WorldWideScience

Sample records for backbone structure based

  1. Slow dynamics of a protein backbone in molecular dynamics simulation revealed by time-structure based independent component analysis

    Energy Technology Data Exchange (ETDEWEB)

    Naritomi, Yusuke [Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 (Japan); Fuchigami, Sotaro, E-mail: sotaro@tsurumi.yokohama-cu.ac.jp [Department of Medical Life Science, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 (Japan)

    2013-12-07

    We recently proposed the method of time-structure based independent component analysis (tICA) to examine the slow dynamics involved in conformational fluctuations of a protein as estimated by molecular dynamics (MD) simulation [Y. Naritomi and S. Fuchigami, J. Chem. Phys. 134, 065101 (2011)]. Our previous study focused on domain motions of the protein and examined its dynamics by using rigid-body domain analysis and tICA. However, the protein changes its conformation not only through domain motions but also by various types of motions involving its backbone and side chains. Some of these motions might occur on a slow time scale: we hypothesize that if so, we could effectively detect and characterize them using tICA. In the present study, we investigated slow dynamics of the protein backbone using MD simulation and tICA. The selected target protein was lysine-, arginine-, ornithine-binding protein (LAO), which comprises two domains and undergoes large domain motions. MD simulation of LAO in explicit water was performed for 1 μs, and the obtained trajectory of C{sub α} atoms in the backbone was analyzed by tICA. This analysis successfully provided us with slow modes for LAO that represented either domain motions or local movements of the backbone. Further analysis elucidated the atomic details of the suggested local motions and confirmed that these motions truly occurred on the expected slow time scale.

  2. External Tank - The Structure Backbone

    Science.gov (United States)

    Welzyn, Kenneth; Pilet, Jeffrey C.; Diecidue-Conners, Dawn; Worden, Michelle; Guillot, Michelle

    2011-01-01

    The External Tank forms the structural backbone of the Space Shuttle in the launch configuration. Because the tank flies to orbital velocity with the Space Shuttle Orbiter, minimization of weight is mandatory, to maximize payload performance. Choice of lightweight materials both for structure and thermal conditioning was necessary. The tank is large, and unique manufacturing facilities, tooling, handling, and transportation operations were required. Weld processes and tooling evolved with the design as it matured through several block changes, to reduce weight. Non Destructive Evaluation methods were used to assure integrity of welds and thermal protection system materials. The aluminum-lithium alloy was used near the end of the program and weld processes and weld repair techniques had to be refined. Development and implementation of friction stir welding was a substantial technology development incorporated during the Program. Automated thermal protection system application processes were developed for the majority of the tank surface. Material obsolescence was an issue throughout the 40 year program. The final configuration and tank weight enabled international space station assembly in a high inclination orbit allowing international cooperation with the Russian Federal Space Agency. Numerous process controls were implemented to assure product quality, and innovative proof testing was accomplished prior to delivery. Process controls were implemented to assure cleanliness in the production environment, to control contaminants, and to preclude corrosion. Each tank was accepted via rigorous inspections, including non-destructive evaluation techniques, proof testing, and all systems testing. In the post STS-107 era, the project focused on ascent debris risk reduction. This was accomplished via stringent process controls, post flight assessment using substantially improved imagery, and selective redesigns. These efforts were supported with a number of test programs to

  3. Backbone cup – a structure design competition based on topology optimization and 3D printing

    Directory of Open Access Journals (Sweden)

    Zhu Ji-Hong

    2016-01-01

    Full Text Available This paper addresses a structure design competition based on topology optimization and 3D Printing, and proposes an experimental approach to efficiently and quickly measure the mechanical performance of the structures designed using topology optimization. Since the topology optimized structure designs are prone to be geometrically complex, it is extremely inconvenient to fabricate these designs with traditional machining. In this study, we not only fabricated the topology optimized structure designs using one kind of 3D Printing technology known as stereolithography (SLA, but also tested the mechanical performance of the produced prototype parts. The finite element method is used to analyze the structure responses, and the consistent results of the numerical simulations and structure experiments prove the validity of this new structure testing approach. This new approach will not only provide a rapid access to topology optimized structure designs verifying, but also cut the turnaround time of structure design significantly.

  4. Nuclear Magnetic Resonance-Based Structural Characterization and Backbone Dynamics of Recombinant Bee Venom Melittin.

    Science.gov (United States)

    Ramirez, Lisa; Shekhtman, Alexander; Pande, Jayanti

    2018-04-30

    In recent years, there has been a resurgence of interest in melittin and its variants as their therapeutic potential has become increasingly evident. Melittin is a 26-residue peptide and a toxic component of honey bee venom. The versatility of melittin in interacting with various biological substrates, such as membranes, glycosaminoglycans, and a variety of proteins, has inspired a slew of studies that aim to improve our understanding of the structural basis of such interactions. However, these studies have largely focused on melittin solutions at high concentrations (>1 mM), even though melittin is generally effective at lower (micromolar) concentrations. Here we present high-resolution nuclear magnetic resonance studies in the lower-concentration regime using a novel method to produce isotope-labeled ( 15 N and 13 C) recombinant melittin. We provide residue-specific structural characterization of melittin in dilute aqueous solution and in 2,2,2-trifluoroethanol/water mixtures, which mimic melittin structure-function and interactions in aqueous and membrane-like environments, respectively. We find that the cis-trans isomerization of Pro14 is key to changes in the secondary structure of melittin. Thus, this study provides residue-specific structural information about melittin in the free state and in a model of the substrate-bound state. These results, taken together with published work from other laboratories, reveal the peptide's structural versatility that resembles that of intrinsically disordered proteins and peptides.

  5. Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15N-NOESY

    KAUST Repository

    Jang, Richard

    2012-03-21

    Background: Chemical shift mapping is an important technique in NMR-based drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule\\'s introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically, which is not efficient for high-throughput drug screening.Results: We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C-labeling, to resolve the ambiguities for a one-to-one mapping. On the three proteins, it achieves an average accuracy of 94% or better.Conclusions: Our mathematical programming approach for modeling chemical shift mapping as a graph problem, while modeling the errors directly, is potentially a time- and cost-effective first step for high-throughput drug screening based on limited NMR data and homologous 3D structures. 2012 Jang et al.; licensee BioMed Central Ltd.

  6. Combining ambiguous chemical shift mapping with structure-based backbone and NOE assignment from 15N-NOESY

    KAUST Repository

    Jang, Richard

    2011-01-01

    Chemical shift mapping is an important technique in NMRbased drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule\\'s introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically. However, automated methods are necessary for high-throughput drug screening. We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C- labeling, to resolve the ambiguities for a one-toone mapping. On the three proteins, it achieves an average accuracy of 94% or better. Copyright © 2011 ACM.

  7. Retrieving Backbone String Neighbors Provides Insights Into Structural Modeling of Membrane Proteins*

    Science.gov (United States)

    Sun, Jiang-Ming; Li, Tong-Hua; Cong, Pei-Sheng; Tang, Sheng-Nan; Xiong, Wen-Wei

    2012-01-01

    Identification of protein structural neighbors to a query is fundamental in structure and function prediction. Here we present BS-align, a systematic method to retrieve backbone string neighbors from primary sequences as templates for protein modeling. The backbone conformation of a protein is represented by the backbone string, as defined in Ramachandran space. The backbone string of a query can be accurately predicted by two innovative technologies: a knowledge-driven sequence alignment and encoding of a backbone string element profile. Then, the predicted backbone string is employed to align against a backbone string database and retrieve a set of backbone string neighbors. The backbone string neighbors were shown to be close to native structures of query proteins. BS-align was successfully employed to predict models of 10 membrane proteins with lengths ranging between 229 and 595 residues, and whose high-resolution structural determinations were difficult to elucidate both by experiment and prediction. The obtained TM-scores and root mean square deviations of the models confirmed that the models based on the backbone string neighbors retrieved by the BS-align were very close to the native membrane structures although the query and the neighbor shared a very low sequence identity. The backbone string system represents a new road for the prediction of protein structure from sequence, and suggests that the similarity of the backbone string would be more informative than describing a protein as belonging to a fold. PMID:22415040

  8. Retrieving backbone string neighbors provides insights into structural modeling of membrane proteins.

    Science.gov (United States)

    Sun, Jiang-Ming; Li, Tong-Hua; Cong, Pei-Sheng; Tang, Sheng-Nan; Xiong, Wen-Wei

    2012-07-01

    Identification of protein structural neighbors to a query is fundamental in structure and function prediction. Here we present BS-align, a systematic method to retrieve backbone string neighbors from primary sequences as templates for protein modeling. The backbone conformation of a protein is represented by the backbone string, as defined in Ramachandran space. The backbone string of a query can be accurately predicted by two innovative technologies: a knowledge-driven sequence alignment and encoding of a backbone string element profile. Then, the predicted backbone string is employed to align against a backbone string database and retrieve a set of backbone string neighbors. The backbone string neighbors were shown to be close to native structures of query proteins. BS-align was successfully employed to predict models of 10 membrane proteins with lengths ranging between 229 and 595 residues, and whose high-resolution structural determinations were difficult to elucidate both by experiment and prediction. The obtained TM-scores and root mean square deviations of the models confirmed that the models based on the backbone string neighbors retrieved by the BS-align were very close to the native membrane structures although the query and the neighbor shared a very low sequence identity. The backbone string system represents a new road for the prediction of protein structure from sequence, and suggests that the similarity of the backbone string would be more informative than describing a protein as belonging to a fold.

  9. Analysis of a systematic search-based algorithm for determining protein backbone structure from a minimum number of residual dipolar couplings.

    Science.gov (United States)

    Wang, Lincong; Donald, Bruce Randall

    2004-01-01

    We have developed an ab initio algorithm for determining a protein backbone structure using global orientational restraints on internuclear vectors derived from residual dipolar couplings (RDCs) measured in one or two different aligning media by solution nuclear magnetic resonance (NMR) spectroscopy [14, 15]. Specifically, the conformation and global orientations of individual secondary structure elements are computed, independently, by an exact solution, systematic search-based minimization algorithm using only 2 RDCs per residue. The systematic search is built upon a quartic equation for computing, exactly and in constant time, the directions of an internuclear vector from RDCs, and linear or quadratic equations for computing the sines and cosines of backbone dihedral (phi, psi) angles from two vectors in consecutive peptide planes. In contrast to heuristic search such as simulated annealing (SA) or Monte-Carlo (MC) used by other NMR structure determination algorithms, our minimization algorithm can be analyzed rigorously in terms of expected algorithmic complexity and the coordinate precision of the protein structure as a function of error in the input data. The algorithm has been successfully applied to compute the backbone structures of three proteins using real NMR data.

  10. Versatile phosphite ligands based on silsesquioxane backbones

    NARCIS (Netherlands)

    van der Vlugt, JI; Ackerstaff, J; Dijkstra, TW; Mills, AM; Kooijman, H; Spek, AL; Meetsma, A; Abbenhuis, HCL; Vogt, D

    Silsesquioxanes are employed as ligand backbones for the synthesis of novel phosphite compounds with 3,3'-5,5'-tetrakis(tert-butyl)-2,2'-di-oxa-1,1'-biphenyl substituents. Both mono- and bidentate phosphites are prepared in good yields. Two types of silsesquioxanes are employed as starting

  11. Computational Protein Design Under a Given Backbone Structure with the ABACUS Statistical Energy Function.

    Science.gov (United States)

    Xiong, Peng; Chen, Quan; Liu, Haiyan

    2017-01-01

    An important objective of computational protein design is to identify amino acid sequences that stably fold into a given backbone structure. A general approach to this problem is to minimize an energy function in the sequence space. We have previously reported a method to derive statistical energies for fixed-backbone protein design and showed that it led to de novo proteins that fold as expected. Here, we present the usage of the program that implements this method, which we now name as ABACUS (A Backbone-based Amino aCid Usage Survey).

  12. APPECT: An Approximate Backbone-Based Clustering Algorithm for Tags

    DEFF Research Database (Denmark)

    Zong, Yu; Xu, Guandong; Jin, Pin

    2011-01-01

    resulting from the severe difficulty of ambiguity, redundancy and less semantic nature of tags. Clustering method is a useful tool to address the aforementioned difficulties. Most of the researches on tag clustering are directly using traditional clustering algorithms such as K-means or Hierarchical...... algorithm for Tags (APPECT). The main steps of APPECT are: (1) we execute the K-means algorithm on a tag similarity matrix for M times and collect a set of tag clustering results Z={C1,C2,…,Cm}; (2) we form the approximate backbone of Z by executing a greedy search; (3) we fix the approximate backbone...... Agglomerative Clustering on tagging data, which possess the inherent drawbacks, such as the sensitivity of initialization. In this paper, we instead make use of the approximate backbone of tag clustering results to find out better tag clusters. In particular, we propose an APProximate backbonE-based Clustering...

  13. Density functional MO calculation for stacked DNA base-pairs with backbones.

    Science.gov (United States)

    Kurita, N; Kobayashi, K

    2000-05-01

    In order to elucidate the effect of the sugar and phosphate backbones on the stable structure and electronic properties of stacked DNA base-pairs, we performed ab initio molecular orbital (MO) calculations based on the density functional theory and Slater-type basis set. As a model cluster for stacked base-pairs, we employed three isomers for the dimer unit of stacked guanine-cytosine pairs composed with backbones as well as base-pairs. These structures were fully optimized and their electronic properties were self-consistently investigated. By including the backbones, the difference in total energy among the isomers was largely enhanced, while the trend in relative stability was not changed. The effect of backbones on the electronic properties is remarkable: the MOs with the character of the PO4 parts of backbones appear just below the highest-occupied MO. This result indicates that the PO4 parts might play a rule as a reaction site in chemical processes concerning DNA. Therefore, we conclude that the DNA backbones are indispensable for investigating the stability and electronic properties of the stacked DNA base-pairs.

  14. A density functional study of backbone structures of polydiacetylene: destabilization of butatriene structure

    International Nuclear Information System (INIS)

    Katagiri, Hideki; Shimoi, Yukihiro; Abe, Shuji

    2004-01-01

    Backbone structures of polydiacetylene are studied with first-principles electronic structure method using plane-waves within generalized gradient approximation (GGA) of density functional theory. In spin-restricted calculations a coarse k-point sampling gives a potential energy curve with two local minima corresponding to acetylene and butatriene structures. However, the potential barrier between the two structures rapidly decreases with increasing number of k-points, which results in destabilization of the butatriene structure. Spin polarization effects also destabilize the butatriene structure, inducing atom-centered spin-density-wave state. These potential energies were compared with those obtained by Hartree-Fock, density functional within local density approximation (LDA) and GGA, and hybrid density functional methods using a gaussian basis set. The comparison shows that the density functional methods within LDA and GGA favor the destabilization of the butatriene structure in contrast to the Hartree-Fock method

  15. Backbone structures in human milk oligosaccharides: trans-glycosylation by metagenomic ß-N-acetylhexosaminidases

    NARCIS (Netherlands)

    Nyffenegger, C.; Nordvang, R.T.; Zeuner, B.; Lezyk, M.; Difilippo, E.; Logtenberg, M.J.; Schols, H.A.; Meyer, A.S.; Mikkelsen, J.D.

    2015-01-01

    This paper describes the discovery and characterization of two novel ß-N-acetylhexosaminidases HEX1 and HEX2, capable of catalyzing the synthesis of human milk oligosaccharides (HMO) backbone structures with fair yields using chitin oligomers as ß-N-acetylglucosamine (GlcNAc) donor. The

  16. L-tyrosine-based backbone-modified poly(amino acids).

    Science.gov (United States)

    Gupta, Anirban Sen; Lopina, Stephanie T

    2002-01-01

    Tyrosine-based pseudo-peptide polymers, first introduced in 1987 by Kohn and Langer, have been identified for potential biomaterial applications. These materials combine the desired polypeptide properties of biocompatibility, biodegradability, non-toxicity, and non-immunogenicity with good processing properties including solubility, thermal stability, and moldability which arise from alternating non-amide bonds along the polymer backbone. This paper focuses on the analysis of two such polymers based on the natural amino acid L-tyrosine. Starting from L-tyrosine and its deaminated analogue, 3-(4-para-hydroxy)-phenylpropionic acid, a diphenolic structure containing an amide linkage, was synthesized following standard procedures of peptide synthesis. This diphenolic structure was then used as a monomer to synthesize a polyiminocarbonate using a cyanogen bromide-initiated reaction and a polycarbonate using a triphosgene-initiated reaction. The polyiminocarbonate has iminocarbonate linkages and the polycarbonate has carbonate linkages alternating with amide linkages in the respective polymer backbone. Analytical studies were performed regarding the feasibility of the reaction procedures, the physical properties of the polymers, and their degradation processes, to gain insight into the potential biomaterial applications of these polymers. These results independently reaffirm the studies published by Kohn et al. working on similar polymeric systems.

  17. Trappist: european project dedicated to an open backbone structure for NDT expertise

    International Nuclear Information System (INIS)

    Nouailhas, B.; Vailhen, O.

    1993-01-01

    Non Destructive Testing (NDT) on critical components such as the reactor vessel, primary coolant pipes and steam generators have already been, and are still the subject of many development concerning the improvement of measuring techniques, data processing and on site operation. The tools developed for these tests are generally closed, difficult to extend and of proprietary type. Productivity could be increased if an open backbone structure common to several types of test were available. Moreover, these components are generally submitted to a test involving a single method. In certain cases, the produced information is an insufficient basis for drawing up a satisfactory diagnosis: the test operator or expert often faces problems in extracting more information from signals that are generally noisy. It may prove necessary to complete the inspection with another NDT method based on different principles in order to obtain better performances. It is then by combining the information obtained by two complementary methods that it will be possible to draw up a more reliable diagnosis. These components have also a complex shape. In the case of ultrasonic testing, the accurate following of probe paths requires 3D representation of the geometry, as it is built, to position and display the data obtained from the inspection. To take these geometric constraints into account, it is imperative to use computer tools allowing the three-dimensional representation of the reconstructed information on the components' actual geometry. This specific difficulty, which has long been appreciated, is the subject of developments resulting to industrial products that are more or less satisfactory. The aim of the European Project TRAPPIST (Race Program) is to study an open backbone structure. A mock-up of an analysis station dedicated to NDT expertise will be built and evaluated with specific examples. (authors). 6 figs., 1 ref

  18. Prediction of backbone dihedral angles and protein secondary structure using support vector machines

    Directory of Open Access Journals (Sweden)

    Hirst Jonathan D

    2009-12-01

    Full Text Available Abstract Background The prediction of the secondary structure of a protein is a critical step in the prediction of its tertiary structure and, potentially, its function. Moreover, the backbone dihedral angles, highly correlated with secondary structures, provide crucial information about the local three-dimensional structure. Results We predict independently both the secondary structure and the backbone dihedral angles and combine the results in a loop to enhance each prediction reciprocally. Support vector machines, a state-of-the-art supervised classification technique, achieve secondary structure predictive accuracy of 80% on a non-redundant set of 513 proteins, significantly higher than other methods on the same dataset. The dihedral angle space is divided into a number of regions using two unsupervised clustering techniques in order to predict the region in which a new residue belongs. The performance of our method is comparable to, and in some cases more accurate than, other multi-class dihedral prediction methods. Conclusions We have created an accurate predictor of backbone dihedral angles and secondary structure. Our method, called DISSPred, is available online at http://comp.chem.nottingham.ac.uk/disspred/.

  19. Annotating the protein-RNA interaction sites in proteins using evolutionary information and protein backbone structure.

    Science.gov (United States)

    Li, Tao; Li, Qian-Zhong

    2012-11-07

    RNA-protein interactions play important roles in various biological processes. The precise detection of RNA-protein interaction sites is very important for understanding essential biological processes and annotating the function of the proteins. In this study, based on various features from amino acid sequence and structure, including evolutionary information, solvent accessible surface area and torsion angles (φ, ψ) in the backbone structure of the polypeptide chain, a computational method for predicting RNA-binding sites in proteins is proposed. When the method is applied to predict RNA-binding sites in three datasets: RBP86 containing 86 protein chains, RBP107 containing 107 proteins chains and RBP109 containing 109 proteins chains, better sensitivities and specificities are obtained compared to previously published methods in five-fold cross-validation tests. In order to make further examination for the efficiency of our method, the RBP107 dataset is used as training set, RBP86 and RBP109 datasets are used as the independent test sets. In addition, as examples of our prediction, RNA-binding sites in a few proteins are presented. The annotated results are consistent with the PDB annotation. These results show that our method is useful for annotating RNA binding sites of novel proteins.

  20. Refinement of the protein backbone angle ψ in NMR structure calculations

    International Nuclear Information System (INIS)

    Sprangers, R.; Bottomley, M.J.; Linge, J.P.; Schultz, J.; Nilges, M.; Sattler, M.

    2000-01-01

    Cross-correlated relaxation rates involving the C α -H α dipolar interaction and the carbonyl (C') chemical shift anisotropy (CSA) have been measured using two complementary 3D experiments. We show that the protein backbone angle ψ can be directly refined against such cross-correlated relaxation rates (Γ HαCα,C' ) and the three-bond H/D isotope effect on the C α chemical shifts ( 3 ΔC α (ND) ). By simultaneously using both experimental parameters as restraints during NMR structure calculations, a unique value for the backbone angle ψ is defined. We have applied the new refinement method to the α-Spectrin SH3 domain (a β-sheet protein) and to the Sgs1p HRDC domain (an α-helical protein) and show that the quality of the NMR structures is substantially improved, judging from the atomic coordinate precision and the Ramachandran map. In addition, the ψ-refined NMR structures of the SH3 domain deviate less from the 1.8 A crystal structure, suggesting an improved accuracy. The proposed refinement method can be used to significantly improve the quality of NMR structures and will be applicable to larger proteins

  1. Congested C2-symmetric aryliodanes based on an anti-dimethanoanthracene backbone.

    Science.gov (United States)

    Murray, Stephen J; Müller-Bunz, Helge; Ibrahim, Hasim

    2012-06-25

    A family of congested aryliodanes based on an anti-dimethanoanthracene backbone has been synthesised and two diaryliodonium salts and the iodyl derivative characterised by X-ray analysis. The latter shows a rare water coordination to the iodine(V) centre in the solid state. Applications of these reagents in functional group transfer reactions are reported.

  2. Correlation between protein secondary structure, backbone bond angles, and side-chain orientations

    Science.gov (United States)

    Lundgren, Martin; Niemi, Antti J.

    2012-08-01

    We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central Cα carbon of a protein backbone, and for this we develop new visualization techniques to analyze high-resolution x-ray structures in the Protein Data Bank. We observe that there is a correlation between the deformations of the ideal tetrahedral symmetry and the local secondary structure of the protein. We propose a universal coarse-grained energy function to describe the ensuing side-chain geometry in terms of the Cβ carbon orientations. The energy function can model the side-chain geometry with a subatomic precision. As an example we construct the Cα-Cβ structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 Å in root-mean-square distance from the experimental x-ray structure.

  3. APSY-NMR for protein backbone assignment in high-throughput structural biology

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, Samit Kumar; Serrano, Pedro; Proudfoot, Andrew; Geralt, Michael [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States); Pedrini, Bill [Paul Scherrer Institute (PSI), SwissFEL Project (Switzerland); Herrmann, Torsten [Université de Lyon, Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1 (France); Wüthrich, Kurt, E-mail: wuthrich@scripps.edu [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States)

    2015-01-15

    A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90 % of the residues. For most proteins the APSY data acquisition was completed in less than 30 h. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [{sup 1}H,{sup 1}H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination.

  4. Backbone chemical shifts assignments, secondary structure, and ligand binding of a family GH-19 chitinase from moss, Bryum coronatum.

    Science.gov (United States)

    Shinya, Shoko; Nagata, Takuya; Ohnuma, Takayuki; Taira, Toki; Nishimura, Shigenori; Fukamizo, Tamo

    2012-10-01

    Family GH19 chitinases have been recognized as important in the plant defense against fungal pathogens. However, their substrate-recognition mechanism is still unknown. We report here the first resonance assignment of NMR spectrum of a GH19 chitinase from moss, Bryum coronatum (BcChi-A). The backbone signals were nearly completely assigned, and the secondary structure was estimated based on the chemical shift values. The addition of the chitin dimer to the enzyme solution perturbed the chemical shifts of HSQC resonances of the amino acid residues forming the putative substrate-binding cleft. Further NMR analysis of the ligand binding to BcChi-A will improve understanding of the substrate-recognition mechanism of GH-19 enzymes.

  5. CORBA and MPI-based 'backbone' for coupling advanced simulation tools

    International Nuclear Information System (INIS)

    Seydaliev, M.; Caswell, D.

    2014-01-01

    There is a growing international interest in using coupled, multidisciplinary computer simulations for a variety of purposes, including nuclear reactor safety analysis. Reactor behaviour can be modeled using a suite of computer programs simulating phenomena or predicting parameters that can be categorized into disciplines such as Thermalhydraulics, Neutronics, Fuel, Fuel Channels, Fission Product Release and Transport, Containment and Atmospheric Dispersion, and Severe Accident Analysis. Traditionally, simulations used for safety analysis individually addressed only the behaviour within a single discipline, based upon static input data from other simulation programs. The limitation of using a suite of stand-alone simulations is that phenomenological interdependencies or temporal feedback between the parameters calculated within individual simulations cannot be adequately captured. To remove this shortcoming, multiple computer simulations for different disciplines must exchange data during runtime to address these interdependencies. This article describes the concept of a new framework, which we refer to as the 'Backbone', to provide the necessary runtime exchange of data. The Backbone, currently under development at AECL for a preliminary feasibility study, is a hybrid design using features taken from the Common Object Request Broker Architecture (CORBA), a standard defined by the Object Management Group, and the Message Passing Interface (MPI), a standard developed by a group of researchers from academia and industry. Both have well-tested and efficient implementations, including some that are freely available under the GNU public licenses. The CORBA component enables individual programs written in different languages and running on different platforms within a network to exchange data with each other, thus behaving like a single application. MPI provides the process-to-process intercommunication between these programs. This paper outlines the different CORBA and

  6. The extension of a DNA double helix by an additional Watson-Crick base pair on the same backbone

    DEFF Research Database (Denmark)

    Kumar, P.; Sharma, P. K.; Madsen, Charlotte S.

    2013-01-01

    Additional base pair: The DNA duplex can be extended with an additional Watson-Crick base pair on the same backbone by the use of double-headed nucleotides. These also work as compressed dinucleotides and form two base pairs with cognate nucleobases on the opposite strand.......Additional base pair: The DNA duplex can be extended with an additional Watson-Crick base pair on the same backbone by the use of double-headed nucleotides. These also work as compressed dinucleotides and form two base pairs with cognate nucleobases on the opposite strand....

  7. 40-Gbps optical backbone network deep packet inspection based on FPGA

    Science.gov (United States)

    Zuo, Yuan; Huang, Zhiping; Su, Shaojing

    2014-11-01

    In the era of information, the big data, which contains huge information, brings about some problems, such as high speed transmission, storage and real-time analysis and process. As the important media for data transmission, the Internet is the significant part for big data processing research. With the large-scale usage of the Internet, the data streaming of network is increasing rapidly. The speed level in the main fiber optic communication of the present has reached 40Gbps, even 100Gbps, therefore data on the optical backbone network shows some features of massive data. Generally, data services are provided via IP packets on the optical backbone network, which is constituted with SDH (Synchronous Digital Hierarchy). Hence this method that IP packets are directly mapped into SDH payload is named POS (Packet over SDH) technology. Aiming at the problems of real time process of high speed massive data, this paper designs a process system platform based on ATCA for 40Gbps POS signal data stream recognition and packet content capture, which employs the FPGA as the CPU. This platform offers pre-processing of clustering algorithms, service traffic identification and data mining for the following big data storage and analysis with high efficiency. Also, the operational procedure is proposed in this paper. Four channels of 10Gbps POS signal decomposed by the analysis module, which chooses FPGA as the kernel, are inputted to the flow classification module and the pattern matching component based on TCAM. Based on the properties of the length of payload and net flows, buffer management is added to the platform to keep the key flow information. According to data stream analysis, DPI (deep packet inspection) and flow balance distribute, the signal is transmitted to the backend machine through the giga Ethernet ports on back board. Practice shows that the proposed platform is superior to the traditional applications based on ASIC and NP.

  8. Solution NMR Structures of Oxidized and Reduced Ehrlichia chaffeensis thioredoxin: NMR-Invisible Structure Owing to Backbone Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Buchko, Garry W.; Hewitt, Stephen N.; Van Voorhis, Wesley C.; Myler, Peter J.

    2018-01-02

    Thioredoxins (Trxs) are small ubiquitous proteins that participate in a diverse variety of redox reactions via the reversible oxidation of two cysteine thiol groups in a structurally conserved active site, CGPC. Here, we describe the NMR solution structures of a Trx from Ehrlichia chaffeensis (Ec-Trx, ECH_0218), the etiological agent responsible for human monocytic ehrlichiosis, in both the oxidized and reduced states. The overall topology of the calculated structures is similar in both redox states and similar to other Trx structures, a five-strand, mixed -sheet (1:3:2:4:5) surrounded by four -helices. Unlike other Trxs studied by NMR in both redox states, the 1H-15N HSQC spectra of reduced Ec-Trx was missing eight amide cross peaks relative to the spectra of oxidized Ec-Trx. These missing amides correspond to residues C32-E39 in the active site containing helix (2) and S72-I75 in a loop near the active site and suggest a substantial change in the backbone dynamics associated with the formation of an intramolecular C32-C35 disulfide bond.

  9. On the geometry and electronic structure of the As-DNA backbone

    Czech Academy of Sciences Publication Activity Database

    Mládek, Arnošt; Šponer, Jiří; Sumpter, B.G.; Fuentes-Cabrera, M.; Šponer, Judit E.

    2011-01-01

    Roč. 2, č. 5 (2011), s. 389-392 ISSN 1948-7185 R&D Projects: GA MŠk(CZ) LC06030; GA AV ČR(CZ) IAA400040802; GA ČR(CZ) GAP208/10/2302; GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GAP208/11/1822; GA ČR(CZ) GD203/09/H046 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : quantum chemistry * DFT * backbone Subject RIV: BO - Biophysics Impact factor: 6.213, year: 2011

  10. Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation

    International Nuclear Information System (INIS)

    Marassi, Francesca M.; Ding, Yi; Schwieters, Charles D.; Tian, Ye; Yao, Yong

    2015-01-01

    The outer membrane protein Ail (attachment invasion locus) is a virulence factor of Yersinia pestis that mediates cell invasion, cell attachment and complement resistance. Here we describe its three-dimensional backbone structure determined in decyl-phosphocholine (DePC) micelles by NMR spectroscopy. The NMR structure was calculated using the membrane function of the implicit solvation potential, eefxPot, which we have developed to facilitate NMR structure calculations in a physically realistic environment. We show that the eefxPot force field guides the protein towards its native fold. The resulting structures provide information about the membrane-embedded global position of Ail, and have higher accuracy, higher precision and improved conformational properties, compared to the structures calculated with the standard repulsive potential

  11. Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation.

    Science.gov (United States)

    Marassi, Francesca M; Ding, Yi; Schwieters, Charles D; Tian, Ye; Yao, Yong

    2015-09-01

    The outer membrane protein Ail (attachment invasion locus) is a virulence factor of Yersinia pestis that mediates cell invasion, cell attachment and complement resistance. Here we describe its three-dimensional backbone structure determined in decyl-phosphocholine (DePC) micelles by NMR spectroscopy. The NMR structure was calculated using the membrane function of the implicit solvation potential, eefxPot, which we have developed to facilitate NMR structure calculations in a physically realistic environment. We show that the eefxPot force field guides the protein towards its native fold. The resulting structures provide information about the membrane-embedded global position of Ail, and have higher accuracy, higher precision and improved conformational properties, compared to the structures calculated with the standard repulsive potential.

  12. Effect of semiconductor polymer backbone structures and side-chain parameters on the facile separation of semiconducting single-walled carbon nanotubes from as-synthesized mixtures

    Science.gov (United States)

    Lee, Dennis T.; Chung, Jong Won; Park, Geonhee; Kim, Yun-Tae; Lee, Chang Young; Cho, Yeonchoo; Yoo, Pil J.; Han, Jae-Hee; Shin, Hyeon-Jin; Kim, Woo-Jae

    2018-01-01

    Semiconducting single-walled carbon nanotubes (SWNTs) show promise as core materials for next-generation solar cells and nanoelectronic devices. However, most commercial SWNT production methods generate mixtures of metallic SWNTs (m-SWNTs) and semiconducting SWNT (sc-SWNTs). Therefore, sc-SWNTs must be separated from their original mixtures before use. In this study, we investigated a polymer-based, noncovalent sc-SWNT separation approach, which is simple to perform and does not disrupt the electrical properties of the SWNTs, thus improving the performance of the corresponding sc-SWNT-based applications. By systematically investigating the effect that different structural features of the semiconductor polymer have on the separation of sc-SWNTs, we discovered that the length and configuration of the alkyl side chains and the rigidity of the backbone structure exert significant effects on the efficiency of sc-SWNT separation. We also found that electron transfer between the semiconductor polymers and sc-SWNTs is strongly affected by their energy-level alignment, which can be tailored by controlling the donor-acceptor configuration in the polymer backbone structures. Among the polymers investigated, the highly planar P8T2Z-C12 semiconductor polymer showed the best sc-SWNT separation efficiency and unprecedentedly strong electronic interaction with the sc-SWNTs, which is important for improving their performance in applications.

  13. The Synthesis and Structural Characterization of Graft Copolymers Composed of γ-PGA Backbone and Oligoesters Pendant Chains

    Science.gov (United States)

    Kwiecień, Iwona; Radecka, Iza; Kowalczuk, Marek; Jelonek, Katarzyna; Orchel, Arkadiusz; Adamus, Grażyna

    2017-10-01

    The novel copolymers composed of poly-γ-glutamic acid (γ-PGA) and oligoesters have been developed. The structures of the obtained copolymers including variety of end groups were determined at the molecular level with the aid of electrospray ionization multistage mass spectrometry (ESI-MSn). The fragmentation experiment performed for the selected sodium adducts of the copolymers confirmed that the developed methods lead to the formation of graft copolymers composed of poly-γ-glutamic acid (γ-PGA) backbone and oligoesters pendant chains. Moreover, it was established that fragmentation of selected sodium adducts of graft copolymers proceeded via random breakage of amide bonds along the backbone and ester bonds of the oligoesters pendant chains. Considering potential applications of the synthesized copolymers in the area of biomaterials, the hydrolytic degradation under laboratory conditions and in vitro cytotoxicity tests were performed. The ESI-MSn technique applied in this study has been proven to be a useful tool in structural studies of novel graft copolymers as well as their degradation products. [Figure not available: see fulltext.

  14. Structural elucidation of a novel core oligosaccharide backbone of the lipopolysaccharide from the new bacterial species Agrobacterium larrymoorei.

    Science.gov (United States)

    Molinaro, Antonio; De Castro, Cristina; Lanzetta, Rosa; Parrilli, Michelangelo; Raio, Aida; Zoina, Astolfo

    2003-11-14

    Agrobacterium larrymoorei is a Gram-negative phytopathogenic bacterium, which produces tumours on Ficus benjamina plants and differs from other Agrobacteria both genetically and biochemically. The lipopolysaccharide (LPS) plays an important role in the pathogenesis of Agrobacteria. The present paper is the first report on the molecular primary structure of the core region of an Agrobacterium LPS. The following structure of the core and lipid A carbohydrate backbone of an R-form LPS of A. larrymoorei was determined by chemical degradations and 1D and 2D NMR spectroscopy: [carbohydrate structure: see text] All sugars are alpha-D-pyranoses if not stated otherwise, Kdo is 3-deoxy-D-manno-oct-2-ulosonic acid, Qui3NAcyl is 3,6-dideoxy-3-(3-hydroxy-2,3-dimethyl-5-oxoprolylamino)glucose, GlcAN and GalAN are amides of GlcA and GalA.

  15. Routing protocol for wireless quantum multi-hop mesh backbone network based on partially entangled GHZ state

    Science.gov (United States)

    Xiong, Pei-Ying; Yu, Xu-Tao; Zhang, Zai-Chen; Zhan, Hai-Tao; Hua, Jing-Yu

    2017-08-01

    Quantum multi-hop teleportation is important in the field of quantum communication. In this study, we propose a quantum multi-hop communication model and a quantum routing protocol with multihop teleportation for wireless mesh backbone networks. Based on an analysis of quantum multi-hop protocols, a partially entangled Greenberger-Horne-Zeilinger (GHZ) state is selected as the quantum channel for the proposed protocol. Both quantum and classical wireless channels exist between two neighboring nodes along the route. With the proposed routing protocol, quantum information can be transmitted hop by hop from the source node to the destination node. Based on multi-hop teleportation based on the partially entangled GHZ state, a quantum route established with the minimum number of hops. The difference between our routing protocol and the classical one is that in the former, the processes used to find a quantum route and establish quantum channel entanglement occur simultaneously. The Bell state measurement results of each hop are piggybacked to quantum route finding information. This method reduces the total number of packets and the magnitude of air interface delay. The deduction of the establishment of a quantum channel between source and destination is also presented here. The final success probability of quantum multi-hop teleportation in wireless mesh backbone networks was simulated and analyzed. Our research shows that quantum multi-hop teleportation in wireless mesh backbone networks through a partially entangled GHZ state is feasible.

  16. Optimized set of two-dimensional experiments for fast sequential assignment, secondary structure determination, and backbone fold validation of 13C/15N-labelled proteins

    International Nuclear Information System (INIS)

    Bersch, Beate; Rossy, Emmanuel; Coves, Jacques; Brutscher, Bernhard

    2003-01-01

    NMR experiments are presented which allow backbone resonance assignment, secondary structure identification, and in favorable cases also molecular fold topology determination from a series of two-dimensional 1 H- 15 N HSQC-like spectra. The 1 H- 15 N correlation peaks are frequency shifted by an amount ± ω X along the 15 N dimension, where ω X is the C α , C β , or H α frequency of the same or the preceding residue. Because of the low dimensionality (2D) of the experiments, high-resolution spectra are obtained in a short overall experimental time. The whole series of seven experiments can be performed in typically less than one day. This approach significantly reduces experimental time when compared to the standard 3D-based methods. The here presented methodology is thus especially appealing in the context of high-throughput NMR studies of protein structure, dynamics or molecular interfaces

  17. A fusion networking model for smart grid power distribution backbone communication network based on PTN

    Directory of Open Access Journals (Sweden)

    Wang Hao

    2016-01-01

    Full Text Available In current communication network for distribution in Chinese power grid systems, the fiber communication backbone network for distribution and TD-LTE power private wireless backhaul network of power grid are both bearing by the SDH optical transmission network, which also carries the communication network of transformer substation and main electric. As the data traffic of the distribution communication and TD-LTE power private wireless network grow rapidly in recent years, it will have a big impact with the SDH network’s bearing capacity which is mainly used for main electric communication in high security level. This paper presents a fusion networking model which use a multiple-layer PTN network as the unified bearing of the TD-LTE power private wireless backhaul network and fiber communication backbone network for distribution. Network dataflow analysis shows that this model can greatly reduce the capacity pressure of the traditional SDH network as well as ensure the reliability of the transmission of the communication network for distribution and TD-LTE power private wireless network.

  18. Folding of RNA tertiary structure: Linkages between backbone phosphates, ions, and water.

    Science.gov (United States)

    Draper, David E

    2013-12-01

    The functional forms of many RNAs have compact architectures. The placement of phosphates within such structures must be influenced not only by the strong electrostatic repulsion between phosphates, but also by networks of interactions between phosphates, water, and mobile ions. This review first explores what has been learned of the basic thermodynamic constraints on these arrangements from studies of hydration and ions in simple DNA molecules, and then gives an overview of what is known about ion and water interactions with RNA structures. A brief survey of RNA crystal structures identifies several interesting architectures in which closely spaced phosphates share hydration shells or phosphates are buried in environments that provide intramolecular hydrogen bonds or site-bound cations. Formation of these structures must require strong coupling between the uptake of ions and release of water. Copyright © 2013 Wiley Periodicals, Inc.

  19. The Effects of NHC-Backbone Substitution on Efficiency in Ruthenium-based Olefin Metathesis

    Science.gov (United States)

    Kuhn, Kevin M.; Bourg, Jean-Baptiste; Chung, Cheol K.; Virgil, Scott C.; Grubbs, Robert H.

    2009-01-01

    A series of ruthenium olefin metathesis catalysts bearing N-heterocyclic carbene (NHC) ligands with varying degrees of backbone and N-aryl substitution have been prepared. These complexes show greater resistance to decomposition through C–H activation of the N-aryl group, resulting in increased catalyst lifetimes. This work has utilized robotic technology to examine the activity and stability of each catalyst in metathesis, providing insights into the relationship between ligand architecture and enhanced efficiency. The development of this robotic methodology has also shown that, under optimized conditions, catalyst loadings as low as 25 ppm can lead to 100% conversion in the ring-closing metathesis of diethyl diallylmalonate. PMID:19351207

  20. A recombinant, chimeric tetravalent dengue vaccine candidate based on a dengue virus serotype 2 backbone.

    Science.gov (United States)

    Osorio, Jorge E; Wallace, Derek; Stinchcomb, Dan T

    2016-01-01

    Dengue fever is caused by infection with one of four dengue virus (DENV) serotypes (DENV-1-4), necessitating tetravalent dengue vaccines that can induce protection against all four DENV. Takeda's live attenuated tetravalent dengue vaccine candidate (TDV) comprises an attenuated DENV-2 strain plus chimeric viruses containing the prM and E genes of DENV-1, -3 and -4 cloned into the attenuated DENV-2 'backbone'. In Phase 1 and 2 studies, TDV was well tolerated by children and adults aged 1.5-45 years, irrespective of prior dengue exposure; mild injection-site symptoms were the most common adverse events. TDV induced neutralizing antibody responses and seroconversion to all four DENV as well as cross-reactive T cell-mediated responses that may be necessary for broad protection against dengue fever.

  1. “Splicing up” drug discovery. Cell-Based Expression and Screening of Genetically-Encoded Libraries of Backbone Cyclized Polypeptides

    Science.gov (United States)

    Sancheti, Harshkumar; Camarero, Julio A.

    2012-01-01

    The present paper reviews the use of protein splicing for the biosynthesis of backbone cyclic polypeptides. This general method allows the in vivo and in vitro biosynthesis of cyclic polypeptides using recombinant DNA expression techniques. Biosynthetic access to backbone cyclic peptides opens the possibility to generate cell-based combinatorial libraries that can be screened inside living cells for their ability to attenuate or inhibit cellular processes thus providing a new way for finding therapeutic agents. PMID:19628015

  2. Design and synthesis of short amphiphilic cationic peptidomimetics based on biphenyl backbone as antibacterial agents.

    Science.gov (United States)

    Kuppusamy, Rajesh; Yasir, Muhammad; Berry, Thomas; Cranfield, Charles G; Nizalapur, Shashidhar; Yee, Eugene; Kimyon, Onder; Taunk, Aditi; Ho, Kitty K K; Cornell, Bruce; Manefield, Mike; Willcox, Mark; Black, David StC; Kumar, Naresh

    2018-01-01

    Antimicrobial peptides (AMPs) and their synthetic mimics have received recent interest as new alternatives to traditional antibiotics in attempts to overcome the rise of antibiotic resistance in many microbes. AMPs are part of the natural defenses of most living organisms and they also have a unique mechanism of action against bacteria. Herein, a new series of short amphiphilic cationic peptidomimetics were synthesized by incorporating the 3'-amino-[1,1'-biphenyl]-3-carboxylic acid backbone to mimic the essential properties of natural AMPs. By altering hydrophobicity and charge, we identified the most potent analogue 25g that was active against both Gram-positive Staphylococcus aureus (MIC = 15.6 μM) and Gram-negative Escherichia coli (MIC = 7.8 μM) bacteria. Cytoplasmic permeability assay results revealed that 25g acts primarily by depolarization of lipids in cytoplasmic membranes. The active compounds were also investigated for their cytotoxicity to human cells, lysis of lipid bilayers using tethered bilayer lipid membranes (tBLMs) and their activity against established biofilms of S. aureus and E. coli. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  3. Solution structure and backbone dynamics of recombinant Cucurbita maxima trypsin inhibitor-V determined by NMR spectroscopy.

    Science.gov (United States)

    Liu, J; Prakash, O; Cai, M; Gong, Y; Huang, Y; Wen, L; Wen, J J; Huang, J K; Krishnamoorthi, R

    1996-02-06

    The solution structure of recombinant Cucurbita maxima trypsin inhibitor-V (rCMTI-V), whose N-terminal is unacetylated and carries an extra glycine residue, was determined by means of two-dimensional (2D) homo and 3D hetero NMR experiments in combination with a distance geometry and simulated annealing algorithm. A total of 927 interproton distances and 123 torsion angle constraints were utilized to generate 18 structures. The root mean squared deviation (RMSD) of the mean structure is 0.53 A for main-chain atoms and 0.95 A for all the non-hydrogen atoms of residues 3-40 and 49-67. The average structure of rCMTI-V is found to be almost the same as that of the native protein [Cai, M., Gong, Y., Kao, J.-L., & Krishnamoorthi, R. (1995) Biochemistry 34, 5201-5211]. The backbone dynamics of uniformly 15N-labeled rCMTI-V were characterized by 2D 1H-15N NMR methods. 15N spin-lattice and spin-spin relaxation rate constants (R1 and R2, respectively) and [1H]-15N steady-state heteronuclear Overhauser effect enhancements were measured for the peptide NH units and, using the model-free formalism [Lipari, G., & Szabo, A. (1982) J. Am. Chem. Soc. 104, 4546-4559, 4559-4570], the following parameters were determined: overall tumbling correlation time for the protein molecule (tau m), generalized order parameters for the individual N-H vectors (S2), effective correlation times for their internal motions (tau e), and terms to account for motions on a slower time scale (second) due to chemical exchange and/or conformational averaging (R(ex)). Most of the backbone NH groups of rCMTI-V are found to be highly constrained ((S2) = 0.83) with the exception of those in the binding loop (residues 41-48, (S2) = 0.71) and the N-terminal region ((S2) = 0.73). Main-chain atoms in these regions show large RMSD values in the average NMR structure. Residues involved in turns also appear to have more mobility ((S2) = 0.80). Dynamical properties of rCMTI-V were compared with those of two other

  4. Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles

    KAUST Repository

    Maadooliat, Mehdi

    2012-08-27

    Despite considerable progress in the past decades, protein structure prediction remains one of the major unsolved problems in computational biology. Angular-sampling-based methods have been extensively studied recently due to their ability to capture the continuous conformational space of protein structures. The literature has focused on using a variety of parametric models of the sequential dependencies between angle pairs along the protein chains. In this article, we present a thorough review of angular-sampling-based methods by assessing three main questions: What is the best distribution type to model the protein angles? What is a reasonable number of components in a mixture model that should be considered to accurately parameterize the joint distribution of the angles? and What is the order of the local sequence-structure dependency that should be considered by a prediction method? We assess the model fits for different methods using bivariate lag-distributions of the dihedral/planar angles. Moreover, the main information across the lags can be extracted using a technique called Lag singular value decomposition (LagSVD), which considers the joint distribution of the dihedral/planar angles over different lags using a nonparametric approach and monitors the behavior of the lag-distribution of the angles using singular value decomposition. As a result, we developed graphical tools and numerical measurements to compare and evaluate the performance of different model fits. Furthermore, we developed a web-tool (http://www.stat.tamu. edu/~madoliat/LagSVD) that can be used to produce informative animations. © The Author 2012. Published by Oxford University Press.

  5. Proton-detected MAS NMR experiments based on dipolar transfers for backbone assignment of highly deuterated proteins

    Science.gov (United States)

    Chevelkov, Veniamin; Habenstein, Birgit; Loquet, Antoine; Giller, Karin; Becker, Stefan; Lange, Adam

    2014-05-01

    Proton-detected solid-state NMR was applied to a highly deuterated insoluble, non-crystalline biological assembly, the Salmonella typhimurium type iii secretion system (T3SS) needle. Spectra of very high resolution and sensitivity were obtained at a low protonation level of 10-20% at exchangeable amide positions. We developed efficient experimental protocols for resonance assignment tailored for this system and the employed experimental conditions. Using exclusively dipolar-based interspin magnetization transfers, we recorded two sets of 3D spectra allowing for an almost complete backbone resonance assignment of the needle subunit PrgI. The additional information provided by the well-resolved proton dimension revealed the presence of two sets of resonances in the N-terminal helix of PrgI, while in previous studies employing 13C detection only a single set of resonances was observed.

  6. Solid State Nuclear Magnetic Resonance Investigation of Polymer Backbone Dynamics in Poly(Ethylene Oxide) Based Lithium and Sodium Polyether-ester-sulfonate Ionomers

    Energy Technology Data Exchange (ETDEWEB)

    Roach, David J.; Dou, Shichen; Colby, Ralph H.; Mueller, Karl T.

    2013-01-01

    Polymer backbone dynamics of single ion conducting poly(ethylene oxide) (PEO)-based ionomer samples with low glass transition temperatures (Tg) have been investigated using solid-state nuclear magnetic resonance (NMR). Experiments detecting 13C with 1H decoupling under magic angle spinning (MAS) conditions identified the different components of the polymer backbone (PEO spacer and isophthalate groups) and their relative mobilities for a suite of lithium- and sodium-containing ionomer samples with varying cation contents. Variable temperature (203-373 K) 1H-13C cross-polarization MAS (CP-MAS) experiments also provided qualitative assessment of the differences in the motions of the polymer backbone components as a function of cation content and identity. Each of the main backbone components exhibit distinct motions, following the trends expected for motional characteristics based on earlier Quasi Elastic Neutron Scattering and 1H spin-lattice relaxation rate measurements. Previous 1H and 7Li spin-lattice relaxation measurements focused on both the polymer backbone and cation motion on the nanosecond timescale. The studies presented here assess the slower timescale motion of the polymer backbone allowing for a more comprehensive understanding of the polymer dynamics. The temperature dependences of 13C linewidths were used to both qualitatively and quantitatively examine the effects of cation content and identity on PEO spacer mobility. Variable contact time 1H-13C CP-MAS experiments were used to further assess the motions of the polymer backbone on the microsecond timescale. The motion of the PEO spacer, reported via the rate of magnetization transfer from 1H to 13C nuclei, becomes similar for T ≳ 1.1 Tg in all ionic samples, indicating that at similar elevated reduced temperatures the motions of the polymer backbones on the microsecond timescale become insensitive to ion interactions. These results present an improved picture, beyond those of previous findings, for

  7. Exact Solutions for Internuclear Vectors and Backbone Dihedral Angles from NH Residual Dipolar Couplings in Two Media, and their Application in a Systematic Search Algorithm for Determining Protein Backbone Structure

    International Nuclear Information System (INIS)

    Wang Lincong; Donald, Bruce Randall

    2004-01-01

    We have derived a quartic equation for computing the direction of an internuclear vector from residual dipolar couplings (RDCs) measured in two aligning media, and two simple trigonometric equations for computing the backbone (φ,ψ) angles from two backbone vectors in consecutive peptide planes. These equations make it possible to compute, exactly and in constant time, the backbone (φ,ψ) angles for a residue from RDCs in two media on any single backbone vector type. Building upon these exact solutions we have designed a novel algorithm for determining a protein backbone substructure consisting of α-helices and β-sheets. Our algorithm employs a systematic search technique to refine the conformation of both α-helices and β-sheets and to determine their orientations using exclusively the angular restraints from RDCs. The algorithm computes the backbone substructure employing very sparse distance restraints between pairs of α-helices and β-sheets refined by the systematic search. The algorithm has been demonstrated on the protein human ubiquitin using only backbone NH RDCs, plus twelve hydrogen bonds and four NOE distance restraints. Further, our results show that both the global orientations and the conformations of α-helices and β-strands can be determined with high accuracy using only two RDCs per residue. The algorithm requires, as its input, backbone resonance assignments, the identification of α-helices and β-sheets as well as sparse NOE distance and hydrogen bond restraints.Abbreviations: NMR - nuclear magnetic resonance; RDC - residual dipolar coupling; NOE - nuclear Overhauser effect; SVD - singular value decomposition; DFS - depth-first search; RMSD - root mean square deviation; POF - principal order frame; PDB - protein data bank; SA - simulated annealing; MD - molecular dynamics

  8. Network Traffic Prediction Based on Deep Belief Network and Spatiotemporal Compressive Sensing in Wireless Mesh Backbone Networks

    Directory of Open Access Journals (Sweden)

    Laisen Nie

    2018-01-01

    Full Text Available Wireless mesh network is prevalent for providing a decentralized access for users and other intelligent devices. Meanwhile, it can be employed as the infrastructure of the last few miles connectivity for various network applications, for example, Internet of Things (IoT and mobile networks. For a wireless mesh backbone network, it has obtained extensive attention because of its large capacity and low cost. Network traffic prediction is important for network planning and routing configurations that are implemented to improve the quality of service for users. This paper proposes a network traffic prediction method based on a deep learning architecture and the Spatiotemporal Compressive Sensing method. The proposed method first adopts discrete wavelet transform to extract the low-pass component of network traffic that describes the long-range dependence of itself. Then, a prediction model is built by learning a deep architecture based on the deep belief network from the extracted low-pass component. Otherwise, for the remaining high-pass component that expresses the gusty and irregular fluctuations of network traffic, the Spatiotemporal Compressive Sensing method is adopted to predict it. Based on the predictors of two components, we can obtain a predictor of network traffic. From the simulation, the proposed prediction method outperforms three existing methods.

  9. Testing Backbone.js

    CERN Document Server

    Roemer, Ryan

    2013-01-01

    This book is packed with the step by step tutorial and instructions in recipe format helping you setup test infrastructure and gradually advance your skills to plan, develop, and test your backbone applications.If you are a JavaScript developer looking for recipes to create and implement test support for your backbone application, then this book is ideal for you.

  10. Stability of maximum-likelihood-based clustering methods: exploring the backbone of classifications

    International Nuclear Information System (INIS)

    Mungan, Muhittin; Ramasco, José J

    2010-01-01

    Components of complex systems are often classified according to the way they interact with each other. In graph theory such groups are known as clusters or communities. Many different techniques have been recently proposed to detect them, some of which involve inference methods using either Bayesian or maximum likelihood approaches. In this paper, we study a statistical model designed for detecting clusters based on connection similarity. The basic assumption of the model is that the graph was generated by a certain grouping of the nodes and an expectation maximization algorithm is employed to infer that grouping. We show that the method admits further development to yield a stability analysis of the groupings that quantifies the extent to which each node influences its neighbors' group membership. Our approach naturally allows for the identification of the key elements responsible for the grouping and their resilience to changes in the network. Given the generality of the assumptions underlying the statistical model, such nodes are likely to play special roles in the original system. We illustrate this point by analyzing several empirical networks for which further information about the properties of the nodes is available. The search and identification of stabilizing nodes constitutes thus a novel technique to characterize the relevance of nodes in complex networks

  11. Progress in palladium-based catalytic systems for the sustainable synthesis of annulated heterocycles: a focus on indole backbones.

    Science.gov (United States)

    Platon, Mélanie; Amardeil, Régine; Djakovitch, Laurent; Hierso, Jean-Cyrille

    2012-05-21

    A survey highlighting the most recent palladium catalytic systems produced and their performances for progress in direct synthesis of indole backbones by heterocarbocyclization of reactive substrates is provided. The discussion is developed in relation with the principles of sustainable chemistry concerning atom and mass economy. In this respect, the general convergent character of the syntheses is of particular interest (one-pot, domino, cascade or tandem reactions), and the substrates accessibility and reactivity, together with the final waste production, are also important. This critical review clearly indicates that the development of ligand chemistry, mainly phosphines and carbenes, in the last few decades gave a significant impetus to powerful functionalization of indoles at virtually all positions of this ubiquitous backbone (118 references).

  12. Backbone amide linker strategy

    DEFF Research Database (Denmark)

    Shelton, Anne Pernille Tofteng; Jensen, Knud Jørgen

    2013-01-01

    In the backbone amide linker (BAL) strategy, the peptide is anchored not at the C-terminus but through a backbone amide, which leaves the C-terminal available for various modifications. This is thus a very general strategy for the introduction of C-terminal modifications. The BAL strategy...... to assemble the final peptide. One useful application of this strategy is in the synthesis of C-terminal peptide aldehydes. The C-terminal aldehyde is masked as an acetal during synthesis and then conveniently demasked in the final cleavage step to generate the free aldehyde. Another application...

  13. Improved site-specific recombinase-based method to produce selectable marker- and vector-backbone-free transgenic cells

    Science.gov (United States)

    Yu, Yuan; Tong, Qi; Li, Zhongxia; Tian, Jinhai; Wang, Yizhi; Su, Feng; Wang, Yongsheng; Liu, Jun; Zhang, Yong

    2014-02-01

    PhiC31 integrase-mediated gene delivery has been extensively used in gene therapy and animal transgenesis. However, random integration events are observed in phiC31-mediated integration in different types of mammalian cells; as a result, the efficiencies of pseudo attP site integration and evaluation of site-specific integration are compromised. To improve this system, we used an attB-TK fusion gene as a negative selection marker, thereby eliminating random integration during phiC31-mediated transfection. We also excised the selection system and plasmid bacterial backbone by using two other site-specific recombinases, Cre and Dre. Thus, we generated clean transgenic bovine fetal fibroblast cells free of selectable marker and plasmid bacterial backbone. These clean cells were used as donor nuclei for somatic cell nuclear transfer (SCNT), indicating a similar developmental competence of SCNT embryos to that of non-transgenic cells. Therefore, the present gene delivery system facilitated the development of gene therapy and agricultural biotechnology.

  14. 1990s: High Capacity Backbones

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. 1990s: High Capacity Backbones. Backbone capacities increased from 2.5 Gb/s to 100s of Gb/s during the 1990's. Wavelength division multiplexing with 160 waves of 10 Gb/s was commercially available. Several high-capacity backbones built in the US and Europe.

  15. Molecular Data for a Biochemical Model of DNA Radiation Damage: Electron Impact Ionization and Dissociative Ionization of DNA Bases and Sugar-Phosphate Backbone

    Science.gov (United States)

    Dateo, Christopher E.; Fletcher, Graham D.

    2004-01-01

    As part of the database for building up a biochemical model of DNA radiation damage, electron impact ionization cross sections of sugar-phosphate backbone and DNA bases have been calculated using the improved binary-encounter dipole (iBED) model. It is found that the total ionization cross sections of C3'- and C5'-deoxyribose-phospate, two conformers of the sugar-phosphate backbone, are close to each other. Furthermore, the sum of the ionization cross sections of the separate deoxyribose and phosphate fragments is in close agreement with the C3'- and C5'-deoxyribose-phospate cross sections, differing by less than 10%. Of the four DNA bases, the ionization cross section of guanine is the largest, then in decreasing order, adenine, thymine, and cytosine. The order is in accordance with the known propensity of oxidation of the bases by ionizing radiation. Dissociative ionization (DI), a process that both ionizes and dissociates a molecule, is investigated for cytosine. The DI cross section for the formation of H and (cytosine-Hl)(+), with the cytosine ion losing H at the 1 position, is also reported. The threshold of this process is calculated to be 17.1 eV. Detailed analysis of ionization products such as in DI is important to trace the sequential steps in the biochemical process of DNA damage.

  16. Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design

    Directory of Open Access Journals (Sweden)

    Bordner Andrew J

    2010-04-01

    Full Text Available Abstract Background Empirical scoring functions have proven useful in protein structure modeling. Most such scoring functions depend on protein side chain conformations. However, backbone-only scoring functions do not require computationally intensive structure optimization and so are well suited to protein design, which requires fast score evaluation. Furthermore, scoring functions that account for the distinctive relative position and orientation preferences of residue pairs are expected to be more accurate than those that depend only on the separation distance. Results Residue pair scoring functions for fixed backbone protein design were derived using only backbone geometry. Unlike previous studies that used spherical harmonics to fit 2D angular distributions, Gaussian Mixture Models were used to fit the full 3D (position only and 6D (position and orientation distributions of residue pairs. The performance of the 1D (residue separation only, 3D, and 6D scoring functions were compared by their ability to identify correct threading solutions for a non-redundant benchmark set of protein backbone structures. The threading accuracy was found to steadily increase with increasing dimension, with the 6D scoring function achieving the highest accuracy. Furthermore, the 3D and 6D scoring functions were shown to outperform side chain-dependent empirical potentials from three other studies. Next, two computational methods that take advantage of the speed and pairwise form of these new backbone-only scoring functions were investigated. The first is a procedure that exploits available sequence data by averaging scores over threading solutions for homologs. This was evaluated by applying it to the challenging problem of identifying interacting transmembrane alpha-helices and found to further improve prediction accuracy. The second is a protein design method for determining the optimal sequence for a backbone structure by applying Belief Propagation

  17. Calculation of Structural Behavior of Indirect NMR Spin-Spin Couplings in the Backbone of Nucleic Acids

    Czech Academy of Sciences Publication Activity Database

    Sychrovský, Vladimír; Vokáčová, Zuzana; Šponer, Jiří; Špačková, Naďa; Schneider, Bohdan

    2006-01-01

    Roč. 110, č. 45 (2006), s. 22894-22902 ISSN 1520-6106 R&D Projects: GA ČR(CZ) GA203/05/0388; GA MŠk(CZ) LC512 Grant - others:NSF(US) DBI 0110076 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z50040507 Keywords : nucleic acids * RNA * DNA * molecular structure Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.115, year: 2006

  18. (nBuCp)2ZrCl2-catalyzed Ethylene-4M1P Copolymerization: Copolymer Backbone Structure, Melt Behavior, and Crystallization

    KAUST Repository

    Atiqullah, Muhammad

    2016-01-08

    The judicious design of methylaluminoxane (MAO) anions expands the scope for developing industrial metallocene catalysts. Therefore, the effects of MAO anion design on the backbone structure, melt behavior, and crystallization of ethylene−4-methyl-1-pentene (E−4M1P) copolymer were investigated. Ethylene was homopolymerized, as well as copolymerized with 4M1P, using (i) MAO anion A (unsupported [MAOCl2]−) premixed with dehydroxylated silica, (nBuCp)2ZrCl2, and Me2SiCl2; and (ii) MAO anion B (Si−O−Me2Si−[MAOCl2]−) supported with (nBuCp)2ZrCl2 on Me2SiCl2-functionalized silica. Unsupported Me2SiCl2, opposite to the supported analogue, acted as a co-chain transfer agent with 4M1P. The modeling of polyethylene melting and crystallization kinetics, including critical crystallite stability, produced insightful results. This study especially illustrates how branched polyethylene can be prepared from ethylene alone using particularly one metallocene-MAO ion pair, and how a compound, that functionalizes silica as well as terminates the chain, can synthesize ethylene−α-olefin copolymers with novel structures. Hence, it unfolds prospective future research niches in polyethyne systhesis. This article is protected by copyright. All rights reserved.

  19. Vibrational Relaxation of the Backbone and Base Modes in LacDNA Complexes by UV Resonance Raman Spectroscopy.

    Science.gov (United States)

    Muntean, Cristina M; Bratu, Ioan; Hernanz, Antonio

    2017-07-20

    Vibrational band shape analysis through time correlation function concept is widely used to obtain experimental information on the molecular dynamics of medium-size molecules in different environments. Interesting details are revealed by extending this technique to biomolecules such as functional groups of the nucleic acids in media approaching the physiological conditions. In this work a study into the UV resonance Raman (UVRR) vibrational half bandwidths of functional groups in LacDNA, upon lowering the pH (pH 6.4, pH 3.45) and in the presence of Mn 2+ and Ca 2+ ions, respectively, was of interest. The corresponding global relaxation times have been derived. Also, the 793 cm -1 UVRR band, corresponding to ν (backbone O-P-O, dT) oscillator of LacDNA in aqueous solutions, was selected for band shape-analysis. Vibrational relaxation appears as the dominant relaxation process for this mode, with vibrational dephasing being the most efficient for this oscillator. Current theories developed for vibrational dephasing have been applied to this profile, and relevant relaxation parameters have been obtained and discussed. To our knowledge this is the first study on DNA oligomers vibrational band shape analysis through time correlation function concept.

  20. Backbone dynamics and solution structure refinement of the 15N-labeled human oncogenic protein p13MTCP1: Comparison with X-ray data

    Energy Technology Data Exchange (ETDEWEB)

    Guignard, Laurent; Padilla, Andre [Universite de Montpellier I, Faculte de Pharmacie, Centre de Biochimie Structurale, CNRS-UMR 9955, INSERM-U414 (France); Mispelter, Joel [Unite INSERM U350, Institut Curie, Biologie (France); Yang, Y.-S. [Universite de Montpellier I, Faculte de Pharmacie, Centre de Biochimie Structurale, CNRS-UMR 9955, INSERM-U414 (France); Stern, Marc-Henri [Hopital Saint-Louis, Unite INSERM U462 (France); Lhoste, Jean-Marc; Roumestand, Christian [Universite de Montpellier I, Faculte de Pharmacie, Centre de Biochimie Structurale, CNRS-UMR 9955, INSERM-U414 (France)

    2000-07-15

    Two related oncogenes, TCL1 and MTCP1, are overexpressed in certain T-cell prolymphocytic leukemias as a result of chromosomal rearrangements that involve the translocation of one T-cell receptor gene to either chromosome 14q32 or Xq28, respectively. The human oncoprotein p13{sup MTCP1} is coded by the MTCP1 gene and its primary sequence is highly and only homologous to that of p14{sup TCL1}, the product of TCL1. These two proteins likely represent the first members of a new family of oncogenic proteins. A previous model of the three-dimensional solution structure of p13{sup MTCP1} was determined recently using exclusively homonuclear proton two-dimensional NMR methods and, almost simultaneously, high-resolution crystal structures of p13{sup MTCP1} and p14{sup TCL1} appeared in the literature. In order to gain more insight into the details of the solution structure, we uniformly labeled p13{sup MTCP1} with nitrogen-15. The refined structure benefits from 520 additional NOEs, extracted from either {sup 15}N-edited 3D experiments or homonuclear 2D NOESY recorded at 800 MHz, and from a nearly complete set of {phi} angular restraints. Measurements of {sup 15}N spin relaxation times and heteronuclear {sup 15}N{l_brace}{sup 1}H{r_brace}NOEs at two magnetic field strengths provided additional insights into the dynamics of the protein backbone. On the basis of these new results, a putative binding surface for this particular class of oncogenes is discussed.

  1. Backbone structures in human milk oligosaccharides: trans-glycosylation by metagenomic β-N-acetylhexosaminidases

    DEFF Research Database (Denmark)

    Nyffenegger, Christian; Nordvang, Rune Thorbjørn; Zeuner, Birgitte

    2015-01-01

    -encoding genes were identified by functional screening of a soil-derived metagenomic library. The β-N-acetylhexosaminidases were expressed in Escherichia coli with an N-terminal His6-tag and were purified by nickel affinity chromatography. The sequence similarities of the enzymes with their respective closest...... homologues are 59 % for HEX1 and 51 % for HEX2 on the protein level. Both β-N-acetylhexosaminidases are classified into glycosyl hydrolase family 20 (GH 20) are able to hydrolyze para-nitrophenyl-β-N-acetylglucosamine (pNP-GlcNAc) as well as para-nitrophenyl-β-N-acetylgalactosamine (pNP-GalNAc) and exhibit p...... milk oligosaccharide precursor lacto-N-triose II (LNT2) with yields of 2 and 8 % based on the donor substrate. In total, trans-glycosylation reactions were tested with the disaccharide acceptors β-lactose, sucrose, and maltose, as well as with the monosaccharides galactose and glucose resulting...

  2. Refined solution structure and backbone dynamics of 15N-labeled C12A-p8MTCP studied by NMR relaxation

    Energy Technology Data Exchange (ETDEWEB)

    Barthe, Philippe; Chiche, Laurent; Declerck, Nathalie; Delsuc, Marc-Andre [Universite de Montpellier I, Faculte de Pharmacie, Centre de Biochimie Structurale, CNRS-UMR 9955, INSERM-U414 (France); Lefevre, Jean-Francois [Universite Louis Pasteur, CNRS UPR-9003, ESBS (France); Malliavin, Therese [Universite de Montpellier I, Faculte de Pharmacie, Centre de Biochimie Structurale, CNRS-UMR 9955, INSERM-U414 (France); Mispelter, Joel [Centre Universitaire Bat 112, INSERM-U350, Institut Curie, Biologie (France); Stern, Marc-Henri [Hopital Saint-Louis, Unite INSERM-U462 (France); Lhoste, Jean-Marc; Roumestand, Christian [Universite de Montpellier I, Faculte de Pharmacie, Centre de Biochimie Structurale, CNRS-UMR 9955, INSERM-U414 (France)

    1999-12-15

    MTCP1 (for Mature-T-Cell Proliferation) was the first gene unequivocally identified in the group of uncommon leukemias with a mature phenotype. The three-dimensional solution structure of the human p8{sup MTCP} protein encoded by the MTCP1 oncogene has been previously determined by homonuclear proton two-dimensional NMR methods at 600 MHz: it consists of an original scaffold comprising three {alpha}-helices, associated with a new cysteine motif. Two of the helices are covalently paired by two disulfide bridges, forming an {alpha}-hairpin which resembles an antiparallel coiled-coil. The third helix is orientated roughly parallel to the plane defined by the {alpha}-antiparallel motif and appears less well defined. In order to gain more insight into the details of this new scaffold, we uniformly labeled with nitrogen-15 a mutant of this protein (C12A-p8{sup MTCP1}) in which the unbound cysteine at position 12 has been replaced by an alanine residue, thus allowing reproducibly high yields of recombinant protein. The refined structure benefits from 211 additional NOEs, extracted from {sup 15}N-edited 3D experiments, and from a nearly complete set of {phi} angular restraints allowing the estimation of the helical content of the structured part of the protein. Moreover, measurements of {sup 15} N spin relaxation times and heteronuclear {sup 15} N{sup 1}HNOEs provided additional insights into the dynamics of the protein backbone. The analysis of the linear correlation between J(0) and J({omega}) was used to interpret relaxation parameters. It appears that the apparent relative disorder seen in helix III is not simply due to a lack of experimental constraints, but associated with substantial contributions of sub-nanosecond motions in this segment.

  3. Preparation of stable micelle-like particles with rigid backbones based on pyridyl-terminated poly (aryl ether ketone)

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Shuling; Liu, Lingzhi; Zhang, Limei; Jiang, Zhenhua [Alan G. MacDiarmid Institute, College of Chemistry, Jilin University, Changchun 130012 (China); Wang, Guibin, E-mail: wgb@jlu.edu.cn [Alan G. MacDiarmid Institute, College of Chemistry, Jilin University, Changchun 130012 (China)

    2012-10-15

    A new pyridyl-containing phenol (3-(2-hydroxyphenylimine) pyridine, PY-PH) and pyridyl-terminated poly(aryl ether ketone) (PAEK-py) were first synthesized. Furthermore, micelle-like particles were successfully prepared in a selective solvent (water, H{sub 2}O) based on the graft-like complexes formed by hydrogen-bonding interactions between pyridyl groups of rigid PAEK-py and carboxyl groups of flexible poly(acrylic acid) (PAA) in their common solvent (tetrahydrofuran, THF), as proven by the measurements of scanning electron microscopy (SEM), transmission electron microscopy (TEM) and surface tension. The diameters of the resulted micelle-like particles with PAEK-py as the inner core and PAA as the outer shell were about 100-350 nm. It was found that the formation and size of micelle-like particles depended on pH value and weight ratio of PAEK-py to PAA, respectively. The structure of the micelle-like particles could be stabilized by the cross-linking reaction between pyridyl groups of PAEK-py and 1,4-dibromobutane, and the diameters of the micelle-like particles obviously decreased after the cross-linking reaction due to falling off of the PAA shell of the micelle-like particles. -- Highlights: Black-Right-Pointing-Pointer A new pyridyl-terminated poly(aryl ether ketone) (PAEK-py) were first synthesized. Black-Right-Pointing-Pointer Micelle-like particles based on rigid PAEK-py and flexible PAA were successfully prepared. Black-Right-Pointing-Pointer The structure of the micelle-like particles could be stabilized by the cross-linking reaction.

  4. Structural elements involved in proton translocation by cytochrome c oxidase as revealed by backbone amide hydrogen-deuterium exchange of the E286H mutant.

    Science.gov (United States)

    Busenlehner, Laura S; Brändén, Gisela; Namslauer, Ida; Brzezinski, Peter; Armstrong, Richard N

    2008-01-08

    Cytochrome c oxidase is the terminal electron acceptor in the respiratory chains of aerobic organisms and energetically couples the reduction of oxygen to water to proton pumping across the membrane. The mechanisms of proton uptake, gating, and pumping have yet to be completely elucidated at the molecular level for these enzymes. For Rhodobacter sphaeroides CytcO (cytochrome aa3), it appears as though the E286 side chain of subunit I is a branching point from which protons are shuttled either to the catalytic site for O2 reduction or to the acceptor site for pumped protons. Amide hydrogen-deuterium exchange mass spectrometry was used to investigate how mutation of this key branching residue to histidine (E286H) affects the structures and dynamics of four redox intermediate states. A functional characterization of this mutant reveals that E286H CytcO retains approximately 1% steady-state activity that is uncoupled from proton pumping and that proton transfer from H286 is significantly slowed. Backbone amide H-D exchange kinetics indicates that specific regions of CytcO, perturbed by the E286H mutation, are likely to be involved in proton gating and in the exit pathway for pumped protons. The results indicate that redox-dependent conformational changes around E286 are essential for internal proton transfer. E286H CytcO, however, is incapable of these specific conformational changes and therefore is insensitive to the redox state of the enzyme. These data support a model where the side chain conformation of E286 controls proton translocation in CytcO through its interactions with the proton gate, which directs the flow of protons either to the active site or to the exit pathway. In the E286H mutant, the proton gate does not function properly and the exit channel is unresponsive. These results provide new insight into the structure and mechanism of proton translocation by CytcO.

  5. Investigation of novel solid oxide fuel cell cathodes based on impregnation of SrTixFe1-xO3-δ into ceria-based backbones

    DEFF Research Database (Denmark)

    Brinch-Larsen, Mathias; Søgaard, Martin; Hjelm, Johan

    2013-01-01

    Solid oxide fuel cell (SOFC) cathodes were prepared by impregnating the nitrates corresponding to SrTixFe1-xO3-δ (STF), x= 0; 0.1; 0.2; 0.3; 0.4 and 0.5, into a porous backbone of Ce 0.9Gd0.1O2-δ (CGO). STF was chosen as very high oxygen surface exchange rate, high ionic conductivity and electroc......Solid oxide fuel cell (SOFC) cathodes were prepared by impregnating the nitrates corresponding to SrTixFe1-xO3-δ (STF), x= 0; 0.1; 0.2; 0.3; 0.4 and 0.5, into a porous backbone of Ce 0.9Gd0.1O2-δ (CGO). STF was chosen as very high oxygen surface exchange rate, high ionic conductivity...... performance is believed to originate from poor electronic conduction in the electrodes and possibly also reactions between Sr-containing compounds and CGO. To circumvent the low electronic conductivity, backbones of a composite cathode containing LaCo0.4Ni0.6O 3-δ (LCN60) and CGO were also tried infiltrated...

  6. Pairwise NMR experiments for the determination of protein backbone dihedral angle Φ based on cross-correlated spin relaxation

    International Nuclear Information System (INIS)

    Takahashi, Hideo; Shimada, Ichio

    2007-01-01

    Novel cross-correlated spin relaxation (CCR) experiments are described, which measure pairwise CCR rates for obtaining peptide dihedral angles Φ. The experiments utilize intra-HNCA type coherence transfer to refocus 2-bond J NCα coupling evolution and generate the N (i)-C α (i) or C'(i-1)-C α (i) multiple quantum coherences which are required for measuring the desired CCR rates. The contribution from other coherences is also discussed and an appropriate setting of the evolution delays is presented. These CCR experiments were applied to 15 N- and 13 C-labeled human ubiquitin. The relevant CCR rates showed a high degree of correlation with the Φ angles observed in the X-ray structure. By utilizing these CCR experiments in combination with those previously established for obtaining dihedral angle Ψ, we can determine high resolution structures of peptides that bind weakly to large target molecules

  7. Mechanical reliability of porous low-k dielectrics for advanced interconnect: Study of the instability mechanisms in porous low-k dielectrics and their mediation through inert plasma induced re-polymerization of the backbone structure

    Science.gov (United States)

    Sa, Yoonki

    siloxane backbone structure under 300˜400°C by reaction with -OH, and simultaneously creating a new Si-O-Si crosslink. As an alternative way of increasing the thermo-mechanical reliability, PLK dielectric film with an intrinsically robust structure by controlling pore morphology is fabricated. Since pore surface is susceptible to be damaged by BEOL integration damage, pore morphology in terms of size, distribution, and connectivity should be controlled in order to increase the robustness of PLK dielectrics. Generally, pores in PLK matrix are created by depositing organic fragment (called 'porogen') into the film and removed later by thermal and electron beam cure to form porous PLK layer (; Subtractive deposition). However, during the curing Si-O-Si backbone crosslink is broken and pores are easily interconnected, leading to vulnerable structure to the extrinsic damage. Constitutive deposition approach is feasible for the introduction of smaller nano-pores with little or no interconnectivity by steric hindrance. Due to the closed pore system, thermally-induced stress and plasma-induced damage is restricted merely to the surface of the dielectric film. This is attributed to the stable siloxane (Si-O-Si) backbone and the terminally bonded methyl group attached to silicon (Si-CH3), inducing steric hindrance that lowers the density of the films. The low dielectric constant and mechanical stability are closely involved with the formation of the Si-O-Si cage-like structure and an appropriate combination of stable Si-O-Si, Si-CH3 groups. Based on the FTIR and XPS spectra, it is concluded that the formation of the Si-O-Si cage-like structure was enhanced by structural method. It is believed that all these changes are beneficial for improving PLK stability as will be detailed in this dissertation. Especially, the originality and particular advantage of this study regarding plasma-induced damage repair will be highlighted.

  8. Backbone resonance assignments of the PRYSPRY domain of TRIM25.

    Science.gov (United States)

    Kong, Chen; Penumutchu, Srinivasa R; Hung, Kuo-Wei; Huang, Huiying; Lin, Tianwei; Yu, Chin

    2015-10-01

    TRIM25 is a member of the tripartite motif (TRIM) family and has been implicated in the regulation of innate immune signaling via the RIG-I (retinoic acid-inducible gene-I) pathway for antiviral defense. As the essential first step towards the structural and functional characterization of the TRIM25/RIG-I interaction, the backbone resonance of the PRYSPRY domain of TRIM25 is assigned here based on triple-resonance experiments using uniformly [(2)H, (13)C, (15)N]-labeled protein.

  9. High Performance Infiltrated Backbones for Cathode-Supported SOFC's

    DEFF Research Database (Denmark)

    Gil, Vanesa; Kammer Hansen, Kent

    2014-01-01

    The concept of using highly ionic conducting backbones with subsequent infiltration of electronically conducting particles has widely been used to develop alternative anode-supported SOFC's. In this work, the idea was to develop infiltrated backbones as an alternative design based on cathode......-supported SOFC. The cathodes are obtained by infiltrating LSM into a sintered either thick (300 μm) yttria stabilized zirconia (YSZ) backbone or a thin YSZ backbone (10-15 μm) integrated onto a thick (300 μm) porous strontium substituted lanthanum manganite (LSM) and YSZ composite. Fabrication challenges...... printed symmetrical cells. Samples with LSM/YSZ composite and YSZ backbones made with graphite+PMMA as pore formers exhibited comparable Rp values to the screen printed LSM/YSZ cathode. This route was chosen as the best to fabricate the cathode supported cells. SEM micrograph of a cathode supported cell...

  10. The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies

    Czech Academy of Sciences Publication Activity Database

    Šponer, Jiří; Mládek, Arnošt; Šponer, Judit E.; Svozil, Daniel; Zgarbová, M.; Banáš, Pavel; Jurečka, P.; Otyepka, M.

    2012-01-01

    Roč. 14, č. 44 (2012), s. 15257-15277 ISSN 1463-9076 R&D Projects: GA ČR(CZ) GD203/09/H046; GA ČR(CZ) GAP208/10/2302; GA ČR(CZ) GAP208/11/1822; GA ČR(CZ) GAP208/12/1878; GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GBP305/12/G034 Institutional research plan: CEZ:AV0Z50040702 Keywords : DNA * RNA * sugar-phosphate backbone Subject RIV: BO - Biophysics Impact factor: 3.829, year: 2012

  11. A sampling approach for protein backbone fragment conformations.

    Science.gov (United States)

    Yu, J Y; Zhang, W

    2013-01-01

    In protein structure prediction, backbone fragment bias information can narrow down the conformational space of the whole polypeptide chain significantly. Unlike existing methods that use fragments as building blocks, the paper presents a probabilistic sampling approach for protein backbone torsion angles by modelling angular correlation of (phi, psi) with a directional statistics distribution. Given a protein sequence and secondary structure information, this method samples backbone fragments conformations by using a backtrack sampling algorithm for the hidden Markov model with multiple inputs and a single output. The proposed approach is applied to a fragment library, and some well-known structural motifs are sampled very well on the optimal path. Computational results show that the method can help to obtain native-like backbone fragments conformations.

  12. Criteria for folding in structure-based models of proteins

    Energy Technology Data Exchange (ETDEWEB)

    Wołek, Karol; Cieplak, Marek, E-mail: mc@ifpan.edu.pl [Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw (Poland)

    2016-05-14

    In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very low thermodynamic stability, especially when the contact map used is too sparse. We consider six different structure-based models and show that allowing for a small, but model-dependent, percentage of the native contacts not being established boosts the folding temperature substantially while affecting the time scales of folding only in a minor way. We also compare other properties of the six models. We show that the choice of the description of the backbone stiffness has a substantial effect on the values of characteristic temperatures that relate both to equilibrium and kinetic properties. Models without any backbone stiffness (like the self-organized polymer) are found to perform similar to those with the stiffness, including in the studies of stretching.

  13. Evolution of robust network topologies: emergence of central backbones.

    Science.gov (United States)

    Peixoto, Tiago P; Bornholdt, Stefan

    2012-09-14

    We model the robustness against random failure or an intentional attack of networks with an arbitrary large-scale structure. We construct a block-based model which incorporates--in a general fashion--both connectivity and interdependence links, as well as arbitrary degree distributions and block correlations. By optimizing the percolation properties of this general class of networks, we identify a simple core-periphery structure as the topology most robust against random failure. In such networks, a distinct and small "core" of nodes with higher degree is responsible for most of the connectivity, functioning as a central "backbone" of the system. This centralized topology remains the optimal structure when other constraints are imposed, such as a given fraction of interdependence links and fixed degree distributions. This distinguishes simple centralized topologies as the most likely to emerge, when robustness against failure is the dominant evolutionary force.

  14. Live Virus Vaccines Based on a Yellow Fever Vaccine Backbone: Standardized Template with Key Considerations for a Risk/Benefit Assessment*

    Science.gov (United States)

    Monath, Thomas P.; Seligman, Stephen J.; Robertson, James S.; Guy, Bruno; Hayes, Edward B.; Condit, Richard C.; Excler, Jean Louis; Mac, Lisa Marie; Carbery, Baevin; Chen, Robert T

    2015-01-01

    The Brighton Collaboration Viral Vector Vaccines Safety Working Group (V3SWG) was formed to evaluate the safety of live, recombinant viral vaccines incorporating genes from heterologous viruses inserted into the backbone of another virus (so-called “chimeric virus vaccines”). Many viral vector vaccines are in advanced clinical trials. The first such vaccine to be approved for marketing (to date in Australia, Thailand, Malaysia, and the Philippines) is a vaccine against the flavivirus Japanese encephalitis (JE), which employs a licensed vaccine (yellow fever 17D) as a vector. In this vaccine, two envelope proteins (prM-E) of YF 17D virus were replaced by the corresponding genes of JE virus, with additional attenuating mutations incorporated into the JE gene inserts. Similar vaccines have been constructed by inserting prM-E genes of dengue and West Nile into YF 17D virus and are in late stage clinical studies. The dengue vaccine is, however, more complex in that it requires a mixture of four live vectors each expressing one of the four dengue serotypes. This vaccine has been evaluated in multiple clinical trials. No significant safety concerns have been found. The Phase 3 trials met their endpoints in terms of overall reduction of confirmed dengue fever, and, most importantly a significant reduction in severe dengue and hospitalization due to dengue. However, based on results that have been published so far, efficacy in preventing serotype 2 infection is less than that for the other three serotypes. In the development of these chimeric vaccines, an important series of comparative studies of safety and efficacy were made using the parental YF 17D vaccine virus as a benchmark. In this paper, we use a standardized template describing the key characteristics of the novel flavivirus vaccine vectors, in comparison to the parental YF 17D vaccine. The template facilitates scientific discourse among key stakeholders by increasing the transparency and comparability of

  15. Live virus vaccines based on a yellow fever vaccine backbone: standardized template with key considerations for a risk/benefit assessment.

    Science.gov (United States)

    Monath, Thomas P; Seligman, Stephen J; Robertson, James S; Guy, Bruno; Hayes, Edward B; Condit, Richard C; Excler, Jean Louis; Mac, Lisa Marie; Carbery, Baevin; Chen, Robert T

    2015-01-01

    The Brighton Collaboration Viral Vector Vaccines Safety Working Group (V3SWG) was formed to evaluate the safety of live, recombinant viral vaccines incorporating genes from heterologous viruses inserted into the backbone of another virus (so-called "chimeric virus vaccines"). Many viral vector vaccines are in advanced clinical trials. The first such vaccine to be approved for marketing (to date in Australia, Thailand, Malaysia, and the Philippines) is a vaccine against the flavivirus, Japanese encephalitis (JE), which employs a licensed vaccine (yellow fever 17D) as a vector. In this vaccine, two envelope proteins (prM-E) of YF 17D virus were exchanged for the corresponding genes of JE virus, with additional attenuating mutations incorporated into the JE gene inserts. Similar vaccines have been constructed by inserting prM-E genes of dengue and West Nile into YF 17D virus and are in late stage clinical studies. The dengue vaccine is, however, more complex in that it requires a mixture of four live vectors each expressing one of the four dengue serotypes. This vaccine has been evaluated in multiple clinical trials. No significant safety concerns have been found. The Phase 3 trials met their endpoints in terms of overall reduction of confirmed dengue fever, and, most importantly a significant reduction in severe dengue and hospitalization due to dengue. However, based on results that have been published so far, efficacy in preventing serotype 2 infection is less than that for the other three serotypes. In the development of these chimeric vaccines, an important series of comparative studies of safety and efficacy were made using the parental YF 17D vaccine virus as a benchmark. In this paper, we use a standardized template describing the key characteristics of the novel flavivirus vaccine vectors, in comparison to the parental YF 17D vaccine. The template facilitates scientific discourse among key stakeholders by increasing the transparency and comparability of

  16. Detecting the solution space of vertex cover by mutual determinations and backbones.

    Science.gov (United States)

    Wei, Wei; Zhang, Renquan; Guo, Binghui; Zheng, Zhiming

    2012-07-01

    To solve the combinatorial optimization problems, especially the minimal Vertex-cover problem with high efficiency, is a significant task in theoretical computer science and many other subjects. Aiming at detecting the solution space of Vertex-cover, a new structure named mutual-determination is defined and discovered for Vertex-cover on general graphs, which results in the emergence of strong correlations among the unfrozen nodes. Based on the backbones and mutual-determinations with node ranks by leaf removal, we propose a Mutual-determination and Backbone Evolution Algorithm to achieve the reduced solution graph, which provides a graphical expression of the solution space of Vertex-cover. By this algorithm, the whole solution space and detailed structures such as backbones can be obtained strictly when there is no leaf-removal core on the given graph. Compared with the current algorithms, the Mutual-determination and Backbone Evolution Algorithm performs as well as the replica symmetry one in a certain interval but has a small gap higher than the replica symmetric breaking one and has a relatively small error for the exact results. The algorithm with the mutual-determination provides a new viewpoint to solve Vertex-cover and understand the organizations of the solution spaces, and the reduced solution graph gives an alternative way to catch detailed information of the ground/steady states.

  17. Peptoid-Peptide hybrid backbone architectures

    DEFF Research Database (Denmark)

    Olsen, Christian Adam

    2010-01-01

    Peptidomimetic oligomers and foldamers have received considerable attention for over a decade, with beta-peptides and the so-called peptoids (N-alkylglycine oligomers) representing prominent examples of such architectures. Lately, hybrid or mixed backbones consisting of both alpha- and beta......-amino acids (alpha/beta-peptides) have been investigated in some detail as well. The present Minireview is a survey of the literature concerning hybrid structures of alpha-amino acids and peptoids, including beta-peptoids (N-alkyl-beta-alanine oligomers), and is intended to give an overview of this area...

  18. Backbone upgrades and DEC equipment replacement

    Science.gov (United States)

    Vancamp, Warren

    1991-01-01

    The NASA Science Internet (NSI) dual protocol backbone is outlined. It includes DECnet link upgrades to match TCP/IP link performance. It also includes the integration of backbone resources and central management. The phase 1 transition process is outlined.

  19. NMR study of non-structural proteins-part III:1H,13C,15N backbone and side-chain resonance assignment of macro domain from Chikungunya virus (CHIKV).

    Science.gov (United States)

    Lykouras, Michail V; Tsika, Aikaterini C; Lichière, Julie; Papageorgiou, Nicolas; Coutard, Bruno; Bentrop, Detlef; Spyroulias, Georgios A

    2018-04-01

    Macro domains are conserved protein domains found in eukaryotic organisms, bacteria, and archaea as well as in certain viruses. They consist of 130-190 amino acids and can bind ADP-ribose. Although the exact role of these domains is not fully understood, the conserved binding affinity for ADP-ribose indicates that this ligand is important for the function of the domain. Such a macro domain is also present in the non-structural protein 3 (nsP3) of Chikungunya Alphavirus (CHIKV) and consists of 160 amino acids. In this study we describe the high yield expression of the macro domain from CHIKV and its preliminary structural analysis via solution NMR spectroscopy. The macro domain seems to be folded in solution and an almost complete backbone assignment was achieved. In addition, the α/β/α sandwich topology with 4 α-helices and 6 β-strands was predicted by TALOS+.

  20. Physics-based side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials for coarse-grained UNRES force field. 2. Comparison with statistical potentials and implementation

    Science.gov (United States)

    Kozłowska, Urszula; Maisuradze, Gia G.; Liwo, Adam; Scheraga, Harold A.

    2009-01-01

    Using the harmonic-approximation approach of the accompanying paper and AM1 energy surfaces of terminally-blocked amino-acid residues, we determined physics-based side-chain-rotamer potentials and the side-chain virtual-bond-deformation potentials of 19 natural amino-acid residues with side chains. The potentials were approximated by analytical formulas and implemented in the UNRES mesoscopic dynamics program. For comparison, the corresponding statistical potentials were determined from 19,682 high-resolution protein structures. The low-free-energy region of both the AM1-derived and the statistical potentials is determined by the valence geometry and the L-chirality, and its size increases with side-chain flexibility and decreases with increasing virtual-bond-angle θ. The differences between the free energies of rotamers are greater for the AM1-derived potentials compared to the statistical potentials and, for alanine and other residues with small side chains, a region corresponding to the Cax7 conformation has remarkably low free energy for the AM1-derived potentials, as opposed to the statistical potentials. These differences probably result from the interactions between neighboring residues and indicate the need for introduction of cooperative terms accounting for the coupling between side-chain-rotamer and backbone interactions. Both AM1-derived and statistical virtual-bond-deformation potentials are multimodal for flexible side chains and are topologically similar; however, the regions of minima of the statistical potentials are much narrower, which probably results from imposing restraints in structure determination. The force field with the new potentials was preliminarily optimized using the FBP WW domain (1E0L) and the engrailed homeodomain (1ENH) as training proteins and assessed to be reasonably transferable. PMID:20017135

  1. Nonribosomal biosynthesis of backbone-modified peptides

    Science.gov (United States)

    Niquille, David L.; Hansen, Douglas A.; Mori, Takahiro; Fercher, David; Kries, Hajo; Hilvert, Donald

    2018-03-01

    Biosynthetic modification of nonribosomal peptide backbones represents a potentially powerful strategy to modulate the structure and properties of an important class of therapeutics. Using a high-throughput assay for catalytic activity, we show here that an L-Phe-specific module of an archetypal nonribosomal peptide synthetase can be reprogrammed to accept and process the backbone-modified amino acid (S)-β-Phe with near-native specificity and efficiency. A co-crystal structure with a non-hydrolysable aminoacyl-AMP analogue reveals the origins of the 40,000-fold α/β-specificity switch, illuminating subtle but precise remodelling of the active site. When the engineered catalyst was paired with downstream module(s), (S)-β-Phe-containing peptides were produced at preparative scale in vitro (~1 mmol) and high titres in vivo (~100 mg l-1), highlighting the potential of biosynthetic pathway engineering for the construction of novel nonribosomal β-frameworks.

  2. CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions.

    Science.gov (United States)

    Hallen, Mark A; Donald, Bruce R

    2017-07-15

    When proteins mutate or bind to ligands, their backbones often move significantly, especially in loop regions. Computational protein design algorithms must model these motions in order to accurately optimize protein stability and binding affinity. However, methods for backbone conformational search in design have been much more limited than for sidechain conformational search. This is especially true for combinatorial protein design algorithms, which aim to search a large sequence space efficiently and thus cannot rely on temporal simulation of each candidate sequence. We alleviate this difficulty with a new parameterization of backbone conformational space, which represents all degrees of freedom of a specified segment of protein chain that maintain valid bonding geometry (by maintaining the original bond lengths and angles and ω dihedrals). In order to search this space, we present an efficient algorithm, CATS, for computing atomic coordinates as a function of our new continuous backbone internal coordinates. CATS generalizes the iMinDEE and EPIC protein design algorithms, which model continuous flexibility in sidechain dihedrals, to model continuous, appropriately localized flexibility in the backbone dihedrals ϕ and ψ as well. We show using 81 test cases based on 29 different protein structures that CATS finds sequences and conformations that are significantly lower in energy than methods with less or no backbone flexibility do. In particular, we show that CATS can model the viability of an antibody mutation known experimentally to increase affinity, but that appears sterically infeasible when modeled with less or no backbone flexibility. Our code is available as free software at https://github.com/donaldlab/OSPREY_refactor . mhallen@ttic.edu or brd+ismb17@cs.duke.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  3. Sequestration of dyes from artificially prepared textile effluent using RSM-CCD optimized hybrid backbone based adsorbent-kinetic and equilibrium studies.

    Science.gov (United States)

    Sukriti; Sharma, Jitender; Chadha, Amritpal Singh; Pruthi, Vaishali; Anand, Prerna; Bhatia, Jaspreet; Kaith, B S

    2017-04-01

    Present work reports the synthesis of semi-Interpenetrating Network Polymer (semi-IPN) using Gelatin-Gum xanthan hybrid backbone and polyvinyl alcohol in presence of l-tartaric acid and ammonium persulphate as the crosslinker-initiator system. Reaction parameters were optimized with Response Surface Methodology (RSM) in order to maximize the percent gel fraction of the synthesized sample. Polyvinyl alcohol, l-Tartaric acid, ammonium persulphate, reaction temperature, time and pH of the reaction medium were found to make an impact on the percentage gel fraction obtained. Incorporation of polyvinyl alcohol chains onto hybrid backbone and crosslinking between the different polymer chains were confirmed through techniques like FTIR, SEM-EDX and XRD. Semi-IPN was found to be very efficient in the removal of cationic dyes rhodamine-B (70%) and auramine-O (63%) from a mixture with an adsorbent dose of 700 mg, initial concentration of rhodamine-B 6 mgL -1 and auramine-O 26 mgL -1 , at an time interval of 22-25 h and 30 °C temp. Further to determine the nature of adsorption Langmuir and Freundlich adsorption isotherm models were studied and it was found that Langmuir adsorption isotherm was the best fit model for the removal of mixture of dyes. Kinetic studies for the sorption of dyes favored the reaction mechanism to occur via a pseudo second order pathway with R 2 value about 0.99. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Receptor structure-based discovery of non-metabolite agonists for the succinate receptor GPR91

    DEFF Research Database (Denmark)

    Trauelsen, Mette; Rexen Ulven, Elisabeth; Hjorth, Siv A

    2017-01-01

    backbone is preferred and that certain backbone modifications are allowed for GPR91 activation. Through receptor modeling over the X-ray structure of the closely related P2Y1 receptor, we discovered that the binding pocket is partly occupied by a segment of an extracellular loop and that succinate...... therefore binds in a very different mode than generally believed. Importantly, an empty side-pocket is identified next to the succinate binding site. All this information formed the basis for a substructure-based search query, which, combined with molecular docking, was used in virtual screening of the ZINC...

  5. Photochemical selectivity in guanine–cytosine base-pair structures

    Science.gov (United States)

    Abo-Riziq, Ali; Grace, Louis; Nir, Eyal; Kabelac, Martin; Hobza, Pavel; de Vries, Mattanjah S.

    2005-01-01

    Prebiotic chemistry presumably took place before formation of an oxygen-rich atmosphere and thus under conditions of intense short wavelength UV irradiation. Therefore, the UV photochemical stability of the molecular building blocks of life may have been an important selective factor in determining the eventual chemical makeup of critical biomolecules. To investigate the role of UV irradiation in base-pairing we have studied guanine (G) and cytosine (C) base pairs in the absence of the RNA backbone. We distinguished base-pair structures by IR–UV hole-burning spectroscopy as well as by high-level correlated ab initio calculations. The Watson–Crick structure exhibits broad UV absorption, in stark contrast to other GC structures and other base-pair structures. This broad absorption may be explained by a rapid internal conversion that makes this specific base pair arrangement uniquely photochemically stable. PMID:15618394

  6. New insights about pilus formation in gut-adapted Lactobacillus rhamnosus GG from the crystal structure of the SpaA backbone-pilin subunit

    Science.gov (United States)

    Chaurasia, Priyanka; Pratap, Shivendra; von Ossowski, Ingemar; Palva, Airi; Krishnan, Vengadesan

    2016-01-01

    Thus far, all solved structures of pilin-proteins comprising sortase-assembled pili are from pathogenic genera and species. Here, we present the first crystal structure of a pilin subunit (SpaA) from a non-pathogen host (Lactobacillus rhamnosus GG). SpaA consists of two tandem CnaB-type domains, each with an isopeptide bond and E-box motif. Intriguingly, while the isopeptide bond in the N-terminal domain forms between lysine and asparagine, the one in the C-terminal domain atypically involves aspartate. We also solved crystal structures of mutant proteins where residues implicated in forming isopeptide bonds were replaced. Expectedly, the E-box-substituted E139A mutant lacks an isopeptide bond in the N-terminal domain. However, the C-terminal E269A substitution gave two structures; one of both domains with their isopeptide bonds present, and another of only the N-terminal domain, but with an unformed isopeptide bond and significant conformational changes. This latter crystal structure has never been observed for any other Gram-positive pilin. Notably, the C-terminal isopeptide bond still forms in D295N-substituted SpaA, irrespective of E269 being present or absent. Although E-box mutations affect SpaA proteolytic and thermal stability, a cumulative effect perturbing normal pilus polymerization was unobserved. A model showing the polymerized arrangement of SpaA within the SpaCBA pilus is proposed. PMID:27349405

  7. Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design.

    Directory of Open Access Journals (Sweden)

    Kevin Drew

    Full Text Available Peptidomimetics are classes of molecules that mimic structural and functional attributes of polypeptides. Peptidomimetic oligomers can frequently be synthesized using efficient solid phase synthesis procedures similar to peptide synthesis. Conformationally ordered peptidomimetic oligomers are finding broad applications for molecular recognition and for inhibiting protein-protein interactions. One critical limitation is the limited set of design tools for identifying oligomer sequences that can adopt desired conformations. Here, we present expansions to the ROSETTA platform that enable structure prediction and design of five non-peptidic oligomer scaffolds (noncanonical backbones, oligooxopiperazines, oligo-peptoids, [Formula: see text]-peptides, hydrogen bond surrogate helices and oligosaccharides. This work is complementary to prior additions to model noncanonical protein side chains in ROSETTA. The main purpose of our manuscript is to give a detailed description to current and future developers of how each of these noncanonical backbones was implemented. Furthermore, we provide a general outline for implementation of new backbone types not discussed here. To illustrate the utility of this approach, we describe the first tests of the ROSETTA molecular mechanics energy function in the context of oligooxopiperazines, using quantum mechanical calculations as comparison points, scanning through backbone and side chain torsion angles for a model peptidomimetic. Finally, as an example of a novel design application, we describe the automated design of an oligooxopiperazine that inhibits the p53-MDM2 protein-protein interaction. For the general biological and bioengineering community, several noncanonical backbones have been incorporated into web applications that allow users to freely and rapidly test the presented protocols (http://rosie.rosettacommons.org. This work helps address the peptidomimetic community's need for an automated and expandable

  8. A novel dengue virus serotype 1 vaccine candidate based on Japanese encephalitis virus vaccine strain SA14-14-2 as the backbone.

    Science.gov (United States)

    Yang, Huiqiang; Li, Zhushi; Lin, Hua; Wang, Wei; Yang, Jian; Liu, Lina; Zeng, Xianwu; Wu, Yonglin; Yu, Yongxin; Li, Yuhua

    2016-06-01

    To develop a potential dengue vaccine candidate, a full-length cDNA clone of a novel chimeric virus was constructed using recombinant DNA technology, with Japanese encephalitis virus (JEV) vaccine strain SA14-14-2 as the backbone, with its premembrane (prM) and envelope (E) genes substituted by their counterparts from dengue virus type 1 (DENV1). The chimeric virus (JEV/DENV1) was successfully recovered from primary hamster kidney (PHK) cells by transfection with the in vitro transcription products of JEV/DENV1 cDNA and was identified by complete genome sequencing and immunofluorescent staining. No neuroinvasiveness of this chimeric virus was observed in mice inoculated by the subcutaneous route (s.c.) or by the intraperitoneal route (i.p.), while some neurovirulence was displayed in mice that were inoculated directly by the intracerebral route (i.c.). The chimeric virus was able to stimulate high-titer production of antibodies against DENV1 and provided protection against lethal challenge with neuroadapted dengue virus in mice. These results suggest that the chimeric virus is a promising dengue vaccine candidate.

  9. 3D-TROSY-based backbone and ILV-methyl resonance assignments of a 319-residue homodimer from a single protein sample

    Energy Technology Data Exchange (ETDEWEB)

    Krejcirikova, Anna; Tugarinov, Vitali, E-mail: vitali@umd.edu [University of Maryland, Department of Chemistry and Biochemistry (United States)

    2012-10-15

    The feasibility of practically complete backbone and ILV methyl chemical shift assignments from a single [U-{sup 2}H,{sup 15}N,{sup 13}C; Ile{delta}1-{l_brace}{sup 13}CH{sub 3}{r_brace}; Leu,Val-{l_brace}{sup 13}CH{sub 3}/{sup 12}CD{sub 3}{r_brace}]-labeled protein sample of the truncated form of ligand-free Bst-Tyrosyl tRNA Synthetase (Bst-{Delta}YRS), a 319-residue predominantly helical homodimer, is established. Protonation of ILV residues at methyl positions does not appreciably detract from the quality of TROSY triple resonance data. The assignments are performed at 40 Degree-Sign C to improve the sensitivity of the measurements and alleviate the overlap of {sup 1}H-{sup 15}N correlations in the abundant {alpha}-helical segments of the protein. A number of auxiliary approaches are used to assist in the assignment process: (1) selection of {sup 1}H-{sup 15}N amide correlations of certain residue types (Ala, Thr/Ser) that simplifies 2D {sup 1}H-{sup 15}N TROSY spectra, (2) straightforward identification of ILV residue types from the methyl-detected 'out-and-back' HMCM(CG)CBCA experiment, and (3) strong sequential HN-HN NOE connectivities in the helical regions. The two subunits of Bst-YRS were predicted earlier to exist in two different conformations in the absence of ligands. In agreement with our earlier findings (Godoy-Ruiz in J Am Chem Soc 133:19578-195781, 2011), no evidence of dimer asymmetry has been observed in either amide- or methyl-detected experiments.

  10. A hierarchical virtual backbone construction protocol for mobile ad hoc networks

    Directory of Open Access Journals (Sweden)

    Bharti Sharma

    2016-07-01

    Full Text Available We propose a hierarchical backbone construction protocol for mobile ad hoc networks. Our protocol is based on the idea of using an efficient extrema finding method to create clusters comprising the nodes that are within certain prespecified wireless hop distance. Afterward, we apply our ‘diameter’ algorithm among clusters to identify the dominating nodes that are, finally, connected via multi-hop virtual links to construct the backbone. We present the analytic as well as simulation study of our algorithm and also a method for the dynamic maintenance of constructed backbone. In the end, we illustrate the use of the virtual backbone with the help of an interesting application.

  11. Mapping the backbone of science.

    Energy Technology Data Exchange (ETDEWEB)

    Klavans, Richard (Indiana University, Bloomington, IN); BÞorner, Katy (Strategies for Science & Technology, Incorporation, Berwyn, PA); Boyack, Kevin W.

    2004-11-01

    This paper presents a new map representing the structure of all of science, based on journal articles, including both the natural and social sciences. Similar to cartographic maps of our world, the map of science provides a bird's eye view of today's scientific landscape. It can be used to visually identify major areas of science, their size, similarity, and interconnectedness. In order to be useful, the map needs to be accurate on a local and on a global scale. While our recent work has focused on the former aspect, this paper summarizes results on how to achieve structural accuracy. Eight alternative measures of journal similarity were applied to a data set of 7,121 journals covering over 1 million documents in the combined Science Citation and Social Science Citation Indexes. For each journal similarity measure we generated two-dimensional spatial layouts using the force-directed graph layout tool, VxOrd. Next, mutual information values were calculated for each graph at different clustering levels to give a measure of structural accuracy for each map. The best co-citation and inter-citation maps according to local and structural accuracy were selected and are presented and characterized. These two maps are compared to establish robustness. The inter-citation map is then used to examine linkages between disciplines. Biochemistry appears as the most interdisciplinary discipline in science.

  12. Solution Structure and Backbone Dynamics of the Pleckstrin Homology Domain of the Human Protein Kinase B (PKB/Akt). Interaction with Inositol Phosphates

    International Nuclear Information System (INIS)

    Auguin, Daniel; Barthe, Philippe; Auge-Senegas, Marie-Therese; Stern, Marc-Henri; Noguchi, Masayuki; Roumestand, Christian

    2004-01-01

    The programmed cell death occurs as part of normal mammalian development. The induction of developmental cell death is a highly regulated process and can be suppressed by a variety of extracellular stimuli. Recently, the ability of trophic factors to promote survival have been attributed, at least in part, to the phosphatidylinositide 3'-OH kinase (PI3K)/Protein Kinase B (PKB, also named Akt) cascade. Several targets of the PI3K/PKB signaling pathway have been identified that may underlie the ability of this regulatory cascade to promote cell survival. PKB possesses a N-terminal Pleckstrin Homology (PH) domain that binds specifically and with high affinity to PtIns(3,4,5)P 3 and PtIns(3,4)P 2 , the PI3K second messengers. PKB is then recruited to the plasma membrane by virtue of its interaction with 3'-OH phosphatidylinositides and activated. Recent evidence indicates that PKB is active in various types of human cancer; constitutive PKB signaling activation is believed to promote proliferation and increased cell survival, thereby contributing to cancer progression. Thus, it has been shown that induction of PKB activity is augmented by the TCL1/MTCP1 oncoproteins through a physical association requiring the PKB PH domain. Here we present the three-dimensional solution structure of the PH domain of the human protein PKB (isoform β). PKBβ-PH is an electrostatically polarized molecule that adopts the same fold and topology as other PH-domains, consisting of a β-sandwich of seven strands capped on one top by an α-helix. The opposite face presents three variable loops that appear poorly defined in the NMR structure. Measurements of 15 N spin relaxation times and heteronuclear 15 N{ 1 H}NOEs showed that this poor definition is due to intrinsic flexibility, involving complex motions on different time scales. Chemical shift mapping studies correctly defined the binding site of Ins(1,3,4,5)P 4 (the head group of PtIns(3,4,5)P 3 ), as was previously proposed from a

  13. Structure-based druggability assessment of the mammalian structural proteome with inclusion of light protein flexibility.

    Directory of Open Access Journals (Sweden)

    Kathryn A Loving

    2014-07-01

    Full Text Available Advances reported over the last few years and the increasing availability of protein crystal structure data have greatly improved structure-based druggability approaches. However, in practice, nearly all druggability estimation methods are applied to protein crystal structures as rigid proteins, with protein flexibility often not directly addressed. The inclusion of protein flexibility is important in correctly identifying the druggability of pockets that would be missed by methods based solely on the rigid crystal structure. These include cryptic pockets and flexible pockets often found at protein-protein interaction interfaces. Here, we apply an approach that uses protein modeling in concert with druggability estimation to account for light protein backbone movement and protein side-chain flexibility in protein binding sites. We assess the advantages and limitations of this approach on widely-used protein druggability sets. Applying the approach to all mammalian protein crystal structures in the PDB results in identification of 69 proteins with potential druggable cryptic pockets.

  14. Contribution of peptide backbone to Anti-citrulline-dependent antibody reactivity

    DEFF Research Database (Denmark)

    Trier, Nicole Hartwig; Dam, Catharina; Olsen, Dorthe

    2015-01-01

    . As ACPAs have been suggested to be involved in the development of RA, knowledge about these antibodies may be crucial. In this study, we examined the influence of peptide backbone for ACPA reactivity in immunoassays. The antibodies were found to be reactive with a central Cit-Gly motif being essential...... is essential for antibody reactivity. Based on these findings it was speculated that any amino acid sequence, which brings the peptide into a properly folded structure for antibody recognition is sufficient for antibody reactivity. These findings are in accordance with the current hypothesis that structural...

  15. Green Network Planning Model for Optical Backbones

    DEFF Research Database (Denmark)

    Gutierrez Lopez, Jose Manuel; Riaz, M. Tahir; Jensen, Michael

    2010-01-01

    Communication networks are becoming more essential for our daily lives and critically important for industry and governments. The intense growth in the backbone traffic implies an increment of the power demands of the transmission systems. This power usage might have a significant negative effect...... on the environment in general. In network planning there are existing planning models focused on QoS provisioning, investment minimization or combinations of both and other parameters. But there is a lack of a model for designing green optical backbones. This paper presents novel ideas to be able to define...... an analytical model to consider environmental aspects in the planning stage of backbones design....

  16. The dominant folding route minimizes backbone distortion in SH3.

    Directory of Open Access Journals (Sweden)

    Heiko Lammert

    Full Text Available Energetic frustration in protein folding is minimized by evolution to create a smooth and robust energy landscape. As a result the geometry of the native structure provides key constraints that shape protein folding mechanisms. Chain connectivity in particular has been identified as an essential component for realistic behavior of protein folding models. We study the quantitative balance of energetic and geometrical influences on the folding of SH3 in a structure-based model with minimal energetic frustration. A decomposition of the two-dimensional free energy landscape for the folding reaction into relevant energy and entropy contributions reveals that the entropy of the chain is not responsible for the folding mechanism. Instead the preferred folding route through the transition state arises from a cooperative energetic effect. Off-pathway structures are penalized by excess distortion in local backbone configurations and contact pair distances. This energy cost is a new ingredient in the malleable balance of interactions that controls the choice of routes during protein folding.

  17. Triazole linkages and backbone branches in nucleic acids for biological and extra-biological applications

    Science.gov (United States)

    Paredes, Eduardo

    The recently increasing evidence of nucleic acids' alternative roles in biology and potential as useful nanomaterials and therapeutic agents has enabled the development of useful probes, elaborate nanostructures and therapeutic effectors based on nucleic acids. The study of alternative nucleic acid structure and function, particularly RNA, hinges on the ability to introduce site-specific modifications that either provide clues to the nucleic acid structure function relationship or alter the nucleic acid's function. Although the available chemistries allow for the conjugation of useful labels and molecules, their limitations lie in their tedious conjugation conditions or the lability of the installed probes. The development and optimization of click chemistry with RNA now provides the access to a robust and orthogonal conjugation methodology while providing stable conjugates. Our ability to introduce click reactive groups enzymatically, rather than only in the solid-phase, allows for the modification of larger, more cell relevant RNAs. Additionally, ligation of modified RNAs with larger RNA constructs through click chemistry represents an improvement over traditional ligation techniques. We determined that the triazole linkage generated through click chemistry is compatible in diverse nucleic acid based biological systems. Click chemistry has also been developed for extra-biological applications, particularly with DNA. We have expanded its use to generate useful polymer-DNA conjugates which can form controllable soft nanoparticles which take advantage of DNA's properties, i.e. DNA hybridization and computing. Additionally, we have generated protein-DNA conjugates and assembled protein-polymer hybrids mediated by DNA hybridization. The use of click chemistry in these reactions allows for the facile synthesis of these unnatural conjugates. We have also developed backbone branched DNA through click chemistry and showed that these branched DNAs are useful in generating

  18. Design bases - Concrete structures

    International Nuclear Information System (INIS)

    Diaz-Llanos Ros, M.

    1993-01-01

    The most suitable title for Section 2 is 'Design Bases', which covers not only calculation but also the following areas: - Structural design concepts. - Project criteria. - Material specifications. These concepts are developed in more detail in the following sections. The numbering in this document is neither complete nor hierarchical since, for easier cross referencing, it corresponds to the paragraphs of Eurocode 2 Part 1 (hereinafter 'EUR-2') which are commented on. (author)

  19. Backbone dynamics of the EIAV-Tat protein from 15N relaxation studies

    International Nuclear Information System (INIS)

    Ejchart, A.; Herrmann, F.; Roesch, P.; Sticht, H.; Willbold, D.

    1994-01-01

    The work investigates the mobility of EIAV-Tat protein backbone by measuring the relaxation parameters of the 15 N nitrogens. High degree of the flexibility, non-typical of rigid, well structured proteins was shown

  20. High Speed Fibre Optic Backbone LAN

    Science.gov (United States)

    Tanimoto, Masaaki; Hara, Shingo; Kajita, Yuji; Kashu, Fumitoshi; Ikeuchi, Masaru; Hagihara, Satoshi; Tsuzuki, Shinji

    1987-09-01

    Our firm has developed the SUMINET-4100 series, a fibre optic local area network (LAN), to serve the communications system trunk line needs for facilities, such as steel refineries, automobile plants and university campuses, that require large transmission capacity, and for the backbone networks used in intelligent building systems. The SUMINET-4100 series is already in service in various fields of application. Of the networks available in this series, the SUMINET-4150 has a trunk line speed of 128 Mbps and the multiplexer used for time division multiplexing (TDM) was enabled by designing an ECL-TTL gate array (3000 gates) based custom LSI. The synchronous, full-duplex V.24 and V.3.5 interfaces (SUMINET-2100) are provided for use with general purpose lines. And the IBM token ring network, the SUMINET-3200, designed for heterogeneous PCs and the Ethernet can all be connected to sub loops. Further, the IBM 3270 TCA and 5080 CADAM can be connected in the local mode. Interfaces are also provided for the NTT high-speed digital service, the digital PBX systems, and the Video CODEC system. The built-in loop monitor (LM) and network supervisory processor (NSP) provide management of loop utilization and send loop status signals to the host CPU's network configuration and control facility (NCCF). These built-in functions allow both the computer system and LAN to be managed from a single source at the host. This paper outlines features of the SUMINET-4150 and provides an example of its installation.

  1. Controlled Conjugated Backbone Twisting for an Increased Open-Circuit Voltage while Having a High Short-Circuit Current in Poly(hexylthiophene) Derivatives

    KAUST Repository

    Ko, Sangwon

    2012-03-21

    Conjugated polymers with nearly planar backbones have been the most commonly investigated materials for organic-based electronic devices. More twisted polymer backbones have been shown to achieve larger open-circuit voltages in solar cells, though with decreased short-circuit current densities. We systematically impose twists within a family of poly(hexylthiophene)s and examine their influence on the performance of polymer:fullerene bulk heterojunction (BHJ) solar cells. A simple chemical modification concerning the number and placement of alkyl side chains along the conjugated backbone is used to control the degree of backbone twisting. Density functional theory calculations were carried out on a series of oligothiophene structures to provide insights on how the sterically induced twisting influences the geometric, electronic, and optical properties. Grazing incidence X-ray scattering measurements were performed to investigate how the thin-film packing structure was affected. The open-circuit voltage and charge-transfer state energy of the polymer:fullerene BHJ solar cells increased substantially with the degree of twist induced within the conjugated backbone-due to an increase in the polymer ionization potential-while the short-circuit current decreased as a result of a larger optical gap and lower hole mobility. A controlled, moderate degree of twist along the poly(3,4-dihexyl-2,2′:5′,2′′- terthiophene) (PDHTT) conjugated backbone led to a 19% enhancement in the open-circuit voltage (0.735 V) vs poly(3-hexylthiophene)-based devices, while similar short-circuit current densities, fill factors, and hole-carrier mobilities were maintained. These factors resulted in a power conversion efficiency of 4.2% for a PDHTT:[6,6]-phenyl-C 71-butyric acid methyl ester (PC 71BM) blend solar cell without thermal annealing. This simple approach reveals a molecular design avenue to increase open-circuit voltage while retaining the short-circuit current. © 2012 American

  2. Bulk Heterojunction Solar Cells: Impact of Minor Structural Modifications to the Polymer Backbone on the Polymer-Fullerene Mixing and Packing and on the Fullerene-Fullerene Connecting Network

    KAUST Repository

    Wang, Tonghui

    2018-01-25

    The morphology of the active layer of a bulk heterojunction solar cell, made of a blend of an electron-donating polymer and an electron-accepting fullerene derivative, is known to play a determining role in device performance. Here, a combination of molecular dynamics simulations and long-range corrected density functional theory calculations is used to elucidate the molecular-scale effects that even minor structural changes to the polymer backbone can have on the “local” morphology; this study focuses on the extent of polymer–fullerene mixing, on their packing, and on the characteristics of the fullerene–fullerene connecting network in the mixed regions, aspects that are difficult to access experimentally. Three representative polymer donors are investigated: (i) poly[(5,6-difluoro-2,1,3-benzothiadiazol-4,7-diyl)-alt-(3,3′″-di(2-octyldodecyl)-2,2′;5′,2″;5″,2′″-quaterthiophen-5,5′″-diyl)] (PffBT4T-2OD); (ii) poly[(2,1,3-benzothiadiazol-4,7-diyl)-alt-(3,3′″-di(2-octyldodecyl)-2,2′;5′,2″;5″,2′″-quaterthiophen-5,5′″-diyl)] (PBT4T-2OD), where the fluorine atoms in the benzothiadiazole moieties of PffBT4T-2OD are replaced with hydrogen atoms; and (iii) poly[(2,2′-bithiophene)-alt-(4,7-bis((2-decyltetradecyl)thiophen-2-yl)-5,6-difluoro-2-propyl-2H-benzo[d][1,2,3]triazole)] (PT2-FTAZ), where the sulfur atoms in the benzothiadiazole moieties of PffBT4T-2OD are replaced with nitrogen atoms carrying a linear C3H7 side-chain; these polymers are mixed with the phenyl-C71-butyric acid methyl ester (PC71BM) acceptor. This study also discusses the nature of the charge-transfer electronic states appearing at the donor–acceptor interfaces, the electronic couplings relevant for the charge-recombination process, and the electron-transfer features between neighboring PC71BM molecules.

  3. Mechanistic Insight into Reversible Core Structural Changes of Dinuclear μ-Hydroxoruthenium(II) Complexes with a 2,8-Di-2-pyridyl-1,9,10-anthyridine Backbone Prior to Water Oxidation Catalysis.

    Science.gov (United States)

    Hirahara, Masanari; Nagai, Sho; Takahashi, Kosuke; Watabe, Shunsuke; Sato, Taisei; Saito, Kenji; Yui, Tatsuto; Umemura, Yasushi; Yagi, Masayuki

    2017-09-05

    proximal,proximal-(p,p)-[Ru II 2 (tpy) 2 LXY] n+ (tpy = 2,2';6',2″-terpyridine, L = 5-phenyl-2,8-di-2-pyridyl-1,9,10-anthyridine, and X and Y = other coordination sites) yields the structurally and functionally unusual Ru II (μ-OH)Ru II core, which is capable of catalyzing water oxidation with key water insertion to the core (Inorg. Chem. 2015, 54, 7627). Herein, we studied a sequence of bridging-ligand substitution among p,p-[Ru 2 (tpy) 2 L(μ-Cl)] 3+ (Ru 2 (μ-Cl)), p,p-[Ru 2 (tpy) 2 L(μ-OH)] 3+ (Ru 2 (μ-OH)), p,p-[Ru 2 (tpy) 2 L(OH)(OH 2 )] 3+ (Ru 2 (OH)(OH 2 )), and p,p-[Ru 2 (tpy) 2 L(OH) 2 ] 2+ (Ru 2 (OH) 2 ) in aqueous solution. Ru 2 (μ-Cl) converted slowly (10 -4 s -1 ) to Ru 2 (μ-OH), and further Ru 2 (μ-OH) converted very slowly (10 -6 s -1 ) to Ru 2 (OH)(OH 2 ) by the insertion of water to reach equilibrium at pH 8.5-12.3. On the basis of density functional theory (DFT) calculations, Ru 2 (OH)(OH 2 ) was predicted to be thermodynamically stable by 13.3 kJ mol -1 in water compared to Ru 2 (μ-OH) because of the specially stabilized core structure by multiple hydrogen-bonding interactions involving aquo, hydroxo, and L backbone ligands. The observed rate from Ru 2 (μ-OH) to Ru 2 (OH) 2 by the insertion of an OH - ion increased linearly with an increase in the OH - concentration from 10 to 100 mM. The water insertion to the core is very slow (∼10 -6 s -1 ) in aqueous solution at pH 8.5-12.3, whereas the insertion of OH - ions is accelerated (10 -5 -10 -4 s -1 ) above pH 13.4 by 2 orders of magnitude. The kinetic data including activation parameters suggest that the associative mechanism for the insertion of water to the Ru II (μ-OH)Ru II core of Ru 2 (μ-OH) at pH 8.5-12.3 alters the interchange mechanism for the insertion of an OH - ion to the core above pH 13.4 because of relatively stronger nucleophilic attack of OH - ions. The hypothesized p,p-[Ru 2 (tpy) 2 L(μ-OH 2 )] 4+ and p,p-[Ru 2 (tpy) 2 L(OH 2 ) 2 ] 4+ formed by protonation from Ru 2

  4. Polystyrene Backbone Polymers Consisting of Alkyl-Substituted Triazine Side Groups for Phosphorescent OLEDs

    Directory of Open Access Journals (Sweden)

    Beatrice Ch. D. Salert

    2012-01-01

    Full Text Available This paper describes the synthesis of new electron-transporting styrene monomers and their corresponding polystyrenes all with a 2,4,6-triphenyl-1,3,5-triazine basic structure in the side group. The monomers differ in the alkyl substitution and in the meta-/paralinkage of the triazine to the polymer backbone. The thermal and spectroscopic properties of the new electron-transporting polymers are discussed in regard to their chemical structures. Phosphorescent OLEDs were prepared using the obtained electron-transporting polymers as the emissive layer material in blend systems together with a green iridium-based emitter 13 and a small molecule as an additional cohost with wideband gap characteristics (CoH-001. The performance of the OLEDs was characterized and discussed in regard to the chemical structure of the new electron-transporting polymers.

  5. Green IGP Link Weights for Energy-efficiency and Load-balancing in IP Backbone Networks

    OpenAIRE

    Francois, Frederic; Wang, Ning; Moessner, Klaus; Georgoulas, Stylianos; Xu, Ke

    2013-01-01

    The energy consumption of backbone networks has become a primary concern for network operators and regulators due to the pervasive deployment of wired backbone networks to meet the requirements of bandwidth-hungry applications. While traditional optimization of IGP link weights has been used in IP based load-balancing operations, in this paper we introduce a novel link weight setting algorithm, the Green Load-balancing Algorithm (GLA), which is able to jointly optimize both energy efficiency ...

  6. Recombinant expression of backbone-cyclized polypeptides.

    Science.gov (United States)

    Borra, Radhika; Camarero, Julio A

    2013-09-01

    Here we review the different biochemical approaches available for the expression of backbone-cyclized polypeptides, including peptides and proteins. These methods allow for the production of circular polypeptides either in vitro or in vivo using standard recombinant DNA expression techniques. Polypeptide circularization provides a valuable tool to study the effects of topology on protein stability and folding kinetics. Furthermore, having biosynthetic access to backbone-cyclized polypeptides makes the production of genetically encoded libraries of cyclic polypeptides possible. The production of such libraries, which was previously restricted to the domain of synthetic chemistry, now offers biologists access to highly diverse and stable molecular libraries that can be screened using high-throughput methods for the rapid selection of novel cyclic polypeptide sequences with new biological activities. Copyright © 2013 Wiley Periodicals, Inc.

  7. Protein structure refinement using a quantum mechanics-based chemical shielding predictor

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen; Jensen, Jan Halborg

    2017-01-01

    The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor...... of a protein backbone and CB chemical shifts (ProCS15, PeerJ, 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic...... geometry optimized X-ray structures as starting points: simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers...

  8. Reliability based structural design

    NARCIS (Netherlands)

    Vrouwenvelder, A.C.W.M.

    2013-01-01

    According to ISO 2394, structures shall be designed, constructed and maintained in such a way that they are suited for their use during the design working life in an economic way. To fulfil this requirement one needs insight into the risk and reliability under expected and non-expected actions. A

  9. Internet Backbone in the Democratic Republic of Congo : Feasibility ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    The participants noted the following priorities for the DRC: a national Internet backbone, urban networks and computing equipment. The national Internet backbone was given highest priority. This project aims to study the feasibility of establishing an Internet backbone en RDC. Researchers will identify suitable technological ...

  10. Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank.

    Science.gov (United States)

    Zhang, Qian; Xu, Zhijian; Shi, Jiye; Zhu, Weiliang

    2017-07-24

    Halogen bonds (XBs) are attracting increasing attention in biological systems. Protein Data Bank (PDB) archives experimentally determined XBs in biological macromolecules. However, no software for structure refinement in X-ray crystallography takes into account XBs, which might result in the weakening or even vanishing of experimentally determined XBs in PDB. In our previous study, we showed that side-chain XBs forming with protein side chains are underestimated in PDB on the basis of the phenomenon that the proportion of side-chain XBs to overall XBs decreases as structural resolution becomes lower and lower. However, whether the dominant backbone XBs forming with protein backbone are overlooked is still a mystery. Here, with the help of the ratio (R F ) of the observed XBs' frequency of occurrence to their frequency expected at random, we demonstrated that backbone XBs are largely overlooked in PDB, too. Furthermore, three cases were discovered possessing backbone XBs in high resolution structures while losing the XBs in low resolution structures. In the last two cases, even at 1.80 Å resolution, the backbone XBs were lost, manifesting the urgent need to consider XBs in the refinement process during X-ray crystallography study.

  11. Control of polymer-packing orientation in thin films through synthetic tailoring of backbone coplanarity

    KAUST Repository

    Chen, Mark S.

    2013-10-22

    Controlling solid-state order of π-conjugated polymers through macromolecular design is essential for achieving high electronic device performance; yet, it remains a challenge, especially with respect to polymer-packing orientation. Our work investigates the influence of backbone coplanarity on a polymer\\'s preference to pack face-on or edge-on relative to the substrate. Isoindigo-based polymers were synthesized with increasing planarity by systematically substituting thiophenes for phenyl rings in the acceptor comonomer. This increasing backbone coplanarity, supported by density functional theory (DFT) calculations of representative trimers, leads to the narrowing of polymer band gaps as characterized by ultraviolet-visible-near infrared (UV-vis-NIR) spectroscopy and cyclic voltammetry. Among the polymers studied, regiosymmetric II and TII polymers exhibited the highest hole mobilities in organic field-effect transistors (OFETs), while in organic photovoltaics (OPVs), TBII polymers that display intermediate levels of planarity provided the highest power conversion efficiencies. Upon thin-film analysis by atomic force microscropy (AFM) and grazing-incidence X-ray diffraction (GIXD), we discovered that polymer-packing orientation could be controlled by tuning polymer planarity and solubility. Highly soluble, planar polymers favor face-on orientation in thin films while the less soluble, nonplanar polymers favor an edge-on orientation. This study advances our fundamental understanding of how polymer structure influences nanostructural order and reveals a new synthetic strategy for the design of semiconducting materials with rationally engineered solid-state properties. © 2013 American Chemical Society.

  12. Antibacterial Studies of Cationic Polymers with Alternating, Random and Uniform Backbones

    Science.gov (United States)

    Song, Airong; Walker, Stephen G.; Parker, Kathlyn A.; Sampson, Nicole S.

    2011-01-01

    Antibacterial polymers have potential as pharmaceuticals and as coatings for implantation devices. The design of these materials will be optimized when we have a complete understanding of the structural features that impart activity toward target organisms and those that are benign with respect to the mammalian host. In this work, four series of polymers in which cationic and hydrophobic groups were distributed along the backbone were tested against six different bacterial species (both Gram positive and Gram negative) and for host cytotoxicities (red blood cell lysis). The most effective of the polymers studied are regularly spaced, featuring a 6–8 carbon stretch along the backbone between side chains that present positively charged groups. They cause potassium efflux, disorder the bacterial cytoplasmic membrane, and disrupt the membrane potential. These polymers, available from alternating ring opening metathesis polymerization (AROMP), offer proof of principle for the importance of regular spacing in antibacterial polymers and for the synthesis of additional functional materials based on regularly spaced scaffolds. PMID:21370918

  13. Porous solid backbone impregnation for electrochemical energy conversion systems

    KAUST Repository

    Boulfrad, Samir

    2013-09-19

    An apparatus and method for impregnating a porous solid backbone. The apparatus may include a platform for holding a porous solid backbone, an ink jet nozzle configured to dispense a liquid solution onto the porous solid backbone, a positioning mechanism configured to position the ink jet nozzle proximate to a plurality of locations of the porous solid backbone, and a control unit configured to control the positioning mechanism to position the ink jet nozzle proximate to the plurality of locations and cause the ink jet nozzle to dispense the liquid solution onto the porous solid backbone.

  14. Flexibility of backbone fibrils in α-chitin crystals with different degree of acetylation.

    Science.gov (United States)

    Yu, Zechuan; Lau, Denvid

    2017-10-15

    Acetyl groups are backbone outreaches that enhance inter-fibril connection in chitin and chitosan fibril bundle. Removal of acetyl groups affects flexibility of chitosan fibril bundle, thereby affecting mechanical strength of chitosan-based products. Understandings of relationship between degree of acetylation and flexibility of chitin fibril bundle conduce to optimization of synthetic chitin materials. Here, the relationship is examined by performing molecular dynamics simulations. Coiling of chitin and chitosan fibril bundle with different degree of acetylation is observed and flexibility of fibrils is measured. Number and alignment of acetyl groups are found to be important factors determining the flexibility of chitin and chitosan fibril bundle. Structural instability can be caused by incompatible alignment of acetyl groups. Our findings on synthetic chitin-based materials indicate that adding a small amount of acetyl groups to chitosan can significantly enhance the integrity of fibril bundle. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Sulfolobus acidocaldarius UDG Can Remove dU from the RNA Backbone: Insight into the Specific Recognition of Uracil Linked with Deoxyribose

    Directory of Open Access Journals (Sweden)

    Gang-Shun Yi

    2017-01-01

    Full Text Available Sulfolobus acidocaldarius encodes family 4 and 5 uracil-DNA glycosylase (UDG. Two recombinant S. acidocaldarius UDGs (SacUDG were prepared and biochemically characterized using oligonucleotides carrying a deaminated base. Both SacUDGs can remove deoxyuracil (dU base from both double-stranded DNA and single-stranded DNA. Interestingly, they can remove U linked with deoxyribose from single-stranded RNA backbone, suggesting that the riboses on the backbone have less effect on the recognition of dU and hydrolysis of the C-N glycosidic bond. However, the removal of rU from DNA backbone is inefficient, suggesting strong steric hindrance comes from the 2′ hydroxyl of ribose linked to uracil. Both SacUDGs cannot remove 2,2′-anhydro uridine, hypoxanthine, and 7-deazaxanthine from single-stranded DNA and single-stranded DNA. Compared with the family 2 MUG, other family UDGs have an extra N-terminal structure consisting of about 50 residues. Removal of the 46 N-terminal residues of family 5 SacUDG resulted in only a 40% decrease in activity, indicating that the [4Fe-4S] cluster and truncated secondary structure are not the key elements in hydrolyzing the glycosidic bond. Combining our biochemical and structural results with those of other groups, we discussed the UDGs’ catalytic mechanism and the possible repair reactions of deaminated bases in prokaryotes.

  16. Backbone NMR assignment of a hypothetical protein MJ0754 from Methanococcus jannaschii DSM 2661

    Directory of Open Access Journals (Sweden)

    Kwang Yeon Hwang

    2011-06-01

    Full Text Available MJ0754 is an unknown hypothetical protein from hyperthermophilic archaeon Methanococcus jannaschii DSM 2661. Here we report the protein purification and NMR spectroscopic study of the N-terminal deleted truncated form of recombinant MJ0754 protein (Δ10-MJ0754. We aquired 3D NMR spectra and assigned all the backbone chemical shifts including Cα, Cβ, CO, HN, and N of Δ10-MJ0754. The secondary structure of Δ10-MJ0754 was estimated from the assigned backbone chemical shifts. This NMR result is very useful for further structural and functional study of MJ0754 protein.

  17. Constructing Battery-Aware Virtual Backbones in Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Chi Ma

    2007-05-01

    Full Text Available A critical issue in battery-powered sensor networks is to construct energy efficient virtual backbones for network routing. Recent study in battery technology reveals that batteries tend to discharge more power than needed and reimburse the over-discharged power if they are recovered. In this paper we first provide a mathematical battery model suitable for implementation in sensor networks. We then introduce the concept of battery-aware connected dominating set (BACDS and show that in general the minimum BACDS (MBACDS can achieve longer lifetime than the previous backbone structures. Then we show that finding a MBACDS is NP-hard and give a distributed approximation algorithm to construct the BACDS. The resulting BACDS constructed by our algorithm is at most (8+Δopt size, where Δ is the maximum node degree and opt is the size of an optimal BACDS. Simulation results show that the BACDS can save a significant amount of energy and achieve up to 30% longer network lifetime than previous schemes.

  18. Plasma-based accelerator structures

    International Nuclear Information System (INIS)

    Schroeder, Carl B.

    1999-01-01

    Plasma-based accelerators have the ability to sustain extremely large accelerating gradients, with possible high-energy physics applications. This dissertation further develops the theory of plasma-based accelerators by addressing three topics: the performance of a hollow plasma channel as an accelerating structure, the generation of ultrashort electron bunches, and the propagation of laser pulses is underdense plasmas

  19. Extracting the information backbone in online system.

    Science.gov (United States)

    Zhang, Qian-Ming; Zeng, An; Shang, Ming-Sheng

    2013-01-01

    Information overload is a serious problem in modern society and many solutions such as recommender system have been proposed to filter out irrelevant information. In the literature, researchers have been mainly dedicated to improving the recommendation performance (accuracy and diversity) of the algorithms while they have overlooked the influence of topology of the online user-object bipartite networks. In this paper, we find that some information provided by the bipartite networks is not only redundant but also misleading. With such "less can be more" feature, we design some algorithms to improve the recommendation performance by eliminating some links from the original networks. Moreover, we propose a hybrid method combining the time-aware and topology-aware link removal algorithms to extract the backbone which contains the essential information for the recommender systems. From the practical point of view, our method can improve the performance and reduce the computational time of the recommendation system, thus improving both of their effectiveness and efficiency.

  20. Structural Analysis of Plate Based Tensegrity Structures

    DEFF Research Database (Denmark)

    Hald, Frederik; Kirkegaard, Poul Henning; Damkilde, Lars

    2013-01-01

    Plate tensegrity structures combine tension cables with a cross laminated timber plate and can then form e.g. a roof structure. The topology of plate tensegrity structures is investigated through a parametric investigation. Plate tensegrity structures are investigated, and a method...

  1. Impact of Backbone Fluorination on π-Conjugated Polymers in Organic Photovoltaic Devices: A Review

    Directory of Open Access Journals (Sweden)

    Nicolas Leclerc

    2016-01-01

    Full Text Available Solution-processed bulk heterojunction solar cells have experienced a remarkable acceleration in performances in the last two decades, reaching power conversion efficiencies above 10%. This impressive progress is the outcome of a simultaneous development of more advanced device architectures and of optimized semiconducting polymers. Several chemical approaches have been developed to fine-tune the optoelectronics and structural polymer parameters required to reach high efficiencies. Fluorination of the conjugated polymer backbone has appeared recently to be an especially promising approach for the development of efficient semiconducting polymers. As a matter of fact, most currently best-performing semiconducting polymers are using fluorine atoms in their conjugated backbone. In this review, we attempt to give an up-to-date overview of the latest results achieved on fluorinated polymers for solar cells and to highlight general polymer properties’ evolution trends related to the fluorination of their conjugated backbone.

  2. From Raw Data to Protein Backbone Chemical Shifts Using NMRFx Processing and NMRViewJ Analysis.

    Science.gov (United States)

    Johnson, Bruce A

    2018-01-01

    Assignment of the chemical shifts of the backbone atoms (HN, N, CA, CB, and C) of proteins is often a prerequisite to using NMR information in the study of proteins. These chemical shifts and their perturbations are the basis for the analysis of protein dynamics, ligand binding, and backbone conformation. They are generally assigned prior to full side-chain assignments and the determination of the complete three-dimensional molecular structure. This chapter describes the use of two software packages, NMRFx Processor and NMRViewJ, in going from raw NMR data to backbone assignments. The step-by-step procedure describes processing of the data and the use of manual and automated features of the RunAbout tool in NMRViewJ to perform the assignments.

  3. Backbone dynamics of the EIAV-Tat protein from {sup 15}N relaxation studies

    Energy Technology Data Exchange (ETDEWEB)

    Ejchart, A.; Herrmann, F.; Roesch, P.; Sticht, H.; Willbold, D. [Bayreuth Univ., Bayreuth (Germany)

    1994-12-31

    The work investigates the mobility of EIAV-Tat protein backbone by measuring the relaxation parameters of the {sup 15}N nitrogens. High degree of the flexibility, non-typical of rigid, well structured proteins was shown. 3 refs, 2 figs.

  4. “Pinning strategy”: a novel approach for predicting the backbone ...

    Indian Academy of Sciences (India)

    Prakash

    a high performance rate. For instance, prediction in ... [de Brevern A G, Etchebest C, Benros C and Hazout S 2006 “Pinning strategy”: a novel approach for predicting the backbone structure in terms of protein blocks from sequence; ..... are confronted to a dilemma: (i) the necessity to trap the main sequence determinants.

  5. AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences.

    Science.gov (United States)

    Lapidoth, Gideon D; Baran, Dror; Pszolla, Gabriele M; Norn, Christoffer; Alon, Assaf; Tyka, Michael D; Fleishman, Sarel J

    2015-08-01

    Computational design of protein function has made substantial progress, generating new enzymes, binders, inhibitors, and nanomaterials not previously seen in nature. However, the ability to design new protein backbones for function--essential to exert control over all polypeptide degrees of freedom--remains a critical challenge. Most previous attempts to design new backbones computed the mainchain from scratch. Here, instead, we describe a combinatorial backbone and sequence optimization algorithm called AbDesign, which leverages the large number of sequences and experimentally determined molecular structures of antibodies to construct new antibody models, dock them against target surfaces and optimize their sequence and backbone conformation for high stability and binding affinity. We used the algorithm to produce antibody designs that target the same molecular surfaces as nine natural, high-affinity antibodies; in five cases interface sequence identity is above 30%, and in four of those the backbone conformation at the core of the antibody binding surface is within 1 Å root-mean square deviation from the natural antibodies. Designs recapitulate polar interaction networks observed in natural complexes, and amino acid sidechain rigidity at the designed binding surface, which is likely important for affinity and specificity, is high compared to previous design studies. In designed anti-lysozyme antibodies, complementarity-determining regions (CDRs) at the periphery of the interface, such as L1 and H2, show greater backbone conformation diversity than the CDRs at the core of the interface, and increase the binding surface area compared to the natural antibody, potentially enhancing affinity and specificity. © 2015 Wiley Periodicals, Inc.

  6. NHC Backbone Configuration in Ruthenium-Catalyzed Olefin Metathesis.

    Science.gov (United States)

    Paradiso, Veronica; Costabile, Chiara; Grisi, Fabia

    2016-01-20

    The catalytic properties of olefin metathesis ruthenium complexes bearing N-heterocyclic carbene ligands with stereogenic centers on the backbone are described. Differences in catalytic behavior depending on the backbone configurations of symmetrical and unsymmetrical NHCs are discussed. In addition, an overview on asymmetric olefin metathesis promoted by chiral catalysts bearing C₂-symmetric and C₁-symmetric NHCs is provided.

  7. NHC Backbone Configuration in Ruthenium-Catalyzed Olefin Metathesis

    Directory of Open Access Journals (Sweden)

    Veronica Paradiso

    2016-01-01

    Full Text Available The catalytic properties of olefin metathesis ruthenium complexes bearing N-heterocyclic carbene ligands with stereogenic centers on the backbone are described. Differences in catalytic behavior depending on the backbone configurations of symmetrical and unsymmetrical NHCs are discussed. In addition, an overview on asymmetric olefin metathesis promoted by chiral catalysts bearing C2-symmetric and C1-symmetric NHCs is provided.

  8. Transforming plastic surfaces with electrophilic backbones from hydrophobic to hydrophilic.

    Science.gov (United States)

    Kim, Samuel; Bowen, Raffick A R; Zare, Richard N

    2015-01-28

    We demonstrate a simple nonaqueous reaction scheme for transforming the surface of plastics from hydrophobic to hydrophilic. The chemical modification is achieved by base-catalyzed trans-esterification with polyols. It is permanent, does not release contaminants, and causes no optical or mechanical distortion of the plastic. We present contact angle measurements to show successful modification of several types of plastics including poly(ethylene terephthalate) (PET) and polycarbonate (PC). Its applicability to blood analysis is explored using chemically modified PET blood collection tubes and found to be quite satisfactory. We expect this approach will reduce the cost of manufacturing plastic devices with optimized wettability and can be generalized to other types of plastic materials having an electrophilic linkage as its backbone.

  9. Extracting the information backbone in online system.

    Directory of Open Access Journals (Sweden)

    Qian-Ming Zhang

    Full Text Available Information overload is a serious problem in modern society and many solutions such as recommender system have been proposed to filter out irrelevant information. In the literature, researchers have been mainly dedicated to improving the recommendation performance (accuracy and diversity of the algorithms while they have overlooked the influence of topology of the online user-object bipartite networks. In this paper, we find that some information provided by the bipartite networks is not only redundant but also misleading. With such "less can be more" feature, we design some algorithms to improve the recommendation performance by eliminating some links from the original networks. Moreover, we propose a hybrid method combining the time-aware and topology-aware link removal algorithms to extract the backbone which contains the essential information for the recommender systems. From the practical point of view, our method can improve the performance and reduce the computational time of the recommendation system, thus improving both of their effectiveness and efficiency.

  10. Extracting the Information Backbone in Online System

    Science.gov (United States)

    Zhang, Qian-Ming; Zeng, An; Shang, Ming-Sheng

    2013-01-01

    Information overload is a serious problem in modern society and many solutions such as recommender system have been proposed to filter out irrelevant information. In the literature, researchers have been mainly dedicated to improving the recommendation performance (accuracy and diversity) of the algorithms while they have overlooked the influence of topology of the online user-object bipartite networks. In this paper, we find that some information provided by the bipartite networks is not only redundant but also misleading. With such “less can be more” feature, we design some algorithms to improve the recommendation performance by eliminating some links from the original networks. Moreover, we propose a hybrid method combining the time-aware and topology-aware link removal algorithms to extract the backbone which contains the essential information for the recommender systems. From the practical point of view, our method can improve the performance and reduce the computational time of the recommendation system, thus improving both of their effectiveness and efficiency. PMID:23690946

  11. Reliability Based Ship Structural Design

    DEFF Research Database (Denmark)

    Dogliani, M.; Østergaard, C.; Parmentier, G.

    1996-01-01

    This paper deals with the development of different methods that allow the reliability-based design of ship structures to be transferred from the area of research to the systematic application in current design. It summarises the achievements of a three-year collaborative research project dealing...... with developments of models of load effects and of structural collapse adopted in reliability formulations which aim at calibrating partial safety factors for ship structural design. New probabilistic models of still-water load effects are developed both for tankers and for containerships. New results are presented...... of non-linear wave induced load effects and the corresponding long-term formulations. Methods to combine linear and non-linear components of wave induced load effects have been developed and checked by alternative methods.These improved models were used for the reliability assessment of the primary hull...

  12. Structural analysis of base substitutions in Thermus thermophilus 16S rRNA conferring streptomycin resistance.

    Science.gov (United States)

    Demirci, Hasan; Murphy, Frank V; Murphy, Eileen L; Connetti, Jacqueline L; Dahlberg, Albert E; Jogl, Gerwald; Gregory, Steven T

    2014-08-01

    Streptomycin is a bactericidal antibiotic that induces translational errors. It binds to the 30S ribosomal subunit, interacting with ribosomal protein S12 and with 16S rRNA through contacts with the phosphodiester backbone. To explore the structural basis for streptomycin resistance, we determined the X-ray crystal structures of 30S ribosomal subunits from six streptomycin-resistant mutants of Thermus thermophilus both in the apo form and in complex with streptomycin. Base substitutions at highly conserved residues in the central pseudoknot of 16S rRNA produce novel hydrogen-bonding and base-stacking interactions. These rearrangements in secondary structure produce only minor adjustments in the three-dimensional fold of the pseudoknot. These results illustrate how antibiotic resistance can occur as a result of small changes in binding site conformation. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  13. Toward water-solvation of rice proteins via backbone hybridization by casein.

    Science.gov (United States)

    Wang, Tao; Yue, Ming; Xu, Pengcheng; Wang, Ren; Chen, Zhengxing

    2018-08-30

    Water insolubility is one of the major bottlenecks restricting the commercial availability of such food proteins as rice proteins (RPs), zein, etc. Here, we report that the structural hybridization of RPs and casein in a mass ratio of 1:0.01 can boost the solubility of RPs to over 90%. A structural analysis demonstrated that the backbones of the RPs and casein were integrated in basic solution (pH 12.0) and folded together into higher structures with subsequent neutralization. The hybrid backbones obtained improved the molecules' resistance to structural changes during neutralization, and formed protein bodies with appreciable exposed polar groups, which may have been buried in the absence of casein. Morphological observations confirmed the formation of well-defined nanoscale particles with no visible aggregation. Both proteins also retained their intact primary peptide chains, thus significantly protecting the original nature of the plant and animal derivatives. Copyright © 2018 Elsevier Ltd. All rights reserved.

  14. Receptor structure-based discovery of non-metabolite agonists for the succinate receptor GPR91.

    Science.gov (United States)

    Trauelsen, Mette; Rexen Ulven, Elisabeth; Hjorth, Siv A; Brvar, Matjaz; Monaco, Claudia; Frimurer, Thomas M; Schwartz, Thue W

    2017-12-01

    Besides functioning as an intracellular metabolite, succinate acts as a stress-induced extracellular signal through activation of GPR91 (SUCNR1) for which we lack suitable pharmacological tools. Here we first determined that the cis conformation of the succinate backbone is preferred and that certain backbone modifications are allowed for GPR91 activation. Through receptor modeling over the X-ray structure of the closely related P2Y1 receptor, we discovered that the binding pocket is partly occupied by a segment of an extracellular loop and that succinate therefore binds in a very different mode than generally believed. Importantly, an empty side-pocket is identified next to the succinate binding site. All this information formed the basis for a substructure-based search query, which, combined with molecular docking, was used in virtual screening of the ZINC database to pick two serial mini-libraries of a total of only 245 compounds from which sub-micromolar, selective GPR91 agonists of unique structures were identified. The best compounds were backbone-modified succinate analogs in which an amide-linked hydrophobic moiety docked into the side-pocket next to succinate as shown by both loss- and gain-of-function mutagenesis. These compounds displayed GPR91-dependent activity in altering cytokine expression in human M2 macrophages similar to succinate, and importantly were devoid of any effect on the major intracellular target, succinate dehydrogenase. These novel, synthetic non-metabolite GPR91 agonists will be valuable both as pharmacological tools to delineate the GPR91-mediated functions of succinate and as leads for the development of GPR91-targeted drugs to potentially treat low grade metabolic inflammation and diabetic complications such as retinopathy and nephropathy. Copyright © 2017 The Authors. Published by Elsevier GmbH.. All rights reserved.

  15. Stereodependent and solvent-specific formation of unusual β-structure through side chain-backbone H-bonding in C4(S)-(NH2/OH/NHCHO)-L-prolyl polypeptides.

    Science.gov (United States)

    Bansode, Nitin D; Madhanagopal, B; Sonar, Mahesh V; Ganesh, Krishna N

    2017-01-01

    It is shown that C4(S)-NH 2 /OH/NHCHO-prolyl polypeptides exhibit PPII conformation in aqueous medium, but in a relatively hydrophobic solvent trifluoroethanol (TFE) transform into an unusual β-structure. The stereospecific directing effect of H-bonding in defining the specific structure is demonstrated by the absence of β-structure in the corresponding C4(S)-guanidinyl/(NH/O)-acetyl derivatives and retention of β-structure in C4(S)-(NHCHO)-prolyl polypeptides in TFE. The distinct conformations are identified by the characteristic CD patterns and supported by Raman spectroscopic data. The solvent dependent conformational effects are interpreted in terms of intraresidue H-bonding that promotes PPII conformation in water, switching over to interchain H-bonding in TFE. The present observations add a new design principle to the growing repertoire of strategies for engineering peptide secondary structural motifs for innovative nanoassemblies and new biomaterials. © 2016 Wiley Periodicals, Inc.

  16. Radiation Safety System (RSS) backbones: Design, engineering, fabrication, and installation

    Science.gov (United States)

    Wilmarth, J. E.; Sturrock, J. C.; Gallegos, F. R.

    1998-12-01

    The Radiation Safety System (RSS) backbones are part of an electrical/electronic/mechanical system ensuring safe access and exclusion of personnel to areas at the Los Alamos Neutron Science Center (LANSCE) accelerator. The RSS backbones control the safety-fusible beam plugs which terminate transmission of accelerated ion beams in response to predefined conditions. Any beam or access fault of the backbone inputs will cause insertion of the beam plugs in the low-energy beam transport. The backbones serve the function of tying the beam plugs to the access control systems, beam spill monitoring systems and current-level limiting systems. In some ways the backbones may be thought of as a spinal column with beam plugs at the head and nerve centers along the spinal column. The two linac backbone segments and the experimental area segments form a continuous cable plant over 3500 feet from the beam plugs to the tip on the longest tail. The backbones were installed in compliance with current safety standards, such as installation of the two segments in separate conduits or tray. Monitoring for ground-faults and input wiring verification was an added enhancement to the system. The system has the capability to be tested remotely.

  17. Radiation safety system (RSS) backbones: Design, engineering, fabrication and installation

    International Nuclear Information System (INIS)

    Wilmarth, J.E.; Sturrock, J.C.; Gallegos, F.R.

    1998-01-01

    The Radiation Safety System (RSS) Backbones are part of an electrical/electronic/mechanical system insuring safe access and exclusion of personnel to areas at the Los Alamos Neutron Science Center (LANSCE) accelerator. The RSS Backbones control the safety fusible beam plugs which terminate transmission of accelerated ion beams in response to predefined conditions. Any beam or access fault of the backbone inputs will cause insertion of the beam plugs in the low energy beam transport. The Backbones serve the function of tying the beam plugs to the access control systems, beam spill monitoring systems and current-level limiting systems. In some ways the Backbones may be thought of as a spinal column with beam plugs at the head and nerve centers along the spinal column. The two Linac Backbone segments and experimental area segments form a continuous cable plant over 3,500 feet from beam plugs to the tip on the longest tail. The Backbones were installed in compliance with current safety standards, such as installation of the two segments in separate conduits or tray. Monitoring for ground-faults and input wiring verification was an added enhancement to the system. The system has the capability to be tested remotely

  18. On the relationship between NMR-derived amide order parameters and protein backbone entropy changes.

    Science.gov (United States)

    Sharp, Kim A; O'Brien, Evan; Kasinath, Vignesh; Wand, A Joshua

    2015-05-01

    Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O(2) NH ) are largely determined by the secondary structure and average values appear unrelated to the overall flexibility of the protein. However, analysis of the more flexible subset (O(2) NH  entropy than that reported by the side chain methyl axis order parameters, O(2) axis . A calibration curve for backbone entropy vs. O(2) NH is developed, which accounts for both correlations between amide group motions of different residues, and correlations between backbone and side chain motions. This calibration curve can be used with experimental values of O(2) NH changes obtained by NMR relaxation measurements to extract backbone entropy changes, for example, upon ligand binding. In conjunction with our previous calibration for side chain entropy derived from measured O(2) axis values this provides a prescription for determination of the total protein conformational entropy changes from NMR relaxation measurements. © 2015 Wiley Periodicals, Inc.

  19. Program structure-based blocking

    Science.gov (United States)

    Bertolli, Carlo; Eichenberger, Alexandre E.; O'Brien, John K.; Sura, Zehra N.

    2017-09-26

    Embodiments relate to program structure-based blocking. An aspect includes receiving source code corresponding to a computer program by a compiler of a computer system. Another aspect includes determining a prefetching section in the source code by a marking module of the compiler. Yet another aspect includes performing, by a blocking module of the compiler, blocking of instructions located in the prefetching section into instruction blocks, such that the instruction blocks of the prefetching section only contain instructions that are located in the prefetching section.

  20. Reliability-based optimization of engineering structures

    DEFF Research Database (Denmark)

    Sørensen, John Dalsgaard

    2008-01-01

    The theoretical basis for reliability-based structural optimization within the framework of Bayesian statistical decision theory is briefly described. Reliability-based cost benefit problems are formulated and exemplitied with structural optimization. The basic reliability-based optimization prob...

  1. Vibration-based structural health monitoring of harbor caisson structure

    Science.gov (United States)

    Lee, So-Young; Lee, So-Ra; Kim, Jeong-Tae

    2011-04-01

    This study presents vibration-based structural health monitoring method in foundation-structure interface of harbor caisson structure. In order to achieve the objective, the following approaches are implemented. Firstly, vibration-based response analysis method is selected and structural health monitoring (SHM) technique is designed for harbor caisson structure. Secondly, the performance of designed SHM technique for harbor structure is examined by FE analysis. Finally, the applicability of designed SHM technique for harbor structure is evaluated by dynamic tests on a lab-scaled caisson structure.

  2. Structural Interpretation of J Coupling Constants in Guanosine and Deoxyguanosine: Modeling the Effects of Sugar Pucker, Backbone Conformation, and Base Paging

    Czech Academy of Sciences Publication Activity Database

    Vokáčová, Zuzana; Bickelhaupt, F. M.; Šponer, Jiří; Sychrovský, Vladimír

    2009-01-01

    Roč. 113, č. 29 (2009), s. 8379-8386 ISSN 1089-5639 R&D Projects: GA AV ČR IAA400550701 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z50040702 Keywords : guanosin * DFT * J-coupling Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.899, year: 2009

  3. Synthesis, photophysics, structure-tunable photoluminescence, and electrochemical properties of soluble poly(p-phenylenevinylene)-based polymers with adjacent 1,3,4-oxadiazoles in the backbone

    Czech Academy of Sciences Publication Activity Database

    Mikroyannidis, J. A.; Hlídková, Helena; Výprachtický, Drahomír; Cimrová, Věra

    2005-01-01

    Roč. 43, č. 14 (2005), s. 3079-3090 ISSN 0887-624X R&D Projects: GA AV ČR IAA4050409 Institutional research plan: CEZ:AV0Z40500505 Keywords : electrochemical properties * Heck coupling * light emitting polymers Subject RIV: CD - Macromolecular Chemistry Impact factor: 3.027, year: 2005

  4. Retrospective Validation of a Structure-Based Virtual Screening Protocol to Identify Ligands for Estrogen Receptor Alpha and Its Application to Identify the Alpha-Mangostin Binding Pose

    OpenAIRE

    Agustina Setiawati; Florentinus Dika Octa Riswanto; Sri Hartati Yuliani; Enade Perdana Istyastono

    2014-01-01

    The publicly available enhanced data of ligands and decoys for estrogen receptor alpha (ERα) which were recently published has made the retrospective validation of a structure-based virtual screening (SBVS) protocol to identify ligands for ERα possible. In this article, we present the retrospective validation of an SBVS protocol using PLANTS molecular docking software version 1.2 (PLANTS1.2) as the backbone software. The protocol shows better enrichment factor at 1% false positives (EF1%) val...

  5. Towards a natural classification and backbone tree for Sordariomycete

    Digital Repository Service at National Institute of Oceanography (India)

    Maharachchikumbura, S.S.N.; Hyde, K.D.; Jones, E.B.G.; McKenzie, E.H.C.; Huang, S.-K.; Abdel-Wahab, M.A.; Daranagama, D.A.; Dayarathne, M.; D'souza, M.J.; Goonasekara, I.D.; Hongsanan, S.; Jayawardena, R.S.; Kirk, P.M.; Konta, S.; Liu, J.-K.; Liu, Z.-Y.; Norphanphoun, C.; Pang, K.-L.; Perera, R.H.; Senanayake, I.C.; Shang, Q.; Shenoy, B.D.; Xiao, Y.; Bahkali, A.H.; Kang, J.; Somrothipol, S.; Suetrong, S.; Wen, T.; Xu, J.

    , lichenized or lichenicolous taxa The class includes freshwater, marine and terrestrial taxa and has a worldwide distribution This paper provides an updated outline of the Sordariomycetes and a backbone tree incorporating asexual and sexual genera in the class...

  6. Topologia dos backbones de internet no Brasil / Internet backbone topology in Brazil

    Directory of Open Access Journals (Sweden)

    Marcelo Paiva da Motta

    2012-04-01

    Full Text Available Este artigo visa reafirmar o papel do espaço no estudo das Novas Tecnologias de Informação e Comunicação (NTICs. Examinamos a topologia dos backbones de internet no Brasil usando as ferramentas matemáticas da teoria dos grafos. Através do cálculo de índices de centralidade (proximidade e intermediação, bem como de outras técnicas quantitativas, as redes físicas que compõem a internet são relacionadas à rede urbana preexistente, mostrando que em suas características gerais o funcionamento não subverte a geografia econômica do país, a despeito do ideário antigeográfico suscitado por parte da literatura sobre os impactos da tecnologia.

  7. ADAR RNA editing below the backbone.

    Science.gov (United States)

    Keegan, Liam; Khan, Anzer; Vukic, Dragana; O'Connell, Mary

    2017-09-01

    ADAR RNA editing enzymes ( a denosine d e a minases acting on R NA) that convert adenosine bases to inosines were first identified biochemically 30 years ago. Since then, studies on ADARs in genetic model organisms, and evolutionary comparisons between them, continue to reveal a surprising range of pleiotropic biological effects of ADARs. This review focuses on Drosophila melanogaster , which has a single Adar gene encoding a homolog of vertebrate ADAR2 that site-specifically edits hundreds of transcripts to change individual codons in ion channel subunits and membrane and cytoskeletal proteins. Drosophila ADAR is involved in the control of neuronal excitability and neurodegeneration and, intriguingly, in the control of neuronal plasticity and sleep. Drosophila ADAR also interacts strongly with RNA interference, a key antiviral defense mechanism in invertebrates. Recent crystal structures of human ADAR2 deaminase domain-RNA complexes help to interpret available information on Drosophila ADAR isoforms and on the evolution of ADARs from tRNA deaminase ADAT proteins. ADAR RNA editing is a paradigm for the now rapidly expanding range of RNA modifications in mRNAs and ncRNAs. Even with recent progress, much remains to be understood about these groundbreaking ADAR RNA modification systems. © 2017 Keegan et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  8. Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

    Energy Technology Data Exchange (ETDEWEB)

    Shen Yang; Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    2013-07-15

    A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, {>=}90 % fraction of the residues, with an error rate smaller than ca 3.5 %, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed ({phi}, {psi}) torsion angles of ca 12 Masculine-Ordinal-Indicator . TALOS-N also reports sidechain {chi}{sup 1} rotameric states for about 50 % of the residues, and a consistency with reference structures of 89 %. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts.

  9. Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

    International Nuclear Information System (INIS)

    Shen Yang; Bax, Ad

    2013-01-01

    A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, ≥90 % fraction of the residues, with an error rate smaller than ca 3.5 %, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed (φ, ψ) torsion angles of ca 12º. TALOS-N also reports sidechain χ 1 rotameric states for about 50 % of the residues, and a consistency with reference structures of 89 %. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts

  10. Automating unambiguous NOE data usage in NVR for NMR protein structure-based assignments.

    Science.gov (United States)

    Akhmedov, Murodzhon; Çatay, Bülent; Apaydın, Mehmet Serkan

    2015-12-01

    Nuclear Magnetic Resonance (NMR) Spectroscopy is an important technique that allows determining protein structure in solution. An important problem in protein structure determination using NMR spectroscopy is the mapping of peaks to corresponding amino acids, also known as the assignment problem. Structure-Based Assignment (SBA) is an approach to solve this problem using a template structure that is homologous to the target. Our previously developed approach Nuclear Vector Replacement-Binary Integer Programming (NVR-BIP) computed the optimal solution for small proteins, but was unable to solve the assignments of large proteins. NVR-Ant Colony Optimization (ACO) extended the applicability of the NVR approach for such proteins. One of the input data utilized in these approaches is the Nuclear Overhauser Effect (NOE) data. NOE is an interaction observed between two protons if the protons are located close in space. These protons could be amide protons, protons attached to the alpha-carbon atom in the backbone of the protein, or side chain protons. NVR only uses backbone protons. In this paper, we reformulate the NVR-BIP model to distinguish the type of proton in NOE data and use the corresponding proton coordinates in the extended formulation. In addition, the threshold value over interproton distances is set in a standard manner for all proteins by extracting the NOE upper bound distance information from the data. We also convert NOE intensities into distance thresholds. Our new approach thus handles the NOE data correctly and without manually determined parameters. We accordingly adapt NVR-ACO solution methodology to these changes. Computational results show that our approaches obtain optimal solutions for small proteins. For the large proteins our ant colony optimization-based approach obtains promising results.

  11. Nucleic Acid Backbone Structure Variations: Peptide Nucleic Acids

    DEFF Research Database (Denmark)

    Nielsen, Peter E.

    2010-01-01

    Synthetic analogues and mimics of the natural genetic material deoxyribonucleic acid (DNA) are potential gene therapeutic (antisense or antigene) drugs. One of these mimics, peptide nucleic acids (PNAs), are chemically closer to peptides and proteins than to DNA, but nonetheless have retained many...

  12. Smart-Grid Backbone Network Real-Time Delay Reduction via Integer Programming.

    Science.gov (United States)

    Pagadrai, Sasikanth; Yilmaz, Muhittin; Valluri, Pratyush

    2016-08-01

    This research investigates an optimal delay-based virtual topology design using integer linear programming (ILP), which is applied to the current backbone networks such as smart-grid real-time communication systems. A network traffic matrix is applied and the corresponding virtual topology problem is solved using the ILP formulations that include a network delay-dependent objective function and lightpath routing, wavelength assignment, wavelength continuity, flow routing, and traffic loss constraints. The proposed optimization approach provides an efficient deterministic integration of intelligent sensing and decision making, and network learning features for superior smart grid operations by adaptively responding the time-varying network traffic data as well as operational constraints to maintain optimal virtual topologies. A representative optical backbone network has been utilized to demonstrate the proposed optimization framework whose simulation results indicate that superior smart-grid network performance can be achieved using commercial networks and integer programming.

  13. Self-assembly of diphenylalanine backbone homologues and their combination with functionalized carbon nanotubes.

    Science.gov (United States)

    Dinesh, Bhimareddy; Squillaci, Marco A; Ménard-Moyon, Cécilia; Samorì, Paolo; Bianco, Alberto

    2015-10-14

    The integration of carbon nanotubes (CNTs) into organized nanostructures is of great interest for applications in materials science and biomedicine. In this work we studied the self-assembly of β and γ homologues of diphenylalanine peptides under different solvent and pH conditions. We aimed to investigate the role of peptide backbone in tuning the formation of different types of nanostructures alone or in combination with carbon nanotubes. In spite of having the same side chain, β and γ peptides formed distinctively different nanofibers, a clear indication of the role played by the backbone homologation on the self-assembly. The variation of the pH allowed to transform the nanofibers into spherical structures. Moreover, the co-assembly of β and γ peptides with carbon nanotubes covalently functionalized with the same peptide generated unique dendritic assemblies. This comparative study on self-assembly using diphenylalanine backbone homologues and of the co-assembly with CNT covalent conjugates is the first example exploring the capacity of β and γ peptides to adopt precise nanostructures, particularly in combination with carbon nanotubes. The dendritic organization obtained by mixing carbon nanotubes and peptides might find interesting applications in tissue engineering and neuronal interfacing.

  14. Comparison of sequence-based and structure-based phylogenetic ...

    Indian Academy of Sciences (India)

    Prakash

    Sequence-based and structure-based phylogeny. 85. J. Biosci. 32(1), January 2007 dispersion is independent of phylogenetic tree construction algorithms. 3. ... two groups only. 3.1 Families with high correlation between sequence- based and structure-based phylogenetic trees. There are 27 families with considerably high ...

  15. Direct observation of backbone planarization via side-chain alignment in single bulky-substituted polythiophenes

    Science.gov (United States)

    Raithel, Dominic; Simine, Lena; Pickel, Sebastian; Schötz, Konstantin; Panzer, Fabian; Baderschneider, Sebastian; Schiefer, Daniel; Lohwasser, Ruth; Köhler, Jürgen; Thelakkat, Mukundan; Sommer, Michael; Köhler, Anna; Rossky, Peter J.; Hildner, Richard

    2018-03-01

    The backbone conformation of conjugated polymers affects, to a large extent, their optical and electronic properties. The usually flexible substituents provide solubility and influence the packing behavior of conjugated polymers in films or in bad solvents. However, the role of the side chains in determining and potentially controlling the backbone conformation, and thus the optical and electronic properties on the single polymer level, is currently under debate. Here, we investigate directly the impact of the side chains by studying the bulky-substituted poly(3-(2,5-dioctylphenyl)thiophene) (PDOPT) and the common poly(3-hexylthiophene) (P3HT), both with a defined molecular weight and high regioregularity, using low-temperature single-chain photoluminescence (PL) spectroscopy and quantum-classical simulations. Surprisingly, the optical transition energy of PDOPT is significantly (˜2,000 cm‑1 or 0.25 eV) red-shifted relative to P3HT despite a higher static and dynamic disorder in the former. We ascribe this red shift to a side-chain induced backbone planarization in PDOPT, supported by temperature-dependent ensemble PL spectroscopy. Our atomistic simulations reveal that the bulkier 2,5-dioctylphenyl side chains of PDOPT adopt a clear secondary helical structural motif and thus protect conjugation, i.e., enforce backbone planarity, whereas, for P3HT, this is not the case. These different degrees of planarity in both thiophenes do not result in different conjugation lengths, which we found to be similar. It is rather the stronger electronic coupling between the repeating units in the more planar PDOPT which gives rise to the observed spectral red shift as well as to a reduced calculated electron‑hole polarization.

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

    Science.gov (United States)

    Ghobadi, Ahmadreza F; Jayaraman, Arthi

    2016-02-28

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

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

    International Nuclear Information System (INIS)

    Li, Dawei; Brüschweiler, Rafael

    2015-01-01

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

  18. Cellular Uptake Mechanism of Cationic Branched Polypeptides with Poly[l-Lys] Backbone.

    Science.gov (United States)

    Szabó, Rita; Sebestyén, Mónika; Kóczán, György; Orosz, Ádám; Mező, Gábor; Hudecz, Ferenc

    2017-04-10

    Cationic macromolecular carriers can be effective carriers for small molecular compounds, drugs, epitopes, or nucleic acids. Polylysine-based polymeric branched polypeptides have been systematically studied on the level of cells and organisms as well. In the present study, we report our findings on the cellular uptake characteristics of nine structurally related polylysine-based polypeptides with cationic side chains composed of (i) single amino acid (poly[Lys(X i )], X i K) or (ii) oligo[dl-alanine] (poly[Lys(dl-Ala m )], AK) or (iii) oligo[dl-alanine] with an additional amino acid (X) at the terminal position (poly[Lys(X i -dl-Ala m )] (XAK)) or (iv) at the position next to the polylysine backbone (poly[Lys(dl-Ala m -X i )] (AXK)). In vitro cytotoxicity and cellular uptake were characterized on HT-29 human colon carcinoma and HepG2 human hepatocarcinoma cell lines. Data indicate that the polycationic polypeptides studied are essentially nontoxic in the concentration range studied, and their uptake is very much dependent on the side chain structure (length, identity of amino acid X, and distance between the terminal positive charges) and also on the cell lines. Our findings in uptake inhibition studies suggest that predominantly macropinocytosis and caveole/lipid raft mediated endocytosis are involved. The efficacy of their internalization is markedly influenced by the hydrophobicity and charge properties of the amino acid X. Interestingly, the uptake properties of the these polypeptides show certain similarities to the entry pathways of several cell penetrating peptides.

  19. Sortase-mediated backbone cyclization of proteins and peptides

    NARCIS (Netherlands)

    van 't Hof, W.; Hansenová Maňásková, S.; Veerman, E.C.I.; Bolscher, J.G.M.

    2015-01-01

    Backbone cyclization has a profound impact on the biological activity and thermal and proteolytic stability of proteins and peptides. Chemical methods for cyclization are not always feasible, especially for large peptides or proteins. Recombinant Staphylococcus aureus sortase A shows potential as a

  20. Stabilizing cations in the backbones of conjugated polymers

    NARCIS (Netherlands)

    Voortman, Thomas P.; de Gier, Hilde D.; Havenith, Remco W. A.; Chiechi, Ryan C.

    2014-01-01

    We synthesized a cross-conjugated polymer containing ketones in the backbone and converted it to a linearly conjugated, cationic polyarylmethine via a process we call "spinless doping" to create a new class of materials, conjugated polyions. This process involves activating the ketones with a Lewis

  1. The Graphical Representation of the Digital Astronaut Physiology Backbone

    Science.gov (United States)

    Briers, Demarcus

    2010-01-01

    This report summarizes my internship project with the NASA Digital Astronaut Project to analyze the Digital Astronaut (DA) physiology backbone model. The Digital Astronaut Project (DAP) applies integrated physiology models to support space biomedical operations, and to assist NASA researchers in closing knowledge gaps related to human physiologic responses to space flight. The DA physiology backbone is a set of integrated physiological equations and functions that model the interacting systems of the human body. The current release of the model is HumMod (Human Model) version 1.5 and was developed over forty years at the University of Mississippi Medical Center (UMMC). The physiology equations and functions are scripted in an XML schema specifically designed for physiology modeling by Dr. Thomas G. Coleman at UMMC. Currently it is difficult to examine the physiology backbone without being knowledgeable of the XML schema. While investigating and documenting the tags and algorithms used in the XML schema, I proposed a standard methodology for a graphical representation. This standard methodology may be used to transcribe graphical representations from the DA physiology backbone. In turn, the graphical representations can allow examination of the physiological functions and equations without the need to be familiar with the computer programming languages or markup languages used by DA modeling software.

  2. Performance of Flow-Aware Networking in LTE backbone

    DEFF Research Database (Denmark)

    Sniady, Aleksander; Soler, José

    2012-01-01

    technologies, such as Long Term Evolution (LTE). This paper proposes usage of a modified Flow Aware Networking (FAN) technique for enhancing Quality of Service (QoS) in the all-IP transport networks underlying LTE backbone. The results obtained with OPNET Modeler show that FAN, in spite of being relatively...

  3. Internet Backbone in the Democratic Republic of Congo : Feasibility ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Internet Backbone in the Democratic Republic of Congo : Feasibility Study and Advocacy. During 7-10 February 2005, representatives of five francophone African countries (Cameroon, Morocco, Niger, Sénégal, and the Democratic Republic of Congo - DRC) met to consider ways and means of galvanizing the appropriation ...

  4. The Structural Location of DNA Lesions in Nucleosome Core Particles Determines Accessibility by Base Excision Repair Enzymes*

    Science.gov (United States)

    Rodriguez, Yesenia; Smerdon, Michael J.

    2013-01-01

    Packaging of DNA into chromatin affects accessibility of DNA regulatory factors involved in transcription, replication, and repair. Evidence suggests that even in the nucleosome core particle (NCP), accessibility to damaged DNA is hindered by the presence of the histone octamer. Base excision repair is the major pathway in mammalian cells responsible for correcting a large number of chemically modified bases. We have measured the repair of site-specific uracil and single nucleotide gaps along the surface of the NCP. Our results indicate that removal of DNA lesions is greatly dependent on their rotational and translational positioning in NCPs. Significantly, the rate of uracil removal with outwardly oriented DNA backbones is 2–10-fold higher than those with inwardly oriented backbones. In general, uracils with inwardly oriented backbones farther away from the dyad center of the NCP are more accessible than those near the dyad. The translational positioning of outwardly oriented gaps is the key factor driving gap filling activity. An outwardly oriented gap near the DNA ends exhibits a 3-fold increase in gap filling activity as compared with one near the dyad with the same rotational orientation. Near the dyad, uracil DNA glycosylase/APE1 removes an outwardly oriented uracil efficiently; however, polymerase β activity is significantly inhibited at this site. These data suggest that the hindrance presented by the location of a DNA lesion is dependent on the structural requirements for enzyme catalysis. Therefore, remodeling at DNA damage sites in NCPs is critical for preventing accumulation of aborted intermediates and ensuring completion of base excision repair. PMID:23543741

  5. Building an Archive Backbone Extending TAP

    Science.gov (United States)

    Molinaro, M.; Apollo, P.; Knapic, C.; Smareglia, R.

    2014-05-01

    A data center (DC) willing to add VO (Virtual Observatory) capabilities to existing archival resources, or new ones, will probably face some issues regarding the constraints on the existing structure of the datasets. On the opposite direction a DC may want to give priority to VO flavored data access but maintain flexibility on proprietary or dedicated access solutions. This contribution tries to delineate a solution, feasible for both approaches, taking advantage of the IVOA (International Virtual Observatory Alliance) existing standards and, at the same time, forcing no constraint at archive generation or ingestion level. The IVOA TAP (Table Access Protocol) specification generalizes the way a set of database schemas and tables, related or not, can be deployed as a queryable resource in the framewok of the Virtual Observatory. The TAP protocol itself has, at its core, a DB schema, named TAP_SCHEMA, that actually acts as an attribute-extended information schema for the exposed set of tables; the TAP_SCHEMA, in short, describes the content of the schemas and tables, and their connections, in a VO aware flavour. It seems then quite immediate to think about pushing the generalization step a little further, i.e. to extend the TAP_SCHEMA itself to provide a more general description of an astrophysical archive (or part of it). Here we discuss on how, adding optional tables and columns to the TAP_SCHEMA, it would be possible to create an archive thin layer solution in terms of this DB schema alongside with a content manager application for it. The goal is to provide a re-usable, configurable connection between an archive's back end and front end, having the benefit of creating a VO translation layer to ease VO resource and service deployment and preserving custom data access and publishing.

  6. The Legal Ethical Backbone of Conscientious Refusal

    DEFF Research Database (Denmark)

    Munthe, Christian; Nielsen, Morten Ebbe Juul

    2017-01-01

    identity and the fostering of a critical atmosphere might provide some support, if no countervailing factors apply. One such factor is that a legal right to healthcare professionals’ conscientious refusal must comply with basic legal ethical tenets regarding the rule of law and equal treatment......This article analyzes the idea of a legal right to conscientious refusal for healthcare professionals from a basic legal ethical standpoint, using refusal to perform tasks related to legal abortion (in cases of voluntary employment) as a case in point. The idea of a legal right to conscientious...... refusal is distinguished from ideas regarding moral rights or reasons related to conscientious refusal, and none of the latter are found to support the notion of a legal right. Reasons for allowing some sort of room for conscientious refusal for healthcare professionals based on the importance of cultural...

  7. SEVA Linkers: A Versatile and Automatable DNA Backbone Exchange Standard for Synthetic Biology.

    Science.gov (United States)

    Kim, Se Hyeuk; Cavaleiro, Ana Mafalda; Rennig, Maja; Nørholm, Morten H H

    2016-10-21

    DNA vectors serve to maintain and select recombinant DNA in cell factories, and as design complexity increases, there is a greater need for well-characterized parts and methods for their assembly. Standards in synthetic biology are top priority, but standardizing molecular cloning contrasts flexibility, and different researchers prefer and master different molecular technologies. Here, we describe a new, highly versatile and automatable standard "SEVA linkers" for vector exchange. SEVA linkers enable backbone swapping with 20 combinations of classical enzymatic restriction/ligation, Gibson isothermal assembly, uracil excision cloning, and a nicking enzyme-based methodology we term SEVA cloning. SEVA cloning is a simplistic one-tube protocol for backbone swapping directly from plasmid stock solutions. We demonstrate the different performance of 30 plasmid backbones for small molecule and protein production and obtain more than 10-fold improvement from a four-gene biosynthetic pathway and 430-fold improvement with a difficult-to-express membrane protein. The standardized linkers and protocols add to the Standard European Vectors Architecture (SEVA) resource and are freely available to the synthetic biology community.

  8. Receptor structure-based discovery of non-metabolite agonists for the succinate receptor GPR91

    DEFF Research Database (Denmark)

    Trauelsen, Mette; Rexen Ulven, Elisabeth; Hjorth, Siv A

    2017-01-01

    OBJECTIVE: Besides functioning as an intracellular metabolite, succinate acts as a stress-induced extracellular signal through activation of GPR91 (SUCNR1) for which we lack suitable pharmacological tools. METHODS AND RESULTS: Here we first determined that the cis conformation of the succinate...... backbone is preferred and that certain backbone modifications are allowed for GPR91 activation. Through receptor modeling over the X-ray structure of the closely related P2Y1 receptor, we discovered that the binding pocket is partly occupied by a segment of an extracellular loop and that succinate...

  9. A Consistent Phylogenetic Backbone for the Fungi

    Science.gov (United States)

    Ebersberger, Ingo; de Matos Simoes, Ricardo; Kupczok, Anne; Gube, Matthias; Kothe, Erika; Voigt, Kerstin; von Haeseler, Arndt

    2012-01-01

    The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data—a common practice in phylogenomic analyses—introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses. PMID:22114356

  10. The Legal Ethical Backbone of Conscientious Refusal.

    Science.gov (United States)

    Munthe, Christian; Nielsen, Morten Ebbe Juul

    2017-01-01

    This article analyzes the idea of a legal right to conscientious refusal for healthcare professionals from a basic legal ethical standpoint, using refusal to perform tasks related to legal abortion (in cases of voluntary employment) as a case in point. The idea of a legal right to conscientious refusal is distinguished from ideas regarding moral rights or reasons related to conscientious refusal, and none of the latter are found to support the notion of a legal right. Reasons for allowing some sort of room for conscientious refusal for healthcare professionals based on the importance of cultural identity and the fostering of a critical atmosphere might provide some support, if no countervailing factors apply. One such factor is that a legal right to healthcare professionals' conscientious refusal must comply with basic legal ethical tenets regarding the rule of law and equal treatment, and this requirement is found to create serious problems for those wishing to defend the idea under consideration. We conclude that the notion of a legal right to conscientious refusal for any profession is either fundamentally incompatible with elementary legal ethical requirements, or implausible because it undermines the functioning of a related professional sector (healthcare) or even of society as a whole.

  11. A consistent phylogenetic backbone for the fungi.

    Science.gov (United States)

    Ebersberger, Ingo; de Matos Simoes, Ricardo; Kupczok, Anne; Gube, Matthias; Kothe, Erika; Voigt, Kerstin; von Haeseler, Arndt

    2012-05-01

    The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data-a common practice in phylogenomic analyses-introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses.

  12. Reliability-Based Optimization in Structural Engineering

    DEFF Research Database (Denmark)

    Enevoldsen, I.; Sørensen, John Dalsgaard

    1994-01-01

    In this paper reliability-based optimization problems in structural engineering are formulated on the basis of the classical decision theory. Several formulations are presented: Reliability-based optimal design of structural systems with component or systems reliability constraints, reliability-b...

  13. Distribution-Based Cluster Structure Selection.

    Science.gov (United States)

    Yu, Zhiwen; Zhu, Xianjun; Wong, Hau-San; You, Jane; Zhang, Jun; Han, Guoqiang

    2017-11-01

    The objective of cluster structure ensemble is to find a unified cluster structure from multiple cluster structures obtained from different datasets. Unfortunately, not all the cluster structures contribute to the unified cluster structure. This paper investigates the problem of how to select the suitable cluster structures in the ensemble which will be summarized to a more representative cluster structure. Specifically, the cluster structure is first represented by a mixture of Gaussian distributions, the parameters of which are estimated using the expectation-maximization algorithm. Then, several distribution-based distance functions are designed to evaluate the similarity between two cluster structures. Based on the similarity comparison results, we propose a new approach, which is referred to as the distribution-based cluster structure ensemble (DCSE) framework, to find the most representative unified cluster structure. We then design a new technique, the distribution-based cluster structure selection strategy (DCSSS), to select a subset of cluster structures. Finally, we propose using a distribution-based normalized hypergraph cut algorithm to generate the final result. In our experiments, a nonparametric test is adopted to evaluate the difference between DCSE and its competitors. We adopt 20 real-world datasets obtained from the University of California, Irvine and knowledge extraction based on evolutionary learning repositories, and a number of cancer gene expression profiles to evaluate the performance of the proposed methods. The experimental results show that: 1) DCSE works well on the real-world datasets and 2) DCSE based on DCSSS can further improve the performance of the algorithm.

  14. Palaeosols as geomorphic backbones in landscape development

    Science.gov (United States)

    van mourik, J. M.; Cammeraat, L. H.

    2012-04-01

    Landscapes in SE Spain are strongly affected by calcretes. Calcretes are especially found in many geomorphic positions, often attached to a backwall which are part of hill or ridge systems. These calcretes which can be perceived as palaeosols with a petrocalcic nature and that are typical for soil formation processes under a non-leaching semi-arid or sub-humid environment. Different phases of calcrete development have existed over time which is expressed by their reoccurrence at up to six geomorphic levels in the landscape. They develop on both calcaric and non-calcaric rocks and are often disconnected from their original back wall by backward gully erosion. They have typical low angular concave surfaces and be followed over long distances in the landscape . They can be related to different paleo-geomorphic surfaces corresponding to former base levels of erosion, which were later dissected through regional uplift or tectonic activity or climate change. Especially the highest paleosols are badly preserved and only parts of the lower sub horizons of the petrocalcic are preserved in these cases. The lithifiedpetrocalcic horizons can be several meters thick and also shows a very high spatial heterogeneity in thickness or degree of induration. In lower landscape positions they are often seamless connected to river terraces which can also be lithified at their surface. In these positions also other types of paleosols occur where luvisols and stagnosols are overprinted with calcic properties, indicating changing climatic conditions during their formation, from leaching wet conditions earlier in late Pleistocene to non-leaching conditions under current conditions. Even spodic horizons can be observed at some locations in sandy and gravelly river terraces, often overlain by current calcic horizon development in the topsoil.

  15. Protein structure refinement using a quantum mechanics-based chemical shielding predictor.

    Science.gov (United States)

    Bratholm, Lars A; Jensen, Jan H

    2017-03-01

    The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of a protein backbone and CB chemical shifts (ProCS15, PeerJ , 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1-0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If an amino acid specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiments that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differ in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural

  16. Backbone assignments for the SPOUT methyltransferase MTT Tm , a knotted protein from Thermotoga maritima.

    Science.gov (United States)

    Burban, David J; Jennings, Patricia A

    2017-10-01

    The SPOUT family of methyltransferase proteins is noted for containing a deep trefoil knot in their defining backbone fold. This unique fold is of high interest for furthering the understanding of knots in proteins. Here, we report the 1 H, 13 C, 15 N assignments for MTT Tm , a canonical member of the SPOUT family. This protein is unique, as it is one of the smallest members of the family, making it an ideal system for probing the unique properties of the knot. Our present work represents the foundation for further studies into the topology of MTT Tm , and understanding how its structure affects both its folding and function.

  17. Neurocardiology: Structure-Based Function.

    Science.gov (United States)

    Ardell, Jeffrey L; Armour, John Andrew

    2016-09-15

    Cardiac control is mediated via a series of reflex control networks involving somata in the (i) intrinsic cardiac ganglia (heart), (ii) intrathoracic extracardiac ganglia (stellate, middle cervical), (iii) superior cervical ganglia, (iv) spinal cord, (v) brainstem, and (vi) higher centers. Each of these processing centers contains afferent, efferent, and local circuit neurons, which interact locally and in an interdependent fashion with the other levels to coordinate regional cardiac electrical and mechanical indices on a beat-to-beat basis. This control system is optimized to respond to normal physiological stressors (standing, exercise, and temperature); however, it can be catastrophically disrupted by pathological events such as myocardial ischemia. In fact, it is now recognized that autonomic dysregulation is central to the evolution of heart failure and arrhythmias. Autonomic regulation therapy is an emerging modality in the management of acute and chronic cardiac pathologies. Neuromodulation-based approaches that target select nexus points of this hierarchy for cardiac control offer unique opportunities to positively affect therapeutic outcomes via improved efficacy of cardiovascular reflex control. As such, understanding the anatomical and physiological basis for such control is necessary to implement effectively novel neuromodulation therapies. © 2016 American Physiological Society. Compr Physiol 6:1635-1653, 2016. Copyright © 2016 John Wiley & Sons, Inc.

  18. Towards fully automated structure-based NMR resonance assignment of 15N-labeled proteins from automatically picked peaks

    KAUST Repository

    Jang, Richard

    2011-03-01

    In NMR resonance assignment, an indispensable step in NMR protein studies, manually processed peaks from both N-labeled and C-labeled spectra are typically used as inputs. However, the use of homologous structures can allow one to use only N-labeled NMR data and avoid the added expense of using C-labeled data. We propose a novel integer programming framework for structure-based backbone resonance assignment using N-labeled data. The core consists of a pair of integer programming models: one for spin system forming and amino acid typing, and the other for backbone resonance assignment. The goal is to perform the assignment directly from spectra without any manual intervention via automatically picked peaks, which are much noisier than manually picked peaks, so methods must be error-tolerant. In the case of semi-automated/manually processed peak data, we compare our system with the Xiong-Pandurangan-Bailey- Kellogg\\'s contact replacement (CR) method, which is the most error-tolerant method for structure-based resonance assignment. Our system, on average, reduces the error rate of the CR method by five folds on their data set. In addition, by using an iterative algorithm, our system has the added capability of using the NOESY data to correct assignment errors due to errors in predicting the amino acid and secondary structure type of each spin system. On a publicly available data set for human ubiquitin, where the typing accuracy is 83%, we achieve 91% accuracy, compared to the 59% accuracy obtained without correcting for such errors. In the case of automatically picked peaks, using assignment information from yeast ubiquitin, we achieve a fully automatic assignment with 97% accuracy. To our knowledge, this is the first system that can achieve fully automatic structure-based assignment directly from spectra. This has implications in NMR protein mutant studies, where the assignment step is repeated for each mutant. © Copyright 2011, Mary Ann Liebert, Inc.

  19. Quantification of the curvature of the spine by a method based on the projection harmful structured light; Cuantificacion de la curvatura de la columna vertebral mediante un metodo no lesivo basado en la proyeccion de luz estructurada

    Energy Technology Data Exchange (ETDEWEB)

    Lopez de la O, F. J.; Cibrian, R.; Salvador, R.; Gonzalez-Pena, R.; Minguez, M. F.; Pino, L.; Jover, A.; Guillen, J.; Reinado, D.; Cortina, T.; Chinillach, N.; Dalmases, F.; Romero, M. C.; Martinez-Celerio, R.; Diez, R.; Rosello, J.

    2011-07-01

    This paper shows the application of a method for determining harmful surface topography based on structured light, to find back the topography of the variables that create a characteristic pattern and differentiating between different groups. Once the topography has calculated three angles along the backbone that characterize its curvature. This pattern has been determined for two study groups, one of athletes and other patients with scoliosis.

  20. On the role of thermal backbone fluctuations in myoglobin ligand gate dynamics

    Science.gov (United States)

    Krokhotin, Andrey; Niemi, Antti J.; Peng, Xubiao

    2013-05-01

    We construct an energy function that describes the crystallographic structure of sperm whale myoglobin backbone. As a model in our construction, we use the Protein Data Bank entry 1ABS that has been measured at liquid helium temperature. Consequently, the thermal B-factor fluctuations are very small, which is an advantage in our construction. The energy function that we utilize resembles that of the discrete nonlinear Schrödinger equation. Likewise, ours supports topological solitons as local minimum energy configurations. We describe the 1ABS backbone in terms of topological solitons with a precision that deviates from 1ABS by an average root-mean-square distance, which is less than the experimentally observed Debye-Waller B-factor fluctuation distance. We then subject the topological multi-soliton solution to extensive numerical heating and cooling experiments, over a very wide range of temperatures. We concentrate in particular to temperatures above 300 K and below the Θ-point unfolding temperature, which is around 348 K. We confirm that the behavior of the topological multi-soliton is fully consistent with Anfinsen's thermodynamic principle, up to very high temperatures. We observe that the structure responds to an increase of temperature consistently in a very similar manner. This enables us to characterize the onset of thermally induced conformational changes in terms of three distinct backbone ligand gates. One of the gates is made of the helix F and the helix E. The two other gates are chosen similarly, when open they provide a direct access route for a ligand to reach the heme. We find that out of the three gates we investigate, the one which is formed by helices B and G is the most sensitive to thermally induced conformational changes. Our approach provides a novel perspective to the important problem of ligand entry and exit.

  1. Reliability based Design of Coastal Structures

    DEFF Research Database (Denmark)

    Burcharth, H. F.

    2003-01-01

    Conventional design practice for coastal structures is deterministic in nature and is based on the concept of a design load which should not exceed the resistance (carrying capacity) of the structure. The design load is usually defined on a probabilistic basis as a characteristic value of the loa...

  2. The determinants of bond angle variability in protein/peptide backbones: A comprehensive statistical/quantum mechanics analysis.

    Science.gov (United States)

    Improta, Roberto; Vitagliano, Luigi; Esposito, Luciana

    2015-11-01

    The elucidation of the mutual influence between peptide bond geometry and local conformation has important implications for protein structure refinement, validation, and prediction. To gain insights into the structural determinants and the energetic contributions associated with protein/peptide backbone plasticity, we here report an extensive analysis of the variability of the peptide bond angles by combining statistical analyses of protein structures and quantum mechanics calculations on small model peptide systems. Our analyses demonstrate that all the backbone bond angles strongly depend on the peptide conformation and unveil the existence of regular trends as function of ψ and/or φ. The excellent agreement of the quantum mechanics calculations with the statistical surveys of protein structures validates the computational scheme here employed and demonstrates that the valence geometry of protein/peptide backbone is primarily dictated by local interactions. Notably, for the first time we show that the position of the H(α) hydrogen atom, which is an important parameter in NMR structural studies, is also dependent on the local conformation. Most of the trends observed may be satisfactorily explained by invoking steric repulsive interactions; in some specific cases the valence bond variability is also influenced by hydrogen-bond like interactions. Moreover, we can provide a reliable estimate of the energies involved in the interplay between geometry and conformations. © 2015 Wiley Periodicals, Inc.

  3. Higher order structural effects stabilizing the reverse watson-crick guanine-cytosine base pair in functional RNAs

    KAUST Repository

    Chawla, Mohit

    2013-10-10

    The G:C reverse Watson-Crick (W:W trans) base pair, also known as Levitt base pair in the context of tRNAs, is a structurally and functionally important base pair that contributes to tertiary interactions joining distant domains in functional RNA molecules and also participates in metabolite binding in riboswitches. We previously indicated that the isolated G:C W:W trans base pair is a rather unstable geometry, and that dicationic metal binding to the Guanine base or posttranscriptional modification of the Guanine can increase its stability. Herein, we extend our survey and report on other H-bonding interactions that can increase the stability of this base pair. To this aim, we performed a bioinformatics search of the PDB to locate all the occurencies of G:C trans base pairs. Interestingly, 66% of the G:C trans base pairs in the PDB are engaged in additional H-bonding interactions with other bases, the RNA backbone or structured water molecules. High level quantum mechanical calculations on a data set of representative crystal structures were performed to shed light on the structural stability and energetics of the various crystallographic motifs. This analysis was extended to the binding of the preQ1 metabolite to a preQ1-II riboswitch. 2013 The Author(s).

  4. Backbone tuning in indenylidene–ruthenium complexes bearing an unsaturated N-heterocyclic carbene

    Directory of Open Access Journals (Sweden)

    César A. Urbina-Blanco

    2010-11-01

    Full Text Available The steric and electronic influence of backbone substitution in IMes-based (IMes = 1,3-bis(2,4,6-trimethylphenylimidazol-2-ylidene N-heterocyclic carbenes (NHC was probed by synthesizing the [RhCl(CO2(NHC] series of complexes to quantify experimentally the Tolman electronic parameter (electronic and the percent buried volume (%Vbur, steric parameters. The corresponding ruthenium–indenylidene complexes were also synthesized and tested in benchmark metathesis transformations to establish possible correlations between reactivity and NHC electronic and steric parameters.

  5. Biocompatible Soft Nanoparticles with Multiple Morphologies Obtained from Nanoprecipitation of Amphiphilic Graft Copolymers in a Backbone-Selective Solvent.

    Science.gov (United States)

    Le Fer, Gaëlle; Le Cœur, Clémence; Guigner, Jean-Michel; Amiel, Catherine; Volet, Gisèle

    2017-03-21

    Stealth nanocarriers are a promising technology for the treatment of diseases. However, the preparation and characterization of well-defined soft nanoparticulate systems remain challenging. Here we describe a platform of amphiphilic graft copolymers leading to nanoparticles with multiple morphologies and the role of the hydrophilic backbone in their interaction with a model protein. The amphiphilic graft copolymers platform was composed of hydrophilic backbone poly(2-methyl-2-oxazoline-co-2-pentyl-2-oxazoline) (P(MeOx-co-PentOx)), prepared via cationic ring-opening polymerization. Hydrophobic poly(d,l-lactide) (PLA) chains were grafted on the backbone via Huisgen 1,3-dipolar cycloaddition. The "click" copper-catalyzed cycloaddition reactions of azides with alkynes (CuAAC) were successfully carried out, and a series of amphiphilic copolymers were prepared containing a backbone with a number-average molecular weight of 14.2 × 10 3 g mol -1 and different hydrophobic PLA grafts with various molecular weights (2.8 × 10 3 -12.4 × 10 3 g mol -1 ). These original architectures of copolymers, when nanoprecipitated in water, the backbone-selective solvent, allowed us to obtain various structures of nanoparticles with a hydrodynamic diameter in the range of 65-99 nm. More interestingly, a plurality of morphologies going from unilamellar, multilamellar, and large compound vesicles to core-shell nanoparticles and depending on the PLA molecular weights were evidenced by combining cryo-transmission electron microscopy (cryo-TEM) and small-angle neutron scattering (SANS) studies. A first evaluation of their stealthiness by studying the stability and the interaction of these nano-objects with a model protein revealed the role played by the P(MeOx-co-PentOx) in these interactions, demonstrating the utility of this amphiphilic graft copolymers platform with well-defined architectures for the design of nanocarriers in drug delivery applications.

  6. First-line HIV treatment: evaluation of backbone choice and its budget impact

    Directory of Open Access Journals (Sweden)

    Orietta Zaniolo

    2013-06-01

    Full Text Available OBJECTIVE: The gradual increase of persons living with HIV, mainly due to the reduced mortality achieved with effective antiretroviral therapies, calls for increased rationality and awareness in health resources consumption also during the early illness phases. Aim of this work is the estimation of the budget impact related to the variation in backbone prescribing trends in naïve patients.METHODS: Target population is the number of patients starting antiretroviral therapy each year, according to the Italian HIV surveillance registry, excluding patients receiving non-authorized or non-recommended regimens. We modeled 3-year mortality and durability rates on a dynamic cohort, basing on international literature. A prevalent patients analysis has also been conducted, for which the model is fed by a closed cohort consisting of all the patients without experience of virologic failure. The aim of this collateral analysis is to estimate the difference in current annual expenditures if the past prescription trends for patients starting therapy would have led to the evaluated hypothetical scenarios. Current Italian market shares of triple regimens containing first-choice or alternative backbones (tenofovir/emtricitabine, abacavir/lamivudine, tenofovir/lamivudine and zidovudine/lamivudine are compared to three hypothetical scenarios (base-case, minimum and maximum in which increasing shares of patients eligible to abacavir/lamivudine start first line treatment with this backbone. Annual cost for each regimen comprises drugs acquisition under hospital pricing rules, monitoring exams and preventive tests, valued basing on regional reimbursement tariffs.RESULTS: According to current prescribing trends, in the next three years about 13,000 patients starting HIV therapy will receive tenofovir/emtricitabine (83% of the target population, and minor portions other regimens (9% abacavir/lamivudine, 8% zidovudine/lamivudine. Patients that would be eligible to

  7. Protein structure--based drug design.

    Science.gov (United States)

    Whittle, P J; Blundell, T L

    1994-01-01

    Design cycles will undoubtedly play an increasingly important role in drug discovery in the coming years, as the amount of structural information on protein targets continues to rise. However, the traditional method of drug discovery, based upon random screening and systematic modification of leads by medicinal chemistry techniques, will probably not be abandoned completely because it has a potentially important advantage over more structure-based methods--namely, leads identified in this way are unlikely to show a close resemblance to the natural ligand or substrate. They may, therefore, have advantages in terms of patent novelty, selectivity, or pharmacokinetic profile. However, such leads could then serve as the basis for structure-based, rational modification programs, in which their interactions with target receptors are defined (as we have described) and improved molecules are designed. A final important point to be made about structure-based design in drug discovery is that, while it can be of great use in the initial process of identifying ligands with improved affinity and selectivity in vitro, it can usually say very little about other essential aspects of the drug discovery process, e.g. the need to achieve an adequate pharmacokinetic profile and low toxicity in vivo. This observation reminds us that drug design is a multidisciplinary process, involving molecular biologists, biochemists, pharmacologists, organic chemists, crystallographers, and others. In order to be effective, therefore, structure-based design must be properly integrated into the overall discovery effort.

  8. NMR backbone resonance assignments of the prodomain variants of BDNF in the urea denatured state.

    Science.gov (United States)

    Wang, Jing; Bains, Henrietta; Anastasia, Agustin; Bracken, Clay

    2018-04-01

    Brain derived neurotrophic factor (BDNF) is a member of the neurotrophin family of proteins which plays a central role in neuronal survival, growth, plasticity and memory. A single Val66Met variant has been identified in the prodomain of human BDNF that is associated with anxiety, depression and memory disorders. The structural differences within the full-length prodomain Val66 and Met66 isoforms could shed light on the mechanism of action of the Met66 and its impact on the development of neuropsychiatric-associated disorders. In the present study, we report the backbone 1 H, 13 C, and 15 N NMR assignments of both full-length Val66 and Met66 prodomains in the presence of 2 M urea. These conditions were utilized to suppress residual structure and aid subsequent native state structural investigations aimed at mapping and identifying variant-dependent conformational differences under native-state conditions.

  9. Data base on structural materials aging properties

    International Nuclear Information System (INIS)

    Oland, C.B.

    1992-01-01

    The US Nuclear Regulatory Commission has initiated a Structural Aging Program at the Oak Ridge National Laboratory to identify potential structural safety issues related to continued service of nuclear power plants and to establish criteria for evaluating and resolving these issues. One of the tasks in this program focuses on the establishment of a Structural Materials Information Center where long-term and environment-dependent properties of concretes and other structural materials are being collected and assembled into a data base. These properties will be used to evaluate the current condition of critical structural components in nuclear power plants and to estimate the future performance of these materials during the continued service period

  10. IPE data base structure and insights

    International Nuclear Information System (INIS)

    Lehner, J.; Youngblood, R.

    1994-01-01

    A data base (the open-quotes IPE Insights Data Baseclose quotes), has been developed that stores data obtained from the Individual Plant Examinations (IPEs) which licensees of nuclear power plants are conducting in response to the Nuclear Regulatory Commission's (NRC) Generic Letter GL88-20. The data base, which is a collection of linked dBase files, stores information about individual plant designs, core damage frequency, and containment performance in a uniform, structured way. This data base can be queried and used as a computational tool to derive insights regarding the plants for which data is stored. This paper sets out the objectives of the IPE Insights Data Base, describes its structure and contents, illustrates sample queries, and discusses possible future uses

  11. Empirical correlation between protein backbone 15N and 13C secondary chemical shifts and its application to nitrogen chemical shift re-referencing

    International Nuclear Information System (INIS)

    Wang Liya; Markley, John L.

    2009-01-01

    The linear analysis of chemical shifts (LACS) has provided a robust method for identifying and correcting 13 C chemical shift referencing problems in data from protein NMR spectroscopy. Unlike other approaches, LACS does not require prior knowledge of the three-dimensional structure or inference of the secondary structure of the protein. It also does not require extensive assignment of the NMR data. We report here a way of extending the LACS approach to 15 N NMR data from proteins, so as to enable the detection and correction of inconsistencies in chemical shift referencing for this nucleus. The approach is based on our finding that the secondary 15 N chemical shift of the backbone nitrogen atom of residue i is strongly correlated with the secondary chemical shift difference (experimental minus random coil) between the alpha and beta carbons of residue i - 1. Thus once alpha and beta 13 C chemical shifts are available (their difference is referencing error-free), the 15 N referencing can be validated, and an appropriate offset correction can be derived. This approach can be implemented prior to a structure determination and can be used to analyze potential referencing problems in database data not associated with three-dimensional structure. Application of the LACS algorithm to the current BMRB protein chemical shift database, revealed that nearly 35% of the BMRB entries have δ 15 N values mis-referenced by over 0.7 ppm and over 25% of them have δ 1 H N values mis-referenced by over 0.12 ppm. One implication of the findings reported here is that a backbone 15 N chemical shift provides a better indicator of the conformation of the preceding residue than of the residue itself

  12. Comparison of sequence-based and structure-based phylogenetic ...

    Indian Academy of Sciences (India)

    Prakash

    pairs of proteins which are inputs into the construction of phylogenetic trees. We find that correlation between the structure-based dissimilarity measures and the sequence-based dissimilarity measures is usually good if the sequence similarity among the homologues is about 30% or more. For protein families with low ...

  13. Backbone Dynamics of the Monomeric λ Repressor Denatured State Ensemble under Nondenaturing Conditions†

    Science.gov (United States)

    Chugha, Preeti; Oas, Terrence G.

    2014-01-01

    Oxidizing two native methionine residues predominantly populates the denatured state of monomeric λ repressor (MetO-λLS) under nondenaturing conditions. NMR was used to characterize the secondary structure and dynamics of MetO-λLS in standard phosphate buffer. 13Cα and 1Hα chemical shift indices reveal a region of significant helicity between residues 9 and 29. This helical content is further supported by the observation of medium-range amide NOEs. The remaining residues do not exhibit significant helicity as determined by NMR. We determined 15N relaxation parameters for 64 of 85 residues at 600 and 800 MHz. There are two distinct regions of reduced flexibility, residues 8–32 in the N-terminal third and residues 50–83 in the C-terminal third. The middle third, residues 33–50, has greater flexibility. We have analyzed the amplitude of the backbone motions in terms of the physical properties of the amino acids and conclude that conformational restriction of the backbone MetO-λLS is due to nascent helix formation in the region corresponding to native helix 1. The bulkiness of amino acid residues in the C-terminal third leads to the potential for hydrophobic interactions, which is suggested by chemical exchange detected by the difference in spectral density J(0) at the two static magnetic fields. The more flexible middle region is the result of a predominance of small side chains in this region. PMID:17260944

  14. Vibrational Based Inspection of Civil Engineering Structures

    DEFF Research Database (Denmark)

    Rytter, Anders

    and Structural Engineering at the University of Aalborg since the beginning of 1992. Both projects have been supported by the Danish Technical Research Council. Further, the first mentioned project was supported by the Danish Energy Agency. Their financial support is gratefully acknowledged.......The thesis has been written in relation to two different research projects. Firstly, an offshore test programme, Integrated Experimental/Numerical Analysis of the Dynamic behavior of offshore structures, which was performed at the department of Building Technology and Structural Engineering...... at the University of Aalborg from 1988 to 1991. Secondly, a research project, In-Field Vibration Based Inspection of Civil Engineering Structures, which has been performed as a pilot project by the Consulting Engineers Rambøll, Hannemann and Højlund in cooperation with the department of Building Technology...

  15. Electronic structure of Fe-based superconductors

    Indian Academy of Sciences (India)

    2015-05-29

    May 29, 2015 ... Fe-based superconductors have drawn much attention during the last decade due to the presence of superconductivity in materials containing the magnetic element, Fe, and the coexistence of superconductivity and magnetism. Extensive study of the electronic structure of these systems suggested the ...

  16. Electronic structure of Fe-based superconductors

    Indian Academy of Sciences (India)

    Abstract. Fe-based superconductors have drawn much attention during the last decade due to the presence of superconductivity in materials containing the magnetic element, Fe, and the coexistence of superconductivity and magnetism. Extensive study of the electronic structure of these systems suggested the dominant ...

  17. Effect of oligonucleic acid (ONA) backbone features on assembly of ONA-star polymer conjugates: a coarse-grained molecular simulation study.

    Science.gov (United States)

    Condon, Joshua E; Jayaraman, Arthi

    2017-10-04

    Understanding the impact of incorporating new physical and chemical features in oligomeric DNA mimics, termed generally as "oligonucleic acids" (ONAs), on their structure and thermodynamics will be beneficial in designing novel materials for a variety of applications. In this work, we conduct coarse-grained molecular simulations of ONA-star polymer conjugates with varying ONA backbone flexibility, ONA backbone charge, and number of arms in the star polymer at a constant ONA strand volume fraction to elucidate the effect of these design parameters on the thermodynamics and assembly of multi-arm ONA-star polymer conjugates. We quantify the thermo-reversible behavior of the ONA-star polymer conjugates by quantifying the hybridization of the ONA strands in the system as a function of temperature (i.e. melting curve). Additionally, we characterize the assembly of the ONA-star polymer conjugates by tracking cluster formation and percolation as a function of temperature, as well as cluster size distribution at temperatures near the assembly transition region. The key results are as follows. The melting temperature (T m ) of the ONA strands decreases upon going from a neutral to a charged ONA backbone and upon increasing flexibility of the ONA backbone. Similar behavior is seen for the assembly transition temperature (T a ) with varying ONA backbone charge and flexibility. While the number of arms in the ONA-star polymer conjugate has a negligible effect on the ONA T m in these systems, as the number of ONA-star polymer arms increase, the assembly temperature T a increases and local ordering in the assembled state improves. By understanding how factors like ONA backbone charge, backbone flexibility, and ONA-star polymer conjugate architecture impact the behavior of ONA-star polymer conjugate systems, we can better inform how the selection of ONA chemistry will influence resulting ONA-star polymer assembly.

  18. Protein Structural Analysis via Mass Spectrometry-Based Proteomics

    Science.gov (United States)

    Artigues, Antonio; Nadeau, Owen W.; Rimmer, Mary Ashley; Villar, Maria T.; Du, Xiuxia; Fenton, Aron W.; Carlson, Gerald M.

    2017-01-01

    Modern mass spectrometry (MS) technologies have provided a versatile platform that can be combined with a large number of techniques to analyze protein structure and dynamics. These techniques include the three detailed in this chapter: 1) hydrogen/deuterium exchange (HDX), 2) limited proteolysis, and 3) chemical crosslinking (CX). HDX relies on the change in mass of a protein upon its dilution into deuterated buffer, which results in varied deuterium content within its backbone amides. Structural information on surface exposed, flexible or disordered linker regions of proteins can be achieved through limited proteolysis, using a variety of proteases and only small extents of digestion. CX refers to the covalent coupling of distinct chemical species and has been used to analyze the structure, function and interactions of proteins by identifying crosslinking sites that are formed by small multi-functional reagents, termed crosslinkers. Each of these MS applications is capable of revealing structural information for proteins when used either with or without other typical high resolution techniques, including NMR and X-ray crystallography. PMID:27975228

  19. Geography-based structural analysis of the Internet

    Energy Technology Data Exchange (ETDEWEB)

    Kasiviswanathan, Shiva [Los Alamos National Laboratory; Eidenbenz, Stephan [Los Alamos National Laboratory; Yan, Guanhua [Los Alamos National Laboratory

    2010-01-01

    In this paper, we study some geographic aspects of the Internet. We base our analysis on a large set of geolocated IP hop-level session data (including about 300,000 backbone routers, 150 million end hosts, and 1 billion sessions) that we synthesized from a variety of different input sources such as US census data, computer usage statistics, Internet market share data, IP geolocation data sets, CAJDA's Skitter data set for backbone connectivity, and BGP routing tables. We use this model to perform a nationwide and statewide geographic analysis of the Internet. Our main observations are: (1) There is a dominant coast-to-coast pattern in the US Internet traffic. In fact, in many instances even if the end-devices are not near either coast, still the traffic between them takes a long detour through the coasts. (2) More than half of the Internet paths are inflated by 100% or more compared to their corresponding geometric straight-line distance. This circuitousness makes the average ratio between the routing distance and geometric distance big (around 10). (3) The weighted mean hop count is around 5, but the hop counts are very loosely correlated with the distances. The weighted mean AS count (number of ASes traversed) is around 3. (4) The AS size and the AS location number distributions are heavy-tailed and strongly correlated. Most of the ASes are medium sized and there is a wide variability in the geographic dispersion size (measured in terms of the convex hull area) of these ASes.

  20. NMR in structure-based drug design.

    Science.gov (United States)

    Carneiro, Marta G; Ab, Eiso; Theisgen, Stephan; Siegal, Gregg

    2017-11-08

    NMR spectroscopy is a powerful technique that can provide valuable structural information for drug discovery endeavors. Here, we discuss the strengths (and limitations) of NMR applications to structure-based drug discovery, highlighting the different levels of resolution and throughput obtainable. Additionally, the emerging field of paramagnetic NMR in drug discovery and recent developments in approaches to speed up and automate protein-observed NMR data collection and analysis are discussed. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  1. Investigating the Tradeoffs between Power Consumption and Quality of Service in a Backbone Network

    Directory of Open Access Journals (Sweden)

    Erol Gelenbe

    2013-05-01

    Full Text Available Energy saving in networks has traditionally focussed on reducing battery consumption through smart wireless network design. Recently, researchers have turned their attention to the energy cost and carbon emissions of the backbone network that both fixed and mobile communications depend on, proposing primarily mechanisms that turn equipments OFF or put them into deep sleep. This is an effective way of saving energy, provided that the nodes can return to working condition quickly, but it introduces increased delays and packet losses that directly affect the quality of communication experienced by the users. Here we investigate the associated tradeoffs between power consumption and quality of service in backbone networks that employ deep sleep energy savings. We examine these tradeoffs by conducting experiments on a real PC-based network topology, where nodes are put into deep sleep at random times and intervals, resulting in a continuously changing network with reduced total power consumption. The average power consumption, the packet loss and the average delay of this network are examined with respect to the average value of the ON rate and the ON/OFF cycle of the nodes.

  2. Marburg virus VP35 can both fully coat the backbone and cap the ends of dsRNA for interferon antagonism.

    Directory of Open Access Journals (Sweden)

    Shridhar Bale

    2012-09-01

    Full Text Available Filoviruses, including Marburg virus (MARV and Ebola virus (EBOV, cause fatal hemorrhagic fever in humans and non-human primates. All filoviruses encode a unique multi-functional protein termed VP35. The C-terminal double-stranded (dsRNA-binding domain (RBD of VP35 has been implicated in interferon antagonism and immune evasion. Crystal structures of the VP35 RBD from two ebolaviruses have previously demonstrated that the viral protein caps the ends of dsRNA. However, it is not yet understood how the expanses of dsRNA backbone, between the ends, are masked from immune surveillance during filovirus infection. Here, we report the crystal structure of MARV VP35 RBD bound to dsRNA. In the crystal structure, molecules of dsRNA stack end-to-end to form a pseudo-continuous oligonucleotide. This oligonucleotide is continuously and completely coated along its sugar-phosphate backbone by the MARV VP35 RBD. Analysis of dsRNA binding by dot-blot and isothermal titration calorimetry reveals that multiple copies of MARV VP35 RBD can indeed bind the dsRNA sugar-phosphate backbone in a cooperative manner in solution. Further, MARV VP35 RBD can also cap the ends of the dsRNA in solution, although this arrangement was not captured in crystals. Together, these studies suggest that MARV VP35 can both coat the backbone and cap the ends, and that for MARV, coating of the dsRNA backbone may be an essential mechanism by which dsRNA is masked from backbone-sensing immune surveillance molecules.

  3. UV-POSIT: Web-Based Tools for Rapid and Facile Structural Interpretation of Ultraviolet Photodissociation (UVPD) Mass Spectra.

    Science.gov (United States)

    Rosenberg, Jake; Parker, W Ryan; Cammarata, Michael B; Brodbelt, Jennifer S

    2018-04-06

    UV-POSIT (Ultraviolet Photodissociation Online Structure Interrogation Tools) is a suite of web-based tools designed to facilitate the rapid interpretation of data from native mass spectrometry experiments making use of 193 nm ultraviolet photodissociation (UVPD). The suite includes four separate utilities which assist in the calculation of fragment ion abundances as a function of backbone cleavage sites and sequence position; the localization of charge sites in intact proteins; the calculation of hydrogen elimination propensity for a-type fragment ions; and mass-offset searching of UVPD spectra to identify unknown modifications and assess false positive fragment identifications. UV-POSIT is implemented as a Python/Flask web application hosted at http://uv-posit.cm.utexas.edu . UV-POSIT is available under the MIT license, and the source code is available at https://github.com/jarosenb/UV_POSIT . Graphical Abstract.

  4. Deployable structures for a human lunar base

    Science.gov (United States)

    Gruber, Petra; Häuplik, Sandra; Imhof, Barbara; Özdemir, Kürsad; Waclavicek, Rene; Perino, Maria Antoinetta

    2007-06-01

    The study Lunar exploration architecture—deployable structures for a lunar base was performed within the Alcatel Alenia Space “Lunar Exploration Architecture” study for the European Space Agency. The purpose of the study was to investigate bionic concepts applicable to deployable structures and to interpret the findings for possible implementation concepts. The study aimed at finding innovative solutions for deployment possibilities. Translating folding/unfolding principles from nature, candidate geometries were developed and researched using models, drawings and visualisations. The use of materials, joints between structural elements and construction details were investigated for these conceptual approaches. Reference scenarios were used to identify the technical and environmental conditions, which served as design drivers. Mechanical issues and the investigation of deployment processes narrowed the selection down to six chosen concepts. Their applicability was evaluated at a conceptual stage in relation to the timescale of the mission.

  5. Reliability Based Optimization of Structural Systems

    DEFF Research Database (Denmark)

    Sørensen, John Dalsgaard

    1987-01-01

    The optimization problem to design structural systems such that the reliability is satisfactory during the whole lifetime of the structure is considered in this paper. Some of the quantities modelling the loads and the strength of the structure are modelled as random variables. The reliability...... is estimated using first. order reliability methods ( FORM ). The design problem is formulated as the optimization problem to minimize a given cost function such that the reliability of the single elements satisfies given requirements or such that the systems reliability satisfies a given requirement....... For these optimization problems it is described how a sensitivity analysis can be performed. Next, new optimization procedures to solve the optimization problems are presented. Two of these procedures solve the system reliability based optimization problem sequentially using quasi-analytical derivatives. Finally...

  6. Backbones of evolutionary history test biodiversity theory for microbes.

    Science.gov (United States)

    O'Dwyer, James P; Kembel, Steven W; Sharpton, Thomas J

    2015-07-07

    Identifying the ecological and evolutionary mechanisms that determine biological diversity is a central question in ecology. In microbial ecology, phylogenetic diversity is an increasingly common and relevant means of quantifying community diversity, particularly given the challenges in defining unambiguous species units from environmental sequence data. We explore patterns of phylogenetic diversity across multiple bacterial communities drawn from different habitats and compare these data to evolutionary trees generated using theoretical models of biodiversity. We have two central findings. First, although on finer scales the empirical trees are highly idiosyncratic, on coarse scales the backbone of these trees is simple and robust, consistent across habitats, and displays bursts of diversification dotted throughout. Second, we find that these data demonstrate a clear departure from the predictions of standard neutral theories of biodiversity and that an alternative family of generalized models provides a qualitatively better description. Together, these results lay the groundwork for a theoretical framework to connect ecological mechanisms to observed phylogenetic patterns in microbial communities.

  7. Intraresidue HNCA and COHNCA Experiments for Protein Backbone Resonance Assignment

    Science.gov (United States)

    Brutscher, Bernhard

    2002-05-01

    Two novel experiments, intra-HNCA and intra-COHNCA, are presented for sequential backbone resonance assignment of 13C, 15N labeled proteins. The advantage with respect to conventional pulse schemes is the suppression of the sequential 15N→13Cα coherence transfer pathway, which can be separately obtained from a HNCOCA correlation experiment. This results in a two-fold reduction of the number of detected correlation peaks. Spectral simplification is especially important for efficient automated assignment protocols as required in the context of high-throughput protein studies by NMR. The performance of the new experiments is demonstrated on an 18-kDa protein fragment of the E. coli sulfite reductase and compared to conventional techniques in terms of sensitivity and resolution.

  8. Design of an IPTV Multicast System for Internet Backbone Networks

    Directory of Open Access Journals (Sweden)

    T. H. Szymanski

    2010-01-01

    Full Text Available The design of an IPTV multicast system for the Internet backbone network is presented and explored through extensive simulations. In the proposed system, a resource reservation algorithm such as RSVP, IntServ, or DiffServ is used to reserve resources (i.e., bandwidth and buffer space in each router in an IP multicast tree. Each router uses an Input-Queued, Output-Queued, or Crosspoint-Queued switch architecture with unity speedup. A recently proposed Recursive Fair Stochastic Matrix Decomposition algorithm used to compute near-perfect transmission schedules for each IP router. The IPTV traffic is shaped at the sources using Application-Specific Token Bucker Traffic Shapers, to limit the burstiness of incoming network traffic. The IPTV traffic is shaped at the destinations using Application-Specific Playback Queues, to remove residual network jitter and reconstruct the original bursty IPTV video streams at each destination. All IPTV traffic flows are regenerated at the destinations with essentially zero delay jitter and essentially-perfect QoS. The destination nodes deliver the IPTV streams to the ultimate end users using the same IPTV multicast system over a regional Metropolitan Area Network. It is shown that all IPTV traffic is delivered with essentially-perfect end-to-end QoS, with deterministic bounds on the maximum delay and jitter on each video frame. Detailed simulations of an IPTV distribution system, multicasting several hundred high-definition IPTV video streams over several essentially saturated IP backbone networks are presented.

  9. Base isolation strategies for structures and components

    International Nuclear Information System (INIS)

    Varma, Veto; Reddy, G.R.; Vaze, K.K.; Kushwaha, H.S.

    2003-08-01

    In the present report the effect of laminated rubber bearing (LRB) system on the dynamic response of the structure was studied. A LRB system was designed and tested in the laboratory for its dynamic characteristics. Finite element analysis was also performed and based on this analysis, isolator for PHWR nuclear power plant was designed. Analysis of the building was performed with and without isolator. Comparison of responses was made in terms of frequencies, accelerations and displacements and floor response spectra. (author)

  10. Side chain and backbone contributions of Phe508 to CFTR folding

    Energy Technology Data Exchange (ETDEWEB)

    Thibodeau, Patrick H.; Brautigam, Chad A.; Machius, Mischa; Thomas, Philip J. (U. of Texas-SMED)

    2010-12-07

    Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an integral membrane protein, cause cystic fibrosis (CF). The most common CF-causing mutant, deletion of Phe508, fails to properly fold. To elucidate the role Phe508 plays in the folding of CFTR, missense mutations at this position were generated. Only one missense mutation had a pronounced effect on the stability and folding of the isolated domain in vitro. In contrast, many substitutions, including those of charged and bulky residues, disrupted folding of full-length CFTR in cells. Structures of two mutant nucleotide-binding domains (NBDs) reveal only local alterations of the surface near position 508. These results suggest that the peptide backbone plays a role in the proper folding of the domain, whereas the side chain plays a role in defining a surface of NBD1 that potentially interacts with other domains during the maturation of intact CFTR.

  11. Cross-correlated relaxation rates between protein backbone H–X dipolar interactions

    Energy Technology Data Exchange (ETDEWEB)

    Vögeli, Beat, E-mail: beat.vogeli@ucdenver.edu [University of Colorado Denver, Department of Biochemistry and Molecular Genetics (United States)

    2017-03-15

    The relaxation interference between dipole–dipole interactions of two separate spin pairs carries structural and dynamics information. In particular, when compared to individual dynamic behavior of those spin pairs, such cross-correlated relaxation (CCR) rates report on the correlation between the spin pairs. We have recently mapped out correlated motion along the backbone of the protein GB3, using CCR rates among and between consecutive H{sup N}–N and H{sup α}–C{sup α} dipole–dipole interactions. Here, we provide a detailed account of the measurement of the four types of CCR rates. All rates were obtained from at least two different pulse sequences, of which the yet unpublished ones are presented. Detailed comparisons between the different methods and corrections for unwanted pathways demonstrate that the averaged CCR rates are highly accurate and precise with errors of 1.5–3% of the entire value ranges.

  12. Cross-correlated relaxation rates between protein backbone H–X dipolar interactions

    International Nuclear Information System (INIS)

    Vögeli, Beat

    2017-01-01

    The relaxation interference between dipole–dipole interactions of two separate spin pairs carries structural and dynamics information. In particular, when compared to individual dynamic behavior of those spin pairs, such cross-correlated relaxation (CCR) rates report on the correlation between the spin pairs. We have recently mapped out correlated motion along the backbone of the protein GB3, using CCR rates among and between consecutive H N –N and H α –C α dipole–dipole interactions. Here, we provide a detailed account of the measurement of the four types of CCR rates. All rates were obtained from at least two different pulse sequences, of which the yet unpublished ones are presented. Detailed comparisons between the different methods and corrections for unwanted pathways demonstrate that the averaged CCR rates are highly accurate and precise with errors of 1.5–3% of the entire value ranges.

  13. A renormalization approach to describe charge transport in quasiperiodic dangling backbone ladder (DBL)-DNA molecules

    Energy Technology Data Exchange (ETDEWEB)

    Sarmento, R.G. [Departamento de Fisica, Universidade Federal do Rio Grande do Norte, 59072-970 Natal, RN (Brazil); Fulco, U.L. [Departamento de Biofisica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal, RN (Brazil); Albuquerque, E.L., E-mail: eudenilson@gmail.com [Departamento de Biofisica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal, RN (Brazil); Caetano, E.W.S. [Instituto Federal de Educacao, Ciencia e Tecnologia do Ceara, 60040-531 Fortaleza, CE (Brazil); Freire, V.N. [Departamento de Fisica, Universidade Federal do Ceara, 60455-760 Fortaleza, CE (Brazil)

    2011-10-31

    Highlights: → One-step renormalization approach to describe the DBL-DNA molecule. → Electronic tight-binding Hamiltonian model. → A quasiperiodic sequence to mimic the DNA nucleotides arrangement. → Electronic transmission spectra. → I-V characteristics. -- Abstract: We study the charge transport properties of a dangling backbone ladder (DBL)-DNA molecule focusing on a quasiperiodic arrangement of its constituent nucleotides forming a Rudin-Shapiro (RS) and Fibonacci (FB) Poly (CG) sequences, as well as a natural DNA sequence (Ch22) for the sake of comparison. Making use of a one-step renormalization process, the DBL-DNA molecule is modeled in terms of a one-dimensional tight-binding Hamiltonian to investigate its transmissivity and current-voltage (I-V) profiles. Beyond the semiconductor I-V characteristics, a striking similarity between the electronic transport properties of the RS quasiperiodic structure and the natural DNA sequence was found.

  14. Assignment of protein backbone resonances using connectivity, torsion angles and 13Cα chemical shifts

    International Nuclear Information System (INIS)

    Morris, Laura C.; Valafar, Homayoun; Prestegard, James H.

    2004-01-01

    A program is presented which will return the most probable sequence location for a short connected set of residues in a protein given just 13 C α chemical shifts (δ( 13 C α )) and data restricting the φ and ψ backbone angles. Data taken from both the BioMagResBank and the Protein Data Bank were used to create a probability density function (PDF) using a multivariate normal distribution in δ( 13 C α ), φ, and ψ space for each amino acid residue. Extracting and combining probabilities for particular amino acid residues in a short proposed sequence yields a score indicative of the correctness of the proposed assignment. The program is illustrated using several proteins for which structure and 13 C α chemical shift data are available

  15. Structure-based ligand design for flexible proteins: Application of new F-DycoBlock

    Science.gov (United States)

    Zhu, Jiang; Fan, Hao; Liu, Haiyan; Shi, Yunyu

    2001-11-01

    A method of structure-based ligand design - DycoBlock - has been proposed and tested by Liu et al.[1]. It was further improved by Zhu et al. and applied to design new selective inhibitors of cyclooxygenase 2 [2]. In the current work, we present a new methodology - F-DycoBlock that allows for the incorporation of receptor flexibility. During the designing procedure, both the receptor and molecular building blocks are subjected to the multiple-copy stochastic molecular dynamics (MCSMD) simulation [1], while the protein moves in the mean field of all copies. It is tested for two enzymes studied previously - cyclooxygenase 2 (COX-2) and human immunodeficiency type 1 (HIV-1) protease. To identify the applicability of F-DycoBlock, the binding protein structure was used as starting point to explore the conformational space around the bound state. This method can be easily extended to accommodate the flexibility in different degree. Four types of treatment of the receptor flexibility - all-atom restrained, backbone restrained, intramolecular hydrogen-bond restrained and active-site flexible - were tested with or without the grid approximation. Two inhibitors, SC-558 for COX-2 and L700417 for HIV-1 protease, are used in this testing study for comparison with previous results. The accuracy of recovery, binding energy, solvent accessible surface area (SASA) and positional root-mean-square (RMS) deviation are used as criteria. The results indicate that F-DycoBlock is a robust methodology for flexible drug design. It is particularly notable that the protein flexibility has been perfectly associated with each stage of drug design - search for the binding sites, dynamic assembly and optimization of candidate compounds. When all protein atoms were restrained, F-DycoBlock yielded higher accuracy of recovery than DycoBlock (100%). If backbone atoms were restrained, the same ratio of accuracy was achieved. Moreover, with the intramolecular hydrogen bonds restrained, reasonable

  16. Automated probabilistic method for assigning backbone resonances of (13C,15N)-labeled proteins

    Energy Technology Data Exchange (ETDEWEB)

    Lukin, Jonathan A. [Carnegie Mellon University, Department of Biological Sciences (United States); Gove, Andrew P.; Talukdar, Sarosh N. [Carnegie Mellon University, Robotics Institute (United States); Ho Chien [Carnegie Mellon University, Department of Biological Sciences (United States)

    1997-02-15

    We present a computer algorithm for the automated assignment of polypeptide backbone and 13C{beta} resonances of a protein of known primary sequence. Input to the algorithm consists of cross peaks from several 3D NMR experiments: HNCA, HN(CA)CO, HN(CA)HA,HNCACB, COCAH, HCA(CO)N, HNCO, HN(CO)CA, HN(COCA)HA, and CBCA(CO)NH. Data from these experiments performed on glutamine-binding protein are analyzed statistically using Bayes' theorem to yield objective probability scoring functions for matching chemical shifts. Such scoring is used in the first stage of the algorithm to combine cross peaks from the first five experiments to form intraresidue segments of chemical shifts{l_brace}Ni,HiN,Ci{alpha},Ci{beta},C'i{r_brace}, while the latter five are combined into interresidue segments {l_brace}Ci{alpha},Ci{beta},C'i,Ni+1,HNi+1{r_brace}. Given a tentative assignment of segments,the second stage of the procedure calculates probability scores based on the likelihood of matching the chemical shifts of each segment with (i) overlapping segments; and (ii) chemical shift distributions of the underlying amino acid type (and secondary structure, if known). This joint probability is maximized by rearranging segments using a simulated annealing program,optimized for efficiency. The automated assignment program was tested using CBCANH and CBCA(CO)NH cross peaks of the two previously assigned proteins, calmodulin and CheA.The agreement between the results of our method and the published assignments was excellent. Our algorithm was also applied to the observed cross peaks of glutamine-binding protein of Escherichia coli, yielding an assignment in excellent agreement with that obtained by time-consuming, manual methods. The chemical shift assignment procedure described here should be most useful for NMR studies of large proteins, which are now feasible with the use of pulsed-field gradients and random partial deuteration of samples.

  17. Molecular couplings and energy exchange between DNA and water mapped by femtosecond infrared spectroscopy of backbone vibrations

    Directory of Open Access Journals (Sweden)

    Yingliang Liu

    2017-07-01

    Full Text Available Molecular couplings between DNA and water together with the accompanying processes of energy exchange are mapped via the ultrafast response of DNA backbone vibrations after OH stretch excitation of the water shell. Native salmon testes DNA is studied in femtosecond pump-probe experiments under conditions of full hydration and at a reduced hydration level with two water layers around the double helix. Independent of their local hydration patterns, all backbone vibrations in the frequency range from 940 to 1120 cm–1 display a quasi-instantaneous reshaping of the spectral envelopes of their fundamental absorption bands upon excitation of the water shell. The subsequent reshaping kinetics encompass a one-picosecond component, reflecting the formation of a hot ground state of the water shell, and a slower contribution on a time scale of tens of picoseconds. Such results are benchmarked by measurements with resonant excitation of the backbone modes, resulting in distinctly different absorption changes. We assign the fast changes of DNA absorption after OH stretch excitation to structural changes in the water shell which couple to DNA through the local electric fields. The second slower process is attributed to a flow of excess energy from the water shell into DNA, establishing a common heated ground state in the molecular ensemble. This interpretation is supported by theoretical calculations of the electric fields exerted by the water shell at different temperatures.

  18. Protein structure based prediction of catalytic residues

    Science.gov (United States)

    2013-01-01

    Background Worldwide structural genomics projects continue to release new protein structures at an unprecedented pace, so far nearly 6000, but only about 60% of these proteins have any sort of functional annotation. Results We explored a range of features that can be used for the prediction of functional residues given a known three-dimensional structure. These features include various centrality measures of nodes in graphs of interacting residues: closeness, betweenness and page-rank centrality. We also analyzed the distance of functional amino acids to the general center of mass (GCM) of the structure, relative solvent accessibility (RSA), and the use of relative entropy as a measure of sequence conservation. From the selected features, neural networks were trained to identify catalytic residues. We found that using distance to the GCM together with amino acid type provide a good discriminant function, when combined independently with sequence conservation. Using an independent test set of 29 annotated protein structures, the method returned 411 of the initial 9262 residues as the most likely to be involved in function. The output 411 residues contain 70 of the annotated 111 catalytic residues. This represents an approximately 14-fold enrichment of catalytic residues on the entire input set (corresponding to a sensitivity of 63% and a precision of 17%), a performance competitive with that of other state-of-the-art methods. Conclusions We found that several of the graph based measures utilize the same underlying feature of protein structures, which can be simply and more effectively captured with the distance to GCM definition. This also has the added the advantage of simplicity and easy implementation. Meanwhile sequence conservation remains by far the most influential feature in identifying functional residues. We also found that due the rapid changes in size and composition of sequence databases, conservation calculations must be recalibrated for specific

  19. Comparative experimental investigation on the actuation mechanisms of ionic polymer–metal composites with different backbones and water contents

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Zicai; Chang, Longfei; Wang, Yanjie; Chen, Hualing, E-mail: hlchen@mail.xjtu.edu.cn [State Key Laboratory of Mechanical Structure Strength and Vibration, Xi' an Jiaotong University, Xi' an 710049 (China); School of Mechanical Engineering, Xi' an Jiaotong University, Xi' an 710049 (China); Asaka, Kinji [Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Osaka 563-8577 (Japan); Zhao, Hongxia [Niumag Corporation, Shanghai 200333 (China); Li, Dichen [School of Mechanical Engineering, Xi' an Jiaotong University, Xi' an 710049 (China); State Key Laboratory for Manufacturing Systems Engineering, Xi' an Jiaotong University, Xi' an 710049 (China)

    2014-03-28

    Water-based ionic polymer–metal composites (IPMCs) exhibit complex deformation properties, especially when the water content changes. To explore the general actuation mechanisms, both Nafion and Flemion membranes are used as the polymer backbones. IPMC deformation includes three stages: fast anode deformation, relaxation deformation, and slow anode deformation, which is mainly dependent on the water content and the backbone. When the water content decreases from 21 to 14 wt. %, Nafion–IPMC exhibits a large negative relaxation deformation, zero deformation, a positive relaxation deformation, and a positive steady deformation without relaxation in sequence. Despite the slow anode deformation, Flemion–IPMC also shows a slight relaxation deformation, which disappears when the water content is less than 13 wt. %. The different water states are investigated at different water contents using nuclear magnetic resonance spectroscopy. The free water, which decreases rapidly at the beginning through evaporation, is proven to be critical for relaxation deformation. For the backbone, indirect evidence from the steady current response is correlated with the slow anode deformation of Flemion-IPMC. The latter is explained by the secondary dissociation of the weak acid group –COOH. Finally, we thoroughly explain not only the three deformations by swelling but also their evolvement with decreasing water content. A fitting model is also presented based on a multi-diffusion equation to reveal the deformation processes more clearly, the results from which are in good agreement with the experimental results.

  20. Structure-based inhibitors of tau aggregation

    Science.gov (United States)

    Seidler, P. M.; Boyer, D. R.; Rodriguez, J. A.; Sawaya, M. R.; Cascio, D.; Murray, K.; Gonen, T.; Eisenberg, D. S.

    2018-02-01

    Aggregated tau protein is associated with over 20 neurological disorders, which include Alzheimer's disease. Previous work has shown that tau's sequence segments VQIINK and VQIVYK drive its aggregation, but inhibitors based on the structure of the VQIVYK segment only partially inhibit full-length tau aggregation and are ineffective at inhibiting seeding by full-length fibrils. Here we show that the VQIINK segment is the more powerful driver of tau aggregation. Two structures of this segment determined by the cryo-electron microscopy method micro-electron diffraction explain its dominant influence on tau aggregation. Of practical significance, the structures lead to the design of inhibitors that not only inhibit tau aggregation but also inhibit the ability of exogenous full-length tau fibrils to seed intracellular tau in HEK293 biosensor cells into amyloid. We also raise the possibility that the two VQIINK structures represent amyloid polymorphs of tau that may account for a subset of prion-like strains of tau.

  1. (1)H, (13)C, and (15)N backbone resonance assignments of the full-length 40 kDa S. acidocaldarius Y-family DNA polymerase, dinB homolog.

    Science.gov (United States)

    Moro, Sean L; Cocco, Melanie J

    2015-10-01

    The dinB homolog (Dbh) is a member of the Y-family of translesion DNA polymerases, which are specialized to accurately replicate DNA across from a wide variety of lesions in living cells. Lesioned bases block the progression of high-fidelity polymerases and cause detrimental replication fork stalling; Y-family polymerases can bypass these lesions. The active site of the translesion synthesis polymerase is more open than that of a replicative polymerase; consequently Dbh polymerizes with low fidelity. Bypass polymerases also have low processivity. Short extension past the lesion allows the high-fidelity polymerase to switch back onto the site of replication. Dbh and the other Y-family polymerases have been used as structural models to investigate the mechanisms of DNA polymerization and lesion bypass. Many high-resolution crystal structures of Y-family polymerases have been reported. NMR dynamics studies can complement these structures by providing a measure of protein motions. Here we report the (15)N, (1)H, and (13)C backbone resonance assignments at two temperatures (35 and 50 °C) for Sulfolobus acidocaldarius Dbh polymerase. Backbone resonance assignments have been obtained for 86 % of the residues. The polymerase active site is assigned as well as the majority of residues in each of the four domains.

  2. Backbone assignment of the binary complex of the full length Sulfolobus solfataricus DNA polymerase IV and DNA.

    Science.gov (United States)

    Lee, Eunjeong; Fowler, Jason D; Suo, Zucai; Wu, Zhengrong

    2017-04-01

    Sulfolobus solfataricus DNA polymerase IV (Dpo4), a model Y-family DNA polymerase, bypasses a wide range of DNA lesions in vitro and in vivo. In this paper, we report the backbone chemical shift assignments of the full length Dpo4 in its binary complex with a 14/14-mer DNA substrate. Upon DNA binding, several β-stranded regions in the isolated catalytic core and little finger/linker fragments of Dpo4 become more structured. This work serves as a foundation for our ongoing investigation of conformational dynamics of Dpo4 and future determination of the first solution structures of a DNA polymerase and its binary and ternary complexes.

  3. Gas separation performance of 6FDA-based polyimides with different chemical structures

    KAUST Repository

    Qiu, Wulin

    2013-10-01

    This work reports the gas separation performance of several 6FDA-based polyimides with different chemical structures, to correlate chemical structure with gas transport properties with a special focus on CO2 and CH 4 transport and plasticization stability of the polyimides membranes relevant to natural gas purification. The consideration of the other gases (He, O2 and N2) provided additional insights regarding effects of backbone structure on detailed penetrant properties. The polyimides studied include 6FDA-DAM, 6FDA-mPDA, 6FDA-DABA, 6FDA-DAM:DABA (3:2), 6FDA-DAM:mPDA (3:2) and 6FDA-mPDA:DABA (3:2). Both pure and binary gas permeation were investigated. The packing density, which is tunable by adjusting monomer type and composition of the various samples, correlated with transport permeability and selectivity. The separation performance of the polyimides for various gas pairs were also plotted for comparison to the upper bound curves, and it was found that this family of materials shows attractive performance. The CO 2 plasticization responses for the un-cross-linked polyimides showed good plasticization resistance to CO2/CH4 mixed gas with 10% CO2; however, only the cross-linked polyimides showed good plasticization resistance under aggressive gas feed conditions (CO 2/CH4 mixed gas with 50% CO2 or pure CO 2). For future work, asymmetric hollow fibers and carbon molecular sieve membranes based on the most attractive members of the family will be considered. © 2013 Elsevier Ltd. All rights reserved.

  4. A Hub Location Problem with Fully Interconnected Backbone and Access Networks

    DEFF Research Database (Denmark)

    Thomadsen, Tommy; Larsen, Jesper

    2007-01-01

    This paper considers the design of two-layered fully interconnected networks. A two-layered network consists of clusters of nodes, each defining an access network and a backbone network. We consider the integrated problem of determining the access networks and the backbone network simultaneously....

  5. Thin Films Formed from Conjugated Polymers with Ionic, Water-Soluble Backbones

    NARCIS (Netherlands)

    Voortman, Thomas P; Chiechi, Ryan C

    2015-01-01

    This paper compares the morphologies of films of conjugated polymers in which the backbone (main chain) and pendant groups are varied between ionic/hydrophilic and aliphatic/hydrophobic. We observe that conjugated polymers in which the pendant groups and backbone are matched, either ionic-ionic or

  6. Pendant Dynamics of Ethylene-Oxide Containing Polymers with Diverse Backbones

    Science.gov (United States)

    Bartels, Joshua; Wang, Jing-Han Helen; Chen, Quan; Runt, James; Colby, Ralph

    In the last twenty years, a wide variety of ion conducting polymers have used ether oxygens to facilitate ion conduction, and it is therefore important to understand the dynamics of ether oxygens (EOs) when attached to different polymer backbones. Four different EO-containing polymer architectures are studied by dielectric spectroscopy to understand the backbone effect on the EO dipoles. Polysiloxanes, polyphosphazenes, polymethylmethacrylates, and a polyester ether are compared, with different EO pendant lengths for the siloxane and methylmethacrylate backbones. The flexible polysiloxanes and polyphosphazene backbones impart superior segmental mobility with a glass transition temperature 15 K lower than that of the organic backbone polymers. Short EO pendants are found to impart a lower static dielectric constant at comparable EO content as compared to longer EO pendants of either inorganic or organic backbones. The long-pendant polymethylmethacrylate polymers show two relaxations corresponding to fast EOs near the pendant tail end and slow EOs close to the slower backbone, whereas the long-pendant polysiloxane shows a single relaxation due to the siloxane backbone relaxing faster than the EO pendant. Supported by the NSF Division of Materials Research Polymers Program through Grants DMR-1404586 (RHC) and DMR-1505953 (JR).

  7. A Hamiltonian Replica Exchange Approach and Its Application to the Study of Side-Chain Type and Neighbor Effects on Peptide Backbone Conformations.

    Science.gov (United States)

    Xu, Chao; Wang, Jun; Liu, Haiyan

    2008-08-01

    We presented a Hamiltonian replica exchange approach and applied it to investigate the effects of various factors on the conformational equilibrium of peptide backbone. In different replicas, biasing potentials of varying strengths are applied to all backbone (φ,ψ) torsional angle pairs to overcome sampling barriers. A general form of constructing biasing potentials based on a reference free energy surface is employed to minimize sampling in physically irrelevant parts of the conformational space. An extension of the weighted histogram analysis formulation allows for conformational free energy surfaces to be computed using all replicas, including those with biased Hamiltonians. This approach can significantly reduce the statistical uncertainties in computed free energies. For the peptide systems considered, it allows for effects of the order of 0.5-1 kJ/mol to be quantified using explicit solvent simulations. We applied this approach to capped peptides of 2-5 peptide units containing Ala, Phe, or Val in explicit water solvent and focused on how the conformational equilibrium of a single pair of backbone angles are influenced by changing the residue types of the same and neighboring residues as well as conformations of neighboring residues. For the effects of changing side-chain types of the same residue, our results consistently showed increased preference of β for Phe and Val relative to Ala. As for neighbor effects, our results not only indicated that they can be as large as the effects of changing the side-chain type of the same residue but also led to several new insights. We found that for the N-terminal neighbors, their conformations seem to have large effects. Relative to the β conformer of an N-terminal neighbor, its α conformer stabilizes the β conformer of its next Ala disregarding the residue type of the neighbor. For C-terminal neighbors, their chemical identities seem to play more important roles. Val as the C-terminal neighbor significantly

  8. Tungsten - Yttrium Based Nuclear Structural Materials

    Science.gov (United States)

    Ramana, Chintalapalle; Chessa, Jack; Martinenz, Gustavo

    2013-04-01

    The challenging problem currently facing the nuclear science community in this 21st century is design and development of novel structural materials, which will have an impact on the next-generation nuclear reactors. The materials available at present include reduced activation ferritic/martensitic steels, dispersion strengthened reduced activation ferritic steels, and vanadium- or tungsten-based alloys. These materials exhibit one or more specific problems, which are either intrinsic or caused by reactors. This work is focussed towards tungsten-yttrium (W-Y) based alloys and oxide ceramics, which can be utilized in nuclear applications. The goal is to derive a fundamental scientific understanding of W-Y-based materials. In collaboration with University of Califonia -- Davis, the project is designated to demonstrate the W-Y based alloys, ceramics and composites with enhanced physical, mechanical, thermo-chemical properties and higher radiation resistance. Efforts are focussed on understanding the microstructure, manipulating materials behavior under charged-particle and neutron irradiation, and create a knowledge database of defects, elemental diffusion/segregation, and defect trapping along grain boundaries and interfaces. Preliminary results will be discussed.

  9. Detecting the Significant Flux Backbone of Escherichia coli metabolism.

    Science.gov (United States)

    Güell, Oriol; Sagués, Francesc; Serrano, M Ángeles

    2017-05-01

    The heterogeneity of computationally predicted reaction fluxes in metabolic networks within a single flux state can be exploited to detect their significant flux backbone. Here, we disclose the backbone of Escherichia coli, and compare it with the backbones of other bacteria. We find that, in general, the core of the backbones is mainly composed of reactions in energy metabolism corresponding to ancient pathways. In E. coli, the synthesis of nucleotides and the metabolism of lipids form smaller cores which rely critically on energy metabolism. Moreover, the consideration of different media leads to the identification of pathways sensitive to environmental changes. The metabolic backbone of an organism is thus useful to trace simultaneously both its evolution and adaptation fingerprints. © 2017 The Authors FEBS Letters published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.

  10. Data Acquisition Backbone Core DABC release v1.0

    International Nuclear Information System (INIS)

    Adamczewski-Musch, J; Kurz, N; Linev, S; Essel, H G

    2010-01-01

    The Data Acquisition Backbone Core (DABC) is a general purpose software framework designed for the implementation of a wide-range of data acquisition systems - from various small detector test beds to high performance systems. DABC consists of a compact data-flow kernel and a number of plug-ins for various functional components like data inputs, device drivers, user functional modules and applications. DABC provides configurable components for implementing event building over fast networks like InfiniBand or Gigabit Ethernet. A generic Java GUI provides the dynamic control and visualization of control parameters and commands, provided by DIM servers. A first set of application plug-ins has been implemented to use DABC as event builder for the front-end components of the GSI standard DAQ system MBS (Multi Branch System). Another application covers the connection to DAQ readout chains from detector front-end boards (N-XYTER) linked to read-out controller boards (ROC) over UDP into DABC for event building, archiving and data serving. This was applied for data taking in the September 2008 test beamtime for the CBM experiment at GSI. DABC version 1.0 is released and available from the website.

  11. Data Acquisition Backbone Core DABC release v1.0

    Science.gov (United States)

    Adamczewski-Musch, J.; Essel, H. G.; Kurz, N.; Linev, S.

    2010-04-01

    The Data Acquisition Backbone Core (DABC) is a general purpose software framework designed for the implementation of a wide-range of data acquisition systems - from various small detector test beds to high performance systems. DABC consists of a compact data-flow kernel and a number of plug-ins for various functional components like data inputs, device drivers, user functional modules and applications. DABC provides configurable components for implementing event building over fast networks like InfiniBand or Gigabit Ethernet. A generic Java GUI provides the dynamic control and visualization of control parameters and commands, provided by DIM servers. A first set of application plug-ins has been implemented to use DABC as event builder for the front-end components of the GSI standard DAQ system MBS (Multi Branch System). Another application covers the connection to DAQ readout chains from detector front-end boards (N-XYTER) linked to read-out controller boards (ROC) over UDP into DABC for event building, archiving and data serving. This was applied for data taking in the September 2008 test beamtime for the CBM experiment at GSI. DABC version 1.0 is released and available from the website.

  12. Removable Backbone Modification Method for the Chemical Synthesis of Membrane Proteins.

    Science.gov (United States)

    Li, Jia-Bin; Tang, Shan; Zheng, Ji-Shen; Tian, Chang-Lin; Liu, Lei

    2017-05-16

    Chemical synthesis can produce water-soluble globular proteins bearing specifically designed modifications. These synthetic molecules have been used to study the biological functions of proteins and to improve the pharmacological properties of protein drugs. However, the above advances notwithstanding, membrane proteins (MPs), which comprise 20-30% of all proteins in the proteomes of most eukaryotic cells, remain elusive with regard to chemical synthesis. This difficulty stems from the strong hydrophobic character of MPs, which can cause considerable handling issues during ligation, purification, and characterization steps. Considerable efforts have been made to improve the solubility of transmembrane peptides for chemical ligation. These methods can be classified into two main categories: the manipulation of external factors and chemical modification of the peptide. This Account summarizes our research advances in the development of chemical modification especially the two generations of removable backbone modification (RBM) strategy for the chemical synthesis of MPs. In the first RBM generation, we install a removable modification group at the backbone amide of Gly within the transmembrane peptides. In the second RBM generation, the RBM group can be installed into all primary amino acid residues. The second RBM strategy combines the activated intramolecular O-to-N acyl transfer reaction, in which a phenyl group remains unprotected during the coupling process, which can play a catalytic role to generate the activated phenyl ester to assist in the formation of amide. The key feature of the RBM group is its switchable stability in trifluoroacetic acid. The stability of these backbone amide N-modifications toward TFA can be modified by regulating the electronic effects of phenol groups. The free phenol group is acylated to survive the TFA deprotection step, while the acyl phenyl ester will be quantitatively hydrolyzed in a neutral aqueous solution, and the free

  13. Structure-based approach to rationally design a chimeric protein for an effective vaccine against Group B Streptococcus infections.

    Science.gov (United States)

    Nuccitelli, Annalisa; Cozzi, Roberta; Gourlay, Louise J; Donnarumma, Danilo; Necchi, Francesca; Norais, Nathalie; Telford, John L; Rappuoli, Rino; Bolognesi, Martino; Maione, Domenico; Grandi, Guido; Rinaudo, C Daniela

    2011-06-21

    Structural vaccinology is an emerging strategy for the rational design of vaccine candidates. We successfully applied structural vaccinology to design a fully synthetic protein with multivalent protection activity. In Group B Streptococcus, cell-surface pili have aroused great interest because of their direct roles in virulence and importance as protective antigens. The backbone subunit of type 2a pilus (BP-2a) is present in six immunogenically different but structurally similar variants. We determined the 3D structure of one of the variants, and experimentally demonstrated that protective antibodies specifically recognize one of the four domains that comprise the protein. We therefore constructed a synthetic protein constituted by the protective domain of each one of the six variants and showed that the chimeric protein protects mice against the challenge with all of the type 2a pilus-carrying strains. This work demonstrates the power of structural vaccinology and will facilitate the development of an optimized, broadly protective pilus-based vaccine against Group B Streptococcus by combining the uniquely generated chimeric protein with protective pilin subunits from two other previously identified pilus types. In addition, this work describes a template procedure that can be followed to develop vaccines against other bacterial pathogens.

  14. Backbone resonance assignments for G protein α(i3) subunit in the GDP-bound state.

    Science.gov (United States)

    Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio

    2014-10-01

    Guanine-nucleotide binding proteins (G proteins) serve as molecular switches in signaling pathways, by coupling the activation of G protein-coupled receptors (GPCRs) at the cell surface to intracellular responses. In the resting state, G protein forms a heterotrimer, consisting of the G protein α subunit with GDP (Gα·GDP) and the G protein βγ subunit (Gβγ). Ligand binding to GPCRs promotes the GDP-GTP exchange on Gα, leading to the dissociation of the GTP-bound form of Gα (Gα·GTP) and Gβγ. Then, Gα·GTP and Gβγ bind to their downstream effector enzymes or ion channels and regulate their activities, leading to a variety of cellular responses. Finally, Gα hydrolyzes the bound GTP to GDP and returns to the resting state by re-associating with Gβγ. The G proteins are classified with four major families based on the amino acid sequences of Gα: i/o, s, q/11, and 12/13. Here, we established the backbone resonance assignments of human Gαi3, a member of the i/o family with a molecular weight of 41 K, in complex with GDP. The chemical shifts were compared with those of Gα(i3) in complex with a GTP-analogue, GTPγS, which we recently reported, indicating that the residues with significant chemical shift differences are mostly consistent with the regions with the structural differences between the GDP- and GTPγS-bound states, as indicated in the crystal structures. The assignments of Gα(i3)·GDP would be useful for the analyses of the dynamics of Gα(i3) and its interactions with various target molecules.

  15. Backbone ¹H, ¹³C, ¹⁵N NMR assignments of yeast OMP synthase in unliganded form and in complex with orotidine 5'-monophosphate.

    Science.gov (United States)

    Hansen, Michael Riis; Harris, Richard; Barr, Eric W; Cheng, Hong; Girvin, Mark E; Grubmeyer, Charles

    2014-04-01

    The type I phosphoribosyltransferase OMP synthase (EC 2.4.2.10) is involved in de novo synthesis of pyrimidine nucleotides forming the UMP precursor orotidine 5'-monophosphate (OMP). The homodimeric enzyme has a Rossman α/β core topped by a base-enclosing "hood" domain and a flexible domain-swapped catalytic loop. High-resolution X-ray structures of the homologous Salmonella typhimurium and yeast enzymes show that a general compacting of the core as well as movement of the hood and a major disorder-to-order transition of the loop occur upon binding of ligands MgPRPP and orotate. Here we present backbone NMR assignments for the unliganded yeast enzyme (49 kDa) and its complex with product OMP. We were able to assign 212-213 of the 225 non-proline backbone (15)N and amide proton resonances. Significant difference in chemical shifts of the amide cross peaks occur in regions of the structure that undergo movement upon ligand occupancy in the S. typhimurium enzyme.

  16. Structural constraints-based evaluation of immunogenic avirulent toxins from Clostridium botulinum C2 and C3 toxins as subunit vaccines.

    Science.gov (United States)

    Prisilla, A; Prathiviraj, R; Sasikala, R; Chellapandi, P

    2016-10-01

    Clostridium botulinum (group-III) is an anaerobic bacterium producing C2 and C3 toxins in addition to botulinum neurotoxins in avian and mammalian cells. C2 and C3 toxins are members of bacterial ADP-ribosyltransferase superfamily, which modify the eukaryotic cell surface proteins by ADP-ribosylation reaction. Herein, the mutant proteins with lack of catalytic and pore forming function derived from C2 (C2I and C2II) and C3 toxins were computationally evaluated to understand their structure-function integrity. We have chosen many structural constraints including local structural environment, folding process, backbone conformation, conformational dynamic sub-space, NAD-binding specificity and antigenic determinants for screening of suitable avirulent toxins. A total of 20 avirulent mutants were identified out of 23 mutants, which were experimentally produced by site-directed mutagenesis. No changes in secondary structural elements in particular to α-helices and β-sheets and also in fold rate of all-β classes. Structural stability was maintained by reordered hydrophobic and hydrogen bonding patterns. Molecular dynamic studies suggested that coupled mutations may restrain the binding affinity to NAD(+) or protein substrate upon structural destabilization. Avirulent toxins of this study have stable energetic backbone conformation with a common blue print of folding process. Molecular docking studies revealed that avirulent mutants formed more favorable hydrogen bonding with the side-chain of amino acids near to conserved NAD-binding core, despite of restraining NAD-binding specificity. Thus, structural constraints in the avirulent toxins would determine their immunogenic nature for the prioritization of protein-based subunit vaccine/immunogens to avian and veterinary animals infected with C. botulinum. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Vision based condition assessment of structures

    International Nuclear Information System (INIS)

    Uhl, Tadeusz; Kohut, Piotr; Holak, Krzysztof; Krupinski, Krzysztof

    2011-01-01

    In this paper, a vision-based method for measuring a civil engineering construction's in-plane deflection curves is presented. The displacement field of the analyzed object which results from loads was computed by means of a digital image correlation coefficient. Image registration techniques were introduced to increase the flexibility of the method. The application of homography mapping enabled the deflection field to be computed from two images of the structure, acquired from two different points in space. An automatic shape filter and a corner detector were implemented to calculate the homography mapping between the two views. The developed methodology, created architecture and the capabilities of software tools, as well as experimental results obtained from tests made on a lab set-up and civil engineering constructions, are discussed.

  18. Vision based condition assessment of structures

    Energy Technology Data Exchange (ETDEWEB)

    Uhl, Tadeusz; Kohut, Piotr; Holak, Krzysztof; Krupinski, Krzysztof, E-mail: tuhl@agh.edu.pl, E-mail: pko@agh.edu.pl, E-mail: holak@agh.edu.pl, E-mail: krzysiek.krupinski@wp.pl [Department of Robotics and Mechatronics, AGH-University of Science and Technology, Al.Mickiewicza 30, 30-059 Cracow (Poland)

    2011-07-19

    In this paper, a vision-based method for measuring a civil engineering construction's in-plane deflection curves is presented. The displacement field of the analyzed object which results from loads was computed by means of a digital image correlation coefficient. Image registration techniques were introduced to increase the flexibility of the method. The application of homography mapping enabled the deflection field to be computed from two images of the structure, acquired from two different points in space. An automatic shape filter and a corner detector were implemented to calculate the homography mapping between the two views. The developed methodology, created architecture and the capabilities of software tools, as well as experimental results obtained from tests made on a lab set-up and civil engineering constructions, are discussed.

  19. Structure Based Antibody-Like Peptidomimetics

    Directory of Open Access Journals (Sweden)

    Mark I. Greene

    2012-02-01

    Full Text Available Biologics such as monoclonal antibodies (mAb and soluble receptors represent new classes of therapeutic agents for treatment of several diseases. High affinity and high specificity biologics can be utilized for variety of clinical purposes. Monoclonal antibodies have been used as diagnostic agents when coupled with radionuclide, immune modulatory agents or in the treatment of cancers. Among other limitations of using large molecules for therapy the actual cost of biologics has become an issue. There is an effort among chemists and biologists to reduce the size of biologics which includes monoclonal antibodies and receptors without a reduction of biological efficacy. Single chain antibody, camel antibodies, Fv fragments are examples of this type of deconstructive process. Small high-affinity peptides have been identified using phage screening. Our laboratory used a structure-based approach to develop small-size peptidomimetics from the three-dimensional structure of proteins with immunoglobulin folds as exemplified by CD4 and antibodies. Peptides derived either from the receptor or their cognate ligand mimics the functions of the parental macromolecule. These constrained peptides not only provide a platform for developing small molecule drugs, but also provide insight into the atomic features of protein-protein interactions. A general overview of the reduction of monoclonal antibodies to small exocyclic peptide and its prospects as a useful diagnostic and as a drug in the treatment of cancer are discussed.

  20. An Unusual Conformational Isomer of Verrucosidin Backbone from a Hydrothermal Vent Fungus, Penicillium sp. Y-50-10

    Directory of Open Access Journals (Sweden)

    Chengqian Pan

    2016-08-01

    Full Text Available A new verrucosidin derivative, methyl isoverrucosidinol (1, was isolated from the marine fungus Penicillium sp. Y-50-10, dwelling in sulfur rich sediment in the Kueishantao hydrothermal vents off Taiwan. The structure was established by spectroscopic means including HRMS and 2D-NMR spectroscopic analysis. The absolute configuration was defined mainly by comparison of quantum chemical TDDFT calculated and experimental ECD spectra. Among hitherto known compounds with a verrucosidine backbone isolated from natural resource, compound 1 represents the first example of a new conformational isomer of its skeleton, exhibiting antibiotic activity against Bacillus subtilis with MIC value 32 μg/mL.

  1. Backbone resonance assignments of the human p73 DNA binding domain.

    Science.gov (United States)

    Cino, Elio A; Soares, Iaci N; Freitas, Mônica S; Silva, Jerson L

    2016-04-01

    p53, p63, p73 family of proteins are transcription factors with crucial roles in regulating cellular processes such apoptosis, proliferation, differentiation, and DNA damage response. The three family members have both overlapping and unique biological functions. Sequence and structural homology are greatest in the DNA binding domains (DBD), which is the site of the majority of p53 mutations. Structurally unstable p53 DBD mutants can associate with themselves or p63 and p73 DBDs, impeding tumor suppressor functions. Evidence suggests that these proteins associate to form amyloid-like oligomers and fibrils through an aggregation-prone sequence within the DBDs. Despite having high sequence and structure similarities, p63 and p73 DBDs appear to have considerably lower tendencies to be incorporated into p53 aggregates, relative to p53. The backbone resonance assignments of p73 DBD reported here complement those previously reported for p53 and p63, allowing comparisons and providing molecular insights into their biological functions and roles in aggregation and tumor development.

  2. Structure-Based Algorithms for Microvessel Classification

    KAUST Repository

    Smith, Amy F.

    2015-02-01

    © 2014 The Authors. Microcirculation published by John Wiley & Sons Ltd. Objective: Recent developments in high-resolution imaging techniques have enabled digital reconstruction of three-dimensional sections of microvascular networks down to the capillary scale. To better interpret these large data sets, our goal is to distinguish branching trees of arterioles and venules from capillaries. Methods: Two novel algorithms are presented for classifying vessels in microvascular anatomical data sets without requiring flow information. The algorithms are compared with a classification based on observed flow directions (considered the gold standard), and with an existing resistance-based method that relies only on structural data. Results: The first algorithm, developed for networks with one arteriolar and one venular tree, performs well in identifying arterioles and venules and is robust to parameter changes, but incorrectly labels a significant number of capillaries as arterioles or venules. The second algorithm, developed for networks with multiple inlets and outlets, correctly identifies more arterioles and venules, but is more sensitive to parameter changes. Conclusions: The algorithms presented here can be used to classify microvessels in large microvascular data sets lacking flow information. This provides a basis for analyzing the distinct geometrical properties and modelling the functional behavior of arterioles, capillaries, and venules.

  3. A Synthetic HIV-1 Subtype C Backbone Generates Comparable PR and RT Resistance Profiles to a Subtype B Backbone in a Recombinant Virus Assay

    Science.gov (United States)

    Nauwelaers, David; Van Houtte, Margriet; Winters, Bart; Steegen, Kim; Van Baelen, Kurt; Chi, Ellen; Zhou, Mimi; Steiner, Derek; Bonesteel, Rachelle; Aston, Colin; Stuyver, Lieven J.

    2011-01-01

    In order to determine phenotypic protease and reverse transcriptase inhibitor-associated resistance in HIV subtype C virus, we have synthetically constructed an HIV-1 subtype C (HIV-1-C) viral backbone for use in a recombinant virus assay. The in silico designed viral genome was divided into 4 fragments, which were chemically synthesized and joined together by conventional subcloning. Subsequently, gag-protease-reverse-transcriptase (GPRT) fragments from 8 HIV-1 subtype C-infected patient samples were RT-PCR-amplified and cloned into the HIV-1-C backbone (deleted for GPRT) using In-Fusion reagents. Recombinant viruses (1 to 5 per patient sample) were produced in MT4-eGFP cells where cyto-pathogenic effect (CPE), p24 and Viral Load (VL) were monitored. The resulting HIV-1-C recombinant virus stocks (RVS) were added to MT4-eGFP cells in the presence of serial dilutions of antiretroviral drugs (PI, NNRTI, NRTI) to determine the fold-change in IC50 compared to the IC50 of wild-type HIV-1 virus. Additionally, viral RNA was extracted from the HIV-1-C RVS and the amplified GPRT products were used to generate recombinant virus in a subtype B backbone. Phenotypic resistance profiles in a subtype B and subtype C backbone were compared. The following observations were made: i) functional, infectious HIV-1 subtype C viruses were generated, confirmed by VL and p24 measurements; ii) their rate of infection was slower than viruses generated in the subtype B backbone; iii) they did not produce clear CPE in MT4 cells; and iv) drug resistance profiles generated in both backbones were very similar, including re-sensitizing effects like M184V on AZT. PMID:21629677

  4. A synthetic HIV-1 subtype C backbone generates comparable PR and RT resistance profiles to a subtype B backbone in a recombinant virus assay.

    Directory of Open Access Journals (Sweden)

    David Nauwelaers

    Full Text Available In order to determine phenotypic protease and reverse transcriptase inhibitor-associated resistance in HIV subtype C virus, we have synthetically constructed an HIV-1 subtype C (HIV-1-C viral backbone for use in a recombinant virus assay. The in silico designed viral genome was divided into 4 fragments, which were chemically synthesized and joined together by conventional subcloning. Subsequently, gag-protease-reverse-transcriptase (GPRT fragments from 8 HIV-1 subtype C-infected patient samples were RT-PCR-amplified and cloned into the HIV-1-C backbone (deleted for GPRT using In-Fusion reagents. Recombinant viruses (1 to 5 per patient sample were produced in MT4-eGFP cells where cyto-pathogenic effect (CPE, p24 and Viral Load (VL were monitored. The resulting HIV-1-C recombinant virus stocks (RVS were added to MT4-eGFP cells in the presence of serial dilutions of antiretroviral drugs (PI, NNRTI, NRTI to determine the fold-change in IC50 compared to the IC50 of wild-type HIV-1 virus. Additionally, viral RNA was extracted from the HIV-1-C RVS and the amplified GPRT products were used to generate recombinant virus in a subtype B backbone. Phenotypic resistance profiles in a subtype B and subtype C backbone were compared. The following observations were made: i functional, infectious HIV-1 subtype C viruses were generated, confirmed by VL and p24 measurements; ii their rate of infection was slower than viruses generated in the subtype B backbone; iii they did not produce clear CPE in MT4 cells; and iv drug resistance profiles generated in both backbones were very similar, including re-sensitizing effects like M184V on AZT.

  5. A synthetic HIV-1 subtype C backbone generates comparable PR and RT resistance profiles to a subtype B backbone in a recombinant virus assay.

    Science.gov (United States)

    Nauwelaers, David; Van Houtte, Margriet; Winters, Bart; Steegen, Kim; Van Baelen, Kurt; Chi, Ellen; Zhou, Mimi; Steiner, Derek; Bonesteel, Rachelle; Aston, Colin; Stuyver, Lieven J

    2011-01-01

    In order to determine phenotypic protease and reverse transcriptase inhibitor-associated resistance in HIV subtype C virus, we have synthetically constructed an HIV-1 subtype C (HIV-1-C) viral backbone for use in a recombinant virus assay. The in silico designed viral genome was divided into 4 fragments, which were chemically synthesized and joined together by conventional subcloning. Subsequently, gag-protease-reverse-transcriptase (GPRT) fragments from 8 HIV-1 subtype C-infected patient samples were RT-PCR-amplified and cloned into the HIV-1-C backbone (deleted for GPRT) using In-Fusion reagents. Recombinant viruses (1 to 5 per patient sample) were produced in MT4-eGFP cells where cyto-pathogenic effect (CPE), p24 and Viral Load (VL) were monitored. The resulting HIV-1-C recombinant virus stocks (RVS) were added to MT4-eGFP cells in the presence of serial dilutions of antiretroviral drugs (PI, NNRTI, NRTI) to determine the fold-change in IC50 compared to the IC50 of wild-type HIV-1 virus. Additionally, viral RNA was extracted from the HIV-1-C RVS and the amplified GPRT products were used to generate recombinant virus in a subtype B backbone. Phenotypic resistance profiles in a subtype B and subtype C backbone were compared. The following observations were made: i) functional, infectious HIV-1 subtype C viruses were generated, confirmed by VL and p24 measurements; ii) their rate of infection was slower than viruses generated in the subtype B backbone; iii) they did not produce clear CPE in MT4 cells; and iv) drug resistance profiles generated in both backbones were very similar, including re-sensitizing effects like M184V on AZT.

  6. SDSL-ESR-based protein structure characterization

    NARCIS (Netherlands)

    Strancar, J.; Kavalenka, A.A.; Urbancic, I.; Ljubetic, A.; Hemminga, M.A.

    2010-01-01

    As proteins are key molecules in living cells, knowledge about their structure can provide important insights and applications in science, biotechnology, and medicine. However, many protein structures are still a big challenge for existing high-resolution structure-determination methods, as can be

  7. Reliability-Based Optimization of Structural Elements

    DEFF Research Database (Denmark)

    Sørensen, John Dalsgaard

    In this paper structural elements from an optimization point of view are considered, i.e. only the geometry of a structural element is optimized. Reliability modelling of the structural element is discussed both from an element point of view and from a system point of view. The optimization...

  8. 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

    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...

  9. Mucosal immunization of rhesus monkeys against respiratory syncytial virus subgroups A and B and human parainfluenza virus type 3 by using a live cDNA-derived vaccine based on a host range-attenuated bovine parainfluenza virus type 3 vector backbone.

    Science.gov (United States)

    Schmidt, Alexander C; Wenzke, Daniel R; McAuliffe, Josephine M; St Claire, Marisa; Elkins, William R; Murphy, Brian R; Collins, Peter L

    2002-02-01

    Reverse genetics was used to develop a two-component, trivalent live attenuated vaccine against human parainfluenza virus type 3 (HPIV3) and respiratory syncytial virus (RSV) subgroups A and B. The backbone for each of the two components of this vaccine was the attenuated recombinant bovine/human PIV3 (rB/HPIV3), a recombinant BPIV3 in which the bovine HN and F protective antigens are replaced by their HPIV3 counterparts (48). This chimera retains the well-characterized host range attenuation phenotype of BPIV3, which appears to be appropriate for immunization of young infants. The open reading frames (ORFs) for the G and F major protective antigens of RSV subgroup A and B were each placed under the control of PIV3 transcription signals and inserted individually or in homologous pairs as supernumerary genes in the promoter proximal position of rB/HPIV3. The level of replication of rB/HPIV3-RSV chimeric viruses in the respiratory tract of rhesus monkeys was similar to that of their parent virus rB/HPIV3, and each of the chimeras induced a robust immune response to both RSV and HPIV3. RSV-neutralizing antibody titers induced by rB/HPIV3-RSV chimeric viruses were equivalent to those induced by infection with wild-type RSV, and HPIV3-specific antibody responses were similar to, or slightly less than, after infection with the rB/HPIV3 vector itself. This study describes a novel vaccine strategy against RSV in which vaccine viruses with a common attenuated backbone, specifically rB/HPIV3 derivatives expressing the G and/or F major protective antigens of RSV subgroup A and of RSV subgroup B, are used to immunize by the intranasal route against RSV and HPIV3, which are the first and second most important viral agents of pediatric respiratory tract disease worldwide.

  10. BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks

    DEFF Research Database (Denmark)

    Alkan, Ferhat; Erten, Cesim

    2014-01-01

    on backbone extraction and merge strategy (BEAMS) for the problem. We finally show, through experiments based on biological significance tests, that the proposed BEAMS algorithm performs better than the state-of-the-art approaches. Furthermore, the computational burden of the BEAMS algorithm in terms...... of execution speed and memory requirements is more reasonable than the competing algorithms. AVAILABILITY AND IMPLEMENTATION: Supplementary material including code implementations in LEDA C++, experimental data and the results are available at http://webprs.khas.edu.tr/~cesim/BEAMS.tar.gz....

  11. Structure based alignment and clustering of proteins (STRALCP)

    Science.gov (United States)

    Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

    2013-06-18

    Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

  12. Reliability-Based Design of Coastal Structures

    DEFF Research Database (Denmark)

    Burcharth, H. F.

    1997-01-01

    is a combination of material presented in the following references: Burcharth, H.F. (1992) Reliability evaluation of a structure at sea. Proceedings of the Short Course on Design and Reliability of Coastal Structures. Venice, Scuola di S. Giovanni Evangelista, 1992. 23rd International Conference on Coastal...

  13. An Enhanced Backbone-Assisted Reliable Framework for Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Amna Ali

    2010-03-01

    Full Text Available An extremely reliable source to sink communication is required for most of the contemporary WSN applications especially pertaining to military, healthcare and disaster-recovery. However, due to their intrinsic energy, bandwidth and computational constraints, Wireless Sensor Networks (WSNs encounter several challenges in reliable source to sink communication. In this paper, we present a novel reliable topology that uses reliable hotlines between sensor gateways to boost the reliability of end-to-end transmissions. This reliable and efficient routing alternative reduces the number of average hops from source to the sink. We prove, with the help of analytical evaluation, that communication using hotlines is considerably more reliable than traditional WSN routing. We use reliability theory to analyze the cost and benefit of adding gateway nodes to a backbone-assisted WSN. However, in hotline assisted routing some scenarios where source and the sink are just a couple of hops away might bring more latency, therefore, we present a Signature Based Routing (SBR scheme. SBR enables the gateways to make intelligent routing decisions, based upon the derived signature, hence providing lesser end-to-end delay between source to the sink communication. Finally, we evaluate our proposed hotline based topology with the help of a simulation tool and show that the proposed topology provides manifold increase in end-to-end reliability.

  14. Degenerate primer MOB typing of multiresistant clinical isolates of E. coli uncovers new plasmid backbones.

    Science.gov (United States)

    Garcillán-Barcia, M Pilar; Ruiz del Castillo, Belén; Alvarado, Andrés; de la Cruz, Fernando; Martínez-Martínez, Luis

    2015-01-01

    Degenerate Primer MOB Typing is a PCR-based protocol for the classification of γ-proteobacterial transmissible plasmids in five phylogenetic relaxase MOB families. It was applied to a multiresistant E. coli collection, previously characterized by PCR-based replicon-typing, in order to compare both methods. Plasmids from 32 clinical isolates of multiresistant E. coli (19 extended spectrum beta-lactamase producers and 13 non producers) and their transconjugants were analyzed. A total of 95 relaxases were detected, at least one per isolate, underscoring the high potential of these strains for antibiotic-resistance transmission. MOBP12 and MOBF12 plasmids were the most abundant. Most MOB subfamilies detected were present in both subsets of the collection, indicating a shared mobilome among multiresistant E. coli. The plasmid profile obtained by both methods was compared, which provided useful data upon which decisions related to the implementation of detection methods in the clinic could be based. The phylogenetic depth at which replicon and MOB-typing classify plasmids is different. While replicon-typing aims at plasmid replication regions with non-degenerate primers, MOB-typing classifies plasmids into relaxase subfamilies using degenerate primers. As a result, MOB-typing provides a deeper phylogenetic depth than replicon-typing and new plasmid groups are uncovered. Significantly, MOB typing identified 17 plasmids and an integrative and conjugative element, which were not detected by replicon-typing. Four of these backbones were different from previously reported elements. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. New theories for smectic and nematic liquid-crystal polymers: Backbone LCPs [liquid crystalline polymers] and their mixtures and side-chain LCPs

    International Nuclear Information System (INIS)

    Dowell, F.

    1987-01-01

    A summary of predictions and explanations from statistical-physics theories for both backbone and side-chain liquid crystalline polymers (LCPs) and for mixtures with backbone LCPs are presented. Trends in the thermodynamic and molecular ordering properties have been calculated as a function of pressure, density, temperature, and molecule chemical structures (including degree of polymerization and the following properties of the chemical structures of the repeat units: lengths and shapes, intra-chain rotation energies, dipole moments, site-site polarizabilities and Lennard-Jones potentials, etc.) in nematic and multiple smectic-A LC phases and in the isotropic liquid phase. The theoretical results are found to be in good agreement with existing experimental data. These theories can also be applied to combined LCPs. Since these theories have no ad hoc or arbitrarily adjustable parameters, these theories can be used to design new LCPs and new solvents as well as to predict and explain properties. 27 refs., 4 tabs

  16. Protein Side-Chain Resonance Assignment and NOE Assignment Using RDC-Defined Backbones without TOCSY Data3

    Science.gov (United States)

    Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

    2011-01-01

    One bottleneck in NMR structure determination lies in the laborious and time-consuming process of side-chain resonance and NOE assignments. Compared to the well-studied backbone resonance assignment problem, automated side-chain resonance and NOE assignments are relatively less explored. Most NOE assignment algorithms require nearly complete side-chain resonance assignments from a series of through-bond experiments such as HCCH-TOCSY or HCCCONH. Unfortunately, these TOCSY experiments perform poorly on large proteins. To overcome this deficiency, we present a novel algorithm, called NASCA (NOE Assignment and Side-Chain Assignment), to automate both side-chain resonance and NOE assignments and to perform high-resolution protein structure determination in the absence of any explicit through-bond experiment to facilitate side-chain resonance assignment, such as HCCH-TOCSY. After casting the assignment problem into a Markov Random Field (MRF), NASCA extends and applies combinatorial protein design algorithms to compute optimal assignments that best interpret the NMR data. The MRF captures the contact map information of the protein derived from NOESY spectra, exploits the backbone structural information determined by RDCs, and considers all possible side-chain rotamers. The complexity of the combinatorial search is reduced by using a dead-end elimination (DEE) algorithm, which prunes side-chain resonance assignments that are provably not part of the optimal solution. Then an A* search algorithm is employed to find a set of optimal side-chain resonance assignments that best fit the NMR data. These side-chain resonance assignments are then used to resolve the NOE assignment ambiguity and compute high-resolution protein structures. Tests on five proteins show that NASCA assigns resonances for more than 90% of side-chain protons, and achieves about 80% correct assignments. The final structures computed using the NOE distance restraints assigned by NASCA have backbone RMSD 0

  17. Optoelectronic Devices Based on Novel Semiconductor Structures

    National Research Council Canada - National Science Library

    Ding, Yujie

    1999-01-01

    .... We have implemented several new schemes for efficiently generating blue and green light. We have grown and characterized several structures towards optically-pumped three- and four-level intersubband lasers...

  18. Modal Based Fatigue Monitoring of Steel Structures

    DEFF Research Database (Denmark)

    Graugaard-Jensen, J.; Brincker, Rune; Hjelm, H. P.

    2005-01-01

    In this paper it is shown how the accumulated fatigue in steel structures can be estimated with high accuracy by continuously measuring the accelerations in a few points of the structure. First step is to obtain a good estimate of the mode shapes by performing a natural input modal analysis. The so...... the damage forecasted by commonly accepted design rules. This points to possibilities of significantly increasing the fatigue lives of structures by performing continuous monitoring....... obtained mode shapes are then used to calibrate a Finite Element model of the structure and to obtain the modal coordinates of the active modes by inverting the mode shape matrix. If the number of active modes is smaller than the number of measurement points, then the problem is solved by regression...

  19. Dependence of crystallite formation and preferential backbone orientations on the side chain pattern in PBDTTPD polymers

    KAUST Repository

    El Labban, Abdulrahman

    2014-11-26

    (Figure Presented) Alkyl substituents appended to the π-conjugated main chain account for the solution-processability and film-forming properties of most π-conjugated polymers for organic electronic device applications, including field-effect transistors (FETs) and bulk-heterojunction (BHJ) solar cells. Beyond film-forming properties, recent work has emphasized the determining role that side-chain substituents play on polymer self-assembly and thin-film nanostructural order, and, in turn, on device performance. However, the factors that determine polymer crystallite orientation in thin-films, implying preferential backbone orientation relative to the device substrate, are a matter of some debate, and these structural changes remain difficult to anticipate. In this report, we show how systematic changes in the side-chain pattern of poly(benzo[1,2-b:4,5-b′]dithiophene-alt-thieno[3,4-c]pyrrole-4,6-dione) (PBDTTPD) polymers can (i) influence the propensity of the polymer to order in the π-stacking direction, and (ii) direct the preferential orientation of the polymer crystallites in thin films (e.g., "face-on" vs "edge-on"). Oriented crystallites, specifically crystallites that are well-ordered in the π-stacking direction, are believed to be a key contributor to improved thin-film device performance in both FETs and BHJ solar cells.

  20. Navigating the massive world of reddit: using backbone networks to map user interests in social media

    Directory of Open Access Journals (Sweden)

    Randal S. Olson

    2015-05-01

    Full Text Available In the massive online worlds of social media, users frequently rely on organizing themselves around specific topics of interest to find and engage with like-minded people. However, navigating these massive worlds and finding topics of specific interest often proves difficult because the worlds are mostly organized haphazardly, leaving users to find relevant interests by word of mouth or using a basic search feature. Here, we report on a method using the backbone of a network to create a map of the primary topics of interest in any social network. To demonstrate the method, we build an interest map for the social news web site reddit and show how such a map could be used to navigate a social media world. Moreover, we analyze the network properties of the reddit social network and find that it has a scale-free, small-world, and modular community structure, much like other online social networks such as Facebook and Twitter. We suggest that the integration of interest maps into popular social media platforms will assist users in organizing themselves into more specific interest groups, which will help alleviate the overcrowding effect often observed in large online communities.

  1. Oligomerized backbone pilin helps piliated Lactococcus lactis to withstand shear flow.

    Science.gov (United States)

    Castelain, Mickaël; Duviau, Marie-Pierre; Oxaran, Virginie; Schmitz, Philippe; Cocaign-Bousquet, Muriel; Loubière, Pascal; Piard, Jean-Christophe; Mercier-Bonin, Muriel

    2016-09-01

    The present work focuses on the role of pili present at the cell surface of Lactococcus lactis in bacterial adhesion to abiotic (hydrophobic polystyrene) and biotic (mucin-coated polystyrene) surfaces. Native pili-displaying strains and isogenic derivatives in which pilins or sortase C structural genes had been modified were used. Surface physico-chemistry, morphology and shear-flow-induced detachment of lactococcal cells were evaluated. The involvement of pili in L. lactis adhesion was clearly demonstrated, irrespective of the surface characteristics (hydrophobic/hydrophilic, presence or not of specific binding sites). The accessory pilin, PilC, and the backbone pilin, PilB, were revealed to play a major role in adhesion, provided that the PilB was present in its polymerized form. Within the population fraction that remained attached to the surface under increasing shear flow, different association behaviors were observed, showing that pili could serve as anchoring sites thus hampering the effect of shear flow on cell orientation and detachment.

  2. Redox-controlled backbone dynamics of human cytochrome c revealed by 15N NMR relaxation measurements

    International Nuclear Information System (INIS)

    Sakamoto, Koichi; Kamiya, Masakatsu; Uchida, Takeshi; Kawano, Keiichi; Ishimori, Koichiro

    2010-01-01

    Research highlights: → The dynamic parameters for the backbone dynamics in Cyt c were determined. → The backbone mobility of Cyt c is highly restricted due to the covalently bound heme. → The backbone mobility of Cyt c is more restricted upon the oxidation of the heme. → The redox-dependent dynamics are shown in the backbone of Cyt c. → The backbone dynamics of Cyt c would regulate the electron transfer from Cyt c. -- Abstract: Redox-controlled backbone dynamics in cytochrome c (Cyt c) were revealed by 2D 15 N NMR relaxation experiments. 15 N T 1 and T 2 values and 1 H- 15 N NOEs of uniformly 15 N-labeled reduced and oxidized Cyt c were measured, and the generalized order parameters (S 2 ), the effective correlation time for internal motion (τ e ), the 15 N exchange broadening contributions (R ex ) for each residue, and the overall correlation time (τ m ) were estimated by model-free dynamics formalism. These dynamic parameters clearly showed that the backbone dynamics of Cyt c are highly restricted due to the covalently bound heme that functions as the stable hydrophobic core. Upon oxidation of the heme iron in Cyt c, the average S 2 value was increased from 0.88 ± 0.01 to 0.92 ± 0.01, demonstrating that the mobility of the backbone is further restricted in the oxidized form. Such increases in the S 2 values were more prominent in the loop regions, including amino acid residues near the thioether bonds to the heme moiety and positively charged region around Lys87. Both of the regions are supposed to form the interaction site for cytochrome c oxidase (CcO) and the electron pathway from Cyt c to CcO. The redox-dependent mobility of the backbone in the interaction site for the electron transfer to CcO suggests an electron transfer mechanism regulated by the backbone dynamics in the Cyt c-CcO system.

  3. Distributed Prognostics Based on Structural Model Decomposition

    Data.gov (United States)

    National Aeronautics and Space Administration — Within systems health management, prognostics focuses on predicting the remaining useful life of a system. In the model-based prognostics paradigm, physics-based...

  4. Phylogenomics resolves a spider backbone phylogeny and rejects a prevailing paradigm for orb web evolution.

    Science.gov (United States)

    Bond, Jason E; Garrison, Nicole L; Hamilton, Chris A; Godwin, Rebecca L; Hedin, Marshal; Agnarsson, Ingi

    2014-08-04

    Spiders represent an ancient predatory lineage known for their extraordinary biomaterials, including venoms and silks. These adaptations make spiders key arthropod predators in most terrestrial ecosystems. Despite ecological, biomedical, and biomaterial importance, relationships among major spider lineages remain unresolved or poorly supported. Current working hypotheses for a spider "backbone" phylogeny are largely based on morphological evidence, as most molecular markers currently employed are generally inadequate for resolving deeper-level relationships. We present here a phylogenomic analysis of spiders including taxa representing all major spider lineages. Our robust phylogenetic hypothesis recovers some fundamental and uncontroversial spider clades, but rejects the prevailing paradigm of a monophyletic Orbiculariae, the most diverse lineage, containing orb-weaving spiders. Based on our results, the orb web either evolved much earlier than previously hypothesized and is ancestral for a majority of spiders or else it has multiple independent origins, as hypothesized by precladistic authors. Cribellate deinopoid orb weavers that use mechanically adhesive silk are more closely related to a diverse clade of mostly webless spiders than to the araneoid orb-weaving spiders that use adhesive droplet silks. The fundamental shift in our understanding of spider phylogeny proposed here has broad implications for interpreting the evolution of spiders, their remarkable biomaterials, and a key extended phenotype--the spider web. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Hydrogen bond rotations as a uniform structural tool for analyzing protein architecture

    Science.gov (United States)

    Penner, Robert C.; Andersen, Ebbe S.; Jensen, Jens L.; Kantcheva, Adriana K.; Bublitz, Maike; Nissen, Poul; Rasmussen, Anton M. H.; Svane, Katrine L.; Hammer, Bjørk; Rezazadegan, Reza; Nielsen, Niels Chr.; Nielsen, Jakob T.; Andersen, Jørgen E.

    2014-12-01

    Proteins fold into three-dimensional structures, which determine their diverse functions. The conformation of the backbone of each structure is locally at each Cα effectively described by conformational angles resulting in Ramachandran plots. These, however, do not describe the conformations around hydrogen bonds, which can be non-local along the backbone and are of major importance for protein structure. Here, we introduce the spatial rotation between hydrogen bonded peptide planes as a new descriptor for protein structure locally around a hydrogen bond. Strikingly, this rotational descriptor sampled over high-quality structures from the protein data base (PDB) concentrates into 30 localized clusters, some of which correlate to the common secondary structures and others to more special motifs, yet generally providing a unifying systematic classification of local structure around protein hydrogen bonds. It further provides a uniform vocabulary for comparison of protein structure near hydrogen bonds even between bonds in different proteins without alignment.

  6. Reliability based Robustness of Timber Structures through NDT Data Updating

    DEFF Research Database (Denmark)

    Sousa, Hélder S.; Sørensen, John Dalsgaard; Kirkegaard, Poul Henning

    2011-01-01

    This work presents a framework for reliability-based assessment of timber structures / members using data gathered from non-destructive test results. These results are used for modeling an update of the mechanical characteristics of timber, using Bayesian methods. Results gathered from ultrasound...... of the structure, thus, being possible to evaluate reliability based in time dependent factors, as well to categorize that structure in terms of robustness. For exemplification of the underlined concepts, three different types of structures are studied....

  7. Robustness and backbone motif of a cancer network regulated by miR-17-92 cluster during the G1/S transition.

    Directory of Open Access Journals (Sweden)

    Lijian Yang

    Full Text Available Based on interactions among transcription factors, oncogenes, tumor suppressors and microRNAs, a Boolean model of cancer network regulated by miR-17-92 cluster is constructed, and the network is associated with the control of G1/S transition in the mammalian cell cycle. The robustness properties of this regulatory network are investigated by virtue of the Boolean network theory. It is found that, during G1/S transition in the cell cycle process, the regulatory networks are robustly constructed, and the robustness property is largely preserved with respect to small perturbations to the network. By using the unique process-based approach, the structure of this network is analyzed. It is shown that the network can be decomposed into a backbone motif which provides the main biological functions, and a remaining motif which makes the regulatory system more stable. The critical role of miR-17-92 in suppressing the G1/S cell cycle checkpoint and increasing the uncontrolled proliferation of the cancer cells by targeting a genetic network of interacting proteins is displayed with our model.

  8. 1H, 15N and 13C backbone resonance assignments of pentaerythritol tetranitrate reductase from Enterobacter cloacae PB2.

    Science.gov (United States)

    Iorgu, Andreea I; Baxter, Nicola J; Cliff, Matthew J; Waltho, Jonathan P; Hay, Sam; Scrutton, Nigel S

    2018-04-01

    Pentaerythritol tetranitrate reductase (PETNR) is a flavoenzyme possessing a broad substrate specificity and is a member of the Old Yellow Enzyme family of oxidoreductases. As well as having high potential as an industrial biocatalyst, PETNR is an excellent model system for studying hydrogen transfer reactions. Mechanistic studies performed with PETNR using stopped-flow methods have shown that tunneling contributes towards hydride transfer from the NAD(P)H coenzyme to the flavin mononucleotide (FMN) cofactor and fast protein dynamics have been inferred to facilitate this catalytic step. Herein, we report the near-complete 1 H, 15 N and 13 C backbone resonance assignments of PETNR in a stoichiometric complex with the FMN cofactor in its native oxidized form, which were obtained using heteronuclear multidimensional NMR spectroscopy. A total of 97% of all backbone resonances were assigned, with 333 out of a possible 344 residues assigned in the 1 H- 15 N TROSY spectrum. This is the first report of an NMR structural study of a flavoenzyme from the Old Yellow Enzyme family and it lays the foundation for future investigations of functional dynamics in hydride transfer catalytic mechanism.

  9. Protein Structure-Function Correlation in Living Human Red Blood Cells Probed by Isotope Exchange-based Mass Spectrometry.

    Science.gov (United States)

    Narayanan, Sreekala; Mitra, Gopa; Muralidharan, Monita; Mathew, Boby; Mandal, Amit K

    2015-12-01

    To gain insight into the underlying mechanisms of various biological events, it is important to study the structure-function correlation of proteins within cells. Structural probes used in spectroscopic tools to investigate protein conformation are similar across all proteins. Therefore, structural studies are restricted to purified proteins in vitro and these findings are extrapolated in cells to correlate their functions in vivo. However, due to cellular complexity, in vivo and in vitro environments are radically different. Here, we show a novel way to monitor the structural transition of human hemoglobin upon oxygen binding in living red blood cells (RBCs), using hydrogen/deuterium exchange-based mass spectrometry (H/DX-MS). Exploiting permeability of D2O across cell membrane, the isotope exchange of polypeptide backbone amide hydrogens of hemoglobin was carried out inside RBCs and monitored using matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). To explore the conformational transition associated with oxygenation of hemoglobin in vivo, the isotope exchange kinetics was simplified using the method of initial rates. RBC might be considered as an in vivo system of pure hemoglobin. Thus, as a proof-of-concept, the observed results were correlated with structural transition of hemoglobin associated with its function established in vitro. This is the first report on structural changes of a protein upon ligand binding in its endogenous environment. The proposed method might be applicable to proteins in their native state, irrespective of location, concentration, and size. The present in-cell approach opens a new avenue to unravel a plethora of biological processes like ligand binding, folding, and post-translational modification of proteins in living cells.

  10. Structuring AHP-based maintenance policy selection

    NARCIS (Netherlands)

    Goossens, Adriaan; Basten, Robertus Johannes Ida; Hummel, J. Marjan; van der Wegen, Leonardus L.M.

    2015-01-01

    We aim to structure the maintenance policy selection process for ships, using the Analytic Hierarchy Process (AHP). Maintenance is an important contributor to reach the intended life-time of capital technical assets, and it is gaining increasing interest and relevance. A maintenance policy is a

  11. Base connections for signal/sign structures.

    Science.gov (United States)

    2012-02-01

    The Atlantic hurricane season of 2004 brought with it a series of four major hurricanes that made landfall across : Florida within a six-week period. During this time, a number of cantilever sign structures along the state interstate system : failed....

  12. Exploring backbone-cation alkyl spacers for multi-cation side chain anion exchange membranes

    Science.gov (United States)

    Zhu, Liang; Yu, Xuedi; Hickner, Michael A.

    2018-01-01

    In order to systematically study how the arrangement of cations on the side chain and length of alkyl spacers between cations impact the performance of multi-cation AEMs for alkaline fuel cells, a series of polyphenylene oxide (PPO)-based AEMs with different cationic side chains were synthesized. This work resulted in samples with two or three cations in a side chain pendant to the PPO backbone. More importantly, the length of the spacer between cations varied from 3 methylene (-CH2-) (C3) groups to 8 methylene (C8) groups. The highest conductivity, up to 99 mS/cm in liquid water at room temperature, was observed for the triple-cation side chain AEM with pentyl (C5) or hexyl (C6) spacers. The multi-cation AEMs were found to have decreased water uptake and ionic conductivity when the spacer chains between cations were lengthened from pentyl (C5) or hexyl (C6) to octyl (C8) linking groups. The triple-cation membranes with pentyl (C5) or hexyl (C6) groups between cations showed greatest stability after immersion in 1 M NaOH at 80 °C for 500 h.

  13. A Novel Structure for MEMS Based Varactors

    Directory of Open Access Journals (Sweden)

    Ebrahim Abbaspour-Sani

    2006-08-01

    Full Text Available A novel structure with electro-mechanically tunable capacitor for RF application is presented. The suspended electrodes are designed in such a way that both are electrostaticaly displaceable. This double plate moveability feature of the capacitor increases the tuning range. In this structure, there is no need for cantilever beams, which introduce considerable series resistance to the capacitor and decrease the quality factor. Therefore, our proposed varactor achieves better Q in a smaller area. The simulated one pF capacitor shows a Q of 40 at 1 GHz and a tuning range of 42%. Pull-in voltage is 3.6 V, which is a reasonable value for submicron CMOS technologies.

  14. Cost-effectiveness analysis of dolutegravir plus backbone compared with raltegravir plus backbone, darunavir+ritonavir plus backbone and efavirenz/tenofovir/emtricitabine in treatment naïve and experienced HIV-positive patients

    Directory of Open Access Journals (Sweden)

    Restelli U

    2017-06-01

    Full Text Available Umberto Restelli,1,2 Giuliano Rizzardini,3,4 Andrea Antinori,5 Adriano Lazzarin,6 Marzia Bonfanti,1 Paolo Bonfanti,7 Davide Croce1,2 1Centre for Research on Health Economics, Social and Health Care Management, LIUC – Università Cattaneo, Castellanza, Varese, Italy; 2School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; 3First and Second Divisions of Infectious Diseases, “Luigi Sacco” Hospital, Milan, Italy; 4School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; 5National Institute for Infectious Diseases “L Spallanzani”, Rome, 6Department of Infectious Diseases, San Raffaele Scientific Institute, 7Department of Infectious and Tropical Diseases, A Manzoni Hospital, Lecco, Italy Background: In January 2014, the European Medicines Agency issued a marketing authorization for dolutegravir (DTG, a second-generation integrase strand transfer inhibitor for HIV treatment. The study aimed at determining the incremental cost-effectiveness ratio (ICER of the use of DTG+backbone compared with raltegravir (RAL+backbone, darunavir (DRV+ritonavir(r+backbone and efavirenz/tenofovir/emtricitabine (EFV/TDF/FTC in HIV-positive treatment-naïve patients and compared with RAL+backbone in treatment-experienced patients, from the Italian National Health Service’s point of view.Materials and methods: A published Monte Carlo Individual Simulation Model (ARAMIS-DTG model was used to perform the analysis. Patients pass through mutually exclusive health states (defined in terms of diagnosis of HIV with or without opportunistic infections [OIs] and cardiovascular disease [CVD] and successive lines of therapy. The model considers costs (2014 and quality of life per monthly cycle in a lifetime horizon. Costs and quality-adjusted life years (QALYs are dependent on OI, CVD, AIDS events, adverse events and antiretroviral therapies.Results: In

  15. Quantification of protein backbone hydrogen-deuterium exchange rates by solid state NMR spectroscopy.

    Science.gov (United States)

    del Amo, Juan-Miguel Lopez; Fink, Uwe; Reif, Bernd

    2010-12-01

    We present the quantification of backbone amide hydrogen-deuterium exchange rates (HDX) for immobilized proteins. The experiments make use of the deuterium isotope effect on the amide nitrogen chemical shift, as well as on proton dilution by deuteration. We find that backbone amides in the microcrystalline α-spectrin SH3 domain exchange rather slowly with the solvent (with exchange rates negligible within the individual (15)N-T (1) timescales). We observed chemical exchange for 6 residues with HDX exchange rates in the range from 0.2 to 5 s(-1). Backbone amide (15)N longitudinal relaxation times that we determined previously are not significantly affected for most residues, yielding no systematic artifacts upon quantification of backbone dynamics (Chevelkov et al. 2008b). Significant exchange was observed for the backbone amides of R21, S36 and K60, as well as for the sidechain amides of N38, N35 and for W41ε. These residues could not be fit in our previous motional analysis, demonstrating that amide proton chemical exchange needs to be considered in the analysis of protein dynamics in the solid-state, in case D(2)O is employed as a solvent for sample preparation. Due to the intrinsically long (15)N relaxation times in the solid-state, the approach proposed here can expand the range of accessible HDX rates in the intermediate regime that is not accessible so far with exchange quench and MEXICO type experiments.

  16. Quantification of protein backbone hydrogen-deuterium exchange rates by solid state NMR spectroscopy

    International Nuclear Information System (INIS)

    Lopez del Amo, Juan-Miguel; Fink, Uwe; Reif, Bernd

    2010-01-01

    We present the quantification of backbone amide hydrogen-deuterium exchange rates (HDX) for immobilized proteins. The experiments make use of the deuterium isotope effect on the amide nitrogen chemical shift, as well as on proton dilution by deuteration. We find that backbone amides in the microcrystalline α-spectrin SH3 domain exchange rather slowly with the solvent (with exchange rates negligible within the individual 15 N-T 1 timescales). We observed chemical exchange for 6 residues with HDX exchange rates in the range from 0.2 to 5 s -1 . Backbone amide 15 N longitudinal relaxation times that we determined previously are not significantly affected for most residues, yielding no systematic artifacts upon quantification of backbone dynamics (Chevelkov et al. 2008b). Significant exchange was observed for the backbone amides of R21, S36 and K60, as well as for the sidechain amides of N38, N35 and for W41ε. These residues could not be fit in our previous motional analysis, demonstrating that amide proton chemical exchange needs to be considered in the analysis of protein dynamics in the solid-state, in case D 2 O is employed as a solvent for sample preparation. Due to the intrinsically long 15 N relaxation times in the solid-state, the approach proposed here can expand the range of accessible HDX rates in the intermediate regime that is not accessible so far with exchange quench and MEXICO type experiments.

  17. Use of Just in Time Maintenance of Reinforced Concrete Bridge Structures based on Real Historical Data Deterioration Models

    Directory of Open Access Journals (Sweden)

    Abu-Tair A.

    2016-01-01

    Full Text Available Concrete is the backbone of any developed economy. Concrete can suffer from a large number of deleterious effects including physical, chemical and biological causes. Large owning bridge structures organizations are facing very serious questions when asking for maintenance budgets. The questions range from needing to justify the need for the work, its urgency, to also have to predict or show the consequences of delayed rehabilitation of a particular structure. There is therefore a need for a probabilistic model that can estimate the range of service lives of bridge populations and also the likelihood of level of deteriorations it can reached for every incremental time interval. A model was developed for such estimation based on statistical data from actual inspection records of a large reinforced concrete bridge portfolio. The method used both deterministic and stochastic methods to predict the service life of a bridge, using these service lives in combination with the just in time (JIT principle of management would enable maintenance managers to justify the need for action and the budgets needed, to intervene at the optimum time in the life of the structure and that of the deterioration. The paper will report on the model which is based on a large database of deterioration records of concrete bridges covering a period of over 60 years and include data from over 400 bridge structures. The paper will also illustrate how the service life model was developed and how these service lives combined with the JIT can be used to effectively allocate resources and use them to keep a major infrastructure asset moving with little disruption to the transport system and its users.

  18. Molecular dynamics simulations of ligand-induced backbone conformational changes in the binding site of the periplasmic lysine-, arginine-, ornithine-binding protein

    Science.gov (United States)

    Yang, Ami Y.-C.; Mancera, Ricardo L.

    2008-11-01

    The periplasmic lysine-, arginine-, ornithine-binding protein (LAOBP) traps its ligands by a large hinge bending movement between two globular domains. The overall geometry of the binding site remains largely unchanged between the open (unliganded) and closed (liganded) forms, with only a small number of residues exhibiting limited movement of their side chains. However, in the case of the ornithine-bound structure, the backbone peptide bond between Asp11 and Thr12 undergoes a large rotation. Molecular dynamics simulations have been used to investigate the origin and mechanism of this backbone movement. Simulations allowing flexibility of a limited region and of the whole binding site, with and without bound ligands, suggest that this conformational change is induced by the binding of ornithine, leading to the stabilisation of an energetically favourable alternative conformation.

  19. CSTutor: A Sketch-Based Tool for Visualizing Data Structures

    Science.gov (United States)

    Buchanan, Sarah; Laviola, Joseph J., Jr.

    2014-01-01

    We present CSTutor, a sketch-based interface designed to help students understand data structures, specifically Linked Lists, Binary Search Trees, AVL Trees, and Heaps. CSTutor creates an environment that seamlessly combines a user's sketched diagram and code. In each of these data structure modes, the user can naturally sketch a data structure on…

  20. Strengthening of Concrete Structures with cement based bonded composites

    DEFF Research Database (Denmark)

    Täljsten, Björn; Blanksvärd, Thomas

    2008-01-01

    Due to demands on higher loads, degradation, re-construction etc. there is a constant need for repair or strengthening of existing concrete structures. Many varying methods exist to strengthen concrete structures, one such commonly used technique utilizes surface epoxy bonded FRPs (Fibre Reinforced...... with improved working environment and better compatibility to the base concrete structure. This study gives an overview of different cement based systems, all with very promising results for structural upgrading. Studied parameters are structural retrofit for bending, shear and confinement. It is concluded...

  1. ROMP- and RAFT-Based Guanidinium-Containing Polymers as Scaffolds for Protein Mimic Synthesis.

    Science.gov (United States)

    Sarapas, Joel M; Backlund, Coralie M; deRonde, Brittany M; Minter, Lisa M; Tew, Gregory N

    2017-05-17

    Cell-penetrating peptides are an important class of molecules with promising applications in bioactive cargo delivery. A diverse series of guanidinium-containing polymeric cell-penetrating peptide mimics (CPPMs) with varying backbone chemistries was synthesized and assessed for delivery of both GFP and fluorescently tagged siRNA. Specifically, we examined CPPMs based on norbornene, methacrylate, and styrene backbones to determine how backbone structure impacted internalization of these two cargoes. Either charge content or degree of polymerization was held constant at 20, with diguanidinium norbornene molecules being polymerized to both 10 and 20 repeat units. Generally, homopolymer CPPMs delivered low amounts of siRNA into Jurkat T cells, with no apparent backbone dependence; however, by adding a short hydrophobic methyl methacrylate block to the guanidinium-rich methacrylate polymer, siRNA delivery to nearly the entire cell population was achieved. Protein internalization yielded similar results for most of the CPPMs, though the block polymer was unable to deliver proteins. In contrast, the styrene-based CPPM yielded the highest internalization for GFP (≈40 % of cells affected), showing that indeed backbone chemistry impacts protein delivery, specifically through the incorporation of an aromatic group. These results demonstrate that an understanding of how polymer structure affects cargo-dependent internalization is critical to designing new, more effective CPPMs. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Structural Bases of Postresuscitative Heart Failure

    Directory of Open Access Journals (Sweden)

    V. T. Dolgikh

    2005-01-01

    Full Text Available An experiment on 106 non-inbred male albino rats undergone 4-minute clinical death from acute blood loss has revealed that the first three days after resuscitation are marked by a concomitance of vascular disorders and cardiomyocytic dystrophic changes, the leading role being played by sludge, stasis, thrombosis, increased vascular permeability, perivascular edema, and hemorrhages. Cardiomyocytic destruction (various contractures, block-like myofibrillolysis, myocytoly-sis is a structural basis of postresuscitative heart failure. Three days later the heart displayed concomitant processes of recovery and damage. Three types of cardiac morphological changes have been identified in relation to the ratio of these processes.

  3. Structure-based bayesian sparse reconstruction

    KAUST Repository

    Quadeer, Ahmed Abdul

    2012-12-01

    Sparse signal reconstruction algorithms have attracted research attention due to their wide applications in various fields. In this paper, we present a simple Bayesian approach that utilizes the sparsity constraint and a priori statistical information (Gaussian or otherwise) to obtain near optimal estimates. In addition, we make use of the rich structure of the sensing matrix encountered in many signal processing applications to develop a fast sparse recovery algorithm. The computational complexity of the proposed algorithm is very low compared with the widely used convex relaxation methods as well as greedy matching pursuit techniques, especially at high sparsity. © 1991-2012 IEEE.

  4. Benefits of Risk Based Inspection Planning for Offshore Structures

    DEFF Research Database (Denmark)

    Straub, D.M.; Goyet, J.; Sørensen, John Dalsgaard

    2006-01-01

    The economical benefits of applying risk-based inspection planning (RBI) for offshore structures subject to fatigue are evaluated based on experiences from past industrial projects. To this end, the factors influencing the cost of inspection, repair and failure of structures are discussed......, the financial benefit of RBI is assessed....

  5. Base pairing in RNA structures: A computational analysis of ...

    Indian Academy of Sciences (India)

    The base pairing patterns in RNA structures are more versatile and completely different as compared to DNA. We present here results of ab-initio studies of structures and interaction energies of eight selected RNA base pairs reported in literature. Interaction energies, including BSSE correction, of hydrogen added crystal ...

  6. [Structuralization of digestive endoscopy report based on NLP].

    Science.gov (United States)

    Kong, Xiao-feng; Li, Ying; Li, Hao-min; Lu, Xu-dong

    2008-09-01

    This paper presents a method based on NLP to realize structuralization of digestive endoscopy reports. The method is taking advantage of existing NLP's processing technologies and introducing minimal standard terminology (MST) to transform a narrative gastroscopy report into the structuralization report based on MST, whose accuracy rate is 92.3%.

  7. Base pairing in RNA structures: A computational analysis

    Indian Academy of Sciences (India)

    The base pairing patterns in RNA structures are more versatile and completely different as compared to DNA. We present here results of ab-initio studies of structures and interaction energies of eight selected RNA base pairs reported in literature. Interaction energies, including BSSE correction, of hydrogen added crystal ...

  8. A Synthetic HIV-1 Subtype C Backbone Generates Comparable PR and RT Resistance Profiles to a Subtype B Backbone in a Recombinant Virus Assay

    OpenAIRE

    Nauwelaers, David; Van Houtte, Margriet; Winters, Bart; Steegen, Kim; Van Baelen, Kurt; Chi, Ellen; Zhou, Mimi; Steiner, Derek; Bonesteel, Rachelle; Aston, Colin; Stuyver, Lieven J.

    2011-01-01

    In order to determine phenotypic protease and reverse transcriptase inhibitor-associated resistance in HIV subtype C virus, we have synthetically constructed an HIV-1 subtype C (HIV-1-C) viral backbone for use in a recombinant virus assay. The in silico designed viral genome was divided into 4 fragments, which were chemically synthesized and joined together by conventional subcloning. Subsequently, gag-protease-reverse-transcriptase (GPRT) fragments from 8 HIV-1 subtype C-infected patient sam...

  9. Characterizing structural transitions using localized free energy landscape analysis.

    Directory of Open Access Journals (Sweden)

    Nilesh K Banavali

    Full Text Available Structural changes in molecules are frequently observed during biological processes like replication, transcription and translation. These structural changes can usually be traced to specific distortions in the backbones of the macromolecules involved. Quantitative energetic characterization of such distortions can greatly advance the atomic-level understanding of the dynamic character of these biological processes.Molecular dynamics simulations combined with a variation of the Weighted Histogram Analysis Method for potential of mean force determination are applied to characterize localized structural changes for the test case of cytosine (underlined base flipping in a GTCAGCGCATGG DNA duplex. Free energy landscapes for backbone torsion and sugar pucker degrees of freedom in the DNA are used to understand their behavior in response to the base flipping perturbation. By simplifying the base flipping structural change into a two-state model, a free energy difference of upto 14 kcal/mol can be attributed to the flipped state relative to the stacked Watson-Crick base paired state. This two-state classification allows precise evaluation of the effect of base flipping on local backbone degrees of freedom.The calculated free energy landscapes of individual backbone and sugar degrees of freedom expectedly show the greatest change in the vicinity of the flipping base itself, but specific delocalized effects can be discerned upto four nucleotide positions away in both 5' and 3' directions. Free energy landscape analysis thus provides a quantitative method to pinpoint the determinants of structural change on the atomic scale and also delineate the extent of propagation of the perturbation along the molecule. In addition to nucleic acids, this methodology is anticipated to be useful for studying conformational changes in all macromolecules, including carbohydrates, lipids, and proteins.

  10. The Reticular Cell Network : A Robust Backbone for Immune Responses

    NARCIS (Netherlands)

    Textor, Johannes; Mandl, Judith N; de Boer, Rob J

    2016-01-01

    Lymph nodes are meeting points for circulating immune cells. A network of reticular cells that ensheathe a mesh of collagen fibers crisscrosses the tissue in each lymph node. This reticular cell network distributes key molecules and provides a structure for immune cells to move around on. During

  11. Traditionally, sardine Sardinops sagax has been the backbone of ...

    African Journals Online (AJOL)

    denise

    1 January. Although dividing cohorts from length frequencies is not the best method for determining age structure of a stock, it is believed to give an indication adequate for the purpose of the present study. Splitting 0-group fish from older cohorts was carried out in an easy and precise manner. Failing to divide the I- from the.

  12. Electronic structure of Fe-based superconductors

    Indian Academy of Sciences (India)

    pounds [2,3] renewed great interest in the study of high-temperature superconductivity. Fe-based systems are significantly different from the cuprates. The parent compounds in cuprates are antiferromagnetic Mott insulators, where the insulating property arises due to strong electron correlation compared to the width of their ...

  13. Wetting of nonconserved residue-backbones: A feature indicative of aggregation associated regions of proteins.

    Science.gov (United States)

    Pradhan, Mohan R; Pal, Arumay; Hu, Zhongqiao; Kannan, Srinivasaraghavan; Chee Keong, Kwoh; Lane, David P; Verma, Chandra S

    2016-02-01

    Aggregation is an irreversible form of protein complexation and often toxic to cells. The process entails partial or major unfolding that is largely driven by hydration. We model the role of hydration in aggregation using "Dehydrons." "Dehydrons" are unsatisfied backbone hydrogen bonds in proteins that seek shielding from water molecules by associating with ligands or proteins. We find that the residues at aggregation interfaces have hydrated backbones, and in contrast to other forms of protein-protein interactions, are under less evolutionary pressure to be conserved. Combining evolutionary conservation of residues and extent of backbone hydration allows us to distinguish regions on proteins associated with aggregation (non-conserved dehydron-residues) from other interaction interfaces (conserved dehydron-residues). This novel feature can complement the existing strategies used to investigate protein aggregation/complexation. © 2015 Wiley Periodicals, Inc.

  14. Crystalline Structure of Starch Based Nano Composites

    OpenAIRE

    Farid Amidi Fazli; Afshin Babazadeh; Farnaz Amidi Fazli

    2015-01-01

    In contrast with literal meaning of nano, researchers have been achieved mega adventures in this area and every day more nanomaterials are being introduced to the market. After long time application of fossil-based plastics, nowadays accumulation of their waste seems to be a big problem to the environment. On the other hand, mankind has more attention to safety and living environment. Replacing common plastic packaging materials with degradable ones that degrade faster an...

  15. Ca-C backbone fragmentation dominates in electron detachment dissociation of gas-phase polypeptide polyanions

    DEFF Research Database (Denmark)

    Kjeldsen, Frank; Silivra, Oleg A; Ivonin, Igor A

    2005-01-01

    the dissociation of oxidized radical anions [M-nH]((n-1)-*. We demonstrate that C(alpha)-C cleavages, which are otherwise rarely observed in tandem mass spectrometry, can account for most of the backbone fragmentation, with even-electron x fragments dominating over radical a* ions. Ab initio calculations at the B3......Fragmentation of peptide polyanions by electron detachment dissociation (EDD) has been induced by electron irradiation of deprotonated polypeptides [M-nH](n-) with >10 eV electrons. EDD has been found to lead preferentially to a* and x fragment ions (C(alpha)-C backbone cleavage) arising from...

  16. On the purported "backbone fluorescence" in protein three-dimensional fluorescence spectra

    DEFF Research Database (Denmark)

    Bortolotti, Annalisa; Wong, Yin How; Korsholm, Stine S.

    2016-01-01

    claiming that this fluorescence originates from the protein backbone, contrary to the established knowledge that UV protein emission is due to aromatic amino acids only. Overall, our data clearly demonstrate that the observed emission upon excitation at 220-230 nm is due to the excitation of Tyr and/or Trp......, with subsequent emission from the lowest excited state (i.e. the same as obtained with 280 nm excitation) in agreement with Kasha's rule. Therefore, this fluorescence peak does not provide any information on backbone conformation, but simply reports on the local environment around the aromatic side chains, just...

  17. Convenient and Scalable Synthesis of Fmoc-Protected Peptide Nucleic Acid Backbone

    Directory of Open Access Journals (Sweden)

    Trevor A. Feagin

    2012-01-01

    Full Text Available The peptide nucleic acid backbone Fmoc-AEG-OBn has been synthesized via a scalable and cost-effective route. Ethylenediamine is mono-Boc protected, then alkylated with benzyl bromoacetate. The Boc group is removed and replaced with an Fmoc group. The synthesis was performed starting with 50 g of Boc anhydride to give 31 g of product in 32% overall yield. The Fmoc-protected PNA backbone is a key intermediate in the synthesis of nucleobase-modified PNA monomers. Thus, improved access to this molecule is anticipated to facilitate future investigations into the chemical properties and applications of nucleobase-modified PNA.

  18. Tuning the structural and electronic properties of novel thiophene-pyrrole based 1,2,3,4-tetrazine

    Science.gov (United States)

    Dutta, Rakesh; Kalita, Dhruba Jyoti

    2017-04-01

    Here, we have studied the structural and optoelectronic behaviour of a series of conjugated heterocyclic polymers. The basic monomer unit of the conjugated polymers contains a backbone of novel thiophene and pyrrole based 1,2,3,4-tetrazine. The other oligomers are designed by substituting the basic monomer unit with different electron-donating and electron-withdrawing groups at the nitrogen and the 3rd C-atom of the pyrrole and the thiophene ring respectively. We have calculated dihedral angles, HOMO-LUMO gaps, excitation energies and oscillator strengths by employing TD-DFT method. Our study reveals that compounds having bulky substituents exhibit larger dihedral angles. This in turn renders an increase in the band gaps (ΔH - L). Presence of the electron-withdrawing substituents also increases the ΔH - L values of the oligomers. However, the electron-donating groups decrease the ΔH - L values of the oligomers. Therefore, small electron-donating substituents have an overwhelming effect on the optoelectronic properties of the conjugated polymers which in turn makes them interesting materials with good conduction properties for fabrication of optoelectronic devices such as OLEDs, OFETs and solar cells.

  19. A structural informatics approach to mine kinase knowledge bases.

    Science.gov (United States)

    Brooijmans, Natasja; Mobilio, Dominick; Walker, Gary; Nilakantan, Ramaswamy; Denny, Rajiah A; Feyfant, Eric; Diller, David; Bikker, Jack; Humblet, Christine

    2010-03-01

    In this paper, we describe a combination of structural informatics approaches developed to mine data extracted from existing structure knowledge bases (Protein Data Bank and the GVK database) with a focus on kinase ATP-binding site data. In contrast to existing systems that retrieve and analyze protein structures, our techniques are centered on a database of ligand-bound geometries in relation to residues lining the binding site and transparent access to ligand-based SAR data. We illustrate the systems in the context of the Abelson kinase and related inhibitor structures. 2009 Elsevier Ltd. All rights reserved.

  20. The Deuterator: software for the determination of backbone amide deuterium levels from H/D exchange MS data

    Directory of Open Access Journals (Sweden)

    Tsinoremas NF

    2007-05-01

    Full Text Available Abstract Background The combination of mass spectrometry and solution phase amide hydrogen/deuterium exchange (H/D exchange experiments is an effective method for characterizing protein dynamics, and protein-protein or protein-ligand interactions. Despite methodological advancements and improvements in instrumentation and automation, data analysis and display remains a tedious process. The factors that contribute to this bottleneck are the large number of data points produced in a typical experiment, each requiring manual curation and validation, and then calculation of the level of backbone amide exchange. Tools have become available that address some of these issues, but lack sufficient integration, functionality, and accessibility required to address the needs of the H/D exchange community. To date there is no software for the analysis of H/D exchange data that comprehensively addresses these issues. Results We have developed an integrated software system for the automated analysis and representation of H/D exchange data that has been titled "The Deuterator". Novel approaches have been implemented that enable high throughput analysis, automated determination of deuterium incorporation, and deconvolution of overlapping peptides. This has been achieved by using methods involving iterative theoretical envelope fitting, and consideration of peak data within expected m/z ranges. Existing common file formats have been leveraged to allow compatibility with the output from the myriad of MS instrument platforms and peptide sequence database search engines. A web-based interface is used to integrate the components of The Deuterator that are able to analyze and present mass spectral data from instruments with varying resolving powers. The results, if necessary, can then be confirmed, adjusted, re-calculated and saved. Additional tools synchronize the curated calculation parameters with replicate time points, increasing throughput. Saved results can then

  1. Evaluating Functional and Structural Condition Based Maintenances of Airfield Pavements

    Directory of Open Access Journals (Sweden)

    Tarefder R.

    2013-01-01

    Full Text Available This study evaluates airfield pavements’ functional- and structural-condition to determine the most economical maintenance method. As a part of the analysis, Pavement Condition Index (PCI for several runways, taxiways, and aprons has been determined by MicroPAVER. Structural evaluation of airport pavements has been performed by Falling Weight Deflectometer (FWD test. Evaluation of Layer Moduli and Overlay Design (ELMOD also determines the required overlay thickness based on the E-values, i.e. FWD data analysis. Damage analysis determines the time of repeated overlay application. In addition, functional parameters have been included to determine the time of functional maintenance. Maintenance and rehabilitation alternatives have been selected to develop different program strategies. Life Cycle Cost Analysis (LCCA has been performed to determine the maintenance cost. Structural condition based maintenance cost is compared to functional condition based maintenance cost. Comparison shows that structural condition based approach yields cheaper maintenance strategies than functional condition based maintenance approach.

  2. Structural Health Monitoring Based on Combined Structural Global and Local Frequencies

    Directory of Open Access Journals (Sweden)

    Jilin Hou

    2014-01-01

    Full Text Available This paper presents a parameter estimation method for Structural Health Monitoring based on the combined measured structural global frequencies and structural local frequencies. First, the global test is experimented to obtain the low order modes which can reflect the global information of the structure. Secondly, the mass is added on the member of structure to increase the local dynamic characteristic and to make the member have local primary frequency, which belongs to structural local frequency and is sensitive to local parameters. Then the parameters of the structure can be optimized accurately using the combined structural global frequencies and structural local frequencies. The effectiveness and accuracy of the proposed method are verified by the experiment of a space truss.

  3. Performance-based shape optimization of continuum structures

    International Nuclear Information System (INIS)

    Liang Qingquan

    2010-01-01

    This paper presents a performance-based optimization (PBO) method for optimal shape design of continuum structures with stiffness constraints. Performance-based design concepts are incorporated in the shape optimization theory to achieve optimal designs. In the PBO method, the traditional shape optimization problem of minimizing the weight of a continuum structure with displacement or mean compliance constraints is transformed to the problem of maximizing the performance of the structure. The optimal shape of a continuum structure is obtained by gradually eliminating inefficient finite elements from the structure until its performance is maximized. Performance indices are employed to monitor the performance of optimized shapes in an optimization process. Performance-based optimality criteria are incorporated in the PBO method to identify the optimum from the optimization process. The PBO method is used to produce optimal shapes of plane stress continuum structures and plates in bending. Benchmark numerical results are provided to demonstrate the effectiveness of the PBO method for generating the maximum stiffness shape design of continuum structures. It is shown that the PBO method developed overcomes the limitations of traditional shape optimization methods in optimal design of continuum structures. Performance-based optimality criteria presented can be incorporated in any shape and topology optimization methods to obtain optimal designs of continuum structures.

  4. Mnn10 Maintains Pathogenicity in Candida albicans by Extending α-1,6-Mannose Backbone to Evade Host Dectin-1 Mediated Antifungal Immunity

    Science.gov (United States)

    Zhang, Shi Qun; Zou, Zui; Shen, Hui; Shen, Shuai Shuai; Miao, Qi; Huang, Xin; Liu, Wei; Li, Li Ping; Chen, Si Min; Yan, Lan; Zhang, Jun Dong; Zhao, Jing Jun; Xu, Guo Tong; An, Mao Mao; Jiang, Yuan Ying

    2016-01-01

    The cell wall is a dynamic structure that is important for the pathogenicity of Candida albicans. Mannan, which is located in the outermost layer of the cell wall, has been shown to contribute to the pathogenesis of C. albicans, however, the molecular mechanism by which this occurs remains unclear. Here we identified a novel α-1,6-mannosyltransferase encoded by MNN10 in C. albicans. We found that Mnn10 is required for cell wall α-1,6-mannose backbone biosynthesis and polysaccharides organization. Deletion of MNN10 resulted in significant attenuation of the pathogenesis of C. albicans in a murine systemic candidiasis model. Inhibition of α-1,6-mannose backbone extension did not, however, impact the invasive ability of C. albicans in vitro. Notably, mnn10 mutant restored the invasive capacity in athymic nude mice, which further supports the notion of an enhanced host antifungal defense related to this backbone change. Mnn10 mutant induced enhanced Th1 and Th17 cell mediated antifungal immunity, and resulted in enhanced recruitment of neutrophils and monocytes for pathogen clearance in vivo. We also demonstrated that MNN10 could unmask the surface β-(1,3)-glucan, a crucial pathogen-associated molecular pattern (PAMP) of C. albicans recognized by host Dectin-1. Our results demonstrate that mnn10 mutant could stimulate an enhanced Dectin-1 dependent immune response of macrophages in vitro, including the activation of nuclear factor-κB, mitogen-activated protein kinase pathways, and secretion of specific cytokines such as TNF-α, IL-6, IL-1β and IL-12p40. In summary, our study indicated that α-1,6-mannose backbone is critical for the pathogenesis of C. albicans via shielding β-glucan from recognition by host Dectin-1 mediated immune recognition. Moreover, our work suggests that inhibition of α-1,6-mannose extension by Mnn10 may represent a novel modality to reduce the pathogenicity of C. albicans. PMID:27144456

  5. Mnn10 Maintains Pathogenicity in Candida albicans by Extending α-1,6-Mannose Backbone to Evade Host Dectin-1 Mediated Antifungal Immunity.

    Directory of Open Access Journals (Sweden)

    Shi Qun Zhang

    2016-05-01

    Full Text Available The cell wall is a dynamic structure that is important for the pathogenicity of Candida albicans. Mannan, which is located in the outermost layer of the cell wall, has been shown to contribute to the pathogenesis of C. albicans, however, the molecular mechanism by which this occurs remains unclear. Here we identified a novel α-1,6-mannosyltransferase encoded by MNN10 in C. albicans. We found that Mnn10 is required for cell wall α-1,6-mannose backbone biosynthesis and polysaccharides organization. Deletion of MNN10 resulted in significant attenuation of the pathogenesis of C. albicans in a murine systemic candidiasis model. Inhibition of α-1,6-mannose backbone extension did not, however, impact the invasive ability of C. albicans in vitro. Notably, mnn10 mutant restored the invasive capacity in athymic nude mice, which further supports the notion of an enhanced host antifungal defense related to this backbone change. Mnn10 mutant induced enhanced Th1 and Th17 cell mediated antifungal immunity, and resulted in enhanced recruitment of neutrophils and monocytes for pathogen clearance in vivo. We also demonstrated that MNN10 could unmask the surface β-(1,3-glucan, a crucial pathogen-associated molecular pattern (PAMP of C. albicans recognized by host Dectin-1. Our results demonstrate that mnn10 mutant could stimulate an enhanced Dectin-1 dependent immune response of macrophages in vitro, including the activation of nuclear factor-κB, mitogen-activated protein kinase pathways, and secretion of specific cytokines such as TNF-α, IL-6, IL-1β and IL-12p40. In summary, our study indicated that α-1,6-mannose backbone is critical for the pathogenesis of C. albicans via shielding β-glucan from recognition by host Dectin-1 mediated immune recognition. Moreover, our work suggests that inhibition of α-1,6-mannose extension by Mnn10 may represent a novel modality to reduce the pathogenicity of C. albicans.

  6. Base pairing in RNA structures: A computational analysis of ...

    Indian Academy of Sciences (India)

    WINTEC

    PDB files using RASMOL18 software. Hydrogen atoms were added to these base pairs using MOLDEN19 software. The sugar portions attached to base pairs in. RNA structures were removed, and C1′ atoms were respectively replaced by hydrogen atoms during model building. The change in base pair geometry on re-.

  7. The Latent Structure of Secure Base Script Knowledge

    Science.gov (United States)

    Waters, Theodore E. A.; Fraley, R. Chris; Groh, Ashley M.; Steele, Ryan D.; Vaughn, Brian E.; Bost, Kelly K.; Veríssimo, Manuela; Coppola, Gabrielle; Roisman, Glenn I.

    2015-01-01

    There is increasing evidence that attachment representations abstracted from childhood experiences with primary caregivers are organized as a cognitive script describing secure base use and support (i.e., the "secure base script"). To date, however, the latent structure of secure base script knowledge has gone unexamined--this despite…

  8. A data base for aging of structural materials

    International Nuclear Information System (INIS)

    Oland, C.B.; Naus, D.J.; Jerath, S.

    1993-01-01

    The U.S. Nuclear Regulatory Commission (USNRC) initiated a Structural Aging (SAG) Program at the Oak Ridge National Laboratory (ORNL). The objective of the program is to provide assistance in identifying potential structural safety issues and to establish acceptance criteria for use in nuclear power plant evaluations for continued service. One of the main parts of the program focuses on the development of a Structural Materials Information Center where long-term and environment-dependent material properties are being collected and assembled into a data base. This data base is presented in two complementary formats. The Structural Materials Handbook is an expandable, hard-copy reference document that contains the complete data base for each material. The Structural Materials Electronic Data Base is accessible using an IBM-compatible personal computer. This paper presents an overview of the Structural Materials Information Center and briefly describes the features of the handbook and the electronic data base. In addition, a proposed method for using the data base to establish current property values for materials in existing concrete structures and to estimate the future performance of these materials is also presented. (author)

  9. A data base for aging of structural materials

    International Nuclear Information System (INIS)

    Oland, C.B.; Naus, D.J.; Jerath, S.

    1993-01-01

    USNRC initiated a Structural Aging (SAG) Program ORNL. The objective of the program is to provide assistance in identifying potential structural safety issues and to establish acceptance criteria for use in nuclear power plant evaluations for continued service. One main part focuses on the development of a Structural Materials Information Center where long-term and environment-dependent material properties are being collected and assembled into a data base. This data base is presented in two complementary formats. The Structural Materials Handbook is an expandable, hard-copy reference document that contains the complete data base for each material. The Structural Materials Electronic Data Base is accessible using an IBM-compatible personal computer. This paper presents an overview of the Structural Materials Information Center and briefly describes the features of the handbook and the electronic data base. In addition, a proposed method for using the data base to establish current property values for materials in existing concrete structures and to estimate the future performance of these materials is also presented

  10. Comparing the Reliability of Regular Topologies on a Backbone Network. A Case Study

    DEFF Research Database (Denmark)

    Cecilio, Sergio Labeage; Gutierrez Lopez, Jose Manuel; Riaz, M. Tahir

    2009-01-01

    The aim of this paper is to compare the reliability of regular topologies on a backbone network. The study is focused on a large-scale fiberoptic network. Different regular topological solutions as single ring, double ring or 4-Regular grid are applied to the case study, and compared in terms...

  11. High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins

    Czech Academy of Sciences Publication Activity Database

    Zawadzka-Kazimierczuk, A.; Kozminski, W.; Šanderová, Hana; Krásný, Libor

    2012-01-01

    Roč. 52, č. 4 (2012), s. 329-337 ISSN 0925-2738 R&D Projects: GA ČR GA204/09/0583 Institutional research plan: CEZ:AV0Z50200510 Keywords : Intrinsically disordered proteins * Non-uniform sampling * Backbone assignment Subject RIV: EE - Microbiology, Virology Impact factor: 2.845, year: 2012

  12. Integrative technology of massage manipulations in physical rehabilitation of students with backbone pathology

    Directory of Open Access Journals (Sweden)

    V.I. Kotelevskiy

    2016-06-01

    Full Text Available Purpose:to analyze effectiveness of massage manipulations’ integrative technology in physical rehabilitation of higher educational establishments’ students with backbone pathology. Material: in the research 195 students of 19-20 years’ age participated. All students had periodical initial neurological symptoms of functional pathology and first stage osteochondrosis in different parts of backbone. We conducted a course of 10 sessions of therapeutic massage. Results: the sense of massage integrative technology is that every specialist shall have certain optimal set of skills and knowledge in technique of manipulation sessions of massage. Integrative technology of massage manipulations consists of psycho-corrective and manipulation parts. It considers psycho-somatic, mechanical and reflex rehabilitation aspects of patho-genesis of backbone functional disorders and vertebral osteochondrosis. Conclusions: depending on pathological process or backbone functional state of every person (peculiarities of his (her psycho-somatic status or, even, his (her bents. Individual approach in choice of strategy, tactic and methodological provisioning of massage session shall be used.

  13. Synthesis of a Backbone Hexasaccharide Fragment of the Pectic Polysaccharide Rhamnogalacturonan I

    DEFF Research Database (Denmark)

    Zakharova, Alexandra N.; Madsen, Robert; Clausen, Mads H.

    2013-01-01

    Synthesis of the fully unprotected hexasaccharide backbone of the pectic polysaccharide rhamnogalacturonan I is described. The strategy relies on iterative coupling of a common pentenyl disaccharide glycosyl donor followed by a late-stage oxidation of the C-6 positions of the galactose residues...

  14. Quantum Chemical Benchmark Study on 46 RNA Backbone Families Using a Dinucleotide Unit

    Czech Academy of Sciences Publication Activity Database

    Kruse, H.; Mládek, Arnošt; Gkionis, Konstantinos; Hansen, A.; Grimme, S.; Šponer, Jiří

    2015-01-01

    Roč. 11, č. 10 (2015), s. 4972-4991 ISSN 1549-9618 R&D Projects: GA ČR(CZ) GBP305/12/G034 Institutional support: RVO:68081707 Keywords : MOLECULAR-DYNAMICS SIMULATIONS * DENSITY-FUNCTIONAL THEORY * SUGAR -PHOSPHATE BACKBONE Subject RIV: BO - Biophysics Impact factor: 5.301, year: 2015

  15. Treatment Results of Injuries of Thoracic and Lumbar Backbone Departments at Osteoporosis Patients

    Directory of Open Access Journals (Sweden)

    D.Y. Sumin

    2009-06-01

    Full Text Available Information relates to radiologic (computer tomography manifestations providing the visualization of thoracic and lumbar backbone department injuries at osteoporotic patients. Contemporary methods of transcutaneous and trans-pedicle vertebroplasty with bone cement allows to obtain a stable positive healing effect against such pathologies.

  16. Exploiting Oligo(amido amine) Backbones for the Multivalent Presentation of Coiled-Coil Peptides.

    Science.gov (United States)

    Gerling-Driessen, Ulla I M; Mujkic-Ninnemann, Nina; Ponader, Daniela; Schöne, Daniel; Hartmann, Laura; Koksch, Beate; Gerling-Driessen, U I M; Schöne, D; Koksch, B; Ponader, D; Mujkic-Ninnemann, N; Hartmann, L

    2015-08-10

    The investigation of coiled coil formation for one mono- and two divalent peptide-polymer conjugates is presented. Through the assembly of the full conjugates on solid support, monodisperse sequence-defined conjugates are obtained with defined positions and distances between the peptide side chains along the polymeric backbone. A heteromeric peptide design was chosen, where peptide K is attached to the polymer backbone, and coiled-coil formation is only expected through complexation with the complementary peptide E. Indeed, the monovalent peptide K-polymer conjugate displays rapid coiled-coil formation when mixed with the complementary peptide E sequence. The divalent systems show intramolecular homomeric coiled-coil formation on the polymer backbone despite the peptide design. Interestingly, this intramolecular assembly undergoes a conformational rearrangement by the addition of the complementary peptide E leading to the formation of heteromeric coiled coil-polymer aggregates. The polymer backbone acts as a template bringing the covalently bound peptide strands in close proximity to each other, increasing the local concentration and inducing the otherwise nonfavorable formation of intramolecular helical assemblies.

  17. First-principles study of the effect of functional groups on polyaniline backbone

    NARCIS (Netherlands)

    Chen, X.P.; Jiang, J.K.; Liang, Q.H.; Yang, N.; Ye, H.Y.; Cai, M.; Shen, L.; Yang, D.G.; Ren, T.L.

    2015-01-01

    We present a first-principles density functional theory study focused on how the chemical and electronic properties of polyaniline are adjusted by introducing suitable substituents on a polymer backbone. Analyses of the obtained energy barriers, reaction energies and minimum energy paths indicate

  18. Structured Simulation-Based Training Programs: History and Lessons Learned

    National Research Council Canada - National Science Library

    Shlechter, Theodore

    2000-01-01

    ...) research and development (R&D) efforts on structured simulation-based training (SST). These R&D efforts have led to the development of 30 research reports, 14 conference papers, and over 200 training support packages (TSPs...

  19. Development of a Structure-Based Turbulence Model

    National Research Council Canada - National Science Library

    Reynolds, W

    2000-01-01

    Work in the current period was aimed at the construction of extensions of the structure-based Particle Representation and one-point models to flows with slow or moderate mean deformations and wall proximity effects...

  20. Global stability-based design optimization of truss structures using ...

    Indian Academy of Sciences (India)

    objective optimization; island models; genetic algorithm; arc-length method. ... Furthermore, a pure pareto-ranking based multi-objective optimization model is employed for the design optimization of the truss structure with multiple objectives.

  1. Protein structure-based design of anti-protozoal drugs

    Directory of Open Access Journals (Sweden)

    Verlinde Christophe L. M. J.

    2002-01-01

    Full Text Available The repertory of drugs to fight protozoal diseases such as malaria, Chagas' disease, leishmaniasis, and African trypanosomiasis is woefully inadequate. Now, genome sequencing and structural genomics projects are quickly elucidating new drug targets, providing incredible opportunities for medicinal chemists. Here, we illustrate the power of structure-based drug design in this process by our efforts to selectively block trypanosomal glycolysis.

  2. Polarity classification using structure-based vector representations of text

    NARCIS (Netherlands)

    Hogenboom, Alexander; Frasincar, Flavius; de Jong, Franciska M.G.; Kaymak, Uzay

    The exploitation of structural aspects of content is becoming increasingly popular in rule-based polarity classification systems. Such systems typically weight the sentiment conveyed by text segments in accordance with these segments' roles in the structure of a text, as identified by deep

  3. RNA structural motif recognition based on least-squares distance.

    Science.gov (United States)

    Shen, Ying; Wong, Hau-San; Zhang, Shaohong; Zhang, Lin

    2013-09-01

    RNA structural motifs are recurrent structural elements occurring in RNA molecules. RNA structural motif recognition aims to find RNA substructures that are similar to a query motif, and it is important for RNA structure analysis and RNA function prediction. In view of this, we propose a new method known as RNA Structural Motif Recognition based on Least-Squares distance (LS-RSMR) to effectively recognize RNA structural motifs. A test set consisting of five types of RNA structural motifs occurring in Escherichia coli ribosomal RNA is compiled by us. Experiments are conducted for recognizing these five types of motifs. The experimental results fully reveal the superiority of the proposed LS-RSMR compared with four other state-of-the-art methods.

  4. Probability based high temperature engineering creep and structural fire resistance

    CERN Document Server

    Razdolsky, Leo

    2017-01-01

    This volume on structural fire resistance is for aerospace, structural, and fire prevention engineers; architects, and educators. It bridges the gap between prescriptive- and performance-based methods and simplifies very complex and comprehensive computer analyses to the point that the structural fire resistance and high temperature creep deformations will have a simple, approximate analytical expression that can be used in structural analysis and design. The book emphasizes methods of the theory of engineering creep (stress-strain diagrams) and mathematical operations quite distinct from those of solid mechanics absent high-temperature creep deformations, in particular the classical theory of elasticity and structural engineering. Dr. Razdolsky’s previous books focused on methods of computing the ultimate structural design load to the different fire scenarios. The current work is devoted to the computing of the estimated ultimate resistance of the structure taking into account the effect of high temperatur...

  5. Microstructure and structural phase transitions in iron-based superconductors

    International Nuclear Information System (INIS)

    Wang Zhen; Cai Yao; Yang Huai-Xin; Tian Huan-Fang; Wang Zhi-Wei; Ma Chao; Chen Zhen; Li Jian-Qi

    2013-01-01

    Crystal structures and microstructural features, such as structural phase transitions, defect structures, and chemical and structural inhomogeneities, are known to have profound effects on the physical properties of superconducting materials. Recently, many studies on the structural properties of Fe-based high-T c superconductors have been published. This review article will mainly focus on the typical microstructural features in samples that have been well characterized by physical measurements. (i) Certain common structural features are discussed, in particular, the crystal structural features for different superconducting families, the local structural distortions in the Fe 2 Pn 2 (Pn = P As, Sb) or Fe 2 Ch 2 (Ch = S, Se, Te) blocks, and the structural transformations in the 122 system. (ii) In FeTe(Se) (11 family), the superconductivity, chemical and structural inhomogeneities are investigated and discussed in correlation with superconductivity. (iii) In the K 0.8 Fe 1.6+x Se 2 system, we focus on the typical compounds with emphasis on the Fe-vacancy order and phase separations. The microstructural features in other superconducting materials are also briefly discussed. (topical review - iron-based high temperature superconductors)

  6. Three-Dimensional Protein Fold Determination from Backbone Amide Pseudocontact Shifts Generated by Lanthanide Tags at Multiple Sites

    KAUST Repository

    Yagi, Hiromasa

    2013-06-01

    Site-specific attachment of paramagnetic lanthanide ions to a protein generates pseudocontact shifts (PCS) in the nuclear magnetic resonance (NMR) spectra of the protein that are easily measured as changes in chemical shifts. By labeling the protein with lanthanide tags at four different sites, PCSs are observed for most amide protons and accurate information is obtained about their coordinates in three-dimensional space. The approach is demonstrated with the chaperone ERp29, for which large differences have been reported between X-ray and NMR structures of the C-terminal domain, ERp29-C. The results unambiguously show that the structure of rat ERp29-C in solution is similar to the crystal structure of human ERp29-C. PCSs of backbone amides were the only structural restraints required. Because these can be measured for more dilute protein solutions than other NMR restraints, the approach greatly widens the range of proteins amenable to structural studies in solution. © 2013 Elsevier Ltd. All rights reserved.

  7. Protein structure prediction provides comparable performance to crystallographic structures in docking-based virtual screening.

    Science.gov (United States)

    Du, Hongying; Brender, Jeffrey R; Zhang, Jian; Zhang, Yang

    2015-01-01

    Structure based virtual screening has largely been limited to protein targets for which either an experimental structure is available or a strongly homologous template exists so that a high-resolution model can be constructed. The performance of state of the art protein structure predictions in virtual screening in systems where only weakly homologous templates are available is largely untested. Using the challenging DUD database of structural decoys, we show here that even using templates with only weak sequence homology (identity) structural models can be constructed by I-TASSER which achieve comparable enrichment rates to using the experimental bound crystal structure in the majority of the cases studied. For 65% of the targets, the I-TASSER models, which are constructed essentially in the apo conformations, reached 70% of the virtual screening performance of using the holo-crystal structures. A correlation was observed between the success of I-TASSER in modeling the global fold and local structures in the binding pockets of the proteins versus the relative success in virtual screening. The virtual screening performance can be further improved by the recognition of chemical features of the ligand compounds. These results suggest that the combination of structure-based docking and advanced protein structure modeling methods should be a valuable approach to the large-scale drug screening and discovery studies, especially for the proteins lacking crystallographic structures. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. Current NMR Techniques for Structure-Based Drug Discovery.

    Science.gov (United States)

    Sugiki, Toshihiko; Furuita, Kyoko; Fujiwara, Toshimichi; Kojima, Chojiro

    2018-01-12

    A variety of nuclear magnetic resonance (NMR) applications have been developed for structure-based drug discovery (SBDD). NMR provides many advantages over other methods, such as the ability to directly observe chemical compounds and target biomolecules, and to be used for ligand-based and protein-based approaches. NMR can also provide important information about the interactions in a protein-ligand complex, such as structure, dynamics, and affinity, even when the interaction is too weak to be detected by ELISA or fluorescence resonance energy transfer (FRET)-based high-throughput screening (HTS) or to be crystalized. In this study, we reviewed current NMR techniques. We focused on recent progress in NMR measurement and sample preparation techniques that have expanded the potential of NMR-based SBDD, such as fluorine NMR ( 19 F-NMR) screening, structure modeling of weak complexes, and site-specific isotope labeling of challenging targets.

  9. Neighboring Structure Visualization on a Grid-based Layout.

    Science.gov (United States)

    Marcou, G; Horvath, D; Varnek, A

    2017-10-01

    Here, we describe an algorithm to visualize chemical structures on a grid-based layout in such a way that similar structures are neighboring. It is based on structure reordering with the help of the Hilbert Schmidt Independence Criterion, representing an empirical estimate of the Hilbert-Schmidt norm of the cross-covariance operator. The method can be applied to any layout of bi- or three-dimensional shape. The approach is demonstrated on a set of dopamine D5 ligands visualized on squared, disk and spherical layouts. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Structure of 2,4-Diaminopyrimidine - Theobromine Alternate Base Pairs

    Science.gov (United States)

    Gengeliczki, Zsolt; Callahan, Michael P.; Kabelac, Martin; Rijs, Anouk M.; deVries, Mattanjah S.

    2011-01-01

    We report the structure of clusters of 2,4-diaminopyrimidine with 3,7-dimethylxanthine (theobromine) in the gas phase determined by IR-UV double resonance spectroscopy in both the near-IR and mid-IR regions in combination with ab initio computations. These clusters represent potential alternate nucleobase pairs, geometrically equivalent to guanine-cytosine. We have found the four lowest energy structures, which include the Watson-Crick base pairing motif. This Watson-Crick structure has not been observed by resonant two-photon ionization (R2PI) in the gas phase for the canonical DNA base pairs.

  11. Data base on avian mortality on man-made structures

    Energy Technology Data Exchange (ETDEWEB)

    Dailey, N. S.

    1978-01-01

    A computerized data base concerning avian mortality on man-made structures is available for searching at the Ecological Sciences Information Center of the Information Center Complex, Information Division, Oak Ridge National Laboratory. This data base, which contains entries from the available literature, provides information on avian mortality from either collision into or electrocution on man-made structures. Primary emphasis has been placed on avian collision with obstacles such as television and radio towers, airport ceilometers, transmission lines, and cooling towers. Other structures included in the studies are fences, glass walls and windows, lighthouses, telegraph and telephone wires, buildings, monuments, smokestacks, and water towers.

  12. Reliability-Based Structural Optimization of Wave Energy Converters

    DEFF Research Database (Denmark)

    Ambühl, Simon; Kramer, Morten; Sørensen, John Dalsgaard

    2014-01-01

    More and more wave energy converter (WEC) concepts are reaching prototype level. Once the prototype level is reached, the next step in order to further decrease the levelized cost of energy (LCOE) is optimizing the overall system with a focus on structural and maintenance (inspection) costs...... objectives and will be located at different locations, as well as receive various subsidies. These points should be accounted for when performing structural optimizations of WECs. An illustrative example on the gravity-based foundation of the Wavestar device is performed showing how structural design can...... be optimized taking target reliability levels and different structural failure modes due to extreme loads into account....

  13. Isolation of Pristine Electronics Grade Semiconducting Carbon Nanotubes by Switching the Rigidity of the Wrapping Polymer Backbone on Demand.

    Science.gov (United States)

    Joo, Yongho; Brady, Gerald J; Shea, Matthew J; Oviedo, M Belén; Kanimozhi, Catherine; Schmitt, Samantha K; Wong, Bryan M; Arnold, Michael S; Gopalan, Padma

    2015-10-27

    Conjugated polymers are among the most selective carbon nanotube sorting agents discovered and enable the isolation of ultrahigh purity semiconducting singled-walled carbon nanotubes (s-SWCNTs) from heterogeneous mixtures that contain problematic metallic nanotubes. The strong selectivity though highly desirable for sorting, also leads to irreversible adsorption of the polymer on the s-SWCNTs, limiting their electronic and optoelectronic properties. We demonstrate how changes in polymer backbone rigidity can trigger its release from the nanotube surface. To do so, we choose a model polymer, namely poly[(9,9-dioctylfluorenyl-2,7-diyl)-alt-co-(6,60-(2,20-bipyridine))] (PFO-BPy), which provides ultrahigh selectivity for s-SWCNTs, which are useful specifically for FETs, and has the chemical functionality (BPy) to alter the rigidity using mild chemistry. Upon addition of Re(CO)5Cl to the solution of PFO-BPy wrapped s-SWCNTs, selective chelation with the BPy unit in the copolymer leads to the unwrapping of PFO-BPy. UV-vis, XPS, and Raman spectroscopy studies show that binding of the metal ligand complex to BPy triggers up to 85% removal of the PFO-BPy from arc-discharge s-SWCNTs (diameter = 1.3-1.7 nm) and up to 72% from CoMoCAT s-SWCNTs (diameter = 0.7-0.8 nm). Importantly, Raman studies show that the electronic structure of the s-SWCNTs is preserved through this process. The generalizability of this method is demonstrated with two other transition metal salts. Molecular dynamics simulations support our experimental findings that the complexation of BPy with Re(CO)5Cl in the PFO-BPy backbone induces a dramatic conformational change that leads to a dynamic unwrapping of the polymer off the nanotube yielding pristine s-SWCNTs.

  14. The backbone of the post-synaptic density originated in a unicellular ancestor of choanoflagellates and metazoans

    Directory of Open Access Journals (Sweden)

    Manuel Michaël

    2010-02-01

    Full Text Available Abstract Background Comparative genomics of the early diverging metazoan lineages and of their unicellular sister-groups opens new window to reconstructing the genetic changes which preceded or accompanied the evolution of multicellular body plans. A recent analysis found that the genome of the nerve-less sponges encodes the homologues of most vertebrate post-synaptic proteins. In vertebrate excitatory synapses, these proteins assemble to form the post-synaptic density, a complex molecular platform linking membrane receptors, components of their signalling pathways, and the cytoskeleton. Newly available genomes from Monosiga brevicollis (a member of Choanoflagellata, the closest unicellular relatives of animals and Trichoplax adhaerens (a member of Placozoa: besides sponges, the only nerve-less metazoans offer an opportunity to refine our understanding of post-synaptic protein evolution. Results Searches for orthologous proteins and reconstruction of gene gains/losses based on the taxon phylogeny indicate that post-synaptic proteins originated in two main steps. The backbone scaffold proteins (Shank, Homer, DLG and some of their partners were acquired in a unicellular ancestor of choanoflagellates and metazoans. A substantial additional set appeared in an exclusive ancestor of the Metazoa. The placozoan genome contains most post-synaptic genes but lacks some of them. Notably, the master-scaffold protein Shank might have been lost secondarily in the placozoan lineage. Conclusions The time of origination of most post-synaptic proteins was not concomitant with the acquisition of synapses or neural-like cells. The backbone of the scaffold emerged in a unicellular context and was probably not involved in cell-cell communication. Based on the reconstructed protein composition and potential interactions, its ancestral function could have been to link calcium signalling and cytoskeleton regulation. The complex later became integrated into the evolving

  15. Gradient-based optimization in nonlinear structural dynamics

    DEFF Research Database (Denmark)

    Dou, Suguang

    , frequency stabilization, and disk resonator gyroscope. For advanced design of these structures, it is of considerable value to extend current optimization in linear structural dynamics into nonlinear structural dynamics. In this thesis, we present a framework for modelling, analysis, characterization......The intrinsic nonlinearity of mechanical structures can give rise to rich nonlinear dynamics. Recently, nonlinear dynamics of micro-mechanical structures have contributed to developing new Micro-Electro-Mechanical Systems (MEMS), for example, atomic force microscope, passive frequency divider...... coefficients are calculated directly from a nonlinear finite element model. Based on the analysis and the characterization, a new class of optimization problems is studied. In the optimization, design sensitivity analysis is performed by using the adjoint method which is suitable for large-scale structural...

  16. General enumeration of RNA secondary structures based on new ...

    African Journals Online (AJOL)

    Crick base pairs between AU and GC. Based on the new representation, this paper also computes the number of various types of constrained secondary structures taking the minimum stack length 1 and minimum size m for each bonding loop as ...

  17. Towards Computerized Adaptive Assessment Based on Structured Tasks

    NARCIS (Netherlands)

    Tvarožek, Jozef; Kravcik, Milos; Bieliková, Mária

    2008-01-01

    Tvarožek, J., Kravčík, M., & Bieliková, M. (2008). Towards Computerized Adaptive Assessment Based on Structured Tasks. In W. Nejdl et al. (Eds.), Adaptive Hypermedia and Adaptive Web-Based Systems (pp. 224-234). Springer Berlin / Heidelberg.

  18. Inter-domain orientation and motions in VAT-N explored by residual dipolar couplings and 15N backbone relaxation.

    Science.gov (United States)

    Deshmukh, Mandar V; John, Michael; Coles, Murray; Peters, Jürgen; Baumeister, Wolfgang; Kessler, Horst

    2006-07-01

    The N-terminal domain of VAT (Valosine-containing protein-like ATPase of Thermoplasma acidophilum), VAT-N (20.5 kDa), is considered to be the primary substrate-recognition site of the complex. The solution structure of VAT-N derived in our laboratory using conventionally obtained NMR restraints shows the existence of two equally sized sub-domains, VAT-Nn and VAT-Nc, together forming a kidney-shaped overall structure. The putative substrate-binding site of VAT-N involves free loops and a highly charged groove located on the surface of the protein. Alternatively, the opening of the cleft between the domains to accommodate substrate has been proposed to be part of the functional mechanism. We have used the residual dipolar couplings (RDCs) obtained in a bicelle medium to refine the structure of VAT-N. The long-range information available from RDCs both defines the sub-domain orientation and probes possible inter-domain motions. In addition, 15N backbone relaxation data were obtained and analysed within the model-free framework. Together, the data provides a refined structure with improved local geometry, but with the overall kidney shape intact. Further, the protein is rigid overall, with no evidence of inter-domain motions. Copyright 2006 John Wiley & Sons, Ltd.

  19. First principles based multiparadigm modeling of electronic structures and dynamics

    Science.gov (United States)

    Xiao, Hai

    enabling the tunability of CBO. We predict that Na further improves the CBO through electrostatically elevating the valence levels to decrease the CBO, explaining the observed essential role of Na for high performance. Moreover we find that K leads to a dramatic decrease in the CBO to 0.05 eV, much better than Na. We suggest that the efficiency of CIGS devices might be improved substantially by tuning the ratio of Na to K, with the improved phase stability of Na balancing phase instability from K. All these defects reduce interfacial stability slightly, but not significantly. A number of exotic structures have been formed through high pressure chemistry, but applications have been hindered by difficulties in recovering the high pressure phase to ambient conditions (i.e., one atmosphere and room temperature). Here we use dispersion-corrected DFT (PBE-ulg flavor) to predict that above 60 GPa the most stable form of N2O (the laughing gas in its molecular form) is a 1D polymer with an all-nitrogen backbone analogous to cis-polyacetylene in which alternate N are bonded (ionic covalent) to O. The analogous trans-polymer is only 0.03-0.10 eV/molecular unit less stable. Upon relaxation to ambient conditions both polymers relax below 14 GPa to the same stable non-planar trans-polymer, accompanied by possible electronic structure transitions. The predicted phonon spectrum and dissociation kinetics validate the stability of this trans-poly-NNO at ambient conditions, which has potential applications as a new type of conducting polymer with all-nitrogen chains and as a high-energy oxidizer for rocket propulsion. This work illustrates in silico materials discovery particularly in the realm of extreme conditions. Modeling non-adiabatic electron dynamics has been a long-standing challenge for computational chemistry and materials science, and the eFF method presents a cost-efficient alternative. However, due to the deficiency of FSG representation, eFF is limited to low-Z elements with

  20. Structure-based classification and ontology in chemistry

    Directory of Open Access Journals (Sweden)

    Hastings Janna

    2012-04-01

    Full Text Available Abstract Background Recent years have seen an explosion in the availability of data in the chemistry domain. With this information explosion, however, retrieving relevant results from the available information, and organising those results, become even harder problems. Computational processing is essential to filter and organise the available resources so as to better facilitate the work of scientists. Ontologies encode expert domain knowledge in a hierarchically organised machine-processable format. One such ontology for the chemical domain is ChEBI. ChEBI provides a classification of chemicals based on their structural features and a role or activity-based classification. An example of a structure-based class is 'pentacyclic compound' (compounds containing five-ring structures, while an example of a role-based class is 'analgesic', since many different chemicals can act as analgesics without sharing structural features. Structure-based classification in chemistry exploits elegant regularities and symmetries in the underlying chemical domain. As yet, there has been neither a systematic analysis of the types of structural classification in use in chemistry nor a comparison to the capabilities of available technologies. Results We analyze the different categories of structural classes in chemistry, presenting a list of patterns for features found in class definitions. We compare these patterns of class definition to tools which allow for automation of hierarchy construction within cheminformatics and within logic-based ontology technology, going into detail in the latter case with respect to the expressive capabilities of the Web Ontology Language and recent extensions for modelling structured objects. Finally we discuss the relationships and interactions between cheminformatics approaches and logic-based approaches. Conclusion Systems that perform intelligent reasoning tasks on chemistry data require a diverse set of underlying computational

  1. Performance based investigations of structural systems under fire

    DEFF Research Database (Denmark)

    Gentili, Filippo; Crosti, Chiara; Giuliani, Luisa

    2010-01-01

    Prescriptive measures and procedures developed over the past here are mostly aimed at preventing structural failures of single elements for the time required for the evacuation. The response to fire and fire effects of the structural system as a whole remains often unknown and the survival of the...... structures are presented and discussed, with particular attention to methodological aspects. The effects of different assumptions in the modeling and in the definition of the collapse are highlighted, as critical aspects of a performance-based investigation....... these kinds of events, the mitigation of possible collapse induced by fire should be achieved. In this respect, a performance-based investigation of the structure aimed at highlight fire effects and fire-induced collapse mechanisms becomes of interest. In the paper collapse mechanisms of some simple...

  2. Self-assembly of boron-based supramolecular structures

    OpenAIRE

    Christinat, Nicolas

    2008-01-01

    This work describes the synthesis and characterization of boronic acid-based supramolecular structures. Macrocycles, dendritic structures, polymers, rotaxanes, and cages were assembled using four types of reversible reactions. The key point of the strategy is the parallel utilization of two –or more– of these reactions. Initially, aryl and alkylboronic acids were condensed with dihydroxypyridine ligands to give tetrameric or pentameric macrocycles, in which four or five boronate esters are co...

  3. Structure-Based Simulations Reveal Concerted Dynamics of GPCR Activation

    OpenAIRE

    Leioatts, Nicholas; Suresh, Pooja; Romo, Tod D.; Grossfield, Alan

    2014-01-01

    G protein-coupled receptors (GPCRs) are a vital class of proteins that transduce biological signals across the cell membrane. However, their allosteric activation mechanism is not fully understood; crystal structures of active and inactive receptors have been reported, but the functional pathway between these two states remains elusive. Here, we employ structure-based (Gō-like) models to simulate activation of two GPCRs, rhodopsin and the β2 adrenergic receptor (β2AR). We used data-derived re...

  4. 1H, 13C, 15N backbone NMR assignments of the Staphylococcus aureus small multidrug-resistance pump (Smr) in a functionally active conformation.

    Science.gov (United States)

    Poget, Sébastien F; Harris, Richard; Cahill, Sean M; Girvin, Mark E

    2010-10-01

    The plasmid-encoded small multidrug resistance pump from S. aureus transports a variety of quaternary ammonium and other hydrophobic compounds, enhancing the bacterial host's resistance to common hospital disinfectants. The protein folds as a homo-dimer of four transmembrane helices each, and appears to be fully functional only in lipid bilayers. Here we report the backbone resonance assignments and implied secondary structure for (2)H(13)C(15)N Smr reconstituted into lipid bicelles. Significant changes were observed between the chemical shifts of the protein in lipid bicelles compared to those in detergent micelles.

  5. Smartphone based hemispherical photography for canopy structure measurement

    Science.gov (United States)

    Wan, Xuefen; Cui, Jian; Jiang, Xueqin; Zhang, Jingwen; Yang, Yi; Zheng, Tao

    2018-01-01

    The canopy is the most direct and active interface layer of the interaction between plant and environment, and has important influence on energy exchange, biodiversity, ecosystem matter and climate change. The measurement about canopy structure of plant is an important foundation to analyze the pattern, process and operation mechanism of forest ecosystem. Through the study of canopy structure of plant, solar radiation, ambient wind speed, air temperature and humidity, soil evaporation, soil temperature and other forest environmental climate characteristics can be evaluated. Because of its accuracy and effectiveness, canopy structure measurement based on hemispherical photography has been widely studied. However, the traditional method of canopy structure hemispherical photogrammetry based on SLR camera and fisheye lens. This method is expensive and difficult to be used in some low-cost occasions. In recent years, smartphone technology has been developing rapidly. The smartphone not only has excellent image acquisition ability, but also has the considerable computational processing ability. In addition, the gyroscope and positioning function on the smartphone will also help to measure the structure of the canopy. In this paper, we present a smartphone based hemispherical photography system. The system consists of smart phones, low-cost fisheye lenses and PMMA adapters. We designed an Android based App to obtain the canopy hemisphere images through low-cost fisheye lenses and provide horizontal collimation information. In addition, the App will add the acquisition location tag obtained by GPS and auxiliary positioning method in hemisphere image information after the canopy structure hemisphere image acquisition. The system was tested in the urban forest after it was completed. The test results show that the smartphone based hemispherical photography system can effectively collect the high-resolution canopy structure image of the plant.

  6. Hard and soft acids and bases: structure and process.

    Science.gov (United States)

    Reed, James L

    2012-07-05

    Under investigation is the structure and process that gives rise to hard-soft behavior in simple anionic atomic bases. That for simple atomic bases the chemical hardness is expected to be the only extrinsic component of acid-base strength, has been substantiated in the current study. A thermochemically based operational scale of chemical hardness was used to identify the structure within anionic atomic bases that is responsible for chemical hardness. The base's responding electrons have been identified as the structure, and the relaxation that occurs during charge transfer has been identified as the process giving rise to hard-soft behavior. This is in contrast the commonly accepted explanations that attribute hard-soft behavior to varying degrees of electrostatic and covalent contributions to the acid-base interaction. The ability of the atomic ion's responding electrons to cause hard-soft behavior has been assessed by examining the correlation of the estimated relaxation energies of the responding electrons with the operational chemical hardness. It has been demonstrated that the responding electrons are able to give rise to hard-soft behavior in simple anionic bases.

  7. Assessment of Performance-based Requirements for Structural Design

    DEFF Research Database (Denmark)

    Hertz, Kristian Dahl

    2005-01-01

    The paper presents how actions can be assessed for a performance-based structural fire safety design from the first formulations in the building program to the final derivations of the fire load to be applied for each structural member. In order to indicate what is of importance for the assessment...... of the requirements, a couple of simple analyses of structural response are made. The examples are chosen deliberately to show the difference between a traditional design based on standard fire resistance and a performance-based approach. A methodology is developed for a decision on the safety level...... and for a detailed assessment of the requirements. The design requirements to be used for a factory producing elements for industrial housing for unknown costumers are discussed, and a fully developed fire is recommended as a common requirement for domestic houses, hotels, offices, schools and hospitals. In addition...

  8. A Tensor-Based Structural Damage Identification and Severity Assessment

    Science.gov (United States)

    Anaissi, Ali; Makki Alamdari, Mehrisadat; Rakotoarivelo, Thierry; Khoa, Nguyen Lu Dang

    2018-01-01

    Early damage detection is critical for a large set of global ageing infrastructure. Structural Health Monitoring systems provide a sensor-based quantitative and objective approach to continuously monitor these structures, as opposed to traditional engineering visual inspection. Analysing these sensed data is one of the major Structural Health Monitoring (SHM) challenges. This paper presents a novel algorithm to detect and assess damage in structures such as bridges. This method applies tensor analysis for data fusion and feature extraction, and further uses one-class support vector machine on this feature to detect anomalies, i.e., structural damage. To evaluate this approach, we collected acceleration data from a sensor-based SHM system, which we deployed on a real bridge and on a laboratory specimen. The results show that our tensor method outperforms a state-of-the-art approach using the wavelet energy spectrum of the measured data. In the specimen case, our approach succeeded in detecting 92.5% of induced damage cases, as opposed to 61.1% for the wavelet-based approach. While our method was applied to bridges, its algorithm and computation can be used on other structures or sensor-data analysis problems, which involve large series of correlated data from multiple sensors. PMID:29301314

  9. Research on backbone node deployment for Wireless Mesh Networks in dynamic environments

    Science.gov (United States)

    Li, Meiyi; Cao, Shengling

    2017-08-01

    Wireless Mesh Network is a type of wireless networks in which demands of bandwidth for users has mobility. The backbone node placement of wireless mesh networks in a dynamic scenario is investigated, and the TSDPSO algorithm is used to adapt the dynamic environment, which updates node deployment location to adapt to changes in demand if it detects environmental changes at the beginning of the cycle time. In order to meet the demands of bandwidth for users and network connectivity, particle swarm optimization algorithm is employed to select the gateway location, then nodes to the backbone network is added constantly until all requirement is covered. The experimental results show that algorithm could get effective solution in dynamic environment.

  10. Aromatic Copolyamides with Anthrazoline Units in the Backbone: Synthesis, Characterization, Pervaporation Application

    Directory of Open Access Journals (Sweden)

    Galina A. Polotskaya

    2016-10-01

    Full Text Available Copolyamides with anthrazoline units in the backbone (coPA were synthesized and dense nonporous films were prepared by solvent evaporation. Glass transition temperature, density, and fractional free volume were determined for the dense nonporous films composed of polyamide and two of its copolymers containing 20 and 30 mol % anthrazoline units in the backbone. Transport properties of the polymer films were estimated by sorption and pervaporation tests toward methanol, toluene, and their mixtures. An increase in anthrazoline fragments content leads to an increasing degree of methanol sorption but to a decreasing degree of toluene sorption. Pervaporation of a methanol–toluene mixture was studied over a wide range of feed concentration (10–90 wt % methanol. Maximal separation factor was observed for coPA-20 containing 20 mol % fragments with anthrazoline units; maximal total flux was observed for coPA-30 with the highest fractional free volume.

  11. Optical-based smart structures for tamper-indicating applications

    International Nuclear Information System (INIS)

    Sliva, P.; Anheier, N.C.; Simmons, K.L.; Undem, H.A.

    1996-11-01

    This report is a compilation of several related projects performed from 1991 through 1996 concerning the design, construction, and application of optical-based smart structure to tamper-indicating and sensing secure containers. Due to several influences, the projects were carried through to varying degrees of completion. Cancellation of the overall project at the client level motivated the authors to gather all of the technology and ideas about smart structures developed during these several projects, whether completed or just conceptualized, into one document. Although each section individually discusses a specific project, the overall document is written chronologically with each successive section showing how increased smart structure complexity was integrated into the container

  12. Hybrid structures based on quantum dots and graphene nanobelts

    Science.gov (United States)

    Reznik, I. A.; Gromova, Yu. A.; Zlatov, A. S.; Baranov, M. A.; Orlova, A. O.; Moshkalev, S. A.; Maslov, V. G.; Baranov, A. V.; Fedorov, A. V.

    2017-01-01

    Luminescence and photoelectric properties of hybrid structures based on CdSe/ZnS quantum dots (QDs) and multilayer graphene have been investigated. A correlation between the luminescence quantum yield of QDs and their photoelectric properties in hybrid structures is established. It is shown that a decrease in the QD luminescence quantum yield due to adsorption of 1-(2-pyridylazo)-2-naphtol azo dye molecules onto the QD surface and a photoinduced increase in the QD luminescence quantum yield are accompanied by a symbate change in the hybrid structure photoconductivity.

  13. Tunable reflecting terahertz filter based on chirped metamaterial structure

    Science.gov (United States)

    Yang, Jing; Gong, Cheng; Sun, Lu; Chen, Ping; Lin, Lie; Liu, Weiwei

    2016-01-01

    Tunable reflecting terahertz bandstop filter based on chirped metamaterial structure is demonstrated by numerical simulation. In the metamaterial, the metal bars are concatenated to silicon bars with different lengths. By varying the conductivity of the silicon bars, the reflectivity, central frequency and bandwidth of the metamaterial could be tuned. Light illumination could be introduced to change the conductivity of the silicon bars. Numerical simulations also show that the chirped metamaterial structure is insensitive to the incident angle and polarization-dependent. The proposed chirped metamaterial structure can be operated as a tunable bandstop filter whose modulation depth, bandwidth, shape factor and center frequency can be controlled by light pumping. PMID:27941833

  14. Integrated Reliability-Based Optimal Design of Structures

    DEFF Research Database (Denmark)

    Sørensen, John Dalsgaard; Thoft-Christensen, Palle

    1987-01-01

    the reliability decreases with time it is often necessary to design an inspection and repair programme. For example the reliability of offshore steel structures decreases with time due to corrosion and development of fatigue cracks. Until now most inspection and repair strategies are based on experience rather......In conventional optimal design of structural systems the weight or the initial cost of the structure is usually used as objective function. Further, the constraints require that the stresses and/or strains at some critical points have to be less than some given values. Finally, all variables...

  15. Secure data structures based on multi-party computation

    DEFF Research Database (Denmark)

    Toft, Tomas

    2011-01-01

    This work considers data structures based on multi-party computation (MPC) primitives: structuring secret (e.g. secret shared and potentially unknown) data such that it can both be queried and updated efficiently. Implementing an oblivious RAM (ORAM) using MPC allows any existing data structure t...... shown that any information theoretically secure ORAM with n memory locations requires at least log n random bits per read/write to hide the access pattern. In contrast, the present construction achieves security with a completely deterministic access pattern....

  16. Backbone resonance assignments of human cytosolic dNT-1 nucleotidase

    Czech Academy of Sciences Publication Activity Database

    Hnízda, Aleš; Skleničková, Radka; Pachl, Petr; Fábry, Milan; Tošner, Z.; Brynda, Jiří; Veverka, Václav

    2014-01-01

    Roč. 8, č. 2 (2014), s. 425-428 ISSN 1874-2718 R&D Projects: GA MŠk(CZ) LK11205; GA ČR GA203/09/0820 Institutional support: RVO:61388963 ; RVO:68378050 Keywords : 5 '-nucleotidase * haloacid dehalogenase superfamily * backbone assignments * NMR * perdeuterated protein * dimer * pyrimidine nucleotides Subject RIV: CE - Biochemistry; EB - Genetics ; Molecular Biology (UMG-J) Impact factor: 0.760, year: 2014

  17. NMR backbone assignments of the tyrosine kinase domain of human fibroblast growth factor receptor 1.

    Science.gov (United States)

    Vajpai, Navratna; Schott, Anne-Kathrin; Vogtherr, Martin; Breeze, Alexander L

    2014-04-01

    Members of the fibroblast growth factor receptor tyrosine kinase family (FGFR1-4) play an important role in many signalling cascades. Although tightly regulated, aberrant activity of these enzymes may lead to, or become features of, disease pathologies including cancer. FGFR isoforms have been the subject of drug discovery programmes, with a number of kinase-domain inhibitors in pre-clinical and clinical development. Here, we present the first (83% complete) backbone resonance assignments of apo-FGFR1 kinase.

  18. Survivability Improvement Against Earthquakes in Backbone Optical Networks Using Actual Seismic Zone Information

    OpenAIRE

    Agrawal, Anuj; Sharma, Purva; Bhatia, Vimal; Prakash, Shashi

    2017-01-01

    Optical backbone networks carry a huge amount of bandwidth and serve as a key enabling technology to provide telecommunication connectivity across the world. Hence, in events of network component (node/link) failures, communication networks may suffer from huge amount of bandwidth loss and service disruptions. Natural disasters such as earthquakes, hurricanes, tornadoes, etc., occur at different places around the world, causing severe communication service disruptions due to network component...

  19. Backbone resonance assignments of the outer membrane lipoprotein FrpD from Neisseria meningitidis

    Czech Academy of Sciences Publication Activity Database

    Bumba, Ladislav; Sviridova, E.; Kutá-Smatanová, Ivana; Řezáčová, Pavlína; Veverka, Václav

    2014-01-01

    Roč. 8, č. 1 (2014), s. 53-55 ISSN 1874-2718 R&D Projects: GA ČR(CZ) GAP207/11/0717; GA MŠk(CZ) LK11205 Institutional support: RVO:61388963 ; RVO:61388971 ; RVO:67179843 Keywords : Neisseria meningitidis * FrpC * FrpD * backbone assignments * NMR * iron-regulated protein Subject RIV: CE - Biochemistry Impact factor: 0.760, year: 2014

  20. Tritium containing polymers having a polymer backbone substantially void of tritium

    Science.gov (United States)

    Jensen, G.A.; Nelson, D.A.; Molton, P.M.

    1992-03-31

    A radioluminescent light source comprises a solid mixture of a phosphorescent substance and a tritiated polymer. The solid mixture forms a solid mass having length, width, and thickness dimensions, and is capable of self-support. In one aspect of the invention, the phosphorescent substance comprises solid phosphor particles supported or surrounded within a solid matrix by a tritium containing polymer. The tritium containing polymer comprises a polymer backbone which is essentially void of tritium. 2 figs.

  1. Performance Analysis of Space Information Networks with Backbone Satellite Relaying for Vehicular Networks

    Directory of Open Access Journals (Sweden)

    Jian Jiao

    2017-01-01

    Full Text Available Space Information Network (SIN with backbone satellites relaying for vehicular network (VN communications is regarded as an effective strategy to provide diverse vehicular services in a seamless, efficient, and cost-effective manner in rural areas and highways. In this paper, we investigate the performance of SIN return channel cooperative communications via an amplify-and-forward (AF backbone satellite relaying for VN communications, where we assume that both of the source-destination and relay-destination links undergo Shadowed-Rician fading and the source-relay link follows Rician fading, respectively. In this SIN-assisted VN communication scenario, we first obtain the approximate statistical distributions of the equivalent end-to-end signal-to-noise ratio (SNR of the system. Then, we derive the closed-form expressions to efficiently evaluate the average symbol error rate (ASER of the system. Furthermore, the ASER expressions are taking into account the effect of satellite perturbation of the backbone relaying satellite, which reveal the accumulated error of the antenna pointing error. Finally, simulation results are provided to verify the accuracy of our theoretical analysis and show the impact of various parameters on the system performance.

  2. Backbone assignment and secondary structure of the PsbQ protein from Photosystem II

    Czech Academy of Sciences Publication Activity Database

    Horničáková, M.; Kohoutová, Jaroslava; Schlagnitweit, J.; Wohlschlager, Ch.; Ettrich, Rüdiger; Fiala, R.; Schoefberger, W.; Müller, N.

    2011-01-01

    Roč. 5, č. 2 (2011), s. 169-175 ISSN 1874-2718 R&D Projects: GA MŠk(CZ) LC06010 Institutional research plan: CEZ:AV0Z60870520 Keywords : Photosystem II * PsbQ * Missing link * NMR resonance assignment * Protein-protein interaction Subject RIV: BO - Biophysics Impact factor: 0.720, year: 2011 http://www.springerlink.com/content/3n38075w5h1l1082/fulltext.pdf

  3. Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids

    Czech Academy of Sciences Publication Activity Database

    Svozil, Daniel; Šponer, Judit E.; Marchan, I.; Pérez, A.; Cheatham III., T.E.; Forti, F.; Luque, F.J.; Orözcö, M.; Šponer, Jiří

    2008-01-01

    Roč. 112, č. 27 (2008), s. 8188-8197 ISSN 1520-6106 R&D Projects: GA MŠk(CZ) LC512; GA AV ČR(CZ) IAA400550701; GA AV ČR(CZ) 1QS500040581 Grant - others:GA AV ČR(CZ) IAA400040802 Program:IA Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702; CEZ:AV0Z40550506 Keywords : molecular dynamics * force field * quantum chemistry Subject RIV: BO - Biophysics Impact factor: 4.189, year: 2008

  4. Stochastic collocation-based finite element of structural nonlinear dynamics with application in composite structures

    Directory of Open Access Journals (Sweden)

    Sepahvand K.

    2016-01-01

    Full Text Available Stochastic analysis of structures having nonlinearity by means of sampling methods leads to expensive cost in term of computational time. In contrast, non-sampling methods based on the spectral representation of uncertainty are very efficient with comparable accurate results. In this pa- per, the application of spectral methods to nonlinear dynamics of structures with random parameters is investigated. The impact of the parameter randomness on structural responses has been consid- ered. To this end, uncertain parameters and the structure responses are represented using the gPC expansions with unknown deterministic coefficients and random orthogonal polynomial basis. The deterministic finite element model of the structure is used as black-box and it is executed on a set of random collocation points. As the sample structure responses are estimated, a nonlinear optimization process is employed to calculate the unknown coefficients. The method has this main advantage that can be used for complicated nonlinear structural dynamic problems for which the deterministic FEM model has been already developed. Furthermore, it is very time efficient in comparison with sampling methods, as MC simulations. The application of the method is applied to the nonlinear transient analysis of composite beam structures including uncertain quadratic random damping. The results show that the proposed method can capture the large range of uncertainty in input parameters as well as in structural dynamic responses while it is too time-efficient.

  5. Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes.

    Science.gov (United States)

    Lavender, Christopher A; Gorelick, Robert J; Weeks, Kevin M

    2015-05-01

    HIV and related primate lentiviruses possess single-stranded RNA genomes. Multiple regions of these genomes participate in critical steps in the viral replication cycle, and the functions of many RNA elements are dependent on the formation of defined structures. The structures of these elements are still not fully understood, and additional functional elements likely exist that have not been identified. In this work, we compared three full-length HIV-related viral genomes: HIV-1NL4-3, SIVcpz, and SIVmac (the latter two strains are progenitors for all HIV-1 and HIV-2 strains, respectively). Model-free RNA structure comparisons were performed using whole-genome structure information experimentally derived from nucleotide-resolution SHAPE reactivities. Consensus secondary structures were constructed for strongly correlated regions by taking into account both SHAPE probing structural data and nucleotide covariation information from structure-based alignments. In these consensus models, all known functional RNA elements were recapitulated with high accuracy. In addition, we identified multiple previously unannotated structural elements in the HIV-1 genome likely to function in translation, splicing and other replication cycle processes; these are compelling targets for future functional analyses. The structure-informed alignment strategy developed here will be broadly useful for efficient RNA motif discovery.

  6. Tunable, omnidirectional structural color on reflection based on metal-SiOx-metal structure

    Science.gov (United States)

    Yang, Chenying; Mao, Kening; Shen, Weidong; Fang, Bo; Fang, Xu; Zhang, Xing; Zhang, Yueguang; Liu, Xu

    2016-12-01

    An omnidirectional structural color based on the metal-SiOx-metal stack structure is proposed, which can present the same perceived color for a broad range of incidence angles. The tunable structural color can be obtained with adjustable intermediate dielectric layer by simply adjusting the deposition condition, especially the oxygen flow rate during the deposition processes. The resonance condition can be satisfied across the whole visible light region with this special dielectric. The strong absorption caused by the resonance within the metal-SiOx-metal structure accounts for the efficient spectral filtering feature, and the constant phase shift within the dielectric layer leads to angle insensitivity of this color filter. This simple color tuning method for omnidirectional structural colors can have a great potential in various applications such as displaying, imaging, colorful decoration, anti-counterfeiting and so forth.

  7. Strain Concentration at Structural Discontinuities and Its Prediction Based on Characteristics of Compliance Change in Structures

    Science.gov (United States)

    Kasahara, Naoto

    Elevated temperature structural design codes pay attention to strain concentration at structural discontinuities due to creep and plasticity, since it causes an increase in creep-fatigue damage of materials. One of the difficulties in predicting strain concentration is its dependence on the magnitude of loading, the constitutive equations, and the duration of loading. In this study, the author investigated the fundamental mechanism of strain concentration and its main factors. The results revealed that strain concentration is caused by strain redistribution between elastic and inelastic regions, which can be quantified by the characteristics of structural compliance. The characteristics of structural compliance are controlled by elastic region in structures and are insensitive to constitutive equations. It means that inelastic analysis can be easily applied to obtain compliance characteristics. By utilizing this fact, a simplified inelastic analysis method was proposed based on the characteristics of compliance change for the prediction of strain concentration.

  8. Structural parameter study on polymer-based ultrasonic motor

    Science.gov (United States)

    Wu, Jiang; Mizuno, Yosuke; Nakamura, Kentaro

    2017-11-01

    Our previous study has shown that traveling-wave rotary ultrasonic motors using polymer-based vibrators can work in the same way as conventional motors with metal-based vibrators. It is feasible to enhance the performance, particularly output torques, of polymer-based motors by adjusting several key dimensions of their vibrators. In this study, poly phenylene sulfide, a functional polymer exhibiting low attenuation at ultrasonic frequency, is selected as the vibrating body, which is activated with a piezoelectric ceramic element bonded on its back surface. The optimal thicknesses of the polymer-based motors are higher than those of metal-based motors. When the same voltages were applied, the maximum torques and output powers available with the polymer-based motors were lower than the values of the metal-based motors with the same structures. The reasons for the lower torque were explained on the basis of vibration modes. First, the force factors of the polymer-based vibrators are lower than those of metal-based vibrators owing to the great difference in the mechanical constants between polymers and piezoelectric ceramics. Subsequently, though the force factors of polymer-based vibrators can be slightly enhanced by increasing their thicknesses, the unavoidable radial vibrations become higher and cause undesirable friction loss, which reduces the output torques. Though the polymer-based motors have rotation speeds comparable to those of metal-based motors, their output power are lower due to the low electromechanical coupling factors of the polymer-based vibrators.

  9. Proposed Doctrine Based Structure of the Armored Reconnaissance Squadron

    Science.gov (United States)

    2017-06-09

    the literature reviewed, specifically in professional Canadian Army publications such as the Army Journal and the Armour Bulletin, where one would...expect to find capability based discourse; there is a lack of proposed structure based on capability, task or equipment. The Armour Bulletin serves...Lieutenant Joe and De Silva, Lieutenant Jon. 2014. “RCD Lessons Learned During Exercise MAPLE RESOLVE 1401.” Armour Bulletin: 27-29. Childs, Major Dale

  10. Structural bases of GM1 gangliosidosis and Morquio B disease.

    Science.gov (United States)

    Morita, Mizuki; Saito, Seiji; Ikeda, Kazuyoshi; Ohno, Kazuki; Sugawara, Kanako; Suzuki, Toshihiro; Togawa, Tadayasu; Sakuraba, Hitoshi

    2009-09-01

    Allelic mutations of the lysosomal beta-galactosidase gene cause heterogeneous clinical phenotypes, such as GM1 gangliosidosis and Morquio B disease, the former being further classified into three variants, namely infantile, juvenile and adult forms; and heterogeneous biochemical phenotypes were shown in these forms. We tried to elucidate the bases of these diseases from a structural viewpoint. We first constructed a three-dimensional structural model of human beta-galactosidase by means of homology modeling. The human beta-galactosidase consists of three domains, such as, a TIM barrel fold domain, which functions as a catalytic domain, and two galactose-binding domain-like fold domains. We then constructed structural models of representative mutant beta-galactosidase proteins (G123R, R201C, I51T and Y83H) and predicted the structural change associated with each phenotype by calculating the number of affected atoms, determining the root-mean-square deviation and the solvent-accessible surface area, and by color imaging. The results show that there is a good correlation between the structural changes caused by amino-acid substitutions in the beta-galactosidase molecule, as well as biochemical and clinical phenotypes in these representative cases. Protein structural study is useful for elucidating the bases of these diseases.

  11. Tamper indicating and sensing optical-based smart structures

    International Nuclear Information System (INIS)

    Sliva, P.; Anheier, N.C.; Gordon, N.R.; Simmons, K.L.; Stahl, K.A.; Undem, H.A.

    1995-05-01

    This paper has presented an overview of the type of optical-based structures that can be designed and constructed. These smart structures are capable of responding to their environment. The examples given represent a modest sampling of the complexity that can be achieved in both design and practice. Tamper-indicating containers and smart, sensing windows demonstrate just a few of the applications. We have shown that optical-based smart structures can be made multifunctional with the sensing built in. The next generation smart structure will combine the sensing functionality of these optical-based smart structures with other sensors such as piezoelectrics and electro-rheological fluids to not only be able to respond to the environment, but to adapt to it as well. An example of functionality in this regime would be a piezosensor that senses pressure changes (e.g., shock waves), which then causes an electro-rheological fluid to change viscosity. A fiber sensor located in or near the electro-rheological fluid senses the stiffness change and sends a signal through a feedback loop back to the piezosensor for additional adjustments to the electro-rheological fluid

  12. Classification of the Pospiviroidae based on their structural hallmarks.

    Directory of Open Access Journals (Sweden)

    Tamara Giguère

    Full Text Available The simplest known plant pathogens are the viroids. Because of their non-coding single-stranded circular RNA genome, they depend on both their sequence and their structure for both a successful infection and their replication. In the recent years, important progress in the elucidation of their structures was achieved using an adaptation of the selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE protocol in order to probe viroid structures in solution. Previously, SHAPE has been adapted to elucidate the structures of all of the members of the family Avsunviroidae, as well as those of a few members of the family Pospiviroidae. In this study, with the goal of providing an entire compendium of the secondary structures of the various viroid species, a total of thirteen new Pospiviroidae members were probed in solution using the SHAPE protocol. More specifically, the secondary structures of eleven species for which the genus was previously known were initially elucidated. At this point, considering all of the SHAPE elucidated secondary structures, a classification system for viroids in their respective genera was proposed. On the basis of the structural classification reported here, the probings of both the Grapevine latent viroid and the Dahlia latent viroid provide sound arguments for the determination of their respective genera, which appear to be Apscaviroid and Hostuviroid, respectively. More importantly, this study provides the complete repertoire of the secondary structures, mapped in solution, of all of the accepted viroid species reported thus far. In addition, a classification scheme based on structural hallmarks, an important tool for many biological studies, is proposed.

  13. Structural Topology Optimization Based on the Smoothed Finite Element Method

    Directory of Open Access Journals (Sweden)

    Vahid Shobeiri

    Full Text Available Abstract In this paper, the smoothed finite element method, incorporated with the level set method, is employed to carry out the topology optimization of continuum structures. The structural compliance is minimized subject to a constraint on the weight of material used. The cell-based smoothed finite element method is employed to improve the accuracy and stability of the standard finite element method. Several numerical examples are presented to prove the validity and utility of the proposed method. The obtained results are compared with those obtained by several standard finite element-based examples in order to access the applicability and effectiveness of the proposed method. The common numerical instabilities of the structural topology optimization problems such as checkerboard pattern and mesh dependency are studied in the examples.

  14. Biomedical application of hierarchically built structures based on metal oxides

    Science.gov (United States)

    Korovin, M. S.; Fomenko, A. N.

    2017-12-01

    Nowadays, the use of hierarchically built structures in biology and medicine arouses much interest. The aim of this work is to review and summarize the available literature data about hierarchically organized structures in biomedical application. Nanoparticles can serve as an example of such structures. Medicine holds a special place among various application methods of similar systems. Special attention is paid to inorganic nanoparticles based on different metal oxides and hydroxides, such as iron, zinc, copper, and aluminum. Our investigations show that low-dimensional nanostructures based on aluminum oxides and hydroxides have an inhibitory effect on tumor cells and possess an antimicrobial activity. At the same time, it is obvious that the large-scale use of nanoparticles by humans needs to thoroughly study their properties. Special attention should be paid to the study of nanoparticle interaction with living biological objects. The numerous data show that there is no clear understanding of interaction mechanisms between nanoparticles and various cell types.

  15. Reliability analysis of offshore structures using OMA based fatigue stresses

    DEFF Research Database (Denmark)

    Silva Nabuco, Bruna; Aissani, Amina; Glindtvad Tarpø, Marius

    2017-01-01

    points of the structure, the stress history can be calculated in any arbitrary point of the structure. The accuracy of the estimated actual stress is analyzed by experimental tests on a scale model where the obtained stresses are compared to strain gauges measurements. After evaluating the fatigue...... affect the accuracy of the performance evaluation. It can be mentioned mainly the uncertainties related to the materials, the uncertainty on Miner’s rule and the uncertainty on the SN curve but most importantly is the uncertainty on the stress ranges induced by the wave loading. In this paper, the mainly...... focus is on the uncertainty observed on the different stresses used to predict the damage. This uncertainty can be reduced by Modal Based Fatigue Monitoring which is a technique based on continuously measuring of the accelerations in few points of the structure with the use of accelerometers known...

  16. A new entropy based method for computing software structural complexity

    CERN Document Server

    Roca, J L

    2002-01-01

    In this paper a new methodology for the evaluation of software structural complexity is described. It is based on the entropy evaluation of the random uniform response function associated with the so called software characteristic function SCF. The behavior of the SCF with the different software structures and their relationship with the number of inherent errors is investigated. It is also investigated how the entropy concept can be used to evaluate the complexity of a software structure considering the SCF as a canonical representation of the graph associated with the control flow diagram. The functions, parameters and algorithms that allow to carry out this evaluation are also introduced. After this analytic phase follows the experimental phase, verifying the consistency of the proposed metric and their boundary conditions. The conclusion is that the degree of software structural complexity can be measured as the entropy of the random uniform response function of the SCF. That entropy is in direct relation...

  17. Inelastic Structural Control Based on MBC and FAM

    Directory of Open Access Journals (Sweden)

    Li Gang

    2011-01-01

    Full Text Available A complex structure has the characters of many degrees of freedom and intricate shape, especially inelastic behavior under strong external loadings. It is hard to apply the structural control technology to it. In this paper, a new method that combines the Market-Based Control (MBC strategy and Force Analogy Method (FAM is presented to analyze the inelastic behavior of structure with magnetorheological dampers. The MBC is used to reduce the structural vibration response, and FAM is proposed to perform the inelastic analysis. A numerical example is used to compare the control effect of the new method and LQR algorithm, which show the accuracy and efficiency of the proposed computational method.

  18. A fingerprint based metric for measuring similarities of crystalline structures

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Li; Fuhrer, Tobias; Schaefer, Bastian; Grauzinyte, Migle; Goedecker, Stefan, E-mail: stefan.goedecker@unibas.ch [Department of Physics, Universität Basel, Klingelbergstr. 82, 4056 Basel (Switzerland); Amsler, Maximilian [Department of Physics, Universität Basel, Klingelbergstr. 82, 4056 Basel (Switzerland); Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208 (United States); Faraji, Somayeh; Rostami, Samare; Ghasemi, S. Alireza [Institute for Advanced Studies in Basic Sciences, P.O. Box 45195-1159, Zanjan (Iran, Islamic Republic of); Sadeghi, Ali [Physics Department, Shahid Beheshti University, G. C., Evin, 19839 Tehran (Iran, Islamic Republic of); Wolverton, Chris [Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208 (United States)

    2016-01-21

    Measuring similarities/dissimilarities between atomic structures is important for the exploration of potential energy landscapes. However, the cell vectors together with the coordinates of the atoms, which are generally used to describe periodic systems, are quantities not directly suitable as fingerprints to distinguish structures. Based on a characterization of the local environment of all atoms in a cell, we introduce crystal fingerprints that can be calculated easily and define configurational distances between crystalline structures that satisfy the mathematical properties of a metric. This distance between two configurations is a measure of their similarity/dissimilarity and it allows in particular to distinguish structures. The new method can be a useful tool within various energy landscape exploration schemes, such as minima hopping, random search, swarm intelligence algorithms, and high-throughput screenings.

  19. A fingerprint based metric for measuring similarities of crystalline structures

    Science.gov (United States)

    Zhu, Li; Amsler, Maximilian; Fuhrer, Tobias; Schaefer, Bastian; Faraji, Somayeh; Rostami, Samare; Ghasemi, S. Alireza; Sadeghi, Ali; Grauzinyte, Migle; Wolverton, Chris; Goedecker, Stefan

    2016-01-01

    Measuring similarities/dissimilarities between atomic structures is important for the exploration of potential energy landscapes. However, the cell vectors together with the coordinates of the atoms, which are generally used to describe periodic systems, are quantities not directly suitable as fingerprints to distinguish structures. Based on a characterization of the local environment of all atoms in a cell, we introduce crystal fingerprints that can be calculated easily and define configurational distances between crystalline structures that satisfy the mathematical properties of a metric. This distance between two configurations is a measure of their similarity/dissimilarity and it allows in particular to distinguish structures. The new method can be a useful tool within various energy landscape exploration schemes, such as minima hopping, random search, swarm intelligence algorithms, and high-throughput screenings.

  20. A fingerprint based metric for measuring similarities of crystalline structures

    International Nuclear Information System (INIS)

    Zhu, Li; Fuhrer, Tobias; Schaefer, Bastian; Grauzinyte, Migle; Goedecker, Stefan; Amsler, Maximilian; Faraji, Somayeh; Rostami, Samare; Ghasemi, S. Alireza; Sadeghi, Ali; Wolverton, Chris

    2016-01-01

    Measuring similarities/dissimilarities between atomic structures is important for the exploration of potential energy landscapes. However, the cell vectors together with the coordinates of the atoms, which are generally used to describe periodic systems, are quantities not directly suitable as fingerprints to distinguish structures. Based on a characterization of the local environment of all atoms in a cell, we introduce crystal fingerprints that can be calculated easily and define configurational distances between crystalline structures that satisfy the mathematical properties of a metric. This distance between two configurations is a measure of their similarity/dissimilarity and it allows in particular to distinguish structures. The new method can be a useful tool within various energy landscape exploration schemes, such as minima hopping, random search, swarm intelligence algorithms, and high-throughput screenings

  1. Modern earthquake engineering offshore and land-based structures

    CERN Document Server

    Jia, Junbo

    2017-01-01

    This book addresses applications of earthquake engineering for both offshore and land-based structures. It is self-contained as a reference work and covers a wide range of topics, including topics related to engineering seismology, geotechnical earthquake engineering, structural engineering, as well as special contents dedicated to design philosophy, determination of ground motions, shock waves, tsunamis, earthquake damage, seismic response of offshore and arctic structures, spatial varied ground motions, simplified and advanced seismic analysis methods, sudden subsidence of offshore platforms, tank liquid impacts during earthquakes, seismic resistance of non-structural elements, and various types of mitigation measures, etc. The target readership includes professionals in offshore and civil engineering, officials and regulators, as well as researchers and students in this field.

  2. Global stability-based design optimization of truss structures using ...

    Indian Academy of Sciences (India)

    Furthermore, a pure pareto-ranking based multi-objective optimization model is employed for the design optimization of the truss structure with multiple objectives. The computational performance of the optimization model is increased by implementing an island model into its evolutionary search mechanism. The proposed ...

  3. Reliability-Based Inspection Planning for Structural Systems

    DEFF Research Database (Denmark)

    Sørensen, John Dalsgaard

    1993-01-01

    A general model for reliability-based optimal inspection and repair strategies for structural systems is described. The total expected costs in the design lifetime is minimized with the number of inspections, the inspection times and efforts as decision variables. The equivalence of this model wi...

  4. Discrete Discriminant analysis based on tree-structured graphical models

    DEFF Research Database (Denmark)

    Perez de la Cruz, Gonzalo; Eslava, Guillermina

    The purpose of this paper is to illustrate the potential use of discriminant analysis based on tree{structured graphical models for discrete variables. This is done by comparing its empirical performance using estimated error rates for real and simulated data. The results show that discriminant...

  5. Bending-active reciprocal structures based on equilateral polyhedral geometries

    DEFF Research Database (Denmark)

    Popovic Larsen, Olga; BRANCART, Stijn; DE TEMMERMAN, Niels

    2017-01-01

    the principle by developing a design methodology based on polyhedral shapes. As this work is part of a research on transformable, rapidly assembled structures, the focus lies on simplicity of the connections, uniformity of the components and reconfigurability. This paper discusses the development of a kit...

  6. Electronic structure of Fe- vs. Ru-based dye molecules

    DEFF Research Database (Denmark)

    Johnson, Phillip S.; Cook, Peter L.; Zegkinoglou, Ioannis

    2013-01-01

    In order to explore whether Ru can be replaced by inexpensive Fe in dye molecules for solar cells, the differences in the electronic structure of Fe- and Ru-based dyes are investigated by X-ray absorption spectroscopy and first-principles calculations. Molecules with the metal in a sixfold, octah...

  7. Internal Structure of DISCOVER: A Performance-based Assessment.

    Science.gov (United States)

    Sarouphim, Ketty M.

    2000-01-01

    A study involving 257 Navajo and Mexican-American elementary students investigated the internal structure of the DISCOVER assessment, a performance-based assessment grounded in Gardner's theory of multiple intelligence. Results showed low interrating correlations among the five assessment activities, indicating students gifted in one intelligence…

  8. Structure and properties of compositions based on petroleum sulfonic acids

    Energy Technology Data Exchange (ETDEWEB)

    Tutorskii, I.A.; Sultanova, A.S.; Belkina, E.V.; Fomin, A.G. [Lomonosov Academy of Fine Chemical Technology, Moscow (Russian Federation)

    1995-03-01

    Colloidal characteristics of compositions based on petroleum sulfonic acids were studied. Neutralized heavy oil residue exhibits surface-active properties and contains an ultradisperse filler. Analysis of the compositions by size-exclusion-chromatography shows deep structural changes in the heavy acid residue upon neutralization with calcium carbonate.

  9. An improved AODV routing protocol based on tower structure

    Directory of Open Access Journals (Sweden)

    Li Yong Qiang

    2016-01-01

    Full Text Available The paper proposed a new routing protocol(IAODV based on tower structure in the Ad Hoc network for the problem which Location Routing Protocol need hardware and Complex algorithm. By the simulation, The complexity of the new routing protocol is reduced without reducing the performance of the network.

  10. Backbone and side-chain assignments for a novel CBM69 starch binding domain AmyP-SBD.

    Science.gov (United States)

    Li, Xinxin; Yu, Jigang; Zhang, Jiahai; Sun, Hongbin; Zhang, Xuecheng

    2017-10-01

    Starch binding domains (SBDs) are important for the functions of glycoside hydrolysis enzymes such as α-amylases, they have great application potential in biotechnology and industries. AmyP is a newly identified α-amylase belonging to a new subfamily 37 of glycoside hydrolysis enzyme family 13. AmyP shows preferential degradation to soluble starch, in which its C-terminal starch binding domain, AmyP-SBD, plays an important role. AmyP-SBD shares very low sequence similarity with other biochemically characterized SBDs and was assigned to a new carbohydrate binding module family CBM69. Intriguingly, AmyP-SBD is unfolded in free form, and substrate analogue β-cyclodextrin may induce it to fold into a relatively rigid state. Structure determination for AmyP-SBD will be helpful for understanding its unique properties. Here, we report the backbone and side-chain 1 H, 13 C and 15 N resonance assignments of folded AmyP-SBD, as a basis for structure determination and further studies.

  11. High resolution 4D HPCH experiment for sequential assignment of {sup 13}C-labeled RNAs via phosphodiester backbone

    Energy Technology Data Exchange (ETDEWEB)

    Saxena, Saurabh; Stanek, Jan [University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre (Poland); Cevec, Mirko; Plavec, Janez [National Institute of Chemistry, Slovenian NMR Centre (Slovenia); Koźmiński, Wiktor, E-mail: kozmin@chem.uw.edu.pl [University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre (Poland)

    2015-11-15

    The three-dimensional structure determination of RNAs by NMR spectroscopy requires sequential resonance assignment, often hampered by assignment ambiguities and limited dispersion of {sup 1}H and {sup 13}C chemical shifts, especially of C4′/H4′. Here we present a novel through-bond 4D HPCH NMR experiment involving phosphate backbone where C4′–H4′ correlations are resolved along the {sup 1}H3′–{sup 31}P spectral planes. The experiment provides high peak resolution and effectively removes ambiguities encountered during assignments. Enhanced peak dispersion is provided by the inclusion of additional {sup 31}P and {sup 1}H3′ dimensions and constant-time evolution of chemical shifts. High spectral resolution is obtained by using non-uniform sampling in three indirect dimensions. The experiment fully utilizes the isotopic {sup 13}C-labeling with evolution of C4′ carbons. Band selective {sup 13}C inversion pulses are used to achieve selectivity and prevent signal dephasing due to the C4′–C3′ and C4′–C5′ homonuclear couplings. Multiple quantum line narrowing is employed to minimize sensitivity loses. The 4D HPCH experiment is verified and successfully applied to a non-coding 34-nt RNA consisting typical structure elements and a 14-nt RNA hairpin capped by cUUCGg tetraloop.

  12. Quality assessment of protein model-structures based on structural and functional similarities.

    Science.gov (United States)

    Konopka, Bogumil M; Nebel, Jean-Christophe; Kotulska, Malgorzata

    2012-09-21

    Experimental determination of protein 3D structures is expensive, time consuming and sometimes impossible. A gap between number of protein structures deposited in the World Wide Protein Data Bank and the number of sequenced proteins constantly broadens. Computational modeling is deemed to be one of the ways to deal with the problem. Although protein 3D structure prediction is a difficult task, many tools are available. These tools can model it from a sequence or partial structural information, e.g. contact maps. Consequently, biologists have the ability to generate automatically a putative 3D structure model of any protein. However, the main issue becomes evaluation of the model quality, which is one of the most important challenges of structural biology. GOBA--Gene Ontology-Based Assessment is a novel Protein Model Quality Assessment Program. It estimates the compatibility between a model-structure and its expected function. GOBA is based on the assumption that a high quality model is expected to be structurally similar to proteins functionally similar to the prediction target. Whereas DALI is used to measure structure similarity, protein functional similarity is quantified using standardized and hierarchical description of proteins provided by Gene Ontology combined with Wang's algorithm for calculating semantic similarity. Two approaches are proposed to express the quality of protein model-structures. One is a single model quality assessment method, the other is its modification, which provides a relative measure of model quality. Exhaustive evaluation is performed on data sets of model-structures submitted to the CASP8 and CASP9 contests. The validation shows that the method is able to discriminate between good and bad model-structures. The best of tested GOBA scores achieved 0.74 and 0.8 as a mean Pearson correlation to the observed quality of models in our CASP8 and CASP9-based validation sets. GOBA also obtained the best result for two targets of CASP8, and

  13. Probabilistic structural damage identification based on vibration data

    International Nuclear Information System (INIS)

    Hao, H.; Xia, Y.

    2001-01-01

    Vibration-based methods are being rapidly developed and applied to detect structural damage in civil, mechanical and aerospace engineering communities in the last two decades. But uncertainties existing in the structural model and measured vibration data might lead to unreliable results. This paper will present some recent research results to tackle the above mentioned uncertainty problems. By assuming each of the FE model parameters and measured vibration data as a normally distributed random variable, a probabilistic damage detection procedure is developed based on perturbation method and validated by Monte Carlo simulation technique. With this technique, the damage probability of each structural element can be determined. The method developed has been verified by applying it to identify the damages of laboratory tested structures. It was proven that, as compared to the deterministic damage identification method, the present method can not only reduce the possibility of false identification, but also give the identification results in terms of probability. which is deemed more realistic and practical in detecting possible damages in a structure. It has also been found that the modal data included in damage identification analysis have a great influence on the identification results. With a sensitivity study, an optimal measurement set for damage detection is determined. This set includes the optimal measurement locations and the most appropriate modes that should be used in the damage identification analysis. Numerical results indicated that if the optimal set determined in a pre-analysis is used in the damage detection better results will be achieved. (author)

  14. Image quality assessment based on textural structure and normalized noise

    Science.gov (United States)

    Zhang, Chun-e.; Qiu, Zhengding

    2006-01-01

    Traditional image quality assessments are mostly based on error analysis and the errors only stem from the absolute differences of pixel values or transform coefficients between the two compared images. With consideration of Human Vision System this paper proposes a quality assessment based on textural structure and normalized noise, SNPSNR. The time-frequency property of wavelet transform is utilized to represent images' textural structure and then the structural noise is figured as the difference between wavelet transform coefficients emphasized by textural structure. The noises on each level, i.e., each channel, are weighted by HVS. Due to the energy distribution property of wavelet transform, the noise quantity difference on each transform level is quite large and is not proportional to the influence caused by them. We normalize the structural noise on different levels by normalizing the coefficients on each level. SNPSNR computation adopting the PSNR form and the result data are fitted with Differential Mean Opinion Scores (DMOS) using logistic function. SNPSNR gains better performance when compared with MSSIM, HVSNR and PSNR.

  15. Blind Test of Physics-Based Prediction of Protein Structures

    Science.gov (United States)

    Shell, M. Scott; Ozkan, S. Banu; Voelz, Vincent; Wu, Guohong Albert; Dill, Ken A.

    2009-01-01

    We report here a multiprotein blind test of a computer method to predict native protein structures based solely on an all-atom physics-based force field. We use the AMBER 96 potential function with an implicit (GB/SA) model of solvation, combined with replica-exchange molecular-dynamics simulations. Coarse conformational sampling is performed using the zipping and assembly method (ZAM), an approach that is designed to mimic the putative physical routes of protein folding. ZAM was applied to the folding of six proteins, from 76 to 112 monomers in length, in CASP7, a community-wide blind test of protein structure prediction. Because these predictions have about the same level of accuracy as typical bioinformatics methods, and do not utilize information from databases of known native structures, this work opens up the possibility of predicting the structures of membrane proteins, synthetic peptides, or other foldable polymers, for which there is little prior knowledge of native structures. This approach may also be useful for predicting physical protein folding routes, non-native conformations, and other physical properties from amino acid sequences. PMID:19186130

  16. Single-Walled Carbon-Nanotubes-Based Organic Memory Structures

    Directory of Open Access Journals (Sweden)

    Sundes Fakher

    2016-09-01

    Full Text Available The electrical behaviour of organic memory structures, based on single-walled carbon-nanotubes (SWCNTs, metal–insulator–semiconductor (MIS and thin film transistor (TFT structures, using poly(methyl methacrylate (PMMA as the gate dielectric, are reported. The drain and source electrodes were fabricated by evaporating 50 nm gold, and the gate electrode was made from 50 nm-evaporated aluminium on a clean glass substrate. Thin films of SWCNTs, embedded within the insulating layer, were used as the floating gate. SWCNTs-based memory devices exhibited clear hysteresis in their electrical characteristics (capacitance–voltage (C–V for MIS structures, as well as output and transfer characteristics for transistors. Both structures were shown to produce reliable and large memory windows by virtue of high capacity and reduced charge leakage. The hysteresis in the output and transfer characteristics, the shifts in the threshold voltage of the transfer characteristics, and the flat-band voltage shift in the MIS structures were attributed to the charging and discharging of the SWCNTs floating gate. Under an appropriate gate bias (1 s pulses, the floating gate is charged and discharged, resulting in significant threshold voltage shifts. Pulses as low as 1 V resulted in clear write and erase states.

  17. Single-Walled Carbon-Nanotubes-Based Organic Memory Structures.

    Science.gov (United States)

    Fakher, Sundes; Nejm, Razan; Ayesh, Ahmad; Al-Ghaferi, Amal; Zeze, Dagou; Mabrook, Mohammed

    2016-09-02

    The electrical behaviour of organic memory structures, based on single-walled carbon-nanotubes (SWCNTs), metal-insulator-semiconductor (MIS) and thin film transistor (TFT) structures, using poly(methyl methacrylate) (PMMA) as the gate dielectric, are reported. The drain and source electrodes were fabricated by evaporating 50 nm gold, and the gate electrode was made from 50 nm-evaporated aluminium on a clean glass substrate. Thin films of SWCNTs, embedded within the insulating layer, were used as the floating gate. SWCNTs-based memory devices exhibited clear hysteresis in their electrical characteristics (capacitance-voltage (C-V) for MIS structures, as well as output and transfer characteristics for transistors). Both structures were shown to produce reliable and large memory windows by virtue of high capacity and reduced charge leakage. The hysteresis in the output and transfer characteristics, the shifts in the threshold voltage of the transfer characteristics, and the flat-band voltage shift in the MIS structures were attributed to the charging and discharging of the SWCNTs floating gate. Under an appropriate gate bias (1 s pulses), the floating gate is charged and discharged, resulting in significant threshold voltage shifts. Pulses as low as 1 V resulted in clear write and erase states.

  18. Oxidation Responsive Polymers with a Triggered Degradation via Arylboronate Self-Immolative Motifs on a Polyphosphazene Backbone.

    Science.gov (United States)

    Iturmendi, Aitziber; Monkowius, Uwe; Teasdale, Ian

    2017-02-21

    Oxidation responsive polymers with triggered degradation pathways have been prepared via attachment of self-immolative moieties onto a hydrolytically unstable polyphosphazene backbone. After controlled main-chain growth, postpolymerization functionalization allows the preparation of hydrolytically stable poly(organo)phosphazenes decorated with a phenylboronic ester caging group. In oxidative environments, triggered cleavage of the caging group is followed by self-immolation, exposing the unstable glycine-substituted polyphosphazene which subsequently undergoes to backbone degradation to low-molecular weight molecules. As well as giving mechanistic insights, detailed GPC and 1 H and 31 P NMR analysis reveal the polymers to be stable in aqueous solutions, but show a selective, fast degradation upon exposure to hydrogen peroxide containing solutions. Since the post-polymerization functionalization route allows simple access to polymer backbones with a broad range of molecular weights, the approach of using the inorganic backbone as a platform significantly expands the toolbox of polymers capable of stimuli-responsive degradation.

  19. Structural kinematics based damage zone prediction in gradient structures using vibration database

    Science.gov (United States)

    Talha, Mohammad; Ashokkumar, Chimpalthradi R.

    2014-05-01

    To explore the applications of functionally graded materials (FGMs) in dynamic structures, structural kinematics based health monitoring technique becomes an important problem. Depending upon the displacements in three dimensions, the health of the material to withstand dynamic loads is inferred in this paper, which is based on the net compressive and tensile displacements that each structural degree of freedom takes. These net displacements at each finite element node predicts damage zones of the FGM where the material is likely to fail due to a vibration response which is categorized according to loading condition. The damage zone prediction of a dynamically active FGMs plate have been accomplished using Reddy's higher-order theory. The constituent material properties are assumed to vary in the thickness direction according to the power-law behavior. The proposed C0 finite element model (FEM) is applied to get net tensile and compressive displacement distributions across the structures. A plate made of Aluminum/Ziconia is considered to illustrate the concept of structural kinematics-based health monitoring aspects of FGMs.

  20. Reliability-Based Structural Optimization of Wave Energy Converters

    Directory of Open Access Journals (Sweden)

    Simon Ambühl

    2014-12-01

    Full Text Available More and more wave energy converter (WEC concepts are reaching prototypelevel. Once the prototype level is reached, the next step in order to further decrease thelevelized cost of energy (LCOE is optimizing the overall system with a focus on structuraland maintenance (inspection costs, as well as on the harvested power from the waves.The target of a fully-developed WEC technology is not maximizing its power output,but minimizing the resulting LCOE. This paper presents a methodology to optimize thestructural design of WECs based on a reliability-based optimization problem and the intentto maximize the investor’s benefits by maximizing the difference between income (e.g., fromselling electricity and the expected expenses (e.g., structural building costs or failure costs.Furthermore, different development levels, like prototype or commercial devices, may havedifferent main objectives and will be located at different locations, as well as receive varioussubsidies. These points should be accounted for when performing structural optimizationsof WECs. An illustrative example on the gravity-based foundation of the Wavestar deviceis performed showing how structural design can be optimized taking target reliability levelsand different structural failure modes due to extreme loads into account.

  1. Protein NMR Structure Refinement based on Bayesian Inference

    Science.gov (United States)

    Ikeya, Teppei; Ikeda, Shiro; Kigawa, Takanori; Ito, Yutaka; Güntert, Peter

    2016-03-01

    Nuclear Magnetic Resonance (NMR) spectroscopy is a tool to investigate threedimensional (3D) structures and dynamics of biomacromolecules at atomic resolution in solution or more natural environments such as living cells. Since NMR data are principally only spectra with peak signals, it is required to properly deduce structural information from the sparse experimental data with their imperfections and uncertainty, and to visualize 3D conformations by NMR structure calculation. In order to efficiently analyse the data, Rieping et al. proposed a new structure calculation method based on Bayes’ theorem. We implemented a similar approach into the program CYANA with some modifications. It allows us to handle automatic NOE cross peak assignments in unambiguous and ambiguous usages, and to create a prior distribution based on a physical force field with the generalized Born implicit water model. The sampling scheme for obtaining the posterior is performed by a hybrid Monte Carlo algorithm combined with Markov chain Monte Carlo (MCMC) by the Gibbs sampler, and molecular dynamics simulation (MD) for obtaining a canonical ensemble of conformations. Since it is not trivial to search the entire function space particularly for exploring the conformational prior due to the extraordinarily large conformation space of proteins, the replica exchange method is performed, in which several MCMC calculations with different temperatures run in parallel as replicas. It is shown with simulated data or randomly deleted experimental peaks that the new structure calculation method can provide accurate structures even with less peaks, especially compared with the conventional method. In particular, it dramatically improves in-cell structures of the proteins GB1 and TTHA1718 using exclusively information obtained in living Escherichia coli (E. coli) cells.

  2. Optimization of morphing flaps based on fluid structure interaction modeling

    DEFF Research Database (Denmark)

    Barlas, Athanasios; Akay, Busra

    2018-01-01

    This article describes the design optimization of morphing trailing edge flaps for wind turbines with ‘smart blades’. A high fidelity Fluid Structure Interaction (FSI) simulation framework is utilized, comprised of 2D Finite Element Analysis (FEA) and Computational Fluid Dynamics (CFD) models....... A coupled aero-structural simulation of a 10% chordwise length morphing trailing edge flap for a 4 MW wind turbine rotor is carried out and response surfaces are produced with respect to the flap internal geometry design parameters for the design conditions. Surrogate model based optimization is applied...

  3. Miniature Microwave Bandpass Filter Based on EBG Structures

    DEFF Research Database (Denmark)

    Zhurbenko, Vitaliy; Krozer, Viktor; Meincke, Peter

    2006-01-01

    as compared to stepped-impedance hairpin (SIH) resonators with similar response. The new bandpass filter has a reduced footprint and can be fabricated in standard thick-film manufacturing technology. Measured and simulated results exhibit good agreement. The measured results show improvement in the filter......A new design of a planar microwave filter, based on rejection band properties of an electrically small electromagnetic bandgap (EBG) structure, is proposed. The proposed EBG structure demonstrates effective impedance manipulation, exhibits a simple analysis, and is about three times smaller...... characteristics in comparison to existing SIH filter design....

  4. Correlation of crystal structures, electronic structures and photocatalytic properties in W-based oxides

    International Nuclear Information System (INIS)

    Shi Haifeng; Huang Xianli; Tian Hanmin; Lv Jun; Li Zhaosheng; Zou Zhigang; Ye Jinhua

    2009-01-01

    We reported a novel W-based oxide NaBi(WO 4 ) 2 with WO 4 tetrahedral crystal structure as a photocatalyst for decomposition of 2-propanol. The physical characteristics of the sample were examined by XRD, BET measurement and SEM, respectively. The band gap of NaBi(WO 4 ) 2 was determined to be 3.6 eV according to the diffuse reflectance spectra of the sample. The photocatalytic activity of NaBi(WO 4 ) 2 was confirmed by decomposing 2-propanol into acetone and CO 2 . It showed a higher acetone generation rate (211 ppm h -1 ) in contrast to that of WO 3 (120 ppm h -1 ), which consisted of WO 6 octahedra. Their electronic structures were further investigated by the plane-wave based density function theory. The results suggested that the crystal field (WO 6 and WO 4 ) significantly influenced the electronic structures and hence affected the photocatalytic activity.

  5. Value of information-based inspection planning for offshore structures

    DEFF Research Database (Denmark)

    Irman, Arifian Agusta; Thöns, Sebastian; Leira, Bernt J.

    2017-01-01

    and risk- based inspection (RRBI) constitutes an efficient method to optimize inspection planning. Basing the inspection planning on pre-posterior Bayesian decision analysis and especially a Value of Information analysis allows to explicitly quantify the expected benefits, costs and risks associated...... with each inspection strategy. A simplified and generic risk-based inspection planning utilizing pre- posterior Bayesian decision analysis had been proposed by Faber et al. [1] and Straub [2]. This paper provides considerations on the theoretical background and a Value of Information analysis......-based inspection planning. The paper will start out with a review of the state-of-art RBI planning procedure based on Bayesian decision theory and its application in offshore structure integrity management. An example of the Value of Information approach is illustrated and it is pointed to further research...

  6. Gradient based structural optimization with fatigue constraints of jacket structures for offshore wind turbines

    DEFF Research Database (Denmark)

    Oest, Jacob; Overgaard, Lars Christian; Lund, Erik

    2015-01-01

    without the need for extensive manual post-processing. Ultimately, the optimized design may be lighter and thus reduce both production and installation cost. The aim of this work is to present such a gradient based optimization method with fatigue constraints of jacket structures for the preliminary......Investigating the fatigue life of support structures of offshore wind turbines is imperative to avoid unexpected failure. Therefore, in the context of structural optimization, including fatigue constraints is crucial, as the optimized design will meet the design criteria early in the design process...... design phase. The key challenge is to efficiently deal with the very large number of non-linear fatigue constraints and the very large time-history loads that are used in the design of offshore support structures. In this paper main emphasis will be on the analytical design sensitivity analysis used...

  7. Design and Additive Manufacturing of 3D Phononic Band Gap Structures Based on Gradient Based Optimization

    Directory of Open Access Journals (Sweden)

    Maximilian Wormser

    2017-09-01

    Full Text Available We present a novel approach for gradient based maximization of phononic band gaps. The approach is a geometry projection method combining parametric shape optimization with density based topology optimization. By this approach, we obtain, in a two dimension setting, cellular structures exhibiting relative and normalized band gaps of more than 8 and 1.6, respectively. The controlling parameter is the minimal strut size, which also corresponds with the obtained stiffness of the structure. The resulting design principle is manually interpreted into a three dimensional structure from which cellular metal samples are fabricated by selective electron beam melting. Frequency response diagrams experimentally verify the numerically determined phononic band gaps of the structures. The resulting structures have band gaps down to the audible frequency range, qualifying the structures for an application in noise isolation.

  8. Design and Additive Manufacturing of 3D Phononic Band Gap Structures Based on Gradient Based Optimization.

    Science.gov (United States)

    Wormser, Maximilian; Wein, Fabian; Stingl, Michael; Körner, Carolin

    2017-09-22

    We present a novel approach for gradient based maximization of phononic band gaps. The approach is a geometry projection method combining parametric shape optimization with density based topology optimization. By this approach, we obtain, in a two dimension setting, cellular structures exhibiting relative and normalized band gaps of more than 8 and 1.6, respectively. The controlling parameter is the minimal strut size, which also corresponds with the obtained stiffness of the structure. The resulting design principle is manually interpreted into a three dimensional structure from which cellular metal samples are fabricated by selective electron beam melting. Frequency response diagrams experimentally verify the numerically determined phononic band gaps of the structures. The resulting structures have band gaps down to the audible frequency range, qualifying the structures for an application in noise isolation.

  9. Structures of human cytosolic and mitochondrial nucleotidases: implications for structure-based design of selective inhibitors

    Czech Academy of Sciences Publication Activity Database

    Pachl, Petr; Fábry, Milan; Rosenberg, Ivan; Šimák, Ondřej; Řezáčová, Pavlína; Brynda, Jiří

    2014-01-01

    Roč. 70, February (2014), s. 461-470 ISSN 0907-4449 R&D Projects: GA ČR GA203/09/0820 Institutional support: RVO:68378050 ; RVO:61388963 Keywords : 5′(3′)-deoxyribonucleotidases * enzyme inhibition * hydrolases * structure-based drug design Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 7.232, year: 2013

  10. Significant role of the DNA backbone in mediating the transition origin of electronic excitations of B-DNA--implication from long range corrected TDDFT and quantified NTO analysis.

    Science.gov (United States)

    Li, Jian-Hao; Chai, Jeng-Da; Guo, Guang-Yu; Hayashi, Michitoshi

    2012-07-07

    We systematically investigate the possible complex transition origin of electronic excitations of giant molecular systems by using the recently proposed QNTO analysis [J.-H. Li, J.-D. Chai, G. Y. Guo and M. Hayashi, Chem. Phys. Lett., 2011, 514, 362.] combined with long-range corrected TDDFT calculations. Thymine (Thy) related excitations of a B-DNA biomolecule are then studied as examples, where the model systems have been constructed by extracting from the perfect or an X-ray crystal (PDB code 3BSE) B-DNA structure with at least one Thy included. In the first part, we consider the systems composed of a core molecular segment (e.g. Thy, or di-Thy) and a surrounding physical/chemical environment of interest (e.g. backbone, adjacent stacking nucleobases) in gas phase and examine how the excitation properties of the core vary in response to the environment. We find that the orbitals contributed by the DNA backbone and surrounding nucleobases often participate in a transition of Thy-related excitations affecting their composition, absorption energy, and oscillator strength. A vast number of strongly backbone-orbital involved excitations are also found at an absorption wavelength below ∼180 nm predicted by TD-ωB97X. In the second part, we take into account geometrically induced variation of the excitation properties of various B-DNA segments, e.g. di-Thy, dTpdT etc., obtained from different sources (ideal and 3BSE). It is found that the transition origin of several Thy-related excitations of these segments is sensitive to slight conformational variations, suggesting that DNA with thermal motions may from time to time exhibit very different photo-induced physical and/or chemical processes.

  11. Performance based analysis of hidden beams in reinforced concrete structures

    Directory of Open Access Journals (Sweden)

    Helou Samir H.

    2014-01-01

    Full Text Available Local and perhaps regional vernacular reinforced concrete building construction leans heavily against designing slabs with imbedded hidden beams for flooring systems in most structures including major edifices. The practice is distinctive in both framed and in shear wall structures. Hidden beams are favoured structural elements due to their many inherent features that characterize them; they save on floor height clearance; they also save on formwork, labour and material cost. Moreover, hidden beams form an acceptable aesthetic appearance that does not hinder efficient interior space partitioning. Such beams have the added advantage of clearing the way for horizontal electromechanical ductwork. However, seismic considerations, in all likelihood, are seldom seriously addressed. The mentioned structural system of shallow beams is adopted in ribbed slabs, waffle slabs and at times with solid slabs. Ribbed slabs and waffle slabs are more prone to hidden beam inclusion due to the added effective height of the concrete section. Due to the presence of a relatively high reinforcement ratio at the joints the sections at such location tend to become less ductile with unreliable contribution to spandrel force resistance. In the following study the structural influence of hidden beams within slabs is investigated. With the primary focus on a performance based analysis of such elements within a structure. This is investigated with due attention to shear wall contribution to the overall behaviour of such structures. Numerical results point in the direction that the function of hidden beams is not as adequate as desired. Therefore it is strongly believed that they are generally superfluous and maybe eliminated altogether. Conversely, shallow beams seem to render the overall seismic capacity of the structure unreliable. Since such an argument is rarely manifested within the linear analysis domain; a pushover analysis exercise is thus mandatory for behaviour

  12. Vibration-based monitoring of civil structures with subspace-based damage detection

    OpenAIRE

    Döhler , Michael; Hille , Falk; Mevel , Laurent

    2018-01-01

    International audience; Automatic vibration-based structural health monitoring has been recognized as a useful alternative or addition to visual inspections or local non-destructive testing performed manually. It is, in particular, suitable for mechanical and aeronautical structures as well as on civil structures, including cultural heritage sites. The main challenge is to provide a robust damage diagnosis from the recorded vibration measurements, for which statistical signal processing metho...

  13. High performance anodes with tailored catalytic properties for La5.6WO11.4-δ based proton conducting fuel cells

    DEFF Research Database (Denmark)

    Balaguer, M.; Solis, C.; Bozza, Francesco

    2013-01-01

    A new generation of anodes for PC-SOFCs based on catalytically promoted La0.75Ce0.1Sr0.15CrO3−δ (LSCCe) is presented. LSCCe is selected as the electrode backbone structure, due to its superior total conductivity over that of LSC. The infiltration of catalytically highly active nickel nanoparticle...

  14. Evidence of structural order recovery in LDPE based copolymers prepared by gamma irradiation

    Science.gov (United States)

    Ferreira, L. M.; Leal, J. P.; Casimiro, M. H.; Cruz, C.; Lancastre, J. J. H.; Falcão, A. N.

    2014-01-01

    PE-g-HEMA films prepared by the mutual gamma irradiation method were prepared to be used as catalyst support in catalytic membrane reactors (CMR). These copolymeric films showed good structural stability, even the high grafted ones, with a consistent correlation between their grafting degree and crystallinity. However, it was observed that above a certain radiation dose threshold, the structural changes induced in polyethylene (PE) backbone do not depend only on the extend of poly(HEMA) graft but also in what seems to be the reorganization of the amorphous regions in the PE matrix. The recovery of some crystallinity (up to 8%) in the copolymeric films was attested by DSC data. FTIR analysis confirmed this observation, revealing a slight increase in intensity and definition of the characteristic peak indicator of high crystalline regions in PE. This process seems to result from a radiation protective effect on copolymers matrix carried out by grafted poly(HEMA) which give to PE the ability to recover some of the lost structural order.

  15. Integrated Teaching of Structure-Based Drug Design and Biopharmaceutics: A Computer-Based Approach

    Science.gov (United States)

    Sutch, Brian T.; Romero, Rebecca M.; Neamati, Nouri; Haworth, Ian S.

    2012-01-01

    Rational drug design requires expertise in structural biology, medicinal chemistry, physiology, and related fields. In teaching structure-based drug design, it is important to develop an understanding of the need for early recognition of molecules with "drug-like" properties as a key component. That is, it is not merely sufficient to teach…

  16. Diode rectifier bridge-based structure for DFIG-based wind turbine

    DEFF Research Database (Denmark)

    Zhu, Rongwu; Chen, Zhe; Wu, Xiaojie

    2015-01-01

    This paper proposes a new structure for the doubly-fed induction generator (DFIG)-based wind turbine. The proposed structure consists of a DFIG controlled by a partial rated power converter in the rotor side, a three-phase diode rectifier bridge (DRB) connected to the stator, and a DC/AC full rated...

  17. High Triplet Energy Level Achieved by Tuning the Arrangement of Building Blocks in Phosphorescent Polymer Backbones for Furnishing High Electroluminescent Performances in Both Blue and White Organic Light-Emitting Devices.

    Science.gov (United States)

    Liu, Boao; Dang, Feifan; Tian, Zhuanzhuan; Feng, Zhao; Jin, Deyuan; Dang, Wanping; Yang, Xiaolong; Zhou, Guijiang; Wu, Zhaoxin

    2017-05-17

    A high triplet energy level (E T ) of ca. 2.83 eV has been achieved in a novel polymer backbone through tuning the arrangement of two kinds of building blocks, showing enhanced hole injection/transporting capacity. Based on this new polymer backbone with high E T , both blue and white phosphorescent polymers were successfully developed with a trade-off between high E T and enhanced charge-carrier transporting ability. In addition, their photophysical features, electrochemical behaviors, and electroluminescent (EL) properties have been characterized in detail. Benefitting from the advantages associated with the novel polymer backbone, the blue phosphorescent polymers show top-ranking EL performances with a maximum luminance efficiency (η L ) of 15.22 cd A -1 , corresponding to a power efficiency (η P ) of 12.64 lm W -1 , and external quantum efficiency (η ext ) of 6.22% and the stable Commission Internationale de L'Eclairage (CIE) coordinates of (0.19, 0.38). Furthermore, blue-orange (B-O) complementary-colored white phosphorescent polymers based on this novel polymer backbone were also obtained showing encouraging EL efficiencies of 12.34 cd A -1 , 9.59 lm W -1 , and 4.10% in the optimized WOLED together with exceptionally stable CIE coordinates of (Δx = 0.014, Δy = 0.010) in a wide driving voltage range from 4 to 16 V. All of these attractive EL results achieved by these novel phosphorescent polymers show the great potential of this new polymer backbone in developing highly efficient phosphorescent polymers.

  18. Management of Adolescent Low-Risk Classical Hodgkin Lymphoma: Which Chemotherapy Backbone Gives the Best Chance of Omitting Radiotherapy Safely.

    Science.gov (United States)

    Algiraigri, Ali H; Essa, Mohammed F

    2016-03-01

    Even though more than 90% of adolescents with low-risk classical Hodgkin lymphoma (LRcHL) will be cured with first-line therapy, many will suffer serious late toxic effects from radiotherapy (RT). The goals for care have shifted toward minimizing late toxic effects without compromising the outstanding cure rates by adapting a risk and response-based therapy. Recent published and ongoing randomized clinical trials, using functional imaging, may allow for better identification of those patients for whom RT may be safely omitted while maintaining excellent cure rates. To evaluate the best chemotherapy regimens with a reasonable toxicity profile and that are expected to have a high chance of omitting RT based on a response-directed therapy while maintaining high cure rates, a mini review was conducted of the recent clinical trials in pediatric and adult LRcHL. The UK RAPID trial chemotherapy backbone (3 × ABVD) followed by a response-based positron emission tomography scan offers up to a 75% chance of safely omitting RT without compromising the cure rate, which remained well above 90%.

  19. CING: an integrated residue-based structure validation program suite

    International Nuclear Information System (INIS)

    Doreleijers, Jurgen F.; Sousa da Silva, Alan W.; Krieger, Elmar; Nabuurs, Sander B.; Spronk, Christian A. E. M.; Stevens, Tim J.; Vranken, Wim F.; Vriend, Gert; Vuister, Geerten W.

    2012-01-01

    We present a suite of programs, named CING for Common Interface for NMR Structure Generation that provides for a residue-based, integrated validation of the structural NMR ensemble in conjunction with the experimental restraints and other input data. External validation programs and new internal validation routines compare the NMR-derived models with empirical data, measured chemical shifts, distance- and dihedral restraints and the results are visualized in a dynamic Web 2.0 report. A red–orange–green score is used for residues and restraints to direct the user to those critiques that warrant further investigation. Overall green scores below ∼20 % accompanied by red scores over ∼50 % are strongly indicative of poorly modelled structures. The publically accessible, secure iCing webserver (https://nmr.le.ac.ukhttps://nmr.le.ac.uk) allows individual users to upload the NMR data and run a CING validation analysis.

  20. Structural color-tunable mesoporous bragg stack layers based on graft copolymer self-assembly for high-efficiency solid-state dye-sensitized solar cells

    Science.gov (United States)

    Lee, Chang Soo; Park, Jung Tae; Kim, Jong Hak

    2016-08-01

    We present a facile fabrication route for structural color-tunable mesoporous Bragg stack (BS) layers based on the self-assembly of a cost-effective graft copolymer. The mesoporous BS layers are prepared through the alternating deposition of organized mesoporous-TiO2 (OM-TiO2) and -SiO2 (OM-SiO2) films on the non-conducting side of the counter electrode in dye-sensitized solar cells (DSSCs). The OM layers with controlled porosity, pore size, and refractive index are templated with amphiphilic graft copolymers consisting of poly(vinyl chloride) backbones and poly(oxyethylene methacrylate) side chains, i.e., PVC-g-POEM. The morphology and properties of the structural color-tunable mesoporous BS-functionalized electrodes are characterized using energy filtered transmission electron microscopy (EF-TEM), field emission-scanning electron microscopy (FE-SEM), spectroscopic ellipsometry, and reflectance spectroscopy. The solid-state DSSCs (ssDSSCs) based on a structural color-tunable mesoporous BS counter electrode with a single-component solid electrolyte show an energy conversion efficiency (η) of 7.1%, which is much greater than that of conventional nanocrystalline TiO2-based cells and one of the highest values for N719 dye-based ssDSSCs. The enhancement of η is due to the enhancement of current density (Jsc), attributed to the improved light harvesting properties without considerable decrease in fill factor (FF) or open-circuit voltage (Voc), as confirmed by incident photon-to-electron conversion efficiency (IPCE) and electrochemical impedance spectroscopy (EIS).

  1. Accuracy of structure-based sequence alignment of automatic methods

    Directory of Open Access Journals (Sweden)

    Lee Byungkook

    2007-09-01

    similarity is low, structure-based methods produce better sequence alignments than by using sequence similarities alone. However, current structure-based methods still mis-align 11–19% of the conserved core residues when compared to the human-curated CDD alignments. The alignment quality of each program depends on the protein structural type and similarity, with DaliLite showing the most agreement with CDD on average.

  2. Pore- and micro-structural characterization of a novel structural binder based on iron carbonation

    Energy Technology Data Exchange (ETDEWEB)

    Das, Sumanta, E-mail: Sumanta.Das@asu.edu [School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ (United States); Stone, David, E-mail: dajstone@gmail.com [Iron Shell LLC, Tucson, AZ (United States); Convey, Diana, E-mail: Diana.Convey@asu.edu [LeRoy Eyring Center for Solid State Science, Arizona State University, Tempe, AZ (United States); Neithalath, Narayanan, E-mail: Narayanan.Neithalath@asu.edu [School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ (United States)

    2014-12-15

    The pore- and micro-structural features of a novel binding material based on the carbonation of waste metallic iron powder are reported in this paper. The binder contains metallic iron powder as the major ingredient, followed by additives containing silica and alumina to facilitate favorable reaction product formation. Compressive strengths sufficient for a majority of concrete applications are attained. The material pore structure is investigated primarily through mercury intrusion porosimetry whereas electron microscopy is used for microstructural characterization. Reduction in the overall porosity and the average pore size with an increase in carbonation duration from 1 day to 4 days is noticed. The pore structure features are used in predictive models for gas and moisture transport (water vapor diffusivity and moisture permeability) through the porous medium which dictates its long-term durability when used in structural applications. Comparisons of the pore structure with those of a Portland cement paste are also provided. The morphology of the reaction products in the iron-based binder, and the distribution of constituent elements in the microstructure are also reported. - Highlights: • Carbonation of iron produces a dense microstructure. • Pore volume in iron carbonate lower, critical size higher than those in OPC pastes • Reaction product contains iron, carbon, silicon, aluminum and calcium. • Power-law for porosity-moisture permeability relationship was established.

  3. Experimental demonstration of dielectric structure based two beam acceleration

    International Nuclear Information System (INIS)

    Gai, W.; Conde, M. E.; Konecny, R.; Power, J. G.; Schoessow, P.; Sun, X.; Zou, P.

    2000-01-01

    We report on the experimental results of the dielectric based two beam accelerator (step-up transformer). By using a single high charge beam, we have generated and extracted a high power RF pulse from a 7.8 GHz primary dielectric structure and then subsequently transferred to a second accelerating structure with higher dielectric constant and smaller transverse dimensions. We have measured the energy change of a second (witness) beam passing through the acceleration stage. The measured gradient is >4 times the deceleration gradient. The detailed experiment of set-up and results of the measurements are dimmed. Future plans for the development of a 100 MeV demonstration accelerator based on this technique is presented

  4. Structural system identification based on variational mode decomposition

    Science.gov (United States)

    Bagheri, Abdollah; Ozbulut, Osman E.; Harris, Devin K.

    2018-03-01

    In this paper, a new structural identification method is proposed to identify the modal properties of engineering structures based on dynamic response decomposition using the variational mode decomposition (VMD). The VMD approach is a decomposition algorithm that has been developed as a means to overcome some of the drawbacks and limitations of the empirical mode decomposition method. The VMD-based modal identification algorithm decomposes the acceleration signal into a series of distinct modal responses and their respective center frequencies, such that when combined their cumulative modal responses reproduce the original acceleration response. The decaying amplitude of the extracted modal responses is then used to identify the modal damping ratios using a linear fitting function on modal response data. Finally, after extracting modal responses from available sensors, the mode shape vector for each of the decomposed modes in the system is identified from all obtained modal response data. To demonstrate the efficiency of the algorithm, a series of numerical, laboratory, and field case studies were evaluated. The laboratory case study utilized the vibration response of a three-story shear frame, whereas the field study leveraged the ambient vibration response of a pedestrian bridge to characterize the modal properties of the structure. The modal properties of the shear frame were computed using analytical approach for a comparison with the experimental modal frequencies. Results from these case studies demonstrated that the proposed method is efficient and accurate in identifying modal data of the structures.

  5. Structural design systems using knowledge-based techniques

    International Nuclear Information System (INIS)

    Orsborn, K.

    1993-01-01

    Engineering information management and the corresponding information systems are of a strategic importance for industrial enterprises. This thesis treats the interdisciplinary field of designing computing systems for structural design and analysis using knowledge-based techniques. Specific conceptual models have been designed for representing the structure and the process of objects and activities in a structural design and analysis domain. In this thesis, it is shown how domain knowledge can be structured along several classification principles in order to reduce complexity and increase flexibility. By increasing the conceptual level of the problem description and representation of the domain knowledge in a declarative form, it is possible to enhance the development, maintenance and use of software for mechanical engineering. This will result in a corresponding increase of the efficiency of the mechanical engineering design process. These ideas together with the rule-based control point out the leverage of declarative knowledge representation within this domain. Used appropriately, a declarative knowledge representation preserves information better, is more problem-oriented and change-tolerant than procedural representations. 74 refs

  6. SAGPAR: structural grammar-based automated pathway reconstruction.

    Science.gov (United States)

    Tagore, Somnath; De, Rajat K

    2012-06-01

    In-silico metabolic engineering is a very useful branch of systems biology for modeling, analysis and prediction of various outcomes of metabolic pathways. It can also be used for detecting interactions and dynamics within a network. Various protocols have been proposed for modeling a pathway. But most of these protocols have various disadvantages and shortcomings with respect to automated pathway modeling and analysis. In the present article, we have proposed a novel algorithm for automated pathway reconstruction. We have also made a comparative study of our algorithm with other standard protocols and discussed its advantages over others. We present StructurAl Grammar-based automated PAthway Reconstruction (SAGPAR), a fast and robust algorithm that generates any metabolic pathway using some given structural representations of metabolites. Users can model any pathway based on some pre-required features that are asked as an input by the algorithm. The algorithm also takes into considerations various thermodynamic thresholds and structural properties while modeling a pathway. The given algorithm has been tested on the standard pathway datasets of 25 pathways of Mycoplasma pneumoniae M129 and 24 pathways of Homo sapiens. The dataset is taken from KEGG and PubChem Compound data repositories. SAGPAR performs much better than some already present metabolic pathway analysis tools like Copasi, PHT, Gepasi, Jarnac and Path-A.

  7. Image-Based Structural Modeling of the Cardiac Purkinje Network

    Directory of Open Access Journals (Sweden)

    Benjamin R. Liu

    2015-01-01

    Full Text Available The Purkinje network is a specialized conduction system within the heart that ensures the proper activation of the ventricles to produce effective contraction. Its role during ventricular arrhythmias is less clear, but some experimental studies have suggested that the Purkinje network may significantly affect the genesis and maintenance of ventricular arrhythmias. Despite its importance, few structural models of the Purkinje network have been developed, primarily because current physical limitations prevent examination of the intact Purkinje network. In previous modeling efforts Purkinje-like structures have been developed through either automated or hand-drawn procedures, but these networks have been created according to general principles rather than based on real networks. To allow for greater realism in Purkinje structural models, we present a method for creating three-dimensional Purkinje networks based directly on imaging data. Our approach uses Purkinje network structures extracted from photographs of dissected ventricles and projects these flat networks onto realistic endocardial surfaces. Using this method, we create models for the combined ventricle-Purkinje system that can fully activate the ventricles through a stimulus delivered to the Purkinje network and can produce simulated activation sequences that match experimental observations. The combined models have the potential to help elucidate Purkinje network contributions during ventricular arrhythmias.

  8. A protein relational database and protein family knowledge bases to facilitate structure-based design analyses.

    Science.gov (United States)

    Mobilio, Dominick; Walker, Gary; Brooijmans, Natasja; Nilakantan, Ramaswamy; Denny, R Aldrin; Dejoannis, Jason; Feyfant, Eric; Kowticwar, Rupesh K; Mankala, Jyoti; Palli, Satish; Punyamantula, Sairam; Tatipally, Maneesh; John, Reji K; Humblet, Christine

    2010-08-01

    The Protein Data Bank is the most comprehensive source of experimental macromolecular structures. It can, however, be difficult at times to locate relevant structures with the Protein Data Bank search interface. This is particularly true when searching for complexes containing specific interactions between protein and ligand atoms. Moreover, searching within a family of proteins can be tedious. For example, one cannot search for some conserved residue as residue numbers vary across structures. We describe herein three databases, Protein Relational Database, Kinase Knowledge Base, and Matrix Metalloproteinase Knowledge Base, containing protein structures from the Protein Data Bank. In Protein Relational Database, atom-atom distances between protein and ligand have been precalculated allowing for millisecond retrieval based on atom identity and distance constraints. Ring centroids, centroid-centroid and centroid-atom distances and angles have also been included permitting queries for pi-stacking interactions and other structural motifs involving rings. Other geometric features can be searched through the inclusion of residue pair and triplet distances. In Kinase Knowledge Base and Matrix Metalloproteinase Knowledge Base, the catalytic domains have been aligned into common residue numbering schemes. Thus, by searching across Protein Relational Database and Kinase Knowledge Base, one can easily retrieve structures wherein, for example, a ligand of interest is making contact with the gatekeeper residue.

  9. ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using next generation sequence.

    Science.gov (United States)

    Blanca, Jose M; Pascual, Laura; Ziarsolo, Peio; Nuez, Fernando; Cañizares, Joaquin

    2011-06-02

    The possibilities offered by next generation sequencing (NGS) platforms are revolutionizing biotechnological laboratories. Moreover, the combination of NGS sequencing and affordable high-throughput genotyping technologies is facilitating the rapid discovery and use of SNPs in non-model species. However, this abundance of sequences and polymorphisms creates new software needs. To fulfill these needs, we have developed a powerful, yet easy-to-use application. The ngs_backbone software is a parallel pipeline capable of analyzing Sanger, 454, Illumina and SOLiD (Sequencing by Oligonucleotide Ligation and Detection) sequence reads. Its main supported analyses are: read cleaning, transcriptome assembly and annotation, read mapping and single nucleotide polymorphism (SNP) calling and selection. In order to build a truly useful tool, the software development was paired with a laboratory experiment. All public tomato Sanger EST reads plus 14.2 million Illumina reads were employed to test the tool and predict polymorphism in tomato. The cleaned reads were mapped to the SGN tomato transcriptome obtaining a coverage of 4.2 for Sanger and 8.5 for Illumina. 23,360 single nucleotide variations (SNVs) were predicted. A total of 76 SNVs were experimentally validated, and 85% were found to be real. ngs_backbone is a new software package capable of analyzing sequences produced by NGS technologies and predicting SNVs with great accuracy. In our tomato example, we created a highly polymorphic collection of SNVs that will be a useful resource for tomato researchers and breeders. The software developed along with its documentation is freely available under the AGPL license and can be downloaded from http://bioinf.comav.upv.es/ngs_backbone/ or http://github.com/JoseBlanca/franklin.

  10. ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence

    Directory of Open Access Journals (Sweden)

    Cañizares Joaquin

    2011-06-01

    Full Text Available Abstract Background The possibilities offered by next generation sequencing (NGS platforms are revolutionizing biotechnological laboratories. Moreover, the combination of NGS sequencing and affordable high-throughput genotyping technologies is facilitating the rapid discovery and use of SNPs in non-model species. However, this abundance of sequences and polymorphisms creates new software needs. To fulfill these needs, we have developed a powerful, yet easy-to-use application. Results The ngs_backbone software is a parallel pipeline capable of analyzing Sanger, 454, Illumina and SOLiD (Sequencing by Oligonucleotide Ligation and Detection sequence reads. Its main supported analyses are: read cleaning, transcriptome assembly and annotation, read mapping and single nucleotide polymorphism (SNP calling and selection. In order to build a truly useful tool, the software development was paired with a laboratory experiment. All public tomato Sanger EST reads plus 14.2 million Illumina reads were employed to test the tool and predict polymorphism in tomato. The cleaned reads were mapped to the SGN tomato transcriptome obtaining a coverage of 4.2 for Sanger and 8.5 for Illumina. 23,360 single nucleotide variations (SNVs were predicted. A total of 76 SNVs were experimentally validated, and 85% were found to be real. Conclusions ngs_backbone is a new software package capable of analyzing sequences produced by NGS technologies and predicting SNVs with great accuracy. In our tomato example, we created a highly polymorphic collection of SNVs that will be a useful resource for tomato researchers and breeders. The software developed along with its documentation is freely available under the AGPL license and can be downloaded from http://bioinf.comav.upv.es/ngs_backbone/ or http://github.com/JoseBlanca/franklin.

  11. From crystal to compound: structure-based antimalarial drug discovery.

    Science.gov (United States)

    Drinkwater, Nyssa; McGowan, Sheena

    2014-08-01

    Despite a century of control and eradication campaigns, malaria remains one of the world's most devastating diseases. Our once-powerful therapeutic weapons are losing the war against the Plasmodium parasite, whose ability to rapidly develop and spread drug resistance hamper past and present malaria-control efforts. Finding new and effective treatments for malaria is now a top global health priority, fuelling an increase in funding and promoting open-source collaborations between researchers and pharmaceutical consortia around the world. The result of this is rapid advances in drug discovery approaches and technologies, with three major methods for antimalarial drug development emerging: (i) chemistry-based, (ii) target-based, and (iii) cell-based. Common to all three of these approaches is the unique ability of structural biology to inform and accelerate drug development. Where possible, SBDD (structure-based drug discovery) is a foundation for antimalarial drug development programmes, and has been invaluable to the development of a number of current pre-clinical and clinical candidates. However, as we expand our understanding of the malarial life cycle and mechanisms of resistance development, SBDD as a field must continue to evolve in order to develop compounds that adhere to the ideal characteristics for novel antimalarial therapeutics and to avoid high attrition rates pre- and post-clinic. In the present review, we aim to examine the contribution that SBDD has made to current antimalarial drug development efforts, covering hit discovery to lead optimization and prevention of parasite resistance. Finally, the potential for structural biology, particularly high-throughput structural genomics programmes, to identify future targets for drug discovery are discussed.

  12. Automated Glioblastoma Segmentation Based on a Multiparametric Structured Unsupervised Classification

    Science.gov (United States)

    Juan-Albarracín, Javier; Fuster-Garcia, Elies; Manjón, José V.; Robles, Montserrat; Aparici, F.; Martí-Bonmatí, L.; García-Gómez, Juan M.

    2015-01-01

    Automatic brain tumour segmentation has become a key component for the future of brain tumour treatment. Currently, most of brain tumour segmentation approaches arise from the supervised learning standpoint, which requires a labelled training dataset from which to infer the models of the classes. The performance of these models is directly determined by the size and quality of the training corpus, whose retrieval becomes a tedious and time-consuming task. On the other hand, unsupervised approaches avoid these limitations but often do not reach comparable results than the supervised methods. In this sense, we propose an automated unsupervised method for brain tumour segmentation based on anatomical Magnetic Resonance (MR) images. Four unsupervised classification algorithms, grouped by their structured or non-structured condition, were evaluated within our pipeline. Considering the non-structured algorithms, we evaluated K-means, Fuzzy K-means and Gaussian Mixture Model (GMM), whereas as structured classification algorithms we evaluated Gaussian Hidden Markov Random Field (GHMRF). An automated postprocess based on a statistical approach supported by tissue probability maps is proposed to automatically identify the tumour classes after the segmentations. We evaluated our brain tumour segmentation method with the public BRAin Tumor Segmentation (BRATS) 2013 Test and Leaderboard datasets. Our approach based on the GMM model improves the results obtained by most of the supervised methods evaluated with the Leaderboard set and reaches the second position in the ranking. Our variant based on the GHMRF achieves the first position in the Test ranking of the unsupervised approaches and the seventh position in the general Test ranking, which confirms the method as a viable alternative for brain tumour segmentation. PMID:25978453

  13. Quality-based Multimodal Classification Using Tree-Structured Sparsity

    Science.gov (United States)

    2014-03-08

    ASI Series F, Computer and Systems Sciences, 163:446–456, 1999. 5 [7] D. Hall and J. Llinas. An introduction to multisensor data fusion . Proceedings of...advantages of in- formation fusion based on sparsity models for multi- modal classification. Among several sparsity models, tree- structured sparsity provides...rithm is proposed to solve the optimization problem, which is an efficient tool for feature-level fusion among either ho- mogeneous or heterogeneous

  14. Simulations for irradiation of silicon-based structures

    International Nuclear Information System (INIS)

    Sagatova, A.; Pavlovic, M.; Sedlackova, K.; Necas, V.; Hybler, P.; Zatko, B.

    2013-01-01

    The software ModePEB for modelling of electron beam processing in multilayer flat objects was shown to be a very useful tool for optimization of the irradiation of silicon based structures. Except its significant help in setting-up the accelerator parameters corresponding to a desired dose, its proven reliability and consistency with the measured data makes the ModePEB an inevitable instrument for design and optimization of electron irradiation experiments. (authors)

  15. Automated glioblastoma segmentation based on a multiparametric structured unsupervised classification.

    Science.gov (United States)

    Juan-Albarracín, Javier; Fuster-Garcia, Elies; Manjón, José V; Robles, Montserrat; Aparici, F; Martí-Bonmatí, L; García-Gómez, Juan M

    2015-01-01

    Automatic brain tumour segmentation has become a key component for the future of brain tumour treatment. Currently, most of brain tumour segmentation approaches arise from the supervised learning standpoint, which requires a labelled training dataset from which to infer the models of the classes. The performance of these models is directly determined by the size and quality of the training corpus, whose retrieval becomes a tedious and time-consuming task. On the other hand, unsupervised approaches avoid these limitations but often do not reach comparable results than the supervised methods. In this sense, we propose an automated unsupervised method for brain tumour segmentation based on anatomical Magnetic Resonance (MR) images. Four unsupervised classification algorithms, grouped by their structured or non-structured condition, were evaluated within our pipeline. Considering the non-structured algorithms, we evaluated K-means, Fuzzy K-means and Gaussian Mixture Model (GMM), whereas as structured classification algorithms we evaluated Gaussian Hidden Markov Random Field (GHMRF). An automated postprocess based on a statistical approach supported by tissue probability maps is proposed to automatically identify the tumour classes after the segmentations. We evaluated our brain tumour segmentation method with the public BRAin Tumor Segmentation (BRATS) 2013 Test and Leaderboard datasets. Our approach based on the GMM model improves the results obtained by most of the supervised methods evaluated with the Leaderboard set and reaches the second position in the ranking. Our variant based on the GHMRF achieves the first position in the Test ranking of the unsupervised approaches and the seventh position in the general Test ranking, which confirms the method as a viable alternative for brain tumour segmentation.

  16. A new entropy based method for computing software structural complexity

    International Nuclear Information System (INIS)

    Roca, Jose L.

    2002-01-01

    In this paper a new methodology for the evaluation of software structural complexity is described. It is based on the entropy evaluation of the random uniform response function associated with the so called software characteristic function SCF. The behavior of the SCF with the different software structures and their relationship with the number of inherent errors is investigated. It is also investigated how the entropy concept can be used to evaluate the complexity of a software structure considering the SCF as a canonical representation of the graph associated with the control flow diagram. The functions, parameters and algorithms that allow to carry out this evaluation are also introduced. After this analytic phase follows the experimental phase, verifying the consistency of the proposed metric and their boundary conditions. The conclusion is that the degree of software structural complexity can be measured as the entropy of the random uniform response function of the SCF. That entropy is in direct relationship with the number of inherent software errors and it implies a basic hazard failure rate for it, so that a minimum structure assures a certain stability and maturity of the program. This metric can be used, either to evaluate the product or the process of software development, as development tool or for monitoring the stability and the quality of the final product. (author)

  17. Module-based structure design of wheeled mobile robot

    Directory of Open Access Journals (Sweden)

    Z. Luo

    2018-02-01

    Full Text Available This paper proposes an innovative and systematic approach for synthesizing mechanical structures of wheeled mobile robots. The principle and terminologies used for the proposed synthesis method are presented by adopting the concept of modular design, isomorphic and non-isomorphic, and set theory with its associated combinatorial mathematics. The modular-based innovative synthesis and design of wheeled robots were conducted at two levels. Firstly at the module level, by creative design and analysing the structures of classic wheeled robots, a wheel module set containing four types of wheel mechanisms, a suspension module set consisting of five types of suspension frames and a chassis module set composed of five types of rigid or articulated chassis were designed and generalized. Secondly at the synthesis level, two kinds of structure synthesis modes, namely the isomorphic-combination mode and the non-isomorphic combination mode were proposed to synthesize mechanical structures of wheeled robots; which led to 241 structures for wheeled mobile robots including 236 novel ones. Further, mathematical models and a software platform were developed to provide appropriate and intuitive tools for simulating and evaluating performance of the wheeled robots that were proposed in this paper. Eventually, physical prototypes of sample wheeled robots/rovers were developed and tested so as to prove and validate the principle and methodology presented in this paper.

  18. Structural reliability analysis based on the cokriging technique

    International Nuclear Information System (INIS)

    Zhao Wei; Wang Wei; Dai Hongzhe; Xue Guofeng

    2010-01-01

    Approximation methods are widely used in structural reliability analysis because they are simple to create and provide explicit functional relationships between the responses and variables in stead of the implicit limit state function. Recently, the kriging method which is a semi-parameter interpolation technique that can be used for deterministic optimization and structural reliability has gained popularity. However, to fully exploit the kriging method, especially in high-dimensional problems, a large number of sample points should be generated to fill the design space and this can be very expensive and even impractical in practical engineering analysis. Therefore, in this paper, a new method-the cokriging method, which is an extension of kriging, is proposed to calculate the structural reliability. cokriging approximation incorporates secondary information such as the values of the gradients of the function being approximated. This paper explores the use of the cokriging method for structural reliability problems by comparing it with the Kriging method based on some numerical examples. The results indicate that the cokriging procedure described in this work can generate approximation models to improve on the accuracy and efficiency for structural reliability problems and is a viable alternative to the kriging.

  19. ¹H, ¹³C, and ¹⁵N backbone and side chain resonance assignments of the C-terminal DNA binding and dimerization domain of v-Myc.

    Science.gov (United States)

    Kızılsavaş, Gönül; Saxena, Saurabh; Żerko, Szymon; Koźmiński, Wiktor; Bister, Klaus; Konrat, Robert

    2013-10-01

    The oncogenic transcription factor Myc is one of the most interesting members of the basic-helix-loop-helix-zipper (bHLHZip) protein family. Deregulation of Myc via gene amplification, chromosomal translocation or other mechanisms lead to tumorigenesis including Burkitt lymphoma, multiple myeloma, and many other malignancies. The oncogene myc is a highly potent transforming gene and capable to transform various cell types in vivo and in vitro. Its oncogenic activity initialized by deregulated expression leads to a shift of the equilibrium in the Myc/Max/Mad network towards Myc/Max complexes. The Myc/Max heterodimerization is a prerequisite for transcriptional functionality of Myc. Primarily, we are focusing on the apo-state of the C-terminal domain of v-Myc, the retroviral homolog of human c-Myc. Based on multi-dimensional NMR measurements v-Myc appears to be neither a fully structured nor a completely unstructured protein. The bHLHZip domain of v-Myc does not exist as a random coil but exhibits partially pre-formed α-helical regions in its apo-state. In order to elucidate the structural propensities of Myc in more detail, the backbone and side-chain assignments obtained here for apo-Myc are a crucial prerequisite for further NMR measurements.

  20. SEVA Linkers: A Versatile and Automatable DNA Backbone Exchange Standard for Synthetic Biology

    DEFF Research Database (Denmark)

    Kim, Se Hyeuk; Cavaleiro, Mafalda; Rennig, Maja

    2016-01-01

    DNA vectors serve to maintain and select recombinant DNA in cell factories, and as design complexity increases, there is a greater need for well-characterized parts and methods for their assembly. Standards in synthetic biology are top priority, but standardizing molecular cloning contrasts...... flexibility, and different researchers prefer and master different molecular technologies. Here, we describe a new, highly versatile and automatable standard “SEVA linkers” for vector exchange. SEVA linkers enable backbone swapping with 20 combinations of classical enzymatic restriction/ligation, Gibson...

  1. Backbone-Fluorinated 1,2,3-Triazole-Containing Dipeptide Surrogates

    DEFF Research Database (Denmark)

    Engel-Andreasen, Jens; Wellhöfer, Isabelle; Wich, Kathrine

    2017-01-01

    The 1,2,3-triazole moiety can be incorporated as a peptide bond bioisostere to provide protease resistance in peptidomimetics. Herein, we report the synthesis of peptidomimetic building blocks containing backbone-fluorinated 1,4-disubstituted 1,2,3-triazole moieties. Synthetic protocols...... for the preparation of various Xaa-Gly dipeptide surrogates in the form of Xaa-ψ[triazole]-F2Gly building blocks were established, and selected examples were introduced into the endogenous peptide opioid receptor ligand Leu-enkephalin as a model compound....

  2. Microscopic neural image registration based on the structure of mitochondria

    Science.gov (United States)

    Cao, Huiwen; Han, Hua; Rao, Qiang; Xiao, Chi; Chen, Xi

    2017-02-01

    Microscopic image registration is a key component of the neural structure reconstruction with serial sections of neural tissue. The goal of microscopic neural image registration is to recover the 3D continuity and geometrical properties of specimen. During image registration, various distortions need to be corrected, including image rotation, translation, tissue deformation et.al, which come from the procedure of sample cutting, staining and imaging. Furthermore, there is only certain similarity between adjacent sections, and the degree of similarity depends on local structure of the tissue and the thickness of the sections. These factors make the microscopic neural image registration a challenging problem. To tackle the difficulty of corresponding landmarks extraction, we introduce a novel image registration method for Scanning Electron Microscopy (SEM) images of serial neural tissue sections based on the structure of mitochondria. The ellipsoidal shape of mitochondria ensures that the same mitochondria has similar shape between adjacent sections, and its characteristic of broad distribution in the neural tissue guarantees that landmarks based on the mitochondria distributed widely in the image. The proposed image registration method contains three parts: landmarks extraction between adjacent sections, corresponding landmarks matching and image deformation based on the correspondences. We demonstrate the performance of our method with SEM images of drosophila brain.

  3. Pressure dependence of backbone chemical shifts in the model peptides Ac-Gly-Gly-Xxx-Ala-NH2.

    Science.gov (United States)

    Erlach, Markus Beck; Koehler, Joerg; Crusca, Edson; Kremer, Werner; Munte, Claudia E; Kalbitzer, Hans Robert

    2016-06-01

    For a better understanding of nuclear magnetic resonance (NMR) detected pressure responses of folded as well as unstructured proteins the availability of data from well-defined model systems are indispensable. In this work we report the pressure dependence of chemical shifts of the backbone atoms (1)H(α), (13)C(α) and (13)C' in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of these nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The polynomial pressure coefficients B 1 and B 2 are dependent on the type of amino acid studied. The coefficients of a given nucleus show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure are also weakly correlated.

  4. Revised Backbone-Virtual-Bond-Angle Potentials to Treat the l- and d-Amino Acid Residues in the Coarse-Grained United Residue (UNRES) Force Field.

    Science.gov (United States)

    Sieradzan, Adam K; Niadzvedtski, Andrei; Scheraga, Harold A; Liwo, Adam

    2014-05-13

    Continuing our effort to introduce d-amino-acid residues in the united residue (UNRES) force field developed in our laboratory, in this work the C α ··· C α ··· C α backbone-virtual-bond-valence-angle (θ) potentials for systems containing d-amino-acid residues have been developed. The potentials were determined by integrating the combined energy surfaces of all possible triplets of terminally blocked glycine, alanine, and proline obtained with ab initio molecular quantum mechanics at the MP2/6-31G(d,p) level to calculate the corresponding potentials of mean force (PMFs). Subsequently, analytical expressions were fitted to the PMFs to give the virtual-bond-valence potentials to be used in UNRES. Alanine represented all types of amino-acid residues except glycine and proline. The blocking groups were either the N -acetyl and N ', N '-dimethyl or N -acetyl and pyrrolidyl group, depending on whether the residue next in sequence was an alanine-type or a proline residue. A total of 126 potentials (63 symmetry-unrelated potentials for each set of terminally blocking groups) were determined. Together with the torsional, double-torsional, and side-chain-rotamer potentials for polypeptide chains containing d-amino-acid residues determined in our earlier work (Sieradzan et al. J. Chem. Theory Comput. , 2012 , 8, 4746), the new virtual-bond-angle (θ) potentials now constitute the complete set of physics-based potentials with which to run coarse-grained simulations of systems containing d-amino-acid residues. The ability of the extended UNRES force field to reproduce thermodynamics of polypeptide systems with d-amino-acid residues was tested by comparing the experimentally measured and the calculated free energies of helix formation of model KLALKLALxxLKLALKLA peptides, where x denotes any d- or l- amino-acid residue. The obtained results demonstrate that the UNRES force field with the new potentials reproduce the changes of free energies of helix formation upon d

  5. Frequency Response Function Based Damage Identification for Aerospace Structures

    Science.gov (United States)

    Oliver, Joseph Acton

    Structural health monitoring technologies continue to be pursued for aerospace structures in the interests of increased safety and, when combined with health prognosis, efficiency in life-cycle management. The current dissertation develops and validates damage identification technology as a critical component for structural health monitoring of aerospace structures and, in particular, composite unmanned aerial vehicles. The primary innovation is a statistical least-squares damage identification algorithm based in concepts of parameter estimation and model update. The algorithm uses frequency response function based residual force vectors derived from distributed vibration measurements to update a structural finite element model through statistically weighted least-squares minimization producing location and quantification of the damage, estimation uncertainty, and an updated model. Advantages compared to other approaches include robust applicability to systems which are heavily damped, large, and noisy, with a relatively low number of distributed measurement points compared to the number of analytical degrees-of-freedom of an associated analytical structural model (e.g., modal finite element model). Motivation, research objectives, and a dissertation summary are discussed in Chapter 1 followed by a literature review in Chapter 2. Chapter 3 gives background theory and the damage identification algorithm derivation followed by a study of fundamental algorithm behavior on a two degree-of-freedom mass-spring system with generalized damping. Chapter 4 investigates the impact of noise then successfully proves the algorithm against competing methods using an analytical eight degree-of-freedom mass-spring system with non-proportional structural damping. Chapter 5 extends use of the algorithm to finite element models, including solutions for numerical issues, approaches for modeling damping approximately in reduced coordinates, and analytical validation using a composite

  6. A Review of the Piezoelectric Electromechanical Impedance Based Structural Health Monitoring Technique for Engineering Structures

    Directory of Open Access Journals (Sweden)

    Wongi S. Na

    2018-04-01

    Full Text Available The birth of smart materials such as piezoelectric (PZT transducers has aided in revolutionizing the field of structural health monitoring (SHM based on non-destructive testing (NDT methods. While a relatively new NDT method known as the electromechanical (EMI technique has been investigated for more than two decades, there are still various problems that must be solved before it is applied to real structures. The technique, which has a significant potential to contribute to the creation of one of the most effective SHM systems, involves the use of a single PZT for exciting and sensing of the host structure. In this paper, studies applied for the past decade related to the EMI technique have been reviewed to understand its trend. In addition, new concepts and ideas proposed by various authors are also surveyed, and the paper concludes with a discussion of the potential directions for future works.

  7. Simulation of chloride transport based description soil structure

    International Nuclear Information System (INIS)

    Mahmood-ul-Hassan, M.; Akhtar, M.S.; Gill, S.M.; Nabi, G.

    2003-01-01

    There is a need of environmental implications of rapid appearance of surface by applying chemical at depths below the vadose zone (tile line or shallow groundwater) for developing better insight into solute flow mechanism through the arable lands. Transport of chloride, a representative non-adsorbing solute, through a moderately structured silty clay loam soil (Gujranwala series, Typic Ustochrepts) and an un-structured sandy loam soil (Nabipur series, Typic Camborthid) was characterized and two existing models viz. convection dispersion equation (CDE) and preferential flow models were tested. The flux average of solute concentration in the outflow as a function of cumulative drainage was fitted to the models. The CDE fitted, relatively, better in the non-structured soil than in the moderately structured soil. Dispersivity value determined by CDE was very high for the structured soil which is physically not possible. The preferential flow model fitted well in the Gujranwala soil, but not in the Nabipur soil. The breakthrough characteristics i.e. drainage to peak concentration (Dp), symmetry coefficient (SC), skewness, and kurtosis were compared. Chloride breakthrough was earlier than expected based on piston flow. It indicated preferential flow in both the soils, yet, immediate appearance of the tracer in the Gujranwala soil demonstrated even larger magnitude of the preferential flow. Breakthrough curves' parameters indicated a large amount of the solute movement through the preferred pathways by passing the soil matrix in the Gujranwala soil. The study suggests that some soil structure parameters (size/shape and degree of aggregation) should be incorporated in the solute transport models.(author)

  8. Dissimilarity-based classification of anatomical tree structures

    DEFF Research Database (Denmark)

    Sørensen, Lauge; Lo, Pechin Chien Pau; Dirksen, Asger

    2011-01-01

    A novel method for classification of abnormality in anatomical tree structures is presented. A tree is classified based on direct comparisons with other trees in a dissimilarity-based classification scheme. The pair-wise dissimilarity measure between two trees is based on a linear assignment...... between the branch feature vectors representing those trees. Hereby, localized information in the branches is collectively used in classification and variations in feature values across the tree are taken into account. An approximate anatomical correspondence between matched branches can be achieved...... by including anatomical features in the branch feature vectors. The proposed approach is applied to classify airway trees in computed tomography images of subjects with and without chronic obstructive pulmonary disease (COPD). Using the wall area percentage (WA%), a common measure of airway abnormality in COPD...

  9. Magnetic properties of FeV/MgO-based structures

    Science.gov (United States)

    Bersweiler, Mathias; Watanabe, Kyota; Sato, Hideo; Matsukura, Fumihiro; Ohno, Hideo

    2017-08-01

    We investigate the magnetic properties of Fe100- x V x /MgO-based structures with a V composition x up to 20 at. %. The introduction of V results in the reduction of spontaneous magnetization, the damping constant, and both interfacial and bulk perpendicular magnetic anisotropies. However, the insertion of thin Fe layers at the FeV/MgO interfaces results in an effective perpendicular magnetic anisotropy as large as that of Fe/MgO. The result shows potential for lowering the threshold current for magnetization switching in FeV/MgO-based magnetic tunnel junctions, while maintaining a thermal stability factor similar to that in Fe/MgO-based junctions.

  10. Pillar-structured neutron detector based multiplicity system

    Science.gov (United States)

    Murphy, John W.; Shao, Qinghui; Voss, Lars F.; Kerr, Phil L.; Fabris, Lorenzo; Conway, Adam M.; Nikolic, Rebecca J.

    2018-01-01

    This work demonstrates the potential of silicon pillars filled with boron-10 as a sensor technology for a compact and portable neutron multiplicity system. Solid-state, semiconductor based neutron detectors may enable completely new detector form factors, offer an alternate approach to helium-3 based systems, and reduce detector weight and volume requirements. Thirty-two pillar-structured neutron detectors were assembled into a system with an active area of over 20 cm2 and were used in this work to demonstrate the feasibility of this sensor technology as a potential replacement for helium-3 based gas detectors. Multiplicity measurements were successfully carried out using a californium-252 neutron source, in which the source mass, system efficiency, and die-away time were determined. This demonstration shows that these solid-state detectors could allow for a more compact and portable system that could be used for special nuclear material identification in the field.

  11. Structural analysis of paintings based on brush strokes

    Science.gov (United States)

    Sablatnig, Robert; Kammerer, Paul; Zolda, Ernestine

    1998-05-01

    The origin of works of art can often not be attributed to a certain artist. Likewise it is difficult to say whether paintings or drawings are originals or forgeries. In various fields of art new technical methods are used to examine the age, the state of preservation and the origin of the materials used. For the examination of paintings, radiological methods like X-ray and infra-red diagnosis, digital radiography, computer-tomography, etc. and color analyzes are employed to authenticate art. But all these methods do not relate certain characteristics in art work to a specific artist -- the artist's personal style. In order to study this personal style of a painter, experts in art history and image processing try to examine the 'structural signature' based on brush strokes within paintings, in particular in portrait miniatures. A computer-aided classification and recognition system for portrait miniatures is developed, which enables a semi- automatic classification and forgery detection based on content, color, and brush strokes. A hierarchically structured classification scheme is introduced which separates the classification into three different levels of information: color, shape of region, and structure of brush strokes.

  12. MEMS-Based Fuel Reformer with Suspended Membrane Structure

    Science.gov (United States)

    Chang, Kuei-Sung; Tanaka, Shuji; Esashi, Masayoshi

    We report a MEMS-based fuel reformer for supplying hydrogen to micro-fuel cells for portable applications. A combustor and a reforming chamber are fabricated at either side of a suspended membrane structure. This design is used to improve the overall thermal efficiency, which is a critical issue to realize a micro-fuel reformer. The suspended membrane structure design provided good thermal isolation. The micro-heaters consumed 0.97W to maintain the reaction zone of the MEMS-based fuel reformer at 200°C, but further power saving is necessary by improving design and fabrication. The conversion rate of methanol to hydrogen was about 19% at 180°C by using evaporated copper as a reforming catalyst. The catalytic combustion of hydrogen started without any assistance of micro-heaters. By feeding the fuel mixture of an equivalence ratio of 0.35, the temperature of the suspended membrane structure was maintained stable at 100°C with a combustion efficiency of 30%. In future works, we will test a micro-fuel reformer by using a micro-combustor to supply heat.

  13. DNA nanotechnology based on i-motif structures.

    Science.gov (United States)

    Dong, Yuanchen; Yang, Zhongqiang; Liu, Dongsheng

    2014-06-17

    CONSPECTUS: Most biological processes happen at the nanometer scale, and understanding the energy transformations and material transportation mechanisms within living organisms has proved challenging. To better understand the secrets of life, researchers have investigated artificial molecular motors and devices over the past decade because such systems can mimic certain biological processes. DNA nanotechnology based on i-motif structures is one system that has played an important role in these investigations. In this Account, we summarize recent advances in functional DNA nanotechnology based on i-motif structures. The i-motif is a DNA quadruplex that occurs as four stretches of cytosine repeat sequences form C·CH(+) base pairs, and their stabilization requires slightly acidic conditions. This unique property has produced the first DNA molecular motor driven by pH changes. The motor is reliable, and studies show that it is capable of millisecond running speeds, comparable to the speed of natural protein motors. With careful design, the output of these types of motors was combined to drive micrometer-sized cantilevers bend. Using established DNA nanostructure assembly and functionalization methods, researchers can easily integrate the motor within other DNA assembled structures and functional units, producing DNA molecular devices with new functions such as suprahydrophobic/suprahydrophilic smart surfaces that switch, intelligent nanopores triggered by pH changes, molecular logic gates, and DNA nanosprings. Recently, researchers have produced motors driven by light and electricity, which have allowed DNA motors to be integrated within silicon-based nanodevices. Moreover, some devices based on i-motif structures have proven useful for investigating processes within living cells. The pH-responsiveness of the i-motif structure also provides a way to control the stepwise assembly of DNA nanostructures. In addition, because of the stability of the i-motif, this

  14. Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings

    International Nuclear Information System (INIS)

    Montalvao, Rinaldo W.; De Simone, Alfonso; Vendruscolo, Michele

    2012-01-01

    Residual dipolar couplings (RDCs) have the potential of providing detailed information about the conformational fluctuations of proteins. It is very challenging, however, to extract such information because of the complex relationship between RDCs and protein structures. A promising approach to decode this relationship involves structure-based calculations of the alignment tensors of protein conformations. By implementing this strategy to generate structural restraints in molecular dynamics simulations we show that it is possible to extract effectively the information provided by RDCs about the conformational fluctuations in the native states of proteins. The approach that we present can be used in a wide range of alignment media, including Pf1, charged bicelles and gels. The accuracy of the method is demonstrated by the analysis of the Q factors for RDCs not used as restraints in the calculations, which are significantly lower than those corresponding to existing high-resolution structures and structural ensembles, hence showing that we capture effectively the contributions to RDCs from conformational fluctuations.

  15. Improving VANETs Connectivity with a Totally Ad Hoc Living Mobile Backbone

    Directory of Open Access Journals (Sweden)

    Joilson Alves Junior

    2015-01-01

    Full Text Available The vehicular ad hoc network (VANET for intelligent transportation systems is an emerging concept to improve transportation security, reliability, and management. The network behavior can be totally different in topological aspects because of the mobility of vehicular nodes. The topology can be fully connected when the flow of vehicles is high and may have low connectivity or be invalid when the flow of vehicles is low or unbalanced. In big cities, the metropolitan buses that travel on exclusive lanes may be used to set up a metropolitan vehicular data network (backbone, raising the connectivity among the vehicles. Therefore, this paper proposes the implementation of a living mobile backbone, totally ad hoc (MOB-NET, which will provide infrastructure and raise the network connectivity. In order to show the viability of MOB-NET, statistical analyses were made with real data of express buses that travel through exclusive lanes, besides evaluations through simulations and analytic models. The statistic, analytic, and simulation results prove that the buses that travel through exclusive lanes can be used to build a communication network totally ad hoc and provide connectivity in more than 99% of the time, besides raising the delivery rate up to 95%.

  16. On contribution of known atomic partial charges of protein backbone in electrostatic potential density maps.

    Science.gov (United States)

    Wang, Jimin

    2017-06-01

    Partial charges of atoms in a molecule and electrostatic potential (ESP) density for that molecule are known to bear a strong correlation. In order to generate a set of point-field force field parameters for molecular dynamics, Kollman and coworkers have extracted atomic partial charges for each of all 20 amino acids using restrained partial charge-fitting procedures from theoretical ESP density obtained from condensed-state quantum mechanics. The magnitude of atomic partial charges for neutral peptide backbone they have obtained is similar to that of partial atomic charges for ionized carboxylate side chain atoms. In this study, the effect of these known atomic partial charges on ESP is examined using computer simulations and compared with the experimental ESP density recently obtained for proteins using electron microscopy. It is found that the observed ESP density maps are most consistent with the simulations that include atomic partial charges of protein backbone. Therefore, atomic partial charges are integral part of atomic properties in protein molecules and should be included in model refinement. © 2017 The Protein Society.

  17. Influence of Backbone Fluorination in Regioregular Poly(3-alkyl-4-fluoro)thiophenes

    KAUST Repository

    Fei, Zhuping

    2015-06-03

    © 2015 American Chemical Society. We report two strategies toward the synthesis of 3-alkyl-4-fluorothiophenes containing straight (hexyl and octyl) and branched (2-ethylhexyl) alkyl groups. We demonstrate that treatment of the dibrominated monomer with 1 equiv of alkyl Grignard reagent leads to the formation of a single regioisomer as a result of the pronounced directing effect of the fluorine group. Polymerization of the resulting species affords highly regioregular poly(3-alkyl-4-fluoro)thiophenes. Comparison of their properties to those of the analogous non-fluorinated polymers shows that backbone fluorination leads to an increase in the polymer ionization potential without a significant change in optical band gap. Fluorination also results in an enhanced tendency to aggregate in solution, which is ascribed to a more co-planar backbone on the basis of Raman and DFT calculations. Average charge carrier mobilities in field-effect transistors are found to increase by up to a factor of 5 for the fluorinated polymers.

  18. A Novel SMA-based Concept for Airfoil Structural Morphing

    Science.gov (United States)

    Barbarino, S.; Pecora, R.; Lecce, L.; Concilio, A.; Ameduri, S.; Calvi, E.

    2009-08-01

    The adaptive structures concept is of great interest in the aerospace field because of the several benefits which can be accomplished in the fields including noise reduction, load alleviation, weight reduction, etc., at a level in which they can be considered as compulsory in the design of future aircraft. Improvements in terms of the aerodynamic efficiency, aeroelastic behavior, stability, and manoeuvrability performance have already been proved through many international studies in the past. In the family of the Smart Materials, Shape Memory Alloys (SMA) seem to be a suitable solution for many static applications. Their high structural integrability in conjunction with actuation capabilities and a favorable performance per weight ratio, allows the development of original architectures. In this study, a morphing wing trailing edge concept is presented; morphing ability was introduced with the aim of replacing a conventional flap device. A compliant rib structure was designed, based on SMA actuators exhibiting structural potential (bearing external aerodynamic loads). Numerical results, achieved through a FE approach, are presented in terms of trailing edge induced displacement and morphed shape.

  19. Coordinate-based versus structural approaches to brain image analysis.

    Science.gov (United States)

    Mangin, J-F; Rivière, D; Coulon, O; Poupon, C; Cachia, A; Cointepas, Y; Poline, J-B; Le Bihan, D; Régis, J; Papadopoulos-Orfanos, D

    2004-02-01

    A basic issue in neurosciences is to look for possible relationships between brain architecture and cognitive models. The lack of architectural information in magnetic resonance images, however, has led the neuroimaging community to develop brain mapping strategies based on various coordinate systems without accurate architectural content. Therefore, the relationships between architectural and functional brain organizations are difficult to study when analyzing neuroimaging experiments. This paper advocates that the design of new brain image analysis methods inspired by the structural strategies often used in computer vision may provide better ways to address these relationships. The key point underlying this new framework is the conversion of the raw images into structural representations before analysis. These representations are made up of data-driven elementary features like activated clusters, cortical folds or fiber bundles. Two classes of methods are introduced. Inference of structural models via matching across a set of individuals is described first. This inference problem is illustrated by the group analysis of functional statistical parametric maps (SPMs). Then, the matching of new individual data with a priori known structural models is described, using the recognition of the cortical sulci as a prototypical example.

  20. Table of periodic properties of fullerenes based on structural parameters.

    Science.gov (United States)

    Torrens, Francisco

    2004-01-01

    The periodic table (PT) of the elements suggests that hydrogen could be the origin of everything else. The construction principle is an evolutionary process that is formally similar to those of Darwin and Oparin. The Kekulé structure count and permanence of the adjacency matrix of fullerenes are related to structural parameters involving the presence of contiguous pentagons p, q and r. Let p be the number of edges common to two pentagons, q the number of vertices common to three pentagons, and r the number of pairs of nonadjacent pentagon edges shared between two other pentagons. Principal component analysis (PCA) of the structural parameters and cluster analysis (CA) of the fullerenes permit classifying them and agree. A PT of the fullerenes is built based on the structural parameters, PCA and CA. The periodic law does not have the rank of the laws of physics. (1) The properties of the fullerenes are not repeated; only, and perhaps, their chemical character. (2) The order relationships are repeated, although with exceptions. The proposed statement is the following: The relationships that any fullerene p has with its neighbor p + 1 are approximately repeated for each period.

  1. Monaural Sound Localization Based on Reflective Structure and Homomorphic Deconvolution.

    Science.gov (United States)

    Park, Yeonseok; Choi, Anthony; Kim, Keonwook

    2017-09-23

    The asymmetric structure around the receiver provides a particular time delay for the specific incoming propagation. This paper designs a monaural sound localization system based on the reflective structure around the microphone. The reflective plates are placed to present the direction-wise time delay, which is naturally processed by convolutional operation with a sound source. The received signal is separated for estimating the dominant time delay by using homomorphic deconvolution, which utilizes the real cepstrum and inverse cepstrum sequentially to derive the propagation response's autocorrelation. Once the localization system accurately estimates the information, the time delay model computes the corresponding reflection for localization. Because of the structure limitation, two stages of the localization process perform the estimation procedure as range and angle. The software toolchain from propagation physics and algorithm simulation realizes the optimal 3D-printed structure. The acoustic experiments in the anechoic chamber denote that 79.0% of the study range data from the isotropic signal is properly detected by the response value, and 87.5% of the specific direction data from the study range signal is properly estimated by the response time. The product of both rates shows the overall hit rate to be 69.1%.

  2. Carbon Nanotube-Based Structural Health Monitoring Sensors

    Science.gov (United States)

    Wincheski, Russell; Jordan, Jeffrey; Oglesby, Donald; Watkins, Anthony; Patry, JoAnne; Smits, Jan; Williams, Phillip

    2011-01-01

    Carbon nanotube (CNT)-based sensors for structural health monitoring (SHM) can be embedded in structures of all geometries to monitor conditions both inside and at the surface of the structure to continuously sense changes. These CNTs can be manipulated into specific orientations to create small, powerful, and flexible sensors. One of the sensors is a highly flexible sensor for crack growth detection and strain field mapping that features a very dense and highly ordered array of single-walled CNTs. CNT structural health sensors can be mass-produced, are inexpensive, can be packaged in small sizes (0.5 micron(sup 2)), require less power than electronic or piezoelectric transducers, and produce less waste heat per square centimeter than electronic or piezoelectric transducers. Chemically functionalized lithographic patterns are used to deposit and align the CNTs onto metallic electrodes. This method consistently produces aligned CNTs in the defined locations. Using photo- and electron-beam lithography, simple Cr/Au thin-film circuits are patterned onto oxidized silicon substrates. The samples are then re-patterned with a CNT-attracting, self-assembled monolayer of 3-aminopropyltriethoxysilane (APTES) to delineate the desired CNT locations between electrodes. During the deposition of the solution-suspended single- wall CNTs, the application of an electric field to the metallic contacts causes alignment of the CNTs along the field direction. This innovation is a prime candidate for smart skin technologies with applications ranging from military, to aerospace, to private industry.

  3. Stabilising emulsion-based colloidal structures with mixed food ingredients.

    Science.gov (United States)

    Dickinson, Eric

    2013-03-15

    The physical scientist views food as a complex form of soft matter. The complexity has its origin in the numerous ingredients that are typically mixed together and the subtle variations in microstructure and texture induced by thermal and mechanical processing. The colloid science approach to food product formulation is based on the assumption that the major product attributes such as appearance, rheology and physical stability are determined by the spatial distribution and interactions of a small number of generic structural entities (biopolymers, particles, droplets, bubbles, crystals) organised in various kinds of structural arrangements (layers, complexes, aggregates, networks). This review describes some recent advances in this field with reference to three discrete classes of dispersed systems: particle-stabilised emulsions, emulsion gels and aerated emulsions. Particular attention is directed towards explaining the crucial role of the macromolecular ingredients (proteins and polysaccharides) in controlling the formation and stabilisation of the colloidal structures. The ultimate objective of this research is to provide the basic physicochemical insight required for the reliable manufacture of novel structured foods with an appealing taste and texture, whilst incorporating a more healthy set of ingredients than those found in many existing traditional products. © 2012 Society of Chemical Industry.

  4. Rational design of a cytotoxic dinuclear Cu2 complex that binds by molecular recognition at two neighboring phosphates of the DNA backbone.

    Science.gov (United States)

    Jany, Thomas; Moreth, Alexander; Gruschka, Claudia; Sischka, Andy; Spiering, Andre; Dieding, Mareike; Wang, Ying; Samo, Susan Haji; Stammler, Anja; Bögge, Hartmut; Fischer von Mollard, Gabriele; Anselmetti, Dario; Glaser, Thorsten

    2015-03-16

    The mechanism of the cytotoxic function of cisplatin and related anticancer drugs is based on their binding to the nucleobases of DNA. The development of new classes of anticancer drugs requires establishing other binding modes. Therefore, we performed a rational design for complexes that target two neighboring phosphates of the DNA backbone by molecular recognition resulting in a family of dinuclear complexes based on 2,7-disubstituted 1,8-naphthalenediol. This rigid backbone preorganizes the two metal ions for molecular recognition at the distance of two neighboring phosphates in DNA of 6-7 Å. Additionally, bulky chelating pendant arms in the 2,7-position impede nucleobase complexation by steric hindrance. We successfully synthesized the Cu(II)2 complex of the designed family of dinuclear complexes and studied its binding to dsDNA by independent ensemble and single-molecule methods like gel electrophoresis, precipitation, and titration experiments followed by UV-vis spectroscopy, atomic force microscopy (AFM), as well as optical tweezers (OT) and magnetic tweezers (MT) DNA stretching. The observed irreversible binding of our dinuclear Cu(II)2 complex to dsDNA leads to a blocking of DNA synthesis as studied by polymerase chain reactions and cytotoxicity for human cancer cells.

  5. Structural level characterization of base oils using advanced analytical techniques

    KAUST Repository

    Hourani, Nadim

    2015-05-21

    Base oils, blended for finished lubricant formulations, are classified by the American Petroleum Institute into five groups, viz., groups I-V. Groups I-III consist of petroleum based hydrocarbons whereas groups IV and V are made of synthetic polymers. In the present study, five base oil samples belonging to groups I and III were extensively characterized using high performance liquid chromatography (HPLC), comprehensive two-dimensional gas chromatography (GC×GC), and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) equipped with atmospheric pressure chemical ionization (APCI) and atmospheric pressure photoionization (APPI) sources. First, the capabilities and limitations of each analytical technique were evaluated, and then the availed information was combined to reveal compositional details on the base oil samples studied. HPLC showed the overwhelming presence of saturated over aromatic compounds in all five base oils. A similar trend was further corroborated using GC×GC, which yielded semiquantitative information on the compound classes present in the samples and provided further details on the carbon number distributions within these classes. In addition to chromatography methods, FT-ICR MS supplemented the compositional information on the base oil samples by resolving the aromatics compounds into alkyl- and naphtheno-subtituted families. APCI proved more effective for the ionization of the highly saturated base oil components compared to APPI. Furthermore, for the detailed information on hydrocarbon molecules FT-ICR MS revealed the presence of saturated and aromatic sulfur species in all base oil samples. The results presented herein offer a unique perspective into the detailed molecular structure of base oils typically used to formulate lubricants. © 2015 American Chemical Society.

  6. Kr-86 Ion-Beam Irradiation of Hydrated DNA: Free Radical and Unaltered Base Yields

    Science.gov (United States)

    Becker, David; Adhikary, Amitava; Tetteh, Smedley T.; Bull, Arthur W.; Sevilla, Michael D.

    2012-01-01

    This work reports an ESR and product analysis investigation of Kr-86 ion-beam irradiation of hydrated DNA at 77 K. The irradiation results in the formation and trapping of both base radicals and sugar phosphate radicals (DNA backbone radicals). The absolute yields (G, μmol/J) of the base radicals are smaller than the yields found in similarly prepared γ-irradiated DNA samples, and the relative yields of backbone radicals relative to base radicals are much higher than that found in γ-irradiated samples. From these results, we have elaborated our radiation chemical model of the track structure for ion-beam irradiated DNA as it applies to krypton ion-beams. The base radicals, which are trapped as ion radicals or reversibly protonated or deprotonated ion radicals, are formed almost entirely in the track penumbra, a region in which radiation chemical effects are similar to those found in γ-irradiated samples. By comparing the yields of base radicals in ion-beam samples to the yields of the same radicals in γ-irradiated samples, the partition of energy between the low-LET region (penumbra) and the core is experimentally determined. The neutral sugar and other backbone radicals, which are not as susceptible to recombination as are ion radicals, are formed largely in the track core. The backbone radicals show a linear dose response up to very high doses. Unaltered base release yields in Kr-86 irradiated hydrated DNA are equal to sugar radical yields within experimental error limits, consistent with radiation-chemical processes in which all base release originates with sugar radicals. Two phosphorus-centered radicals from fragmentation of the DNA backbone are found in low yields. PMID:23106211

  7. Structure-based control of complex networks with nonlinear dynamics

    Science.gov (United States)

    Zañudo, Jorge Gomez Tejeda; Yang, Gang; Albert, Réka

    2017-01-01

    What can we learn about controlling a system solely from its underlying network structure? Here we adapt a recently developed framework for control of networks governed by a broad class of nonlinear dynamics that includes the major dynamic models of biological, technological, and social processes. This feedback-based framework provides realizable node overrides that steer a system toward any of its natural long-term dynamic behaviors, regardless of the specific functional forms and system parameters. We use this framework on several real networks, identify the topological characteristics that underlie the predicted node overrides, and compare its predictions to those of structural controllability in control theory. Finally, we demonstrate this framework’s applicability in dynamic models of gene regulatory networks and identify nodes whose override is necessary for control in the general case but not in specific model instances. PMID:28655847

  8. Support system of a structure on a support base

    International Nuclear Information System (INIS)

    Arene, G.; Renaux, C.; Minguet, J.L.; Chantot, H.

    1984-01-01

    Two series of strips are fixed to the structure to be supported and to the base to define each one a closed convex envelope; the strips are flexible in the radial direction with regard to the envelope. The two series of strips are connected by a treillis of rigid bars set to form juxtaposed V or X. A good transversal rigidity and a certain radial flexibility are obtained. The invention can be applied to a fast neutron nuclear reactor, the reactor comprising a vertical axis vessel filled with liquid metal; the vessel rests on a support foundation by means of the support system proposed by the invention. The support system allows the supported structure to resist the effects of an eventual earthquake and brutal temperature variations [fr

  9. Calculation of Sentence Semantic Similarity Based on Syntactic Structure

    Directory of Open Access Journals (Sweden)

    Xiao Li

    2015-01-01

    Full Text Available Combined with the problem of single direction of the solution of the existing sentence similarity algorithms, an algorithm for sentence semantic similarity based on syntactic structure was proposed. Firstly, analyze the sentence constituent, then through analysis convert sentence similarity into words similarity on the basis of syntactic structure, then convert words similarity into concept similarity through words disambiguation, and, finally, realize the semantic similarity comparison. It also gives the comparison rules in more detail for the modifier words in the sentence which also have certain contributions to the sentence. Under the same test condition, the experiments show that the proposed algorithm is more intuitive understanding of people and has higher accuracy.

  10. Edge detection based on computational ghost imaging with structured illuminations

    Science.gov (United States)

    Yuan, Sheng; Xiang, Dong; Liu, Xuemei; Zhou, Xin; Bing, Pibin

    2018-03-01

    Edge detection is one of the most important tools to recognize the features of an object. In this paper, we propose an optical edge detection method based on computational ghost imaging (CGI) with structured illuminations which are generated by an interference system. The structured intensity patterns are designed to make the edge of an object be directly imaged from detected data in CGI. This edge detection method can extract the boundaries for both binary and grayscale objects in any direction at one time. We also numerically test the influence of distance deviations in the interference system on edge extraction, i.e., the tolerance of the optical edge detection system to distance deviation. Hopefully, it may provide a guideline for scholars to build an experimental system.

  11. A community detection algorithm based on structural similarity

    Science.gov (United States)

    Guo, Xuchao; Hao, Xia; Liu, Yaqiong; Zhang, Li; Wang, Lu

    2017-09-01

    In order to further improve the efficiency and accuracy of community detection algorithm, a new algorithm named SSTCA (the community detection algorithm based on structural similarity with threshold) is proposed. In this algorithm, the structural similarities are taken as the weights of edges, and the threshold k is considered to remove multiple edges whose weights are less than the threshold, and improve the computational efficiency. Tests were done on the Zachary’s network, Dolphins’ social network and Football dataset by the proposed algorithm, and compared with GN and SSNCA algorithm. The results show that the new algorithm is superior to other algorithms in accuracy for the dense networks and the operating efficiency is improved obviously.

  12. Structure-based control of complex networks with nonlinear dynamics

    Science.gov (United States)

    Zanudo, Jorge G. T.; Yang, Gang; Albert, Reka

    What can we learn about controlling a system solely from its underlying network structure? Here we use a framework for control of networks governed by a broad class of nonlinear dynamics that includes the major dynamic models of biological, technological, and social processes. This feedback-based framework provides realizable node overrides that steer a system towards any of its natural long term dynamic behaviors, regardless of the dynamic details and system parameters. We use this framework on several real networks, identify the topological characteristics that underlie the predicted node overrides, and compare its predictions to those of classical structural control theory. Finally, we demonstrate this framework's applicability in dynamic models of gene regulatory networks and identify nodes whose override is necessary for control in the general case, but not in specific model instances. This work was supported by NSF Grants PHY 1205840 and IIS 1160995. JGTZ is a recipient of a Stand Up To Cancer - The V Foundation Convergence Scholar Award.

  13. Photophysical properties and computational investigation on substituent effects on the structural and electronic properties of 3,6-di(thiophene-2-yl)-carbazole-based derivatives

    Science.gov (United States)

    Sriyab, Suwannee; Gleeson, Matthew Paul; Hannongbua, Supa; Suramitr, Songwut

    2016-12-01

    A series of 3,6-carbazole-based derivatives, 3,6-CzTh-(1), 3,6-CzTh-(2), 3,6-CzTh-(3) and 3,6-CzTh-(4), were synthesized to investigate the influence of structural distortion on intramolecular charge transfer (ICT) complexation between the conjugation components and carbazole core unit of the 3,6-carbazole-based derivatives. The 3,6-carbazole-based derivatives were synthesized and analysed using UV-Visible, photoluminescence spectroscopy and DFT calculations. The electron-donating substituents on the carbazole core unit, which was linked by formyl and acetyl at the 3,6-positions of the carbazole core so as to directly involve the electron-donating edge substituents in backbone, exhibited conjugation breaks in the middle of the carbazole core units. The break lead to a planar structure with an extraordinary ability to stabilize on the excited state resulting in a strong fluorescence quantum yield (Фfluo ≈ 0.6-0.7). The results of the Time-dependent density functional theory (TD-DFT) calculations were in agreement with the experimental results, and indicated that the low fluorescence of 3,6-CzTh-(1) and 3,6-CzTh-(2) is derived not only from intersystem crossing but also from internal conversion due to the proximity effect; this inference was also supported by the measurements of the photoluminescence spectra at low temperatures. In addition, factors leading efficiently to non-radiative processes were shown to be absent in 3,6-CzTh-(3) and 3,6-CzTh-(4). This work deepens our understanding of 3,6-di(thiophen-2-yl)-carbazole-based derivatives and provides insight into the future design of novel materials for improved fluorescence efficiencies and optoelectronic devices.

  14. Structure-based, rational design of T cell receptors

    Directory of Open Access Journals (Sweden)

    Vincent eZoete

    2013-09-01

    Full Text Available Adoptive cell transfer using engineered T cells is emerging as a promising treatment for metastatic melanoma. Such an approach allows one to introduce TCR modifications that, while maintaining the specificity for the targeted antigen, can enhance the binding and kinetic parameters for the interaction pMHC. Using the well-characterized 2C TCR/SIYR/H-2K(b structure as a model system, we demonstrated that a binding free energy decomposition based on the MM-GBSA approach provides a detailed and reliable description of the TCR/pMHC interactions at the structural and thermodynamic levels. Starting from this result, we developed a new structure-based approach, to rationally design new TCR sequences, and applied it to the BC1 TCR targeting the HLA-A2 restricted NY-ESO-1157-165 cancer-testis epitope. 54% of the designed sequence replacements exhibited improved pMHC-binding as compared to the native TCR, with up to 150 fold increase in affinity, while preserving specificity. Genetically-engineered CD8+ T cells expressing these modified TCRs showed an improved functional activity compared to those expressing BC1 TCR. We measured maximum levels of activities for TCRs within the upper limit of natural affinity. Beyond the affinity threshold at KD < 1 μM we observed an attenuation in cellular function. We have also developed a homology modeling-based approach, TCRep 3D, to obtain accurate structural models of any TCR-pMHC complexes. We have complemented the approach with a simplified rigid method to predict the TCR orientation over pMHC. These methods potentially extend the use of our TCR engineering method to entire TCR repertoires for which no X-ray structure is available. We have also performed a steered molecular dynamics study of the unbinding of the TCR-pMHC complex to get a better understanding of how TCRs interact with pMHCs. This entire rational TCR design pipeline is now being used to produce rationally optimized TCRs for adoptive cell therapies of

  15. Backbone resonance assignments for G protein α(i3) subunit in the GTP-bound state.

    Science.gov (United States)

    Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio

    2012-10-01

    Guanine-nucleotide binding proteins (G proteins) act as molecular switches in signaling pathways, by coupling the activation of G protein-coupled receptors (GPCRs) at the cell surface to intracellular responses. In the resting state, G protein forms a heterotrimer, consisting of GDP-bound form of the G protein α subunit (Gα(GDP)) and G protein βγ subunit (Gβγ). Ligand binding to GPCRs promotes the GDP-GTP exchange on Gα, leading to the dissociation of the GTP-bound form of Gα (Gα(GTP)) and Gβγ. Then, Gα(GTP) and Gβγ bind to their downstream effector enzymes or ion channels and regulate their activities, leading to a variety of cellular responses. Finally, Gα hydrolyzes the bound GTP to GDP and returns to the resting state by re-associating with Gβγ. G proteins are classified with four major families based on the amino acid sequences of Gα: i/o, s, q/11, and 12/13. Each family transduces the signaling from different GPCRs to the specific effectors. Here, we established the backbone resonance assignments of human Gα(i3), a member of the i/o family, with a molecular weight of 41 K in complex with a GTP analogue, GTPγS.

  16. An Analysis of Rheological Properties of Inconel 625 Superalloy Feedstocks Formulated with Backbone Binder Polypropylene System for Powder Injection Molding

    Directory of Open Access Journals (Sweden)

    Gökmen U.

    2017-12-01

    Full Text Available Binder formula is one of the most significant factors which has a considerable influence on powder injection molding (PIM processes. In the study, rheological behaviors and properties of different binder systems containing PIM feedstocks, Inconel 625 powder commonly used in space industry, were investigated. The feedstocks were prepared 59%-69% (volume powder loading ratios with three diversified binder systems by use of Polypropylene as backbone binder. The average particle size of the Inconel 625 powder used was 12.86 microns. Components used in the binder were mixed for 30 minutes as dry in three dimensional mixing to prepare binder systems. Rheological features of the feedstock were characterized by using a capillary rheometer. Viscosities of the feedstocks were calculated within the range of 37.996-1900 Pa.s based on the shear rate, shear stress, binder formula and temperature. “n” parameters for PIM feedstocks were determined to be less than 1. Influences of temperature on the viscosities of the feedstocks were also studied and “Ea” under various shear stresses were determined within the range of 24.41-70.89 kJ/mol.

  17. Current trends in virtual high throughput screening using ligand-based and structure-based methods.

    Science.gov (United States)

    Sukumar, Nagamani; Das, Sourav

    2011-12-01

    High throughput in silico methods have offered the tantalizing potential to drastically accelerate the drug discovery process. Yet despite significant efforts expended by academia, national labs and industry over the years, many of these methods have not lived up to their initial promise of reducing the time and costs associated with the drug discovery enterprise, a process that can typically take over a decade and cost hundreds of millions of dollars from conception to final approval and marketing of a drug. Nevertheless structure-based modeling has become a mainstay of computational biology and medicinal chemistry, helping to leverage our knowledge of the biological target and the chemistry of protein-ligand interactions. While ligand-based methods utilize the chemistry of molecules that are known to bind to the biological target, structure-based drug design methods rely on knowledge of the three-dimensional structure of the target, as obtained through crystallographic, spectroscopic or bioinformatics techniques. Here we review recent developments in the methodology and applications of structure-based and ligand-based methods and target-based chemogenomics in Virtual High Throughput Screening (VHTS), highlighting some case studies of recent applications, as well as current research in further development of these methods. The limitations of these approaches will also be discussed, to give the reader an indication of what might be expected in years to come.

  18. Density-based and transport-based core-periphery structures in networks.

    Science.gov (United States)

    Lee, Sang Hoon; Cucuringu, Mihai; Porter, Mason A

    2014-03-01

    Networks often possess mesoscale structures, and studying them can yield insights into both structure and function. It is most common to study community structure, but numerous other types of mesoscale structures also exist. In this paper, we examine core-periphery structures based on both density and transport. In such structures, core network components are well-connected both among themselves and to peripheral components, which are not well-connected to anything. We examine core-periphery structures in a wide range of examples of transportation, social, and financial networks-including road networks in large urban areas, a rabbit warren, a dolphin social network, a European interbank network, and a migration network between counties in the United States. We illustrate that a recently developed transport-based notion of node coreness is very useful for characterizing transportation networks. We also generalize this notion to examine core versus peripheral edges, and we show that the resulting diagnostic is also useful for transportation networks. To examine the properties of transportation networks further, we develop a family of generative models of roadlike networks. We illustrate the effect of the dimensionality of the embedding space on transportation networks, and we demonstrate that the correlations between different measures of coreness can be very different for different types of networks.

  19. Retrospective Validation of a Structure-Based Virtual Screening Protocol to Identify Ligands for Estrogen Receptor Alpha and Its Application to Identify the Alpha-Mangostin Binding Pose

    Directory of Open Access Journals (Sweden)

    Agustina Setiawati

    2014-07-01

    Full Text Available The publicly available enhanced data of ligands and decoys for estrogen receptor alpha (ERα which were recently published has made the retrospective validation of a structure-based virtual screening (SBVS protocol to identify ligands for ERα possible. In this article, we present the retrospective validation of an SBVS protocol using PLANTS molecular docking software version 1.2 (PLANTS1.2 as the backbone software. The protocol shows better enrichment factor at 1% false positives (EF1% value and the Area Under Curve (AUC value of the Receiver Operator Characteristic (ROC compared to the original published protocol. Moreover, in all 1000 iterative attempts the protocol could reproduce the co-crystal pose of 4-hydroxitamoxifen in ERα binding pocket. It shows that the protocol is not only able to identify potent ligands for ERα but also able to be employed in examining binding pose of known ligand. Thence, the protocol was successfully employed to examine the binding poses of α-mangostin, an ERα ligand found in the Garcinia mangostana, L. pericarp.

  20. Synthesis/literature review for determining structural layer coefficients (SLC) of bases.

    Science.gov (United States)

    2014-12-01

    FDOTs current method of determining a base material structural layer coefficient (SLC) is detailed in the : Materials Manual, Chapter 2.1, Structural Layer Coefficients for Flexible Pavement Base Materials. : Currently, any new base material not a...

  1. Performance characterization of structured light-based fingerprint scanner

    Science.gov (United States)

    Hassebrook, Laurence G.; Wang, Minghao; Daley, Raymond C.

    2013-05-01

    Our group believes that the evolution of fingerprint capture technology is in transition to include 3-D non-contact fingerprint capture. More specifically we believe that systems based on structured light illumination provide the highest level of depth measurement accuracy. However, for these new technologies to be fully accepted by the biometric community, they must be compliant with federal standards of performance. At present these standards do not exist for this new biometric technology. We propose and define a set of test procedures to be used to verify compliance with the Federal Bureau of Investigation's image quality specification for Personal Identity Verification single fingerprint capture devices. The proposed test procedures include: geometric accuracy, lateral resolution based on intensity or depth, gray level uniformity and flattened fingerprint image quality. Several 2-D contact analogies, performance tradeoffs and optimization dilemmas are evaluated and proposed solutions are presented.

  2. Guided wave based structural health monitoring: A review

    Science.gov (United States)

    Mitra, Mira; Gopalakrishnan, S.

    2016-05-01

    The paper provides a state of the art review of guided wave based structural health monitoring (SHM). First, the fundamental concepts of guided wave propagation and its implementation for SHM is explained. Following sections present the different modeling schemes adopted, developments in the area of transducers for generation, and sensing of wave, signal processing and imaging technique, statistical and machine learning schemes for feature extraction. Next, a section is presented on the recent advancements in nonlinear guided wave for SHM. This is followed by section on Rayleigh and SH waves. Next is a section on real-life implementation of guided wave for industrial problems. The paper, though briefly talks about the early development for completeness, is primarily focussed on the recent progress made in the last decade. The paper ends by discussing and highlighting the future directions and open areas of research in guided wave based SHM.

  3. Guided wave based structural health monitoring: A review

    International Nuclear Information System (INIS)

    Mitra, Mira; Gopalakrishnan, S

    2016-01-01

    The paper provides a state of the art review of guided wave based structural health monitoring (SHM). First, the fundamental concepts of guided wave propagation and its implementation for SHM is explained. Following sections present the different modeling schemes adopted, developments in the area of transducers for generation, and sensing of wave, signal processing and imaging technique, statistical and machine learning schemes for feature extraction. Next, a section is presented on the recent advancements in nonlinear guided wave for SHM. This is followed by section on Rayleigh and SH waves. Next is a section on real-life implementation of guided wave for industrial problems. The paper, though briefly talks about the early development for completeness, is primarily focussed on the recent progress made in the last decade. The paper ends by discussing and highlighting the future directions and open areas of research in guided wave based SHM. (topical review)

  4. Neuronal bases of structural coherence in contemporary dance observation.

    Science.gov (United States)

    Bachrach, Asaf; Jola, Corinne; Pallier, Christophe

    2016-01-01

    The neuronal processes underlying dance observation have been the focus of an increasing number of brain imaging studies over the past decade. However, the existing literature mainly dealt with effects of motor and visual expertise, whereas the neural and cognitive mechanisms that underlie the interpretation of dance choreographies remained unexplored. Hence, much attention has been given to the action observation network (AON) whereas the role of other potentially relevant neuro-cognitive mechanisms such as mentalizing (theory of mind) or language (narrative comprehension) in dance understanding is yet to be elucidated. We report the results of an fMRI study where the structural coherence of short contemporary dance choreographies was manipulated parametrically using the same taped movement material. Our participants were all trained dancers. The whole-brain analysis argues that the interpretation of structurally coherent dance phrases involves a subpart (superior parietal) of the AON as well as mentalizing regions in the dorsomedial prefrontal cortex. An ROI analysis based on a similar study using linguistic materials (Pallier et al., 2011) suggests that structural processing in language and dance might share certain neural mechanisms. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. Identification of Novel Smoothened Ligands Using Structure-Based Docking

    Science.gov (United States)

    Torosyan, Hayarpi; Parathaman, Pranavan; Irwin, John J.; Shoichet, Brian K.

    2016-01-01

    The seven transmembrane protein Smoothened is required for Hedgehog signaling during embryonic development and adult tissue homeostasis. Inappropriate activation of the Hedgehog signalling pathway leads to cancers such as basal cell carcinoma and medulloblastoma, and Smoothened inhibitors are now available clinically to treat these diseases. However, resistance to these inhibitors rapidly develops thereby limiting their efficacy. The determination of Smoothened crystal structures enables structure-based discovery of new ligands with new chemotypes that will be critical to combat resistance. In this study, we docked 3.2 million available, lead-like molecules against Smoothened, looking for those with high physical complementarity to its structure; this represents the first such campaign against the class Frizzled G-protein coupled receptor family. Twenty-one high-ranking compounds were selected for experimental testing, and four, representing three different chemotypes, were identified to antagonize Smoothened with IC50 values better than 50 μM. A screen for analogs revealed another six molecules, with IC50 values in the low micromolar range. Importantly, one of the most active of the new antagonists continued to be efficacious at the D473H mutant of Smoothened, which confers clinical resistance to the antagonist vismodegib in cancer treatment. PMID:27490099

  6. Scalable, ultra-resistant structural colors based on network metamaterials

    KAUST Repository

    Galinski, Henning

    2017-05-05

    Structural colors have drawn wide attention for their potential as a future printing technology for various applications, ranging from biomimetic tissues to adaptive camouflage materials. However, an efficient approach to realize robust colors with a scalable fabrication technique is still lacking, hampering the realization of practical applications with this platform. Here, we develop a new approach based on large-scale network metamaterials that combine dealloyed subwavelength structures at the nanoscale with lossless, ultra-thin dielectric coatings. By using theory and experiments, we show how subwavelength dielectric coatings control a mechanism of resonant light coupling with epsilon-near-zero regions generated in the metallic network, generating the formation of saturated structural colors that cover a wide portion of the spectrum. Ellipsometry measurements support the efficient observation of these colors, even at angles of 70°. The network-like architecture of these nanomaterials allows for high mechanical resistance, which is quantified in a series of nano-scratch tests. With such remarkable properties, these metastructures represent a robust design technology for real-world, large-scale commercial applications.

  7. A Structurally Based Viscosity Model for Oxide Melts

    Science.gov (United States)

    Zhang, Guo-Hua; Chou, Kuo-Chih; Mills, Ken

    2014-04-01

    A structurally based viscosity model is proposed to represent the viscosity of oxide melts as functions of both temperature and composition; The oxide melts cover the following constituents: Li2O, Na2O, K2O, MgO, CaO, SrO, BaO, FeO, MnO, Al2O3, SiO2, CaF2, TiO2, Fe2O3, and P2O5. The model describes the slag structure in terms of the various forms of oxygen ions which are classified according to the metal cations they bond with. Approximate methods for calculating the concentrations of these oxygen ions are proposed and are then used to describe the effect of melt structure on viscosity. The model provides a good description of the variations in viscosity with composition and temperature. The measured viscosities were compared with values calculated with the model, and the current model was found to provide reliable estimates of viscosities of slags used in various industrial processes ( e.g., blast furnace, basic oxygen steelmaking, ladle refining, continuous casting of steel, coal gasification, and electroslag remelting).

  8. Poly(Ethylene Glycol-Based Backbones with High Peptide Loading Capacities

    Directory of Open Access Journals (Sweden)

    Aoife O'Connor

    2014-10-01

    Full Text Available Polymer-peptide conjugates are a promising class of compounds, where polymers can be used to overcome some of the limitations associated with peptides intended for therapeutic and/or diagnostic applications. Linear polymers such as poly(ethylene glycol can be conjugated through terminal moieties and have therefore limited loading capacities. In this research, functionalised linear poly(ethylene glycols are utilised for peptide conjugation, to increase their potential loading capacities. These poly(ethylene glycol derivatives are conjugated to peptide sequences containing representative side-chain functionalised amino acids, using different conjugation chemistries, including copper-catalysed azide-alkyne cycloaddition, amide coupling and thiol-ene reactions. Conjugation of a sequence containing the RGD motif to poly(allyl glycidyl ether by the thiol-ene reaction, provided a conjugate which could be used in platelet adhesion studies.

  9. Analytical Model based on Green Criteria for Optical Backbone Network Interconnection

    DEFF Research Database (Denmark)

    Gutierrez Lopez, Jose Manuel; Riaz, M. Tahir; Pedersen, Jens Myrup

    2011-01-01

    to the evaluation of the environmental impact of networks from physical interconnection point of view. Networks deployment, usage, and disposal are analyzed as contributing elements to ICT’s (Information and Communications Technology) CO2 emissions. This paper presents an analytical model for evaluating...... for backbone’s interconnection, since minimization of CO2 emissions is becoming an important factor. In addition, two case studies are presented to illustrate the use and application of this model, and the need for de facto and international standards to reduce CO2 emissions through good network planning....

  10. Spectral methods and cluster structure in correlation-based networks

    Science.gov (United States)

    Heimo, Tapio; Tibély, Gergely; Saramäki, Jari; Kaski, Kimmo; Kertész, János

    2008-10-01

    We investigate how in complex systems the eigenpairs of the matrices derived from the correlations of multichannel observations reflect the cluster structure of the underlying networks. For this we use daily return data from the NYSE and focus specifically on the spectral properties of weight W=|-δ and diffusion matrices D=W/sj-δ, where C is the correlation matrix and si=∑jW the strength of node j. The eigenvalues (and corresponding eigenvectors) of the weight matrix are ranked in descending order. As in the earlier observations, the first eigenvector stands for a measure of the market correlations. Its components are, to first approximation, equal to the strengths of the nodes and there is a second order, roughly linear, correction. The high ranking eigenvectors, excluding the highest ranking one, are usually assigned to market sectors and industrial branches. Our study shows that both for weight and diffusion matrices the eigenpair analysis is not capable of easily deducing the cluster structure of the network without a priori knowledge. In addition we have studied the clustering of stocks using the asset graph approach with and without spectrum based noise filtering. It turns out that asset graphs are quite insensitive to noise and there is no sharp percolation transition as a function of the ratio of bonds included, thus no natural threshold value for that ratio seems to exist. We suggest that these observations can be of use for other correlation based networks as well.

  11. Protein Function Prediction Based on Sequence and Structure Information

    KAUST Repository

    Smaili, Fatima Z.

    2016-05-25

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

  12. (Biodegradable Ionomeric Polyurethanes Based on Xanthan: Synthesis, Properties, and Structure

    Directory of Open Access Journals (Sweden)

    T. V. Travinskaya

    2017-01-01

    Full Text Available New (biodegradable environmentally friendly film-forming ionomeric polyurethanes (IPU based on renewable biotechnological polysaccharide xanthan (Xa have been obtained. The influence of the component composition on the colloidal-chemical and physic-mechanical properties of IPU/Xa and based films, as well as the change of their properties under the influence of environmental factors, have been studied. The results of IR-, PMS-, DMA-, and X-ray scattering study indicate that incorporation of Xa into the polyurethane chain initiates the formation of a new polymer structure different from the structure of the pure IPU (matrix: an amorphous polymer-polymer microdomain has occurred as a result of the chemical interaction of Xa and IPU. It predetermines the degradation of the IPU/Xa films as a whole, unlike the mixed polymer systems, and plays a key role in the improvement of material performance. The results of acid, alkaline hydrolysis, and incubation into the soil indicate the increase of the intensity of degradation processes occurring in the IPU/Xa in comparison with the pure IPU. It has been shown that the introduction of Xa not only imparts the biodegradability property to polyurethane, but also improves the mechanical properties.

  13. Development of structural materials on the base of new technology

    International Nuclear Information System (INIS)

    Belov, A.F.; Anoshkin, N.F.

    1982-01-01

    Some results are considered and possibilities which discovered in development of structural materials connected with development of such new technological processes as skull melting of titanium alloys, granule metallurgy, hot isostatic, diffusion welding are estimated. The method of skull melting with remelted skull is developed. The method assures sufficient possibilities for dissolving of high-heat components of charge and obtaining homogeneous ingots of series of new alloys. Granule metallurgy based on crystallization of the metal with high rate in the form of small (up to 300 μkm) particles and subsequent consolidation of them into compact billet discoveres a wide possibilities of creation of new structural material with more high operation indexes. It is noted that developed processes of granule production, their treatment, compacting and thermal treatment of the billets assure production of metal of high quality, satisfied the strong requirements of present standards. The process of hot isostatic pressing at which the workable metal is subjected to through uniform pressure by compressed gas after heating or semultaneously with its heating up to the temperatures of working in gasostats is one of new technological processes. A certain experience of the HIP use for production of compact billets from granules for diffusion welding of the billets is accumulated. This process has a great possibilities for densification of shaped castings. Investigation and application of the diffusion welding represent combination of elements into details of complex form in vacuum at the temperatures low of melting point under effect of small pressures are investigated both in our country and abroad. Diffusion welding gives a wide possibilities in the development of materials with higher properties at the expence of production of products of large dimensions from thin elements with fine-grained structure as well as products with assigned gradient of chemical composition, structure

  14. Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models.

    Science.gov (United States)

    Jonikas, Magdalena A; Radmer, Randall J; Altman, Russ B

    2009-12-15

    The recent development of methods for modeling RNA 3D structures using coarse-grain approaches creates a need to bridge low- and high-resolution modeling methods. Although they contain topological information, coarse-grain models lack atomic detail, which limits their utility for some applications. We have developed a method for adding full atomic detail to coarse-grain models of RNA 3D structures. Our method [Coarse to Atomic (C2A)] uses geometries observed in known RNA crystal structures. Our method rebuilds full atomic detail from ideal coarse-grain backbones taken from crystal structures to within 1.87-3.31 A RMSD of the full atomic crystal structure. When starting from coarse-grain models generated by the modeling tool NAST, our method builds full atomic structures that are within 1.00 A RMSD of the starting structure. The resulting full atomic structures can be used as starting points for higher resolution modeling, thus bridging high- and low-resolution approaches to modeling RNA 3D structure. Code for the C2A method, as well as the examples discussed in this article, are freely available at www.simtk.org/home/c2a. russ.altman@stanford.edu

  15. Life estimation and analysis of dielectric strength, hydrocarbon backbone and oxidation of high voltage multi stressed EPDM composites

    Science.gov (United States)

    Khattak, Abraiz; Amin, Muhammad; Iqbal, Muhammad; Abbas, Naveed

    2018-02-01

    Micro and nanocomposites of ethylene propylene diene monomer (EPDM) are recently studied for different characteristics. Study on life estimation and effects of multiple stresses on its dielectric strength and backbone scission and oxidation is also vital for endorsement of these composites for high voltage insulation and other outdoor applications. In order to achieve these goals, unfilled EPDM and its micro and nanocomposites are prepared at 23 phr micro silica and 6 phr nanosilica loadings respectively. Prepared samples are energized at 2.5 kV AC voltage and subjected for a long time to heat, ultraviolet radiation, acid rain, humidity and salt fog in accelerated manner in laboratory. Dielectric strength, leakage current and intensity of saturated backbone and carbonyl group are periodically measured. Loss in dielectric strength, increase in leakage current and backbone degradation and oxidation were observed in all samples. These effects were least in the case of EPDM nanocomposite. The nanocomposite sample also demonstrated longest shelf life.

  16. Prediction of atomic structure from sequence for double helical DNA oligomers.

    Science.gov (United States)

    Farwer, Jochen; Packer, Martin J; Hunter, Christopher A

    2006-01-01

    DNA can adopt different conformations depending on the base sequence, solvent, electrolyte composition and concentration, pH, temperature, and interaction with proteins. Here we present a model for calculating the three-dimensional atomic structure of double-stranded DNA oligomers. A theoretical energy function is used for calculating the interactions within the base steps and an empirical backbone function is used to restrict the conformational space accessible to the bases and to account for the conformational coupling of neighboring steps in a sequence. Conformational searching on large structures or a large number of structures is possible, because each base step can be described by just two primary degrees of freedom (slide and shift). A genetic algorithm is used to search for low-energy structures in slide-shift space, and this allows very rapid optimization of DNA oligomers. The other base step parameters have been previously optimized for all possible slide-shift sequence combinations, and a heuristic algorithm is used to add the atomic details of the backbone conformation in the final step of the calculation. The structures obtained by this method are very similar to the corresponding X-ray crystal structures observed experimentally. The average RMSD is 2.24 Angstroms for a set of 20 oligomer structures. For 15 of these sequences, the X-ray crystal structure is the global energy minimum. The other 5 are bistable sequences that have B-form global energy minima but crystallize as A-DNA. Copyright 2005 Wiley Periodicals, Inc.

  17. Quantifying vegetation distribution and structure using high resolution drone-based structure-from-motion photogrammetry

    Science.gov (United States)

    Zhang, J.; Okin, G.

    2017-12-01

    Vegetation is one of the most important driving factors of different ecosystem processes in drylands. The structure of vegetation controls the spatial distribution of moisture and heat in the canopy and the surrounding area. Also, the structure of vegetation influences both airflow and boundary layer resistance above the land surface. Multispectral satellite remote sensing has been widely used to monitor vegetation coverage and its change; however, it can only capture 2D images, which do not contain the vertical information of vegetation. In situ observation uses different methods to measure the structure of vegetation, and their results are accurate; however, these methods are laborious and time-consuming, and susceptible to undersampling in spatial heterogeneity. Drylands are sparsely covered by short plants, which allows the drone fly at a relatively low height to obtain ultra-high resolution images. Structure-from-motion (SfM) is a photogrammetric method that was proved to produce 3D model based on 2D images. Drone-based remote sensing can obtain the multiangle images for one object, which can be used to constructed 3D models of vegetation in drylands. Using these images detected by the drone, the orthomosaics and digital surface model (DSM) can be built. In this study, the drone-based remote sensing was conducted in Jornada Basin, New Mexico, in the spring of 2016 and 2017, and three derived vegetation parameters (i.e., canopy size, bare soil gap size, and plant height) were compared with those obtained with field measurement. The correlation coefficient of canopy size, bare soil gap size, and plant height between drone images and field data are 0.91, 0.96, and 0.84, respectively. The two-year averaged root-mean-square error (RMSE) of canopy size, bare soil gap size, and plant height between drone images and field data are 0.61 m, 1.21 m, and 0.25 cm, respectively. The two-year averaged measure error (ME) of canopy size, bare soil gap size, and plant height

  18. Structure Based Predictive Model for Coal Char Combustion

    Energy Technology Data Exchange (ETDEWEB)

    Robert Hurt; Joseph Calo; Robert Essenhigh; Christopher Hadad

    2000-12-30

    This unique collaborative project has taken a very fundamental look at the origin of structure, and combustion reactivity of coal chars. It was a combined experimental and theoretical effort involving three universities and collaborators from universities outside the U.S. and from U.S. National Laboratories and contract research companies. The project goal was to improve our understanding of char structure and behavior by examining the fundamental chemistry of its polyaromatic building blocks. The project team investigated the elementary oxidative attack on polyaromatic systems, and coupled with a study of the assembly processes that convert these polyaromatic clusters to mature carbon materials (or chars). We believe that the work done in this project has defined a powerful new science-based approach to the understanding of char behavior. The work on aromatic oxidation pathways made extensive use of computational chemistry, and was led by Professor Christopher Hadad in the Department of Chemistry at Ohio State University. Laboratory experiments on char structure, properties, and combustion reactivity were carried out at both OSU and Brown, led by Principle Investigators Joseph Calo, Robert Essenhigh, and Robert Hurt. Modeling activities were divided into two parts: first unique models of crystal structure development were formulated by the team at Brown (PI'S Hurt and Calo) with input from Boston University and significant collaboration with Dr. Alan Kerstein at Sandia and with Dr. Zhong-Ying chen at SAIC. Secondly, new combustion models were developed and tested, led by Professor Essenhigh at OSU, Dieter Foertsch (a collaborator at the University of Stuttgart), and Professor Hurt at Brown. One product of this work is the CBK8 model of carbon burnout, which has already found practical use in CFD codes and in other numerical models of pulverized fuel combustion processes, such as EPRI's NOxLOI Predictor. The remainder of the report consists of detailed

  19. Backbone resonance assignments of the outer membrane lipoprotein FrpD from Neisseria meningitidis.

    Science.gov (United States)

    Bumba, Ladislav; Sviridova, Ekaterina; Kutá Smatanová, Ivana; Řezáčová, Pavlína; Veverka, Václav

    2014-04-01

    The iron-regulated FrpD protein is a unique lipoprotein embedded into the outer membrane of the Gram-negative bacterium Neisseria meningitidis. The biological function of FrpD remains unknown but might consist in anchoring to the bacterial cell surface the Type I-secreted FrpC protein, which belongs to a Repeat in ToXins (RTX) protein family and binds FrpD with very high affinity (K(d) = 0.2 nM). Here, we report the backbone (1)H, (13)C, and (15)N chemical shift assignments for the FrpD(43-271) protein that allow us to characterize the intimate interaction between FrpD and the N-terminal domain of FrpC.

  20. Extensive Air Showers: from the muonic smoking guns to the hadronic backbone

    Directory of Open Access Journals (Sweden)

    Cazon L.

    2013-06-01

    Full Text Available Extensive Air Showers are complex macroscopic objects initiated by single ultra-high energy particles. They are the result of millions of high energy reactions in the atmosphere and can be described as the superposition of hadronic and electromagnetic cascades. The hadronic cascade is the air shower backbone, and it is mainly made of pions. Decays of neutral pions initiate electromagnetic cascades, while the decays of charged pions produce muons which leave the hadronic core and travel many kilometers almost unaffected. Muons are smoking guns of the hadronic cascade: the energy, transverse momentum, spatial distribution and depth of production are key to reconstruct the history of the air shower. In this work, we overview the phenomenology of muons on the air shower and its relation to the hadronic cascade. We briefly review the experimental efforts to analyze muons within air showers and discuss possible paths to use this information.