dicyan-argentate

    International Nuclear Information System (INIS)

    Sattarova, M.A.; Solojenkin, P.M.

    1997-01-01

    This work is devoted to obtaining of potassium dicyan-argentate. By means of exchange reaction between silver nitrate and potassium cyanide the potassium dicyan-argentate was synthesized. The analysis of obtained samples was carried out by means of titration and potentiometry.

  12. Treating shale oil to obtain sulfonates

    Energy Technology Data Exchange (ETDEWEB)

    Schaeffer, H

    1921-01-21

    The process shows as its principal characteristics: (1) treating the oil with chlorsulfonic acid at a temperature of about 100/sup 0/C; (2) the transformation of the sulfonic acid obtained into salts; (3) as new industrial products, the sulfonates obtained and their industrial application as disinfectants for hides and wood.

  13. Strategies for obtaining unpublished drug trial data

    DEFF Research Database (Denmark)

    Wolfe, Nicole; Gøtzsche, Peter C.; Bero, Lisa Anne

    2013-01-01

    Authors of systematic reviews have difficulty obtaining unpublished data for their reviews. This project aimed to provide an in-depth description of the experiences of authors in searching for and gaining access to unpublished data for their systematic reviews, and to give guidance on best...... practices for identifying, obtaining and using unpublished data....

  14. 38 CFR 21.5725 - Obtaining benefits.

    Science.gov (United States)

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false Obtaining benefits. 21... benefits. (a) Actions required of the individual. In order to obtain benefits under the educational assistance and subsistence allowance program, an individual must— (1) File a claim for benefits with VA, and...

  15. Obtaining of polycrystalline silicon for semiconductor industry

    International Nuclear Information System (INIS)

    Mukashev, F.; Nauryzbaev, M.; Kolesnikov, B.; Ivanov, Y.

    1996-01-01

    The purpose of the project is to create pilot equipment and optimize the process of obtaining polycrystalline silicon on semi-industrial level. In the past several decades, the historical experience in the developing countries has shown that one of the most promising ways to improve the economy,of a country is to establish semiconductor industry. First of all, the results can help increase defense, national security and create industrial production. The silane method, which has been traditionally' used for obtaining technical and polycrystalline silicon, is to obtain and then to pyrolyzed mono-and poly silanes. Although the traditional methods of obtaining silicon hydrides have specific advantages, such as utilizing by-products, they also have clear shortcomings, i.e. either low output of the ultimate product ( through hydrolysis of Mg 2 Si) or high contents of by-products in it or high contents of dissolving vapors (through decomposing Mg 2 Si in non-water solutions)

  16. Production and characterization of pectinases obtained from ...

    African Journals Online (AJOL)

    Production and characterization of pectinases obtained from Aspergillus fumigatus in submerged fermentation system using pectin extracted from mango peels as carbon source. AL Ezugwu, SOO Eze, FC Chilaka, CU Anyanwu ...

  17. Treatment of biomass to obtain ethanol

    Science.gov (United States)

    Dunson, Jr., James B.; Elander, Richard T [Evergreen, CO; Tucker, III, Melvin P.; Hennessey, Susan Marie [Avondale, PA

    2011-08-16

    Ethanol was produced using biocatalysts that are able to ferment sugars derived from treated biomass. Sugars were obtained by pretreating biomass under conditions of high solids and low ammonia concentration, followed by saccharification.

  18. Silicon dioxide obtained by Polymeric Precursor Method

    International Nuclear Information System (INIS)

    Oliveira, C.T.; Granado, S.R.; Lopes, S.A.; Cavalheiro, A.A.

    2011-01-01

    The Polymeric Precursor Method is able for obtaining several oxide material types with high surface area even obtained in particle form. Several MO 2 oxide types such as titanium, silicon and zirconium ones can be obtained by this methodology. In this work, the synthesis of silicon oxide was monitored by thermal analysis, XRD and surface area analysis in order to demonstrate the influence of the several synthesis and calcining parameters. Surface area values as higher as 370m2/g and increasing in the micropore volume nm were obtained when the material was synthesized by using ethylene glycol as polymerizing agent. XRD analysis showed that the material is amorphous when calcinated at 600°C in despite of the time of calcining, but the material morphology is strongly influenced by the polymeric resin composition. Using Glycerol as polymerizing agent, the pore size increase and the surface area goes down with the increasing in decomposition time, when compared to ethylene glycol. (author)

  19. Process for obtaining cobalt and lanthanum nickelate

    International Nuclear Information System (INIS)

    Tapcov, V.; Samusi, N.; Gulea, A.; Horosun, I.; Stasiuc, V.; Petrenco, P.

    1999-01-01

    The invention relates to the process for obtaining polycrystalline ceramics of cobalt and lanthanum nickelate with the perovskite structure from coordinative hetero metallic compounds. The obtained products can be utilized in the industry in the capacity of catalysts. Summary of the invention consists in obtaining polycrystalline ceramics LaCoO 3 and LaNiO 3 with the perovskite structure by pyrolysis of the parent compounds, namely, the coordinative hetero metallic compounds of the lanthanum cobalt or lanthanum nickel. The pyrolysis of the parent compound runs during one hour at 800 C. The technical result of the invention consists in lowering the temperature of the parent compound pyrolysis containing the precise ratio of metals necessary for ceramics obtaining

  20. Structure-wise discrimination of cytosine, thymine, and uracil by proteins in terms of their nonbonded interactions.

    Science.gov (United States)

    Usha, S; Selvaraj, S

    2014-01-01

    The molecular recognition and discrimination of very similar ligand moieties by proteins are important subjects in protein-ligand interaction studies. Specificity in the recognition of molecules is determined by the arrangement of protein and ligand atoms in space. The three pyrimidine bases, viz. cytosine, thymine, and uracil, are structurally similar, but the proteins that bind to them are able to discriminate them and form interactions. Since nonbonded interactions are responsible for molecular recognition processes in biological systems, our work attempts to understand some of the underlying principles of such recognition of pyrimidine molecular structures by proteins. The preferences of the amino acid residues to contact the pyrimidine bases in terms of nonbonded interactions; amino acid residue-ligand atom preferences; main chain and side chain atom contributions of amino acid residues; and solvent-accessible surface area of ligand atoms when forming complexes are analyzed. Our analysis shows that the amino acid residues, tyrosine and phenyl alanine, are highly involved in the pyrimidine interactions. Arginine prefers contacts with the cytosine base. The similarities and differences that exist between the interactions of the amino acid residues with each of the three pyrimidine base atoms in our analysis provide insights that can be exploited in designing specific inhibitors competitive to the ligands.

  1. Obtaining of ceramics biphasic dense and porous

    International Nuclear Information System (INIS)

    Pallone, E.M.J.A.; Rigo, E.C.S.; Fraga, A.F.

    2010-01-01

    Among the bioceramic hydroxyapatite (HAP) and beta-tricalcium phosphate (beta-TCP) are materials commonly used in biomedical field. Their combined properties result in a material with absorbable and at the same time with bioactive surface. Called biphasic ceramics such materials respond more quickly when exposed to physiological environment. In this work, powders of HAP/beta-TCP were obtained by chemical precipitation. After obtaining the post-phase was added at a ratio of 0, 15% and 30w% aqueous solutions of corn starch in order to obtain porous bodies. After mixing the resulting solutions were dried, resigned in tablet form and sintered at 1300 deg C. The initial powder was characterized by X-ray diffraction with Rietveld refinement to quantify the phases present. Bodies-of-evidence has been characterized by calculating the bulk density, X-ray diffraction (XRD), scanning electron microscopy and diametral compression. (author)

  2. Organoclays obtaining starting up of clays sodium

    International Nuclear Information System (INIS)

    Silva, M.M. da; Mota, M.F.; Oliveira, G.C. de; Rodrigues, M.G.F.

    2012-01-01

    Clays have several applications in many areas of fields of technology, however, modification of these materials using organic compounds can be performed to obtain further hydrophobic materials, for applications in the adsorption of organic pollutants. This study aimed to analyze the effects of modifying two clays using sodium quaternary ammonium surfactants through ion exchange reaction process, in obtaining organoclays. The samples with sodium and organoclays were characterized by the techniques of X-ray diffraction (XRD), Infrared Spectroscopy in the region (IV), Gravimetric and Differential Thermal Analysis (DTA / TG) and organic adsorption tests. The results show that the process of obtaining organoclay is efficient, and materials have the potential for future applications in removing organic contaminants. (author)

  3. Obtain of uranium concentrates from fertil liquids

    International Nuclear Information System (INIS)

    Narvaez Castillo, W.A.

    1992-01-01

    This research tried to encounter the form to remove uranium from the rock in the best way, for that it was used different process like leaching, extraction, concentration and precipitation. To leach the mineral was chosen basic leaching, using a mixture of carbonate-sodium bicarbonate, this method is more adequated for the basic nature of the mineral. In extraction was used specific uranium ionic interchanges, so was chosen a tertiary amine like Alamina 336. The concentration phase is intimately binding with the extraction by ionic interchange, for the capability of resine's extraction to obtain concentrated liquids. When the liquids were obtained with high concentration of uranium in the same time were purified and then were precipitated, for that we employed a precipitant agent like: Sodium hydroxide, Amonium hydroxide, Magnesium hydroxide, Hydrogen peroxide and phosphates. With all concentrates we obtain the YELLOW CAKE

  4. Obtaining the Andersen's chart, triangulation algorithm

    DEFF Research Database (Denmark)

    Sabaliauskas, Tomas; Ibsen, Lars Bo

    Andersen’s chart (Andersen & Berre, 1999) is a graphical method of observing cyclic soil response. It allows observing soil response to various stress amplitudes that can lead to liquefaction, excess plastic deformation or stabilizing soil response. The process of obtaining the original chart has...

  5. Purification of alcohol obtained from molasses

    Energy Technology Data Exchange (ETDEWEB)

    Visnevskaya, G L; Egorov, A S; Sokol' skaya, E V

    1960-01-01

    A study of the composition of alcohol liquids on different plates of a fractionation column of indirect action during purification of alcohol obtained from normal and defective molasses, and from starch raw material, showed that there were two local strength minima in the lower part of the column and on the plates (adjacent and feed). Aldehydes behaved as a typical head impurity; a noticeable increase in their concentration occurred only on the highest plates in the fractionation column. In the zone of the column containing liquids of a strength of 86 to 94% alcohol by weight a sharply pronounced local maximum of ester accumulation were observed, provisionally designated as intermediate, whose presence is apparently one of the causes of the specific sharp taste of alcohol obtained from molasses. These esters hinder the obtaining of high-grade alcohols which are standard in respect to ester content and oxidizability test. Reduction with 0.05N KMnO/sub 4/ occurs most rapidly with alcohol liquids in the zone of ester accumulation; purification of alcohols obtained from grain and potato raw material resulted in no zones of ester accumulation in the column.

  6. Obtaining shale distillate free from sulphur

    Energy Technology Data Exchange (ETDEWEB)

    Heyl, G E

    1917-09-14

    A process whereby, from sulfur-containing shale, products free from sulfur may be obtained, consisting of mixing with the finely ground shale a portion of iron salts containing sufficient metal to unite with all the sulfur in the shale and form sulfide therewith, grinding the mixture to a fine state of subdivision and subsequently subjecting it to destructive distillation.

  7. Obtaining a minimal set of rewrite rules

    CSIR Research Space (South Africa)

    Davel, M

    2005-11-01

    Full Text Available In this paper the authors describe a new approach to rewrite rule extraction and analysis, using Minimal Representation Graphs. This approach provides a mechanism for obtaining the smallest possible rule set – within a context-dependent rewrite rule...

  8. Obtainment of tantalum oxide from national ores

    International Nuclear Information System (INIS)

    Pinatti, D.G.; Ribeiro, S.; Martins, A.H.

    1988-01-01

    The experimental results of tantalum oxides (Ta 2 O 5 ) obtainment from Brazilian ores of tantalite and columbite are described. This study is a part of the technologic and scientific research design of refractory metals (Ti, Zr, Hf, V, Nb, Ta, Cr, Mo and W) and correlate ceramics. (C.G.C.) [pt

  9. Isolation and characterization of microcrystalline cellulose obtained ...

    African Journals Online (AJOL)

    In this study, microcrystalline cellulose, coded MCC-PNF, was obtained from palm nut (Elaeis guineensis) fibres. MCC-PNF was examined for its physicochemical and powder properties. The powder properties of MCC-PNF were compared to those of the best commercial microcrystalline cellulose grade, Avicel PH 101.

  10. 47 CFR 54.615 - Obtaining services.

    Science.gov (United States)

    2010-10-01

    ... provided under § 54.621, that the requester cannot obtain toll-free access to an Internet service provider... thing of value; (6) If the service or services are being purchased as part of an aggregated purchase... submitted and select the most cost-effective alternative. (b) Receiving supported rate. Except with regard...

  11. Interacting boson model with surface delta interaction between nucleons: Structure and interaction of bosons

    International Nuclear Information System (INIS)

    Druce, C.H.; Moszkowski, S.A.

    1986-01-01

    The surface delta interaction is used as an effective nucleon-nucleon interaction to investigate the structure and interaction of the bosons in the interacting boson model. We have obtained analytical expressions for the coefficients of a multipole expansion of the neutron-boson-proton-boson interaction for the case of degenerate orbits. A connection is made between these coefficients and the parameters of the interaction boson model Hamiltonian. A link between the latter parameters and the single boson energies is suggested

  12. Interacting boson model with surface delta interaction between nucleons: Structure and interaction of bosons

    Energy Technology Data Exchange (ETDEWEB)

    Druce, C.H.; Moszkowski, S.A.

    1986-01-01

    The surface delta interaction is used as an effective nucleon-nucleon interaction to investigate the structure and interaction of the bosons in the interacting boson model. We have obtained analytical expressions for the coefficients of a multipole expansion of the neutron-boson-proton-boson interaction for the case of degenerate orbits. A connection is made between these coefficients and the parameters of the interaction boson model Hamiltonian. A link between the latter parameters and the single boson energies is suggested.

  13. Superconductive ceramics obtained with sol gel method

    International Nuclear Information System (INIS)

    Arcangeli, A.; Mosci, A.; Nardi, A.; Vatteroni, R.; Zondini, C.

    1988-01-01

    Several sol gel routes have been considered, studied and developed to produce large quantities of granulates which can be processed to obtain ceramics having good superconducting characteristics. In the considered process a mixture of commercial nitrates is atomized, at room temperature, in a solution 1:1 of Primene JMT and Benzene and a pale blue gel of the starting elements is suddently formed. The granulates obtained are free flowing, very reactive and well suited for pressing. For their intrinsic characteristics they could be very good precursors for the production of large quantities of superconductive ceramics in different forms. The precipitated gel is dried, calcinated, pressed in the form of cylindrical pellets which are sintered up to 960 degrees C. No griding or different thermal treatments are needed. The sintered material has low electric resistence, shows a clear Meissner effect and has a transition temperature of between 91 and 95 K

  14. Acoustic barriers obtained from industrial wastes.

    Science.gov (United States)

    Garcia-Valles, M; Avila, G; Martinez, S; Terradas, R; Nogués, J M

    2008-07-01

    Acoustic pollution is an environmental problem that is becoming increasingly more important in our society. Likewise, the accumulation of generated waste and the need for waste management are also becoming more and more pressing. In this study we describe a new material--called PROUSO--obtained from industrial wastes. PROUSO has a variety of commercial and engineering, as well as building, applications. The main raw materials used for this environmentally friendly material come from slag from the aluminium recycling process, dust from the marble industry, foundry sands, and recycled expanded polystyrene from recycled packaging. Some natural materials, such as plastic clays, are also used. To obtain PROUSO we used a conventional ceramic process, forming new mineral phases and incorporating polluted elements into the structure. Its physical properties make PROUSO an excellent acoustic and thermal insulation material. It absorbs 95% of the sound in the frequency band of the 500 Hz. Its compressive strength makes it ideal for use in ceramic wall building.

  15. Processing of hydroxyapatite obtained by combustion synthesis

    International Nuclear Information System (INIS)

    Canillas, M.; Rivero, R.; García-Carrodeguas, R.; Barba, F.; Rodríguez, M.A.

    2017-01-01

    One of the reasons of implants failure are the stress forces appearing in the material–tissue interface due to the differences between their mechanical properties. For this reason, similar mechanical properties to the surrounding tissue are desirable. The synthesis of hydroxyapatite by solution combustion method and its processing have been studied in order to obtain fully dense ceramic bodies with improved mechanical strength. Combustion synthesis provides nanostructured powders characterized by a high surface area to facilitate the following sintering. Moreover, synthesis was conducted in aqueous and oxidizing media. Oxidizing media improve homogenization and increase the energy released during combustion. It gives rise to particles whose morphology and size suggest lower surface energies compared with aqueous media. The obtained powders were sintered by using a controlled sintering rate schedule. Lower surfaces energies minimize the shrinkage during sintering and relative densities measurements and diametral compression test confirm improved densification and consequently mechanical properties. [es

  16. Process for obtaining luminescent glass layers

    International Nuclear Information System (INIS)

    Heindi, R.; Robert, A.

    1984-01-01

    Process for obtaining luminescent glass layers, application to the production of devices provided with said layers and to the construction of photoscintillators. The process comprises projecting onto a support, by cathodic sputtering, the material of at least one target, each target including silica and at least one chemical compound able to give luminescent centers, such as a cerium oxide, so as to form at least one luminescent glass layer of the said support. The layer or layers formed preferably undergo a heat treatment such as annealing in order to increase the luminous efficiency thereof. It is in this way possible to form a scintillating glass layer on the previously frosted entrance window of a photomultiplier in order to obtain an integrated photoscintillator

  17. Processing of hydroxyapatite obtained by combustion synthesis

    Directory of Open Access Journals (Sweden)

    M. Canillas

    2017-09-01

    Full Text Available One of the reasons of implants failure are the stress forces appearing in the material–tissue interface due to the differences between their mechanical properties. For this reason, similar mechanical properties to the surrounding tissue are desirable. The synthesis of hydroxyapatite by solution combustion method and its processing have been studied in order to obtain fully dense ceramic bodies with improved mechanical strength. Combustion synthesis provides nanostructured powders characterized by a high surface area to facilitate the following sintering. Moreover, synthesis was conducted in aqueous and oxidizing media. Oxidizing media improve homogenization and increase the energy released during combustion. It gives rise to particles whose morphology and size suggest lower surface energies compared with aqueous media. The obtained powders were sintered by using a controlled sintering rate schedule. Lower surfaces energies minimize the shrinkage during sintering and relative densities measurements and diametral compression test confirm improved densification and consequently mechanical properties.

  18. Process for obtaining ammonium uranyl tri carbonate

    International Nuclear Information System (INIS)

    Santos, L.R. dos; Riella, H.G.

    1992-01-01

    The procedure adopted for obtaining Ammonium Uranyl Carbonate (AUC) from uranium hexafluoride (U F 6 ) in a aqueous solutions of ammonium hydrogen carbonate is described in this work. The precipitation is made in temperature and pH controlled. This process consists of three steps: evaporation of U F 6 , AUC precipitation and filtration of the AUC slurry. An attempt is made of correlate the parameters involved in the precipitation process of AUC with its and U O 2 characteristics. (author)

  19. Superconducting materials fabrication process and materials obtained

    International Nuclear Information System (INIS)

    Lafon, M.O.; Magnier, C.

    1989-01-01

    The preparation process of a fine powder of YBaCuO type superconductors of easy sintering comprises: mixing in presence of alcohol an aqueous solution of rare earth nitrate or acetate, alkaline earth nitrate or acetate and copper nitrate or acetate and an oxalic acid solution, the pH value of the mixture is comprised between 2 and 4, the obtained precipitate is separated, dried, calcined and eventually crushed [fr

  20. PULP OBTAINING METHOD FOR PACKAGE PRODUCTION

    Directory of Open Access Journals (Sweden)

    V. V. Kuzmich

    2015-01-01

    Full Text Available The paper presents a new method for obtaining pulp which is used for production of cardboard, paper and package while using carbon dioxide and hydrazine hydrate and neutral-sulfite  shive cooking. Output increase of  the desired product can be explained by reduction in destruction of plant raw material carbohydrates during its cooking process. Quality improvement of the desired product (improvement in bleaching and output is attributed to the fact that usage of carbon dioxide and hydrazine contributes to provision of polysaccharide chain resistance to destruction due to the presence of  end links having structure of metasaccharinic and aldonic acids.The author has developed a new method for pulp obtaining on the basis of the executed investigations  and literature data.  СО2 and hydrazine hydrate have been used for obtaining pulp. Method invention concerns pulp obtaining and it can be used for paper and cardboard package manufacturing in pulp and paper industry.The method is to be carried in the following way: pulp-containing plant raw material is loaded into an autoclave and then aqua solution of sodium monosulfite containing hydrazine hydrate that constitutes 4–5 % of absolute dry pulp-containing raw material mass with liquid module 1:6–1:8 is supplied into the autoclave. The autoclave is closed for operation under pressure and the solution is carbonated under pressure which constitutes 5–8 % of absolute dry plant raw material (shover. Temperature is subsequently raised up to 180 °С in the space of 2 hours and cooking is carried out in the course of 4 hours. Usage of  the proposed method for shover cooking makes it possible to reduce monosulfite cooking process and improve qualitative characteristics and output of the desired product.  In addition to above mentioned fact there is a possibility to improve bleaching and final product output. 

  1. Lifetime obtained by ion beam assisted deposition

    Energy Technology Data Exchange (ETDEWEB)

    Chakaroun, M. [XLIM-MINACOM-UMR 6172, Faculte des Sciences et Techniques, 123 av. Albert Thomas, 87060 Limoges cedex (France); Antony, R. [XLIM-MINACOM-UMR 6172, Faculte des Sciences et Techniques, 123 av. Albert Thomas, 87060 Limoges cedex (France)], E-mail: remi.antony@unilim.fr; Taillepierre, P.; Moliton, A. [XLIM-MINACOM-UMR 6172, Faculte des Sciences et Techniques, 123 av. Albert Thomas, 87060 Limoges cedex (France)

    2007-09-15

    We have fabricated green organic light-emitting diodes based on tris-(8-hydroxyquinoline)aluminium (Alq3) thin films. In order to favor the charge carriers transport from the anode, we have deposited a N,N'-diphenyl-N,N'-bis (3-methylphenyl)-1,1'-diphenyl-4,4'-diamine (TPD) layer (hole transport layer) on a ITO anode. Cathode is obtained with a calcium layer covered with a silver layer. This silver layer is used to protect the other layers against oxygen during the OLED use. All the depositions are performed under vacuum and the devices are not exposed to air during their realisation. In order to improve the silver layer characteristics, we have realized this layer with the ion beam assisted deposition process. The aim of this process is to densify the layer and then reduce the permeation of H{sub 2}O and O{sub 2}. We have used argon ions to assist the silver deposition. All the OLEDs optoelectronic characterizations (I = f(V), L = f(V)) are performed in the ambient air. We compare the results obtained with the assisted layer with those obtained with a classical cathode realized by thermal unassisted evaporation. We have realized lifetime measurements in the ambient air and we discuss about the assisted layer influence on the OLEDs performances.

  2. Antiproton-nucleus interaction

    International Nuclear Information System (INIS)

    Gibbs, W.R.

    1984-01-01

    Several facets of antinucleon-nucleus interactions are explored. The topics treated are: coherent interactions, production of unusual states and particles in the nuclear medium, and the creation of extreme states of matter by antimatter annihilation. It is found that temperatures of the magnitude necessary to achieve the predicted quark-gluon phase transition are obtained. 20 references

  3. Protein-protein interactions: an application of Tus-Ter mediated protein microarray system.

    Science.gov (United States)

    Sitaraman, Kalavathy; Chatterjee, Deb K

    2011-01-01

    In this chapter, we present a novel, cost-effective microarray strategy that utilizes expression-ready plasmid DNAs to generate protein arrays on-demand and its use to validate protein-protein interactions. These expression plasmids were constructed in such a way so as to serve a dual purpose of synthesizing the protein of interest as well as capturing the synthesized protein. The microarray system is based on the high affinity binding of Escherichia coli "Tus" protein to "Ter," a 20 bp DNA sequence involved in the regulation of DNA replication. The protein expression is carried out in a cell-free protein synthesis system, with rabbit reticulocyte lysates, and the target proteins are detected either by labeled incorporated tag specific or by gene-specific antibodies. This microarray system has been successfully used for the detection of protein-protein interaction because both the target protein and the query protein can be transcribed and translated simultaneously in the microarray slides. The utility of this system for detecting protein-protein interaction is demonstrated by a few well-known examples: Jun/Fos, FRB/FKBP12, p53/MDM2, and CDK4/p16. In all these cases, the presence of protein complexes resulted in the localization of fluorophores at the specific sites of the immobilized target plasmids. Interestingly, during our interactions studies we also detected a previously unknown interaction between CDK2 and p16. Thus, this Tus-Ter based system of protein microarray can be used for the validation of known protein interactions as well as for identifying new protein-protein interactions. In addition, it can be used to examine and identify targets of nucleic acid-protein, ligand-receptor, enzyme-substrate, and drug-protein interactions.

  4. DIFFERENCES IN RESULTS OBTAINED BY STUDENTS OF DIFFERENT FACULTIES

    Directory of Open Access Journals (Sweden)

    OTAVOVÁ, Miroslava

    2016-03-01

    Full Text Available The paper presents and discusses the results of statistical analysis of differences among scores obtained by students of different faculties of the University of Economics in Prague. The analysed dataset contains the scores for 2256 students that took basic mathematics course during the academic year 2013/2014. A two way analysis of variance was performed with semester and faculty as main factors. The interaction between these two factors was also considered. Students have to take two tests. At first, the sum of the scores obtained from both tests is analysed and then, the two tests are analysed separately. It turns out that the significance of factors is the same in the three analyses. The assumptions of linear models are verified. Due to problem of heteroscedasticity, weighted least squares are used and the possibility of using Box-Cox transformation is also discussed, as the errors are not normally distributed. Finally, the differences between the faculties are described.

  5. Characterization of Wastewaters obtained from Hatay Tanneries

    Directory of Open Access Journals (Sweden)

    Şana Sungur

    2017-06-01

    Full Text Available The leather tanning industry is one of the most significant pollutants in terms of both conventional and toxic parameters. On the other hand, leather industry has an important economic role both in Turkey and in the World. In this study, wastewater samples were taken from 15 different tanneries in the Hatay Region. Wastewaters obtained from liming process and chromium tanning process was analyzed. Sulfide, chromium (III, chromium (VI, oil and grease, total suspended solids (TSS, organic matters, biochemical oxygen demand (BOD, chemical oxygen demand (COD, pH and alkalinity were determined according to Turkish Standard Methods. The determined averages values belong to wastewaters obtained from liming process were as following: pH 11.71; COD 16821 mg L-1; BOD 4357 mg L-1; TSS 39023 mg L-1; oil and grease 364 mg L-1; S-2 concentration 802 mg L-1; alkalinity 2115 mg L-1. The determined averages values belong to wastewaters obtained from chromium tanning process were also as following: pH 4.23; COD 6740 mg L-1; BOD 377 mg L-1; Cr+3 concentrations 372 mg L-1; Cr+6 concentrations 127 mg L-1; TSS 14553 mg L-1; oil and grease 343 mg L-1. The results of all analyzes were higher than wastewater discharge standards. As a result, it’s necessary to use more effective treatments in order to reduce the negative impacts of leather tanning industry that affect environment, natural water resources and at last human health and welfare.

  6. Propensity for obtaining alcohol through shoulder tapping.

    Science.gov (United States)

    Toomey, Traci L; Fabian, Lindsey E A; Erickson, Darin J; Lenk, Kathleen M

    2007-07-01

    Underage youth often obtain alcohol from adults who illegally provide the alcohol. One method for obtaining alcohol from adults is shoulder tapping, where youth approach an adult outside an alcohol establishment and ask the adult to purchase alcohol for them. The goal of this study was to assess what percentage of the general and youth-targeted adult population approached outside of a convenience/liquor store will agree to purchase and then provide alcohol to individuals who appear under age 21. We conducted 2 waves of pseudo-underage shoulder tap request attempts, using requesters who were age 21 or older but appeared 18 to 20 years old. In both waves, requests were conducted at randomly selected liquor and convenience stores, requesters explained that the reason they were asking the adult was because they did not have their identification with them, and requesters asked the adults to purchase a 6-pack of beer. During wave 1, we conducted 102 attempts, with the requester approaching the first adult entering the store alone. During wave 2, we conducted 102 attempts where the requester approached the first casually dressed male entering the store alone who appeared to be 21 to 30 years old. During wave 1, 8% of the general sample of approached adults provided alcohol to the pseudo-underage requesters. The odds of adults providing alcohol in urban areas were 9.4 times greater than in suburban areas. During wave 2, 19% of the approached young men provided alcohol to the requesters. No requester, request attempt, establishment, or community characteristics were associated with request attempt outcomes during wave 2. A small percentage of the general population of adults will agree to provide alcohol to underage youth when approached outside an alcohol establishment. The likelihood of underage youth obtaining alcohol through shoulder tapping increases substantially if the youth approach young men.

  7. A general scheme for obtaining graviton spectrums

    International Nuclear Information System (INIS)

    GarcIa-Cuadrado, G

    2006-01-01

    The aim of this contribution is to present a general scheme for obtaining graviton spectra from modified gravity theories, based on a theory developed by Grishchuk in the mid 1970s. We try to be pedagogical, putting in order some basic ideas in a compact procedure and also giving a review of the current trends in this arena. With the aim to fill a gap for the interface between quantum field theorists and observational cosmologist in this matter, we highlight two interesting applications to cosmology: clues as to the nature of dark energy; and the possibility of reconstruction of the scalar potential in scalar-tensor gravity theories

  8. Obtaining high purity silica from rice hulls

    Directory of Open Access Journals (Sweden)

    José da Silva Júnior

    2010-01-01

    Full Text Available Many routes for extracting silica from rice hulls are based on direct calcining. These methods, though, often produce silica contaminated with inorganic impurities. This work presents the study of a strategy for obtaining silica from rice hulls with a purity level adequate for applications in electronics. The technique is based on two leaching steps, using respectively aqua regia and Piranha solutions, which extract the organic matrix and inorganic impurities. The material was characterized by Fourier-transform infrared spectroscopy (FTIR, powder x-ray diffraction (XRD, x-ray fluorescence (XRF, scanning electron microscopy (SEM, particle size analysis by laser diffraction (LPSA and thermal analysis.

  9. Diaphragms obtained by radiochemical grafting in PTFE

    International Nuclear Information System (INIS)

    Nenner, T.; Fahrasmane, A.

    1984-01-01

    Diaphragms for alkaline water electrolysis are prepared by radiochemical grafting of PTFE fabric with styrene, which is later on sulfonated, or with acrylic acid. The diaphragms obtained are mechanically resistant to potash at temperatures up to 200 0 C, but show some degrafting, which limits the lifetime. The sulfonated styrene group has been found to be more stable in electrolysis than the acrylic acid. In both cases, the incorporation of a cross-linking agent like divinyl benzene improves the lifetime of the diaphragms. Electrolysis during 500 hours at 120 0 C and 10 kAm 2 could be performed. (author)

  10. Reliability of "Google" for obtaining medical information

    Directory of Open Access Journals (Sweden)

    Mihir Kothari

    2015-01-01

    Full Text Available Internet is used by many patients to obtain relevant medical information. We assessed the impact of "Google" search on the knowledge of the parents whose ward suffered from squint. In 21 consecutive patients, the "Google" search improved the mean score of the correct answers from 47% to 62%. We found that "Google" search was useful and reliable source of information for the patients with regards to the disease etiopathogenesis and the problems caused by the disease. The internet-based information, however, was incomplete and not reliable with regards to the disease treatment.

  11. Carbon nanofibers obtained from electrospinning process

    Science.gov (United States)

    Bovi de Oliveira, Juliana; Müller Guerrini, Lília; Sizuka Oishi, Silvia; Rogerio de Oliveira Hein, Luis; dos Santos Conejo, Luíza; Cerqueira Rezende, Mirabel; Cocchieri Botelho, Edson

    2018-02-01

    In recent years, reinforcements consisting of carbon nanostructures, such as carbon nanotubes, fullerenes, graphenes, and carbon nanofibers have received significant attention due mainly to their chemical inertness and good mechanical, electrical and thermal properties. Since carbon nanofibers comprise a continuous reinforcing with high specific surface area, associated with the fact that they can be obtained at a low cost and in a large amount, they have shown to be advantageous compared to traditional carbon nanotubes. The main objective of this work is the processing of carbon nanofibers, using polyacrylonitrile (PAN) as a precursor, obtained by the electrospinning process via polymer solution, with subsequent use for airspace applications as reinforcement in polymer composites. In this work, firstly PAN nanofibers were produced by electrospinning with diameters in the range of (375 ± 85) nm, using a dimethylformamide solution. Using a furnace, the PAN nanofiber was converted into carbon nanofiber. Morphologies and structures of PAN and carbon nanofibers were investigated by scanning electron microscopy, Raman Spectroscopy, thermogravimetric analyses and differential scanning calorimeter. The resulting residual weight after carbonization was approximately 38% in weight, with a diameters reduction of 50%, and the same showed a carbon yield of 25%. From the analysis of the crystalline structure of the carbonized material, it was found that the material presented a disordered structure.

  12. Experimental methodology for obtaining sound absorption coefficients

    Directory of Open Access Journals (Sweden)

    Carlos A. Macía M

    2011-07-01

    Full Text Available Objective: the authors propose a new methodology for estimating sound absorption coefficients using genetic algorithms. Methodology: sound waves are generated and conducted along a rectangular silencer. The waves are then attenuated by the absorbing material covering the silencer’s walls. The attenuated sound pressure level is used in a genetic algorithm-based search to find the parameters of the proposed attenuation expressions that include geometric factors, the wavelength and the absorption coefficient. Results: a variety of adjusted mathematical models were found that make it possible to estimate the absorption coefficients based on the characteristics of a rectangular silencer used for measuring the attenuation of the noise that passes through it. Conclusions: this methodology makes it possible to obtain the absorption coefficients of new materials in a cheap and simple manner. Although these coefficients might be slightly different from those obtained through other methodologies, they provide solutions within the engineering accuracy ranges that are used for designing noise control systems.

  13. Alcoholic Beverages Obtained from Black Mulberry

    Directory of Open Access Journals (Sweden)

    Jacinto Darias-Martín

    2003-01-01

    Full Text Available Black mulberry (Morus nigra is a fruit not known only for its nutritional qualities and its flavour, but also for its traditional use in natural medicine as it has a high content of active therapeutic compounds. However, this fruit is not widely produced in Spain but some trees are still found growing in the Canary Islands, particularly on the edges of the ravine. The inhabitants of these islands (Tenerife, La Gomera, La Palma, El Hierro and Lanzarote collect the fruit and prepare homemade beverages for medicinal purposes. Numerous authors have reported that type II diabetes mellitus can be controlled by taking a mixture containing black mulberry and water. Apart from that, this fruit has been used for the treatment of mouth, tongue and throat inflammations. In this study we present some characteristics of black mulberry juice (TSS, pH, titratable acidity, citric acid, lactic acid, polyphenols, anthocyanins, the potassium etc. and alcoholic beverages (alcoholic grade, pH, total acidity, volatile acidity, tannins, phenols etc. obtained from black mulberry. Moreover, we have studied the quality of liquors obtained from black mulberry in Canary Islands.

  14. Cotton nanofibers obtained by different acid conditions

    International Nuclear Information System (INIS)

    Teixeira, Eliangela de M.; Oliveira, Caue Ribeiro de; Mattoso, Luiz H.C.; Correa, Ana Carolina; Palladin, Priscila

    2009-01-01

    The thermal stability of cellulose nanofibers is related to their application and especially to polymer processing which temperatures of processing are around 200 deg C. In this work, nanofibers of commercial cotton were obtained by acid hydrolysis employing different acids: sulfuric, hydrochloric and a mixture (2:1; sulfuric acid: hydrochloric acid).The morphology of the nanofibers were characterized by transmission microscopy (TEM), crystallinity by x-ray diffraction (XRD) and thermal stability in air atmosphere by thermogravimetric analysis (TGA). The results indicated a very similar morphology and crystallinity among them. The main differences were relative to aggregation state e and thermal stability. The aggregation state of the suspensions decreases in the order HCl 2 SO 4 :HCl 2 SO 4- . The hydrolysis with a mix of HCl and H 2 SO 4 resulted in cellulose nanofibers with higher thermal stability than those hydrolyzed with H 2 SO 4 . The hydrolysis employed with a mixture of sulphuric and hydrochloric acids also showed a better dispersion than those suspensions of nanofibers obtained by hydrolysis with only HCl. (author)

  15. Polypropylene obtained through zeolite supported catalysts

    International Nuclear Information System (INIS)

    Bastos, Queli C.; Marques, Maria de Fatima V.

    2004-01-01

    Propylene polymerizations were carried out with φ 2 C(Flu)(Cp)ZrCl 2 and SiMe 2 (Ind)2ZrCl 2 catalysts supported on silica, zeolite sodic mordenite (NaM) and acid mordenite (HM). The polymerizations were performed at different temperatures and varying aluminium/zirconium molar ratios ([Al]/[Zr]). The effect of these reaction parameters on the catalyst activity was investigated using a proposed statistical experimental planning. In the case of f 2 C(Flu)(Cp)ZrCl 2 , SiO 2 and NaM were used as support and the catalyst performance evaluated using toluene and pentane as polymerization solvent. The molecular weight, molecular weight distribution, melting point and crystallinity of the polymers were examined. The results indicate very high activities for the syndiospecific heterogeneous system. Also, the polymers obtained had superior Mw and stereo regularity. (author)

  16. Polypropylene obtained through zeolite supported catalysts

    Directory of Open Access Journals (Sweden)

    Queli C. Bastos

    2004-01-01

    Full Text Available Propylene polymerizations were carried out with f2C(Flu(CpZrCl2 and SiMe2(Ind2ZrCl2 catalysts supported on silica, zeolite sodic mordenite (NaM and acid mordenite (HM. The polymerizations were performed at different temperatures and varying aluminium/zirconium molar ratios ([Al]/[Zr]. The effect of these reaction parameters on the catalyst activity was investigated using a proposed statistical experimental planning. In the case of f2C(Flu(CpZrCl2, SiO2 and NaM were used as support and the catalyst performance evaluated using toluene and pentane as polymerization solvent. The molecular weight, molecular weight distribution, melting point and crystallinity of the polymers were examined. The results indicate very high activities for the syndiospecific heterogeneous system. Also, the polymers obtained had superior Mw and stereoregularity.

  17. Process to Obtain Quick Counts from PREP

    Directory of Open Access Journals (Sweden)

    Martínez–Cruz M.Á.

    2011-10-01

    Full Text Available Considering the Preliminary Electoral Results Program (PERP as a database of the federal elections for president of the Mexican Republic, a methodology was developed in order to find representative samples of ballot boxes installed in the election’s day (quick count in different hours, due to its characteristics of gathering of information, the PREP in the first hours forms a non-representative sample of data. In a particular way, in the election of July 2, 2006, after 3 hours of opening the PREP, it was observed that the accuracy of the process of the quick counts was better than the one obtained by the IFE. Among other things, this allows to lower the cost, to increase the confidentiality of the ballot boxes used in the sampling and to distinguish in a precise moment the winning candidate long before PREP finishes.

  18. The method of obtaining of decorative varnish

    International Nuclear Information System (INIS)

    Salidzhanova, N.S.; Tashbekova, D.M.

    1997-01-01

    The method of obtaining of decorative varnish allowing to remove inhibition action of air oxygen and to improve the varnish hardness is described. It is includes the impregnation of texture paper with mixture of PE-284 type polyether lacquer on the basis of unsaturated oligoethylenglycolfumarath resin and cation type salt, putting it on wooden or asbestos cement slabs and further hardening by pulsed beams of accelerated electrons on moving belt. The radiation dose for one pulse is 1,10 -2 - 9,10 -3 MGy, the number of pulses is 180 - 250, the duration of pulses is 2.3 ms, their frequency is 50 KHz. Chloride, bromide, benzylbromide or iodide of N, N-dialkylaminoethyl (benzil) (met)acrylate are used as cation type salt. (author)

  19. Devices for obtaining information about radiation sources

    International Nuclear Information System (INIS)

    Tosswill, C.H.

    1981-01-01

    The invention provides a sensitive, fast high-resolution device for obtaining information about the distribution of gamma and X-radiation sources and provides a radiation detector useful in such a device. It comprises a slit collimator with a multiplicity of slits each with slit-defining walls of material and thickness to absorb beam components impinging on them. The slits extend further in one direction than the other. The detector for separately detecting beam components passing through the slits also provides data output signals. It comprises a plurality of radiation transducing portions which are not photoconductor elements each at the end of a slit. A positioner operates to change the transverse position of the slits and radiation transducing portions relative to the source, wherein each radiation transducing element is positioned within its respective slit between the slit defining walls. Full details and preferred embodiments are given. (U.K.)

  20. Devices for obtaining information about radiation sources

    International Nuclear Information System (INIS)

    Tosswill, C.H.

    1981-01-01

    The invention provides a sensitive, fast, high-resolution device for obtaining information about the distribution of gamma and X-radiation sources and provides a radiation detector useful in such a device. It comprises a slit collimator with a multiplicity of slits each with slit-defining walls of material and thickness to absorb beam components impinging on them. The slits extend further in one transverse direction than the other. The detector for separately detecting beam components passing through the slits also provides data output signals. It comprises a plurality of radiation transducing portions, each at the end of a slit. A positioner changes the transverse position of the slits and radiation transducer (a photoconductor) relative to the source. Applications are in nuclear medicine and industry. Full details and preferred embodiments are given. (U.K.)

  1. Obtaining the electrostatic screening from first principles

    International Nuclear Information System (INIS)

    Shaviv, N.J.; Shaviv, G.

    2003-01-01

    We derive the electrostatic screening effect from first principles and show the basic properties of the screening process. We in particular show that under the conditions prevailing in the Sun the number of particles in the Debye sphere is of the order of unity. Consequently; fluctuations play a dominant role in the screening process. The fluctuations lead to an effective time dependent potential. Particles with low kinetic energy lose on the average energy to the plasma and vice versa with high energy particles. We derive general conditions on the screening energy and show under what conditions the Salpeter approximation is obtained. The connection between the screening and relaxation processes in the plasma is exposed

  2. ORIENTATION OF ENTERPRISES TOWARD OBTAINING COMPETITIVE

    Directory of Open Access Journals (Sweden)

    PAUL BOGDAN ZAMFIR

    2015-10-01

    Full Text Available In this paper I proposed to emphasize the importance of obtaining competitive advantage by companies on EU internal market. The huge EU market, offers for participating companies the possibility to achieve significant economies of scale and numerous niches (segments market, which can be covered with large quantities of goods, the condition is that niches to be discovered in time, and the firms to be able to adapt promptly at their needs. Thus, the most important positive effect derives from the fact that companies have at their disposal a vast market consisting approximately 500 million consumers, free of customs duties and other restrictions inhindering the movement of goods. On this background, the companies can achieve high series production and thereby can reduce their cost of production and increase their competitiveness. In this context, the companies must meet the standards of the European Union, if they really want to gain competitive advantage on EU market.

  3. Dependence of Interaction Free Energy between Solutes on an External Electrostatic Field

    Directory of Open Access Journals (Sweden)

    Pei-Kun Yang

    2013-07-01

    Full Text Available To explore the athermal effect of an external electrostatic field on the stabilities of protein conformations and the binding affinities of protein-protein/ligand interactions, the dependences of the polar and hydrophobic interactions on the external electrostatic field, −Eext, were studied using molecular dynamics (MD simulations. By decomposing Eext into, along, and perpendicular to the direction formed by the two solutes, the effect of Eext on the interactions between these two solutes can be estimated based on the effects from these two components. Eext was applied along the direction of the electric dipole formed by two solutes with opposite charges. The attractive interaction free energy between these two solutes decreased for solutes treated as point charges. In contrast, the attractive interaction free energy between these two solutes increased, as observed by MD simulations, for Eext = 40 or 60 MV/cm. Eext was applied perpendicular to the direction of the electric dipole formed by these two solutes. The attractive interaction free energy was increased for Eext = 100 MV/cm as a result of dielectric saturation. The force on the solutes along the direction of Eext computed from MD simulations was greater than that estimated from a continuum solvent in which the solutes were treated as point charges. To explore the hydrophobic interactions, Eext was applied to a water cluster containing two neutral solutes. The repulsive force between these solutes was decreased/increased for Eext along/perpendicular to the direction of the electric dipole formed by these two solutes.

  4. Optimizing scoring function of protein-nucleic acid interactions with both affinity and specificity.

    Directory of Open Access Journals (Sweden)

    Zhiqiang Yan

    Full Text Available Protein-nucleic acid (protein-DNA and protein-RNA recognition is fundamental to the regulation of gene expression. Determination of the structures of the protein-nucleic acid recognition and insight into their interactions at molecular level are vital to understanding the regulation function. Recently, quantitative computational approach has been becoming an alternative of experimental technique for predicting the structures and interactions of biomolecular recognition. However, the progress of protein-nucleic acid structure prediction, especially protein-RNA, is far behind that of the protein-ligand and protein-protein structure predictions due to the lack of reliable and accurate scoring function for quantifying the protein-nucleic acid interactions. In this work, we developed an accurate scoring function (named as SPA-PN, SPecificity and Affinity of the Protein-Nucleic acid interactions for protein-nucleic acid interactions by incorporating both the specificity and affinity into the optimization strategy. Specificity and affinity are two requirements of highly efficient and specific biomolecular recognition. Previous quantitative descriptions of the biomolecular interactions considered the affinity, but often ignored the specificity owing to the challenge of specificity quantification. We applied our concept of intrinsic specificity to connect the conventional specificity, which circumvents the challenge of specificity quantification. In addition to the affinity optimization, we incorporated the quantified intrinsic specificity into the optimization strategy of SPA-PN. The testing results and comparisons with other scoring functions validated that SPA-PN performs well on both the prediction of binding affinity and identification of native conformation. In terms of its performance, SPA-PN can be widely used to predict the protein-nucleic acid structures and quantify their interactions.

  5. A Novel Protein Interaction between Nucleotide Binding Domain of Hsp70 and p53 Motif

    Directory of Open Access Journals (Sweden)

    Asita Elengoe

    2015-01-01

    Full Text Available Currently, protein interaction of Homo sapiens nucleotide binding domain (NBD of heat shock 70 kDa protein (PDB: 1HJO with p53 motif remains to be elucidated. The NBD-p53 motif complex enhances the p53 stabilization, thereby increasing the tumor suppression activity in cancer treatment. Therefore, we identified the interaction between NBD and p53 using STRING version 9.1 program. Then, we modeled the three-dimensional structure of p53 motif through homology modeling and determined the binding affinity and stability of NBD-p53 motif complex structure via molecular docking and dynamics (MD simulation. Human DNA binding domain of p53 motif (SCMGGMNR retrieved from UniProt (UniProtKB: P04637 was docked with the NBD protein, using the Autodock version 4.2 program. The binding energy and intermolecular energy for the NBD-p53 motif complex were −0.44 Kcal/mol and −9.90 Kcal/mol, respectively. Moreover, RMSD, RMSF, hydrogen bonds, salt bridge, and secondary structure analyses revealed that the NBD protein had a strong bond with p53 motif and the protein-ligand complex was stable. Thus, the current data would be highly encouraging for designing Hsp70 structure based drug in cancer therapy.

  6. Biodegradable Polyelectrolyte Obtained by Radiation Polymerization

    International Nuclear Information System (INIS)

    Craciun, G.; Martin, D.; Manaila, E.; Nemtanu, M.; Brasoveanu, M.; Ighigeanu, D.

    2009-01-01

    Poly electrolytes are water-soluble polymers carrying ionic charge along the polymer chain. Depending upon the charge, these polymers are anionic or cationic. The inherent solid - liquid separating efficiency makes these poly electrolytes a unique class of polymers which find extensive application in potable water, industrial raw and process water, municipal sewage treatment, mineral processing and metallurgy, oil drilling and recovery, etc. Also, due to their ability to produce advanced induced coagulation, a considerable amount of bacteria and viruses are precipitated together with the suspended solids. Especially the acrylamide polymers are very efficacious for water treatment but acrylamide is a toxic monomer and therefore their use are governed by international standards that provide the residual acrylamide monomer content (RAMC) in them be less than 0.05%. Under these circumstances our attention was focused on the following research steps that are presented in this paper: 1) Preparation of a special class of poly electrolytes, named Pn, with very low RAMC values, based on electron beam (EB), microwave (MW) and EB + MW induced co-polymerization of aqueous solutions containing appropriate mixtures of acrylamide (AMD) and acrylic acid (AA) monomers (AMD - AA co-polymers). The Pn were obtained by radiation technology with very small RAMC (under 0.01%) as well as in a wide range of molecular weights and charge densities. Very low AMD monomer content of Pn is due to the major advantages of radiation induced polymerization in aqueous solution containing monomers. Due to water presence in the EB irradiated system, irradiated water radicals facilitate the polymerization process and increase rate and level of monomers conversion in co-polymers. Also, once again, by the presence of water, which absorbs MW energy very strongly, the MW polymerization reaction rate is much enhanced resulting in a reaction time about 50-100 times lowers than by conventional heating. Also

  7. HOW TO OBTAIN BOOKS FOR YOUR GROUP

    CERN Multimedia

    Head Librarian

    2000-01-01

    The wide variety of scientific and technical activity engaged in by people working at CERN means that the Library cannot always provide a deep on-site coverage in areas which are outside the core subjects of particle physics and accelerators. As many of you have already experienced, one way of solving this is to borrow books from other libraries. Our Inter-Library Loan (ILL) service currently obtains about 1000 books on loan per year for readers at CERN. However, there may be books which groups need on a more permanent basis, in which case a loan from either our own collection or via ILL is not the appropriate solution. Instead, groups might prefer to purchase such books from their own budgets. To facilitate this, the CERN Library has set up a procedure with the SPL Division, by which you can submit your purchase request to us and be charged via a TID when you receive the book. In addition, via our database interface WebLib, we can provide you with a private virtual catalogue of your group's collection, which...

  8. Evaluation of biodiesel obtained from cottonseed oil

    Energy Technology Data Exchange (ETDEWEB)

    Rashid, Umer [Department of Chemistry and Biochemistry, University of Agriculture, Faisalabad-38040 (Pakistan); Department of Industrial Chemistry, Government College University, Faisalabad-38000 (Pakistan); Anwar, Farooq [Department of Chemistry and Biochemistry, University of Agriculture, Faisalabad-38040 (Pakistan); Knothe, Gerhard [United States Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, IL 61604 (United States)

    2009-09-15

    Esters from vegetable oils have attracted a great deal of interest as substitutes for petrodiesel to reduce dependence on imported petroleum and provide a fuel with more benign environmental properties. In this work biodiesel was prepared from cottonseed oil by transesterification with methanol, using sodium hydroxide, potassium hydroxide, sodium methoxide and potassium methoxide as catalysts. A series of experiments were conducted in order to evaluate the effects of reaction variables such as methanol/oil molar ratio (3:1-15:1), catalyst concentration (0.25-1.50%), temperature (25-65 C), and stirring intensity (180-600 rpm) to achieve the maximum yield and quality. The optimized variables of 6:1 methanol/oil molar ratio (mol/mol), 0.75% sodium methoxide concentration (wt.%), 65 C reaction temperature, 600 rpm agitation speed and 90 min reaction time offered the maximum methyl ester yield (96.9%). The obtained fatty acid methyl esters (FAME) were analyzed by gas chromatography (GC) and {sup 1}H NMR spectroscopy. The fuel properties of cottonseed oil methyl esters (COME), cetane number, kinematic viscosity, oxidative stability, lubricity, cloud point, pour point, cold filter plugging point, flash point, ash content, sulfur content, acid value, copper strip corrosion value, density, higher heating value, methanol content, free and bound glycerol were determined and are discussed in the light of biodiesel standards such as ASTM D6751 and EN 14214. (author)

  9. Electrolytic Hydrogen obtaining by a photovoltaic source

    International Nuclear Information System (INIS)

    Pasculete, E.; Condrea, F.; Stanoiu, L.

    2005-01-01

    At present, the developed countries allocate large funds for the financing of some global programs for fundamental and applicative research for development of hydrogen non-conventional production technologies. One of these technologies is the photo-assisted electrolysis. This technology is adopted in the research, which results are presented in this paper. The experimental model includes as basic equipment 100 W photovoltaic source, electrolysis battery press filter type, control unit of the electric energy discharged, accumulator, hydrogen storage unit. Five types of material have been tested for the electrolysis cell diaphragm: asbestos; Netrom- unwoven material from fibers of polypropylene; ion changing composite membrane - polysulfone support with an active layer of sulfonated poly-sulfone (PSS/PSJ) and poly-sulfone support with an active layer of sulfonated poly-eter cetone (SPEEK/PSf); ion-exchange membrane made from sulfonated poly-eter cetone (SPEEK). The graphics and results from the test system are presented. The analysis of the experimental results lead to the establishment of the optimal configuration of battery and of the operational conditions of the assembly. The experimental results give the opportunity to obtain electrolytic hydrogen with a photovoltaic source, in an efficient system, and promote the Romanian research at a level of a demonstrative installation

  10. WAYS OF OBTAINING FINANCING BY TOUR OPERATORS

    Directory of Open Access Journals (Sweden)

    CARLAN ADRIANA

    2015-12-01

    Full Text Available domanin.Romania is a country with highly touristic potential that is not exploited to maximum. In order to reach a high quality level of tourism permanent development and modernization are needed and also the establishment of new businesses That conducts other activities other than those which takes place in our country. Ways of getting funds are multiple, depending on individual needs.To develop tourism activities it is necessary to require some funding that can come from various sources: auto-financing, loans from various banks or from third parties and grants offered by the European Union. There are many programs designed to support the development of tourism, such as ROP that allows people to access grants in order to implement projects for the establishment and the development of the activity in the touristic field. The purpose of this article is to highlight funding opportunities for the tourism operators and to assist them in choosing the appropriate form of financing of the current activity or the activity they want to implement in the future and description of how to obtain the necessary funds from various sources.

  11. Shielding design to obtain compact marine reactor

    International Nuclear Information System (INIS)

    Yamaji, Akio; Sako, Kiyoshi

    1994-01-01

    The marine reactors equipped in previously constructed nuclear ships are in need of the secondary shield which is installed outside the containment vessel. Most of the weight and volume of the reactor plants are occupied by this secondary shield. An advanced marine reactor called MRX (Marine Reactor X) has been designed to obtain a more compact and lightweight marine reactor with enhanced safety. The MRX is a new type of marine reactor which is an integral PWR (The steam generator is installed in the pressure vessel.) with adopting a water-filled containment vessel and a new shielding design method of no installation of the secondary shield. As a result, MRX is considerably lighter in weight and more compact in size as compared with the reactors equipped in previously constructed nuclear ships. For instance, the plant weight and volume of the containment vessel of MRX are about 50% and 70% of those of the Nuclear Ship MUTSU, in spite of the power of MRX is 2.8 times as large as the MUTSU's reactor. The shielding design calculation was made using the ANISN, DOT3.5, QAD-CGGP2 and ORIGEN codes. The computational accuracy was confirmed by experimental analyses. (author)

  12. Obtaining cementitious material from municipal solid waste

    Directory of Open Access Journals (Sweden)

    Macías, A.

    2007-06-01

    Full Text Available The primary purpose of the present study was to determine the viability of using incinerator ash and slag from municipal solid waste as a secondary source of cementitious materials. The combustion products used were taken from two types of Spanish MSW incinerators, one located at Valdemingómez, in Madrid, and the other in Melilla, with different incineration systems: one with fluidised bed combustion and other with mass burn waterwall. The effect of temperature (from 800 to 1,200 ºC on washed and unwashed incinerator residue was studied, in particular with regard to phase formation in washed products with a high NaCl and KCl content. The solid phases obtained were characterized by X-ray diffraction and BET-N2 specific surface procedures.El principal objetivo del trabajo ha sido determinar la viabilidad del uso de las cenizas y escorias procedentes de la incineración de residuos sólidos urbanos, como materia prima secundaria para la obtención de fases cementantes. Para ello se han empleado los residuos generados en dos tipos de incineradoras españolas de residuos sólidos urbanos: la incineradora de Valdemingómez y la incineradora de Melilla. Se ha estudiado la transformación de los residuos, sin tratamiento previo, en función de la temperatura de calentamiento (desde 800 ºC hasta 1.200 ºC, así como la influencia del lavado de los residuos con alto contenido en NaCl y KCl en la formación de fases obtenidas a las diferentes temperaturas de calcinación. Las fases obtenidas fueron caracterizadas por difracción de rayos X y área superficial por el método BET-N2.

  13. Reduced sensitivity RDX obtained from bachmann RDX

    Energy Technology Data Exchange (ETDEWEB)

    Spyckerelle, Christian; Eck, Genevieve [EURENCO France, Sorgues Plant 1928 route d' Avignon, BP 311, 84706 Sorgues Cedex (France); Sjoeberg, Per; Amneus, Anna-Maria [EURENCO Sweden, SE-69186 Karlskoga (Sweden)

    2008-02-15

    In recent years much interest has been generated in a quality of reduced sensitivity RDX (RS-RDX), like I-RDX {sup registered} which, when incorporated in cast cure and even pressable plastic bonded explosives (PBX compositions), can confer reduced shock sensitivity as measured through gap test. At crystal level, lot of work has been done to try to determine which property or properties may explain the behaviour of the corresponding cast PBX composition. But up to now, and despite an international inter-laboratory comparison (Round Robin) of seven lots of RDX from five different manufacturers conducted from 2003 to 2005, even if some techniques lead to interesting results, there is no dedicated specification to apply to RS-RDX. This quality (I-RDX {sup registered}) has proved to retain its low sensitivity even after ageing, which does not seem to be the case for standard RDX produced by the Bachmann process (when re-crystallized under I-RDX conditions in order to obtain RS-RDX). It has been shown that the higher sensitivity of RDX produced by the Bachmann process, or the evolution of sensitivity after ageing of RS-RDX produced from Bachmann RDX may be linked to the presence of octogen (HMX) during the crystallization process. In order to check such hypothesis, low HMX content RDX produced by the Bachmann process has been prepared and evaluated in cast PBX composition (PBX N 109). Results of the characterization of such quality of RDX and its evaluation in cast PBX composition as well as ageing behaviour are presented and discussed; there are indications that removal of HMX from Bachmann RDX may lead to RS-RDX, which retains its RS character even after ageing. (Abstract Copyright [2008], Wiley Periodicals, Inc.)

  14. Instrumental interaction

    OpenAIRE

    Luciani , Annie

    2007-01-01

    International audience; The expression instrumental interaction as been introduced by Claude Cadoz to identify a human-object interaction during which a human manipulates a physical object - an instrument - in order to perform a manual task. Classical examples of instrumental interaction are all the professional manual tasks: playing violin, cutting fabrics by hand, moulding a paste, etc.... Instrumental interaction differs from other types of interaction (called symbolic or iconic interactio...

  15. Grasp interaction with tablets

    CERN Document Server

    Wolf, Katrin

    2015-01-01

    This book presents guidelines for a future device type: a tablet that allows ergonomic front- and back-of-device interaction. These guidelines help designers and developers of user interfaces to build ergonomic applications for tablet devices, in particular for devices that enable back-of-device interaction. In addition, manufacturers of tablet devices obtain arguments that back-of-device interaction is a promising extension of the interaction design space and results in increased input capabilities, enriched design possibilities, and proven usability. The guidelines are derived from empirical studies and developed to fit the users’ skills to the way the novel device type is held. Three particular research areas that are relevant to develop design guidelines for tablet interaction are investigated: ergonomic gestures, interaction areas, and pointing techniques.

  16. Component Repair Times Obtained from MSPI Data

    International Nuclear Information System (INIS)

    Eide, Steven A.; Cadwallader, Lee

    2015-01-01

    Information concerning times to repair or restore equipment to service given a failure is valuable to probabilistic risk assessments (PRAs). Examples of such uses in modern PRAs include estimation of the probability of failing to restore a failed component within a specified time period (typically tied to recovering a mitigating system before core damage occurs at nuclear power plants) and the determination of mission times for support system initiating event (SSIE) fault tree models. Information on equipment repair or restoration times applicable to PRA modeling is limited and dated for U.S. commercial nuclear power plants. However, the Mitigating Systems Performance Index (MSPI) program covering all U.S. commercial nuclear power plants provides up-to-date information on restoration times for a limited set of component types. This paper describes the MSPI program data available and analyzes the data to obtain median and mean component restoration times as well as non-restoration cumulative probability curves. The MSPI program provides guidance for monitoring both planned and unplanned outages of trains of selected mitigating systems deemed important to safety. For systems included within the MSPI program, plants monitor both train UA and component unreliability (UR) against baseline values. If the combined system UA and UR increases sufficiently above established baseline results (converted to an estimated change in core damage frequency or CDF), a ''white'' (or worse) indicator is generated for that system. That in turn results in increased oversight by the US Nuclear Regulatory Commission (NRC) and can impact a plant's insurance rating. Therefore, there is pressure to return MSPI program components to service as soon as possible after a failure occurs. Three sets of unplanned outages might be used to determine the component repair durations desired in this article: all unplanned outages for the train type that includes the component of

  17. Component Repair Times Obtained from MSPI Data

    Energy Technology Data Exchange (ETDEWEB)

    Eide, Steven A. [Curtiss-Wright/Scietech, Ketchum, ID (United States); Cadwallader, Lee [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2015-05-01

    Information concerning times to repair or restore equipment to service given a failure is valuable to probabilistic risk assessments (PRAs). Examples of such uses in modern PRAs include estimation of the probability of failing to restore a failed component within a specified time period (typically tied to recovering a mitigating system before core damage occurs at nuclear power plants) and the determination of mission times for support system initiating event (SSIE) fault tree models. Information on equipment repair or restoration times applicable to PRA modeling is limited and dated for U.S. commercial nuclear power plants. However, the Mitigating Systems Performance Index (MSPI) program covering all U.S. commercial nuclear power plants provides up-to-date information on restoration times for a limited set of component types. This paper describes the MSPI program data available and analyzes the data to obtain median and mean component restoration times as well as non-restoration cumulative probability curves. The MSPI program provides guidance for monitoring both planned and unplanned outages of trains of selected mitigating systems deemed important to safety. For systems included within the MSPI program, plants monitor both train UA and component unreliability (UR) against baseline values. If the combined system UA and UR increases sufficiently above established baseline results (converted to an estimated change in core damage frequency or CDF), a “white” (or worse) indicator is generated for that system. That in turn results in increased oversight by the US Nuclear Regulatory Commission (NRC) and can impact a plant’s insurance rating. Therefore, there is pressure to return MSPI program components to service as soon as possible after a failure occurs. Three sets of unplanned outages might be used to determine the component repair durations desired in this article: all unplanned outages for the train type that includes the component of interest, only

  18. Obtaining and characterization of thin films polyelectrolyte with gold nanoparticles

    International Nuclear Information System (INIS)

    Popiolski, Tatiane M.; Crespo, Janaina S.; Silva, Renato B.

    2011-01-01

    Thin films of polyelectrolytes are manufactured via sequential adsorption of weak polyelectrolytes from aqueous solutions based on electrostatic interaction of oppositely charged polymers. Metal containing polymeric compounds are of particular interest to the production of materials with electrical interface and optical properties. In this sense, the objective of this study was to obtain thin films of weak polyelectrolytes and analyze the distribution of gold nanoparticles stabilized by sodium citrate and by poly (vinylpyrrolidone). The characterization was performed using UV-visible, X-ray diffraction and atomic force microscopy. The techniques of UV-visible and X-ray diffraction was confirmed the presence of gold in the films, the atomic force microscopy images were used to analyze the morphology of the films and check the behavior of the diffusion of gold nanoparticles. (author)

  19. Manipulating surface diffusion and elastic interactions to obtain quantum dot multilayer arrangements over different length scales

    Energy Technology Data Exchange (ETDEWEB)

    Placidi, E., E-mail: ernesto.placidi@ism.cnr.it; Arciprete, F. [Istituto di Struttura della Materia, CNR, Via del Fosso del Cavaliere 100, 00133 Rome (Italy); Università di Roma “Tor Vergata”, Dipartimento di Fisica, via della Ricerca Scientifica 1, 00133 Rome (Italy); Latini, V.; Latini, S.; Patella, F. [Università di Roma “Tor Vergata”, Dipartimento di Fisica, via della Ricerca Scientifica 1, 00133 Rome (Italy); Magri, R. [Dipartimento di Scienze Fisiche, Informatiche e Matematiche (FIM), Università di Modena e Reggio Emilia, and Centro S3 CNR-Istituto Nanoscienze, Via Campi 213/A, 4100 Modena (Italy); Scuderi, M.; Nicotra, G. [CNR-IMM, Strada VIII, 5, 95121 Catania (Italy)

    2014-09-15

    An innovative multilayer growth of InAs quantum dots on GaAs(100) is demonstrated to lead to self-aggregation of correlated quantum dot chains over mesoscopic distances. The fundamental idea is that at critical growth conditions is possible to drive the dot nucleation only at precise locations corresponding to the local minima of the Indium chemical potential. Differently from the known dot multilayers, where nucleation of new dots on top of the buried ones is driven by the surface strain originating from the dots below, here the spatial correlations and nucleation of additional dots are mostly dictated by a self-engineering of the surface occurring during the growth, close to the critical conditions for dot formation under the fixed oblique direction of the incoming As flux, that drives the In surface diffusion.

  20. Interaction and observation, categorically

    Directory of Open Access Journals (Sweden)

    Vincenzo Ciancia

    2011-07-01

    Full Text Available This paper proposes to use dialgebras to specify the semantics of interactive systems in a natural way. Dialgebras are a conservative extension of coalgebras. In this categorical model, from the point of view that we provide, the notions of observation and interaction are separate features. This is useful, for example, in the specification of process equivalences, which are obtained as kernels of the homomorphisms of dialgebras. As an example we present the asynchronous semantics of the CCS.

  1. Elucidation of relaxin-3 binding interactions in the extracellular loops of RXFP3

    Directory of Open Access Journals (Sweden)

    Ross eBathgate

    2013-02-01

    Full Text Available Relaxin-3 is a highly conserved neuropeptide in vertebrate species and binds to the Class A G protein-coupled receptor RXFP3. Relaxin-3 is involved in a wide range of behaviours, including feeding, stress responses, arousal and cognitive processes and therefore targeting of RXFP3 may be relevant for a range of neurological diseases. Structural knowledge of RXFP3 and its interaction with relaxin-3 would both increase our understanding of ligand recognition in GPCRs that respond to protein ligands and enable acceleration of the design of drug leads. In this study we have used comparative sequence analysis, molecular modelling and receptor mutagenesis to investigate the binding site of the native ligand human relaxin-3 (H3 relaxin on the human RXFP3 receptor. Previous structure function studies have demonstrated that arginine residues in the H3 relaxin B-chain are critical for binding interactions with the receptor extracellular loops and/or N-terminal domain. Hence we have concentrated on determining the ligand interacting sites in these domains and have focussed on glutamic (E and aspartic acid (D residues in these regions that may form electrostatic interactions with these critical arginine residues. Conserved D/E residues identified from vertebrate species multiple sequence alignments were mutated to Ala in human RXFP3 to test the effect of loss of amino acid side chain on receptor binding using both Eu-labelled relaxin-3 agonist. Finally data from mutagenesis experiments have been used in ligand docking simulations to a homology model of human RXFP3 based on the peptide-bound CXCR4 structure. These studies have resulted in a model of the relaxin-3 interaction with RXFP3 which will inform further interrogation of the agonist binding site.

  2. DARC 2.0: Improved Docking and Virtual Screening at Protein Interaction Sites.

    Directory of Open Access Journals (Sweden)

    Ragul Gowthaman

    Full Text Available Over the past decade, protein-protein interactions have emerged as attractive but challenging targets for therapeutic intervention using small molecules. Due to the relatively flat surfaces that typify protein interaction sites, modern virtual screening tools developed for optimal performance against "traditional" protein targets perform less well when applied instead at protein interaction sites. Previously, we described a docking method specifically catered to the shallow binding modes characteristic of small-molecule inhibitors of protein interaction sites. This method, called DARC (Docking Approach using Ray Casting, operates by comparing the topography of the protein surface when "viewed" from a vantage point inside the protein against the topography of a bound ligand when "viewed" from the same vantage point. Here, we present five key enhancements to DARC. First, we use multiple vantage points to more accurately determine protein-ligand surface complementarity. Second, we describe a new scheme for rapidly determining optimal weights in the DARC scoring function. Third, we incorporate sampling of ligand conformers "on-the-fly" during docking. Fourth, we move beyond simple shape complementarity and introduce a term in the scoring function to capture electrostatic complementarity. Finally, we adjust the control flow in our GPU implementation of DARC to achieve greater speedup of these calculations. At each step of this study, we evaluate the performance of DARC in a "pose recapitulation" experiment: predicting the binding mode of 25 inhibitors each solved in complex with its distinct target protein (a protein interaction site. Whereas the previous version of DARC docked only one of these inhibitors to within 2 Å RMSD of its position in the crystal structure, the newer version achieves this level of accuracy for 12 of the 25 complexes, corresponding to a statistically significant performance improvement (p < 0.001. Collectively then, we find

  3. Weak interactions

    International Nuclear Information System (INIS)

    Chanda, R.

    1981-01-01

    The theoretical and experimental evidences to form a basis for Lagrangian Quantum field theory for Weak Interactions are discussed. In this context, gauge invariance aspects of such interactions are showed. (L.C.) [pt

  4. Intermolecular interactions

    International Nuclear Information System (INIS)

    Kaplan, I.G.; Rodimova, O.B.; AN SSSR, Tomsk. Inst. Optiki Atmosfery)

    1978-01-01

    The present state of the intermolecular interaction theory is described. The general physical picture of the molecular interactions is given, the relative contributions of interactions of different types are analyzed (electrostatic, resonance, induction, dispersion, relativistic, magnetostatic and exchange), and the main ones in each range of separations are picked out. The methods of the potential curve calculations are considered, specific for definite separations between the interacting systems. The special attention is paid to the analysis of approximations used in different theoretical calculation methods

  5. Effective interactions

    International Nuclear Information System (INIS)

    Elliott, J.P.

    1981-01-01

    This chapter attempts to describe and compare some of the more important nucleon-nucleon interactions that have been used in nuclear structure calculations, and to relate them where possible to the real nucleon-nucleon interaction. Explains that different interactions have been used depending on whether one is fitting to total binding energies and densities with a Hartree Fock (HF) calculation or fitting to spectra and spectroscopic data in a shell model calculation. Examines both types of calculation after two preliminary sections concerned with notation and with the philosophy underlying the use of model spaces and effective interactions. Discusses Skyrme interactions, finite range interactions, small model space, large model space, and the Sussex potential matrix elements. Focuses on the more empirical approaches in which a simple form is chosen for the effective interaction in a given model space and the parameters are deduced from fitting many-body data

  6. Effect of inclusion of hydroxycinnamic and chlorogenic acids from green coffee bean in β-cyclodextrin on their interactions with whey, egg white and soy protein isolates.

    Science.gov (United States)

    Budryn, Grażyna; Pałecz, Bartłomiej; Rachwał-Rosiak, Danuta; Oracz, Joanna; Zaczyńska, Donata; Belica, Sylwia; Navarro-González, Inmaculada; Meseguer, Josefina María Vegara; Pérez-Sánchez, Horacio

    2015-02-01

    The aim of the study was to characterise the interactions of hydroxycinnamic and chlorogenic acids (CHAs) from green coffee, with isolates of proteins from egg white (EWP), whey (WPC) and soy (SPI), depending on pH and temperature. The binding degree was determined by liquid chromatography coupled to a diode array detector and an ultrahigh resolution hybrid quadruple-time-of-flight mass spectrometer with ESI source (LC-QTOF-MS/MS). As a result of binding, the concentration of CHAs in proteins ranged from 9.44-12.2, 11.8-13.1 and 12.1-14.4g/100g for SPI, WPC and EWP, respectively. Thermodynamic parameters of protein-ligand interactions were determined by isothermal titration calorimetry (ITC) and energetics of interactions at the atomic level by molecular modelling. The amount of CHAs released during proteolytic digestion was in the range 0.33-2.67g/100g. Inclusion of CHAs with β-cyclodextrin strongly limited these interactions to a level of 0.03-0.06g/100g. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. Food-Drug Interactions

    Directory of Open Access Journals (Sweden)

    Arshad Yar Khan

    2011-03-01

    Full Text Available The effect of drug on a person may be different than expected because that drug interacts with another drug the person is taking (drug-drug interaction, food, beverages, dietary supplements the person is consuming (drug-nutrient/food interaction or another disease the person has (drug-disease interaction. A drug interaction is a situation in which a substance affects the activity of a drug, i.e. the effects are increased or decreased, or they produce a new effect that neither produces on its own. These interactions may occur out of accidental misuse or due to lack of knowledge about the active ingredients involved in the relevant substances. Regarding food-drug interactions physicians and pharmacists recognize that some foods and drugs, when taken simultaneously, can alter the body's ability to utilize a particular food or drug, or cause serious side effects. Clinically significant drug interactions, which pose potential harm to the patient, may result from changes in pharmaceutical, pharmacokinetic, or pharmacodynamic properties. Some may be taken advantage of, to the benefit of patients, but more commonly drug interactions result in adverse drug events. Therefore it is advisable for patients to follow the physician and doctors instructions to obtain maximum benefits with least fooddrug interactions. The literature survey was conducted by extracting data from different review and original articles on general or specific drug interactions with food. This review gives information about various interactions between different foods and drugs and will help physicians and pharmacists prescribe drugs cautiously with only suitable food supplement to get maximum benefit for the patient.

  8. Weak interactions

    International Nuclear Information System (INIS)

    Ogava, S.; Savada, S.; Nakagava, M.

    1983-01-01

    The problem of the use of weak interaction laws to study models of elementary particles is discussed. The most typical examples of weak interaction is beta-decay of nucleons and muons. Beta-interaction is presented by quark currents in the form of universal interaction of the V-A type. Universality of weak interactions is well confirmed using as examples e- and μ-channels of pion decay. Hypothesis on partial preservation of axial current is applicable to the analysis of processes with pion participation. In the framework of the model with four flavours lepton decays of hadrons are considered. Weak interaction without lepton participation are also considered. Properties of neutral currents are described briefly

  9. Floor interaction

    DEFF Research Database (Denmark)

    Petersen, Marianne Graves; Krogh, Peter; Ludvigsen, Martin

    2005-01-01

    Within architecture, there is a long tradition of careful design of floors. The design has been concerned with both decorating floors and designing floors to carry information. Ubiquitous computing technology offers new opportunities for designing interactive floors. This paper presents three...... different interactive floor concepts. Through an urban perspective it draws upon the experiences of floors in architecture, and provides a set of design issues for designing interactive floors....

  10. Foreign language interactive didactics

    Directory of Open Access Journals (Sweden)

    Arnaldo Moisés Gómez

    2016-06-01

    Full Text Available Foreign Language Interactive Didactics is intended for foreign language teachers and would-be teachers since it is an interpretation of the foreign language teaching-learning process is conceived from a reflexive social interaction. This interpretation declares learning based on interactive tasks that provide learners with opportunities to interact meaningfully among them, as a way to develop interactional competence as objective in itself and as a means to obtain communicative competence. Foreign language interactive didactics claims for the unity of reflection and action while learning the language system and using it to communicate, by means of solving problems presented in interactive tasks. It proposes a kind of teaching that is interactive, developmental, collaborative, holist, cognitive, problematizing, reflexive, student centered, humanist, and with a strong affective component that empower the influencing psychological factors in learning. This conception appears in the book: DIDÁCTICA INTERACTIVA DE LENGUAS (2007 y 2010. The book is used as a textbook for the subject of Didactics that is part of the curriculum in language teachers’ formation of all the pedagogical sciences universities, in Spanish teachers’ formation who are not Spanish speaking people at Havana University, and also as a reference book for postgraduate courses, master’s and doctorate’ s degrees.

  11. Molecular Dynamics Simulations and Kinetic Measurements to Estimate and Predict Protein-Ligand Residence Times.

    Science.gov (United States)

    Mollica, Luca; Theret, Isabelle; Antoine, Mathias; Perron-Sierra, Françoise; Charton, Yves; Fourquez, Jean-Marie; Wierzbicki, Michel; Boutin, Jean A; Ferry, Gilles; Decherchi, Sergio; Bottegoni, Giovanni; Ducrot, Pierre; Cavalli, Andrea

    2016-08-11

    Ligand-target residence time is emerging as a key drug discovery parameter because it can reliably predict drug efficacy in vivo. Experimental approaches to binding and unbinding kinetics are nowadays available, but we still lack reliable computational tools for predicting kinetics and residence time. Most attempts have been based on brute-force molecular dynamics (MD) simulations, which are CPU-demanding and not yet particularly accurate. We recently reported a new scaled-MD-based protocol, which showed potential for residence time prediction in drug discovery. Here, we further challenged our procedure's predictive ability by applying our methodology to a series of glucokinase activators that could be useful for treating type 2 diabetes mellitus. We combined scaled MD with experimental kinetics measurements and X-ray crystallography, promptly checking the protocol's reliability by directly comparing computational predictions and experimental measures. The good agreement highlights the potential of our scaled-MD-based approach as an innovative method for computationally estimating and predicting drug residence times.

  12. Calculation of absolute protein-ligand binding free energy using distributed replica sampling.

    Science.gov (United States)

    Rodinger, Tomas; Howell, P Lynne; Pomès, Régis

    2008-10-21

    Distributed replica sampling [T. Rodinger et al., J. Chem. Theory Comput. 2, 725 (2006)] is a simple and general scheme for Boltzmann sampling of conformational space by computer simulation in which multiple replicas of the system undergo a random walk in reaction coordinate or temperature space. Individual replicas are linked through a generalized Hamiltonian containing an extra potential energy term or bias which depends on the distribution of all replicas, thus enforcing the desired sampling distribution along the coordinate or parameter of interest regardless of free energy barriers. In contrast to replica exchange methods, efficient implementation of the algorithm does not require synchronicity of the individual simulations. The algorithm is inherently suited for large-scale simulations using shared or heterogeneous computing platforms such as a distributed network. In this work, we build on our original algorithm by introducing Boltzmann-weighted jumping, which allows moves of a larger magnitude and thus enhances sampling efficiency along the reaction coordinate. The approach is demonstrated using a realistic and biologically relevant application; we calculate the standard binding free energy of benzene to the L99A mutant of T4 lysozyme. Distributed replica sampling is used in conjunction with thermodynamic integration to compute the potential of mean force for extracting the ligand from protein and solvent along a nonphysical spatial coordinate. Dynamic treatment of the reaction coordinate leads to faster statistical convergence of the potential of mean force than a conventional static coordinate, which suffers from slow transitions on a rugged potential energy surface.

  13. G-LoSA for Prediction of Protein-Ligand Binding Sites and Structures.

    Science.gov (United States)

    Lee, Hui Sun; Im, Wonpil

    2017-01-01

    Recent advances in high-throughput structure determination and computational protein structure prediction have significantly enriched the universe of protein structure. However, there is still a large gap between the number of available protein structures and that of proteins with annotated function in high accuracy. Computational structure-based protein function prediction has emerged to reduce this knowledge gap. The identification of a ligand binding site and its structure is critical to the determination of a protein's molecular function. We present a computational methodology for predicting small molecule ligand binding site and ligand structure using G-LoSA, our protein local structure alignment and similarity measurement tool. All the computational procedures described here can be easily implemented using G-LoSA Toolkit, a package of standalone software programs and preprocessed PDB structure libraries. G-LoSA and G-LoSA Toolkit are freely available to academic users at http://compbio.lehigh.edu/GLoSA . We also illustrate a case study to show the potential of our template-based approach harnessing G-LoSA for protein function prediction.

  14. Magnetic levitation as a platform for competitive protein-ligand binding assays.

    Science.gov (United States)

    Shapiro, Nathan D; Soh, Siowling; Mirica, Katherine A; Whitesides, George M

    2012-07-17

    This paper describes a method based on magnetic levitation (MagLev) that is capable of indirectly measuring the binding of unlabeled ligands to unlabeled protein. We demonstrate this method by measuring the affinity of unlabeled bovine carbonic anhydrase (BCA) for a variety of ligands (most of which are benzene sulfonamide derivatives). This method utilizes porous gel beads that are functionalized with a common aryl sulfonamide ligand. The beads are incubated with BCA and allowed to reach an equilibrium state in which the majority of the immobilized ligands are bound to BCA. Since the beads are less dense than the protein, protein binding to the bead increases the overall density of the bead. This change in density can be monitored using MagLev. Transferring the beads to a solution containing no protein creates a situation where net protein efflux from the bead is thermodynamically favorable. The rate at which protein leaves the bead for the solution can be calculated from the rate at which the levitation height of the bead changes. If another small molecule ligand of BCA is dissolved in the solution, the rate of protein efflux is accelerated significantly. This paper develops a reaction-diffusion (RD) model to explain both this observation, and the physical-organic chemistry that underlies it. Using this model, we calculate the dissociation constants of several unlabeled ligands from BCA, using plots of levitation height versus time. Notably, although this method requires no electricity, and only a single piece of inexpensive equipment, it can measure accurately the binding of unlabeled proteins to small molecules over a wide range of dissociation constants (K(d) values within the range from ~10 nM to 100 μM are measured easily). Assays performed using this method generally can be completed within a relatively short time period (20 min-2 h). A deficiency of this system is that it is not, in its present form, applicable to proteins with molecular weight greater than approximately 65 kDa.

  15. Ligand Conformational and Solvation/Desolvation Free Energy in Protein-Ligand Complex Formation

    Czech Academy of Sciences Publication Activity Database

    Kolář, Michal; Fanfrlík, Jindřich; Hobza, Pavel

    2011-01-01

    Roč. 115, č. 16 (2011), s. 4718-4724 ISSN 1520-6106 R&D Projects: GA MŠk LC512; GA ČR GAP208/11/0295 Grant - others:Korea Science and Engineering Foundation(KR) R32-2008-000-10180-0; European Science Fund(XE) CZ.1.05/2.1.00/03.0058 Institutional research plan: CEZ:AV0Z40550506 Keywords : solvation free energy * SMD * HIV protease inhibitors Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.696, year: 2011

  16. Natural HLA-B*2705 Protein Ligands with Glutamine as Anchor Motif

    Science.gov (United States)

    Infantes, Susana; Lorente, Elena; Barnea, Eilon; Beer, Ilan; Barriga, Alejandro; Lasala, Fátima; Jiménez, Mercedes; Admon, Arie; López, Daniel

    2013-01-01

    The presentation of short viral peptide antigens by human leukocyte antigen (HLA) class I molecules on cell surfaces is a key step in the activation of cytotoxic T lymphocytes, which mediate the killing of pathogen-infected cells or initiate autoimmune tissue damage. HLA-B27 is a well known class I molecule that is used to study both facets of the cellular immune response. Using mass spectrometry analysis of complex HLA-bound peptide pools isolated from large amounts of HLA-B*2705+ cells, we identified 200 naturally processed HLA-B*2705 ligands. Our analyses revealed that a change in the position (P) 2 anchor motif was detected in the 3% of HLA-B*2705 ligands identified. B*2705 class I molecules were able to bind these six GlnP2 peptides, which showed significant homology to pathogenic bacterial sequences, with a broad range of affinities. One of these ligands was able to bind with distinct conformations to HLA-B27 subtypes differentially associated with ankylosing spondylitis. These conformational differences could be sufficient to initiate autoimmune damage in patients with ankylosing spondylitis-associated subtypes. Therefore, these kinds of peptides (short, with GlnP2, and similar low affinity to all HLA-B27 subtypes tested but with unlike conformations in differentially ankylosing spondylitis-associated subtypes) must not be excluded from future researches involving potential arthritogenic peptides. PMID:23430249

  17. Generation of pharmacophores and classification of drugs using protein-ligand complexes

    Directory of Open Access Journals (Sweden)

    Eliana Velasquez

    2014-04-01

    Full Text Available Pharmacophore identification is a veryimportant step in de novo design, leadoptimization, chemogenomics, and virtualscreening of drugs. Unfortunately,the high cost of comercial software forpharmacophore detection is a commonlimiting factor for researchers with limitedfunding. This paper presents a set offreely available perl routines that weredesigned to help in the process of 3Dpharmacophore identification and QSARstudies. These routines also allowed theclassification of ligands based on theirtridimensional similarity and bindingmechanism. The family of phosphodiesterasesand their inhibitors were used astest model.

  18. A chemical library to screen protein and protein-ligand crystallization using a versatile microfluidic platform

    OpenAIRE

    Gerard , Charline ,; Ferry , Gilles; Vuillard , Laurent ,; Boutin , Jean ,; Ferte , Nathalie ,; Grossier , Romain ,; Candoni , Nadine ,; Veesler , Stéphane ,

    2018-01-01

    Here, we describe a plug-and-play microfluidic platform, suitable for protein crystallization. The droplet factory is designed to generate hundreds of droplets as small as a few nanoliters (2 to 10nL) for screening and optimization of crystallization conditions. Commercially-available microfluidic junctions and tubing are combined to create the appropriate geometry. In addition, a " chemical library " is produced in tubing. The microfluidic geometry for a " crystallization agent-based chemica...

  19. Preclinical Testing of a Translocator Protein Ligand for the Treatment of Amyotrophic Lateral Sclerosis

    Science.gov (United States)

    2017-03-01

    investigated the neuroprotective effect and therapeutic value of a drug : the translocator protein (TSPO) ligand PK11195 (PK), which we found to be...Translocator protein (TSPO) ligand Neuroprotective drugs In vitro models of neurodegeneration Axon preservation Neuromuscular junctions 5 3...pharmacokinetic data of the JNK study were showing that daily gavage (30 mg/kg/day) allowed an efficient delivery of the drugs in the brain and the spinal

  20. Biotechnological Fluorescent Ligands of the Bradykinin B1 Receptor: Protein Ligands for a Peptide Receptor.

    Directory of Open Access Journals (Sweden)

    Xavier Charest-Morin

    Full Text Available The bradykinin (BK B1 receptor (B1R is a peculiar G protein coupled receptor that is strongly regulated to the point of being inducible in immunopathology. Limited clinical evidence suggests that its expression in peripheral blood mononuclear cells is a biomarker of active inflammatory states. In an effort to develop a novel imaging/diagnostic tool, we report the rational design and testing of a fusion protein that is a ligand of the human B1R but not likely to label peptidases. This ligand is composed of a fluorescent protein (FP (enhanced green FP [EGFP] or mCherry prolonged at its N-terminus by a spacer peptide and a classical peptide agonist or antagonist (des-Arg9-BK, [Leu8]des-Arg9-BK, respectively. The design of the spacer-ligand joint peptide was validated by a competition assay for [3H]Lys-des-Arg9-BK binding to the human B1R applied to 4 synthetic peptides of 18 or 19 residues. The labeling of B1R-expressing cells with EGFP or mCherry fused with 7 of such peptides was performed in parallel (microscopy. Both assays indicated that the best design was FP-(Asn-Glyn-Lys-des-Arg9-BK; n = 15 was superior to n = 5, suggesting benefits from minimizing steric hindrance between the FP and the receptor. Cell labeling concerned mostly plasma membranes and was inhibited by a B1R antagonist. EGFP-(Asn-Gly15-Lys-des-Arg9-BK competed for the binding of [3H]Lys-des-Arg9-BK to human recombinant B1R, being only 10-fold less potent than the unlabeled form of Lys-des-Arg9-BK to do so. The fusion protein did not label HEK 293a cells expressing recombinant human BK B2 receptors or angiotensin converting enzyme. This study identifies a modular C-terminal sequence that can be adapted to protein cargoes, conferring high affinity for the BK B1R, with possible applications in diagnostic cytofluorometry, histology and drug delivery (e.g., in oncology.

  1. Discovering rules for protein-ligand specificity using support vector inductive logic programming.

    Science.gov (United States)

    Kelley, Lawrence A; Shrimpton, Paul J; Muggleton, Stephen H; Sternberg, Michael J E

    2009-09-01

    Structural genomics initiatives are rapidly generating vast numbers of protein structures. Comparative modelling is also capable of producing accurate structural models for many protein sequences. However, for many of the known structures, functions are not yet determined, and in many modelling tasks, an accurate structural model does not necessarily tell us about function. Thus, there is a pressing need for high-throughput methods for determining function from structure. The spatial arrangement of key amino acids in a folded protein, on the surface or buried in clefts, is often the determinants of its biological function. A central aim of molecular biology is to understand the relationship between such substructures or surfaces and biological function, leading both to function prediction and to function design. We present a new general method for discovering the features of binding pockets that confer specificity for particular ligands. Using a recently developed machine-learning technique which couples the rule-discovery approach of inductive logic programming with the statistical learning power of support vector machines, we are able to discriminate, with high precision (90%) and recall (86%) between pockets that bind FAD and those that bind NAD on a large benchmark set given only the geometry and composition of the backbone of the binding pocket without the use of docking. In addition, we learn rules governing this specificity which can feed into protein functional design protocols. An analysis of the rules found suggests that key features of the binding pocket may be tied to conformational freedom in the ligand. The representation is sufficiently general to be applicable to any discriminatory binding problem. All programs and data sets are freely available to non-commercial users at http://www.sbg.bio.ic.ac.uk/svilp_ligand/.

  2. Playful Interaction

    DEFF Research Database (Denmark)

    2003-01-01

    The video Playful Interaction describes a future architectural office, and envisions ideas and concepts for playful interactions between people, materials and appliances in a pervasive and augmented working environment. The video both describes existing developments, technologies and designs...... as well as ideas not yet implemented such as playful modes of interaction with an augmented ball. Playful Interaction has been used as a hybrid of a vision video and a video prototype (1). Externally the video has been used to visualising our new ideas, and internally the video has also worked to inspire...

  3. Process for obtaining oxygen doped zinc telluride monocrystals and scintillator crystals obtained by this process

    International Nuclear Information System (INIS)

    Schneider, Maurice; Moreau, Roland; D'Haenen, J.-P.; Merenda, Pierre.

    1976-01-01

    A process is described for obtaining oxygen doped zinc telluride monocrystals, for use as scintillator crystals for ionising radiation detectors. The following operations are carried out in succession: one or several zinc telluride crystals are introduced into a silica ampoule together with a ternary mixture of zinc tellurium and oxygen, as an oxide or hydroxide of these elements; the ampoule is pumped down to a high vacuum and sealed; the sealed ampoule containing the mixture and monocrystals is placed in a kiln and brought to a uniform temperature sufficient to make the mixture three-phased, depending on its composition; the zinc telluride crystalline compound remains solid; the ampoule is then tempered to bring it quickly back to ambient temperature [fr

  4. Aesthetic interaction

    DEFF Research Database (Denmark)

    Petersen, Marianne Graves; Iversen, Ole Sejer; Krogh, Peter

    2004-01-01

    , as it promotes aesthetics of use, rather than aesthetics of appearance. We coin this approach in the perspective of aesthetic interaction. Finally we make the point that aesthetics is not re-defining everything known about interactive systems. We provide a framework placing this perspective among other...

  5. Interactive benchmarking

    DEFF Research Database (Denmark)

    Lawson, Lartey; Nielsen, Kurt

    2005-01-01

    We discuss individual learning by interactive benchmarking using stochastic frontier models. The interactions allow the user to tailor the performance evaluation to preferences and explore alternative improvement strategies by selecting and searching the different frontiers using directional...... in the suggested benchmarking tool. The study investigates how different characteristics on dairy farms influences the technical efficiency....

  6. Explicit Interaction

    DEFF Research Database (Denmark)

    Löwgren, Jonas; Eriksen, Mette Agger; Linde, Per

    2006-01-01

    We report an ongoing study of palpable computing to support surgical rehabilitation, in the general field of interaction design for ubiquitous computing. Through explorative design, fieldwork and participatory design techniques, we explore the design principle of explicit interaction as an interp...

  7. Kinesthetic Interaction

    DEFF Research Database (Denmark)

    Fogtmann, Maiken Hillerup; Fritsch, Jonas; Kortbek, Karen Johanne

    2008-01-01

    Within the Human-Computer Interaction community there is a growing interest in designing for the whole body in interaction design. The attempts aimed at addressing the body have very different outcomes spanning from theoretical arguments for understanding the body in the design process, to more...... practical examples of designing for bodily potential. This paper presents Kinesthetic Interaction as a unifying concept for describing the body in motion as a foundation for designing interactive systems. Based on the theoretical foundation for Kinesthetic Interaction, a conceptual framework is introduced...... to reveal bodily potential in relation to three design themes – kinesthetic development, kinesthetic means and kinesthetic disorder; and seven design parameters – engagement, sociality, movability, explicit motivation, implicit motivation, expressive meaning and kinesthetic empathy. The framework is a tool...

  8. Protein-binding RNA aptamers affect molecular interactions distantly from their binding sites.

    Directory of Open Access Journals (Sweden)

    Daniel M Dupont

    Full Text Available Nucleic acid aptamer selection is a powerful strategy for the development of regulatory agents for molecular intervention. Accordingly, aptamers have proven their diligence in the intervention with serine protease activities, which play important roles in physiology and pathophysiology. Nonetheless, there are only a few studies on the molecular basis underlying aptamer-protease interactions and the associated mechanisms of inhibition. In the present study, we use site-directed mutagenesis to delineate the binding sites of two 2´-fluoropyrimidine RNA aptamers (upanap-12 and upanap-126 with therapeutic potential, both binding to the serine protease urokinase-type plasminogen activator (uPA. We determine the subsequent impact of aptamer binding on the well-established molecular interactions (plasmin, PAI-1, uPAR, and LRP-1A controlling uPA activities. One of the aptamers (upanap-126 binds to the area around the C-terminal α-helix in pro-uPA, while the other aptamer (upanap-12 binds to both the β-hairpin of the growth factor domain and the kringle domain of uPA. Based on the mapping studies, combined with data from small-angle X-ray scattering analysis, we construct a model for the upanap-12:pro-uPA complex. The results suggest and highlight that the size and shape of an aptamer as well as the domain organization of a multi-domain protein such as uPA, may provide the basis for extensive sterical interference with protein ligand interactions considered distant from the aptamer binding site.

  9. Investigating the Interaction of Fe Nanoparticles with Lysozyme by Biophysical and Molecular Docking Studies.

    Directory of Open Access Journals (Sweden)

    Zahra Aghili

    Full Text Available Herein, the interaction of hen egg white lysozyme (HEWL with iron nanoparticle (Fe NP was investigated by spectroscopic and docking studies. The zeta potential analysis revealed that addition of Fe NP (6.45±1.03 mV to HEWL (8.57±0.54 mV can cause to greater charge distribution of nanoparticle-protein system (17.33±1.84 mV. In addition, dynamic light scattering (DLS study revealed that addition of Fe NP (92.95±6.11 nm to HEWL (2.68±0.37 nm increases suspension potential of protein/nanoparticle system (51.17±3.19 nm. Fluorescence quenching studies reveled that both static and dynamic quenching mechanism occur and hydrogen bond and van der Waals interaction give rise to protein-NP system. Synchronous fluorescence spectroscopy of HEWL in the presence of Fe NP showed that the emission maximum wavelength of tryptophan (Trp residues undergoes a red-shift. ANS fluorescence data indicated a dramatic exposure of hydrophobic residues to the solvent. The considerable reduction in melting temperature (T(m of HEWL after addition of Fe NP determines an unfavorable interaction system. Furthermore circular dichoroism (CD experiments demonstrated that, the secondary structure of HEWL has not changed with increasing Fe NP concentrations; however, some conformational changes occur in tertiary structure of HEWL. Moreover, protein-ligand docking study confirmed that the Fe NP forms hydrogen bond contacts with HEWL.

  10. Polaron mobility obtained by a variational approach for lattice Fröhlich models

    Science.gov (United States)

    Kornjača, Milan; Vukmirović, Nenad

    2018-04-01

    Charge carrier mobility for a class of lattice models with long-range electron-phonon interaction was investigated. The approach for mobility calculation is based on a suitably chosen unitary transformation of the model Hamiltonian which transforms it into the form where the remaining interaction part can be treated as a perturbation. Relevant spectral functions were then obtained using Matsubara Green's functions technique and charge carrier mobility was evaluated using Kubo's linear response formula. Numerical results were presented for a wide range of electron-phonon interaction strengths and temperatures in the case of one-dimensional version of the model. The results indicate that the mobility decreases with increasing temperature for all electron-phonon interaction strengths in the investigated range, while longer interaction range leads to more mobile carriers.

  11. Origin of poor doping efficiency in solution processed organic semiconductors† †Electronic supplementary information (ESI) available: Additional details on sample characterization, quantum chemistry calculations to obtain transition dipole moments of the ions and determine the strength of the Coulomb interaction, two-dimensional correlation analysis has been provided. In addition, this document also contains details of the calculations used to simulate 2D electronic spectra. See DOI: 10.1039/c8sc00758f

    Science.gov (United States)

    Jha, Ajay; Duan, Hong-Guang; Tiwari, Vandana; Thorwart, Michael

    2018-01-01

    Doping is an extremely important process where intentional insertion of impurities in semiconductors controls their electronic properties. In organic semiconductors, one of the convenient, but inefficient, ways of doping is the spin casting of a precursor mixture of components in solution, followed by solvent evaporation. Active control over this process holds the key to significant improvements over current poor doping efficiencies. Yet, an optimized control can only come from a detailed understanding of electronic interactions responsible for the low doping efficiencies. Here, we use two-dimensional nonlinear optical spectroscopy to examine these interactions in the course of the doping process by probing the solution mixture of doped organic semiconductors. A dopant accepts an electron from the semiconductor and the two ions form a duplex of interacting charges known as ion-pair complexes. Well-resolved off-diagonal peaks in the two-dimensional spectra clearly demonstrate the electronic connectivity among the ions in solution. This electronic interaction represents a well resolved electrostatically bound state, as opposed to a random distribution of ions. We developed a theoretical model to recover the experimental data, which reveals an unexpectedly strong electronic coupling of ∼250 cm–1 with an intermolecular distance of ∼4.5 Å between ions in solution, which is approximately the expected distance in processed films. The fact that this relationship persists from solution to the processed film gives direct evidence that Coulomb interactions are retained from the precursor solution to the processed films. This memory effect renders the charge carriers equally bound also in the film and, hence, results in poor doping efficiencies. This new insight will help pave the way towards rational tailoring of the electronic interactions to improve doping efficiencies in processed organic semiconductor thin films. PMID:29896388

  12. Programming Interactivity

    CERN Document Server

    Noble, Joshua

    2012-01-01

    Ready to create rich interactive experiences with your artwork, designs, or prototypes? This is the ideal place to start. With this hands-on guide, you'll explore several themes in interactive art and design-including 3D graphics, sound, physical interaction, computer vision, and geolocation-and learn the basic programming and electronics concepts you need to implement them. No previous experience is necessary. You'll get a complete introduction to three free tools created specifically for artists and designers: the Processing programming language, the Arduino microcontroller, and the openFr

  13. Interaction graphs

    DEFF Research Database (Denmark)

    Seiller, Thomas

    2016-01-01

    Interaction graphs were introduced as a general, uniform, construction of dynamic models of linear logic, encompassing all Geometry of Interaction (GoI) constructions introduced so far. This series of work was inspired from Girard's hyperfinite GoI, and develops a quantitative approach that should...... be understood as a dynamic version of weighted relational models. Until now, the interaction graphs framework has been shown to deal with exponentials for the constrained system ELL (Elementary Linear Logic) while keeping its quantitative aspect. Adapting older constructions by Girard, one can clearly define...... "full" exponentials, but at the cost of these quantitative features. We show here that allowing interpretations of proofs to use continuous (yet finite in a measure-theoretic sense) sets of states, as opposed to earlier Interaction Graphs constructions were these sets of states were discrete (and finite...

  14. Embarrassing Interactions

    DEFF Research Database (Denmark)

    Deterding, Sebastian; Lucero, Andrés; Holopainen, Jussi

    2015-01-01

    Wherever the rapid evolution of interactive technologies disrupts standing situational norms, creates new, often unclear situational audiences, or crosses cultural boundaries, embarrassment is likely. This makes embarrassment a fundamental adoption and engagement hurdle, but also a creative design...

  15. Diffractive interactions

    International Nuclear Information System (INIS)

    Del Duca, V.; Marage, P.

    1996-08-01

    The general framework of diffractive deep inelastic scattering is introduced and reports given in the session on diffractive interactions at the international workshop on deep-inelastic scattering and related phenomena, Rome, April 1996, are presented. (orig.)

  16. Interaction Widget

    DEFF Research Database (Denmark)

    Ingstrup, Mads

    2003-01-01

    This pattern describes the idea of making a user interface of discrete, reusable entities---here called interaction widgets. The idea behind widgets is described using two perspectives, that of the user and that of the developer. It is the forces from these two perspectives that are balanced...... in the pattern. The intended audience of the pattern is developers and researchers within the field of human computer interaction....

  17. Hair Interactions

    OpenAIRE

    Cani , Marie-Paule; Bertails , Florence

    2006-01-01

    International audience; Processing interactions is one of the main challenges in hair animation. Indeed, in addition to the collisions with the body, an extremely large number of contacts with high friction rates are permanently taking place between individual hair strands. Simulating the latter is essential: without hair self-interactions, strands would cross each other during motion or come to rest at the same location, yielding unrealistic behavior and a visible lack of hair volume. This c...

  18. 32 CFR Appendix B to Part 275 - Obtaining Customer Authorization

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 2 2010-07-01 2010-07-01 false Obtaining Customer Authorization B Appendix B to... OF 1978 Pt. 275, App. B Appendix B to Part 275—Obtaining Customer Authorization A. A DoD law... feasible, obtain the customer's consent. B. Any authorization obtained under paragraph A. of this appendix...

  19. Alkane dimers interaction

    DEFF Research Database (Denmark)

    Ferrighi, Lara; Madsen, Georg Kent Hellerup; Hammer, Bjørk

    2010-01-01

    The interaction energies of a series of n-alkane dimers, from methane to decane, have been investigated with Density Functional Theory (DFT), using the MGGA-M06-L density functional. The results are compared both to the available wavefunction-based values as well as to dispersion corrected DFT...... values. The MGGA-M06-L density functional is a semi-local functional designed and has proven to provide accurate estimates of dispersion interactions for several systems at moderate computational cost. In the present application, it reproduces the trends obtained by the more expensive wavefunction...

  20. Numbat: an interactive software tool for fitting Δχ-tensors to molecular coordinates using pseudocontact shifts

    International Nuclear Information System (INIS)

    Schmitz, Christophe; Stanton-Cook, Mitchell J.; Su Xuncheng; Otting, Gottfried; Huber, Thomas

    2008-01-01

    Pseudocontact shift (PCS) effects induced by a paramagnetic lanthanide bound to a protein have become increasingly popular in NMR spectroscopy as they yield a complementary set of orientational and long-range structural restraints. PCS are a manifestation of the χ-tensor anisotropy, the Δχ-tensor, which in turn can be determined from the PCS. Once the Δχ-tensor has been determined, PCS become powerful long-range restraints for the study of protein structure and protein-ligand complexes. Here we present the newly developed package Numbat (New User-friendly Method Built for Automatic Δχ-Tensor determination). With a Graphical User Interface (GUI) that allows a high degree of interactivity, Numbat is specifically designed for the computation of the complete set of Δχ-tensor parameters (including shape, location and orientation with respect to the protein) from a set of experimentally measured PCS and the protein structure coordinates. Use of the program for Linux and Windows operating systems is illustrated by building a model of the complex between the E. coli DNA polymerase III subunits ε186 and θ using PCS

  1. Time-dependent inhibition of Na+/K+-ATPase induced by single and simultaneous exposure to lead and cadmium

    Science.gov (United States)

    Vasić, V.; Kojić, D.; Krinulović, K.; Čolović, M.; Vujačić, A.; Stojić, D.

    2007-09-01

    Time-dependent interactions of Na+/K+-ATPase, isolated from rat brain synaptic plasma membranes (SPMs), with Cd2+ and Pb2+ ions in a single exposure and in a mixture were investigated in vitro. The interference of the enzyme with these metal ions was studied as a function of different protein concentrations and exposure time. The aim of the work was to investigate the possibility of selective recognition of Cd2+ and Pb2+ ions in a mixture, on the basis of the different rates of their protein-ligand interactions. Decreasing protein concentration increased the sensitivity of Na+/K+-ATPase toward both metals. The selectivity in protein-ligand interactions was obtained by variation of preincubation time (incubation before starting the enzymatic reaction).

  2. Automated Hydrophobic Interaction Chromatography Column Selection for Use in Protein Purification

    Science.gov (United States)

    Murphy, Patrick J. M.; Stone, Orrin J.; Anderson, Michelle E.

    2011-01-01

    In contrast to other chromatographic methods for purifying proteins (e.g. gel filtration, affinity, and ion exchange), hydrophobic interaction chromatography (HIC) commonly requires experimental determination (referred to as screening or "scouting") in order to select the most suitable chromatographic medium for purifying a given protein 1. The method presented here describes an automated approach to scouting for an optimal HIC media to be used in protein purification. HIC separates proteins and other biomolecules from a crude lysate based on differences in hydrophobicity. Similar to affinity chromatography (AC) and ion exchange chromatography (IEX), HIC is capable of concentrating the protein of interest as it progresses through the chromatographic process. Proteins best suited for purification by HIC include those with hydrophobic surface regions and able to withstand exposure to salt concentrations in excess of 2 M ammonium sulfate ((NH4)2SO4). HIC is often chosen as a purification method for proteins lacking an affinity tag, and thus unsuitable for AC, and when IEX fails to provide adequate purification. Hydrophobic moieties on the protein surface temporarily bind to a nonpolar ligand coupled to an inert, immobile matrix. The interaction between protein and ligand are highly dependent on the salt concentration of the buffer flowing through the chromatography column, with high ionic concentrations strengthening the protein-ligand interaction and making the protein immobile (i.e. bound inside the column) 2. As salt concentrations decrease, the protein-ligand interaction dissipates, the protein again becomes mobile and elutes from the column. Several HIC media are commercially available in pre-packed columns, each containing one of several hydrophobic ligands (e.g. S-butyl, butyl, octyl, and phenyl) cross-linked at varying densities to agarose beads of a specific diameter 3. Automated column scouting allows for an efficient approach for determining which HIC media

  3. Interactive governance

    DEFF Research Database (Denmark)

    Sørensen, Eva; Torfing, Jacob; Peters, B. Guy

    Governance has become one of the most commonly used concepts in contemporary political science. It is, however, often used to mean a variety of different things. This book helps to clarify this conceptual muddle by concentrating on one variety of governance-interactive governance. The authors argue...... that although the state may remain important for many aspects of governing, interactions between state and society represent an important, and perhaps increasingly important, dimension of governance. These interactions may be with social actors such as networks, with market actors or with other governments......, but all these forms represent means of governing involving mixtures of state action with the actions of other entities.This book explores thoroughly this meaning of governance, and links it to broader questions of governance. In the process of explicating this dimension of governance the authors also...

  4. Multiquark interactions

    International Nuclear Information System (INIS)

    Luk'yanov, V.K.

    1984-01-01

    To study multiquark interactions (MQI) the data of experiments confirming the presence of 3q, 6q, 12q states in interacting nuclear nucleons, in hadron- and lepton-nuclear processes at high energies and high momentum transfers are considered. Experimental data on cumulative processes pointing to the existence of MQI are analyzed. Two-channel model of a nucleus (the model of interacting nucleons) in the theory of coupled channels is discussed. The behaviour of form factor of deuteron and NQI (6q) contributions to ed scattering as well as deep inelastic scattering on nuclei are studied. The data known as EMC effect are discussed. It is pointed out that introduction of the notion MQI and consideration of a nucleus as a system of nucleons with a low MQI addition will help to explain such processes as cumulative reactions, form factors of a deuteron and light nuclei, deep inelastic scattering on nuclei

  5. Interaction region

    International Nuclear Information System (INIS)

    Anon.

    1982-01-01

    The Interaction Region Group addressed the basic questions of how to collide the SLC beams, how to maximize and monitor the luminosity, and how to minimize the detector backgrounds at the interaction region. In practice, five subgroups evolved to study these questions. The final focus group provided three alternative designs to acheive the 1 to 2 micron beam spot size required by the SLC, as well as studying other problems including: eta, eta' matching from the collider arcs, the implementation of soft bends near the interaction region, beam emittance growth, and magnet tolerances in the final focus. The beam position monitor group proposed two devices, a strip line monitor, and a beamstrahlung monitor, to bring the beams into collision. The luminosity monitor group reviewed the possible QED processes that would be insensitive to weak interaction (Z 0 ) effects. The beam dumping group proposed locations for kicker and septum magnets in the final focus that would achieve a high dumping efficiency and would meet the desired beam tolerances at the Moller scattering target in the beam dump line. Working with the Polarization Group, the Moller experiment was designed into the beam dump beam line. A beam dump was proposed that would maintain radiation backgrounds (penetrating muons) at acceptible levels. The detector backgrounds group proposed soft-bend and masking configurations to shield the detector from synchrotron radiation from the hard/soft bends and from the final focus quadrupoles and evaluated the effectiveness of these designs for the three final focus optics designs. Backgrounds were also estimated from: large angle synchrotron radiation, local and distant beam-gas interactions, 2-photon interactions, and from neutrons and backscattered photons from the beamstrahlung dump

  6. Programming Interactivity

    CERN Document Server

    Noble, Joshua

    2009-01-01

    Make cool stuff. If you're a designer or artist without a lot of programming experience, this book will teach you to work with 2D and 3D graphics, sound, physical interaction, and electronic circuitry to create all sorts of interesting and compelling experiences -- online and off. Programming Interactivity explains programming and electrical engineering basics, and introduces three freely available tools created specifically for artists and designers: Processing, a Java-based programming language and environment for building projects on the desktop, Web, or mobile phonesArduino, a system t

  7. Interacting binaries

    International Nuclear Information System (INIS)

    Eggleton, P.P.; Pringle, J.E.

    1985-01-01

    This volume contains 15 review articles in the field of binary stars. The subjects reviewed span considerably, from the shortest period of interacting binaries to the longest, symbiotic stars. Also included are articles on Algols, X-ray binaries and Wolf-Rayet stars (single and binary). Contents: Preface. List of Participants. Activity of Contact Binary Systems. Wolf-Rayet Stars and Binarity. Symbiotic Stars. Massive X-ray Binaries. Stars that go Hump in the Night: The SU UMa Stars. Interacting Binaries - Summing Up

  8. 48 CFR 1815.403 - Obtaining cost or pricing data.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 6 2010-10-01 2010-10-01 true Obtaining cost or pricing... ADMINISTRATION CONTRACTING METHODS AND CONTRACT TYPES CONTRACTING BY NEGOTIATION Contract Pricing 1815.403 Obtaining cost or pricing data. ...

  9. Hadron interactions

    International Nuclear Information System (INIS)

    Fischer, J.; Kolar, P.; Kundrat, V.

    1988-01-01

    The proceedings contain invited lectures and papers presente at the symposium. Attention was devoted to hadron interactions a high energy in QCD, to the structure and decay of hadrons, the production of hadrons and supersymmetric particles in e + e - and ep collisions, to perturbation theory in quantum field theory, and new supersymmetric extensions of relativistic algebra. (Z.J

  10. Interactive Storytelling

    DEFF Research Database (Denmark)

    Schoenau-Fog, Henrik; Reng, Lars

    2015-01-01

    This book constitutes the refereed proceedings of the 8th International Conference on Interactive Digital Storytelling, ICIDS 2015, held in Copenhagen, Denmark, in November/December 2015. The 18 revised full papers and 13 short papers presented together with 9 posters, 9 workshop descriptions, an...

  11. Infrared Fourier spectres of pectin obtained from pumpkin

    International Nuclear Information System (INIS)

    Usmanova, S.R.; Dzhonmurodov, A.S.; Nazirova, Kh.I.; Mukhidinov, Z.K.

    2015-01-01

    Present article is devoted to infrared Fourier spectres of pectin obtained from pumpkin. The analysis of pectin obtained from pumpkin was conducted by means of infrared spectrophotometer with Fourier transformation. The infrared spectroscopic study of pectin polysaccharide fraction of pectin matter, as well as pectin helium and micro helium obtained by means of fast extraction was conducted.

  12. 32 CFR 806b.8 - Obtaining law enforcement records.

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 6 2010-07-01 2010-07-01 false Obtaining law enforcement records. 806b.8 Section 806b.8 National Defense Department of Defense (Continued) DEPARTMENT OF THE AIR FORCE ADMINISTRATION PRIVACY ACT PROGRAM Obtaining Law Enforcement Records and Confidentiality Promises § 806b.8 Obtaining law enforcement records. The Commander, Air...

  13. 15 CFR 748.2 - Obtaining forms; mailing addresses.

    Science.gov (United States)

    2010-01-01

    ... 15 Commerce and Foreign Trade 2 2010-01-01 2010-01-01 false Obtaining forms; mailing addresses... APPLICATIONS (CLASSIFICATION, ADVISORY, AND LICENSE) AND DOCUMENTATION § 748.2 Obtaining forms; mailing addresses. (a) You may obtain the forms required by the EAR from any U.S. Department of Commerce District...

  14. ELECTROCHEMICAL TECHNOLOGIES FOR OBTAINING MOULDS FOR SOLES OF SHOES

    Directory of Open Access Journals (Sweden)

    Cornelia LUCA

    2013-05-01

    Full Text Available The paper presents contributions in the designing of some electrochemical technologiesfor the manufacturing of the moulds used in the footwear soles obtaining. There are presented a fewmethods for the moulds obtaining, using electro-deposit processes. There are presented thetechnological phases of the obtaining process of the electrolytes and electrodes preparing and thetechnological stages of the moulds manufacturing.

  15. Interactions between photodegradation components

    Directory of Open Access Journals (Sweden)

    Abdollahi Yadollah

    2012-09-01

    Full Text Available Abstract Background The interactions of p-cresol photocatalytic degradation components were studied by response surface methodology. The study was designed by central composite design using the irradiation time, pH, the amount of photocatalyst and the p-cresol concentration as variables. The design was performed to obtain photodegradation % as actual responses. The actual responses were fitted with linear, two factor interactions, cubic and quadratic model to select an appropriate model. The selected model was validated by analysis of variance which provided evidences such as high F-value (845.09, very low P-value (2 = 0.999, adjusted R-squared (Radj2 = 0.998, predicted R-squared (Rpred2 = 0.994 and the adequate precision (95.94. Results From the validated model demonstrated that the component had interaction with irradiation time under 180 min of the time while the interaction with pH was above pH 9. Moreover, photocatalyst and p-cresol had interaction at minimal amount of photocatalyst (p-cresol. Conclusion These variables are interdependent and should be simultaneously considered during the photodegradation process, which is one of the advantages of the response surface methodology over the traditional laboratory method.

  16. Interactive cinema : engagement and interaction

    NARCIS (Netherlands)

    Vosmeer, M.; Schouten, B.; Mitchell, A.

    2014-01-01

    Technologies that were initially developed to be applied within the domain of video games are currently being used in experiments to explore their meaning and possibilities for cinema and cinema audiences. In this position paper we examine how narrativity, interactivity and engagement are mutually

  17. Interactive Macroeconomics

    Science.gov (United States)

    Di Guilmi, Corrado; Gallegati, Mauro; Landini, Simone

    2017-04-01

    Preface; List of tables; List of figures, 1. Introduction; Part I. Methodological Notes and Tools: 2. The state space notion; 3. The master equation; Part II. Applications to HIA Based Models: 4. Financial fragility and macroeconomic dynamics I: heterogeneity and interaction; 5. Financial fragility and macroeconomic Dynamics II: learning; Part III. Conclusions: 6. Conclusive remarks; Part IV. Appendices and Complements: Appendix A: Complements to Chapter 3; Appendix B: Solving the ME to solve the ABM; Appendix C: Specifying transition rates; Index.

  18. SiC-Based Composite Materials Obtained by Siliconizing Carbon Matrices

    Science.gov (United States)

    Shikunov, S. L.; Kurlov, V. N.

    2017-12-01

    We have developed a method for fabrication of parts of complicated configuration from composite materials based on SiC ceramics, which employs the interaction of silicon melt with the carbon matrix having a certain composition and porosity. For elevating the operating temperatures of ceramic components, we have developed a method for depositing protective silicon-carbide coatings that is based on the interaction of the silicon melt and vapor with carbon obtained during thermal splitting of hydrocarbon molecules. The new structural ceramics are characterized by higher operating temperatures; chemical stability; mechanical strength; thermal shock, wear and radiation resistance; and parameters stability.

  19. Interactive Governance

    DEFF Research Database (Denmark)

    Bang, Henrik

    2016-01-01

    Governance analysis has exploded in recent years, and it has become nearly impossible to tell what difference the concept and practice of governance makes from those of government and state. In addition governance analysis has been placed more and more in the shadow of the new institutionalisms and...... and growth. However, interactive governance is not a property or effect of institutions; nor does it apply solely to those individuals who seek success above everything else. It is connective more than individualistic or collectivistic in nature; and it manifests a governability capacity which...

  20. Collocated Interaction

    DEFF Research Database (Denmark)

    E. Fischer, Joel; Porcheron, Martin; Lucero, Andrés

    2016-01-01

    interactions. Yet, new challenges abound as people wear and carry more devices than ever, creating fragmented device ecologies at work, and changing the ways we socialise with each other. In this workshop we seek to start a dialogue to look back as well as forward, review best practices, discuss and design......In the 25 years since Ellis, Gibbs, and Rein proposed the time-space taxonomy, research in the ‘same time, same place’ quadrant has diversified, perhaps even fragmented. This one-day workshop will bring together researchers with diverse, yet convergent interests in tabletop, surface, mobile...

  1. Weak interactions

    International Nuclear Information System (INIS)

    Bjorken, J.D.

    1978-01-01

    Weak interactions are studied from a phenomenological point of view, by using a minimal number of theoretical hypotheses. Charged-current phenomenology, and then neutral-current phenomenology are discussed. This all is described in terms of a global SU(2) symmetry plus an electromagnetic correction. The intermediate-boson hypothesis is introduced and lower bounds on the range of the weak force are inferred. This phenomenology does not yet reconstruct all the predictions of the conventional SU(2)xU(1) gauge theory. To do that requires an additional assumption of restoration of SU(2) symmetry at asymptotic energies

  2. Strong interactions

    International Nuclear Information System (INIS)

    Froissart, Marcel

    1976-01-01

    Strong interactions are introduced by their more obvious aspect: nuclear forces. In hadron family, the nucleon octet, OMEGA - decuplet, and quark triply are successively considered. Pion wave having been put at the origin of nuclear forces, low energy phenomena are described, the force being explained as an exchange of structure corresponding to a Regge trajectory in a variable rotating state instead of the exchange of a well defined particle. At high energies the concepts of pomeron, parton and stratons are introduced, pionization and fragmentation are briefly differentiated [fr

  3. Obtaining the Electron Angular Momentum Coupling Spectroscopic Terms, jj

    Science.gov (United States)

    Orofino, Hugo; Faria, Roberto B.

    2010-01-01

    A systematic procedure is developed to obtain the electron angular momentum coupling (jj) spectroscopic terms, which is based on building microstates in which each individual electron is placed in a different m[subscript j] "orbital". This approach is similar to that used to obtain the spectroscopic terms under the Russell-Saunders (LS) coupling…

  4. 17 CFR 10.93 - Obtaining default order.

    Science.gov (United States)

    2010-04-01

    ... 17 Commodity and Securities Exchanges 1 2010-04-01 2010-04-01 false Obtaining default order. 10.93... Disposition Without Full Hearing § 10.93 Obtaining default order. When a respondent has failed to (a) file an... enter findings and conclusions and a default order against that respondent based upon the matters set...

  5. The legal status of evidence obtained through human rights ...

    African Journals Online (AJOL)

    The Constitution of the Republic of Uganda, 1995 is silent on the issue of dealing with evidence obtained through human rights violations. This silence dates to the earlier Constitutions of 1962, 1966 and 1967. It is only the Prohibition and Prevention of Torture Act of 2012 that renders evidence obtained through torture and ...

  6. 7 CFR 29.91 - How to obtain an appeal.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false How to obtain an appeal. 29.91 Section 29.91... REGULATIONS TOBACCO INSPECTION Regulations Appeal § 29.91 How to obtain an appeal. An appeal shall be made in writing and filed with the Division or the office of inspection for the type of tobacco involved. Such...

  7. Investigating Molecular Interactions

    DEFF Research Database (Denmark)

    Clausen, Henrik Fanø

    2010-01-01

    ···π interactions are accommodated by electrostatic complementarity. The crystal structure of both the α- and the β-polymorph of hydroquinone is presented in Chapter 6 with focus on close intermolecular contacts between the molecules via Hirshfeld surface analysis. The charge density distribution of the empty β....... The last chapter of this dissertation presents the analysis of intermolecular interaction using both the Hirshfeld surface and charge density distribution of the acetonitrile β-hydroquinone clathrate. The local packing and related close contacts are examined by breakdown of the fingerprint plots revealing......, are also introduced, as a goal of the analysis of charge density distributions is to obtain further understanding of these macroscopic properties. Neutron diffraction will be used as a complementary tool to the X-ray diffraction experiment, as positional and thermal parameters of hydrogen atoms can...

  8. Mathematical models for correction of images, obtained at radioisotope scan

    International Nuclear Information System (INIS)

    Glaz, A.; Lubans, A.

    2002-01-01

    The images, which obtained at radioisotope scintigraphy, contain distortions. Distortions appear as a result of absorption of radiation by patient's body's tissues. Two mathematical models for reducing of such distortions are proposed. Image obtained by only one gamma camera is used in the first mathematical model. Unfortunately, this model allows processing of the images only in case, when it can be assumed, that the investigated organ has a symmetric form. The images obtained by two gamma cameras are used in the second model. It gives possibility to assume that the investigated organ has non-symmetric form and to acquire more precise results. (authors)

  9. The ion-exchange obtaining of high purity samarium oxide

    International Nuclear Information System (INIS)

    Brzyska, W.; Soltysiak, I.; Cygan, J.

    1987-01-01

    The use of lactic acid - EDTA mixture as an eluent for the obtaining of high purity samarium oxide was studied. The studies were carried out at room temperature on cation exchange resin Wofatit KPS X 8. The best results were obtained for lactic acid (0,26 mol/dm 3 ) - EDTA (0,013 mol/dm 3 ) mixture at pH 3,3. As the result of 57% samarium concentrate elution with column load 1:3 and flow rate 0,4 cm/min, over 99% pure samarium oxide with 73% yield has been obtained. The yield of spectrally pure Sm 2 O 3 exceeded 45%. (author)

  10. Wood-Polymer composites obtained by gamma irradiation

    International Nuclear Information System (INIS)

    Gago, J.; Lopez, A.; Rodriguez, J.; Santiago, J.; Acevedo, M.

    2007-01-01

    In this work we impregnate three Peruvian woods (Calycophy spruceanum Be, Aniba amazonica Meiz and Hura crepitans L) with styrene-polyester resin and methyl methacrylate. The polymerization of the system was promoted by gamma radiation and the experimental optimal condition was obtained with styrene-polyester 1:1 and 15 kGy. The obtained composites show reduced water absorption and better mechanical properties compared to the original wood. The structure of the wood-polymer composites was studied by light microscopy. Water absorption and hardness were also obtained

  11. Wood-Polymer composites obtained by gamma irradiation

    Science.gov (United States)

    Gago, J.; López, A.; Santiago, J.; Acevedo, M.; Rodríguez, J.

    2007-10-01

    In this work we impregnate three Peruvian woods (Calycophy spruceanum Be, Aniba amazonica Meiz and Hura crepitans L) with styrene-polyester resin and methyl methacrylate. The polymerization of the system was promoted by gamma radiation and the experimental optimal condition was obtained with styrene-polyester 1:1 and 15 kGy. The obtained composites show reduced water absorption and better mechanical properties compared to the original wood. The structure of the wood-polymer composites was studied by light microscopy. Water absorption and hardness were also obtained.

  12. Uses of phage display in agriculture: a review of food-related protein-protein interactions discovered by biopanning over diverse baits.

    Science.gov (United States)

    Kushwaha, Rekha; Payne, Christina M; Downie, A Bruce

    2013-01-01

    This review highlights discoveries made using phage display that impact the use of agricultural products. The contribution phage display made to our fundamental understanding of how various protective molecules serve to safeguard plants and seeds from herbivores and microbes is discussed. The utility of phage display for directed evolution of enzymes with enhanced capacities to degrade the complex polymers of the cell wall into molecules useful for biofuel production is surveyed. Food allergies are often directed against components of seeds; this review emphasizes how phage display has been employed to determine the seed component(s) contributing most to the allergenic reaction and how it has played a central role in novel approaches to mitigate patient response. Finally, an overview of the use of phage display in identifying the mature seed proteome protection and repair mechanisms is provided. The identification of specific classes of proteins preferentially bound by such protection and repair proteins leads to hypotheses concerning the importance of safeguarding the translational apparatus from damage during seed quiescence and environmental perturbations during germination. These examples, it is hoped, will spur the use of phage display in future plant science examining protein-ligand interactions.

  13. Uses of Phage Display in Agriculture: A Review of Food-Related Protein-Protein Interactions Discovered by Biopanning over Diverse Baits

    Directory of Open Access Journals (Sweden)

    Rekha Kushwaha

    2013-01-01

    Full Text Available This review highlights discoveries made using phage display that impact the use of agricultural products. The contribution phage display made to our fundamental understanding of how various protective molecules serve to safeguard plants and seeds from herbivores and microbes is discussed. The utility of phage display for directed evolution of enzymes with enhanced capacities to degrade the complex polymers of the cell wall into molecules useful for biofuel production is surveyed. Food allergies are often directed against components of seeds; this review emphasizes how phage display has been employed to determine the seed component(s contributing most to the allergenic reaction and how it has played a central role in novel approaches to mitigate patient response. Finally, an overview of the use of phage display in identifying the mature seed proteome protection and repair mechanisms is provided. The identification of specific classes of proteins preferentially bound by such protection and repair proteins leads to hypotheses concerning the importance of safeguarding the translational apparatus from damage during seed quiescence and environmental perturbations during germination. These examples, it is hoped, will spur the use of phage display in future plant science examining protein-ligand interactions.

  14. Method for obtaining a varnish with a base of mineral oil obtained by distillation of bituminous schists

    Energy Technology Data Exchange (ETDEWEB)

    Marchionni, A

    1945-07-24

    A method for obtaining a varnish is described characterized by the fact that the following ingredients are being used; mineral oil from the distillation of bituminous schists in the proportions already cited in the description, diluted with benzene or turpentine, with admixture of coloring matter. Varnish with a base of mineral oil from the distillation of bituminous schists is obtained.

  15. Interactive Workspaces

    DEFF Research Database (Denmark)

    Mogensen, Preben Holst

    augmented reality, interactive building elements, and mobile devices to support new ways of working in a diversity of application domains with work situations ranging from individual work, through local collaboration, to distributed collaboration. The work situations may take place in offices/project rooms......Many application domains such as architecture, engineering, industrial design, city planning, environmental supervision, health care etc. share the properties of users working collaboratively with complex mixtures of physical and digital materials. Studies in such domains show that it is hard...... to maintain and integrate these heterogeneous materials in traditional desktop computing environments. Our thesis is that pervasive computing technologies can be developed to support a more natural user collaboration in a rich variety of application. This may be achieved by going beyond the traditional...

  16. Electromagnetic interactions

    International Nuclear Information System (INIS)

    Bosanac, Slobodan Danko

    2016-01-01

    This book is devoted to theoretical methods used in the extreme circumstances of very strong electromagnetic fields. The development of high power lasers, ultrafast processes, manipulation of electromagnetic fields and the use of very fast charged particles interacting with other charges requires an adequate theoretical description. Because of the very strong electromagnetic field, traditional theoretical approaches, which have primarily a perturbative character, have to be replaced by descriptions going beyond them. In the book an extension of the semi-classical radiation theory and classical dynamics for particles is performed to analyze single charged atoms and dipoles submitted to electromagnetic pulses. Special attention is given to the important problem of field reaction and controlling dynamics of charges by an electromagnetic field.

  17. Electroweak interactions

    International Nuclear Information System (INIS)

    Bjorken, J.D.

    1980-10-01

    A point of view of the electroweak interaction is presented. It begins phenomenologically and moves in stages toward the conventional gauge theory formalism containing elementary scalar Higgs-fields and then beyond. The purpose in so doing is that the success of the standard SU(2) x U(1) theory in accounting for low energy phenomena need not automatically imply success at high energies. It is deemed unlikely by most theorists that the predicted W +- or Z 0 does not exist or does not have the mass and/or couplings anticipated in the standard model. However, the odds that the standard predictions will work are not 100%. Therefore there is some reason to look at the subject as one would were he forced by a wrong experimental outcome - to go back to fundamentals and ascertain what is the minimal amount of theory necessary to account for the data

  18. On topological RNA interaction structures.

    Science.gov (United States)

    Qin, Jing; Reidys, Christian M

    2013-07-01

    Recently a folding algorithm of topological RNA pseudoknot structures was presented in Reidys et al. (2011). This algorithm folds single-stranded γ-structures, that is, RNA structures composed by distinct motifs of bounded topological genus. In this article, we set the theoretical foundations for the folding of the two backbone analogues of γ structures: the RNA γ-interaction structures. These are RNA-RNA interaction structures that are constructed by a finite number of building blocks over two backbones having genus at most γ. Combinatorial properties of γ-interaction structures are of practical interest since they have direct implications for the folding of topological interaction structures. We compute the generating function of γ-interaction structures and show that it is algebraic, which implies that the numbers of interaction structures can be computed recursively. We obtain simple asymptotic formulas for 0- and 1-interaction structures. The simplest class of interaction structures are the 0-interaction structures, which represent the two backbone analogues of secondary structures.

  19. Treatment of biomass to obtain a target chemical

    Science.gov (United States)

    Dunson, Jr., James B.; Tucker, III, Melvin P.; Elander, Richard T.; Hennessey, Susan Marie

    2010-08-24

    Target chemicals were produced using biocatalysts that are able to ferment sugars derived from treated biomass. Sugars were obtained by pretreating biomass under conditions of high solids and low ammonia concentration, followed by saccharification.

  20. Process modifications of obtaining Tc-99m by solvent extraction

    International Nuclear Information System (INIS)

    Leon, A.; Verdera, S.

    1978-01-01

    This paper describes a modification in the process to obtaining Tc-99m by the extraction method of solvent from Mo-99 produced by irradiation. Tc-99m is considered an ideal radionuclide for medical and biological applications

  1. Synthesis and characterization of zinc ferrite nanoparticles obtained ...

    Indian Academy of Sciences (India)

    Administrator

    (Hamdeh et al 1997), hydrothermal technique (Toledo-. Antonio and ... heptahydrate/zinc nitrate and oxalic acid were dissolved in minimum quantity of water and was stirred well. The respective metal oxalate precipitate obtained was filtered.

  2. High purity zirconium obtainment through the iodine compounds transport method

    International Nuclear Information System (INIS)

    Bolcich, J.C.; Zuzek, E.; Dutrus, S.M.; Corso, H.L.

    1987-01-01

    This paper describes the experimental method and the equipment designed, constructed and actually applied for the high purity zirconium obtainment from a zirconium sponge of the nuclear type. The mechanism of purification is based on the impure metal attack with gaseous iodine (at 200 deg C) to obtain zirconium tetra iodine as main product which is then transformed into a pure zirconium base (at 1000-1300 deg C), precipitating the metallic zirconium and releasing the gaseous iodine. From the first experiences carried out, pure zirconium has been obtained from an initial filament of 0.5 mm of diameter as well as wires up to 2.5 mm of diameter. This work presents the results from the studies and analysis made to characterize the material obtained. Finally, the refining methods to which the zirconium produced may be submitted so as to optimize the final purity are discussed. (Author)

  3. 27 CFR 17.103 - Bonds obtained from surety companies.

    Science.gov (United States)

    2010-04-01

    ... its liability, in terms upon the face of the bond, to a definite, specified amount. This amount shall... obtained from: Surety Bond Branch, Financial Management Service, Department of the Treasury, Washington, DC...

  4. Lambing results obtained with imported Ile de France rarn semen

    African Journals Online (AJOL)

    insemination was carried out either 54,5 h (fixed time single ... Table 1 Conception rate obtained using two batches of frozen lle de France ... Pregnant mare serum gonadotrophin (Fostim, 300 ... Effect of initial freezing temperature, addition.

  5. Process optimization for obtaining nano cellulose from curaua fiber

    International Nuclear Information System (INIS)

    Lunz, Juliana do N.; Cordeiro, Suellem B.; Mota, Jose Carlos F.; Marques, Maria de Fatima V.

    2011-01-01

    This study focuses on the methodology for optimization to obtain nanocellulose from vegetal fibers. An experimental planning was carried out for the treatment of curaua fibers and parameters were estimated, having the concentration of H 2 SO 4 , hydrolysis time, reaction temperature and time of sonication applied as independent variables for further statistical analysis. According to the estimated parameters, the statistically significant effects were determined for the process of obtaining nanocellulose. According to the results obtained from the thermogravimetric analysis (TGA) it was observed that certain conditions led to cellulose with degradation temperatures near or even above that of untreated cellulose fibers. The crystallinity index (IC) obtained after fiber treatment (X-ray diffraction) were higher than that of the pure fiber. Treatments with high acid concentrations led to higher IC. (author)

  6. Acclimatization of Phalaenopsis and Cattleya obtained by micropropagation

    OpenAIRE

    Lucía Primitiva Díaz; Jorge Julio Namur; Sebastián Agustín Bollati; Osvaldo Ernesto Antonio Arce

    2010-01-01

    Título en español: Aclimatización de Phalaenopsis y Cattleya obtenidas por micropropagación ABSTRACT The quality of micropropagated plants relies on the acclimatization stage. This research intends to develop an efficient protocol to obtain the acclimatization of Phalaenopsis and Cattleya. Plants of Phalaenopsis obtained from protocorms were selected. They came from flowering stalks grown at modified Murashige and Skoog (MS) (1962) medium and classified by growth ranks and put into mo...

  7. First donation of human skin obtained from corpse

    International Nuclear Information System (INIS)

    Reyes F, M.L.; Luna Z, D.

    2007-01-01

    The first donation of human skin coming from a cadaverous donor was obtained in the State of Mexico. The skin was obtained of a 34 year-old multi organic donor, the extraction of the same was carried out in an operating theatre by medical personnel, supported by personal of the Radio sterilized Tissue Bank (BTR) of the ININ. The skin was transported to the BTR for it processing. (Author)

  8. Perovskite type nanopowders and thin films obtained by chemical methods

    Directory of Open Access Journals (Sweden)

    Viktor Fruth

    2010-09-01

    Full Text Available The review presents the contribution of the authors, to the preparation of two types of perovskites, namely BiFeO3 and LaCoO3, by innovative methods. The studied perovskites were obtained as powders, films and sintered bodies. Their complex structural and morphological characterization is also presented. The obtained results have underlined the important influence of the method of preparation on the properties of the synthesized perovskites.

  9. Thermoluminescence properties of zinc oxide obtained by solution combustion synthesis

    Energy Technology Data Exchange (ETDEWEB)

    Orante B, V. R.; Escobar O, F. M.; Cruz V, C. [Universidad de Sonora, Departamento de Investigacion en Polimeros y Materiales, Apdo. Postal 130, 83000 Hermosillo, Sonora (Mexico); Bernal, R., E-mail: victor.orante@polimeros.uson.mx [Universidad de Sonora, Departamento de Investigacion en Fisica, Apdo. Postal 5-088, 83190 Hermosillo, Sonora (Mexico)

    2014-08-15

    High-dose thermoluminescence dosimetry properties of novel zinc oxide obtained by solution combustion synthesis in a glycine-nitrate process, with a non-stoichiometric value of the elemental stoichiometric coefficient (Φ{sub c}) are presented in this work. Zn O powder samples obtained were annealed afterwards at 900 grades C during 2 h in air. Sintered particles of sizes between ∼ 0.5 and ∼ 2 μm were obtained, according to scanning electron microscopy results. X-ray diffraction indicates the presence of the hexagonal phase of Zn O for the powder samples obtained, before and after thermal annealing, without any remaining nitrate peaks observed. Thermoluminescence glow curves of Zn O obtained after being exposed to beta radiation consists of two maxima; one located at ∼ 149 grades C and another at ∼ 308 grades C, being the latter the dosimetric component of the curve. Dosimetric characterization of non-stoichiometric zinc oxide provided experimental evidence like asymptotic behavior of the Tl signal fading for times greater than 16 h between irradiation and the corresponding Tl readout, as well as the linear behaviour of the dose response without saturation in the dose interval studied (from 12.5 up to 400 Gy). Such characteristics place Zn O phosphors obtained in this work as a promising material for high-dose radiation dosimetry applications (e.g., radiotherapy and food industry). (author)

  10. Thermoluminescence properties of zinc oxide obtained by solution combustion synthesis

    International Nuclear Information System (INIS)

    Orante B, V. R.; Escobar O, F. M.; Cruz V, C.; Bernal, R.

    2014-08-01

    High-dose thermoluminescence dosimetry properties of novel zinc oxide obtained by solution combustion synthesis in a glycine-nitrate process, with a non-stoichiometric value of the elemental stoichiometric coefficient (Φ c ) are presented in this work. Zn O powder samples obtained were annealed afterwards at 900 grades C during 2 h in air. Sintered particles of sizes between ∼ 0.5 and ∼ 2 μm were obtained, according to scanning electron microscopy results. X-ray diffraction indicates the presence of the hexagonal phase of Zn O for the powder samples obtained, before and after thermal annealing, without any remaining nitrate peaks observed. Thermoluminescence glow curves of Zn O obtained after being exposed to beta radiation consists of two maxima; one located at ∼ 149 grades C and another at ∼ 308 grades C, being the latter the dosimetric component of the curve. Dosimetric characterization of non-stoichiometric zinc oxide provided experimental evidence like asymptotic behavior of the Tl signal fading for times greater than 16 h between irradiation and the corresponding Tl readout, as well as the linear behaviour of the dose response without saturation in the dose interval studied (from 12.5 up to 400 Gy). Such characteristics place Zn O phosphors obtained in this work as a promising material for high-dose radiation dosimetry applications (e.g., radiotherapy and food industry). (author)

  11. Health Outcomes of Obtaining Housing Among Older Homeless Adults

    Science.gov (United States)

    Miao, Yinghui; Mitchell, Susan L.; Bharel, Monica; Patel, Mitkumar; Ard, Kevin L.; Grande, Laura J.; Blazey-Martin, Deborah; Floru, Daniella; Steinman, Michael A.

    2015-01-01

    Objectives. We determined the impact of obtaining housing on geriatric conditions and acute care utilization among older homeless adults. Methods. We conducted a 12-month prospective cohort study of 250 older homeless adults recruited from shelters in Boston, Massachusetts, between January and June 2010. We determined housing status at follow-up, determined number of emergency department visits and hospitalizations over 12 months, and examined 4 measures of geriatric conditions at baseline and 12 months. Using multivariable regression models, we evaluated the association between obtaining housing and our outcomes of interest. Results. At 12-month follow-up, 41% of participants had obtained housing. Compared with participants who remained homeless, those with housing had fewer depressive symptoms. Other measures of health status did not differ by housing status. Participants who obtained housing had a lower rate of acute care use, with an adjusted annualized rate of acute care visits of 2.5 per year among participants who obtained housing and 5.3 per year among participants who remained homeless. Conclusions. Older homeless adults who obtained housing experienced improved depressive symptoms and reduced acute care utilization compared with those who remained homeless. PMID:25973822

  12. Designing "Interaction": How Do Interaction Design Students Address Interaction?

    Science.gov (United States)

    Karlgren, Klas; Ramberg, Robert; Artman, Henrik

    2016-01-01

    Interaction design is usually described as being concerned with interactions with and through artifacts but independent of a specific implementation. Design work has been characterized as a conversation between the designer and the situation and this conversation poses a particular challenge for interaction design as interactions can be elusive…

  13. Comparison of different methodologies for obtaining nickel nanoferrites

    Energy Technology Data Exchange (ETDEWEB)

    Galindo, R.; Menendez, N. [Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, E-28049 Madrid (Spain); Crespo, P.; Velasco, V. [Instituto de Magnetismo Aplicado, UCM, ADIF CSIC, E-28230 Madrid (Spain); Bomati-Miguel, O.; Díaz-Fernández, D. [Departamento de Física Aplicada and Instituto Nicolás Cabrera, Facultad de Ciencias Universidad Autónoma de Madrid, Cantoblanco, E-28049 Madrid (Spain); Herrasti, P., E-mail: pilar.herrasti@uam.es [Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, E-28049 Madrid (Spain)

    2014-06-01

    Nickel nanoferrites were obtained by means of four different synthetic wet-routes: co-precipitation (CP), sonochemistry (SC), sonoelectrochemistry (SE) and electrochemistry (E). The influence of the synthesis method on the structural and magnetic properties of nickel ferrite nanoparticles is studied. Although similar experimental conditions such as temperature, pH and time of synthesis were used, a strong dependence of composition and microstructure on the synthesis procedure is found, as electron microscopy, X-ray diffraction and Mössbauer spectroscopy studies reveal. Whereas by means of the CP and SC methods particles of a small size around 5–10 nm, respectively, and composed by different phases are obtained, the electrochemical routes (E and SE) allow obtaining monodisperse nanoparticles, with sizes ranging from 30 to 40 nm, and very close to stoichiometry. Magnetic characterization evidences a superparamagnetic behavior for samples obtained by CP and SC methods, whereas the electrochemical route leads to ferromagnetic ferrite nanoparticles. - Highlights: • Electrochemical synthesis produces pure NiFe{sub 2}O{sub 4} nanonoparticles with 40 nm particle size. • Coprecipitation and sonochemistry techniques generate NiFe{sub 2}O{sub 4} nanoparticles with impurities. • Nanoparticles obtained by coprecipitation and sonochemistry are superparamagnetic. • Electrochemical and sonoelectrochemical methods produce ferromagnetic nanoparticles.

  14. Entropy in molecular recognition by proteins.

    Science.gov (United States)

    Caro, José A; Harpole, Kyle W; Kasinath, Vignesh; Lim, Jackwee; Granja, Jeffrey; Valentine, Kathleen G; Sharp, Kim A; Wand, A Joshua

    2017-06-20

    Molecular recognition by proteins is fundamental to molecular biology. Dissection of the thermodynamic energy terms governing protein-ligand interactions has proven difficult, with determination of entropic contributions being particularly elusive. NMR relaxation measurements have suggested that changes in protein conformational entropy can be quantitatively obtained through a dynamical proxy, but the generality of this relationship has not been shown. Twenty-eight protein-ligand complexes are used to show a quantitative relationship between measures of fast side-chain motion and the underlying conformational entropy. We find that the contribution of conformational entropy can range from favorable to unfavorable, which demonstrates the potential of this thermodynamic variable to modulate protein-ligand interactions. For about one-quarter of these complexes, the absence of conformational entropy would render the resulting affinity biologically meaningless. The dynamical proxy for conformational entropy or "entropy meter" also allows for refinement of the contributions of solvent entropy and the loss in rotational-translational entropy accompanying formation of high-affinity complexes. Furthermore, structure-based application of the approach can also provide insight into long-lived specific water-protein interactions that escape the generic treatments of solvent entropy based simply on changes in accessible surface area. These results provide a comprehensive and unified view of the general role of entropy in high-affinity molecular recognition by proteins.

  15. DEXTRINIZED SYRUPS OBTAINING THROUGH THE ENZYMATIC HYDROLYSIS OF SORGHUM STARCH

    Directory of Open Access Journals (Sweden)

    Leyanis Rodríguez Rodríguez

    2015-10-01

    Full Text Available The main objective of this work was the production of syrups dextrinized by enzymatic hydrolysis of starch red sorghum CIAPR-132 using α-amylase on solutions at different concentrations, with different concentrations of enzyme and enzyme hydrolysis time. The response variable was the dextrose equivalent in each obtained syrup (ED using the modified Lane-Eynon method. In some of the experiments, we used a full factorial design 23 and in others we worked with intermediate concentration and higher hydrolysis time with different levels of enzyme. The obtained products were syrups dextrinized ED between 10,25 and 33,97% (values we can find within the established ones for these types of syrups, which can be used for their functional properties as intermediates syrups or as raw material for different processes of the food industry. This allows you to set a pattern for the use of sorghum feedstock in unconventional obtaining products from its starch.

  16. Modelling of classical ghost images obtained using scattered light

    International Nuclear Information System (INIS)

    Crosby, S; Castelletto, S; Aruldoss, C; Scholten, R E; Roberts, A

    2007-01-01

    The images obtained in ghost imaging with pseudo-thermal light sources are highly dependent on the spatial coherence properties of the incident light. Pseudo-thermal light is often created by reducing the coherence length of a coherent source by passing it through a turbid mixture of scattering spheres. We describe a model for simulating ghost images obtained with such partially coherent light, using a wave-transport model to calculate the influence of the scattering on initially coherent light. The model is able to predict important properties of the pseudo-thermal source, such as the coherence length and the amplitude of the residual unscattered component of the light which influence the resolution and visibility of the final ghost image. We show that the residual ballistic component introduces an additional background in the reconstructed image, and the spatial resolution obtainable depends on the size of the scattering spheres

  17. Nanocrystalline and ultrafine grain copper obtained by mechanical attrition

    Directory of Open Access Journals (Sweden)

    Rodolfo Rodríguez Baracaldo

    2010-01-01

    Full Text Available This article presents a method for the sample preparation and characterisation of bulk copper having grain size lower than 1 μm (ultra-fine grain and lower than 100 nm grain size (nanocrystalline. Copper is initially manufactured by a milling/alloying me- chanical method thereby obtaining a powder having a nanocrystalline structure which is then consolidated through a process of warm compaction at high pressure. Microstructural characterisation of bulk copper samples showed the evolution of grain size during all stages involved in obtaining it. The results led to determining the necessary conditions for achieving a wide range of grain sizes. Mechanical characterisation indicated an increase in microhardness to values of around 3.40 GPa for unconsolida- ted nanocrystalline powder. Compressivee strength was increased by reducing the grain size, thereby obtaining an elastic limit of 650 MPa for consolidated copper having a ~ 62 nm grain size.

  18. Technical and technological solution for vegetal bio-stimulants obtaining

    Science.gov (United States)

    Anghelache, D. G.; Diaconescu, I.; Pătraşcu, R.

    2017-08-01

    The paper presents a modern technology for bio fertilizers resulted from waste plant mass after harvesting crops Experimental products were obtained rich in nutrients, but unstable in terms of existing microorganisms. Therefore, they conducted further studies to obtaining bio fungicide herb, so in all investigations undertaken so far in the laboratory, were able to conclude that the introduction of medicinal plant extracts with fungicidal effect into the bio fertilizers obtained by degradation of plant material post-harvest can get various bio-stimulants with nourishing effect upon the plants. Following this technology the paper’s objective is to identify a flux scheme for experimental equipment which can produce as final outcome this type of bio-stimulant. Also, in this work, this equipment will be chosen and will be designed following and obeying to the request of every step of the above technology.

  19. Biodiesel obtained from soapstock originated in a refining oil industry

    International Nuclear Information System (INIS)

    Tobio Pérez, Indira; Díaz Domínguez, Yosvany; Piloto-Rodríguez, Ramón

    2017-01-01

    In the vegetable oil chemical refining process is obtained a by-product commonly named as soapstock, due to its physical and aspect properties. The soapstock free fatty acid content can reach to 50%. The present work shows a survey of researches focused on biodiesel obtaining from this by-product. The biodiesel is obtained following different routes and catalyzers features. A variety of reports shown the effectivity of the use of this by-product derived from vegetable oil refining industry to produce biodiesel. Several studies are addressed to the acid oil recovering involving processes without soapstock acidulation, with the aim of lowering costs and finding more attractive yields closing to the concept of zero wastes. (author)

  20. Analysis of ADU structure obtained under different precipitation conditions

    International Nuclear Information System (INIS)

    Ramella, Jose L.; Esteban, Adolfo; Mendez De Leo, Lucia P.; Sassone, Ariel; Novara, Oscar E.; Boero, Norma L.; Leyva, Ana G.

    1999-01-01

    ADU is the nominal name for ammonium poly uranate. It is a very complex compound of polymeric structure, which may have, according to precipitation conditions, different chemical composition and crystallographic structure. ADU is used as uranium oxide precursor in the manufacture of fuel elements. In former papers it was proved that if ultrasound is applied during precipitation and digestion the characteristics of the final product (U 3 O 8 UO 2 ) improve. By studying ADU thermal decomposition obtained by ultrasonic application, it was intended to obtain its composition. Therefore, differential thermal gravimetric and differential thermal analyses were performed. Samples were taken from special points and analyzed by X-ray diffraction, infra-red spectroscopy and scanning. An experiment was also designed to identify the products released during heating. Results and conclusions obtained are presented in this work. (author)

  1. Nanostructured films of metal particles obtained by laser ablation

    Energy Technology Data Exchange (ETDEWEB)

    Muniz-Miranda, M., E-mail: muniz@unifi.it [Dipartimento di Chimica “U. Schiff”, Università di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino (Italy); Gellini, C. [Dipartimento di Chimica “U. Schiff”, Università di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino (Italy); Giorgetti, E.; Margheri, G.; Marsili, P. [Istituto Sistemi Complessi (CNR), Via Madonna del Piano 10, 50019 Sesto Fiorentino (Italy); Lascialfari, L.; Becucci, L. [Dipartimento di Chimica “U. Schiff”, Università di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino (Italy); Trigari, S. [Istituto Sistemi Complessi (CNR), Via Madonna del Piano 10, 50019 Sesto Fiorentino (Italy); Giammanco, F. [Dipartimento di Fisica “E. Fermi”, Università di Pisa, Largo Pontecorvo 3, 56127 Pisa (Italy)

    2013-09-30

    Colloidal dispersions of silver and gold nanoparticles were obtained in pure water by ablation with nanosecond pulsed laser. Then, by filtration of the metal particles on alumina, we fabricated nanostructured films, whose surface morphology was examined by atomic force microscopy (AFM) and related to surface-enhanced Raman scattering (SERS) after adsorption of adenine. - Highlights: • Ag and Au colloidal nanoparticles were obtained by laser ablation. • Nanostructured Ag and Au films were fabricated by filtration of metal nanoparticles. • Surface morphology of metal films was investigated by atomic force microscopy. • Surface-enhanced Raman spectra (SERS) of adenine on metal films were obtained. • SERS enhancements were related to the surface roughness of the metal films.

  2. Modelling of classical ghost images obtained using scattered light

    Energy Technology Data Exchange (ETDEWEB)

    Crosby, S; Castelletto, S; Aruldoss, C; Scholten, R E; Roberts, A [School of Physics, University of Melbourne, Victoria, 3010 (Australia)

    2007-08-15

    The images obtained in ghost imaging with pseudo-thermal light sources are highly dependent on the spatial coherence properties of the incident light. Pseudo-thermal light is often created by reducing the coherence length of a coherent source by passing it through a turbid mixture of scattering spheres. We describe a model for simulating ghost images obtained with such partially coherent light, using a wave-transport model to calculate the influence of the scattering on initially coherent light. The model is able to predict important properties of the pseudo-thermal source, such as the coherence length and the amplitude of the residual unscattered component of the light which influence the resolution and visibility of the final ghost image. We show that the residual ballistic component introduces an additional background in the reconstructed image, and the spatial resolution obtainable depends on the size of the scattering spheres.

  3. Acid formic effect in zinc coatings obtained by galvanostatic deposition

    International Nuclear Information System (INIS)

    Lopes, C.; David, M.; Souza, E.C.

    2016-01-01

    Zinc deposits obtained from electrodeposition is widely used for the purpose of protecting steel substrates from corrosion. They are generally added to Zn deposition bath many additives for improving certain characteristics of the deposit. As far as is known there is no information in literature about the effect of formic acid in corrosion resistance of a Zn deposit. Because it is an acid additive, it has the use of cyclohexylamine, in order for the electrolytic bath continue with a pH equal to the one used commercially, around 5. The main goal of this study is analyze the effect of the formic acid addition in the corrosion resistance of an Zn electrodeposition obtained by galvanostatic deposition. The results obtained by performance tests, cyclic voltammetry and X-ray diffraction showed that the formic acid addition may be promising in combating the corrosion of materials. (author)

  4. Vibrational properties of gold nanoparticles obtained by green synthesis

    Science.gov (United States)

    Alvarez, Ramón A. B.; Cortez-Valadez, M.; Bueno, L. Oscar Neira; Britto Hurtado, R.; Rocha-Rocha, O.; Delgado-Beleño, Y.; Martinez-Nuñez, C. E.; Serrano-Corrales, Luis Ivan; Arizpe-Chávez, H.; Flores-Acosta, M.

    2016-10-01

    This study reports the synthesis and characterization of gold nanoparticles through an ecological method to obtain nanostructures from the extract of the plant Opuntia ficus-indica. Colloidal nanoparticles show sizes that vary between 10-20 nm, and present various geometric morphologies. The samples were characterized through optical absorption, Raman Spectroscopy and Transmission Electron Microscopy (TEM). Additionally, low energy metallic clusters of Aun (n=2-20 atoms) were modeled by computational quantum chemistry. The theoretical results were obtained with Density Functional Theory (DFT). The predicted results of Au clusters show a tendency and are correlated with the experimental results concerning the optical absorption bands and Raman spectroscopy in gold nanoparticles.

  5. UO2 microspheres obtainment through the internal gelation methods

    International Nuclear Information System (INIS)

    Sterba, M.E.; Gomez Constenla, A.

    1987-01-01

    UO 2 microspheres obtainment process through the internal gelation method which allows the spheres' obtainment of uniform size is detailed herein, varying the same among 0.3 and 1.7 mm of diameter. The sintered density reaches 10.78 g/cm 3 , permitting the fuels fabrication dispersed and vibro-compacted fuels. The trichloroethylene use implementation as gelation agent is described, thus reducing the number of stages in the microspheres fabrication. At the same time, the uranium sun composition has been modified so as to be compatible with the use solvent. (Author)

  6. Preparative method to obtain ursolic acid from Clinopodium revolutum

    Directory of Open Access Journals (Sweden)

    Michael Azael Ludeña Huaman

    2018-01-01

    Full Text Available A method to obtain ursolic acid (UA in an easy, fast, and economical way was proposed, having as raw material the medicinal plant Clinopodium revolutum from Peru. This plant is known and marketed as flor de arena or té indio. The selective recrystallization technique used was efficient due to UA crystals were obtained without the need for chromatographic purification methods neither the use of toxic solvents. The purity determined by HPLC is greater than 95%. Thus, the flor de arena becomes an important biosource of this compound.

  7. GHM method for obtaining rationalsolutions of nonlinear differential equations.

    Science.gov (United States)

    Vazquez-Leal, Hector; Sarmiento-Reyes, Arturo

    2015-01-01

    In this paper, we propose the application of the general homotopy method (GHM) to obtain rational solutions of nonlinear differential equations. It delivers a high precision representation of the nonlinear differential equation using a few linear algebraic terms. In order to assess the benefits of this proposal, three nonlinear problems are solved and compared against other semi-analytic methods or numerical methods. The obtained results show that GHM is a powerful tool, capable to generate highly accurate rational solutions. AMS subject classification 34L30.

  8. Improved dielectric functions in metallic films obtained via template stripping

    Science.gov (United States)

    Hyuk Park, Jong; Nagpal, Prashant; Oh, Sang-Hyun; Norris, David J.

    2012-02-01

    We compare the dielectric functions of silver interfaces obtained via thermal evaporation with those obtained with template stripping. Ellipsometry measurements show that the smoother template-stripped surfaces exhibit effective dielectric functions with a more negative real component and a smaller imaginary component, implying higher conductivity and less energy loss, respectively. These results agree with the relation between dielectric function and surface roughness derived from combining the effective-medium model and the Drude-Lorentz model. The improvement in the effective dielectric properties shows that metallic films prepared via template stripping can be favorable for applications in electronics, nanophotonics, and plasmonics.

  9. Photocatalysis application of zinc oxide fibers obtained by electrospinning

    International Nuclear Information System (INIS)

    Gerchman, D.; Alves, A.K.; Berutti, F.A.; Bergmann, C.P.

    2010-01-01

    Using the electrospinning technique, composite fibers of polyvinylbutyral and zinc nitrate were obtained. After a heat treatment at 600 deg C, nanostructured zinc oxide fibers were obtained. The fibers were characterized using X ray diffraction. The photocatalytic activity of the nanostructured fibers was determined using the photodegradation of a methyl orange solution. The increase in the heat treatment temperature decreases the photoactivity of the zinc oxide. The heat treatment, the phases and the surface area, affect the physical, chemical and photocatalytic activity of the zinc oxide. (author)

  10. The use of nuclear energy for obtaining petroleum

    International Nuclear Information System (INIS)

    Waldmann, H.; Koch, C.; Thelen, H.J.; Kappe, P.

    1982-01-01

    After some basic considerations of petroleum demand, petroleum supply and petroleum reserves, the article gives a survey of the various methods of obtaining petroleum. The use of energy in the form of steam and electricity in the previously used processes and in conventional deposits requires up to 50% of the energy contained in the oil obtained. Now unconventional sources of petroleum (tertiary petroleum, heavy fractions and shale oil) could become of interest to West Germany in the near future. The economy of production can be determined by the energy source used, to a large extent. A series of possibilities are discussed for using nuclear steam raising systems for this purpose. (UA) [de

  11. Clinical value of renal images obtained incidentally to bone scintigraphy

    International Nuclear Information System (INIS)

    Ohishi, Y.; Machida, T.; Miki, M.; Kido, A.; Tanaka, A.

    1982-01-01

    Various studies were made on 400 renal (including 325 clinical cases) observed during whole-body bone scintigraphy using 99mTc-MDP. Asymmetrical renal images in bone scintigrams were obtained from 40% of the urologic patients and 7.5% of the nonurologic patients. Out of the asymmetrical images of the urologic patients, 50% provided nonvisualized kidneys and 35% showed unilateral renal high accumulation. It can be said from the above that renal images incidentally obtained during whole-body bone scintigraphy should not be overlooked

  12. Bio-inspired method to obtain multifunctional dynamic nanocomposites

    Science.gov (United States)

    Kushner, Aaron M.; Guan, Zhibin; Williams, Gregory; Chen, Yulin

    2018-04-10

    A method for a polymeric or nanocomposite material. The method includes assembling a multiphase hard-soft structure, where the structure includes a hard micro- or nano-phase, and a soft micro- or nano-phase that includes a polymeric scaffold. In the method, the polymeric scaffold includes dynamically interacting motifs and has a glass transition temperature (T.sub.g) lower than the intended operating temperature of the material.

  13. The colours of strong interaction

    International Nuclear Information System (INIS)

    1995-01-01

    The aim of this session is to draw a consistent framework about the different ways to consider strong interaction. A large part is dedicated to theoretical work and the latest experimental results obtained at the first electron collider HERA are discussed. (A.C.)

  14. Visualizing 3D data obtained from microscopy on the Internet.

    Science.gov (United States)

    Pittet, J J; Henn, C; Engel, A; Heymann, J B

    1999-01-01

    The Internet is a powerful communication medium increasingly exploited by business and science alike, especially in structural biology and bioinformatics. The traditional presentation of static two-dimensional images of real-world objects on the limited medium of paper can now be shown interactively in three dimensions. Many facets of this new capability have already been developed, particularly in the form of VRML (virtual reality modeling language), but there is a need to extend this capability for visualizing scientific data. Here we introduce a real-time isosurfacing node for VRML, based on the marching cube approach, allowing interactive isosurfacing. A second node does three-dimensional (3D) texture-based volume-rendering for a variety of representations. The use of computers in the microscopic and structural biosciences is extensive, and many scientific file formats exist. To overcome the problem of accessing such data from VRML and other tools, we implemented extensions to SGI's IFL (image format library). IFL is a file format abstraction layer defining communication between a program and a data file. These technologies are developed in support of the BioImage project, aiming to establish a database prototype for multidimensional microscopic data with the ability to view the data within a 3D interactive environment. Copyright 1999 Academic Press.

  15. Aqueous Dispersions of Silica Stabilized with Oleic Acid Obtained by Green Chemistry.

    Science.gov (United States)

    Nistor, Cristina Lavinia; Ianchis, Raluca; Ghiurea, Marius; Nicolae, Cristian-Andi; Spataru, Catalin-Ilie; Culita, Daniela Cristina; Pandele Cusu, Jeanina; Fruth, Victor; Oancea, Florin; Donescu, Dan

    2016-01-05

    The present study describes for the first time the synthesis of silica nanoparticles starting from sodium silicate and oleic acid (OLA). The interactions between OLA and sodium silicate require an optimal OLA/OLANa molar ratio able to generate vesicles that can stabilize silica particles obtained by the sol-gel process of sodium silicate. The optimal molar ratio of OLA/OLANa can be ensured by a proper selection of OLA and respectively of sodium silicate concentration. The titration of sodium silicate with OLA revealed a stabilization phenomenon of silica/OLA vesicles and the dependence between their average size and reagent's molar ratio. Dynamic light scattering (DLS) and scanning electron microscopy (SEM) measurements emphasized the successful synthesis of silica nanoparticles starting from renewable materials, in mild condition of green chemistry. By grafting octadecyltrimethoxysilane on the initial silica particles, an increased interaction between silica particles and the OLA/OLANa complex was achieved. This interaction between the oleyl and octadecyl chains resulted in the formation of stable gel-like aqueous systems. Subsequently, olive oil and an oleophylic red dye were solubilized in these stable aqueous systems. This great dispersing capacity of oleosoluble compounds opens new perspectives for future green chemistry applications. After the removal of water and of the organic chains by thermal treatment, mesoporous silica was obtained.

  16. Aqueous Dispersions of Silica Stabilized with Oleic Acid Obtained by Green Chemistry

    Directory of Open Access Journals (Sweden)

    Cristina Lavinia Nistor

    2016-01-01

    Full Text Available The present study describes for the first time the synthesis of silica nanoparticles starting from sodium silicate and oleic acid (OLA. The interactions between OLA and sodium silicate require an optimal OLA/OLANa molar ratio able to generate vesicles that can stabilize silica particles obtained by the sol-gel process of sodium silicate. The optimal molar ratio of OLA/OLANa can be ensured by a proper selection of OLA and respectively of sodium silicate concentration. The titration of sodium silicate with OLA revealed a stabilization phenomenon of silica/OLA vesicles and the dependence between their average size and reagent’s molar ratio. Dynamic light scattering (DLS and scanning electron microscopy (SEM measurements emphasized the successful synthesis of silica nanoparticles starting from renewable materials, in mild condition of green chemistry. By grafting octadecyltrimethoxysilane on the initial silica particles, an increased interaction between silica particles and the OLA/OLANa complex was achieved. This interaction between the oleyl and octadecyl chains resulted in the formation of stable gel-like aqueous systems. Subsequently, olive oil and an oleophylic red dye were solubilized in these stable aqueous systems. This great dispersing capacity of oleosoluble compounds opens new perspectives for future green chemistry applications. After the removal of water and of the organic chains by thermal treatment, mesoporous silica was obtained.

  17. Vortex dynamics during blade-vortex interactions

    Science.gov (United States)

    Peng, Di; Gregory, James W.

    2015-05-01

    Vortex dynamics during parallel blade-vortex interactions (BVIs) were investigated in a subsonic wind tunnel using particle image velocimetry (PIV). Vortices were generated by applying a rapid pitch-up motion to an airfoil through a pneumatic system, and the subsequent interactions with a downstream, unloaded target airfoil were studied. The blade-vortex interactions may be classified into three categories in terms of vortex behavior: close interaction, very close interaction, and collision. For each type of interaction, the vortex trajectory and strength variation were obtained from phase-averaged PIV data. The PIV results revealed the mechanisms of vortex decay and the effects of several key parameters on vortex dynamics, including separation distance (h/c), Reynolds number, and vortex sense. Generally, BVI has two main stages: interaction between vortex and leading edge (vortex-LE interaction) and interaction between vortex and boundary layer (vortex-BL interaction). Vortex-LE interaction, with its small separation distance, is dominated by inviscid decay of vortex strength due to pressure gradients near the leading edge. Therefore, the decay rate is determined by separation distance and vortex strength, but it is relatively insensitive to Reynolds number. Vortex-LE interaction will become a viscous-type interaction if there is enough separation distance. Vortex-BL interaction is inherently dominated by viscous effects, so the decay rate is dependent on Reynolds number. Vortex sense also has great impact on vortex-BL interaction because it changes the velocity field and shear stress near the surface.

  18. Stability of wheat germ oil obtained by supercritical carbon dioxide ...

    African Journals Online (AJOL)

    심정은

    For determination of stability, wheat germ oil obtained by ethanolysis reactants was characterized by ... extract non polar lipids with lipid soluble bioactive com- pounds from different sources (Esquivel et al., 1997; ... thin layer of cotton was placed at the bottom of the extraction vessel. Before plugging with cap another layer of ...

  19. 20 CFR 726.4 - Who must obtain insurance coverage.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 3 2010-04-01 2010-04-01 false Who must obtain insurance coverage. 726.4 Section 726.4 Employees' Benefits EMPLOYMENT STANDARDS ADMINISTRATION, DEPARTMENT OF LABOR FEDERAL COAL MINE HEALTH AND SAFETY ACT OF 1969, AS AMENDED BLACK LUNG BENEFITS; REQUIREMENTS FOR COAL MINE OPERATOR...

  20. Glass transition temperatures of liquid prepolymers obtained by thermal penetrometry

    Science.gov (United States)

    Potts, J. E., Jr.; Ashcraft, A. C.

    1973-01-01

    Thermal penetrometry is experimental technique for detecting temperature at which frozen prepolymer becomes soft enough to be pierced by weighted penetrometer needle; temperature at which this occurs is called penetration temperature. Apparatus used to obtain penetration temperatures can be set up largely from standard parts.

  1. Obtainment of lithium metal by electrolysis of molten salts

    International Nuclear Information System (INIS)

    Silva Costa, M.A.Z. da.

    1988-04-01

    The obtainment metallic lithium through KCL + LiCl, using a stainless steel cathode and a graphite anode is studied. The applications of lithium on nuclear energy, aerospatial program, metalurgy and as refining and degassing agent are also presented. The purification of lithium is still mentioned. (C.G.C.) [pt

  2. Biochemical Characterization of Lipases Obtained from Acinetobacter psychrotolerans Strains

    Directory of Open Access Journals (Sweden)

    Şule SEREN

    2017-12-01

    Full Text Available In this study, extracellular lipases obtained from Acinetobacter psychrotolerans strains (Xg1 and Xg2 were characterized. The effects of varying pH values (3.0-10.0 and various temperatures (10-90 °C on lipase activities were examined. Also the effects of different metal ions, organic solvents and detergents on lipases were studied. The extracellular crude lipases were concentrated using ultrafiltration. Zymogram analysis of these lipases was performed. Lipases exhibited maximum activity at pH 8 and 30 °C.  While lipase obtained from the Xg1 strain exhibited the highest stability in the presence of various organic solvents, including hexane, ethyl acetate, chloroform and N,N dietil formamide, lipase obtained from the Xg2 strain was sensitive in the presence of isopropanol, acetonitrile, and butan-1-ol. The lipases of the Xg1 and Xg2 strains were inhibited in the presence of Cu2+ and Zn2+. Also, the lipase of the Xg1 strain was inhibited in the presence of Fe3+. In the presence of EDTA, the lipase activities of the Xg1 and Xg2 strains were partially inhibited. In presence of SDS, they were exactly inhibited. According to the zymogram results, the molecular weights of the lipases obtained from the Acinetobacter psychrotolerans Xg1 and Xg2 strains have been found approximately 37 and 30 kDa, respectively.

  3. 7 CFR 1205.520 - Procedure for obtaining reimbursement.

    Science.gov (United States)

    2010-01-01

    ... application forms may be filed. In any such case, the reimbursement application shall show the names... Cotton Board shall make reimbursement to the importer. For joint applications, the reimbursement shall be... procedures prescribed in this section. (a) Application form. An importer shall obtain a reimbursement...

  4. Test Beam Results Obtained with the Q4 Prototype

    Energy Technology Data Exchange (ETDEWEB)

    Aguilar-Benitez, M.; Alberdi, J.; Cerrada, M.; Colino, N.; Daniel, M.; Fouz, M. c.; Marin, J.; Mocholi, J.; Oller, J. C.; Puerta, J.; Romero, L.; Salicio, J. M.

    2000-07-01

    A prototype of the CMS Barrel Muon Detector incorporating all the features of the final chambers was built at CIEMAT using the mass production assembly procedures and tools. The performance of this prototype was studied in a muon test beam at CERN and the results obtained are presented here. (Author)

  5. 41 CFR 101-26.308 - Obtaining filing cabinets.

    Science.gov (United States)

    2010-07-01

    ... 41 Public Contracts and Property Management 2 2010-07-01 2010-07-01 true Obtaining filing cabinets. 101-26.308 Section 101-26.308 Public Contracts and Property Management Federal Property Management Regulations System FEDERAL PROPERTY MANAGEMENT REGULATIONS SUPPLY AND PROCUREMENT 26-PROCUREMENT SOURCES AND...

  6. Remarks on the low value obtained for the Hubble constant

    International Nuclear Information System (INIS)

    Jaakkola, Toivo

    1975-01-01

    Some remarks are made on the basis of the data given by Sandage and Tamman, suggesting that these authors have over-estimated the distances to the most luminous galaxies and obtained a value too low for the Hubble constant [fr

  7. A heuristic way of obtaining the Kerr metric

    International Nuclear Information System (INIS)

    Enderlein, J.

    1997-01-01

    An intuitive, straightforward way of finding the metric of a rotating black hole is presented, based on the algebra of differential forms. The representation obtained for the metric displays a simplicity which is not obvious in the usual Boyer Lindquist coordinates. copyright 1997 American Association of Physics Teachers

  8. Chelate forms of biometalls. Theoretical aspects of obtaining and characteristics

    Directory of Open Access Journals (Sweden)

    A. Kapustyan

    2017-04-01

    Full Text Available The problem of microelements bioavailability is highlighted and the correct ways of its solution are substantiated as a result of generalization of theoretical aspects of obtaining of the biometals chelate forms. The characteristics of the main biogenic elements, their physiological significance, electrochemical properties are presented. The main examples of the participation of biometals in various biological processes are given. The properties and the structure peculiarities of biometals coordination complexes are considered in detail. It is shown that in obtaining of biometals chelate forms, there is the mutual selectivity and the affinity of biometals and ligands. The main factors of obtaining a hard metal complex are given. Potential bioligands for obtaining bioavailable forms of microelements are detailed. Among them there are amino acids, peptides, proteins, nucleic acids, carbohydrates. The possible character of complexation depending on the nature of the bioligand is indicated. Practical examples of preparation of biometals mixed ligand complexes are given. The expediency of using metabolic products and processing of lactic acid bacteria as promising components of mixed ligand chelate complexes is substantiated. These substances contain in their composition a mass of potential donor atoms that are capable to form covalent and coordination bonds with biomethalles, and also possess high biological and immunotropic activities. The use of this system in the biocoordination compounds of the "metals of life" can provide a synergistic effect of the components, significantly to expand the range of their physiological activity and to increase the degree of assimilation by the body.

  9. Weather Satellite Pictures and How to Obtain Them.

    Science.gov (United States)

    Petit, Noel J.; Johnson, Philip

    1982-01-01

    An introduction to satellite meteorology is presented to promote use of live weather satellite photographs in the classroom. Topics addressed include weather satellites, how they work, earth emissions, satellite photography, satellite image analysis, obtaining satellite pictures, and future considerations. Includes sources for materials to…

  10. Process for obtaining a distillation product free from sulfur

    Energy Technology Data Exchange (ETDEWEB)

    Heyl, G E

    1920-06-12

    A process is described of obtaining from shale a hydrocarbon product free from sulfur, by distillation, consisting in mixing with the shale a portion of mineral oil and metallic debris, such as turnings and drillings, heating the mixture in a rotary drum and recovering and condensing the vapors distilled.

  11. Stoichiometric hydroxyapatite obtained by precipitation and sol gel processes

    Energy Technology Data Exchange (ETDEWEB)

    Guzman V, C.; Pina B, C.; Munguia, N. [IIM-UNAM, A.P. 70-360, 04510 Mexico D.F. (Mexico)]. e-mail: caroguz@servidor.unam.mx

    2005-07-01

    Three methods for obtaining hydroxyapatite (HA) are described. HA is a very interesting ceramic because of its many medical applications. The first two precipitation methods start from calcium and phosphorous compounds, whereas the third method is a sol-gel process that uses alkoxides. The products were characterized and compared. The observed differences are important for practical applications. (Author)

  12. Apparatus for obtaining electric energy in speed highways

    International Nuclear Information System (INIS)

    Khalatyan, P.R.; Khalatyan, R.P.; Khalatyan, E.P.

    2012-01-01

    The problems of obtaining electricity by means of moving motor-transport are examined. An apparatus installed in the distributive zone of intensive traffic speed highways is proposed. Part of air mass movement of kinetic energy is transformed from the movement of automobiles into electricity

  13. Cyanophycin production from nitrogen-containing chemicals obtained from biomass

    NARCIS (Netherlands)

    Elbahloul, Y.A.K.B.; Scott, E.L.; Mooibroek, H.; Sanders, J.P.M.; Obsts, M.; Steinbüchel, A.

    2006-01-01

    The present invention relates to fermentation processes for the production of cyanophycin in a microorganism whereby a plant-derived nitrogen source is converted by the microorganism into cyanophycin. The plant-derived nitrogen source preferably is a process stream being obtained in the processing

  14. 48 CFR 509.105-1 - Obtaining information.

    Science.gov (United States)

    2010-10-01

    ... Obtaining information. (a) From a prospective contractor. FAR 9.105-1 lists a number of sources of..., Contractor's Qualifications and Financial Information, but only after exhausting other available sources of... finance, and auditors before determining that an offeror is responsible. [74 FR 12732, Mar. 25, 2009] ...

  15. U3O8 obtained from metallic uranium

    International Nuclear Information System (INIS)

    Lopez, Marisol; Gonzalez, Alfredo; Pasqualini, Enrique E.

    2003-01-01

    Enriched uranium oxide, U 3 O 8 , used as nuclear powder in MTR's, can be obtained by direct oxidation of metallic uranium at 800 C degrees. Maximum density, 8.2 gr/cm 3 , is achieved after grinding and a high temperature treatment at 1400 C degrees. All the process is highly controllable and performed in dry environments. (author)

  16. Data Obtained from Prototype Wave Dragon in Nissum Bredning

    DEFF Research Database (Denmark)

    Tedd, James William; Curie, Marie; Kofoed, Jens Peter

    This report is a product of the Project: Sea Testing and Optimisation of Power Production on a Scale 1:4.5 Test Rig of the Offshore Wave Energy Converter Wave Dragon. This report aims to provide access for the project partners to the raw data obtained from the testing period in Nissum Bredning...

  17. 9 CFR 592.100 - Who may obtain service.

    Science.gov (United States)

    2010-01-01

    ... conduct of the service. (c) The applicant must have a tax identification number for billing purposes. ... 9 Animals and Animal Products 2 2010-01-01 2010-01-01 false Who may obtain service. 592.100 Section 592.100 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE...

  18. Sintering of uranium dioxide obtained by continuous precipitation of AUC

    International Nuclear Information System (INIS)

    Amaya, C.D.; Sterba, M.E.; Russo, D.O.

    1993-01-01

    The Nuclear Materials Division in Bariloche Atomic Center evaluates the ceramic behaviour of UO 2 powders obtained from continuously precipitated and reduced AUC (Ammonium Uranyl Tri Carbonate). An analysis is made of powder characteristics (particle morphology and size distribution and specific area) on behaviour of UO 2 during sintering (compaction, sintering, pore and grain microstructure, etc.). 1 ref

  19. Antioxidant properties of volatile oils obtained from Artemisia taurica ...

    African Journals Online (AJOL)

    In this study, the antioxidant properties of volatile oils obtained from the earth parts of the Artemisia taurica Willd. and Salvia kronenburgii Rech. Fil. plants and their effects on xanthine oxidase enzyme were studied. The chemical contents of each volatile oil were determined by applying gas chromatograpghy-mass ...

  20. GINES: first rice mutant obtained from proton irradiation

    International Nuclear Information System (INIS)

    Gonzalez, Maria C; Perez, Noraida; Cristo, Elizabeth

    2009-01-01

    A new rice variety of a good productive potential and salinity tolerance was obtained at the National Institute of Agricultural Sciences (INCA), starting from in vitro culture of J-104 rice seeds irradiated with protons. This is the first report of a variety achieved by proton irradiation

  1. 15 CFR 711.6 - Where to obtain forms.

    Science.gov (United States)

    2010-01-01

    ... 15 Commerce and Foreign Trade 2 2010-01-01 2010-01-01 false Where to obtain forms. 711.6 Section 711.6 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) BUREAU OF INDUSTRY AND SECURITY, DEPARTMENT OF COMMERCE CHEMICAL WEAPONS CONVENTION REGULATIONS GENERAL...

  2. Methods for obtaining a uniform volume concentration of implanted ions

    International Nuclear Information System (INIS)

    Reutov, V.F.

    1995-01-01

    Three simple practical methods of irradiations with high energy particles providing the conditions for obtaining a uniform volume concentration of the implanted ions in the massive samples are described in the present paper. Realization of the condition of two-sided irradiation of a plane sample during its rotation in the flux of the projectiles is the basis of the first method. The use of free air as a filter with varying absorbent ability due to movement of the irradiated sample along ion beam brought to the atmosphere is at the basis of the second method of uniform ion alloying. The third method for obtaining a uniform volume concentration of the implanted ions in a massive sample consists of irradiation of a sample through the absorbent filter in the shape of a foil curved according to the parabolic law moving along its surface. The first method is the most effective for obtaining a great number of the samples, for example, for mechanical tests, the second one - for irradiation in different gaseous media, and the third one - for obtaining high concentrations of the implanted ions under controlled (regulated) thermal and deformation conditions. 2 refs., 7 figs

  3. Mass Media Campaign Impacts Influenza Vaccine Obtainment of University Students

    Science.gov (United States)

    Shropshire, Ali M.; Brent-Hotchkiss, Renee; Andrews, Urkovia K.

    2013-01-01

    Objective: To describe the effectiveness of a mass media campaign in increasing the rate of college student influenza vaccine obtainment. Participants/Methods: Students ("N" = 721) at a large southern university completed a survey between September 2011 and January 2012 assessing what flu clinic media sources were visualized and if they…

  4. 7 CFR 1737.41 - Procedure for obtaining approval.

    Science.gov (United States)

    2010-01-01

    ... RUS financing. (3) The proposed interim financing presents unacceptable loan security risks to RUS, or..., DEPARTMENT OF AGRICULTURE PRE-LOAN POLICIES AND PROCEDURES COMMON TO INSURED AND GUARANTEED TELECOMMUNICATIONS LOANS Interim Financing of Construction of Telephone Facilities § 1737.41 Procedure for obtaining...

  5. Process for encapsulating active agents obtaining a gel

    NARCIS (Netherlands)

    Yilmaz, G.; Jongboom, R.O.J.

    2001-01-01

    The present invention relates to a process for encapsulating an active agent in a biopolymer in the form of a gel, comprising the steps of: a) forming a dispersion or solution of the biopolymer in water; and b) adding the active agent to the dispersion or solution obtained in step a); wherein the

  6. Effective properties of a viscoplastic constitutive model obtained by homogenisation

    NARCIS (Netherlands)

    Sluis, van der O.; Schreurs, P.J.G.; Meijer, H.E.H.

    1999-01-01

    Heterogeneous materials are used more and more frequent due to their enhanced mechanical properties. If the relation between the microscopic deformation and the macroscopic mechanical behaviour can be obtained, it can be used to design new materials with desired properties such as high strength,

  7. 48 CFR 9.105-1 - Obtaining information.

    Science.gov (United States)

    2010-10-01

    ... information required concerning the adequacy of prospective contractors' accounting systems and these systems... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Obtaining information. 9... accounting systems, and these systems' suitability for use in administering the proposed type of contract. (3...

  8. Test beam results obtained with the Q4 prototype

    International Nuclear Information System (INIS)

    Aguilar-Benitez, M.; Alberdi, J.; Cerrada, M.; Colino, N.; Daniel, M.; Fouz, M.C.; Marin, J.; Mocholi, J.; Oller, J. C.; Puerta, J.; Romero, L.; Salicio, J. M.; Willmott, C.

    2000-10-01

    A prototype of the CMS Barrel Muon Detector incorporating all the features of the final chambers was built at CIEMAT using the mass production assembly procedures and tools. The performance of this prototype was studied in a muon test beam at CERN and the results obtained are presented here. (Author)

  9. 32 CFR 564.40 - Procedures for obtaining medical care.

    Science.gov (United States)

    2010-07-01

    ... care. (a) When a member of the ARNG incurs a disease or an injury, while performing training duty under... 32 National Defense 3 2010-07-01 2010-07-01 true Procedures for obtaining medical care. 564.40... benefits. (b) Authorization for care in civilian facility. (1) An individual who desires medical or dental...

  10. 9 CFR 439.10 - Criteria for obtaining accreditation.

    Science.gov (United States)

    2010-01-01

    ... degree in chemistry, food science, food technology, or a related field. (i) For food chemistry... ACT ACCREDITATION OF NON-FEDERAL CHEMISTRY LABORATORIES § 439.10 Criteria for obtaining accreditation. (a) Analytical laboratories may be accredited for the analyses of food chemistry analytes, as defined...

  11. OBTAINING AND PROPERTIES OF AgInS2 FILMS

    Directory of Open Access Journals (Sweden)

    M. A. Abdullaev

    2016-01-01

    Full Text Available Aim. The aim is to obtain AgInS2 films and study their electrical and optical properties.Methods. The samples of thin AgInS2 films for measurement were obtained by the method of magnetron sputtering with direct current. The structure, phase and elemental composition were studied using DRON-2 X-ray diffractometer (СuKа - radiation and the microscope LEO-1450 with EDS attachment for X-ray microanalysis. The optical transmittance and absorption were examined using MDR-2 monochromator in the wavelength range of 400-800 nm with the Keitley electrometer and FD-10G; we applied the spectral resolution of ± 1 meV. The electrical conductivity, Hall effect was measured by the four-point probe method with indium ohmic contacts. Measurements were carried out in the temperature range of 77-400 K.Findings. We obtained indium disulfide and silver films with the thickness of up to 1 μm on quartz substrates by magnetron sputtering. It is shown that increasing the substrate temperature to about 450 0С allows to obtain single phase film with a chalcopyrite structure with a band gap of 1.88 eV and high absorption coefficient (>104см-1.Conclusions. The possibility of obtaining films in a wide range of the electrical resistance and variation of the electrical parameters at constant stoichiometry is of interest for efficient technologies of phototransduction.

  12. Radiochemical schemes of obtaining 89Sr and 90Y radionuclides

    International Nuclear Information System (INIS)

    Usarov, Z. O.

    2010-03-01

    Key words: strontium-89, yttrium-90, extraction and extraction-chromatographic purification of radionuclides, radiopharmaceuticals. Subjects of research: strontium-89 and yttrium-90 radionuclides and their chloride forms. Purpose of work is developing of radiochemical technologies on obtaining of 89 Sr and 90 Y on the WWR-SM reactor with high radionuclide purity. Methods of research: extraction and extraction-chromatographic methods of radionuclides separation, beta- and gamma-spectrometric methods of activity measuring. The results obtained and their novelty: Were determined the conformity to laws of Y and Sr distribution in two-phase systems TBP-HNO 3 , TBP-NH 4 NO 3 , TBP-HCI, HDEHP-NO 3 , HDEHP-NH 4 NO 3 and HDEHP-HCI. Were determined the conformity to laws of Y and Sr distribution in systems with craun ethers DB-18K-6 and DTBDB-18K-6 from water solutions of HNO 3 . Radiochemical technologies on obtaining of 89 Sr and 90 Y radionuclides including radiochemical process of yttrium target with using the systems TBP-HNO 3 and HDEHP/Teflone were developed. Practical value: the radiochemical technology of obtaining 89 Sr with high radionuclide purity was developed. The method of preparation a chloride compound of 89 SrCl 2 which is used as a drug form for preparation of 89 Sr- 'Metastron' was developed. The relatively simple method of on the way obtaining 90 Y in the reactor with high radionuclidic purity that is useful for follow using in medical practice was offered. Degree of embed and economic effectivity: the developed technologies have approbation in manufacturing conditions in Radiopreparat Enterprise of INP AS RU and were offered for receiving of domestic preparations against of import foreign analogues. The statement about using the invention by obtained patent is attached to dissertation. Field of application: the received results will be introduced in manufacture at Radiopreparat Enterprise of INP AS RU for receiving of domestic preparations

  13. Evidence of interstitial microsegregation in iron obtained by ion microscopy

    International Nuclear Information System (INIS)

    Price, C.W.

    1984-01-01

    Segregation of impurity atoms to the strain fields of dislocations and the effective locking of the dislocations by the impurity atmospheres have been suggested earlier by others. The formation of interstitial atmospheres and their effect in iron was first treated mathematically by Cottrell and Bilby (Proc. Phys. Soc.; A62: 49(1949). Hirth and Lothe (Theory of Discolations, McGraw-Hill, New York (1968) reviewed more recent evidence of interstitial effects and theoretical treatments of interstitial dislocation interactions. This paper describes additional evidence of microsegregation of several interstitial elements in iron that were detected using secondary-ion mass spectroscopy (SIMS). 10 references, 2 figures

  14. Molecular profiling of Vitis vinifera Chardonnay obtained by somatic embryogenesis

    Directory of Open Access Journals (Sweden)

    Christophe Bertsch

    2003-12-01

    Full Text Available With the help of microsatellite profiling, we showed that Vitis vinifera Chardonnay clone 96 is a periclinal chimera plant which is composed at least of two distinct cell layers. Performing somatic embryogenesis allowed us to separate the two cell layers and to regenerate L1 plants. These regenerated L1 plants did not show phenotypic differences to the parental clone when grown in greenhouse conditions, suggesting therefore that the phenotype of Chardonnay 96 did not result of an interaction between the two distinct cell layers L1 and L2.

  15. Ultracold fermions with repulsive interactions

    Directory of Open Access Journals (Sweden)

    Ketterle W.

    2013-08-01

    Full Text Available An ultracold Fermi gas with repulsive interaction has been studied. For weak interactions, the atomic gas is metastable, and the interactions were characterized by obtaining the isothermal compressibility from atomic density profiles. For stronger interactions (kFa ≈ 1, rapid conversion into Feshbach molecules is observed. When the conversion rate becomes comparable to the Fermi energy divided by η, the atomic gas cannot reach equilibrium without forming pairs. This precludes the predicted transition to a ferromagnetic state (Stoner transition. The absence of spin fluctuations proves that the gas stays paramagnetic. In free space, a Fermi gas with strong short-range repulsion does not exist because of the rapid coupling to molecular states.

  16. Macrolide drug interactions: an update.

    Science.gov (United States)

    Pai, M P; Graci, D M; Amsden, G W

    2000-04-01

    To describe the current drug interaction profiles for the commonly used macrolides in the US and Europe, and to comment on the clinical impact of these interactions. A MEDLINE search (1975-1998) was performed to identify all pertinent studies, review articles, and case reports. When appropriate information was not available in the literature, data were obtained from the product manufacturers. All available data were reviewed to provide an unbiased account of possible drug interactions. Data for some of the interactions were not available from the literature, but were available from abstracts or company-supplied materials. Although the data were not always explicit, the best attempt was made to deliver pertinent information that clinical practitioners would need to formulate practice opinions. When more in-depth information was supplied in the form of a review or study report, a thorough explanation of pertinent methodology was supplied. Several clinically significant drug interactions have been identified since the approval of erythromycin. These interactions usually were related to the inhibition of the cytochrome P450 enzyme systems, which are responsible for the metabolism of many drugs. The decreased metabolism by the macrolides has in some instances resulted in potentially severe adverse events. The development and marketing of newer macrolides are hoped to improve the drug interaction profile associated with this class. However, this has produced variable success. Some of the newer macrolides demonstrated an interaction profile similar to that of erythromycin; others have improved profiles. The most success in avoiding drug interactions related to the inhibition of cytochrome P450 has been through the development of the azalide subclass, of which azithromycin is the first and only to be marketed. Azithromycin has not been demonstrated to inhibit the cytochrome P450 system in studies using a human liver microsome model, and to date has produced none of the

  17. Obtaining polyester from glycerin for synthesis of polyurethanes

    International Nuclear Information System (INIS)

    Breves, Rodolfo A.; Ghesti, Grace F.; Sales, Maria J.A.

    2014-01-01

    The use of renewable resources has been increasing, due to the development of materials that have viable applications that are environmentally friendly. In this paper, a polyester was synthesized from glycerin, with the addition of adipic acid in a molar ratio of 1: 1.5, with dilauryl tin catalyst, which was added in proportions of 1 to 3% obtained PUs from castor oil (Ricinus communis) and MDI (diphenyl methane diisocyanate). The materials were characterized by infrared spectroscopy (FTIR), nuclear magnetic resonance "1H NMR, thermogravimetry (TG) and derivative thermogravimetry (DTG). The reaction for obtaining the polyester was confirmed by FTIR, the absorption band between 1708-1730 cm"-"1 and "1H NMR, in the region 1.4 to 1.8 ppm and 2.2 to 2.6 ppm. The thermal decomposition of polyester occurred with temperature above 300 ° C. PUs showed similar thermal stability. (author)

  18. Obtaining hydroxyapatite coatings on titanium by the biomimetic method

    International Nuclear Information System (INIS)

    Paz, A.; Martin, Y.; Pazos, L. M.; Parodi, M. B.; Ybarra, G. O.; Gonzalez, J. E.

    2011-01-01

    In this work, a study about the deposition of hydroxyapatite on a titanium substrate employing the biomimetic method is presented. A solution with high content of calcium and phosphorus (SCS) was used. In addition, activation of titanium with hydrogen peroxide and hydrochloric acid and a subsequent heat treatment was performed. The characterization of materials used and the coating obtained was carried out by Infrared Spectroscopy (FT-IR), X-ray Diffraction (XRD), Scanning Electron Microscopy (SEM) and Energy Dispersive X-ray Spectroscopy (EDX). As a result of the activation processes a hydrated titanium oxide was formed. On the active surface, a coating of hydroxyapatite was obtained after a period of 24 h, which has a thickness of about 2-4 μm. (Author) 21 refs.

  19. Simulation of uranium and plutonium oxides compounds obtained in plasma

    Science.gov (United States)

    Novoselov, Ivan Yu.; Karengin, Alexander G.; Babaev, Renat G.

    2018-03-01

    The aim of this paper is to carry out thermodynamic simulation of mixed plutonium and uranium oxides compounds obtained after plasma treatment of plutonium and uranium nitrates and to determine optimal water-salt-organic mixture composition as well as conditions for their plasma treatment (temperature, air mass fraction). Authors conclude that it needs to complete the treatment of nitric solutions in form of water-salt-organic mixtures to guarantee energy saving obtainment of oxide compounds for mixed-oxide fuel and explain the choice of chemical composition of water-salt-organic mixture. It has been confirmed that temperature of 1200 °C is optimal to practice the process. Authors have demonstrated that condensed products after plasma treatment of water-salt-organic mixture contains targeted products (uranium and plutonium oxides) and gaseous products are environmental friendly. In conclusion basic operational modes for practicing the process are showed.

  20. Obtaining and Characterization of Flux-Based Products

    Directory of Open Access Journals (Sweden)

    Cosmina Maria Bogăţean

    2015-11-01

    Full Text Available The purpose of creating this assortment was to remind the public of a long forgotten sugar based product, with a high energy value and which can be easily associated both with plain or mineral water consumption. Also we have taken into consideration the well-known '' home-made'' and ''vintage'' concepts. The purpose of this scientific research is to obtain a laboratory created product, as well as obtaining both the cocoa and the lemon sorbet. In the technological process this type of products can be redefined under a new form. The great advantage comes with the fact that it dosen't currently exit on the market and so it can be considered as being a brand new product. The anbalyses both on the raw materials and on the final deliverable product were done in the Faculty's laboratories and it was proven to meet the standars.

  1. New method in obtaining correction factor of power confirming

    International Nuclear Information System (INIS)

    Deng Yongjun; Li Rundong; Liu Yongkang; Zhou Wei

    2010-01-01

    Westcott theory is the most widely used method in reactor power calibration, which particularly suited to research reactor. But this method is very fussy because lots of correction parameters which rely on empirical formula to special reactor type are needed. The incidence coefficient between foil activity and reactor power was obtained by Monte-Carlo calculation, which was carried out with precise description of the reactor core and the foil arrangement position by MCNP input card. So the reactor power was determined by the core neutron fluence profile and the foil activity placed in the position for normalization use. The characteristic of this new method is simpler, more flexible and accurate than Westcott theory. In this paper, the results of SPRR-300 obtained by the new method in theory were compared with the experimental results, which verified the possibility of this new method. (authors)

  2. A rapid, simple method for obtaining radiochemically pure hepatic heme

    International Nuclear Information System (INIS)

    Bonkowski, H.L.; Bement, W.J.; Erny, R.

    1978-01-01

    Radioactively-labelled heme has usually been isolated from liver to which unlabelled carrier has been added by long, laborious techniques involving organic solvent extraction followed by crystallization. A simpler, rapid method is devised for obtaining radiochemically-pure heme synthesized in vivo in rat liver from delta-amino[4- 14 C]levulinate. This method, in which the heme is extracted into ethyl acetate/glacial acetic acid and in which porphyrins are removed from the heme-containing organic phase with HCl washes, does not require addition of carrier heme. The new method gives better heme recoveries than and heme specific activities identical to, those obtained using the crystallization method. In this new method heme must be synthesized from delta-amino[4- 14 C]levulinate; it is not satisfactory to use [2- 14 C]glycine substrate because non-heme counts are isolated in the heme fraction. (Auth.)

  3. Physicochemical characteristics of ozonated sunflower oils obtained by different procedures

    Energy Technology Data Exchange (ETDEWEB)

    Diaz, M. F.; Sanchez, Y.; Gomez, M.; Hernandez, F.; Veloso, M. C.; Pereira, P. A.; Mangrich, A. S.; Andrade, J. B.

    2012-07-01

    Two ozonation procedures for sunflower oils at different applied ozone dosages were carried out. Ozone was obtained from medicinal oxygen and from air. Peroxide, acidity, and iodine indexes, along with density, viscosity and antimicrobial activity were determined. The fatty acid compositions of the samples were analyzed using GC. The content of oxygen was determined using an elemental analysis. Electronic Paramagnetic Resonance was used to measure the organic free radicals. The reactions were achieved up to peroxide index values of 658 and 675 mmolequiv kg1 using medicinal oxygen and air for 5 and 8 hours, respectively. The samples of ozonized sunflower oil did not present organic free radicals, which is a very important issue if these oils are to be used as drugs. The ozonation reaction is more rapid with medicinal oxygen (5 hours) than with air (8 hours). Ozonized sunflower oil with oxygen as an ozone source was obtained with high potential for antimicrobial activity. (Author) 34 refs.

  4. Obtaining the crystal potential by inversion from electron scattering intensities

    International Nuclear Information System (INIS)

    Allen, L.T.; Josefsson, T.W.; Leeb, H.

    1998-01-01

    A method to obtain the crystal potential from the intensities of the diffracted beams in high energy electron diffraction is proposed. It is based on a series of measurements for specific well determined orientations of the incident beam which determine the moduli of all elements of the scattering matrix. Using unitarity and the specific form of the scattering matrix (including symmetries) an overdetermined set of non-linear equations is obtained from these data. Solution of these equations yields the required phase information and allows the determination of a (projected) crystal potential by inversion which is unique up to an arbitrary shift of the origin. The reconstruction of potentials from intensities is illustrated for two realistic examples, a [111] systematic row case in ZnS and a [110] zone axis orientation in GaAs (both noncentrosymmetric crystals)

  5. LINKING MARKETING AND HUMAN RESOURCES RECRUITMENT TO OBTAIN ORGANIZATIONAL EFFICIENCY

    Directory of Open Access Journals (Sweden)

    Nicoleta Valentina FLOREA

    2010-01-01

    Full Text Available In times of rapid change and technical change, in a complex and dynamic environment, organizations must strive for superiority, in order to survive and to serve the clients who want more quality and lower price. Corporate leaders and human resources strategists have to take up this challenge of changing work attitudes across the organization. This involves guiding, leading, enabling and motivating people. This article is looking at aligning marketing with recruitment efforts, to obtain organizational performance. Anticipating customers’ needs, the organization develop specific plans of recruitment, selection and retention of those candidates who satisfy these needs at the highest level. Only anticipating and retaining those “right people at the right time”, an organization may obtain success into a global, dynamic and changing environment.

  6. Periods found in heat measurements obtained by calorimetry

    International Nuclear Information System (INIS)

    Jordan, K.C.

    1984-01-01

    During a span of 640 days, a periodicity of 1.5158 +- 0.0008 days was discovered in successive heater equilibria on Calorimeter No. 127. Measurements were taken at 12-h intervals, with occasional changes of exactly 3 or 6 h in the schedule of measurements. This schedule eliminated all other possible periods except a period of 0.150156 days. Periods of 1.519125 and 1.511283 days were discovered in data on the excess length of day as obtained by the US Naval Observatory over a period of 24 y. These two periods could equally well represent periods of 0.150189 and 0.150112 days, since measurements were obtained only once every 24 h. It is suggested that periods observed in sensitive calorimeters and in length of day data may be related. 1 reference, 6 figures, 5 tables

  7. Oil and gas processing products to obtain polymers modified bitumen

    Directory of Open Access Journals (Sweden)

    Serhiy Pyshyev

    2017-07-01

    Full Text Available To obtain modified bitumen with excellent adhesive properties, coumarone-indene resin (CIR was used. However, bitumens modified by CIR have somewhat worse plastic properties. For the improvement of the plastic properties of road bitumen modified by coumarone-indene resin, the paper proposes to use plasticizers. Characterized by a high content of rings (aromatic-naphthenic oils, a range of compounds was used as plasticizers. Of all different plasticizers tested, the tar produced from West-Ukrainian oils has been found to be the most effective one. The optimal ratio between modified bitumen components was determined enabling to obtain the commercial product of polymers modified bitumen of BMP 60/90-52 brand. The complex thermogravimetry and differential-thermal analysis has been used to analyze the initial and modified bitumen. Bitumens modified by CIR have shown by far the highest thermal stability under operation conditions. Keywords: Bitumen, Modifier, Coumarone-indene resin, Plasticizer

  8. Carbon/Clay nanostructured composite obtained by hydrothermal method

    International Nuclear Information System (INIS)

    Barin, G.B.; Bispo, T.S.; Gimenez, I.F.; Barreto, L.S.; Souza Filho, A.G.

    2010-01-01

    The development of strategies for converting biomass into useful materials, more efficient energy carrier and / or hydrogen storage is shown a key issue for the present and future. Carbon nanostructure can be obtained by severe processing techniques such as arc discharge, chemical deposition and catalyzed pyrolysis of organic compounds. In this study we used hydrothermal methods for obtaining nanostructured composites of carbon / clay. To this end, we used coir dust and special clays. The samples were characterized by infrared spectroscopy, X-ray diffraction and Raman. The presence of the D band at 1350 cm -1 in the Raman spectrum shows the formation of amorphous carbon with particle size of about 8.85 nm. (author)

  9. Exchange interactions in Fe/Y multilayers

    International Nuclear Information System (INIS)

    Elkabil, R.; Elkaidi, I.; Annouar, F.; Lassri, H.; Hamdoun, A.; Bensassi, B.; Berrada, A.; Krishnan, R.

    2005-01-01

    The magnetization of Fe/Y multilayers has been measured as a function of temperature. A bulk-like T 3/2 temperature dependence of the magnetization is observed for all multilayers in the temperature range 5-300 K. The spin-wave constant B is found to decrease inversely with t Fe . A simple theoretical model with exchange interactions only, and with non-interacting magnons, has been used to explain the temperature dependence of the magnetization and the approximate values for the bulk exchange interaction J b , surface exchange interaction J s and the interlayer exchange interaction J I for various Fe layer thicknesses have been obtained

  10. Structure of Al-CF composites obtained by infiltration methods

    Directory of Open Access Journals (Sweden)

    A. Dolata-Grosz

    2011-04-01

    Full Text Available The structure of the composites obtained in infiltration processes 2D and 3D carbon preform by liquid Al alloy have been presented in thispaper. An aluminum alloy with silicon and manganese AlSi9Mn (trimal 37-TR37 was applied in the researches. As the reinforcementused carbon perform prepared with various protective barriers such as the nickel coating, the coating of silicon carbide and pyrolyticcarbon coating. Carbon preforms was prepared at the Institute for Lightweight Structures and Polymer Technology (ILK TU Dresden andat the Institute of Technology and Ceramic Systems (Fraunhofer-IKTS. The process of infiltration of carbon perform by liquid aluminiumalloy was carried out using a pressure-vacuum infiltration on the Degussa press and gas-pressure infiltration (GPI in an autoclavedesigned and built at the Department of Materials Technology at the Silesian University of Technology. The obtained composites werecharacterized by a regular shape, with no surface casting defects. The best connection of components was observed in AlSi9Mn/Cf(Nicomposite, obtained by gas-pressure infiltration method (GPI. On metallographic specimens, good interface between fibres and thealuminium matrix were observed. The obtained research results justify the application of nickel coatings on the fibres. During the failurecrack propagated across fiber. There was no presence of aluminum carbide on the fiber-matrix. It can be assumed that the composite willbe characterized by the good mechanical properties. However, this requires further experimental verification planned in the next stage of research, in the project realized within the DFG program: "3D textile reinforced aluminium matrix composites for complex loadingsituations in lightweight automobile and machine parts".

  11. Some mutants in maize obtained by irradiation with thermal neutrons

    International Nuclear Information System (INIS)

    Diaconu, P.

    1993-01-01

    Irradiation was carried out at the Bucharest Institute of Atomic Physics and the National Laboratory Brookhaven, USA. A description is given of 22 genic mutants affecting leaf color, plant size, and branching capacity. Characteristics related to pollen fertility and the vegetative period were affected in all the mutants. Improvement of pollen fertility was attempted over four generations without success. The maize mutants obtained by irradiation may be considered as being without practical significance. (author). 7 figs., 1 tab. 11 ref

  12. System for obtaining biogas. System zur Gewinnung von Biogas

    Energy Technology Data Exchange (ETDEWEB)

    Anon.

    1985-01-17

    The invention refers to a system for obtaining biogas from organic substances in at least one drum reactor, which is situated in a container accepting a liquid and which is driven so that it rotates preferably around its horizontal drum axis. It is distinguished by the fact that for at least one drum reactor acting as the main reactor there is at least one further reactor ahead of it for the pre-treatment or pre-fermentation of the substances.

  13. Unsteady aerodynamic coefficients obtained by a compressible vortex lattice method.

    OpenAIRE

    Fabiano Hernandes

    2009-01-01

    Unsteady solutions for the aerodynamic coefficients of a thin airfoil in compressible subsonic or supersonic flows are studied. The lift, the pitch moment, and pressure coefficients are obtained numerically for the following motions: the indicial response (unit step function) of the airfoil, i.e., a sudden change in the angle of attack; a thin airfoil penetrating into a sharp edge gust (for several gust speed ratios); a thin airfoil penetrating into a one-minus-cosine gust and sinusoidal gust...

  14. Microbiological quality of five potato products obtained at retail markets.

    OpenAIRE

    Duran, A P; Swartzentruber, A; Lanier, J M; Wentz, B A; Schwab, A H; Barnard, R J; Read, R B

    1982-01-01

    The microbiological quality of frozen hash brown potatoes, dried hash brown potatoes with onions, frozen french fried potatoes, dried instant mashed potatoes, and potato salad was determined by a national sampling at the retail level. A wide range of results was obtained, with most sampling units of each products having excellent microbiological quality. Geometric mean aerobic plate counts were as follows: dried hash brown potatoes, 270/g; frozen hash brown potatoes with onions, 580/g; frozen...

  15. Comparison of mentha extracts obtained by different extraction methods

    Directory of Open Access Journals (Sweden)

    Milić Slavica

    2006-01-01

    Full Text Available The different methods of mentha extraction, such as steam distillation, extraction by methylene chloride (Soxhlet extraction and supercritical fluid extraction (SFE by carbon dioxide (CO J were investigated. SFE by CO, was performed at pressure of 100 bar and temperature of40°C. The extraction yield, as well as qualitative and quantitative composition of obtained extracts, determined by GC-MS method, were compared.

  16. Bainite obtaining in cast iron with carbides castings

    Directory of Open Access Journals (Sweden)

    S. Pietrowski

    2010-01-01

    Full Text Available In these paper the possibility of upper and lower bainite obtaining in cast iron with carbides castings are presented. Conditions, when in cast iron with carbides castings during continuous free air cooling austenite transformation to upper bainite or its mixture with lower bainte proceeds, have been given. A mechanism of this transformation has been given, Si, Ni, Mn and Mo distribution in the eutectic cell has been tested and hardness of tested castings has been determined.

  17. [Lymphoscintigrams with anatomical landmarks obtained with vector graphics].

    Science.gov (United States)

    Rubini, Giuseppe; Antonica, Filippo; Renna, Maria Antonia; Ferrari, Cristina; Iuele, Francesca; Stabile Ianora, Antonio Amato; Losco, Matteo; Niccoli Asabella, Artor

    2012-11-01

    Nuclear medicine images are difficult to interpret because they do not include anatomical details. The aim of this study was to obtain lymphoscintigrams with anatomical landmarks that could be easily interpreted by General Physicians. Traditional lymphoscintigrams were processed with Adobe© Photoshop® CS6 and converted into vector images created by Illustrator®. The combination with a silhouette vector improved image interpretation, without resulting in longer radiation exposure or acquisition times.

  18. A metastable Mg11Sm phase obtained by rapid solidification

    International Nuclear Information System (INIS)

    Budurov, S.

    1993-01-01

    Molten Mg-Sm alloys with a Sm concentration of 4.93, 6.86, and 8.35 at.% were rapidly soldified with the aid of a shock wave gun device. Investigations of the obtained splats were performed with the aid of DSC, X-ray analysis, and metallography. Rapid soldification of the eutectic MgSm 8.35 alloy forms a new Im3m-type phase. (orig.)

  19. [Biotechnological cultivation of edible macrofungi: an alternative for obtaining nutraceutics].

    Science.gov (United States)

    Suárez Arango, Carolina; Nieto, Ivonne Jeannette

    2013-01-03

    Macromycetes have been part of the human culture for thousand years, and have been reported as food in the most important civilizations in history. Many nutraceutical properties of macromycetes have been described, such as anti-cancer, anti-tumour, cholesterol lowering, antiviral, antibacterial, or immunomodulatory, among others. Given that production of mushrooms by traditional cultivation and extraction of bioactive metabolites is very difficult in some cases, biotechnology is essential for the development of profitable and productive techniques for obtaining these metabolites. It is the development of this technology, and the ease in which it enables the use of its variables that has allowed mycelium to be cultivated in liquid medium of macrofungi, with a significant reduction in time and an increased production of metabolites. This increased production has led to the study of compounds that have medicinal, nutriceutical and quasi-farmaceutical potential, in the exhausted media and the mycelium. The aim of this review is to provide an overview of the use of liquid-state fermentation as a technological tool for obtaining edible fungi, and the study of these and their metabolites, by describing the different cultivation conditions used in recent years, as well as the results obtained. The relevance of Agaricus, Flammulina, Grifola, Pleurotus and Lentinula genera, will also be discussed, with emphasis on the last one, since Shiitake has been always considered as the ultimate medicinal mushroom. Copyright © 2011 Revista Iberoamericana de Micología. Published by Elsevier España, S.L. All rights reserved.

  20. Secondary electron images obtained with a standard PEEM set up

    International Nuclear Information System (INIS)

    Benka, O.; Zeppenfeld, P.

    2004-01-01

    Secondary electron images excited by 3 to 4.3 keV electrons are obtained with a standard photoelectron electron emission microscope (PEEM) set up equipped with an imaging energy filter (IEF). The electron gun was mounted on a standard PEEM entrance flange at an angle of 25 o with respect to the sample surface. A low extraction voltage of 500 V was used to minimize the deflection of the electron beam by the PEEM extraction electrode. The secondary electron images are compared to photoelectron images excited by a standard 4.9 eV UV lamp. In the case of a Cu pattern on a Si substrate it is found that the lateral resolution without the IEF is about the same for electron and photon excitation but that the relative electron emission intensities are very different. The use of the IEF-reduces the lateral resolution. Images for secondary electron energies between eV 1 and eV 2 were obtained by setting the IEF to -V 1 and -V 2 ∼ -(V 1 + 5V) potentials and taking the difference of both images. Images up to 100 eV electron energies were recorded. The lateral resolution is in the range of μm. The material contrast obtained in these difference images are discussed in terms of a secondary electron and photoelectron emission model and secondary electron energy spectra measured with a LEED-Auger spectrometer. (author)

  1. THE TECHNOLOGY OF PASTE FROM SUGAR BEET OBTAINING

    Directory of Open Access Journals (Sweden)

    M. G. Magomedov

    2014-01-01

    Full Text Available We considered a new technology for processing sugar beet into intermediate product for the food industry. Nowadays sugar beet is mainly used for processing into granulated sugar. In the granulated sugar obtaining sugar beet undergoes deep extraction of all nutrients: proteins, minerals, pectin, organic acids, preventing the crystallization process, and then the refined product (granulated sugar with a mass fraction of sucrose not less than 99.75% is obtained. We developed a technology for producing a sugar beet paste, which allows to preserve both sucrose, and almost all useful for human food substances containing in beet. A sugar beet paste is a valuable food product. Carbohydrates, organic acids, minerals, proteins, dietary fibers and vitamins are found in it. The block diagram of a sugar beet paste is given in the article. Technology of obtaining a sugar beet paste was tested under production conditions at the cannery (Joint Stock Company "Sadovoye" Liskinsky district,. Storozhevoe village, Voronezh region. The chemical composition of the paste (Dry Substances = 40% was determined, the degree of meeting of daily requirement for nutrients was calculated. 100 g of the product satisfy the daily requirement for dietary fiber by 42.5%, organic acids by 27.5% potassium by 24.0%, magnesium by 40.0%, iron by 26.7%. The sugar beet paste can be used as a semi-finished product in the confectionery, bakery, food concentrates industry, for products with increased nutritional value, as well as the finished product instead of marmalade and jam.

  2. Obtaining of Peracetic Cellulose from Oat Straw for Paper Manufacturing

    Directory of Open Access Journals (Sweden)

    Tetyana V. Zelenchuk

    2017-10-01

    Full Text Available Background. Development of technology for obtaining peracetic pulp from oat straw and its use in the production of one of the paper mass types. Objective. Determination of peracetic cooking technological parameters’ optimal values for oat straw peracetic cellulose quality indicators. Methods. The oat straw cooking was carried out with peracetic acid at 95 ± 1 °C from 90 to 180 min for hydromodulus 8:1 and 7:1, using a sodium tungstate catalyst. To determine the oat straw peracetic cellulose mechanical indexes, laboratory samples of paper weighing 70 g/m2 were made. Results. Technological parameters’ optimum values (temperature, cooking duration, hydromodulus, hydrogen peroxide and acetic acid concentration for the oat straw delignification process were established. It is shown that the sodium tungstate catalyst addition to the cooking solution at a rate of up to 1 % of the plant raw material weight helps to reduce the lignin content in cellulose to 15 %. A diagram of the cellulose yield dependence on its residual lignin content for various methods of non-wood plant material species delignification is constructed. The high efficiency of the peracetic method for obtaining cellulose from non-wood plant raw materials, in particular from oat straw, has been confirmed. It is determined that the obtained peracetic cellulose from oat straw has high mechanical indexes. Conclusions. Oat straw peracetic cellulose can be used for the production of paper and cardboard mass types, in particular wrapping paper.

  3. Irradiation with protons in order to obtain new rice varieties

    International Nuclear Information System (INIS)

    Gonzalez, Maria C.; Cristo, Elizabeth; Fuentes, Jorge L.

    2001-01-01

    In the Laboratory of Genetics and Improvement of the National Institute of Agricultural Sciences was developed a Program of Genetic Improvement using Biotechnical and Nuclear Techniques in order to obtain new rice varieties of high yield potential under drought stress condition. For them different explants types were used starting from seeds of the Cuban variety of rice Amistad 82 irradiated with protons in dose of 10, 20, 30, 40, 50, 60, 70, 80, 90 and 100 Gy. The explants were cultivated in vitro in order to obtaining callus and later plant regenerate. The plant selected in vitro was multiplied being carried out several selection cycles under field conditions. A remarkable stimulation was observed from the regeneration of plants when using dose of 20 Gy and it was possible to select 4 promising lines that differ of the donor as for cycle, architecture of the plant and tolerance to drought. Tjis result demonstrates the potentialities of this radiation source for obtaining of new rice varieties

  4. Polythiophene films obtained by polymerization under atmospheric pressure plasma conditions

    Energy Technology Data Exchange (ETDEWEB)

    Teslaru, T.; Topala, I., E-mail: ionut.topala@uaic.ro; Dobromir, M.; Pohoata, V.; Curecheriu, L.; Dumitrascu, N.

    2016-02-01

    The present work describes the experimental arrangement used to initiate polymerization reactions of thiophene monomer based on a dielectric barrier discharge with plane – parallel geometry, working at atmospheric pressure in argon, in turn to obtain conductive polymeric films for different applications. The resulting plasma polymerized polythiophene (pPTh) film was characterized by FT-IR, UV–Vis, XPS spectroscopy, AFM and contact angle measurements. Characterization of pPTh films showed a higher hydrophobic character and roughness, as compared with films obtained by chemical methods, and the thickness is depending on polymerization duration. Also it can conclude that our samples represent oxidised state of pPTh. As a possible application, it analysed in situ the iodine absorption phenomenon in the pPTh matrix and its time evolution by UV–Vis spectroscopy. The presence of iodine 3d{sub 5/2} and 3d{sub 3/2} peaks in the pPTh sample after absorption was identified by XPS spectroscopy. The hydrophobic pPTh film is transformed in a super hydrophilic film after absorption of iodine vapors. - Highlights: • We obtained polythiophene films (pPTh) by atmospheric pressure plasma technique. • The pPTh films showed a hydrophobic character and conducting properties. • The pPTh films were used as sensor for iodine vapors in biological environment.

  5. Porous materials based on foaming solutions obtained from industrial waste

    Science.gov (United States)

    Starostina, I. V.; Antipova, A. N.; Ovcharova, I. V.; Starostina, Yu L.

    2018-03-01

    This study analyzes foam concrete production efficiency. Research has shown the possibility of using a newly-designed protein-based foaming agent to produce porous materials using gypsum and cement binders. The protein foaming agent is obtained by alkaline hydrolysis of a raw mixture consisting of industrial waste in an electromagnetic field. The mixture consists of spent biomass of the Aspergillus niger fungus and dust from burning furnaces used in cement production. Varying the content of the foaming agent allows obtaining gypsum binder-based foam concretes with the density of 200-500 kg/m3 and compressive strength of 0.1-1.0 MPa, which can be used for thermal and sound insulation of building interiors. Cement binders were used to obtain structural and thermal insulation materials with the density of 300-950 kg/m3 and compressive strength of 0.9-9.0 MPa. The maximum operating temperature of cement-based foam concretes is 500°C because it provides the shrinkage of less than 2%.

  6. Histology of periapical lesions obtained during apical surgery.

    Science.gov (United States)

    Schulz, Malte; von Arx, Thomas; Altermatt, Hans Jörg; Bosshardt, Dieter

    2009-05-01

    The aim of this was to evaluate the histology of periapical lesions in teeth treated with periapical surgery. After root-end resection, the root tip was removed together with the periapical pathological tissue. Histologic sectioning was performed on calcified specimens embedded in methylmethacrylate (MMA) and on demineralized specimens embedded in LR White (Fluka, Buchs, Switzerland). The samples were evaluated with light and transmission electron microscopy (TEM). The histologic findings were classified into periapical abscesses, granulomas, or cystic lesions (true or pocket cysts). The final material comprised 70% granulomas, 23% cysts and 5% abscesses, 1% scar tissues, and 1% keratocysts. Six of 125 samples could not be used. The cystic lesions could not be subdivided into pocket or true cysts. All cysts had an epithelium-lined cavity, two of them with cilia-lined epithelium. These results show the high incidence of periapical granulomas among periapical lesions obtained during apical surgery. Periapical abscesses were a rare occasion. The histologic findings from samples obtained during apical surgery may differ from findings obtained by teeth extractions. A determination between pocket and true apical cysts is hardly possible when collecting samples by apical surgery.

  7. Synthesis and characterization of carbon fibers obtained through plasma techniques

    International Nuclear Information System (INIS)

    Valdivia B, M.

    2005-01-01

    The study of carbon, particularly the nano technology is a recent field, the one which has important implications in the science of new materials. It investigation is of great interest for industries producers of ceramic, metallurgy, electronic, energy storage, biomedicine, among others. The diverse application fields are a reason at national as international level, so that many works are focused in the production of nano fibers of carbon. The Thermal plasma applications laboratory (LAPT) of the National Institute of Nuclear Research (ININ), it is carrying out works about carbon nano technology. The present work has as purpose to carry out the synthesis and characterization of the carbon nano fibers which are obtained by electric arch of alternating current (CA) to high frequencies and by a plasma gun of non transferred arch, where are used hydrocarbons like benzene, methane, acetylene like carbon source and ferrocene, nickel, yttrium and cerium oxide like catalysts. For both techniques its were thought about a relationship among hydrocarbon-catalyst that it favored to the nano fibers production. The obtained product of each experiment outlined it was analyzed by transmission electron microscopy (TEM), scanning electron microscopy (SEM) and X-ray diffraction (XRD), analysis with those were obtained pictures and diffraction graphs, which were observed to arrive to one conclusion on the operation conditions, same analysis with those were characterized the tests carried out according to the nano structures formation of carbon. (Author)

  8. Fermi and the Theory of Weak Interactions

    Indian Academy of Sciences (India)

    IAS Admin

    Quantum Field Theory created by Dirac and used by Fermi to describe weak ... of classical electrodynamics (from which the electric field and magnetic field can be obtained .... Universe. However, thanks to weak interactions, this can be done.

  9. Symmetric nuclear matter with Skyrme interaction

    International Nuclear Information System (INIS)

    Manisa, K.; Bicer, A.; Atav, U.

    2010-01-01

    The equation of state (EOS) and some properties of symmetric nuclear matter, such as the saturation density, saturation energy and incompressibility, are obtained by using Skyrme's density-dependent effective nucleon-nucleon interaction.

  10. COMPARISON OF ACCEPTOR PROPERTIES FOR INTERACTION ...

    African Journals Online (AJOL)

    Preferred Customer

    determined by UV-Vis titration method for the adducts. Surprisingly, the ... Interaction of. TCNE and DDQ as π-acceptors with hydrocarbon donors such as cycloalkanes, alkenes, ... obtained from a Shimadzu GC-MS model QP5050 instrument.

  11. Interacting Winds in Eclipsing Symbiotic Systems

    Indian Academy of Sciences (India)

    2016-01-27

    Jan 27, 2016 ... Interacting Winds in Eclipsing Symbiotic Systems – The Case Study of EG Andromedae ... to obtain the physical parameters of a quiescent eclipsing symbiotic system. ... Articles are also visible in Web of Science immediately.

  12. Interaction in Balanced Cross Nested Designs

    Science.gov (United States)

    Ramos, Paulo; Mexia, João T.; Carvalho, Francisco; Covas, Ricardo

    2011-09-01

    Commutative Jordan Algebras, CJA, are used in the study of mixed models obtained, through crossing and nesting, from simpler ones. In the study of cross nested models the interaction between nested factors have been systematically discarded. However this can constitutes an artificial simplification of the models. We point out that, when two crossed factors interact, such interaction is symmetric, both factors playing in it equivalent roles, while when two nested factors interact, the interaction is determined by the nesting factor. These interactions will be called interactions with nesting. In this work we present a coherent formulation of the algebraic structure of models enabling the choice of families of interactions between cross and nested factors using binary operations on CJA.

  13. Cellulose acetate nanocomposite with nanocellulose obtained from bagasse of sugarcane

    International Nuclear Information System (INIS)

    Santos, Frirllei Cardozo dos

    2016-01-01

    This study presents a methodology for the extraction of nanocellulose of sugarcane bagasse for use in nanocomposites with cellulose acetate (CA). The bagasse sugarcane was treated with sodium hydroxide (NaOH) and sodium hypochlorite (NaClO) to remove lignin, hemicellulose, pectin and impurities. For removal of the amorphous region of cellulose microfibrils obtained from alkali treatments were submitted to acid hydrolysis with sulfuric acid under different temperature conditions. The nanocellulose obtained through acid hydrolysis heated at 45 ° C was used for the formulation of nanocomposites by smaller dimensions presented. The films were formulated at different concentrations (1, 2, 4 and 6 wt%) by the casting technique at room temperature. Each alkaline treatment was accompanied by spectrophotometry by infrared and fluorescence analysis to confirm the removal of the amorphous fraction, micrographs carried out by Scanning Electron Microscope (SEM) to display the fiber defibration. The efficiency of acid hydrolysis was confirmed by micrographs obtained by transmission electron microscope (TEM). The crystallinity index (CI) of the nanocrystals was determined by X-ray Diffraction (XRD). The surface of the obtained films were characterized by SEM and AFM microscopy of. The results showed that the sugarcane bagasse is an excellent source for nanocellulose extraction, the amorphous fraction of the fiber can be removed with the suggested alkaline treatments, and hydrolysis with H_2SO_4 was efficient both in the removal of amorphous cellulose as in reducing cellulose nanoscale with a length around 250 nm and a diameter of about 10 nm. The use of heated nanocellulose obtained through hydrolysis was selected after analysis of XRD, it was confirmed that this material had higher when compared to IC hydrolysis at room temperature. The nanocomposites showed high rigidity and brittleness with high crystallinity when compared to the pure polymer film was observed by AFM and SEM

  14. Interactions, Starbursts, and Star Formation

    Directory of Open Access Journals (Sweden)

    Johan H. Knapen

    2015-12-01

    Full Text Available We study how interactions between galaxies affect star formation within them by considering a sample of almost 1500 of the nearest galaxies, all within a distance of ∼45 Mpc. We use the far-IR emission to define the massive star formation rate (SFR, and then normalise the SFR by the stellar mass of the galaxy to obtain the specific star formation rate (SSFR. We explore the distribution of (SSFR with morphological type and with stellar mass. We calculate the relative enhancement of SFR and SSFR for each galaxy by normalising them by the median SFR and SSFR values of individual control samples of similar non-interacting galaxies. We find that both the median SFR and SSFR are enhanced in interacting galaxies, and more so as the degree of interaction is higher. The increase is moderate, reaching a maximum of a factor of 1.9 for the highest degree of interaction (mergers. While the SFR and SSFR are enhanced statistically by interactions, in many individual interacting galaxies they are not enhanced at all. Our study is based on a representative sample of nearby galaxies and should be used to place constraints on studies based on samples of galaxies at larger distances.

  15. Verification of the component accuracy prediction obtained by physical modelling and the elastic simulation of the die/component interaction

    DEFF Research Database (Denmark)

    Ravn, Bjarne Gottlieb; Andersen, Claus Bo; Wanheim, Tarras

    2001-01-01

    There are three demands on a component that must undergo a die-cavity elasticity analysis. The demands to the product are specified as: (i) to be able to measure the loading profile which results in elestic die-cavity deflections; (ii) to be able to compute the elestic deflections using FE; (iii...

  16. Structural characterization of HDPE/LLDPE blend-based nano composites obtained by different blending sequence

    International Nuclear Information System (INIS)

    Passador, Fabio R.; Ruvolo Filho, Adhemar; Pessan, Luiz A.

    2011-01-01

    The blending sequence affects the morphology formation of the nanocomposites. In this work, the blending sequences were explored to determine its influence in the rheological behavior of HDPE/LLDPE/OMMT nanocomposites. The nanocomposites were obtained by melt-intercalation using a mixture of LLDPE-g-MA and HDPE-g-MA as compatibilizer system in a torque rheometer at 180 deg C and five blending sequences were studied. The materials structures were characterized by wide angle X-ray diffraction (WAXD) and by rheological properties. The nanoclay's addition increased the shear viscosity at low shear rates, changing the behavior of HDPE/LLDPE matrix to a Bingham model behavior with an apparent yield stress. Intense interactions were obtained for the blending sequence where LLDPE and/or LLDPE-g-MA were first reinforced with organoclay since the intercalation process occurs preferentially in the amorphous phase. (author)

  17. Thrust evaluation of magneto plasma sail that obtains an electromagnetic thrust from the solar wind

    International Nuclear Information System (INIS)

    Kajimura, Yoshihiro; Funaki, Ikkoh; Usui, Hideyuki; Yamakawa, Hiroshi

    2011-01-01

    Magneto Plasma Sail (MPS) is a propulsion system used in space, which generates its force by the interaction between the solar wind and an inflated magnetic field via a plasma injection. The quantitative evaluation of the thrust increment generated by injecting a plasma jet with a β in less than unity was conducted by three-dimensional hybrid particle-in-cell (PIC) simulations in an ion inertia scale. The injected plasma β in is 0.02 and the ratio of Larmor radius of injected ion to the representative length of the magnetic field is 0.5 at the injection point. In this situation, the obtained thrust of the MPS is 1.6 mN compared with the 0.2 mN of the thrust obtained by the pure magnetic sail since the induced current region on magnetosphere expanded by the magnetic inflation. (author)

  18. Obtainment of silica nanofiber and its preliminary investigation and its effects as reinforcement in polymeric matrix

    International Nuclear Information System (INIS)

    Teixeira, R.S.; Oliveira, G.L.; Silva, F.D.C.; Teofilo, E. T.; Farias, R.C.; Menezes, R.R.

    2016-01-01

    Silica is widely used as fillers in polymers, and may confer flame retardant characteristics and improve mechanical properties. their use usually occurs as spherical nanoparticles or short fibers of. Studies using this reinforce in the form of nanofibers are promising. This analysis proposes to obtain silica nanofibers by blowspinning method in solution (SBS), and investigate its application in polymeric matrix. To synthesize the silica nanofibers it was used a precursor solution that has been subjected to SBS process and calcined for forming the silica layer. The DR-X indicated the obtainment of amorphous silica phase and SEM showed the the fibers are at the nanometer scale. Silica nanofibers were incorporated into filmogenic solution Polyamide 6. Preliminary results showed no improvement in mechanical properties. Future stages propose to verify that the surface chemical modification of silica nanofibers enables interaction charge / matrix. (author)

  19. Development of the NAA Laboratory for an Accreditation Obtains

    International Nuclear Information System (INIS)

    Sri Wardani; Rina M, Th.; Sunarko, M.; Ratnawati, E.

    2004-01-01

    The evaluation of capability of the neutron activation analysis comparative method and laboratory equipment at P2TRR have been performed by analyzed a reference standard materials prepared by NIST, namely: SRM 1646a and SRM 1648 by a both of comparative and ko- NAA methods. From the analysis results used a comparative method shown that the method and laboratory equipment used at P2TRR obtained in a good precision, accuracy and high sensitivity. In this experiments a few elements could analyzed, namely: V, Ti, Mn, Cl, As, Sm, La, Na, Sc, Cr, Fe, Co, Se, Br, In, Sb, Ba, Cs, Ce, W, U, and Zn. The deviation values results compared with certificate values (NIST) obtained in a range 2 - 12.5% with confidence levels in range 68 - 98%. While, a reference standard material of SRM 1648 analyzed by k 0 -NAA method shown that the method need more research and study continued. From the qualitatively analysis results for short-lived nuclides category analysis by k 0 -NAA could identified a few elements, namely: V, Cu, Na, As and U with standard deviation values in range 1- 11% and limit detection values are 1.6 (U), 6.4 (Cu), 11.2 (V), 73.3 (As) and 199.9 (Na) μg/g for a SRM 1648. For analysis of CRM 8 the results obtained on standard deviation values in range 1 - 13 % and limit detection of 0.71 (Cu), 1.2 (As), 2.4 (V) and 375.9 (Na) μg/g. (author)

  20. Tin dioxide nanostructured thin films obtained through polymeric precursor method

    Directory of Open Access Journals (Sweden)

    Marcelo Antônio Dal Santos

    2012-11-01

    Full Text Available Tin dioxide (SnO2 nanostructured thin films with low proportion of defects and low roughness were produced through the systematic control of temperature and viscosity of the precursor solutions used for thin films deposition. These solutions were obtained through the citrate method and the films were deposited through the ‘dip-coating’ technique on glass substrate and after thermal treatment at 470ºC/4h, they were characterized both structurally and morphologically through the X-ray diffractometry, optic microscopy, scanning electronic microscopy, atomic force microscopy, X-ray fluorescence, UV-Vis absorption spectroscopy and X-ray excited photoelectrons spectroscopy. The film thickness was obtained through scanning electronic microscopy of the films cross-section and correlated to the proportion of Sn and Si obtained through X-ray fluorescence. X-ray diffractometry of the films revealed the presence of peaks corresponding to the SnO2 crystalline phase, overlapping a wide peak between 20 and 30º (2?, characteristic of the glass substrate. Optic microscopy, Scanning electronic microscopy and atomic force microscopy revealed homogeneous films, with low roughness, suitable to several applications such as sensors and transparent electrodes. It could be observed through the UV-Vis absorption analysis that the films presented high optical transparency and ‘band gap’ energy 4.36 eV. The X-ray excited photoelectron spectroscopy confirmed the presence of SnO2, as well as traces of the elements present in the glass substrate and residual carbon from the thermal treatment of the films.

  1. Preparation of membranes from cellulose obtained of sugarcane bagasse

    International Nuclear Information System (INIS)

    Pereira, Paulo Henrique Fernandes; Cioffi, Maria Odila Hilario; Voorwald, Herman Jacobus Cornelis; Pinho, Maria Noberta de; Silva, Maria Lucia Caetano Pinto da

    2010-01-01

    In this work, cellulose obtained from sugarcane bagasse to produce both cellulose and acetylated cellulose to prepare asymmetric membranes. Membranes was procedure used a mixture of materials of DMAc/ LiCl systemic in different conditions. Cellulose and acetylated cellulose were characterized by thermogravimetric (TG), Xray diffraction (XRD) and scanning Electron Microscopy (SEM). Observed less stability thermal of acetylated cellulose when compared of cellulose. All membranes procedure were asymmetric, characterized by presence of a dense skin and porous support can be observed. SEM showed that the morphology of the superficial of membranes depends on the method preparation. (author)

  2. Antimicrobial material obtained from pulping white paper waste

    International Nuclear Information System (INIS)

    Angioletto, E.; Fiori, M.A.; Pitch, C.T.; Mendes, E.; Oliveira, C.M.; Melo, C.R.; Riella, H.G.

    2011-01-01

    The paper industry produces white waste, consisting of 45% kaolin, 45% calcium carbonate and 10% cellulose. After calcination at 903K for two hours, the cellulose is burnt and decomposed kaolin in metakaolin. Held treatment of the calcined material with hydrochloric acid to remove calcium carbonate. The metakaolin is treated with sodium hydroxide solution to obtain the type of zeolite 4A. The zeolites were characterized using XRD, XRF and SEM. The zeolite was subjected to ion exchange with zinc sulphate and silver nitrate at room temperature, stirring, for six hours. This material was tested with Staphylococcus aureus and Escherichia coli, to get excellent results with regard to bactericidal properties.(author)

  3. Techniques for combining isotopic images obtained at different energies

    International Nuclear Information System (INIS)

    Soussaline, F.; Di Paola, R.; Bazin, J.P.

    1976-01-01

    The technique described should be considered as a first step towards the classification of scintigraphic data where the energy is included. As in all such studies the interpretation of the resulting images is not necessarily at first evident, and certain experience needs to be established. This applies in particular to the images obtained with the higher factors. It is possible that the use of this technique may resolve, without requiring a priori information, the problem previously encountered using the other 'subtraction' type techniques [fr

  4. Easy process to obtain suspended graphene flakes on TEM grids

    International Nuclear Information System (INIS)

    Gonçalves, Hugo; Fernandes, Joel; Moura, Cacilda; Schellenberg, Peter; Belsley, Michael; Alves, Luís

    2015-01-01

    Much of the ongoing research on graphene requires free-hanging (suspended) graphene to eliminate any influence from underlying substrates. Several methods have been developed for its preparation but they are either very complex or not completely reliable. Here, we describe a simple method for the transfer of graphene single layers from glass or silicon substrates onto TEM grids. The method uses a carrier film for the transfer process. By optimizing the process yields greater than 60% were achieved. The integrity of the transferred films was confirmed using Raman spectroscopy; successful suspension of both mono- and double-layer graphene sheets was obtained. (paper)

  5. Concretes of low environmental impact obtained by geopolymerization of Metakaolin

    Science.gov (United States)

    Sandoval, D. C.; Montaño, A. M.; González, C. P.; Gutiérrez, J.

    2018-04-01

    This work shows results of partial replacement of Portland Type I cement®, by geopolymers obtained through alkaline activation of Metakaolin, in concrete mixtures. Replacement was made with 10%, 20% and 30% of geopolymers at 7, 14, 28 and 90 days of setting. Cement samples was mechanical and electrically tested. Mechanical resistance to compression assay shows that the best percentage of replacement is 10% for every setting time; highest value is 26.75MPa at 90 days. Nyquist diagrams at different times of immersion exhibit same trend: decreasing of electrical resistance as time of assay goes by.

  6. Obtaining a new variety of rape by biotechnology

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Z H; Cun, S X; Zhang, Z Z; Wang, W F; Zhang, T H; Li, W B; Zhang, L H [Institute of Genetics, Chinese Academy of Sciences, Beijing (China); [Laboratory of Genetic Engineering, Yunnan Academy of Agricultural Sciences, Kunming (China)

    1990-01-01

    Full text: High-frequency induction of pollen embryoids and plantlets of rape was obtained by stepped float anther culture. In addition, somatic embryoids and plantlets were induced with a high frequency from several species by cell suspension culture. The erucic acid (EA) content of embryoids was analysed by a micro-analysis technique and a semi-micro-analysis of glucosinolates (GS) content in culture was used. A new variety 'H86-166' with low EA and low GS content was selected by these techniques. It gave a yield of 3169 kg/ha and has been released for commercial production on about 1000 ha in Yunnan Province. (author)

  7. Obtainment of cerium dioxide for use as spectrochemical standard

    International Nuclear Information System (INIS)

    Silva Queiroz, C.A. da; Hespanhol, E.C.B.; Abrao, A.

    1992-01-01

    This paper describes a simple method for cerium separation and purification. Cerium is previously precipitated with N H 3 /air/H 2 O 2 system in a mixed chlorides solution obtained from Brazilian monazite treatment. The cerium fraction as cerium chloride is run down throughout a strong cationic resin bed and then the rare earth impurities separation is done by elution of the resin with separation ammonium salt of EDTA. None retainer ion is used in the purification technique by ion exchange. (author)

  8. The obtaining a high-grade gadolinium concentrate

    International Nuclear Information System (INIS)

    Soltysiak, I.; Ozga, W.

    1982-01-01

    Gadolinium concentrates obtained by the fractional precipitation of lanthanon-potassium double chromates were separated by ion exchange with 0,4 M lactic acid solution in the presence of 0,1 M ammonium nitrate at pH of the medium 2,95-3,4. It was found out, that using the fractional precipitation of lanthanon-potassium double chromates (as the fast and cheap method that does not need special equipment) together with ion exchange separation with lactic acid solution as the eluent gave a highgrade gadolinium concentrate in a quick and economical way. (author)

  9. Lithium storage into carbonaceous materials obtained from sugarcane bagasse

    International Nuclear Information System (INIS)

    Matsubara, Elaine Y.; Lala, Stella M.; Rosolen, Jose Mauricio

    2010-01-01

    Carbonaceous materials with different structures are prepared by carbonization of sugarcane bagasse. Depending on carbonization conditions, it is possible to obtain soot rich in flakes or in honeycomb-shaped micrometric particles, whose concentration has large influence on lithium storage into electrodes. The soot rich in honeycomb-shaped particles provides the best electrochemical performance, with a reversible specific capacity of 310 mAh g -1 . The results suggest that the sugarcane bagasse can be potentially used in the design of anodic materials for lithium ion batteries. (author)

  10. Obtaining and Estimating Low Noise Floors in Vibration Sensors

    DEFF Research Database (Denmark)

    Brincker, Rune; Larsen, Jesper Abildgaard

    2007-01-01

    For some applications like seismic applications and measuring ambient vibrations in structures, it is essential that the noise floors of the sensors and other system components are low and known to the user. Some of the most important noise sources are reviewed and it is discussed how the sensor...... can be designed in order to obtain a low noise floor. Techniques to estimate the noise floors for sensors are reviewed and are demonstrated on a commercial commonly used sensor for vibration testing. It is illustrated how the noise floor can be calculated using the coherence between simultaneous...

  11. Peritoneal tuberculosis: how to obtain a confident diagnosis?

    International Nuclear Information System (INIS)

    Peixoto Filho, Anibal Araujo Alves; Peixoto, Mila Correia Gois; D'Ippolito, Giuseppe

    2007-01-01

    The peritoneum is a frequent site of involvement by peritoneal tuberculosis. Generally, computed tomography appears to be the imaging modality of choice in the detection and assessment of abdominal tuberculosis. The computed tomography findings can help in the diagnosis of peritoneal tuberculosis, that is confirmed by a positive culture or hystologic analysis of biopsy obtained through laparoscopic examination. Peritoneal carcinomatosis is the main differential diagnosis. In this article we present the spectrum of tomographic manifestation of peritoneal tuberculosis and how we can differentiate it from peritoneal carcinomatosis. (author)

  12. A novel heuristic method for obtaining S-boxes

    International Nuclear Information System (INIS)

    Chen Guo

    2008-01-01

    An efficient algorithm named chaotic multi-swapping and simulated annealing (CMSSA) for obtaining cryptographically strong 8 x 8 S-boxes is presented. The method is based on chaotic maps and simulated annealing. In addition, cryptographic properties such as bijectivity, strict avalanche criterion, nonlinearity, output bits independence criterion and equiprobable input/output XOR distribution are analyzed in detail for the S-box produced. The results of numerical analysis show that the box has nearly fulfilled the criteria for a cryptographically strong S-box and can effectively resist several attacks

  13. Obtaining and Using Images in the Clinical Setting

    International Nuclear Information System (INIS)

    Cendales, Ricardo

    2009-01-01

    Currently small electronic devices capable of producing high quality images are available. The massive use of these devices has become common in the clinical setting as medical images represent a useful tool to document relevant clinical conditions for patient diagnosis, treatment and follow-up. Besides, clinical images are beneficial for legal, scientific and academic purposes. The extended practice without proper ethical guidelines might represent a significant risk for the protection of patient rights and clinical practice. This document discusses risks and duties when obtaining medical images, and presents some arguments on institutional and professional responsibilities around the definition of policies regarding the protection of privacy and dignity of the patient.

  14. Methods for obtaining sorption data from uranium-series disequilibria

    International Nuclear Information System (INIS)

    Finnegan, D.L.; Bryant, E.A.

    1987-12-01

    Two possible methods have been identified for obtaining in situ retardation factors from measurements of uranium-series disequilibria at Yucca Mountain. The first method would make use of the enhanced 234 U/ 238 U ratio in groundwater to derive a signature for exchangeable uranium sorbed on the rock; the exchangeable uranium would be leached and assayed. The second method would use the ratio of 222 Rn to 234 U in solution, corrected for weathering, to infer the retardation factor for uranium. Similar methods could be applied to thorium and radium

  15. Charm and particle production in neutrino interactions

    International Nuclear Information System (INIS)

    Cazzoli, E.G.; Cnops, A.M.; Connolly, P.L.; Louttit, R.I.; Murtagh, M.J.; Palmer, R.B.; Samios, N.P.; Tso, T.T.; Williams, H.H.

    1976-01-01

    Ten strange particles were observed in a total of 1086 charged current neutrino interactions obtained in the analysis of 482,000 pictures taken in the Brookhaven Cryogenic 7' Bubble Chamber filled with hydrogen and deuterium. Details of these events are presented together with rates for associated strange particle and ΔS = +-ΔQ production in neutrino interactions

  16. Domain Specific Languages for Interactive Web Services

    DEFF Research Database (Denmark)

    Brabrand, Claus

    This dissertation shows how domain specific languages may be applied to the domain of interactive Web services to obtain flexible, safe, and efficient solutions. We show how each of four key aspects of interactive Web services involving sessions, dynamic creation of HTML/XML documents, form field......, , that supports virtually all aspects of the development of interactive Web services and provides flexible, safe, and efficient solutions....

  17. Requirements to obtain the recognition of radiological protection experts

    International Nuclear Information System (INIS)

    Arguelles, R.; Villarroel, R.; Senderos, V.; Campos, R.; Pinos, M.; Ponjuan, G.; Franco, P.; Rueda, D.

    2003-01-01

    The scope of this paper is to summarize the general requirements related to education, training and skill of the individual to obtain the recognition of radiological protection experts on ionizing radiation (experts on radiological protection- RP). There has been established two levels according to the grade of responsibility: Qualified expert provided with a diploma given by de Nuclear Safety Council. Technician expert on radiological protection whose certification is made by the Qualified expert that supervise their work. To obtain the diploma of qualified expert is required an official degree, a title of Architecture, Engineering or equivalent in case of no national degrees; specific training on radiological protection (300 hours) and the knowledge on safety and radiological protection of the facilities to be supervised. Three years of experience on radiological protection must be proved. To get the recognition of technician expert on radiological protection is required Formacion Profesional de Grado Superior or equivalent and specific training on safety and radiological protection. Knowledge on basis and principles of radiological protection are required. According to the type of the facilities to be supervised there are two models: A model: to deal with facilities included in RD 1836/1999 (nuclear and radioactive facilities). B model: to deal with medical X rays facilities approved under RD 1891/1991 three months of experience on the selected model must be proved. (Author)

  18. A model on how to obtain data from botanical practitioners.

    Science.gov (United States)

    Elsas, Siegward M

    2015-11-01

    This paper addresses the challenge on how to obtain information from practitioners with experience in using medicinal plants. Collecting information on medicinal uses of plants is very challenging; since botanical remedies are used within the context of multiple differing medical systems, practitioners differ in training from Western physicians and scientists, and active ingredients of botanicals vary with preparation method, growth, and harvest conditions. A model on how useful data on safety and efficacy can be obtained from botanical practitioners is presented, based on methods developed by the association of anthroposophic physicians in Europe, a system of integrative medicine which includes the use of botanicals and is practiced mostly by medical doctors. Decades of experience by hundreds of practitioners are summarized and made accessible in a manual, which alphabetically lists the most commonly used botanicals and describes the most successful therapeutic experiences which could be confirmed by several of the contributing practitioners. This approach of continuous, multilingual systematic collection of successful therapeutic experiences within a community of practitioners with similar goals and a common therapeutic framework can be used not only for the training of successful future botanical practitioners, but also for helping to identify promising botanicals for scientific research and to further their development, and could support their official registration with governing bodies in countries of their use. This article is part of a Special Issue entitled "Botanicals for Epilepsy". Copyright © 2015 Elsevier Inc. All rights reserved.

  19. Comparison of Vespula germanica venoms obtained from different sources.

    Science.gov (United States)

    Sanchez, F; Blanca, M; Miranda, A; Carmona, M J; Garcia, J; Fernandez, J; Torres, M J; Rondon, M C; Juarez, C

    1994-08-01

    This study was carried out to compare the allergenic potency of Vespula germanica (VG) venoms extracted by different methods and commercially available venoms from Vespula species currently used for in vivo and in vitro studies including immunotherapy. Pure VG venom was used as the reference material. Protein content and enzymatic and allergenic properties of all venoms studied were determined by dye stain reagent, hyaluronidase and phospholipase A1B enzyme activities, and radioallergosorbent test inhibition studies, respectively. Radioallergosorbent test discs sensitized with commercial and pure VG venom were compared using specific IgE antibodies from subjects allergic to VG venom. The data obtained indicate that there were important differences in the allergenic potency between the Vespula species venoms employed for in vivo and/or in vitro assays, VG venom obtained by sac dissection, and pure VG venom. These results indicate that venoms from Vespula species used for in vitro and in vivo tests have a lower concentration of allergens and contain nonvenom proteins. These data should be taken into account when these vespid venoms are used for diagnostic purposes and also when evaluating immunotherapy studies.

  20. Characterisation of Aronia powders obtained by different drying processes.

    Science.gov (United States)

    Horszwald, Anna; Julien, Heritier; Andlauer, Wilfried

    2013-12-01

    Nowadays, food industry is facing challenges connected with the preservation of the highest possible quality of fruit products obtained after processing. Attention has been drawn to Aronia fruits due to numerous health promoting properties of their products. However, processing of Aronia, like other berries, leads to difficulties that stem from the preparation process, as well as changes in the composition of bioactive compounds. Consequently, in this study, Aronia commercial juice was subjected to different drying techniques: spray drying, freeze drying and vacuum drying with the temperature range of 40-80 °C. All powders obtained had a high content of total polyphenols. Powders gained by spray drying had the highest values which corresponded to a high content of total flavonoids, total monomeric anthocyanins, cyaniding-3-glucoside and total proanthocyanidins. Analysis of the results exhibited a correlation between selected bioactive compounds and their antioxidant capacity. In conclusion, drying techniques have an impact on selected quality parameters, and different drying techniques cause changes in the content of bioactives analysed. Spray drying can be recommended for preservation of bioactives in Aronia products. Powder quality depends mainly on the process applied and parameters chosen. Therefore, Aronia powders production should be adapted to the requirements and design of the final product. Copyright © 2013 Elsevier Ltd. All rights reserved.

  1. Genotoxicity of corrosion eluates obtained from orthodontic brackets in vitro.

    Science.gov (United States)

    Angelieri, Fernanda; Marcondes, Joao Paulo C; de Almeida, Danielle Cristina; Salvadori, Daisy M F; Ribeiro, Daniel A

    2011-04-01

    The purpose of this study was to evaluate whether corrosion eluates obtained from commercially available orthodontic brackets are able to induce genetic damage in vitro. Genotoxicity was assessed by the single cell gel (comet) assay using Chinese hamster ovary (CHO) cells. The following orthodontic metallic brackets were used: Morelli (Sorocaba, Brazil); Abzil (São José do Rio Preto, Brazil); Dentaurum (Pforzheim, Germany); and 3M Unitek (Puchheim, Germany). Each dental bracket was submitted to a corrosion process in a solution containing equal amounts of acetic acid and sodium chloride at 0.1 M concentration for 1, 3, 7, 14, 21, 35, and 70 days. CHO cells were exposed to eluates for 30 minutes at 37°C. The negative control was treated with the same solution used for corrosion process for 30 minutes at 37°C. Independent positive control was performed with methyl methanesulfonate (MMS) (Sigma Aldrich, St. Louis, Mo) at 1 ug/mL for 1 hour. None of the eluates was found to exhibit genotoxicity, regardless of the different commercial brands of orthodontic appliance used. In summary, our results indicate corrosion eluates obtained from orthodontic brackets do not induce genetic damage as assessed by single cell gel (comet) assay. Copyright © 2011 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

  2. Thermal Stabilization study of polyacrylonitrile fiber obtained by extrusion

    Directory of Open Access Journals (Sweden)

    Robson Fleming Ribeiro

    2015-12-01

    Full Text Available A low cost and environmental friendly extrusion process of the Polyacrylonitrile (PAN polymer was viabilized by using the 1,2,3-propanetriol (glycerol as a plasticizer. The characterization of the fibers obtained by this process was the object of study in the present work. The PAN fibers were heat treated in the range of 200 °C to 300 °C, which is the temperature range related to the stabilization/oxidation step. This is a limiting phase during the carbon fiber processing. The characterization of the fibers was made using infrared spectroscopy, thermal analysis and microscopy. TGA revealed that the degradation of the extruded PAN co-VA fibers between 250 °C and 350 °C, corresponded to a 9% weight loss to samples analyzed under oxidizing atmosphere and 18% when the samples were analyzed under inert atmosphere. DSC showed that the exothermic reactions on the extruded PAN co-VA fibers under oxidizing synthetic air was broader and the cyclization started at a lower temperature compared under inert atmosphere. Furthermore, FT-IR analysis correlated with thermal anlysis showed that the stabilization/oxidation process of the extruded PAN fiber were coherent with other works that used PAN fibers obtained by other spinning processes.

  3. Nanostructured Thin Films Obtained from Fischer Aminocarbene Complexes

    Directory of Open Access Journals (Sweden)

    Rosa E. Lazo-Jiménez

    2016-03-01

    Full Text Available The synthesis of four amphiphilic organometallic complexes with the general formula RC = M(CO5NH(CH215CH3, where R is a ferrocenyl 2(a-b or a phenyl 4(a-b group as a donor moiety and a Fischer carbene of chromium (0 or tungsten (0 as an acceptor group, are reported. These four push-pull systems formed Langmuir (L monolayers at the air-water interface, which were characterized by isotherms of surface pressure versus molecular area and compression/expansion cycles (hysteresis curves; Brewster angle microscopic images were also obtained. By using the Langmuir–Blodgett (LB method, molecular monolayers were transferred onto glass substrates forming Z-type multilayers. LB films were characterized through ultraviolet-visible spectroscopy, atomic force microscopy and X-ray diffraction techniques. Results indicated that films obtained from 2b complex [(Ferrocenyl(hexadecylaminemethylidene] pentacarbonyl tungsten (0 are the most stable and homogeneous; due to their properties, these materials may be incorporated into organic electronic devices.

  4. Evaluation of quinua lines obtained trough mutagenesis and conventional methods

    International Nuclear Information System (INIS)

    De la Cruz, E.; Garcia, J. M; Gonzalez, J.; Brunner, I.; Rubluo, A.; Guadarrama, S

    2001-01-01

    Chenopodium quinoa is an ancient crop that due to its hardiness, nutritive value, and ability to strive under marginal conditions is considered as a crop for modern times, considering the current demands of highly nutritive products obtained through sustainable agricultural practices. The research on quinua began in Mexico in the early eighties, considering it as an alternative crop to peasants living in impoverished regions, characterised by marginal soils. Research institutions such as the Instituto de Investigacion Agricola del Estado de Mexico (ICAMEX), Colegio de Postgraduados and Universidad Autonoma Chapingo, began to evaluate varieties from South-America and eventually established a breeding programme on quinua. One goal of the quinua research programme in Mexico is the reduction of saponin content, so a mutation breeding approach was designed in the early nineties being the Instituto Nacional de Investigaciones Nucleares (ININ) involved. In the 1999-2000 period, field trials of low saponin putative mutants obtained through irradiation of Barandales variety were performed, including also elite lines supplied by the National Germplasm Bank (NGB) at Chapingo, Mexico. The results from this trials indicate that the low saponin content character in the putative mutants remains in the M5 generation. Also eleven early maturing lines were detected. Climatic conditions prevalent in that period exhibited the resistance of quinua to spring frosts, furthermore, the evaluation of advanced lines from the (NGB) showed high variability regarding to morphological, agronomic and seed quality characters which Hill allow us to advance in the search for superior quinua lines

  5. Combustion behaviour of ultra clean coal obtained by chemical demineralisation

    Energy Technology Data Exchange (ETDEWEB)

    F. Rubiera; A. Arenillas; B. Arias; J.J. Pis; I. Suarez-Ruiz; K.M. Steel; J.W. Patrick [Instituto Nacional del Carbon, CSIC, Oviedo (Spain)

    2003-10-01

    The increasing environmental concern caused by the use of fossil fuels and the concomitant need for improved combustion efficiency is leading to the development of new coal cleaning and utilisation processes. However, the benefits achieved by the removal of most mineral matter from coal either by physical or chemical methods can be annulled if poor coal combustibility characteristics are attained. In this work a high volatile bituminous coal with 6% ash content was subjected to chemical demineralisation via hydrofluoric and nitric acid leaching, the ash content of the clean coal was reduced to 0.3%. The original and treated coals were devolatilised in a drop tube furnace and the structure and morphology of the resultant chars was analysed by optical and scanning electron microscopies. The reactivity characteristics of the chars were studied by isothermal combustion tests in air at different temperatures in a thermogravimetric system. Comparison of the combustion behaviour and pollutant emissions of both coals was conducted in a drop tube furnace operating at 1000{sup o}C. The results of this work indicate that the char obtained from the chemically treated coal presents very different structure, morphology and reactivity behaviour than the char from the original coal. The changes induced by the chemical treatment increased the combustion efficiency determined in the drop tube furnace, in fact higher burnout levels were obtained for the demineralised coal.

  6. Field sludge characterization obtained from inner of pipelines

    Energy Technology Data Exchange (ETDEWEB)

    Nava, N.; Sosa, E.; Alamilla, J.L. [Instituto Mexicano del Petroleo, Programa de Integridad de Ductos, Eje Central Lazaro Cardenas Norte 152, San Bartolo Atepehuacan, C.P. 07730 (Mexico); Knigth, C. [PEMEX Refinacion, Avenida Marina Nacional 329, Edificio B-2, Piso 11, C.P. 11311 (Mexico); Contreras, A. [Instituto Mexicano del Petroleo, Programa de Integridad de Ductos, Eje Central Lazaro Cardenas Norte 152, San Bartolo Atepehuacan, C.P. 07730 (Mexico)], E-mail: acontrer@imp.mx

    2009-11-15

    Physicochemical characterization of sludge obtained from refined hydrocarbons transmission pipeline was carried out through Moessbauer spectroscopy and X-ray diffraction. The Moessbauer and X-ray patterns indicate the presence of corrosion products composed of different iron oxide and sulfide phases. Hematite ({alpha}-Fe{sub 2}O{sub 3}), magnetite (Fe{sub 3}O{sub 4}), maghemite ({gamma}-Fe{sub 2}O{sub 3}), magnetic and superparamagnetic goethite ({alpha}-FeOOH), pyrrhotite (Fe{sub 1-x}S), akaganeite ({beta}-FeOOH), and lepidocrocite ({gamma}-FeOOH) were identified as corrosion products in samples obtained from pipeline transporting Magna and Premium gasoline. For diesel transmission pipeline, hematite, magnetite, and magnetic goethite were identified. Corrosion products follow a simple reaction mechanism of steel dissolution in aerated aqueous media at a near-neutral pH. Chemical composition of the corrosion products depends on H{sub 2}O and sulfur inherent in fluids (traces). These results can be useful for decision-making with regard to pipeline corrosion control.

  7. A method to obtain new cross-sections transport equivalent

    International Nuclear Information System (INIS)

    Palmiotti, G.

    1988-01-01

    We present a method, that allows the calculation, by the mean of variational principle, of equivalent cross-sections in order to take into account the transport and mesh size effects on reactivity variation calculations. The method validation has been made in two and three dimensions geometries. The reactivity variations calculated in three dimensional hexagonal geometry with seven points by subassembly using two sets of equivalent cross-sections for control rods are in a very good agreement with the ones of a transport, extrapolated to zero mesh size, calculation. The difficulty encountered in obtaining a good flux distribution has lead to the utilisation of a single set of equivalent cross-sections calculated by starting from an appropriated R-Z model that allows to take into account also the axial transport effects for the control rod followers. The global results in reactivity variations are still satisfactory with a good performance for the flux distribution. The main interest of the proposed method is the possibility to simulate a full 3D transport calculation, with fine mesh size, using a 3D diffusion code, with a larger mesh size. The results obtained should be affected by uncertainties, which do not exceed ± 4% for a large LMFBR control rod worth and for very different rod configurations. This uncertainty is by far smaller than the experimental uncertainties. (author). 5 refs, 8 figs, 9 tabs

  8. Visual Perception Studies in CT images obtained lo low dose

    International Nuclear Information System (INIS)

    Adame Brooks, D.; Miller-Clemente, R. A.

    2015-01-01

    This paper has as aims to describe a strategy to evaluate the diagnostic quality of obtained images of method for dose reduction, with the purpose of determining the dose value or values from which the image quality is significantly degraded making it insufficient for the diagnostic. To complement and have an estimate of the quality of the images we established a group of measures of objective type, and the diagnostic quality of the images was evaluated through a group of observers using the analysis ROC and LROC. For ROC and LROC analyzes the behavior of the area under the curve in relation to the four proposed dose levels was obtained. For high dose levels, detection was good. The values of area under the curve decreased as the dose rate decreased, falling to values indicating low accuracy in diagnosis. This result indicates that the area under the curve decreases by the dose rate. We conclude that the objective quality measures selected are representative of the changes that occur in the resulting image and provided information on changes in the perception of observers. The experiments ROC and LROC allowed determine the range of dose values from which the image degradation causes a low accuracy in the diagnostic. (Author)

  9. Functional nanostructured titanium nitride films obtained by sputtering magnetron

    International Nuclear Information System (INIS)

    Sanchez, O.; Hernandez-Velez, M.; Navas, D.; Auger, M.A.; Baldonedo, J.L.; Sanz, R.; Pirota, K.R.; Vazquez, M.

    2006-01-01

    Development of new methods in the formation of hollow structures, in particular, nanotubes and nanocages are currently generating a great interest as a consequence of the growing relevance of these nanostructures on many technological fields, ranging from optoelectronics to biotechnology. In this work, we report the formation of titanium nitride (TiN) nanotubes and nanohills via reactive sputtering magnetron processes. Anodic Alumina Membranes (AAM) were used as template substrates to grow the TiN nanostructures. The AAM were obtained through electrochemical anodization processes by using oxalic acid solutions as electrolytes. The nanotubes were produced at temperatures below 100 deg. C, and using a pure titanium (99.995%) sputtering target and nitrogen as reactive gas. The obtained TiN thin films showed surface morphologies adjusted to pore diameter and interpore distance of the substrates, as well as ordered arrays of nanotubes or nanohills depending on the sputtering and template conditions. High Resolution Scanning Electron Microscopy (HRSEM) was used to elucidate both the surface order and morphology of the different grown nanostructures. The crystalline structure of the samples was examined using X-ray Diffraction (XRD) patterns and their qualitative chemical composition by using X-ray Energy Dispersive Spectroscopy (XEDS) in a scanning electron microscopy

  10. Nanostructured Thin Films Obtained from Fischer Aminocarbene Complexes

    Science.gov (United States)

    Lazo-Jiménez, Rosa E.; Ortega-Alfaro, M. Carmen; López-Cortés, José G.; Alvarez-Toledano, Cecilio; Chávez-Carvayar, José Á.; Ignés-Mullol, Jordi; González-Torres, Maykel; Carreón-Castro, Pilar

    2016-01-01

    The synthesis of four amphiphilic organometallic complexes with the general formula RC = M(CO)5NH(CH2)15CH3, where R is a ferrocenyl 2(a-b) or a phenyl 4(a-b) group as a donor moiety and a Fischer carbene of chromium (0) or tungsten (0) as an acceptor group, are reported. These four push-pull systems formed Langmuir (L) monolayers at the air-water interface, which were characterized by isotherms of surface pressure versus molecular area and compression/expansion cycles (hysteresis curves); Brewster angle microscopic images were also obtained. By using the Langmuir–Blodgett (LB) method, molecular monolayers were transferred onto glass substrates forming Z-type multilayers. LB films were characterized through ultraviolet-visible spectroscopy, atomic force microscopy and X-ray diffraction techniques. Results indicated that films obtained from 2b complex [(Ferrocenyl)(hexadecylamine)methylidene] pentacarbonyl tungsten (0) are the most stable and homogeneous; due to their properties, these materials may be incorporated into organic electronic devices. PMID:28773289

  11. Obtaining big data of vegetation using artificial neural network

    Science.gov (United States)

    Ise, T.; Minagawa, M.; Onishi, M.

    2017-12-01

    To carry out predictive studies concerning ecosystems, obtaining appropriate datasets is one of the key factors. Recently, applications of neural network such as deep learning have successfully overcome difficulties in data acquisition and added large datasets for predictive science. For example, deep learning is very powerful in identifying and counting people, cars, etc. However, for vegetation science, deep learning has not been widely used. In general, differing from animals, plants have characteristics of modular growth. For example, numbers of leaves and stems which one individual plant typically possesses are not predetermined but change flexibly according to environmental conditions. This is clearly different from that the standard model of human face has predetermined numbers of parts, such as two eyes, one mouth, and so on. This characteristics of plants can make object identification difficult. In this study, a simple but effective technique was used to overcome the difficulty of visual identification of plants, and automated classification of plant types and quantitative analyses were become possible. For instance, when our method was applied to classify bryophytes, one of the most difficult plant types for computer vision due to their amorphous shapes, the performance of identification model was typically over 90% success. With this technology, it may be possible to obtain the big data of plant type, size, density etc. from satellite and/or drone imageries, in a quantitative manner. this will allow progress in predictive biogeosciences.

  12. Pulsed system for obtaining microdosimetric data with high intensity beams

    International Nuclear Information System (INIS)

    Zaider, M.; Dicello, J.F.; Hiebert, R.D.

    1977-01-01

    The use of heavy particle accelerators for radiation therapy requires high intensity beams in order to produce useful dose rates. The 800-MeV proton beam at LAMPF passes through different production targets to generate secondary pion beams. Conventional microdosimetric techniques are not applicable under these conditions because exceedingly high count rates result in detector damage, gas breakdown, and saturation effects in the electronics. We describe a new microdosimetric system developed at the Pion Biomedical Channel of LAMPF. The accelerator provides a variable low intensity pulse once every ten high intensity macropulses. The voltage on the detector is pulsed in coincidence with the low intensity pulse so that we were able to operate the detector under optimum data-taking conditions. A low noise two-stage preamplifier was built in connection with the pulsed mode operation. A comparison is made between data obtained in pulsed (high intensity beam) and unpulsed (low intensity beam) modes. The spectra obtained by the two methods agree within the experimental uncertainties

  13. PbSe nanocubes obtained by high-energy milling

    Energy Technology Data Exchange (ETDEWEB)

    Rojas-Chavez, H., E-mail: hrojasc@ipn.mx [Centro de Investigacion en Ciencia Aplicada y Tecnologia Avanzada - IPN (Mexico); Reyes-Carmona, F. [Facultad de Quimica - UNAM (Mexico); Achimovicova, M. [Slovak Academy of Sciences, Institute of Geotechnics (Slovakia); Daneu, N. [Jozef Stefan Institute, Department for Nanostructured Materials (Slovenia); Jaramillo-Vigueras, D. [Centro de Investigacion e Innovacion Tecnologica - IPN (Mexico)

    2012-06-15

    In this study, PbSe nanocubes were obtained by high-energy milling, and their optical properties were investigated by measuring the UV-VIS-IR spectra in the range of 200-2,000 nm. The optical absorption of all samples showed a strong UV emission band at 1.45 eV. Previously, to obtain only PbSe nanocubes, an intermediate phase was identified, PbSeO{sub 3}. Although both PbSeO{sub 3} and PbSe were traced through this study, a major effort is devoted to characterize the latter. To trace how chemical transitions evolve from precursors to PbSe, X-ray diffraction and Rietveld refinement were carried out. Therefore, the following parameters were evaluated as a function of milling time: phase percentages, area-to-volume ratio, average crystallite dimensions, specific surface area, and morphology changes. To corroborate previous findings, nitrogen adsorption and transmission electron microscopy techniques were used. All the set experimental results unambiguously confirm that crystallites show a cubic morphology, with its average crystallite size distribution being around 24 nm.

  14. Automatic processing of isotopic dilution curves obtained by precordial detection

    International Nuclear Information System (INIS)

    Verite, J.C.

    1973-01-01

    Dilution curves pose two distinct problems: that of their acquisition and that of their processing. A study devoted to the latter aspect only was presented. It was necessary to satisfy two important conditions: the treatment procedure, although applied to a single category of curves (isotopic dilution curves obtained by precordial detection), had to be as general as possible; to allow dissemination of the method the equipment used had to be relatively modest and inexpensive. A simple method, considering the curve processing as a process identification, was developed and should enable the mean heart cavity volume and certain pulmonary circulation parameters to be determined. Considerable difficulties were encountered, limiting the value of the results obtained though not condemning the method itself. The curve processing question raised the problem of their acquisition, i.e. the number of these curves and their meaning. A list of the difficulties encountered is followed by a set of possible solutions, a solution being understood to mean a curve processing combination where the overlapping between the two aspects of the problem is accounted for [fr

  15. Influence of chemical treatment of clay to obtain polypropylene nanocomposites

    International Nuclear Information System (INIS)

    Rosa, Jeferson L.S.; Marques, Maria F.V.

    2009-01-01

    Commercial clay was chemically treated to prepare a Ziegler-Natta catalyst containing MgCl 2 and clay for the synthesis of polypropylene nanocomposites by in situ polymerization. The performance of this catalyst and materials obtained in propylene polymerization was compared with a reference catalyst (without clay) and with another, whose composition presents the same clay but without prior chemical treatment. Techniques like differential scanning calorimetry (DSC), X-ray diffractometry (XRD) and melt flow index (MFI) measurements were performed. There was a marked reduction in catalytic activity of clay catalysts in comparison with the reference one, and a slight reduction in melting temperature of the polymers produced from first ones. The melt flow index of polymers obtained with treated clay were notably higher than those synthesized with the untreated clay, so the treated clay caused treated the production of PP's with lower molar mass. The clays showed an increase of spacing and irregular stacking of the lamellas, especially if chemically treated. (author)

  16. Optimizing the Operation of Maceration to Obtain Quality White Wines

    Directory of Open Access Journals (Sweden)

    Stegărus Diana

    2014-06-01

    Full Text Available This study monitors the physico-chemical properties of wines from Dragasani under the influence of pectolytic enzymes in various temperature conditions. during maceration contact is made between the grape skins and selected the optimal time leads to wines with more pronounced floral character. The physico-chemical extraction maceration leads to a more pronounced specific compounds, the time of maceration is very important in this case. The curing time is of great importance in producing varieties Muscat Ottonel and Tămâioasă Românească primarily for successful extraction of aromatic components from grape. As noted in the literature flavored grapes contain large amounts of terpene compounds are in free form or bound. To optimize the technological process is able to extract these compounds and to achieve a harmonious and balanced wine. The variants considered in the study presents the results of physico-chemical and aromatic wines obtained from the Muscat Ottonel and Tămâioasă Românească, which took into consideration both during maceration and the use of selected yeasts and enzymes, which form the basis for the selection of the optimal procedure for obtaining aromatic white wines in Dragasani Vineyard.

  17. Variables of synthesis in obtaining nanosilicas with sol-gel

    International Nuclear Information System (INIS)

    Elia, A; Martin-Aispuro, P; Musante, L; Martin-Martinez, J.M; Vazquez, P

    2008-01-01

    Amorphous silica materials and polycrystalline are now being developed for different applications as optic components, superconductors, nano-particles used as charges in adhesives and paints, among others. Some methods of obtaining these materials involve complex techniques and high costs. Generally, the materials constituents are fused, for example, using the pyrogenic silica technique, widely used industrially. Meanwhile, the sol-gel meted is based on a mixture of liquid reagents at the molecular level, to easily obtain amorphous and polycrystalline materials, even at room temperature. Therefore, the sol-gel way is a promising option for producing new materials, due to its cost advantages compared to the traditional methods. The sol-gel technique consists of the simultaneous reaction of the hydrolysis and the condensation. In this process the precursor solution, the TEOS in our case, becomes a polymeric gel network polymer. The partial hydrolysis of the orthosilicate takes place when it is mixed with water and ethanol (EtOH), the reaction that occurs is: S i(OEt) 4 + H 2 O S i(OEt) 3 (OH) + EtOH. The condensation takes place between two OH groups or between an OH group and an ethoxy to form an oxygen bridge plus water or ethanol. S i(OEt) 4 + H 2 O + S i(OEt) 3 (OH)(EtO) 3 Si-O-Si(OEt) 3 (OH) + H 2 O S i-OH + HO-Si S i-O-Si + H 2 O. The addition of a base or of an acid catalyzes the process and changes the pH of the solution influencing the condensation process and size of the final particle. This work focuses on finding different conditions by varying the pH, using HCI, with and without agitation during the addition of the HCI, and washing the solid obtained with ethanol in order to study its effect. The nanosilicas were characterized by TEM-EDX, DTA-TGA, S BET , FT-IR, DRX, DRS, SEM and pH measurements. The morphology of the nanosilicas was characterized with SEM and TEM. Using these techniques a partial conclusion showed that the samples synthesized with HCI

  18. Quantum Uncertainty and Fundamental Interactions

    Directory of Open Access Journals (Sweden)

    Tosto S.

    2013-04-01

    Full Text Available The paper proposes a simplified theoretical approach to infer some essential concepts on the fundamental interactions between charged particles and their relative strengths at comparable energies by exploiting the quantum uncertainty only. The worth of the present approach relies on the way of obtaining the results, rather than on the results themselves: concepts today acknowledged as fingerprints of the electroweak and strong interactions appear indeed rooted in the same theoretical frame including also the basic principles of special and general relativity along with the gravity force.

  19. Collaboration Meets Interactive Surfaces (CMIS)

    DEFF Research Database (Denmark)

    Anslow, Craig; Campos, Pedro; Grisoni, Laurent

    2015-01-01

    This workshop proposes to bring together researchers who are interested in improving collaborative experiences through the combination of multiple interaction surfaces with diverse sizes and formats, ranging from large-scale walls, to tables, mobiles, and wearables. The opportunities for innovation...... exist, but the ITS, CHI, CSCW, and other HCI communities have not yet thoroughly addressed the problem of bringing effective collaboration activities together using multiple interactive surfaces, especially in complex work domains. Of particular interest is the potential synergy that one can obtain...

  20. Causal electromagnetic interaction equations

    International Nuclear Information System (INIS)

    Zinoviev, Yury M.

    2011-01-01

    For the electromagnetic interaction of two particles the relativistic causal quantum mechanics equations are proposed. These equations are solved for the case when the second particle moves freely. The initial wave functions are supposed to be smooth and rapidly decreasing at the infinity. This condition is important for the convergence of the integrals similar to the integrals of quantum electrodynamics. We also consider the singular initial wave functions in the particular case when the second particle mass is equal to zero. The discrete energy spectrum of the first particle wave function is defined by the initial wave function of the free-moving second particle. Choosing the initial wave functions of the free-moving second particle it is possible to obtain a practically arbitrary discrete energy spectrum.

  1. Intracranial CT angiography obtained from a cerebral CT perfusion examination

    International Nuclear Information System (INIS)

    Gratama van Andel, H. A. F.; Venema, H. W.; Majoie, C. B.; Den Heeten, G. J.; Grimbergen, C. A.; Streekstra, G. J.

    2009-01-01

    CT perfusion (CTP) examinations of the brain are performed increasingly for the evaluation of cerebral blood flow in patients with stroke and vasospasm after subarachnoid hemorrhage. Of the same patient often also a CT angiography (CTA) examination is performed. This study investigates the possibility to obtain CTA images from the CTP examination, thereby possibly obviating the CTA examination. This would save the patient exposure to radiation, contrast, and time. Each CTP frame is a CTA image with a varying amount of contrast enhancement and with high noise. To improve the contrast-to-noise ratio (CNR) we combined all 3D images into one 3D image after registration to correct for patient motion between time frames. Image combination consists of weighted averaging in which the weighting factor of each frame is proportional to the arterial contrast. It can be shown that the arterial CNR is maximized in this procedure. An additional advantage of the use of the time series of CTP images is that automatic differentiation between arteries and veins is possible. This feature was used to mask veins in the resulting 3D images to enhance visibility of arteries in maximum intensity projection (MIP) images. With a Philips Brilliance 64 CT scanner (64x0.625 mm) CTP examinations of eight patients were performed on 80 mm of brain using the toggling table technique. The CTP examination consisted of a time series of 15 3D images (2x64x0.625 mm; 80 kV; 150 mAs each) with an interval of 4 s. The authors measured the CNR in images obtained with weighted averaging, images obtained with plain averaging, and images with maximal arterial enhancement. The authors also compared CNR and quality of the images with that of regular CTA examinations and examined the effectiveness of automatic vein masking in MIP images. The CNR of the weighted averaged images is, on the average, 1.73 times the CNR of an image at maximal arterial enhancement in the CTP series, where the use of plain averaging

  2. Study of the Deformation/Interaction Model: How Interactions Increase the Reaction Barrier

    Directory of Open Access Journals (Sweden)

    Zhiling Liang

    2018-01-01

    Full Text Available The interactions (including weak interactions between dienophiles and dienes play an important role in the Diels-Alder reaction. To elucidate the influence of these interactions on the reactivity, a popular DFT functional and a variational DFT functional corrected with dispersion terms are used to investigate different substituent groups incorporated on the dienophiles and dienes. The bond order is used to track the trajectory of the cycloaddition reaction. The deformation/interaction model is used to obtain the interaction energy from the reactant complex to the inflection point until reaching the saddle point. The interaction energy initially increases with a decrease in the interatomic distance, reaching a maximum value, but then decreases when the dienophiles and dienes come closer. Reduced density gradient and chemical energy component analysis are used to analyse the interaction. Traditional transition state theory and variational transition state theory are used to obtain the reaction rates. The influence of tunneling on the reaction rate is also discussed.

  3. COMPARISON OF GINGER (Zingiber officiale Roscoe OLEORESIN OBTAINED WITH ETHANOL AND ISOPROPANOL WITH THAT OBTAINED WITH PRESSURIZED CO2

    Directory of Open Access Journals (Sweden)

    Lia P. NOBREGA

    1997-12-01

    Full Text Available Ginger (Zingiber officinale Roscoe belongs to the Zingiberacea family. It is a spice of great commercial importance. In this work ginger oleoresin was obtained with ethanol, isopropanol and liquid carbon dioxide. The chemical compositions of the extract were compared with each other. All oleoresin samples had monoterpenes and sesquiterpenes. Carboxylic acids were found in organic solvent extracts for an extraction time of 2 hours. The component responsible the for pungent characteristic of the oleoresin, gingerois, were detected in samples obtained with organic solvent for extraction times of 6 hours and in samples obtained with CO2 liquid for extraction times of 2 hours.O gengibre (Zingiber officinale Roscoe pertence à família Zingiberacea. É uma especiaria de grande importância comercial. Neste trabalho realizou-se extrações da oleoresina de gengibre com etanol, isopropanol e dióxido de carbono líquido e comparou-se a composição química de cada um dos extratos. A oleoresina obtida tem componentes das classes dos monoterpenos e sesquiterpenos em todas as amostras. Ácidos carboxílicos foram encontrados nos extratos obtidos com solvente orgânico, quando o tempo de extração foi de 2 horas. Os componentes que dão a característica pungente à oleoresina, os gingerois, foram detectados nas amostras obtidas com solvente orgânico, quando o tempo de extração foi de 6 horas e, nas amostras obtidas com CO2 líquido, com 2 horas de extração.

  4. A method for increase abrasive wear resistance parts by obtaining on methods casting on gasifying models

    Science.gov (United States)

    Sedukhin, V. V.; Anikeev, A. N.; Chumanov, I. V.

    2017-11-01

    Method optimizes hardening working layer parts’, working in high-abrasive conditions looks in this work: bland refractory particles WC and TiC in respect of 70/30 wt. % prepared by beforehand is applied on polystyrene model in casting’ mould. After metal poured in mould, withstand for crystallization, and then a study is carried out. Study macro- and microstructure received samples allows to say that thickness and structure received hardened layer depends on duration interactions blend harder carbides and liquid metal. Different character interactions various dispersed particles and matrix metal observed under the same conditions. Tests abrasive wear resistance received materials of method calculating residual masses was conducted in laboratory’ conditions. Results research wear resistance showed about that method obtaining harder coating of blend carbide tungsten and carbide titanium by means of drawing on surface foam polystyrene model before moulding, allows receive details with surface has wear resistance in 2.5 times higher, than details of analogy steel uncoated. Wherein energy costs necessary for transformation units mass’ substances in powder at obtained harder layer in 2.06 times higher, than materials uncoated.

  5. Luminescent hybrid porphyrinosilica obtained by sol gel chemistry

    Directory of Open Access Journals (Sweden)

    Neri Cláudio Roberto

    2003-01-01

    Full Text Available The sol-gel process is a methodology used to obtain organic-inorganic hybrid solids, which open new possibilities in the field of material science. The sol-gel technique offers a low temperature attractive approach for introducing organic molecules into amorphous materials. In order to introduce tetrakis (2-hydroxy-5-nitrophenylporphyrin covalently bounded to a silicate matrix, the inorganic precursor 3-isocyanatopropyltriethoxysilane was added (molar ratio 2:1 to the porphyrin solution in anhydrous dimethylformamide and triethylamine. The isolated porphyrin and the hybrid porphyrinosilica have excitation maximum centred at 400 nm and 424 nm, respectively and the emission spectra for both materials has bands centred at 650 nm and 713 nm. The formation of hybrid matrix was investigated by FTIR.

  6. Comparative Properties of Amazonian Oils Obtained by Different Extraction Methods

    Directory of Open Access Journals (Sweden)

    Cláudio Galuppo Diniz

    2011-07-01

    Full Text Available Pequi (Caryocar brasiliense Camb., babaçu (Orbignya phalerata Mart., buriti (Mauritia flexuosa, and passion fruit (Passiflora edulis oils were studied to determine their antibacterial, antioxidant and cytotoxic activities, as well as their total phenol and carotenoid contents. The fatty acid contents were determined by GC-MS. The three types of passion fruit oils studied were refined, cold pressed or extracted from seeds in a Soxhlet apparatus. The oils thus obtained showed differences in antioxidant activity and carotenoid content, but were similar in regard to total phenols. Buriti and pequi had the highest carotenoid contents, while refined and cold pressed passion fruit oil displayed the highest antioxidant activity. Pequi oil was the only oil to display antibacterial and cytotoxic activity.

  7. LIGNOCELLULOSE AS AN ALTERNATIVE SOURCE FOR OBTAINING OF BIOBUTANOL

    Directory of Open Access Journals (Sweden)

    S. M. Shulga

    2013-04-01

    Full Text Available Energy and environmental crisis facing the world force us to reconsider the effectiveness or find an alternative use of renewable natural resources, especially organic «waste» by using environmentally friendly technologies. Microbial conversion of renewable resources of biosphere to produce useful products, including biofuels, currently is an actual biotech problem. Anaerobic bacteria of Clostridiaceae family are known as butanol producers, but unfortunately, the microbiological synthesis is currently not economical one. In order to make cost-effective aceton-butanol-ethanol fermentation, solventproducing strains using available cheap raw materials, such as agricultural waste or plant biomass, are required. Opportunities and ways to obtaine economic and ecological processing of lignocellulosic wastes for biobutanol creation are described in the review .

  8. Procedure for obtaining visas for Switzerland and France - Signature rights

    CERN Multimedia

    2016-01-01

    In accordance with the Status Agreements with CERN, Switzerland and France facilitate the entry of members of the Organization’s personnel on to their territories. Where relevant, detailed procedures for obtaining visas apply.   Within the framework of those procedures, only the following individuals are authorised to initiate the Note verbale procedure as well as to sign the Official Invitation Letters and the Conventions d’accueil. Kirsti ASPOLA (EP – CMO) Maria BARROSO LOPEZ (IT – DI) Catherine BRANDT (DG – DI) Michelle CONNOR (TH – GS) Gaëlle DUPERRIER (EP – AGS) Patrick FASSNACHT (EP – ADO) Fernando FERNANDEZ SAVORGNANO (HR – TA) Nathalie GOURIOU (EP – AGS) Nathalie GRÜB (EP – AGS) Laurie HEMERY (BE – ASR) Cécile NOELS (ATS – DO) Tania PARDO (EP – AGS) Maria QUINTAS (HR – TA) Kate RICHARDSON (EP –  A...

  9. Procedure for obtaining visas for Switzerland and France - Signature rights

    CERN Multimedia

    2015-01-01

    In accordance with the Status Agreements with CERN, Switzerland and France facilitate the entry of members of the Organization’s personnel on to their territories. Where relevant, detailed procedures for obtaining visas apply.   Within the framework of those procedures, only the following individuals are authorised to initiate the Note verbale procedure as well as to sign the Official Invitation Letters and the Conventions d’accueil. 1.     Kirsti ASPOLA (PH – CMO) 2.     Catherine BRANDT (DG – IR) 3.     Oliver BRÜNING (BE – HDO) 4.     Michelle CONNOR (PH – DI) 5.     Gaëlle DUPERRIER (PH – DI) 6.     Patrick FASSNACHT (PH – ADO) 7.     Fernando FERN...

  10. Procedure for obtaining visas for Switzerland and France - Signature rights

    CERN Multimedia

    2014-01-01

    In accordance with the Status Agreements with CERN, Switzerland and France facilitate the entry of members of the Organization’s personnel onto their territories. Where relevant, detailed procedures for obtaining visas apply.   Within the framework of those procedures, only the following individuals are authorised to initiate the note verbale procedure as well as to sign the Official Invitation Letters and the Conventions d’accueil. 1. Kirsti ASPOLA (PH – CMO) 2. Catherine BRANDT (DG – IR) 3. Oliver BRÜNING (BE – ABP) 4. Michelle CONNOR (PH – AGS) 5. Patrick FASSNACHT (PH – ADO) 6. Fernando FERNANDEZ SAVORGNANO (HR – TA) 7. David FOSTER (IT – DI) 8. Nathalie GRÜB (PH – AGS) 9. Cécile NOELS (DG – DI) 10. Maria QUINTAS (HR – TA) 11. Kate RICHARDSON (PH –  AGS) 12. Jeanne ROSTANT (PH – AGS) 13. José SALICIO-DIEZ (...

  11. Procedure for obtaining visas for Switzerland and France - Signature rights

    CERN Multimedia

    2016-01-01

    In accordance with the Status Agreements with CERN, Switzerland and France facilitate the entry of members of the Organization’s personnel on to their territories. Where relevant, detailed procedures for obtaining visas apply.   Within the framework of those procedures, only the following individuals are authorised to initiate the Note verbale procedure as well as to sign the Official Invitation Letters and the Conventions d’accueil. Kirsti ASPOLA (EP – CMO) Maite BARROSO LOPEZ (IT – DI) Catherine BRANDT (DG – DI) Michelle CONNOR (TH – GS) Gaëlle DUPERRIER (EP – AGS) Patrick FASSNACHT (EP – ADO) Fernando FERNANDEZ SAVORGNANO (HR – TA) Nathalie GRÜB (EP – AGS) Laurie HEMERY (BE – ASR) Cécile NOELS (ATS – DO) Tania PARDO (EP – AGS) Maria QUINTAS (HR – TA) Kate RICHARDSON (EP –  AGS) Jeanne ROSTANT (TH – GS)...

  12. Obtain and characterization of chitosan / propranolol microparticles by spray drying

    International Nuclear Information System (INIS)

    Nascimento, Ednaldo G. do; Silva Junior, Arnobio A. da; Santos, Katia S.C.R. dos

    2015-01-01

    The study investigated the application of chitosan microparticles as carriers into hard gelatin capsule containing propranolol, evaluating the variability of the molecular weight and the chitosan particles by spray drying. The formulations were characterized by average weight, dosing unit dose uniformity and dissolution profile according to the pharmacopoeia. While the microparticles were characterized by Fourier transformed infrared spectroscopy, scanning electron microscopy and X-ray diffraction. The results showed that chitosan microparticles obtained without the drug and then physically mixed with propranolol promoted a modified release 85% of the drug after 5 hours. While, chitosan microparticles sprayed with propranolol released only 55% at 5 hours is presented both as a modified release system. Samples of dried chitosan showed up amorphous and homogeneous and spherical morphology. (author)

  13. Enhancing the seismic margin review methodology to obtain risk insights

    International Nuclear Information System (INIS)

    Budnitz, R.J.

    1992-01-01

    This paper discusses methods for obtaining risk insights from the seismic margin review (SMR) methodology. The SMR methodology was originally developed in 1984-1987 with the objective of analyzing an individual nuclear power plant to ascertain whether the plant has the ability to withstand earthquakes substantially beyond the design-basis earthquake without suffering a core-damage accident. Recently, in the context of Nuclear Regulatory Commission's (NRC's) Individual Plant Evaluation for External Events (IPEEE) program, the SMR methodology has been developed further by NRC to allow plants to identify plant-specific vulnerabilities (in the IPEEE sense) to seismic events. The objective of these enhancements has been to provide a methodology for IPEEE seismic review that is substantially less expensive than a full-scope seismic PRA, but that achieves the IPEEE's vulnerability-search objectives. In this paper, the steps involved in the enhanced methodology are discussed

  14. ANTIFUNGAL ACTIVITY OF SILVER NANOPARTICLES OBTAINED BY GREEN SYNTHESIS

    Directory of Open Access Journals (Sweden)

    Eduardo José J. MALLMANN

    2015-04-01

    Full Text Available Silver nanoparticles (AgNPs are metal structures at the nanoscale. AgNPs have exhibited antimicrobial activities against fungi and bacteria; however synthesis of AgNPs can generate toxic waste during the reaction process. Accordingly, new routes using non-toxic compounds have been researched. The proposal of the present study was to synthesize AgNPs using ribose as a reducing agent and sodium dodecyl sulfate (SDS as a stabilizer. The antifungal activity of these particles against C. albicans and C. tropicalis was also evaluated. Stable nanoparticles 12.5 ± 4.9 nm (mean ± SD in size were obtained, which showed high activity against Candida spp. and could represent an alternative for fungal infection treatment.

  15. The obtaining of giant laser pulses by optical pumping

    International Nuclear Information System (INIS)

    Briquet, Georges

    1970-12-01

    From coherent pumping studies a laser of short pulse duration was developed. Further study of laser effects in organic substances was envisaged. The first part of the work yielded awaited results, and led to the development of a single mode emitter (due to the small dimensions of the cavity). The principles of laser action were enumerated and the relative parameters defined. Various methods of obtaining pulses were discussed; the reasons behind the particular choice mode were given. A theoretical study was then made leading to the establishment of the fundamental equations defining the pulse formation process. An important part of the test deals with technical implications and the experimental results, which have arisen. The conclusion reviews possible applications. (author) [fr

  16. Uniaxially aligned ceramic nanofibers obtained by chemical mechanical processing

    Energy Technology Data Exchange (ETDEWEB)

    Tararam, R. [Univ Estadual Paulista – UNESP – Instituto de Química, Rua Prof. Francisco Degni n° 55, CEP 14800-900 Araraquara, SP (Brazil); Foschini, C.R. [Univ Estadual Paulista – UNESP – Faculdade de Engenharia de Bauru, Dept. de Eng. Mecanica, Av. Eng. Luiz Edmundo C. Coube 14-01, CEP 17033-360 Bauru, SP (Brazil); Destro, F.B. [Univ Estadual Paulista – UNESP – Faculdade de Engenharia de Guaratinguetá, Guaratinguetá 12516-410, SP (Brazil); Simões, A.Z., E-mail: alezipo@yahoo.com [Univ Estadual Paulista – UNESP – Faculdade de Engenharia de Guaratinguetá, Guaratinguetá 12516-410, SP (Brazil); Longo, E.; Varela, J.A. [Univ Estadual Paulista – UNESP – Instituto de Química, Rua Prof. Francisco Degni n° 55, CEP 14800-900 Araraquara, SP (Brazil)

    2014-08-01

    For this study, we investigated a simple method to generate well aligned nanofibers over large areas using an organic polymer stretched over the substrate surface With this method, ZnO and CuO 3D parallel nanowire arrays were successfully prepared by calcinations of the polymer fibers. X-ray diffraction (XRD) analysis revealed that the copper oxide has a monoclinic structure while the zinc oxide has a hexagonal structure. Scanning electron microscopy (SEM) analysis showed ceramic nanofibers with an average diameter of 120 nm which were composed of small nanoparticles which are 10 nm in diameter. The ability to obtain uniaxially aligned nanofibers reveals a range of interesting properties with potential applications for sensors, catalysts and energy technologies.

  17. Doped ZnS:Mn nanoparticles obtained by sonochemical synthesis.

    Science.gov (United States)

    Korotchenkov, O A; Cantarero, A; Shpak, A P; Kunitskii, Yu A; Senkevich, A I; Borovoy, M O; Nadtochii, A B

    2005-10-01

    A study of sonochemically synthesized ZnS:Mn nanoparticles is presented. The particles prepared at low rf power (about 20 W) and room temperature coalesce to form morphologically amorphous large species (30-100 nm in diameter). As the power is increased in the range from 20 to 70 W, and the solution temperature is raised to 60 to 80 degrees C, finer particles are produced with the size ranging from 2 to 20 nm and improved crystallinity. The results indicate the dispersion of the Mn(2+) ions at near-surface sites in the particles. It is shown that the sonochemically fabricated particles approach the quality of the ones obtained by a standard chemical route and show a reasonable luminescence performance.

  18. How to obtain traceability on optical radiation measurements?

    Science.gov (United States)

    Matamoros García, Carlos H.

    2006-02-01

    Traceability to national standards provides confidence in measurements results, granting a guaranty when carrying out governmental rules and when demonstrating conformity with quality requirements such as ISO 9000 or ISO/IEC 17025 (and the Mexican equivalent standards). The appropriate traceability contributes with confidence of the quality of products or services. This paper presents different ways to obtain traceability in Mexico for the optical radiation measurements, mentioning some applications, and highlighting the necessity of having traceability to the appropriate units of the SI. Additionally it present the national standards maintained by Centro Nacional de Metrologia (CENAM), the national metrology institute in Mexico, that give the technical support to Mexican measurements in this field and the international recognition that the personal of the Optics and Radiometry Division had gained in 10 years of development.

  19. A new methodology to obtain wine yeast strains overproducing mannoproteins.

    Science.gov (United States)

    Quirós, Manuel; Gonzalez-Ramos, Daniel; Tabera, Laura; Gonzalez, Ramon

    2010-04-30

    Yeast mannoproteins are highly glycosylated proteins that are covalently bound to the beta-1,3-glucan present in the yeast cell wall. Among their outstanding enological properties, yeast mannoproteins contribute to several aspects of wine quality by protecting against protein haze, reducing astringency, retaining aroma compounds and stimulating growth of lactic-acid bacteria. The development of a non-recombinant method to obtain enological yeast strains overproducing mannoproteins would therefore be very useful. Our previous experience on the genetic determinants of the release of these molecules by Saccharomyces cerevisiae has allowed us to propose a new methodology to isolate and characterize wine yeast that overproduce mannoproteins. The described methodology is based on the resistance of the killer 9 toxin produced by Williopsis saturnus, a feature linked to an altered biogenesis of the yeast cell wall. Copyright 2010 Elsevier B.V. All rights reserved.

  20. Using surfaces, ligands, and dimensionality to obtain desired nanostructure properties

    Science.gov (United States)

    Nagpal, Prashant; Singh, Vivek; Ding, Yuchen

    2014-03-01

    Nanostructured materials are intensively investigated to obtain material properties different from their bulk counterparts. It has been demonstrated that nanoscaled semiconductor can have interesting size, shape and morphology dependent optoelectronic properties. But the effect of surfaces, ligands and dimensionality (0D quantum dots to 2D nanosheets) has been largely unexplored. Here, we will show how tuning the surface and dimensionality can affect the electronic states of the semiconductor, and how these states can play an important role in their fundamental photophysical properties or thermal transport. Using the specific case for silicon, we will show how ``new'' surface states in small uniform can lead to light absorption/emission without phonon assistance, while hindering the phonon-drag of charge carriers leading to low Seebeck coefficient for thermoelectric applications. These measurements will shed light on designing appropriate surface, size, and dimensionality for desired applications of nanostructured films.