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Sample records for backbone structure based

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

    CERN Document Server

    Christensen, Anders S

    2015-01-01

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

  2. A Multi-Objective Approach for Protein Structure Prediction Based on an Energy Model and Backbone Angle Preferences.

    Science.gov (United States)

    Tsay, Jyh-Jong; Su, Shih-Chieh; Yu, Chin-Sheng

    2015-07-03

    Protein structure prediction (PSP) is concerned with the prediction of protein tertiary structure from primary structure and is a challenging calculation problem. After decades of research effort, numerous solutions have been proposed for optimisation methods based on energy models. However, further investigation and improvement is still needed to increase the accuracy and similarity of structures. This study presents a novel backbone angle preference factor, which is one of the factors inducing protein folding. The proposed multiobjective optimisation approach simultaneously considers energy models and backbone angle preferences to solve the ab initio PSP. To prove the effectiveness of the multiobjective optimisation approach based on the energy models and backbone angle preferences, 75 amino acid sequences with lengths ranging from 22 to 88 amino acids were selected from the CB513 data set to be the benchmarks. The data sets were highly dissimilar, therefore indicating that they are meaningful. The experimental results showed that the root-mean-square deviation (RMSD) of the multiobjective optimization approach based on energy model and backbone angle preferences was superior to those of typical energy models, indicating that the proposed approach can facilitate the ab initio PSP.

  3. A Multi-Objective Approach for Protein Structure Prediction Based on an Energy Model and Backbone Angle Preferences

    Directory of Open Access Journals (Sweden)

    Jyh-Jong Tsay

    2015-07-01

    Full Text Available Protein structure prediction (PSP is concerned with the prediction of protein tertiary structure from primary structure and is a challenging calculation problem. After decades of research effort, numerous solutions have been proposed for optimisation methods based on energy models. However, further investigation and improvement is still needed to increase the accuracy and similarity of structures. This study presents a novel backbone angle preference factor, which is one of the factors inducing protein folding. The proposed multiobjective optimisation approach simultaneously considers energy models and backbone angle preferences to solve the ab initio PSP. To prove the effectiveness of the multiobjective optimisation approach based on the energy models and backbone angle preferences, 75 amino acid sequences with lengths ranging from 22 to 88 amino acids were selected from the CB513 data set to be the benchmarks. The data sets were highly dissimilar, therefore indicating that they are meaningful. The experimental results showed that the root-mean-square deviation (RMSD of the multiobjective optimization approach based on energy model and backbone angle preferences was superior to those of typical energy models, indicating that the proposed approach can facilitate the ab initio PSP.

  4. 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.

  5. HMM-based prediction for protein structural motifs' two local properties: solvent accessibility and backbone torsion angles.

    Science.gov (United States)

    Yu, Jianyong; Xiang, Leijun; Hong, Jiang; Zhang, Weidong

    2013-02-01

    Protein structure prediction is often assisted by predicting one-dimensional structural properties including relative solvent accessibility (RSA) surface and backbone torsion angles (BTA) of residues, and these two properties are continuously varying variables because proteins can move freely in a three-dimensional space. Instead of subdividing them into a few arbitrarily defined states that many popular approaches used, this paper proposes an integrated system for realvalue prediction of protein structural motifs' two local properties, based on the modified Hidden Markov Model that we previously presented. The model was used to capture the relevance of RSA and the dependency of BTA between adjacent residues along the local protein chain in motifs with definite probabilities. These two properties were predicted according to their own probability distribution. The method was applied to a protein fragment library. For nine different classes of motifs, real values of RSA were predicted with mean absolute error (MAE) of 0.122-0.175 and Pearson's correlation coefficient (PCC) of 0.623-0.714 between predicted and actual RSA. Meanwhile, real values of BTA were obtained with MAE of 8.5⁰-29.4⁰ for Φ angles, 11.2⁰-38.5⁰ for ψ angles and PCC of 0.601-0.716 for Φ, 0.597-0.713 for ψ. The results were compared with well-known Real-SPINE Server, and indicate the proposed method may at least serve as the foundation to obtain better local properties from structural motifs for protein structure prediction. PMID:22894152

  6. 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.

  7. 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.

  8. Geometry motivated alternative view on local protein backbone structures

    OpenAIRE

    Zacharias, Jan; Knapp, Ernst Walter

    2013-01-01

    We present an alternative to the classical Ramachandran plot (R-plot) to display local protein backbone structure. Instead of the (ϕ, ψ)-backbone angles relating to the chemical architecture of polypeptides generic helical parameters are used. These are the rotation or twist angle ϑ and the helical rise parameter d. Plots with these parameters provide a different view on the nature of local protein backbone structures. It allows to display the local structures in polar (d, ϑ)-coordinates, whi...

  9. On Backbone Structure for a Future Multipurpose Network

    DEFF Research Database (Denmark)

    Gutierrez Lopez, Jose Manuel; Cuevas, Ruben; Riaz, M. Tahir;

    2008-01-01

    Telecommunications are evolving towards the unification of services and infrastructures. This unification must be achieved at the highest hierarchical level for a complete synergy of services. Therefore, one of the requirements is a multipurpose backbone network capable of supporting all the curr......Telecommunications are evolving towards the unification of services and infrastructures. This unification must be achieved at the highest hierarchical level for a complete synergy of services. Therefore, one of the requirements is a multipurpose backbone network capable of supporting all...... the current and future services over the same infrastructure, offering high QoS levels. This paper analyzes different possibilities of a future backbone in order to find the best option among the studied ones. This option is a two level structure formed by the combination of N2R and Grid topologies which...

  10. Backbone Dynamics of Triple-helical Collagen-like Structure

    OpenAIRE

    Lazarev, Yu.A.; Lazareva, A.V.; Komarov, V.M.

    1999-01-01

    Some details of the backbone dynamics in the collagen-like triple helix is discussed and the role of backbone dynamics in functioning collagen proteins is illustrated. On a series of oligotripeptides synthetic analogs of collagen formation of high-frequency vibrational backbone dynamics and low-frequency nonlinear backbone dynamics upon stepwise elongation of peptide chain have been described using infrared spectroscopy and hydrogen-exchange method. In the fully completed triple helix the lev...

  11. Application of Multicast-based Video Conference on CERNET Backbone

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Multicast-based video conference is a representative application in advanced network. In multi-point video conference using multicast can get better efficiency facilitated by inner-group broadcast mechanism. In the application, the multicast-based network resources assignment, management and security should be considered together. This paper presents a framework model of multicast-based video conferencing application with three layers. And a practical multicast-based video conferencing is implemented in CERNET(China Education and Research Network) backbone. The practice is valuable for the development of multicast-based video conferencing application in China.

  12. Protein structure quality assessment based on the distance profiles of consecutive backbone Cα atoms [v3; ref status: indexed, http://f1000r.es/2kg

    Directory of Open Access Journals (Sweden)

    Sandeep Chakraborty

    2013-12-01

    Full Text Available Predicting the three dimensional native state structure of a protein from its primary sequence is an unsolved grand challenge in molecular biology. Two main computational approaches have evolved to obtain the structure from the protein sequence - ab initio/de novo methods and template-based modeling - both of which typically generate multiple possible native state structures. Model quality assessment programs (MQAP validate these predicted structures in order to identify the correct native state structure. Here, we propose a MQAP for assessing the quality of protein structures based on the distances of consecutive Cα atoms. We hypothesize that the root-mean-square deviation of the distance of consecutive Cα (RDCC atoms from the ideal value of 3.8 Å, derived from a statistical analysis of high quality protein structures (top100H database, is minimized in native structures. Based on tests with the top100H set, we propose a RDCC cutoff value of 0.012 Å, above which a structure can be filtered out as a non-native structure. We applied the RDCC discriminator on decoy sets from the Decoys 'R' Us database to show that the native structures in all decoy sets tested have RDCC below the 0.012 Å cutoff. While most decoy sets were either indistinguishable using this discriminator or had very few violations, all the decoy structures in the fisa decoy set were discriminated by applying the RDCC criterion. This highlights the physical non-viability of the fisa decoy set, and possible issues in benchmarking other methods using this set. The source code and manual is made available at https://github.com/sanchak/mqap and permanently available on 10.5281/zenodo.7134.

  13. Effect of Liquid-Crystalline Epoxy Backbone Structure on Thermal Conductivity of Epoxy-Alumina Composites

    Science.gov (United States)

    Giang, Thanhkieu; Kim, Jinhwan

    2016-06-01

    In a series of papers published recently, we clearly demonstrated that the most important factor governing the thermal conductivity of epoxy-Al2O3 composites is the backbone structure of the epoxy. In this study, three more epoxies based on diglycidyl ester-terminated liquid-crystalline epoxy (LCE) have been synthesized to draw conclusions regarding the effect of the epoxy backbone structure on the thermal conductivity of epoxy-alumina composites. The synthesized structures were characterized by proton nuclear magnetic resonance (1H-NMR) and Fourier-transform infrared (FT-IR) spectroscopy. Differential scanning calorimetry, thermogravimetric analysis, and optical microscopy were also employed to examine the thermal and optical properties of the synthesized LCEs and the cured composites. All three LCE resins exhibited typical liquid-crystalline behaviors: clear solid crystalline state below the melting temperature (T m), sharp crystalline melting at T m, and transition to nematic phase above T m with consequent isotropic phase above the isotropic temperature (T i). The LCE resins displayed distinct nematic liquid-crystalline phase over a wide temperature range and retained liquid-crystalline phase after curing, with high thermal conductivity of the resulting composite. The thermal conductivity values ranged from 3.09 W/m-K to 3.89 W/m-K for LCE-Al2O3 composites with 50 vol.% filler loading. The steric effect played a governing role in the difference. The neat epoxy resin thermal conductivity was obtained as 0.35 W/m-K to 0.49 W/m-K based on analysis using the Agari-Uno model. The results clearly support the objective of this study in that the thermal conductivity of the LCE-containing networks strongly depended on the epoxy backbone structure and the degree of ordering in the cured network.

  14. Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning.

    Science.gov (United States)

    Heffernan, Rhys; Paliwal, Kuldip; Lyons, James; Dehzangi, Abdollah; Sharma, Alok; Wang, Jihua; Sattar, Abdul; Yang, Yuedong; Zhou, Yaoqi

    2015-01-01

    Direct prediction of protein structure from sequence is a challenging problem. An effective approach is to break it up into independent sub-problems. These sub-problems such as prediction of protein secondary structure can then be solved independently. In a previous study, we found that an iterative use of predicted secondary structure and backbone torsion angles can further improve secondary structure and torsion angle prediction. In this study, we expand the iterative features to include solvent accessible surface area and backbone angles and dihedrals based on Cα atoms. By using a deep learning neural network in three iterations, we achieved 82% accuracy for secondary structure prediction, 0.76 for the correlation coefficient between predicted and actual solvent accessible surface area, 19° and 30° for mean absolute errors of backbone φ and ψ angles, respectively, and 8° and 32° for mean absolute errors of Cα-based θ and τ angles, respectively, for an independent test dataset of 1199 proteins. The accuracy of the method is slightly lower for 72 CASP 11 targets but much higher than those of model structures from current state-of-the-art techniques. This suggests the potentially beneficial use of these predicted properties for model assessment and ranking.

  15. 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...... of the structural properties of DNA. These molecules have found applications as probes in genetic diagnostics and are also being developed into antisense (RNA (ribonucleic acid) interference) gene therapeutic drugs, targeting selected genes through sequence-specific recognition of (messenger or micro......)RNA and in the future also antigene applications targeting the double-stranded DNA of the genes themselves leading to gene silencing or guiding specific gene repair. Finally, the special chemical and structural properties of PNA suggest that these or similar molecules might have played a role in the prebiotic origin...

  16. Influence of structures of polymer backbones on cooperative photoreorientation behavior of p-cyanoazobenzene side chains

    DEFF Research Database (Denmark)

    Han, Mina; Kidowaki, Masatoshi; Ichimura, Kunihiro;

    2001-01-01

    Photoinduced orientational behavior of a polymethacrylate (CN6) and a polyester (p6a12) with p-cyanoazobenzene side chains was studied to reveal the structural effect of the liquid crystalline polymer backbones. Irradiation with linearly polarized W light resulted in the reorientation of the azob...

  17. De novo backbone and sequence design of an idealized alpha/beta-barrel protein: Evidence of stable tertiary structure

    OpenAIRE

    Offredi, Fabrice; Dubail, Fabien; Kischel, Philippe; Sarinski, K.; Stern, A S; Van de Weerdt, Cécile; Hoch, J. C.; Prosperi, Christelle; François, Jean-Marie; Mayo, S. L.; Martial, Joseph

    2003-01-01

    We have designed, synthesized, and characterized a 216 amino acid residue sequence encoding a putative idealized alpha/beta-barrel protein. The design was elaborated in two steps. First, the idealized backbone was defined with geometric parameters representing our target fold: a central eight parallel-stranded beta-sheet surrounded by eight parallel alpha-helices, connected together with short structural turns on both sides of the barrel. An automated sequence selection algorithm, based on th...

  18. Structure and backbone dynamics of a microcrystalline metalloprotein by solid-state NMR.

    Science.gov (United States)

    Knight, Michael J; Pell, Andrew J; Bertini, Ivano; Felli, Isabella C; Gonnelli, Leonardo; Pierattelli, Roberta; Herrmann, Torsten; Emsley, Lyndon; Pintacuda, Guido

    2012-07-10

    We introduce a new approach to improve structural and dynamical determination of large metalloproteins using solid-state nuclear magnetic resonance (NMR) with (1)H detection under ultrafast magic angle spinning (MAS). The approach is based on the rapid and sensitive acquisition of an extensive set of (15)N and (13)C nuclear relaxation rates. The system on which we demonstrate these methods is the enzyme Cu, Zn superoxide dismutase (SOD), which coordinates a Cu ion available either in Cu(+) (diamagnetic) or Cu(2+) (paramagnetic) form. Paramagnetic relaxation enhancements are obtained from the difference in rates measured in the two forms and are employed as structural constraints for the determination of the protein structure. When added to (1)H-(1)H distance restraints, they are shown to yield a twofold improvement of the precision of the structure. Site-specific order parameters and timescales of motion are obtained by a gaussian axial fluctuation (GAF) analysis of the relaxation rates of the diamagnetic molecule, and interpreted in relation to backbone structure and metal binding. Timescales for motion are found to be in the range of the overall correlation time in solution, where internal motions characterized here would not be observable.

  19. East vergent structure of Backbone Range: Insights from A-Lan-Yi area and sandbox modeling

    Science.gov (United States)

    Lee, C. A.; Lu, C. Y.

    2015-12-01

    Southern Taiwan, including Pingtung peninsula and Taitung, is the incipient oblique collision zone of Eurasian plate and Philippine Sea plate. The Luzon volcanic arc converged toward Taiwan Island and formed Hengchun Ridge south offshore Taiwan. Thus, Taiwan mountain belt developed from north to south as the Backbone Range, so that we can infer the incipient feature structure from the topography and outcrop study of southern Taiwan. Our field survey of this study concentrated at the southeast coastline of Taiwan, also known as A-Lan-Yi Trail. According to previous study, the deformational structures such as faults and folds are consistent with regional kinematic processes, and the preserved transpression structure is the most important evidence of incipient collision. In this study, we use the sedimentary sequences of study area to trace the regional tectonics from north to south. Discovered structures in this area show the similar kinematic history as the eastern flank of Backbone Range, so that we suggest they are at the same series of a tectonic event. To complete the regional structure mapping in this accessible area, besides the field geological data, we also applied the LiDAR-derived DTM which is a 3D visualization technology to improve our topography information. In addition, we use the sandbox modeling to demonstrate the development of structures in the eastern flank of Backbone Range. After combining the results of field observation and regional structure mapping, this study provides a strong evidence of backthrusting and backfolding deformation during the incipient oblique collision stage.

  20. Synthesis, Characterization and Structure of Chiral Amino Acids and Their Corresponding Amino Alcohols with Camphoric Backbone

    Institute of Scientific and Technical Information of China (English)

    QIAN Hui-Fen; HUANG Wei; LI Hui-Hui; YAO Cheng

    2006-01-01

    Chiral amino acids and their corresponding amino alcohols bearing camphoric backbone were prepared from D-(+)-camphoric imide and characterized by infrared, elemental analysis, ESI-MS, and NMR measurements. Among them, one intermediate (lS,3R)-3-amino-2,2,3-trimethyl cyclopentane-1-carboxylic acid hydrochloride 3 was structurally elucidated by X-ray diffraction techniques. Versatile intermolecular hydrogen bonding interactions observed in its packing structure result in a two-dimensional framework.

  1. Solution structure and backbone dynamics of the defunct domain of calcium vector protein.

    Science.gov (United States)

    Théret, I; Baladi, S; Cox, J A; Gallay, J; Sakamoto, H; Craescu, C T

    2001-11-20

    CaVP (calcium vector protein) is a Ca(2+) sensor of the EF-hand protein family which is highly abundant in the muscle of Amphioxus. Its three-dimensional structure is not known, but according to the sequence analysis, the protein is composed of two domains, each containing a pair of EF-hand motifs. We determined recently the solution structure of the C-terminal domain (Trp81-Ser161) and characterized the large conformational and dynamic changes induced by Ca(2+) binding. In contrast, the N-terminal domain (Ala1-Asp86) has lost the capacity to bind the metal ion due to critical mutations and insertions in the two calcium loops. In this paper, we report the solution structure of the N-terminal domain and its backbone dynamics based on NMR spectroscopy, nuclear relaxation, and molecular modeling. The well-resolved three-dimensional structure is typical of a pair of EF-hand motifs, joined together by a short antiparallel beta-sheet. The tertiary arrangement of the two EF-hands results in a closed-type conformation, with near-antiparallel alpha-helices, similar to other EF-hand pairs in the absence of calcium ions. To characterize the internal dynamics of the protein, we measured the (15)N nuclear relaxation rates and the heteronuclear NOE effect in (15)N-labeled N-CaVP at a magnetic field of 11.74 T and 298 K. The domain is mainly monomeric in solution and undergoes an isotropic Brownian rotational diffusion with a correlation time of 7.1 ns, in good agreement with the fluorescence anisotropy decay measurements. Data analysis using a model-free procedure showed that the amide backbone groups in the alpha-helices and beta-strands undergo highly restricted movements on a picosecond to nanosecond time scale. The amide groups in Ca(2+) binding loops and in the linker fragment also display rapid fluctuations with slightly increased amplitudes. PMID:11705378

  2. Sequential backbone assignment based on dipolar amide-to-amide correlation experiments

    Energy Technology Data Exchange (ETDEWEB)

    Xiang, ShengQi; Grohe, Kristof; Rovó, Petra; Vasa, Suresh Kumar; Giller, Karin; Becker, Stefan; Linser, Rasmus, E-mail: rali@nmr.mpibpc.mpg.de [Max Planck Institute for Biophysical Chemistry, Department for NMR-Based Structural Biology (Germany)

    2015-07-15

    Proton detection in solid-state NMR has seen a tremendous increase in popularity in the last years. New experimental techniques allow to exploit protons as an additional source of information on structure, dynamics, and protein interactions with their surroundings. In addition, sensitivity is mostly improved and ambiguity in assignment experiments reduced. We show here that, in the solid state, sequential amide-to-amide correlations turn out to be an excellent, complementary way to exploit amide shifts for unambiguous backbone assignment. For a general assessment, we compare amide-to-amide experiments with the more common {sup 13}C-shift-based methods. Exploiting efficient CP magnetization transfers rather than less efficient INEPT periods, our results suggest that the approach is very feasible for solid-state NMR.

  3. Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions.

    Science.gov (United States)

    Botan, Alexandru; Favela-Rosales, Fernando; Fuchs, Patrick F J; Javanainen, Matti; Kanduč, Matej; Kulig, Waldemar; Lamberg, Antti; Loison, Claire; Lyubartsev, Alexander; Miettinen, Markus S; Monticelli, Luca; Määttä, Jukka; Ollila, O H Samuli; Retegan, Marius; Róg, Tomasz; Santuz, Hubert; Tynkkynen, Joona

    2015-12-10

    Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR experiments in terms of the highly structurally sensitive C-H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three-dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P-N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using nmrlipids.blogspot.fi as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files ( https

  4. Refinement of the protein backbone angle {psi} in NMR structure calculations

    Energy Technology Data Exchange (ETDEWEB)

    Sprangers, R.; Bottomley, M.J.; Linge, J.P.; Schultz, J.; Nilges, M.; Sattler, M. [European Molecular Biology Laboratory (Germany)

    2000-01-15

    Cross-correlated relaxation rates involving the C{sup {alpha}}-H{sup {alpha}} 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 {psi} can be directly refined against such cross-correlated relaxation rates ({gamma}{sup H{alpha}}{sup C{alpha}}{sup ,C'}) and the three-bond H/D isotope effect on the C{sup {alpha}} chemical shifts ({sup 3}{delta}C{sup {alpha}}{sub (ND)}). By simultaneously using both experimental parameters as restraints during NMR structure calculations, a unique value for the backbone angle {psi} is defined. We have applied the new refinement method to the {alpha}-Spectrin SH3 domain (a {beta}-sheet protein) and to the Sgs1p HRDC domain (an {alpha}-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 {psi}-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.

  5. The structure of the carbohydrate backbone of the lipopolysaccharide of Pectinatus frisingensis strain VTT E-79104.

    Science.gov (United States)

    Vinogradov, Evgeny; Li, Jianjun; Sadovskaya, Irina; Jabbouri, Said; Helander, Ilkka M

    2004-06-22

    The structure of the carbohydrate backbone of the lipopolysaccharide from Pectinatus frisingensis strain VTT E-79104 was analyzed using chemical degradations, NMR spectroscopy, mass spectrometry, and chemical methods. The LPS contains two major structural variants, differing in the presence or absence of an octasaccharide fragment. The largest structure of the carbohydrate backbone of the LPS, that could be deduced from experimental results, consists of 20 monosaccharides arranged in a nonrepetitive sequence: [carbohydrate structure: see text] where R is H or 4-O-Me-alpha-L-Fuc-(1-2)-4-O-Me-beta-Hep-(1-3)-alpha-GlcNAc-(1-2)-beta-Man-(1-3)-beta-ManNAc-(1-4)-alpha-Gal-(1-4)-beta-Hep-(1-3)-beta-GalNAc-(1- where Hep is a residue of D-glycero-D-galacto-heptose; all monosaccharides have the D-configuration except for 4-O-Me-L-Fuc and L-Ara4N. This structure is architecturally similar to the oligosaccharide system reported previously in P. frisingensis VTT E-82164 LPS, but differs from the latter in composition and also in the size of the outer region.

  6. On correlation between protein secondary structure, backbone bond angles, and side-chain orientations

    CERN Document Server

    Lundgren, Martin

    2012-01-01

    We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central C$_\\alpha$ carbon of a protein backbone, and for this we develop new visualization techniques to analyze high resolution X-ray structures in 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 C$_\\beta$ carbon orientations. The energy function can model the side-chain geometry with a sub-atomic precision. As an example we construct the C$_\\alpha$-C$_\\beta$ structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 \\.A in root-mean-square distance from the experimental X-ray structure.

  7. Structure and assembly of group B streptococcus pilus 2b backbone protein.

    Science.gov (United States)

    Cozzi, Roberta; Malito, Enrico; Lazzarin, Maddalena; Nuccitelli, Annalisa; Castagnetti, Andrea; Bottomley, Matthew J; Margarit, Immaculada; Maione, Domenico; Rinaudo, C Daniela

    2015-01-01

    Group B Streptococcus (GBS) is a major cause of invasive disease in infants. Like other Gram-positive bacteria, GBS uses a sortase C-catalyzed transpeptidation mechanism to generate cell surface pili from backbone and ancillary pilin precursor substrates. The three pilus types identified in GBS contain structural subunits that are highly immunogenic and are promising candidates for the development of a broadly-protective vaccine. Here we report the X-ray crystal structure of the backbone protein of pilus 2b (BP-2b) at 1.06Å resolution. The structure reveals a classical IgG-like fold typical of the pilin subunits of other Gram-positive bacteria. The crystallized portion of the protein (residues 185-468) encompasses domains D2 and D3 that together confer high stability to the protein due to the presence of an internal isopeptide bond within each domain. The D2+D3 region, lacking the N-terminal D1 domain, was as potent as the entire protein in conferring protection against GBS challenge in a well-established mouse model. By site-directed mutagenesis and complementation studies in GBS knock-out strains we identified the residues and motives essential for assembly of the BP-2b monomers into high-molecular weight complexes, thus providing new insights into pilus 2b polymerization.

  8. Structure and assembly of group B streptococcus pilus 2b backbone protein.

    Directory of Open Access Journals (Sweden)

    Roberta Cozzi

    Full Text Available Group B Streptococcus (GBS is a major cause of invasive disease in infants. Like other Gram-positive bacteria, GBS uses a sortase C-catalyzed transpeptidation mechanism to generate cell surface pili from backbone and ancillary pilin precursor substrates. The three pilus types identified in GBS contain structural subunits that are highly immunogenic and are promising candidates for the development of a broadly-protective vaccine. Here we report the X-ray crystal structure of the backbone protein of pilus 2b (BP-2b at 1.06Å resolution. The structure reveals a classical IgG-like fold typical of the pilin subunits of other Gram-positive bacteria. The crystallized portion of the protein (residues 185-468 encompasses domains D2 and D3 that together confer high stability to the protein due to the presence of an internal isopeptide bond within each domain. The D2+D3 region, lacking the N-terminal D1 domain, was as potent as the entire protein in conferring protection against GBS challenge in a well-established mouse model. By site-directed mutagenesis and complementation studies in GBS knock-out strains we identified the residues and motives essential for assembly of the BP-2b monomers into high-molecular weight complexes, thus providing new insights into pilus 2b polymerization.

  9. Influence of backbone rigidness on single chain conformation of thiophene-based conjugated polymers.

    Science.gov (United States)

    Hu, Zhongjian; Liu, Jianhua; Simón-Bower, Lauren; Zhai, Lei; Gesquiere, Andre J

    2013-04-25

    Structural order of conjugated polymers at different length scales directs the optoelectronic properties of the corresponding materials; thus it is of critical importance to understand and control conjugated polymer morphology for successful application of these materials in organic optoelectronics. Herein, with the aim of probing the dependence of single chain folding properties on the chemical structure and rigidness of the polymer backbones, single molecule fluorescence spectroscopy was applied to four thiophene-based conjugated polymers. These include regioregular poly(3-hexylthiophene) (RR-P3HT), poly(2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT-14), poly(2,5-bis(3-tetradecylthiophen-2-yl)thiophene-2-yl)thiophen-2-ylthiazolo[5,4-d]thiazole) (PTzQT-12), and poly(3,3-didodecylquaterthiophene)] (PQT-12). Our previous work has shown that RR-P3HT and PBTTT-14 polymer chains fold in their nanostructures, whereas PQT-12 and PTzQT-12 do not fold in their nanostructures. At the single molecule level, it was found that RR-P3HT single chains almost exclusively fold into loosely and strongly aggregated conformations, analogous to the folding properties in nanostructures. PQT-12 displays significant chain folding as well, but only into loosely aggregated conformations, showing an absence of strongly aggregated polymer chains. PBTTT-14 exhibits a significant fraction of rigid polymer chain. The findings made for single molecules of PQT-12 and PBTTT-14 are thus in contrast with the observations made in their corresponding nanostructures. PTzQT-12 appears to be the most rigid and planar conjugated polymer of these four polymers. However, although the presumably nonfolding polymers PQT-12 and PTzQT-12 exhibit less folding than RR-P3HT, there is still a significant occurrence of chain folding for these polymers at the single molecule level. These results suggest that the folding properties of conjugated polymers can be influenced by the architecture of the

  10. Phase behaviors, molecular and supramolecular structures in polymers containing rigid-rod backbones with cyanobiphenyl side chains

    Science.gov (United States)

    Ruan, Jrjeng

    One of the most important and challenging topics in materials chemistry involves designing nano-structures in synthetic materials via self-assembly for various highly technical applications. A specially designed combined liquid crystalline polymer containing a polyester backbone with cyanobiphenyl side chains has been studied in aspects of phase behaviors and crystal structures. The triclinic crystal phases identified in this series of polymer are all found to be constricted by 4-monomer unit cells. This discovery of 4-monomer triclinic unit cells motivates a search for the existence of supramolecular phases and understanding the possible molecular packing. A series of newly designed polyimides, which are composed of aromatic polyimide backbones with 4-cyanobiphenyl mesogens on the side chains has been synthesized. This series of polymers possesses a lesser degree of coupling between the backbones and side chains, which indicates the possibility of microphase separation between them. The representative polyimides of BPDA-7CBBP and BPDA-11CBBP in this series, in which 4-cyanobiphenyl side chains are connected onto the backbones through seven and eleven methylene units respectively have systematically studied in this research. Two crystal forms were recognized in BPDA-11CBBA, and one of them possesses six repeating units in one monoclinic unit cell. Moreover, the existence of a supramolecular phase has been proposed based on 2D WAXD fiber patterns. In the case of BPDA-7CBBP, three crystal forms were identified: two of them are constructed by triclinic lattices with large unit cells. The numbers of repeating units in those unit cells are seven and eight, respectively. Complicated phase behaviors including a second-order transition between the supramolecular phase and a high-order liquid crystal phase have been explored. The fact that large unit cells in both polymers with the numbers of repeating units in unit cells being 6, 7, and 8 leads to an important issue for

  11. 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.

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

    International Nuclear Information System (INIS)

    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

  13. STARD6 on steroids: solution structure, multiple timescale backbone dynamics and ligand binding mechanism

    Science.gov (United States)

    Létourneau, Danny; Bédard, Mikaël; Cabana, Jérôme; Lefebvre, Andrée; LeHoux, Jean-Guy; Lavigne, Pierre

    2016-01-01

    START domain proteins are conserved α/β helix-grip fold that play a role in the non-vesicular and intracellular transport of lipids and sterols. The mechanism and conformational changes permitting the entry of the ligand into their buried binding sites is not well understood. Moreover, their functions and the identification of cognate ligands is still an active area of research. Here, we report the solution structure of STARD6 and the characterization of its backbone dynamics on multiple time-scales through 15N spin-relaxation and amide exchange studies. We reveal for the first time the presence of concerted fluctuations in the Ω1 loop and the C-terminal helix on the microsecond-millisecond time-scale that allows for the opening of the binding site and ligand entry. We also report that STARD6 binds specifically testosterone. Our work represents a milestone for the study of ligand binding mechanism by other START domains and the elucidation of the biological function of STARD6. PMID:27340016

  14. Base-pairing potential identified by in vitro selection predicts the kinked RNA backbone observed in the crystal structure of the alfalfa mosaic virus RNA-coat protein complex.

    Science.gov (United States)

    Boyce, Michael; Scott, Felicia; Guogas, Laura M; Gehrke, Lee

    2006-01-01

    The three-dimensional structure of the 3' terminus of alfalfa mosaic virus RNA in complex with an amino-terminal coat protein peptide revealed an unusual RNA fold with inter-AUGC basepairing stabilized by key arginine residues (Guogas, et al., 2004). To probe viral RNA interactions with the full-length coat protein, we have used in vitro genetic selection to characterize potential folding patterns among RNAs isolated from a complex randomized pool. Nitrocellulose filter retention, electrophoretic mobility bandshift analysis, and hydroxyl radical footprinting techniques were used to define binding affinities and to localize the potential RNA-protein interaction sites. Minimized binding sites were identified that included both the randomized domain and a portion of the constant regions of the selected RNAs. The selected RNAs, identified by their ability to bind full-length coat protein, have the potential to form the same unusual inter-AUGC Watson-Crick base pairs observed in the crystal structure, although the primary sequences diverge from the wild-type RNA. A constant feature of both the wild-type RNA and the selected RNAs is a G ribonucleotide in the third position of an AUGC-like repeat. Competitive binding assays showed that substituting adenosine for the constant guanosine in either the wild-type or selected RNAs impaired coat protein binding. These data suggest that the interactions observed in the RNA-peptide structure are likely recapitulated when the full-length protein binds. Further, the results underscore the power of in vitro genetic selection for probing RNA-protein structure and function. PMID:16312015

  15. 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.

  16. Interaction of Al-induced peptide backbone ring structure with the sidechains of His, Phe, Trp and Tyr

    Institute of Scientific and Technical Information of China (English)

    吴清雷; 宋波

    2015-01-01

    Aluminium is widely used as an antimicrobial coagulant, food additive, and cookware. However, many reports indicate that aluminium may be a critical factor in many amyloid diseases, such as Alzheimer’s disease and Parkinson’s disease. Unfortunately, the underlying mechanism is still poorly understood, which limits efforts to prevent and treat these diseases. In this paper, using an ab initio method, we studied the interaction of Al-backbone ring structure with theπ-electron-rich sidechains of His, Phe, Trp, and Tyr. We found that in the absence of water, the Al-backbone ring can stably bind with those sidechains. In the presence of water, the Al-backbone ring can bind to the His sidechain and cannot bind to the other sidechains. As revealed by further investigations, this could be attributed to the fact that there was a coordinate bond of the Al-backbone ring with the His sidechain, while there were theπ-πstacking and cation-π-like interactions with the other sidechains. These findings potentially provide a molecular understanding of Al-related toxicity, and may be helpful in designing drugs for those aforementioned aluminum-linked diseases and encourage treatment of Al-polluted water.

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

    Energy Technology Data Exchange (ETDEWEB)

    Seydaliev, M.; Caswell, D., E-mail: marat.seydaliev@cnl.ca [Canadian Nuclear Laboratories, Chalk River, Ontario (Canada)

    2014-12-01

    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

  18. 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....

  19. Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture, and an integrated set of spectral analysis tools.

    Science.gov (United States)

    Monleón, Daniel; Colson, Kimberly; Moseley, Hunter N B; Anklin, Clemens; Oswald, Robert; Szyperski, Thomas; Montelione, Gaetano T

    2002-01-01

    Rapid data collection, spectral referencing, processing by time domain deconvolution, peak picking and editing, and assignment of NMR spectra are necessary components of any efficient integrated system for protein NMR structure analysis. We have developed a set of software tools designated AutoProc, AutoPeak, and AutoAssign, which function together with the data processing and peak-picking programs NMRPipe and Sparky, to provide an integrated software system for rapid analysis of protein backbone resonance assignments. In this paper we demonstrate that these tools, together with high-sensitivity triple resonance NMR cryoprobes for data collection and a Linux-based computer cluster architecture, can be combined to provide nearly complete backbone resonance assignments and secondary structures (based on chemical shift data) for a 59-residue protein in less than 30 hours of data collection and processing time. In this optimum case of a small protein providing excellent spectra, extensive backbone resonance assignments could also be obtained using less than 6 hours of data collection and processing time. These results demonstrate the feasibility of high throughput triple resonance NMR for determining resonance assignments and secondary structures of small proteins, and the potential for applying NMR in large scale structural proteomics projects.

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

    International Nuclear Information System (INIS)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    Marassi, Francesca M., E-mail: fmarassi@sbmri.org; Ding, Yi [Sanford-Burnham Medical Research Institute (United States); Schwieters, Charles D. [National Institutes of Health, Division of Computational Bioscience, Center for Information Technology (United States); Tian, Ye; Yao, Yong [Sanford-Burnham Medical Research Institute (United States)

    2015-09-15

    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.

  2. Free vibration analysis of a robotic fish based on a continuous and non-uniform flexible backbone with distributed masses

    Science.gov (United States)

    Coral, W.; Rossi, C.; Curet, O. M.

    2015-12-01

    This paper presents a Differential Quadrature Element Method for free transverse vibration of a robotic fish based on a continuous and non-uniform flexible backbone with distributed masses (fish ribs). The proposed method is based on the theory of a Timoshenko cantilever beam. The effects of the masses (number, magnitude and position) on the value of natural frequencies are investigated. Governing equations, compatibility and boundary conditions are formulated according to the Differential Quadrature rules. The convergence, efficiency and accuracy are compared to other analytical solution proposed in the literature. Moreover, the proposed method has been validate against the physical prototype of a flexible fish backbone. The main advantages of this method, compared to the exact solutions available in the literature are twofold: first, smaller computational cost and second, it allows analysing the free vibration in beams whose section is an arbitrary function, which is normally difficult or even impossible with other analytical methods.

  3. Dialkylaluminium-, -gallium-, and -indium-based poly-Lewis acids with a 1,8-diethynylanthracene backbone.

    Science.gov (United States)

    Chmiel, Jasmin; Neumann, Beate; Stammler, Hans-Georg; Mitzel, Norbert W

    2010-10-18

    Potential host systems based on a rigid 1,8-diethynylanthracendiyl backbone were synthesised by treatment of 1,8-diethynylanthracene with the Group 13 trialkyls AlMe(3), GaMe(3), InMe(3), AlEt(3) and GaEt(3). The resulting products were characterised by IR and multinuclear NMR spectroscopy, elemental analyses and determination of their crystal structures by X-ray diffraction. The compounds are dimeric in the solid state and comprise two M(2)C(2) heterocycles. Depending on the steric demand of the alkyl substituents at the metal atom, different types of binding modes were observed, which can be classified to lie between the ideals of side-on coordination with almost linear primary M-C≡C units and the 3c-2e coordination with symmetrically bridging alkynyl units in M-C-M bonds. As a solution in THF the dimers are broken into monomers and some are found to undergo ligand scrambling reactions. PMID:20827789

  4. Deformation of redox-active polymer gel based on polysiloxane backbone and bis(benzodithiolyl)bithienyl scaffold.

    Science.gov (United States)

    Ohtake, Toshihiro; Tanaka, Hideki; Matsumoto, Tetsuro; Ohta, Akira; Kimura, Mutsumi

    2014-12-01

    Redox-active polymer gels consisting of polysiloxane backbone and bis(benzodithiolyl)bithienyl units have been designed and synthesized. The bis(benzodithiolyl)bithienyl units, which undergo interconversion between cyclic form and opened dicationic form, have been incorporated into polysiloxane backbone via hydrosilylation of vinyl-terminated bis(benzodithiolyl)bithienyl derivative and poly(methylhydrosiloxane) (PMHS) or poly(dimethylsiloxane-co-hydrogenmethylsiloxane) (PDMS-co-PMHS), resulting in polymer gels cross-linked with bis(benzodithiolyl)bithienyl units. After the incorporation of M1 into polysiloxane backbone, these polymer gels (P1 and P2) also exhibit redox responses associated with the electrochemical interconversion of the bis(benzodithiolyl)bithienyl moieties. The polymer gels show swelling behavior upon chemical oxidization, and bending behavior has been observed for the polymer gel immobilized poly(vinylidene difluoride) (PVdF) film. These results provide a useful perspective for fabricating redox-triggered polymer gel actuators based on the conformational change of the functional molecular unit. PMID:25400032

  5. Structure Elucidation of Poly-Faldaprevir: Polymer Backbone Solved Using Solid-State and Solution Nuclear Magnetic Resonance Spectroscopy.

    Science.gov (United States)

    Gonnella, Nina C; Busacca, Carl A; Zhang, Li; Saha, Anjan; Wu, Jiang-Ping; Li, Guisheng; Davis, Mark; Offerdahl, Thomas; Jones, Paul-James; Herfurth, Lars; Reddig, Tim; Wagner, Klaus; Niemann, Michael; Werthmann, Ulrike; Grupe, Julia; Roos, Helmut; Reckzügel, Gaby; Ding, Andreas

    2016-06-01

    A large-scale synthesis of the hepatitis C virus drug Faldaprevir revealed precipitation of an unknown insoluble solid from methanol solutions of the drug substance. The unknown impurity was determined to be a polymer of Faldaprevir based on analytical methods that included size exclusion chromatography in combination with electrospray ionization mass spectrometry, solution nuclear magnetic resonance (NMR), matrix-assisted laser desorption ionization-time of flight, ultracentrifugation, elemental analysis, and sodium quantitation by atom absorption spectroscopy. Structure elucidation of the polymeric backbone was achieved using solid-state NMR cross-polarization/magic angle spinning (CP/MAS), cross polarization-polarization inversion, and heteronuclear correlation (HETCOR) experiments. The polymerization was found to occur at the vinyl cyclopropane via a likely free radical initiation mechanism. Full proton and carbon chemical shift assignments of the polymer were obtained using solution NMR spectroscopy. The polymer structure was corroborated with chemical synthesis of the polymer and solution NMR analysis. PMID:27238486

  6. Poly(meta-phenylene) Derivative with Rigid Twisted Biphenyl Units in Backbone: Synthesis, Structural Characterization,Photophysical Properties and Electroluminescence

    Institute of Scientific and Technical Information of China (English)

    ZHENG Yan; YANG Bing; ZHANG Hai-quan; LU Ping; SHEN Fang-zhong; LIU Lin-lin; XU Hai; YANG Guang-di; MA Yu-guang

    2007-01-01

    A soluble poly(meta-phenylene) derivative with rigid twisted biphenyl unit was synthesized by the Yamamoto coupling reaction. The polymer is soluble in common organic solvents, and the number-average molecular weight is about 6500. The UV-Vis and quantum chemical calculation indicate that the different conformation segments named "conformers" exist in the polymer backbones; it was also further confirmed by the single crystal X-ray diffraction study of the dimeric model compound. The π-π* transition of biphenyl segments of twisted and planar conformations made the polymer exhibit a strong absorption around 256 nm and a weak absorption at about 300 nm. Furthermore,the polymer exhibits a strong UV photoluminescence at 372 nm when the excitation wavelengths are longer than 300 nm. The ultraviolet-emitting electroluminescence(EL) device with the single layer structure shows EL λmax of the derivative at 370 nm.

  7. 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.

  8. Structure of the exceptionally large nonrepetitive carbohydrate backbone of the lipopolysaccharide of Pectinatus frisingensis strain VTT E-82164.

    Science.gov (United States)

    Vinogradov, Evgeny; Petersen, Bent O; Sadovskaya, Irina; Jabbouri, Said; Duus, Jens Ø; Helander, Ilkka M

    2003-07-01

    The structures of the oligosaccharides obtained after acetic acid hydrolysis and alkaline deacylation of the rough-type lipopolysaccharide (LPS) from Pectinatus frisingensis strain VTT E-82164 were analysed using NMR spectroscopy, MS and chemical methods. The LPS contains two major structural variants, differing by a decasaccharide fragment, and some minor variants lacking the terminal glucose residue. The largest structure of the carbohydrate backbone of the LPS that could be deduced from experimental results consists of 25 monosaccharides (including the previously found Ara4NP residue in lipid A) arranged in a well-defined nonrepetitive structure: We presume that the shorter variant with R1 = H represents the core-lipid A part of the LPS, and the additional fragment is present instead of the O-specific polysaccharide. Structures of this type have not been previously described. Analysis of the deacylation products obtained from the LPS of the smooth strain, VTT E-79100T, showed that it contains a very similar core but with one different glycosidic linkage.

  9. An improved algorithm for finding community structure in networks with an application to IPv6 backbone network

    Institute of Scientific and Technical Information of China (English)

    GUO Yingxin; XU Ke

    2007-01-01

    The discovery of community structure in a large number of complex networks has attracted lots of interest in recent years.One category of algorithms for detecting community structure,the divisive algorithms,has been proposed and improved impressively.In this paper,we propose an improved divisive algorithm,the basic idea of which is to take more than one parameters into consideration to describe the networks from different points of view.Although its basic idea appears to be a little simple,it is shown experimentally that it outperforms some other algorithms when it is applied to the networks with a relatively obscure community structure.We also demonstrate its effectiveness by applying it to IPv6 backbone network.The communities detected by our algorithm indicate that although underdeveloped compared with IPv4 network,IPv6 network has already exhibited a preliminary community structure.Moreover,our algorithm can be further extended and adapted in the future.In fact,it suggests a simple yet possibly efficient way to improve algorithms.

  10. 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

  11. 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...... amino acid residue by reductive amination. This can be used as a general approach for the introduction of other C-terminal modifications as well as functionalities, such as fluorophors. The second step is an acylation of a secondary amine, followed by standard Fmoc-based solid-phase synthesis...

  12. Orientation Preferences of Backbone Secondary Amide Functional Groups in Peptide Nucleic Acid Complexes: Quantum Chemical Calculations Reveal an Intrinsic Preference of Cationic D-Amino Acid-Based Chiral PNA Analogues for the P-form

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Jeremy C [ORNL; Topham, Christopher [University of Heidelberg

    2007-01-01

    Geometric descriptions of nonideal interresidue hydrogen bonding and backbone-base water bridging in the minor groove are established in terms of polyamide backbone carbonyl group orientation from analyses of residue junction conformers in experimentally determined peptide nucleic acid (PNA) complexes. Two types of interresidue hydrogen bonding are identified in PNA conformers in heteroduplexes with nucleic acids that adopt A-like base pair stacking. Quantum chemical calculations on the binding of a water molecule to an O2 base atom in glycine-based PNA thymine dimers indicate that junctions modeled with P-form backbone conformations are lower in energy than a dimer comprising the predominant conformation observed in A-like helices. It is further shown in model systems that PNA analogs based on D-lysine are better able to preorganize in a conformation exclusive to P-form helices than is glycine-based PNA. An intrinsic preference for this conformation is also exhibited by positively charged chiral PNA dimers carrying 3-amino-D-alanine or 4-aza-D-leucine residue units that provide for additional rigidity by side-chain hydrogen bonding to the backbone carbonyl oxygen. Structural modifications stabilizing P-form helices may obviate the need for large heterocycles to target DNA pyrimidine bases via PNADNA-PNA triplex formation. Quantum chemical modeling methods are used to propose candidate PNA Hoogsteen strand designs.

  13. Orientation preferences of backbone secondary amide functional groups in peptide nucleic acid complexes: quantum chemical calculations reveal an intrinsic preference of cationic D-amino acid-based chiral PNA analogues for the P-form.

    Science.gov (United States)

    Topham, Christopher M; Smith, Jeremy C

    2007-02-01

    Geometric descriptions of nonideal interresidue hydrogen bonding and backbone-base water bridging in the minor groove are established in terms of polyamide backbone carbonyl group orientation from analyses of residue junction conformers in experimentally determined peptide nucleic acid (PNA) complexes. Two types of interresidue hydrogen bonding are identified in PNA conformers in heteroduplexes with nucleic acids that adopt A-like basepair stacking. Quantum chemical calculations on the binding of a water molecule to an O2 base atom in glycine-based PNA thymine dimers indicate that junctions modeled with P-form backbone conformations are lower in energy than a dimer comprising the predominant conformation observed in A-like helices. It is further shown in model systems that PNA analogs based on D-lysine are better able to preorganize in a conformation exclusive to P-form helices than is glycine-based PNA. An intrinsic preference for this conformation is also exhibited by positively charged chiral PNA dimers carrying 3-amino-D-alanine or 4-aza-D-leucine residue units that provide for additional rigidity by side-chain hydrogen bonding to the backbone carbonyl oxygen. Structural modifications stabilizing P-form helices may obviate the need for large heterocycles to target DNA pyrimidine bases via PNA.DNA-PNA triplex formation. Quantum chemical modeling methods are used to propose candidate PNA Hoogsteen strand designs. PMID:17071666

  14. The structure of the carbohydrate backbone of the LPS from Shewanella spp. MR-4

    OpenAIRE

    Vinogradov, Evgeny; Kubler-Kielb, Joanna; Korenevsky, Anton

    2008-01-01

    The rough type lipopolysaccharide isolated from Shewanella spp. strain MR-4 was analyzed using NMR, mass spectroscopy and chemical methods. Two structural variants have been found, both contained 8-amino-3,8-dideoxy-d-manno-octulosonic acid and lacked l-glycero-d-manno-heptose. A minor variant of the LPS contained phosphoramide substituent.

  15. VIRTUAL BACKBONE CONTENT ROUTING IN WIRELESS AD-HOC NETWORK

    Directory of Open Access Journals (Sweden)

    Longxiang Gao

    2009-11-01

    Full Text Available We developed a new content routing based on the virtual backbone structure, which groups wireless nodes and contents into a virtual architecture. Our approach is scalable, works with local information,and does not rely on address information. The naming system uses flat naming to identify nodes and contents, and organizes these identifiers together. Backbone nodes can be selected automatically or predefined to direct their associated normal nodes in a local area. The normal nodes are guided by the backbone nodes to full fill the searching and routing processes. With a virtual structure, the searching performance can be improved by using the DHT technique.Experiments using ns2 simulator demonstrate that this virtual backbone routing architecture has the following significances: workable without being aware address in a mobile situation; scalable with the size of network; efficient in terms of the reduced hop counts and short end-to-end delay, and also resistant to the dead-end problem.

  16. 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.

  17. 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.

  18. 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

  19. 4-Oxalocrotonate tautomerase, a 41-kDa homohexamer: backbone and side-chain resonance assignments, solution secondary structure, and location of active site residues by heteronuclear NMR spectroscopy.

    OpenAIRE

    Stivers, J T; Abeygunawardana, C; Whitman, C. P.; Mildvan, A. S.

    1996-01-01

    4-Oxalocrotonate tautomerase (4-OT), a homohexamer consisting of 62 residues per subunit, catalyzes the isomerization of unsaturated alpha-keto acids using Pro-1 as a general base (Stivers et al., 1996a, 1996b). We report the backbone and side-chain 1H, 15N, and 13C NMR assignments and the solution secondary structure for 4-OT using 2D and 3D homonuclear and heteronuclear NMR methods. The subunit secondary structure consists of an alpha-helix (residues 13-30), two beta-strands (beta 1, residu...

  20. 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.

  1. Conotoxins containing nonnatural backbone spacers: cladistic-based design, chemical synthesis, and improved analgesic activity.

    Science.gov (United States)

    Green, Brad R; Catlin, Philip; Zhang, Min-Min; Fiedler, Brian; Bayudan, Wendi; Morrison, Alex; Norton, Raymond S; Smith, Brian J; Yoshikami, Doju; Olivera, Baldomero M; Bulaj, Grzegorz

    2007-04-01

    Disulfide-rich neurotoxins from venomous animals continue to provide compounds with therapeutic potential. Minimizing neurotoxins often results in removal of disulfide bridges or critical amino acids. To address this drug-design challenge, we explored the concept of disulfide-rich scaffolds consisting of isostere polymers and peptidic pharmacophores. Flexible spacers, such as amino-3-oxapentanoic or 6-aminohexanoic acids, were used to replace conformationally constrained parts of a three-disulfide-bridged conotoxin, SIIIA. The peptide-polymer hybrids, polytides, were designed based on cladistic identification of nonconserved loci in related peptides. After oxidative folding, the polytides appeared to be better inhibitors of sodium currents in dorsal root ganglia and sciatic nerves in mice. Moreover, the polytides appeared to be significantly more potent and longer-lasting analgesics in the inflammatory pain model in mice, when compared to SIIIA. The resulting polytides provide a promising strategy for transforming disulfide-rich peptides into therapeutics.

  2. A lysosome-targeted drug delivery system based on sorbitol backbone towards efficient cancer therapy.

    Science.gov (United States)

    Maniganda, Santhi; Sankar, Vandana; Nair, Jyothi B; Raghu, K G; Maiti, Kaustabh K

    2014-09-14

    A straightforward synthetic approach was adopted for the construction of a lysosome-targeted drug delivery system (TDDS) using sorbitol scaffold (Sor) linked to octa-guanidine and tetrapeptide GLPG, a peptide substrate of lysosomal cysteine protease, cathepsin B. The main objective was to efficiently deliver the potential anticancer drug, doxorubicin to the target sites, thereby minimizing dose-limiting toxicity. Three TDDS vectors were synthesized viz., DDS1: Sor-GLPG-Fl, DDS2: Sor-Fl (control) and DDS3: Sor-GLPGC-SMCC-Dox. Dox release from DDS3 in the presence of cathepsin B was studied by kinetics measurement based on the fluorescent property of Dox. The cytotoxicity of DDS1 was assessed and found to be non-toxic. Cellular internalization and colocalization studies of all the 3 systems were carried out by flow cytometry and confocal microscopy utilizing cathepsin B-expressing HeLa cells. DDS1 and DDS3 revealed significant localization within the lysosomes, in contrast to DDS2 (control). The doxorubicin-conjugated carrier, DDS3, demonstrated significant cytotoxic effect when compared to free Dox by MTT assay and also by flow cytometric analysis. The targeted approach with DDS3 is expected to be promising, because it is indicated to be advantageous over free Dox, which possesses dose-limiting toxicity, posing risk of injury to normal tissues.

  3. Root-mean-square-deviation-based rapid backbone resonance assignments in proteins.

    Science.gov (United States)

    Rout, Ashok K; Barnwal, Ravi P; Agarwal, Geetika; Chary, Kandala V R

    2010-10-01

    We have shown that the methodology based on the estimation of root-mean-square deviation (RMSD) between two sets of chemical shifts is very useful to rapidly assign the spectral signatures of (1)H(N), (13)C(α), (13)C(β), (13)C', (1)H(α) and (15)N spins of a given protein in one state from the knowledge of its resonance assignments in a different state, without resorting to routine established procedures (manual and automated). We demonstrate the utility of this methodology to rapidly assign the 3D spectra of a metal-binding protein in its holo-state from the knowledge of its assignments in apo-state, the spectra of a protein in its paramagnetic state from the knowledge of its assignments in diamagnetic state and, finally, the spectra of a mutant protein from the knowledge of the chemical shifts of the corresponding wild-type protein. The underlying assumption of this methodology is that, it is impossible for any two amino acid residues in a given protein to have all the six chemical shifts degenerate and that the protein under consideration does not undergo large conformational changes in going from one conformational state to another. The methodology has been tested using experimental data on three proteins, M-crystallin (8.5 kDa, predominantly β-sheet, for apo- to holo-state), Calbindin (7.5 kDa, predominantly α-helical, for diamagnetic to paramagnetic state and apo to holo) and EhCaBP1 (14.3 kDa, α-helical, the wild-type protein with one of its mutant). In all the cases, the extent of assignment is found to be greater than 85%.

  4. 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). PMID:22447100

  5. 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.

  6. Backbone colorings for graphs: Tree and path backbones

    NARCIS (Netherlands)

    Broersma, Hajo; Fomin, Fedor V.; Golovach, Petr A.; Woeginger, Gerhard J.

    2007-01-01

    We introduce and study backbone colorings, a variation on classical vertex colorings: Given a graph $G = (V,E)$ and a spanning subgraph $H$ of $G$ (the backbone of $G$), a backbone coloring for $G$ and $H$ is a proper vertex coloring $V \\to {1,2,\\ldots}$ of $G$ in which the colors assigned to adjace

  7. Backbone colorings for networks: tree and path backbones

    NARCIS (Netherlands)

    Broersma, H.J.; Fomin, F.V.; Golovach, P.A.; Woeginger, G.J.

    2003-01-01

    We introduce and study backbone colorings, a variation on classical vertex colorings: Given a graph $G=(V,E)$ and a spanning subgraph $H$ of $G$ (the backbone of $G$), a backbone coloring for $G$ and $H$ is a proper vertex coloring $V\\rightarrow \\{1,2,\\ldots\\}$ of $G$ in which the colors assigned to

  8. General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Qing; Shi, Chaowei [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Yu, Lu [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui, 230031 (China); Zhang, Longhua [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Xiong, Ying, E-mail: yxiong73@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Tian, Changlin, E-mail: cltian@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui, 230031 (China)

    2015-02-13

    Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of {sup 15}N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S{sup 2}) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in a defined hydrated box at neutral pH were conducted and the general order parameters (S{sup 2}) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S{sup 2} values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S{sup 2} parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S{sup 2} calculated from the experimental NMR relaxation measurements, in a site-specific manner. - Highlights: • Correlation analysis between NMR relaxation measurements and MD simulations. • General order parameter (S{sup 2}) as common reference between the two methods. • Different protein dynamics with different Histidine charge states in neutral pH. • Different protein dynamics with different water models.

  9. ``Pinning strategy": a novel approach for predicting the backbone structure in terms of protein blocks from sequence

    Indian Academy of Sciences (India)

    A G De Brevern; C Etchebest; C Benros; S Hazout

    2007-01-01

    The description of protein 3D structures can be performed through a library of 3D fragments, named a structural alphabet. Our structural alphabet is composed of 16 small protein fragments of 5 C in length, called protein blocks (PBs). It allows an efficient approximation of the 3D protein structures and a correct prediction of the local structure. The 72 most frequent series of 5 consecutive PBs, called structural words (SWs) are able to cover more than 90% of the 3D structures. PBs are highly conditioned by the presence of a limited number of transitions between them. In this study, we propose a new method called “pinning strategy” that used this specific feature to predict long protein fragments. Its goal is to define highly probable successions of PBs. It starts from the most probable SW and is then extended with overlapping SWs. Starting from an initial prediction rate of 34.4%, the use of the SWs instead of the PBs allows a gain of 4.5%. The pinning strategy simply applied to the SWs increases the prediction accuracy to 39.9%. In a second step, the sequence-structure relationship is optimized, the prediction accuracy reaches 43.6%.

  10. Backbone colorings along perfect matchings

    NARCIS (Netherlands)

    Broersma, H.J.; Fujisawa, J.; Yoshimoto, K.

    2003-01-01

    Given a graph $G=(V,E)$ and a spanning subgraph $H$ of $G$ (the backbone of $G$), a backbone coloring for $G$ and $H$ is a proper vertex coloring $V\\rightarrow \\{1,2,\\ldots\\}$ of $G$ in which the colors assigned to adjacent vertices in $H$ differ by at least two. In a recent paper, backbone coloring

  11. 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.

  12. Structural insights into the evolution of a sexy protein: novel topology and restricted backbone flexibility in a hypervariable pheromone from the red-legged salamander, Plethodon shermani.

    Science.gov (United States)

    Wilburn, Damien B; Bowen, Kathleen E; Doty, Kari A; Arumugam, Sengodagounder; Lane, Andrew N; Feldhoff, Pamela W; Feldhoff, Richard C

    2014-01-01

    In response to pervasive sexual selection, protein sex pheromones often display rapid mutation and accelerated evolution of corresponding gene sequences. For proteins, the general dogma is that structure is maintained even as sequence or function may rapidly change. This phenomenon is well exemplified by the three-finger protein (TFP) superfamily: a diverse class of vertebrate proteins co-opted for many biological functions - such as components of snake venoms, regulators of the complement system, and coordinators of amphibian limb regeneration. All of the >200 structurally characterized TFPs adopt the namesake "three-finger" topology. In male red-legged salamanders, the TFP pheromone Plethodontid Modulating Factor (PMF) is a hypervariable protein such that, through extensive gene duplication and pervasive sexual selection, individual male salamanders express more than 30 unique isoforms. However, it remained unclear how this accelerated evolution affected the protein structure of PMF. Using LC/MS-MS and multidimensional NMR, we report the 3D structure of the most abundant PMF isoform, PMF-G. The high resolution structural ensemble revealed a highly modified TFP structure, including a unique disulfide bonding pattern and loss of secondary structure, that define a novel protein topology with greater backbone flexibility in the third peptide finger. Sequence comparison, models of molecular evolution, and homology modeling together support that this flexible third finger is the most rapidly evolving segment of PMF. Combined with PMF sequence hypervariability, this structural flexibility may enhance the plasticity of PMF as a chemical signal by permitting potentially thousands of structural conformers. We propose that the flexible third finger plays a critical role in PMF:receptor interactions. As female receptors co-evolve, this flexibility may allow PMF to still bind its receptor(s) without the immediate need for complementary mutations. Consequently, this unique

  13. Structural insights into the evolution of a sexy protein: novel topology and restricted backbone flexibility in a hypervariable pheromone from the red-legged salamander, Plethodon shermani.

    Directory of Open Access Journals (Sweden)

    Damien B Wilburn

    Full Text Available In response to pervasive sexual selection, protein sex pheromones often display rapid mutation and accelerated evolution of corresponding gene sequences. For proteins, the general dogma is that structure is maintained even as sequence or function may rapidly change. This phenomenon is well exemplified by the three-finger protein (TFP superfamily: a diverse class of vertebrate proteins co-opted for many biological functions - such as components of snake venoms, regulators of the complement system, and coordinators of amphibian limb regeneration. All of the >200 structurally characterized TFPs adopt the namesake "three-finger" topology. In male red-legged salamanders, the TFP pheromone Plethodontid Modulating Factor (PMF is a hypervariable protein such that, through extensive gene duplication and pervasive sexual selection, individual male salamanders express more than 30 unique isoforms. However, it remained unclear how this accelerated evolution affected the protein structure of PMF. Using LC/MS-MS and multidimensional NMR, we report the 3D structure of the most abundant PMF isoform, PMF-G. The high resolution structural ensemble revealed a highly modified TFP structure, including a unique disulfide bonding pattern and loss of secondary structure, that define a novel protein topology with greater backbone flexibility in the third peptide finger. Sequence comparison, models of molecular evolution, and homology modeling together support that this flexible third finger is the most rapidly evolving segment of PMF. Combined with PMF sequence hypervariability, this structural flexibility may enhance the plasticity of PMF as a chemical signal by permitting potentially thousands of structural conformers. We propose that the flexible third finger plays a critical role in PMF:receptor interactions. As female receptors co-evolve, this flexibility may allow PMF to still bind its receptor(s without the immediate need for complementary mutations. Consequently

  14. Orientation Preferences of Backbone Secondary Amide Functional Groups in Peptide Nucleic Acid Complexes: Quantum Chemical Calculations Reveal an Intrinsic Preference of Cationic D-Amino Acid-Based Chiral PNA Analogues for the P-form

    OpenAIRE

    Topham, Christopher M.; Smith, Jeremy C.

    2006-01-01

    Geometric descriptions of nonideal interresidue hydrogen bonding and backbone-base water bridging in the minor groove are established in terms of polyamide backbone carbonyl group orientation from analyses of residue junction conformers in experimentally determined peptide nucleic acid (PNA) complexes. Two types of interresidue hydrogen bonding are identified in PNA conformers in heteroduplexes with nucleic acids that adopt A-like basepair stacking. Quantum chemical calculations on the bindin...

  15. Phase behaviour of two-component bottle-brush polymers with flexible backbones under poor solvent conditions

    International Nuclear Information System (INIS)

    The phase behaviour of two-component bottle-brush polymers with fully flexible backbones under poor solvent conditions is studied via molecular-dynamics simulations, using a coarse-grained bead-spring model and side chains of up to N = 40 effective monomers. We consider a symmetric model where side chains of type A and B are grafted alternately onto a flexible backbone. The aim of this study is to explore the phase behaviour of two-component bottle-brushes depending on parameters, such as as the grafting density σ, the backbone length Nb, the side-chain length N, and the temperature T. Based on a cluster analysis, we identify for our range of parameters the regimes of fully phase separated systems, i.e., A-type side chains form one cluster and B-type chains another, while the interface that separates these two clusters contains the backbone monomers. We find that pearl-necklace or Janus-like structures, which normally occur for bottle-brush polymers with rigid backbones under poor solvent conditions, are fully attributed to the backbone rigidity, and, therefore, such structures are unlikely in the case of bottle brushes with fully flexible backbones. Also, a comparative discussion with earlier work on the phase behaviour of single-component bottle-brush polymers with flexible backbones is performed. (paper)

  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. 2D IR Spectroscopy of Histidine: Probing Side-Chain Structure and Dynamics via Backbone Amide Vibrations

    OpenAIRE

    Ghosh, Ayanjeet; Tucker, Matthew J.; Gai, Feng

    2014-01-01

    It is well known that histidine is involved in many biological functions due to the structural versatility of its side chain. However, probing the conformational transitions of histidine in proteins, especially those occurring on an ultrafast time scale, is difficult. Herein we show, using a histidine dipeptide as a model, that it is possible to probe the tautomer and protonation status of a histidine residue by measuring the two-dimensional infrared (2D IR) spectrum of its amide I vibrationa...

  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. Influence of Backbone Structure on Properties of Directly Polymerized Phenoxy Resins from Epichlorohydrin and Various Aromatic Dihydric Phenols Monomers

    Institute of Scientific and Technical Information of China (English)

    CAI Hong-li; BI Da-wu; SHAO Ke; ZHONG Shuang-ling; NA Hui

    2007-01-01

    A series of phenoxy resins was directly prepared through the polymerization of each of the various aromatic dihydric phenols and epichlorohydrin. FTIR and 1H NMR spectra were recorded to characterize the structures of the resins. The GPC curves were used to determine the molecular weight distribution. In addition, the thermal properties of the resins were studied with differential scanning calorimetry ( DSC ) and thermal gravimetric analysis (TGA). The thermal stabilities of the polymers increased with the content of the benzene ring, pendant group increasing or biphe nyl groups emerging. The adhesive properties of the polymers were evaluated in terms of the lap shear strength with Fe-Fe adherends. The fracture mechanisms were determined by SEM observation and it was found that there was an important participation of cohesive fracture mechanisms. Also, it has been demonstrated that the extension of these micro-cohesive mechanisms is directly correlated with the adhesive strength. According to these results, the phenoxy resin containing biphenyl groups presented a higher adhesive strength and could improve the adhesive property of the epoxy/phenoxy system to a certain extent.

  20. 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

    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......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...... backbone. All prepared electrodes were characterized as symmetric cells using impedance spectroscopy. Within the investigated series the infiltrate with x = 0.1 (STF10) showed the best performance with an area specific resistance (ASR) of ASR ≈ 6.4 Ω cm2 (STF10) at 600°C in air. The relatively poor...

  1. Backbone analysis and algorithm design for the quadratic assignment problem

    Institute of Scientific and Technical Information of China (English)

    JIANG He; ZHANG XianChao; CHEN GuoLiang; LI MingChu

    2008-01-01

    As the hot line in NP-hard problems research in recent years, backbone analysis is crucial for phase transition, hardness, and algorithm design. Whereas theoretical analysis of backbone and its applications in algorithm design are still at a begin-ning state yet, this paper took the quadratic assignment problem (QAP) as a case study and proved by theoretical analysis that it is NP-hard to find the backbone, l.e., no algorithm exists to obtain the backbone of a QAP in polynomial time. Results of this paper showed that it is reasonable to acquire approximate backbone by inter-section of local optimal solutions. Furthermore, with the method of constructing biased instances, this paper proposed a new meta-heuristic - biased instance based approximate backbone (BI-AB), whose basic idea is as follows: firstly, con-struct a new biased instance for every QAP instance (the optimal solution of the new instance is also optimal for the original one); secondly, the approximate backbone is obtained by intersection of multiple local optimal solutions computed by some existing algorithm; finally, search for the optimal solutions in the reduced space by fixing the approximate backbone. Work of the paper enhanced the re-search area of theoretical analysis of backbone. The meta-heuristic proposed in this paper provided a new way for general algorithm design of NP-hard problems as well.

  2. SYNTHESIS AND CHARACTERIZATION OF A NEW COMBLIKE POLYMER BASED ON POLY (VINYL METHYL ETHER-ALT-MALEIC ANHYDRIDE) BACKBONE

    Institute of Scientific and Technical Information of China (English)

    DING Liming; LIN Yunqing; ZHOU Zinan; NI Jianlong; CHEN Donglin

    1995-01-01

    A new comblike polymer host for polymer electrolyte was synthesized by reacting monomethyl ether of poly(ethylene glycol) with poly(vinyl methyl ether-alt-maleic anhydride) and endcapping the residual carboxylic acid with methanol. Butanone was selected as a solvent for the esterification in order to obtain a completely soluble product. The synthesis process was traced through by IR. Compared with the model compounds, the presumed structure of this comblike polymer has been proved to be valid by 13C NMR. The comb polymer is a white rubbery solid. It can be dissolved in butanone and THF, and manifests good film forming ability.

  3. Diketene-based neat four-component synthesis of the dihydropyrimidinones and dihydropyridine backbones using silica sulfuric acid (SSA)

    Institute of Scientific and Technical Information of China (English)

    Sadegh Rostamnia; Kamran Lamei

    2012-01-01

    Heterocyclic skeleton building blocks to afford dihydropyrimidinones and dihydropyridines based on neat adducts of diketene,alcohols and aldehydes via silica sulfuric acid (SSA) catalyzed ring opening of diketene in four-c6mponent Biginelli-type and Hantzsch-type reactions are presented.

  4. EFFICIENT WHITE EMITTING COPOLYMERS BASED ON BIPOLAR FLUORENE-co-DIBENZOTHIOPHENE-S,S-DIOXIDE-co-CARBAZOLE BACKBONE

    Institute of Scientific and Technical Information of China (English)

    Lei Ying; Yan-hu Li; Cai-hong Wei; Min-quan Wang; Wei Yang; Hong-bin Wu; Yong Cao

    2013-01-01

    Efficient white light emitting polymers were synthesized based on poly(9,9-dioctylfluorene-co-dibenzothiopheneS,S-dioxide) as blue emitter and a bisphenylamine functionalized 2,1,3-benzothiadiazole (DPABT) as red emitter.It was found that the incorporation of hole-transporting carbazole moiety into polymer main chain could effectively reduce the hole injection barriers,which can lead to distinctly improved charge balance in the emissive layer.Additionally,the holetransporting carbazole units may form efficient bipolar host with electron-transporting dibenzothiophene-S,S-dioxide units.The white light emitting diodes based on single polymer PFSOCzDPABT showed the maximum luminous efficiency of 3.3 cd/A with the maximum luminance of 10282 cd/m2,and the luminous efficiency showed only 24% roll off at current density of 400 mA/cm2.These Commission Intemationale d'Enclairage (CIE) coordinates of the devices changed slightly with the driving voltages increasing from 8 V to 12 V,and were very close to National Television System Committee (NTSC) standard white light emission of (0.33,0.33).The results indicated that the incorporating bipolar host and low band gap DPABT unit was a promising way to achieve efficient single white light emitting copolymers.

  5. Grid-based backbone correction to the ff12SB protein force field for implicit-solvent simulations.

    Science.gov (United States)

    Perez, Alberto; MacCallum, Justin L; Brini, Emiliano; Simmerling, Carlos; Dill, Ken A

    2015-10-13

    Force fields, such as Amber's ff12SB, can be fairly accurate models of the physical forces in proteins and other biomolecules. When coupled with accurate solvation models, force fields are able to bring insight into the conformational preferences, transitions, pathways, and free energies for these biomolecules. When computational speed/cost matters, implicit solvent is often used but at the cost of accuracy. We present an empirical grid-like correction term, in the spirit of cMAPs, to the combination of the ff12SB protein force field and the GBneck2 implicit-solvent model. Ff12SB-cMAP is parametrized on experimental helicity data. We provide validation on a set of peptides and proteins. Ff12SB-cMAP successfully improves the secondary structure biases observed in ff12SB + Gbneck2. Ff12SB-cMAP can be downloaded ( https://github.com/laufercenter/Amap.git ) and used within the Amber package. It can improve the agreement of force fields + implicit solvent with experiments. PMID:26574266

  6. 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. PMID:23777175

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

    OpenAIRE

    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.

    2014-01-01

    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 mark...

  8. 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

  9. 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

  10. Detection of closed influenza virus hemagglutinin fusion peptide structures in membranes by backbone {sup 13}CO-{sup 15}N rotational-echo double-resonance solid-state NMR

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Ujjayini; Xie Li; Weliky, David P., E-mail: weliky@chemistry.msu.edu [Michigan State University, Department of Chemistry (United States)

    2013-02-15

    The influenza virus fusion peptide is the N-terminal {approx}20 residues of the HA2 subunit of the hemagglutinin protein and this peptide plays a key role in the fusion of the viral and endosomal membranes during initial infection of a cell. The fusion peptide adopts N-helix/turn/C-helix structure in both detergent and membranes with reports of both open and closed interhelical topologies. In the present study, backbone {sup 13}CO-{sup 15}N REDOR solid-state NMR was applied to the membrane-associated fusion peptide to detect the distribution of interhelical distances. The data clearly showed a large fraction of closed and semi-closed topologies and were best-fitted to a mixture of two structures that do not exchange. One of the earlier open structural models may have incorrect G13 dihedral angles derived from TALOS analysis of experimentally correct {sup 13}C shifts.

  11. Peptoid-Peptide hybrid backbone architectures

    DEFF Research Database (Denmark)

    Olsen, Christian Adam

    2010-01-01

    -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......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...

  12. ANSS Backbone Station Quality Assessment

    Science.gov (United States)

    Leeds, A.; McNamara, D.; Benz, H.; Gee, L.

    2006-12-01

    In this study we assess the ambient noise levels of the broadband seismic stations within the United States Geological Survey's (USGS) Advanced National Seismic System (ANSS) backbone network. The backbone consists of stations operated by the USGS as well as several regional network stations operated by universities. We also assess the improved detection capability of the network due to the installation of 13 additional backbone stations and the upgrade of 26 existing stations funded by the Earthscope initiative. This assessment makes use of probability density functions (PDF) of power spectral densities (PSD) (after McNamara and Buland, 2004) computed by a continuous noise monitoring system developed by the USGS- ANSS and the Incorporated Research Institutions in Seismology (IRIS) Data Management Center (DMC). We compute the median and mode of the PDF distribution and rank the stations relative to the Peterson Low noise model (LNM) (Peterson, 1993) for 11 different period bands. The power of the method lies in the fact that there is no need to screen the data for system transients, earthquakes or general data artifacts since they map into a background probability level. Previous studies have shown that most regional stations, instrumented with short period or extended short period instruments, have a higher noise level in all period bands while stations in the US network have lower noise levels at short periods (0.0625-8.0 seconds), high frequencies (8.0- 0.125Hz). The overall network is evaluated with respect to accomplishing the design goals set for the USArray/ANSS backbone project which were intended to increase broadband performance for the national monitoring network.

  13. 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

    Continuous scaling down of critical dimensions in interconnect structures requires the use of ultralow dielectric constant (k) films as interlayer dielectrics to reduce resistance-capacitance delays. Porous carbon-doped silicon oxide (p-SiCOH) dielectrics have been the leading approach to produce these ultralow-k materials. However, embedding of porosity into dielectric layer necessarily decreases the mechanical reliability and increases its susceptibility to adsorption of potentially deleterious chemical species during device fabrication process. Among those, exposure of porous-SiCOH low-k (PLK) dielectrics to oxidizing plasma environment causes the increase in dielectric constant and their vulnerability to mechanical instability of PLKs due to the loss of methyl species and increase in moisture uptake. These changes in PLK properties and physical stability have been persisting challenges for next-generation interconnects because they are the sources of failure in interconnect integration as well as functional and physical failures appearing later in IC device manufacturing. It is therefore essential to study the fundamentals of the interactions on p-SiCOH matrix induced by plasma exposure and find an effective and easy-to-implement way to reverse such changes by repairing damage in PLK structure. From these perspectives, the present dissertation proposes 1) a fundamental understanding of structural transformation occurring during oxidative plasma exposure in PLK matrix structure and 2) its restoration by using silylating treatment, soft x-ray and inert Ar-plasma radiation, respectively. Equally important, 3) as an alternative way of increasing the thermo-mechanical reliability, PLK dielectric film with an intrinsically robust structure by controlling pore morphology is fabricated and investigated. Based on the investigations, stability of PLK films studied by time-dependent ball indentation tester under the elevated temperature, variation in film thickness and

  14. Hash: a program to accurately predict protein H{sup {alpha}} shifts from neighboring backbone shifts

    Energy Technology Data Exchange (ETDEWEB)

    Zeng Jianyang, E-mail: zengjy@gmail.com [Tsinghua University, Institute for Interdisciplinary Information Sciences (China); Zhou Pei [Duke University Medical Center, Department of Biochemistry (United States); Donald, Bruce Randall [Duke University, Department of Computer Science (United States)

    2013-01-15

    Chemical shifts provide not only peak identities for analyzing nuclear magnetic resonance (NMR) data, but also an important source of conformational information for studying protein structures. Current structural studies requiring H{sup {alpha}} chemical shifts suffer from the following limitations. (1) For large proteins, the H{sup {alpha}} chemical shifts can be difficult to assign using conventional NMR triple-resonance experiments, mainly due to the fast transverse relaxation rate of C{sup {alpha}} that restricts the signal sensitivity. (2) Previous chemical shift prediction approaches either require homologous models with high sequence similarity or rely heavily on accurate backbone and side-chain structural coordinates. When neither sequence homologues nor structural coordinates are available, we must resort to other information to predict H{sup {alpha}} chemical shifts. Predicting accurate H{sup {alpha}} chemical shifts using other obtainable information, such as the chemical shifts of nearby backbone atoms (i.e., adjacent atoms in the sequence), can remedy the above dilemmas, and hence advance NMR-based structural studies of proteins. By specifically exploiting the dependencies on chemical shifts of nearby backbone atoms, we propose a novel machine learning algorithm, called Hash, to predict H{sup {alpha}} chemical shifts. Hash combines a new fragment-based chemical shift search approach with a non-parametric regression model, called the generalized additive model, to effectively solve the prediction problem. We demonstrate that the chemical shifts of nearby backbone atoms provide a reliable source of information for predicting accurate H{sup {alpha}} chemical shifts. Our testing results on different possible combinations of input data indicate that Hash has a wide rage of potential NMR applications in structural and biological studies of proteins.

  15. Tuning backbones and side-chains of cationic conjugated polymers for optical signal amplification of fluorescent DNA detection.

    Science.gov (United States)

    Huang, Yan-Qin; Liu, Xing-Fen; Fan, Qu-Li; Wang, Lihua; Song, Shiping; Wang, Lian-Hui; Fan, Chunhai; Huang, Wei

    2009-06-15

    Three cationic conjugated polymers (CCPs) exhibiting different backbone geometries and charge densities were used to investigate how their conjugated backbone and side chain properties, together with the transitions of DNA amphiphilic properties, interplay in the CCP/DNA-C* (DNA-C*: fluorophore-labeled DNA) complexes to influence the optical signal amplification of fluorescent DNA detection based on Förster resonance energy transfer (FRET). By examining the FRET efficiencies to dsDNA-C* (dsDNA: double-stranded DNA) and ssDNA-C* (ssDNA: single-stranded DNA) for each CCP, twisted conjugated backbones and higher charge densities were proved to facilitate electrostatic attraction in CCP/dsDNA-C* complexes, and induced improved sensitivity to DNA hybridization. Especially, by using the CCP with twisted conjugated backbone and the highest charge density, a more than 7-fold higher efficiency of FRET to dsDNA-C* was found than to ssDNA-C*, indicating a high signal amplification for discriminating between dsDNA and ssDNA. By contrast, linear conjugated backbones and lower charge density were demonstrated to favor hydrophobic interactions in CCP/ssDNA-C* complexes. These findings provided guidelines for the design of novel sensitive CCP, which can be useful to recognize many other important DNA activities involving transitions of DNA amphiphilic properties like DNA hybridization, such as specific DNA binding with ions, some secondary or tertiary structural changes of DNA, and so forth.

  16. Future High Capacity Backbone Networks

    DEFF Research Database (Denmark)

    Wang, Jiayuan

    This thesis - Future High Capacity Backbone Networks - deals with the energy efficiency problems associated with the development of future optical networks. In the first half of the thesis, novel approaches for using multiple/single alternative energy sources for improving energy efficiency...... is studied in details with dynamic network simulations using OPNET. Dynamic routing optimization methods are proposed. The influences of re-routing and load-balancing factors on the algorithm are evaluated with a focus on different re-routing thresholds. Results from dynamic network simulations show that re...... aiming for reducing the dynamic part of the energy consumption of the network may increase the fixed part of the energy consumption meanwhile. In the second half of the thesis, the conflict between energy efficiency and Quality of Service (QoS) is addressed by introducing a novel software defined...

  17. 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. PMID:26976137

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

    Science.gov (United States)

    Voortman, Thomas P; Chiechi, Ryan C

    2015-12-30

    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 hydrophobic-hydrophobic, form smooth, structured, homogeneous films from water (ionic) or tetrahydrofuran (hydrophobic). Mismatched conjugated polymers, by contrast, form inhomogeneous films with rough topologies. The polymers with ionic backbone chains are conjugated polyions (conjugated polymers with closed-shell charges in the backbone), which are semiconducting materials with tunable bad-gaps, not unlike uncharged conjugated polymers.

  19. 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

  20. Orientational constraints as three-dimensional structural constraints from chemical shift anisotropy: the polypeptide backbone of gramicidin A in a lipid bilayer.

    OpenAIRE

    Mai, W.; Hu, W; Wang, C; Cross, T A

    1993-01-01

    Chemical shifts observed from samples that are uniformly aligned with respect to the magnetic field can be used as very high-resolution structural constraints. This constraint takes the form of an orientational constraint rather than the more familiar distance constraint. The accuracy of these constraints is dependent upon the quality of the tensor characterization. Both tensor element magnitudes and tensor orientations with respect to the molecular frame need to be considered. Here these con...

  1. 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.

  2. Free backbone carbonyls mediate rhodopsin activation.

    Science.gov (United States)

    Kimata, Naoki; Pope, Andreyah; Sanchez-Reyes, Omar B; Eilers, Markus; Opefi, Chikwado A; Ziliox, Martine; Reeves, Philip J; Smith, Steven O

    2016-08-01

    Conserved prolines in the transmembrane helices of G-protein-coupled receptors (GPCRs) are often considered to function as hinges that divide the helix into two segments capable of independent motion. Depending on their potential to hydrogen-bond, the free C=O groups associated with these prolines can facilitate conformational flexibility, conformational switching or stabilization of the receptor structure. To address the role of conserved prolines in family A GPCRs through solid-state NMR spectroscopy, we focus on bovine rhodopsin, a GPCR in the visual receptor subfamily. The free backbone C=O groups on helices H5 and H7 stabilize the inactive rhodopsin structure through hydrogen-bonds to residues on adjacent helices. In response to light-induced isomerization of the retinal chromophore, hydrogen-bonding interactions involving these C=O groups are released, thus facilitating repacking of H5 and H7 onto the transmembrane core of the receptor. These results provide insights into the multiple structural and functional roles of prolines in membrane proteins. PMID:27376589

  3. Variation of protein backbone amide resonance by electrostatic field

    OpenAIRE

    Sharley, John N.

    2015-01-01

    Amide resonance is found to be sensitive to electrostatic field with component parallel or antiparallel the amide C-N bond. This effect is linear and without threshold in the biologically plausible electrostatic field range -0.005 to 0.005 au. Variation of amide resonance varies Resonance-Assisted Hydrogen Bonding such as occurs in the hydrogen bonded chains of backbone amides of protein secondary structures such as beta sheet and alpha helix, varying the stability of the secondary structure....

  4. Research on the Interconnection Structures and Routing Policies of Operators’ Internet Backbone Network and Metropolitan Area Network%运营商互联网骨干网与城域网互联结构及策略研究

    Institute of Scientific and Technical Information of China (English)

    王泽林; 谢梦楠

    2015-01-01

    众所周知,运营商互联网网络结构和路由策略可以决定网络流量的走向,影响运营商的建网成本和网络运维效率,甚至影响用户体验。分析骨干网与城域网互联的典型结构,选出合理的互联方式;基于优选的网络互联结构,分析路由策略的可行性,研究同一互联结构下不同路由策略的优缺点,为运营商互联网的构建、路由策略的制定以及网络的演进提供指导。%It is wel-know that the network structures and routing policies of operators’networks determine the flow direction,affect the cost of network construction and efficiency of maintenance,and even influence subscriber experience. It analyzes the typical structures of the interconnection between backbone network and metropolitan area networks,and selects the most reasonable way of those topologies. In terms of the selective interconnection structure,it researches the feasibilities and the pros and cons of routing policies,thereby providing guidance for the routing strategies,the construction and evolution of the carriers’net-works.

  5. 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.

  6. Computation-Guided Backbone Grafting of a Discontinuous Motif onto a Protein Scaffold

    Energy Technology Data Exchange (ETDEWEB)

    Azoitei, Mihai L.; Correia, Bruno E.; Ban, Yih-En Andrew; Carrico, Chris; Kalyuzhniy, Oleksandr; Chen, Lei; Schroeter, Alexandria; Huang, Po-Ssu; McLellan, Jason S.; Kwong, Peter D.; Baker, David; Strong, Roland K.; Schief, William R. (UWASH); (FHCRC); (NIAID)

    2012-02-07

    The manipulation of protein backbone structure to control interaction and function is a challenge for protein engineering. We integrated computational design with experimental selection for grafting the backbone and side chains of a two-segment HIV gp120 epitope, targeted by the cross-neutralizing antibody b12, onto an unrelated scaffold protein. The final scaffolds bound b12 with high specificity and with affinity similar to that of gp120, and crystallographic analysis of a scaffold bound to b12 revealed high structural mimicry of the gp120-b12 complex structure. The method can be generalized to design other functional proteins through backbone grafting.

  7. Backbone and sidechain 1H, 15N and 13C assignments of Tyrosine Phosphatase related to Biofilm formation A (TpbA) of Pseudomonas aeruginosa

    OpenAIRE

    Koveal, Dorothy; Jayasundera, Thusitha B.; Wood, Thomas K.; Peti, Wolfgang; Page, Rebecca

    2012-01-01

    The backbone and side chain resonance assignments of the Tyrosine Phosphatase related to Biofilm formation A (TpbA) of Pseudomonas aeruginosa have been determined based on triple-resonance experiments using uniformly [13C,15N]-labeled protein. This assignment is the first step towards the determination of the 3-dimensional structure of TpbA.

  8. Exercise: The Backbone of Spine Treatment

    Science.gov (United States)

    Exercise: The Backbone of Spine Treatment | View Video Back Purchase Video Struggling with Low Back Pain? Many people are surprised to learn that carefully selected exercise can actually reduce back pain. Some exercises can ...

  9. Exercise: The Backbone of Spine Treatment

    Medline Plus

    Full Text Available Exercise: The Backbone of Spine Treatment | View Video Back Purchase Video Struggling with Low Back Pain? Many people are surprised to learn that carefully selected exercise can actually reduce back pain. Some exercises can ...

  10. Exercise: The Backbone of Spine Treatment

    Medline Plus

    Full Text Available Exercise: The Backbone of Spine Treatment | View Video Back Purchase Video Struggling with Low Back Pain? Many people are surprised to learn that carefully selected exercise can ...

  11. Protein-Backbone Thermodynamics across the Membrane Interface.

    Science.gov (United States)

    Bereau, Tristan; Kremer, Kurt

    2016-07-01

    The thermodynamics of insertion of a protein in a membrane depends on the fine interplay between backbone and side-chain contributions interacting with the lipid environment. Using computer simulations, we probe how different descriptions of the backbone glycyl unit affect the thermodynamics of insertion of individual residues, dipeptides, and entire transmembrane helices. Due to the lack of reference data, we first introduce an efficient methodology to estimate atomistic potential of mean force (PMF) curves from a series of representative and uncorrelated coarse-grained (CG) snapshots. We find strong discrepancies between two CG models, Martini and PLUM, against reference atomistic PMFs and experiments. Atomistic simulations suggest a weak free energy of insertion between water and a POPC membrane for the glycyl unit, in overall agreement with experimental results despite severe assumptions in our calculations. We show that refining the backbone contribution in PLUM significantly improves the PMF of insertion of the WALP16 transmembrane peptide. An improper balance between the glycyl backbone and the attached side chain will lead to energetic artifacts, rationalizing Martini's overstabilization of WALP's adsorbed interfacial state. It illustrates difficulties associated with free-energy-based parametrizations of single-residue models, as the relevant free energy of partitioning used for force-field parametrization does not arise from the entire residue but rather the solvent-accessible chemical groups. PMID:27138459

  12. Properties of polyimide liquid crystal alignment layer with different backbone structure%聚酰亚胺主链结构对液晶取向膜性能的影响

    Institute of Scientific and Technical Information of China (English)

    刘露露; 刘明; 龚世铭; 汪映寒

    2015-01-01

    A series polyimides (PIs)were prepared by one-step method.These PIs were comprised of a functional diamine N,N-bis (4-aminophenyl )-4-(dodecylo-xy-biphenyl )-4′-amino-phenylether (C1 2 -BAAPE),one of two commercially available diamines 2,2′-Bis(trifluoromethy-l)-4,4′-diaminobiphe-nyl (TFDB),4,4′-Oxydianiline (ODA)and one of two dianhydride 4,4′-(hexafluoroisopropylidene) diphthalic anhydride (6FDA)and 4,4′-Oxydiphthalic anhydride (ODPA)in order to get different backbone structures.The structures and thermo properties of these PIs were characterized by NMR, FT-IR,DSC and TGA.Pretilt angles and alignment abilities were carried out by pretilt angle tester and polarization microscope.Solubility of PIs was tested by dissolving PIs in various organic solvents. DSC and TGA curves showed that PI-2 had higher glass transition temperature (T g )and decomposi-tion temperature (T d )than PI-1 and PI-3.Three PI films presented vertical alignment before mechan-ical rubbing and only PI-2 maintained it after rubbing process.Conformations of these PIs were simu-lated by Material Studio (MS).The vertical conformation existed in PI-2 ’s backbones improved rubbing resistance and showed vertical alignment ability after rubbing.%采用一步法,以 N,N-二(4-氨基苯基)-4-(十二烷氧基联苯基)-4’-氨基苯醚(C12-BAAPE)为控制预倾角的功能性二胺,2,2’-双三氟甲基-4,4’-联苯二胺(TFDB)或4,4’-二氨基二苯醚(ODA)为辅助二胺,分别与2,2’-双(3,4-二羧苯基)六氟丙烷四羧酸二酐(6FDA)和4,4’-联苯醚二酐(ODPA)聚合,得到三种主链结构不同的聚酰亚胺(PI-1、PI-2和PI-3)。利用 NMR、FT-IR、DSC、TGA、偏光显微镜和预倾角测试仪对聚合物的结构、热性能以及制备的液晶盒的取向性进行了表征,同时测试了3种 PI 的溶解性能。结果表明,PI-2液晶取向膜的耐摩擦性能明显优于 PI-1和 PI-3,且具有更高的玻璃化转变温度(T g )和分解温度(T d ),更好

  13. Post-translational heterocyclic backbone modifications in the 43-peptide antibiotic microcin B17. Structure elucidation and NMR study of a 13C,15N-labelled gyrase inhibitor.

    Science.gov (United States)

    Bayer, A; Freund, S; Jung, G

    1995-12-01

    Microcin B17 (McB17), the first known gyrase inhibitor of peptidic nature, is produced by ribosomal synthesis and post-translational modification of the 69-residue precursor protein by an Escherichia coli strain. To elucidate the chemical structure of the mature 43-residue peptide antibiotic, fermentation and purification protocols were established and optimized which allowed the isolation and purification of substantial amounts of highly pure McB17 (non-labelled, 15N-labelled and 13C/15N-labelled peptide. By ultraviolet-absorption spectroscopy. HPLC-electrospray mass spectrometry and GC-mass spectrometry, amino acid analysis, protein sequencing, and, in particular, multidimensional NMR, we could demonstrate and unequivocally prove that the enzymic modification of the precursor backbone at Gly-Cys and Gly-Ser segments leads to the formation of 2-aminomethylthiazole-4-carboxylic acid and 2-aminomethyloxazole-4-carboxylic acid, respectively. In addition, two bicyclic modifications 2-(2-aminomethyloxazolyl)thiazole-4-carboxylic acid and 2-(2-aminomethylthiazolyl)oxazole-4-carboxylic acid were found that consist of directly linked thiazole and oxazole rings derived from one Gly-Ser-Cys and one Gly-Cys-Ser segment. Analogous to the thiazole and oxazole rings found in antitumor peptides of microbial and marine origin, these heteroaromatic ring systems of McB17 presumably play an important role in its gyrase-inhibiting activity, e.g. interacting with the DNA to trap the covalent protein-DNA intermediate of the breakage-reunion reaction of the gyrase.

  14. Increasing Sequence Diversity with Flexible Backbone Protein Design: The Complete Redesign of a Protein Hydrophobic Core

    Energy Technology Data Exchange (ETDEWEB)

    Murphy, Grant S.; Mills, Jeffrey L.; Miley, Michael J.; Machius, Mischa; Szyperski, Thomas; Kuhlman, Brian (UNC); (Buffalo)

    2015-10-15

    Protein design tests our understanding of protein stability and structure. Successful design methods should allow the exploration of sequence space not found in nature. However, when redesigning naturally occurring protein structures, most fixed backbone design algorithms return amino acid sequences that share strong sequence identity with wild-type sequences, especially in the protein core. This behavior places a restriction on functional space that can be explored and is not consistent with observations from nature, where sequences of low identity have similar structures. Here, we allow backbone flexibility during design to mutate every position in the core (38 residues) of a four-helix bundle protein. Only small perturbations to the backbone, 12 {angstrom}, were needed to entirely mutate the core. The redesigned protein, DRNN, is exceptionally stable (melting point >140C). An NMR and X-ray crystal structure show that the side chains and backbone were accurately modeled (all-atom RMSD = 1.3 {angstrom}).

  15. A data acquisition backbone core library

    International Nuclear Information System (INIS)

    For the new experiments at FAIR new concepts of data acquisition systems have to be developed like the distribution of self-triggered, time stamped data streams over high performance networks for event building. The data acquisition backbone core (DABC) is a general purpose software framework designed for the implementation of such data acquisition systems. It provides the event building over networks like InfiniBand or Gigabit Ethernet. All kinds of data channels (front-end systems) are supported by program plug-ins into functional components of DABC like data input, combiner, scheduler, event builder, analysis and storage components. Commands and parameters of DABC and its application plug-ins are published by DIM servers. A Java based Graphical User Interface provides the dynamic control and visualization of these components. Application specific GUIs can be added. After a testing phase, DABC can be used to develop high performance data acquisition systems. Besides that DABC will be used for the implementation of various test beds needed for the final design of data acquisition systems at FAIR like detector tests, readout components test, and data flow investigations

  16. 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 for...... determination of the structures pre-stresses is used. A parametric investigation is performed to determine a more optimized form of the plate based tensegrity structure. Conclusions of the use of plate based tensegrity in civil engineering and further research areas are discussed....

  17. 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

  18. Backbone of complex networks of corporations: The flow of control

    Science.gov (United States)

    Glattfelder, J. B.; Battiston, S.

    2009-09-01

    We present a methodology to extract the backbone of complex networks based on the weight and direction of links, as well as on nontopological properties of nodes. We show how the methodology can be applied in general to networks in which mass or energy is flowing along the links. In particular, the procedure enables us to address important questions in economics, namely, how control and wealth are structured and concentrated across national markets. We report on the first cross-country investigation of ownership networks, focusing on the stock markets of 48 countries around the world. On the one hand, our analysis confirms results expected on the basis of the literature on corporate control, namely, that in Anglo-Saxon countries control tends to be dispersed among numerous shareholders. On the other hand, it also reveals that in the same countries, control is found to be highly concentrated at the global level, namely, lying in the hands of very few important shareholders. Interestingly, the exact opposite is observed for European countries. These results have previously not been reported as they are not observable without the kind of network analysis developed here.

  19. Efficient White Light Emission Using a Single Copolymer with Red and Green Chromophores on a Conjugated Polyfluorene Backbone Hybridized with InGaN-Based Light-Emitting Diodes

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yong; HOU Qiong; NIU Qiao-Li; ZHENG Shu-Wen; LI Shu-Ti; HE Miao; FAN Guang-Han

    2009-01-01

    We report an efficient white-light emission based on a single copolymer/InGaN hybrid light-emitting diode.The single copolymer consists of a conjugated polyfluorene backbone by incorporating 2,1,3-benzothiadiazole (BT) and 4, 7-bis(2-thienyl)-2,1,3-benzothiadiazole (DBT) as green and red light-emitting units, respectively. For the single eopolymer/lnGaN hybrid device, the Commission Internationale de l'Eclairage (CIE) coordinates,color temperature Tc and color rendering index Ra at 20mA are (0.323,0.329), 5960K and 86, respectively.In comparison with the performance of red copolymer PFO-DBT15 (DOF:DBT=85:15 with DOF being 9'9-dioctylfluorene) and green copolymer PFO-BT35 (DOF:BT=65:35) blend/InGaN hybrid white devices, it is concluded that the chemically doped copolymer hybridized device shows a higher emission intensity and spectral stability at a high driving current than the polymer blend.

  20. mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet.

    Science.gov (United States)

    Léonard, Sylvain; Joseph, Agnel Praveen; Srinivasan, Narayanaswamy; Gelly, Jean-Christophe; de Brevern, Alexandre G

    2014-04-01

    The increasing number of available protein structures requires efficient tools for multiple structure comparison. Indeed, multiple structural alignments are essential for the analysis of function, evolution and architecture of protein structures. For this purpose, we proposed a new web server called multiple Protein Block Alignment (mulPBA). This server implements a method based on a structural alphabet to describe the backbone conformation of a protein chain in terms of dihedral angles. This 'sequence-like' representation enables the use of powerful sequence alignment methods for primary structure comparison, followed by an iterative refinement of the structural superposition. This approach yields alignments superior to most of the rigid-body alignment methods and highly comparable with the flexible structure comparison approaches. We implement this method in a web server designed to do multiple structure superimpositions from a set of structures given by the user. Outputs are given as both sequence alignment and superposed 3D structures visualized directly by static images generated by PyMol or through a Jmol applet allowing dynamic interaction. Multiple global quality measures are given. Relatedness between structures is indicated by a distance dendogram. Superimposed structures in PDB format can be also downloaded, and the results are quickly obtained. mulPBA server can be accessed at www.dsimb.inserm.fr/dsimb_tools/mulpba/ .

  1. Microsoft Operations Framework implementation for The Backbone

    NARCIS (Netherlands)

    Kienhuis, G.H.

    2007-01-01

    Doel The Backbone ontwerpt, implementeert en beheert IT infrastructuren voor bedrijven en instellingen. Beheer wordt proactief uitgevoerd met behulp van Microsoft Operation Manager (MOM) 2005. MOM is een applicatie die de status en gebeurtenissen van systemen zichtbaar maakt vanuit één locatie. Om

  2. 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...

  3. 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.

  4. Radiation damage to DNA: electron scattering from the backbone subunits

    CERN Document Server

    Tonzani, S; Greene, Chris H.; Tonzani, Stefano

    2006-01-01

    In the context of damage to DNA by low-energy electrons, we carry out calculations of electron scattering from tetrahydrofuran and phosphoric acid, models of the subunits in the DNA backbone, as a first step in simulating the electron capture process that occurs in the cell. In the case of tetrahydrofuran, we also compare with previous theoretical and experimental data. A comparison of the shape of the resonant structures to virtual orbitals is also performed to gain insight into the systematic connections with electron scattering from similar molecules and dissociative electron attachment experiments.

  5. Net neutrality at internet backbone provider level

    OpenAIRE

    Baglioni, Laura; Calabrese, Armando; Ghiron, Nathan Levialdi

    2013-01-01

    This paper analysis the Internet interconnection market and combine the main technical (i.e. service quality) and economic aspects (i.e. profits and utility) characterizing relations between market players (end users, EUs; Internet Service Providers, ISPs; Internet Backbone Providers, IBPs) in order to determine possible economic outcomes in the strategic interaction between them. The proposed model enables a comparison to be made between expected values of social welfare (i.e. EU utility and...

  6. A Cooperative Game Based Data Center Backbone Network Bandwidth Allocation Policy%基于合作博弈的数据中心骨干网带宽分配策略

    Institute of Scientific and Technical Information of China (English)

    孟飞; 兰巨龙; 胡宇翔

    2016-01-01

    数据中心(data center ,DC)之间通过部署流量工程来提高连接各个数据中心骨干网的利用率,虽然效率提升显著,但对不同类型汇聚流的带宽分配的公平性没有考虑。将多个汇聚流对带宽分配的竞争行为建模为一个合作博弈,通过寻求此博弈的纳什谈判解(Nash bargaining solution ,NBS)来确定优化的带宽分配策略 CGBA(cooperation game based bandwidth allocation ),权衡各汇聚流的最小带宽保证与带宽分配的公平性。在 Mininet 平台上进行实验仿真并和典型的带宽分配策略对比,结果表明CGBA 不但可保证各汇聚流的最小带宽需求,还确保了各类流对带宽资源竞争的公平性。%Currently ,traffic engineering is typically deployed to improve the utilization of data centers (DC) backbone networks ,which usually belongs to the same online service providers .Although the efficiency is remarkable ,the bandwidth allocation fairness of different aggregate flow isn’t considered . Hence ,the QoS guarantee is restricted .Because the bandwidth resource is expensive and packet loss is typically thought unacceptable ,the bandwidth utilization should be maximized ,at the same time , the QoS guarantee of different flow should be improved .In this paper ,the problem of contending the share bandwidth is modeled as a cooperative game ,and different aggregate flow compets the share bandwidth and maximizes the overall bandwidth resource utilization simultaneously ,and the optimal bandwidth allocation policy ,called cooperation game based bandwidth allocation (CGBA) ,is obtained through searching the Nash bargaining solution (NBS) of the game and balancing the tradeoff between minimum bandwidth guarantee and bandwidth allocation fairness .Simulation on a Mininet testbed shows that the proposed policy can effectively guarantee minimum bandwidth of each aggregate flow while ensuring the allocation fairness , compared with three

  7. 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.

  8. Protonation–deprotonation of the glycine backbone as followed by Raman scattering and multiconformational analysis

    Energy Technology Data Exchange (ETDEWEB)

    Hernández, Belén; Pflüger, Fernando [Groupe de Biophysique Moléculaire, UFR Santé-Médecine-Biologie Humaine, Université Paris 13, Sorbonne Paris Cité, 74 rue Marcel Cachin, 93017 Bobigny cedex (France); Kruglik, Sergei G. [Laboratoire Jean Perrin, FRE 3231, Université Pierre et Marie Curie (Paris 6), Case courrier 138, 75252 Paris Cedex 05 (France); Ghomi, Mahmoud, E-mail: mahmoud.ghomi@univ-paris13.fr [Groupe de Biophysique Moléculaire, UFR Santé-Médecine-Biologie Humaine, Université Paris 13, Sorbonne Paris Cité, 74 rue Marcel Cachin, 93017 Bobigny cedex (France)

    2013-11-08

    Highlights: • New pH-dependent Raman spectra in the middle wavenumber region (1800-300 cm{sup −1}). • New quantum mechanical calculations for exploring the Gly conformational landscape. • Construction of muticonformation based theoretical Raman spectra. - Abstract: Because of the absence of the side chain in its chemical structure and its well defined Raman spectra, glycine was selected here to follow its backbone protonation–deprotonation. The scan of the recorded spectra in the 1800–300 cm{sup −1} region led us to assign those obtained at pH 1, 6 and 12 to the cationic, zwitterionic and anionic species, respectively. These data complete well those previously published by Bykov et al. (2008) [16] devoted to the high wavenumber Raman spectra (>2500 cm{sup −1}). To reinforce our discussion, DFT calculations were carried out on the clusters of glycine + 5H{sub 2}O, mimicking reasonably the first hydration shell of the amino acid. Geometry optimization of 141 initial clusters, reflecting plausible combinations of the backbone torsion angles, allowed exploration of the conformational features, as well as construction of the theoretical Raman spectra by considering the most stable clusters containing each glycine species.

  9. RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone.

    Science.gov (United States)

    Wang, Xueyi; Kapral, Gary; Murray, Laura; Richardson, David; Richardson, Jane; Snoeyink, Jack

    2008-01-01

    Although accurate details in RNA structure are of great importance for understanding RNA function, the backbone conformation is difficult to determine, and most existing RNA structures show serious steric clashes (>or= 0.4 A overlap) when hydrogen atoms are taken into account. We have developed a program called RNABC (RNA Backbone Correction) that performs local perturbations to search for alternative conformations that avoid those steric clashes or other local geometry problems. Its input is an all-atom coordinate file for an RNA crystal structure (usually from the MolProbity web service), with problem areas specified. RNABC rebuilds a suite (the unit from sugar to sugar) by anchoring the phosphorus and base positions, which are clearest in crystallographic electron density, and reconstructing the other atoms using forward kinematics. Geometric parameters are constrained within user-specified tolerance of canonical or original values, and torsion angles are constrained to ranges defined through empirical database analyses. Several optimizations reduce the time required to search the many possible conformations. The output results are clustered and presented to the user, who can choose whether to accept one of the alternative conformations. Two test evaluations show the effectiveness of RNABC, first on the S-motifs from 42 RNA structures, and second on the worst problem suites (clusters of bad clashes, or serious sugar pucker outliers) in 25 unrelated RNA structures. Among the 101 S-motifs, 88 had diagnosed problems, and RNABC produced clash-free conformations with acceptable geometry for 71 of those (about 80%). For the 154 worst problem suites, RNABC proposed alternative conformations for 72. All but 8 of those were judged acceptable after examining electron density (where available) and local conformation. Thus, even for these worst cases, nearly half the time RNABC suggested corrections suitable to initiate further crystallographic refinement. The program is

  10. The optimization issues in an agile all-photonic backbone network

    Science.gov (United States)

    Zhang, Yiming; Yang, Oliver W.; Zhai, Yihua

    2005-02-01

    The Agile All-photonic Backbone Network (AAPN) architecture has been proposed by the telecommunication industry as a potential candidate for the ultra high speed Next Generation Optical Network (NGON) architecture. AAPN network structure is composed of adaptive optical core switches and edge routers in an overlaid star physical topology. In this paper, we examine various optimization issues for AAPN architectures. The optimization procedure is based on a Lagrangean relaxation and subgradient method. Based on the optimization methodology provided in the previous research, we propose a modified algorithm to optimize AAPN networks, with respect to the assumptions used in AAPN. The results for different network configurations are studied and the influence of network resources is also studied. Our algorithm is shown to be very computational effective on the AAPN networks, and the bounds generated are mostly within 1% of the final objective value.

  11. 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.

  12. Relative packing groups in template-based structure prediction: cooperative effects of true positive constraints.

    Science.gov (United States)

    Day, Ryan; Qu, Xiaotao; Swanson, Rosemarie; Bohannan, Zach; Bliss, Robert; Tsai, Jerry

    2011-01-01

    Most current template-based structure prediction methods concentrate on finding the correct backbone conformation and then packing sidechains within that backbone. Our packing-based method derives distance constraints from conserved relative packing groups (RPGs). In our refinement approach, the RPGs provide a level of resolution that restrains global topology while allowing conformational sampling. In this study, we test our template-based structure prediction method using 51 prediction units from CASP7 experiments. RPG-based constraints are able to substantially improve approximately two-thirds of starting templates. Upon deeper investigation, we find that true positive spatial constraints, especially those non-local in sequence, derived from the RPGs were important to building nearer native models. Surprisingly, the fraction of incorrect or false positive constraints does not strongly influence the quality of the final candidate. This result indicates that our RPG-based true positive constraints sample the self-consistent, cooperative interactions of the native structure. The lack of such reinforcing cooperativity explains the weaker effect of false positive constraints. Generally, these findings are encouraging indications that RPGs will improve template-based structure prediction. PMID:21210729

  13. Understanding VoIP from Backbone Measurements

    OpenAIRE

    Birke, Robert Rene' Maria; Petracca, Michele; Mellia, Marco

    2007-01-01

    VoIP has widely been addressed as the technology that will change the Telecommunication model opening the path for convergence. Still today this revolution is far from being complete, since the majority of telephone calls are originated by circuit-oriented networks. In this paper for the first time to the best of our knowledge, we present a large dataset of measurements collected from the FastWeb backbone, which is one of the first worldwide Telecom operator to offer VoIP and high-speed data ...

  14. Instant Backbone.js application development

    CERN Document Server

    Hunter, Thomas

    2013-01-01

    Get to grips with a new technology, understand what it is and what it can do for you, and then get to work with the most important features and tasks. This book is a practical, step-by-step tutorial that will teach you to build Backbone.js applications quickly and efficiently.This book is targeted towards developers. It is assumed that you have at least a basic understanding of JavaScript and jQuery selectors. If you are interested in building dynamic Single Page Applications that interact heavily with a backend server, then this is the book for you.

  15. 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.

  16. Variation of protein backbone amide resonance by electrostatic field

    CERN Document Server

    Sharley, John N

    2015-01-01

    Amide resonance is found to be sensitive to electrostatic field with component parallel or antiparallel the amide C-N bond. This effect is linear and without threshold in the biologically plausible electrostatic field range -0.005 to 0.005 au. Variation of amide resonance varies Resonance Assisted Hydrogen Bonding such as occurs in the hydrogen bonded chains of backbone amides of protein secondary structures such as beta sheet and non-polyproline helix such as alpha helix, varying the stability of the secondary structure. The electrostatic properties including permittivity of amino acid residue sidegroups influence the electrostatic field component parallel or antiparallel the C-N bond of each amide. The significance of this factor relative to other factors in protein folding depends on the magnitude of electrostatic field component parallel or antiparallel the C-N bond of each amide, and preliminary protein-scale calculations of the magnitude of these components suggest this factor warrants investigation in ...

  17. Study of muscular skeletal apparatus’s functional state of junior sportsmen-power lifters, who have backbone verterbral abnormalities

    Directory of Open Access Journals (Sweden)

    Ilmatov V.R.

    2015-10-01

    Full Text Available Purpose: determination of abnormalities and disorders of muscular skeletal apparatuses’ status of power lifters, who have vertebral abnormalities of backbone. Material: 58 junior sportsmen participated in the research. 36 sportsmen were the main group of the research and had vertebral disorders in backbone. For posture testing visual examination was used. Backbone mobility was tested with goniometry method. Flat feet were registered with plantography method. Results: we determined posture abnormalities in sagittal and frontal planes; feet flat, limited maximal movements in thoracic and lumbar spines. It was determined that the most limited were rotational movements and backbone unbending. The next were side bents. These limitations were accompanied by pain syndrome. These observations indirectly confirmed theory of direct interaction of backbone structures with nervous structures. It is also a confirmation of vertebral abnormalities’ presence in junior sportsmen. Conclusions: it was found that in junior sportsmen - power lifters with backbone pathologies in 100% of cases symptoms are determined by local limitations of backbone mobility with pain syndrome. In 35% of cases they are accompanied by posture’s disorders and feet flat. Orientation and methodic of rehabilitation of such sportsmen have been determined.

  18. The orientational preferences of backbones of proteins

    Institute of Scientific and Technical Information of China (English)

    CHEN Ying; WANG Jun; XUE Bin; WANG Wei

    2006-01-01

    The orientation between the backboneresidues of proteins is defined based on the local configurations and the corresponding preferences are analyzed by statistics. It is found that all the residue pairs have some specific preferences of orientations. The statistical analysis is mainly concentrated in the orientational distributions for two kinds of groupings of residues based on the hydrophobicity and secondary structural features. The statistics for such two types of groupings shows different orientational preferences. It is found that for the former grouping the orientational preference is rather weak,while for the later a kind of strong orientational preferences. This suggests that the formation of local structures and of secondary structures are highly related to the orientational preferences.

  19. The role of backbone hydrogen bonds in the transition state for protein folding of a PDZ domain

    DEFF Research Database (Denmark)

    Pedersen, Søren W; Hultqvist, Greta; Strømgaard, Kristian;

    2014-01-01

    Backbone hydrogen bonds are important for the structure and stability of proteins. However, since conventional site-directed mutagenesis cannot be applied to perturb the backbone, the contribution of these hydrogen bonds in protein folding and stability has been assessed only for a very limited set...... of small proteins. We have here investigated effects of five amide-to-ester mutations in the backbone of a PDZ domain, a 90-residue globular protein domain, to probe the influence of hydrogen bonds in a β-sheet for folding and stability. The amide-to-ester mutation removes NH-mediated hydrogen bonds...

  20. Extracting the information backbone in online system

    CERN Document Server

    Zhang, Qian-Ming; 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 mainly dedicated to improve the recommendation performance (accuracy and diversity) of the algorithms while 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 improve both of...

  1. Sofosbuvir as backbone of interferon free treatments.

    Science.gov (United States)

    Bourlière, Marc; Oules, Valèrie; Ansaldi, Christelle; Adhoute, Xavier; Castellani, Paul

    2014-12-15

    Sofosbuvir is the first-in-class NS5B nucleotide analogues to be launched for hepatitis C virus (HCV) treatment. Its viral potency, pangenotypic activity and high barrier to resistance make it the ideal candidate to become a backbone for several IFN-free regimens. Recent data demonstrated that sofosbuvir either with ribavirin alone or in combination with other direct-acting antivirals (DAAs) as daclatasvir, ledipasvir or simeprevir are able to cure HCV in at least 90% or over of patients. Treatment experienced genotype 3 population may remain the most difficult to treat population, but ongoing DAA combination studies will help to fill this gap. Safety profile of sofosbuvir or combination with other DAAs is good. Resistance to sofosbuvir did not appear as a significant issue. The rationale for using this class of drug and the available clinical data are reviewed.

  2. 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.

  3. Plasma-based accelerator structures

    Energy Technology Data Exchange (ETDEWEB)

    Schroeder, Carl B.

    1999-12-01

    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.

  4. Plasma-based accelerator structures

    International Nuclear Information System (INIS)

    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

  5. A Native to Amyloidogenic Transition Regulated by a Backbone Trigger

    Energy Technology Data Exchange (ETDEWEB)

    Eakin,C.; Berman, A.; Miranker, A.

    2006-01-01

    Many polypeptides can self-associate into linear, aggregated assemblies termed amyloid fibers. High-resolution structural insights into the mechanism of fibrillogenesis are elusive owing to the transient and mixed oligomeric nature of assembly intermediates. Here, we report the conformational changes that initiate fiber formation by beta-2-microglobulin (beta2m) in dialysis-related amyloidosis. Access of beta2m to amyloidogenic conformations is catalyzed by selective binding of divalent cations. The chemical basis of this process was determined to be backbone isomerization of a conserved proline. On the basis of this finding, we designed a beta2m variant that closely adopts this intermediate state. The variant has kinetic, thermodynamic and catalytic properties consistent with its being a fibrillogenic intermediate of wild-type beta2m. Furthermore, it is stable and folded, enabling us to unambiguously determine the initiating conformational changes for amyloid assembly at atomic resolution.

  6. A model for the [C+-GxC]n triple helix derived from observation of the C+-GxC base triplet in a crystal structure.

    Science.gov (United States)

    Nunn, C M; Trent, J O; Neidle, S

    1997-10-13

    A molecular modelling study on the [C+-GxC]n triple helix is reported. We have observed the C+-GxC base triplet in the crystal structure of an oligonucleotide-drug complex, between the minor-groove drug netropsin and the decanucleotide d(CGCAATTGCG)2. The complex was crystallised at pH 7.0, but the crystal structure, at a resolution of 2.4 A, shows that a terminal cytosine has become protonated and participates in a parallel C+-GxC base triplet. The structure of this triplet and its associated sugar-phosphate backbones have been energy-refined and then used to generate a triple helix. This has characteristics of the B-type family of DNA structures for two strands, with the third, the C+ strand, having backbone conformations closer to the A family. PMID:9369239

  7. 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...... structure of several tankers and containerships. The results of the reliability analysis were the basis for the definition of a target safety level which was used to asses the partial safety factors suitable for in a new design rules format to be adopted in modern ship structural design. Finally...

  8. INFLUENCE OF BACKBONE RIGIDITY ON THE LIQUID CRYSTALLINITY OF MESOGEN-CONTAINING POLYACETYLENES

    Institute of Scientific and Technical Information of China (English)

    1998-01-01

    Two acetylene polymers containing cyanobiphenyl-based mesogens,poly{10-[((4'-cyano-4-biphenylyl)oxy)carbonyl]-1-decyne} (PA8CN), which has a relatively flexible polyalkyne backbone, and poly {[4-(((12-((4'-cyano-4-biphenylyl)oxy)dodecyl)oxy)carbonyl) phenyl]-acetylene} (PB12CN), which has a fairly rigid poly(phenylacetylene)backbone, were synthesized using respectively WCl6 and [Rh(nbd)Cl]2 as the catalysts.PA8CN exhibits enantiotropic interdigitated smectic A phase (SAd) over a temperature range as wide as ca. 100℃, whereas PB12CN is non-mesomorphic, demonstrating that the backbone rigidity plays an important role in determining the liquid crystallinity of the polyacetylenes.

  9. 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.

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

    Science.gov (United States)

    Paradiso, Veronica; Costabile, Chiara; Grisi, Fabia

    2016-01-01

    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. PMID:26805793

  11. λ-backbone colorings along pairwise disjoint stars and matchings

    NARCIS (Netherlands)

    Broersma, H.J.; Fujisawa, J.; Marchal, L.; Paulusma, D.; Salman, A.N.M.; Yoshimoto, K.

    2009-01-01

    Given an integer $\\lambda \\ge 2$, a graph $G=(V,E)$ and a spanning subgraph $H$ of $G$ (the backbone of $G$), a $\\lambda$-backbone coloring of $(G,H)$ is a proper vertex coloring $V\\to\\{1,2,\\ldots\\}$ of $G$, in which the colors assigned to adjacent vertices in $H$ differ by at least $\\lambda$. We st

  12. 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.

  13. 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.

  14. 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.

  15. Extracting Backbones from Weighted Complex Networks with Incomplete Information

    Directory of Open Access Journals (Sweden)

    Liqiang Qian

    2015-01-01

    Full Text Available The backbone is the natural abstraction of a complex network, which can help people understand a networked system in a more simplified form. Traditional backbone extraction methods tend to include many outliers into the backbone. What is more, they often suffer from the computational inefficiency—the exhaustive search of all nodes or edges is often prohibitively expensive. In this paper, we propose a backbone extraction heuristic with incomplete information (BEHwII to find the backbone in a complex weighted network. First, a strict filtering rule is carefully designed to determine edges to be preserved or discarded. Second, we present a local search model to examine part of edges in an iterative way, which only relies on the local/incomplete knowledge rather than the global view of the network. Experimental results on four real-life networks demonstrate the advantage of BEHwII over the classic disparity filter method by either effectiveness or efficiency validity.

  16. Quantum chemical benchmark study on 46 RNA backbone families using a dinucleotide unit.

    Science.gov (United States)

    Kruse, Holger; Mladek, Arnost; Gkionis, Konstantinos; Hansen, Andreas; Grimme, Stefan; Sponer, Jiri

    2015-10-13

    We have created a benchmark set of quantum chemical structure-energy data denoted as UpU46, which consists of 46 uracil dinucleotides (UpU), representing all known 46 RNA backbone conformational families. Penalty-function-based restrained optimizations with COSMO TPSS-D3/def2-TZVP ensure a balance between keeping the target conformation and geometry relaxation. The backbone geometries are close to the clustering-means of their respective RNA bioinformatics family classification. High-level wave function methods (DLPNO-CCSD(T) as reference) and a wide-range of dispersion-corrected or inclusive DFT methods (DFT-D3, VV10, LC-BOP-LRD, M06-2X, M11, and more) are used to evaluate the conformational energies. The results are compared to the Amber RNA bsc0χOL3 force field. Most dispersion-corrected DFT methods surpass the Amber force field significantly in accuracy and yield mean absolute deviations (MADs) for relative conformational energies of ∼0.4-0.6 kcal/mol. Double-hybrid density functionals represent the most accurate class of density functionals. Low-cost quantum chemical methods such as PM6-D3H+, HF-3c, DFTB3-D3, as well as small basis set calculations corrected for basis set superposition errors (BSSEs) by the gCP procedure are also tested. Unfortunately, the presently available low-cost methods are struggling to describe the UpU conformational energies with satisfactory accuracy. The UpU46 benchmark is an ideal test for benchmarking and development of fast methods to describe nucleic acids, including force fields. PMID:26574283

  17. Animals without Backbones: The Invertebrate Story. Grade Level 5-9.

    Science.gov (United States)

    Jerome, Brian; Fuqua, Paul

    This guide, when used in tandem with the videotape "Animals Without Backbones," helps students learn about invertebrates. These materials promote hands-on discovery and learning. The guide is composed of six curriculum-based teaching units: (1) "Getting Started"; (2) "Porifera"; (3) "Cnidarians"; (4) "Worms"; (5) "Mollusks"; (6) "Arthropods"; and…

  18. Prediction of nonregular secondary structures of proteins based on wavelet analysis

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The secondary structures of proteins fall into two classes: regular structure and nonregular structure. Helices and sheets are termed "regular" structures because their residues have repeating main-chain torsion angles, and their backbone N-H and C-O groups are arranged in a periodic pattern of hydrogen bonding. In contrast, the remaining structures with nonrepeating backbone torsion angles are called nonregular secondary structures. In this note, we performed an extensive sequence analysis of nonregular secondary structures and showed that these nonregular parts could be effectively predicted by continuous wavelet transform.

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

    Energy Technology Data Exchange (ETDEWEB)

    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 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.

  20. Displacement based multilevel structural optimization

    Science.gov (United States)

    Striz, Alfred G.

    1995-01-01

    Multidisciplinary design optimization (MDO) is expected to play a major role in the competitive transportation industries of tomorrow, i.e., in the design of aircraft and spacecraft, of high speed trains, boats, and automobiles. All of these vehicles require maximum performance at minimum weight to keep fuel consumption low and conserve resources. Here, MDO can deliver mathematically based design tools to create systems with optimum performance subject to the constraints of disciplines such as structures, aerodynamics, controls, etc. Although some applications of MDO are beginning to surface, the key to a widespread use of this technology lies in the improvement of its efficiency. This aspect is investigated here for the MDO subset of structural optimization, i.e., for the weight minimization of a given structure under size, strength, and displacement constraints. Specifically, finite element based multilevel optimization of structures (here, statically indeterminate trusses and beams for proof of concept) is performed. In the system level optimization, the design variables are the coefficients of assumed displacement functions, and the load unbalance resulting from the solution of the stiffness equations is minimized. Constraints are placed on the deflection amplitudes and the weight of the structure. In the subsystems level optimizations, the weight of each element is minimized under the action of stress constraints, with the cross sectional dimensions as design variables. This approach is expected to prove very efficient, especially for complex structures, since the design task is broken down into a large number of small and efficiently handled subtasks, each with only a small number of variables. This partitioning will also allow for the use of parallel computing, first, by sending the system and subsystems level computations to two different processors, ultimately, by performing all subsystems level optimizations in a massively parallel manner on separate

  1. LOAD AWARE ADAPTIVE BACKBONE SYNTHESIS IN WIRELESS MESH NETWORKS

    Institute of Scientific and Technical Information of China (English)

    Yuan Yuan; Zheng Baoyu

    2009-01-01

    Wireless Mesh Networks (WMNs) are envisioned to support the wired backbone with a wireless Backbone Networks (BNet) for providing internet connectivity to large-scale areas.With a wide range of internet-oriented applications with different Quality of Service (QoS) requirement,the large-scale WMNs should have good scalability and large bandwidth.In this paper,a Load Aware Adaptive Backbone Synthesis (LAABS) algorithm is proposed to automatically balance the traffic flow in the WMNs.The BNet will dynamically split into smaller size or merge into bigger one according to statistic load information of Backbone Nodes (BNs).Simulation results show LAABS generates moderate BNet size and converges quickly,thus providing scalable and stable BNet to facilitate traffic flow.

  2. 使用Backbone JS搭建SPA

    Institute of Scientific and Technical Information of China (English)

    吕婷

    2012-01-01

    Backbone JSR从2010年发布以来,受到了业界的广泛关注。“豆瓣说”和“豆瓣阅读(阅读器)”是两款以它为基础框架搭建的SPA,本文将结合这两款产品,向读者介绍BackboneJS的方方面面。

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

    DEFF Research Database (Denmark)

    Gil, Vanesa; Kammer Hansen, Kent

    2014-01-01

    -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...... with infiltrated LSM nanoparticles is shown in Fig. 1. Figure 1. Cross section of LSM infiltrated cathode supported cell. [Formula]...

  4. Side chain and backbone ordering in a polypeptide

    CERN Document Server

    Wei, Y; Hansmann, U H E

    2006-01-01

    We report results from multicanonical simulations of polyglutamic acid chains of length of ten residues. For this simple polypeptide we observe a decoupling of backbone and side-chain ordering in the folding process. While the details of the two transitions vary between the peptide in gas phase and in an implicit solvent, our results indicate that, independent of the specific surroundings, upon continuously lowering the temperature side-chain ordering occurs only after the backbone topology is completely formed.

  5. 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...

  6. n Silico Analysis of Envelope Dengue Virus-2 and Envelope Dengue Virus-3 Protein as the Backbone of Dengue Virus Tetravalent Vaccine by Using Homology Modeling Method

    Directory of Open Access Journals (Sweden)

    Rizky I. Taufik

    2009-01-01

    Full Text Available Problem statement: Dengue fever, which was caused by Dengue virus infection, had became a major public health problem in the tropic and subtropical countries. Dengue virus (DENV had four serotypes (DENV-1, DENV-2, DENV-3 and DENV-4, based on their immunogenic in the human body. Preventive measure will be necessary to decrease the prevalence of dengue fever, by developing modern vaccine. Approach: This research was focused on in silico study of dengue virus vaccines, by using envelope (E protein of DENV-2 and DENV-3 as their backbones. T cell epitope prediction was determined by using MULTIPRED server and B cell epitope prediction was determined by using Conformational Epitope Prediction server (CEP. Homology modeling study of E DENV-3 protein as the vaccine backbone had produced six dengue vaccine peptides (HMM Vaccine 1-6. Moreover, homology modeling study of E DENV-2 protein as vaccine backbone had produced six dengue vaccine peptides (ANN vaccine 1-6. Results: The BLAST analysis of HMM and ANN vaccines had produced 93% and 91% identity, respectively. The Ramachandran Plot of both vaccines had shown less than 15% non glycine residue in the disallowed region, therefore it showed the solid stability of the proteins. The VAST analysis of E DENV-3 backbone vaccines had determined, that HMM4 and HMM6 had the highest structure similarity with native E DENV-3. HMM4 and HMM6 had the highest VAST score of 64.5. Moreover, the VAST analysis of E DENV-2 backbone vaccines had determined, that ANN1, ANN3, ANN4, ANN5 and ANN6 had the highest structure similarity with native E DENV-2. ANN1, ANN3, ANN4, ANN5 and ANN6 have the highest VAST score of 64.7. Conclusion/Recommendation: It could be inferred from this research that HMM4; HMM6; ANN1; ANN3; ANN4; ANN5; and ANN6 were the best in silico vaccine design, based on their similarity with native E DENV Proteins. This research could be applied for the wet

  7. 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.

  8. Histidine-Directed Arylation/Alkenylation of Backbone N-H Bonds Mediated by Copper(II).

    Science.gov (United States)

    Ohata, Jun; Minus, Matthew B; Abernathy, Morgan E; Ball, Zachary T

    2016-06-22

    Chemical modification of proteins and peptides represents a challenge of reaction design as well as an important biological tool. In contrast to side-chain modification, synthetic methods to alter backbone structure are extremely limited. In this communication, copper-mediated backbone N-alkenylation or N-arylation of peptides and proteins by direct modification of natural sequences is described. Histidine residues direct oxidative coupling of boronic acids at the backbone NH of a neighboring amino acid. The mild reaction conditions in common physiological buffers, at ambient temperature, are compatible with proteins and biological systems. This simple reaction demonstrates the potential for directed reactions in complex systems to allow modification of N-H bonds that directly affect polypeptide structure, stability, and function. PMID:27249339

  9. 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

    2015-09-01

    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.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

  10. 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...

  11. 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. PMID:26260854

  12. The backbone of the climate network

    CERN Document Server

    Donges, Jonathan F; Marwan, Norbert; Kurths, Juergen; 10.1209/0295-5075/87/48007

    2010-01-01

    We propose a method to reconstruct and analyze a complex network from data generated by a spatio-temporal dynamical system, relying on the nonlinear mutual information of time series analysis and betweenness centrality of complex network theory. We show, that this approach reveals a rich internal structure in complex climate networks constructed from reanalysis and model surface air temperature data. Our novel method uncovers peculiar wave-like structures of high energy flow, that we relate to global surface ocean currents. This points to a major role of the oceanic surface circulation in coupling and stabilizing the global temperature field in the long term mean (140 years for the model run and 60 years for reanalysis data). We find that these results cannot be obtained using classical linear methods of multivariate data analysis, and have ensured their robustness by intensive significance testing.

  13. Solution-based growth and structural characterization of homo- and heterobranched semiconductor nanowires.

    Science.gov (United States)

    Dong, Angang; Tang, Rui; Buhro, William E

    2007-10-10

    Colloidal homobranched ZnSe nanowires (NWs) and heterobranched CdSe-ZnSe NWs are successfully synthesized by combining a sequential seeding strategy with the solution-liquid-solid (SLS) growth process. We have developed an efficient approach to deposit secondary bismuth nanoparticles onto the NW backbone to induce the subsequent SLS branch growth. The density, length, and diameter of branches are rationally controlled by varying reaction conditions. Structural characterization reveals that crystalline branches grow epitaxially from the backbone in both homo- and heterobranched NWs. Two different branching structures are observed in the CdSe-ZnSe heterobranched NWs, owing to the phase admixture, i.e., cubic and hexagonal crystal structures, coexisting in the CdSe NW backbones. These branched NWs with well-designed architectures are expected to have potential as three-dimensional building blocks in the fabrication of nanoscale electronics and photonics.

  14. Preparation of amphiphilic graft copolymer with polyisoprene backbone by combination of anionic polymerization and “click” reaction

    Institute of Scientific and Technical Information of China (English)

    Fei Shao; Xu Feng Ni; Zhi Quan Shen

    2012-01-01

    A novel graft copolymer consisting of polyisoprene backbone and hydrophilic side chain with carbamic acid ester functional group was prepared via thiol-ene “click” reaction and alcohol-isocyanate reactions.Polyisoprene was synthesized by anionic polymerization using n-butyl lithium as initiator,and the pendant hydroxyl groups were introduced by the thiol-ene reaction of mercaptoethanol with the double bond of 1,2-addition units of PI backbone in the presence of radical initiator azobisisobutyronitrile.Isocyanate end group capped poly(ethylene glycol) (mPEG-NCO) was grafted onto the PI backbone through alcoholisocyanate reaction between the pendant hydroxyl groups and isocyanate group of mPEG-NCO.The structure of the graft copolymer were characterized and confirmed by means of size-exclusion chromatography,1H NMR and FTIR spectroscopy.

  15. 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.

  16. 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. PMID:25935050

  17. High performance and highly durable infiltrated cathodes using Pr-modified Ce0.9Gd0.1O1.95 backbone

    DEFF Research Database (Denmark)

    Samson, Alfred Junio; Søgaard, Martin; Bonanos, Nikolaos;

    2014-01-01

    Infiltration of electrocatalysts into ionic conducting backbones (e.g. Sr – doped LaCoO3 (LSC) into Ce0.9Gd0.1O1.95 (CGO)) is becoming a widely popular means of preparing composite cathodes for SOFCs. The high surface area nanoparticle grains of the electrocatalyst obtained using the method...... the CGO backbone with Pr through infiltration into the structure followed by firing. The Pr – modified CGO backbone is then infiltrated with LSC. The electrochemical performance of the infiltrated cathodes with and without Pr modification in the backbone was studied by impedance spectroscopy on symmetric...

  18. Alkali metal salts of formazanate ligands : diverse coordination modes as a result of the nitrogen-rich [NNCNN] ligand backbone

    NARCIS (Netherlands)

    Travieso-Puente, Raquel; Chang, Mu-Chieh; Otten, Edwin

    2014-01-01

    Alkali metal salts of redox-active formazanate ligands were prepared, and their structures in the solid-state and in solution are determined. The nitrogen-rich [NNCNN] backbone of formazanates results in a varied coordination chemistry, with both the internal and terminal nitrogen atoms available fo

  19. 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...

  20. Determination of backbone chain direction of PDA using FFM

    Science.gov (United States)

    Jo, Sadaharu; Okamoto, Kentaro; Takenaga, Mitsuru

    2010-01-01

    The effect of backbone chains on friction force was investigated on both Langmuir-Blodgett (LB) films of 10,12-heptacosadiynoic acid and the (0 1 0) surfaces of single crystals of 2,4-hexadiene-1,6-diol using friction force microscopy (FFM). It was observed that friction force decreased when the scanning direction was parallel to the [0 0 1] direction in both samples. Moreover, friction force decreased when the scanning direction was parallel to the crystallographic [1 0 2], [1 0 1], [1 0 0] and [1 0 1¯] directions in only the single crystals. For the LB films, the [0 0 1] direction corresponds to the backbone chain direction of 10,12-heptacosadiynoic acid. For the single crystals, both the [0 0 1] and [1 0 1] directions correspond to the backbone chain direction, and the [1 0 2], [1 0 0] and [1 0 1¯] directions correspond to the low-index crystallographic direction. In both the LB films and single crystals, the friction force was minimized when the directions of scanning and the backbone chain were parallel.

  1. Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design.

    Directory of Open Access Journals (Sweden)

    Colin A Smith

    Full Text Available Predicting the set of sequences that are tolerated by a protein or protein interface, while maintaining a desired function, is useful for characterizing protein interaction specificity and for computationally designing sequence libraries to engineer proteins with new functions. Here we provide a general method, a detailed set of protocols, and several benchmarks and analyses for estimating tolerated sequences using flexible backbone protein design implemented in the Rosetta molecular modeling software suite. The input to the method is at least one experimentally determined three-dimensional protein structure or high-quality model. The starting structure(s are expanded or refined into a conformational ensemble using Monte Carlo simulations consisting of backrub backbone and side chain moves in Rosetta. The method then uses a combination of simulated annealing and genetic algorithm optimization methods to enrich for low-energy sequences for the individual members of the ensemble. To emphasize certain functional requirements (e.g. forming a binding interface, interactions between and within parts of the structure (e.g. domains can be reweighted in the scoring function. Results from each backbone structure are merged together to create a single estimate for the tolerated sequence space. We provide an extensive description of the protocol and its parameters, all source code, example analysis scripts and three tests applying this method to finding sequences predicted to stabilize proteins or protein interfaces. The generality of this method makes many other applications possible, for example stabilizing interactions with small molecules, DNA, or RNA. Through the use of within-domain reweighting and/or multistate design, it may also be possible to use this method to find sequences that stabilize particular protein conformations or binding interactions over others.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-07-15

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

  3. PESI - a taxonomic backbone for Europe

    Science.gov (United States)

    Kouwenberg, Juliana; Boumans, Louis; Hussey, Charles; Hyam, Roger; Nicolson, Nicola; Kirk, Paul; Paton, Alan; Michel, Ellinor; Guiry, Michael D.; Boegh, Phillip S.; Pedersen, Henrik Ærenlund; Enghoff, Henrik; von Raab-Straube, Eckhard; Güntsch, Anton; Geoffroy, Marc; Müller, Andreas; Kohlbecker, Andreas; Berendsohn, Walter; Appeltans, Ward; Arvanitidis, Christos; Vanhoorne, Bart; Declerck, Joram; Vandepitte, Leen; Hernandez, Francisco; Nash, Róisín; Costello, Mark John; Ouvrard, David; Bezard-Falgas, Pascale; Bourgoin, Thierry; Wetzel, Florian Tobias; Glöckler, Falko; Korb, Günther; Ring, Caroline; Hagedorn, Gregor; Häuser, Christoph; Aktaç, Nihat; Asan, Ahmet; Ardelean, Adorian; Borges, Paulo Alexandre Vieira; Dhora, Dhimiter; Khachatryan, Hasmik; Malicky, Michael; Ibrahimov, Shaig; Tuzikov, Alexander; De Wever, Aaike; Moncheva, Snejana; Spassov, Nikolai; Chobot, Karel; Popov, Alexi; Boršić, Igor; Sfenthourakis, Spyros; Kõljalg, Urmas; Uotila, Pertti; Olivier, Gargominy; Dauvin, Jean-Claude; Tarkhnishvili, David; Chaladze, Giorgi; Tuerkay, Michael; Legakis, Anastasios; Peregovits, László; Gudmundsson, Gudmundur; Ólafsson, Erling; Lysaght, Liam; Galil, Bella Sarah; Raimondo, Francesco M.; Domina, Gianniantonio; Stoch, Fabio; Minelli, Alessandro; Spungis, Voldermars; Budrys, Eduardas; Olenin, Sergej; Turpel, Armand; Walisch, Tania; Krpach, Vladimir; Gambin, Marie Therese; Ungureanu, Laurentia; Karaman, Gordan; Kleukers, Roy M.J.C.; Stur, Elisabeth; Aagaard, Kaare; Valland, Nils; Moen, Toril Loennechen; Bogdanowicz, Wieslaw; Tykarski, Piotr; Węsławski, Jan Marcin; Kędra, Monika; M. de Frias Martins, Antonio; Abreu, António Domingos; Silva, Ricardo; Medvedev, Sergei; Ryss, Alexander; Šimić, Smiljka; Marhold, Karol; Stloukal, Eduard; Tome, Davorin; Ramos, Marian A.; Valdés, Benito; Pina, Francisco; Kullander, Sven; Telenius, Anders; Gonseth, Yves; Tschudin, Pascal; Sergeyeva, Oleksandra; Vladymyrov, Volodymyr; Rizun, Volodymyr Bohdanovych; Raper, Chris; Lear, Dan; Stoev, Pavel; Penev, Lyubomir; Rubio, Ana Casino; Backeljau, Thierry; Saarenmaa, Hannu; Ulenberg, Sandrine

    2015-01-01

    Abstract Background Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools. The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information. New information This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs. PMID:26491393

  4. Laccase-assisted grafting of poly(3-hydroxybutyrate) onto the bacterial cellulose as backbone polymer: development and characterisation.

    Science.gov (United States)

    Iqbal, Hafiz M N; Kyazze, Godfrey; Tron, Thierry; Keshavarz, Tajalli

    2014-11-26

    Bacterial cellulose (BC) exhibits high purity, mechanical strength and an ultra-fine fibrous 3-D network structure with bio-compatible and bio-degradable characteristics, while P(3 HB) are a bio-degradable matrix material derived from natural resources. Herein, we report a mild and eco-friendly fabrication of indigenously isolated P(3 HB) based novel composites consisting of BC (a straight-chain polysaccharide) as a backbone polymer and laccase was used as a grafting tool. The resulting composites were characterised by Fourier-transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), X-ray diffraction (XRD), differential scanning calorimetry (DSC), dynamic mechanical analyser (DMA) and water contact angle analyser (WCA). The FTIR spectra of the pure P(3 HB) and P(3 HB) containing graft composites [P(3 HB)-g-BC] showed their strong characteristic bands at 3358 cm(-1), 1721 cm(-1) and 1651 cm(-1), respectively. A homogenous dispersion of P(3 HB) in the backbone polymer of BC was achieved as evident by the SEM micrographs. XRD pattern for P(3 HB) showed distinct peaks at 2θ values that represent the crystalline nature of P(3 HB). While, in comparison with those of neat P(3 HB), the degree of crystallinity for P(3 HB)-g-BC decreased and this reduction is mainly because of the new cross-linking of P(3 HB) within the backbone polymer that changes the morphology and destroys the crystallites. Laccase-assisted graft composite prepared from P(3 HB) and BC was fairly flexible and strong, judged by the tensile strength (64.5 MPa), elongations at break (15.7%), and Young's modulus (0.98 GPa) because inherently high strength of BC allowed the mechanical properties of P(3 HB) to improve in the P(3 HB)-g-BC composite. The hydrophilic property of the P(3 HB)-g-BC was much better than that of the individual counterparts which is also a desired characteristic to enhance the biocompatibility of the materials for proper cell adhesion and proliferation.

  5. Design of HIV-1 Protease Inhibitors with Amino-bis-tetrahydrofuran Derivatives as P2-Ligands to Enhance Backbone-Binding Interactions. Synthesis, Biological Evaluation, and Protein-Ligand X-ray Studies

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Arun K.; Martyr, Cuthbert D.; Osswald, Heather L.; Sheri, Venkat Reddy; Kassekert, Luke A.; Chen, Shujing; Agniswamy, Johnson; Wang, Yuan-Fang; Hayashi, Hironori; Aoki, Manabu; Weber, Irene T.; Mitsuya, Hiroaki (GSU); (Kumamoto); (Purdue)

    2015-10-30

    Structure-based design, synthesis, and biological evaluation of a series of very potent HIV-1 protease inhibitors are described. In an effort to improve backbone ligand–binding site interactions, we have incorporated basic-amines at the C4 position of the bis-tetrahydrofuran (bis-THF) ring. We speculated that these substituents would make hydrogen bonding interactions in the flap region of HIV-1 protease. Synthesis of these inhibitors was performed diastereoselectively. A number of inhibitors displayed very potent enzyme inhibitory and antiviral activity. Inhibitors 25f, 25i, and 25j were evaluated against a number of highly-PI-resistant HIV-1 strains, and they exhibited improved antiviral activity over darunavir. Two high resolution X-ray structures of 25f- and 25g-bound HIV-1 protease revealed unique hydrogen bonding interactions with the backbone carbonyl group of Gly48 as well as with the backbone NH of Gly48 in the flap region of the enzyme active site. These ligand–binding site interactions are possibly responsible for their potent activity.

  6. SYNTHESIS OF BIMODAL POLYETHYLENE WITH UNSYMMETRICAL α-DIIMINE NICKEL COMPLEXES: INFLUENCE OF LIGAND BACKBONE AND UNSYM-SUBSTITUTED ANILINE MOIETY

    Institute of Scientific and Technical Information of China (English)

    Hai-yang Gao; Feng-shou Liu; Hai-bin Hu; Fang-ming Zhu; Qing Wu

    2013-01-01

    A series of unsymmetrical α-diimine nickel complexes with various backbones and substituted aniline moieties were synthesized and characterized.The crystallographic analysis of the nickel complexes confirmed the existence of mesoand rac-configuration in solid structure.Nickel complexes after activation by MAO were screened for ethylene polymerization to evaluate backbone substituent effect on synthesis of bimodal PE.Acenaphthyl nickel complex with planar backbone afforded a bimodal PE with a broad polydispersity,whereas camphyl nickel complex with rigid and bulky backbone afforded a monomodal PE with a narrow polydispersity.Steric effect of aniline moiety for acenaphthyl nickel complex was also examined,and bimodal PE with dominant high-molecular-weight fraction was obtained by modifying substituents on aniline moiety.

  7. B-DNA structure is intrinsically polymorphic: even at the level of base pair positions

    Energy Technology Data Exchange (ETDEWEB)

    Maehigashi, Tatsuya; Hsiao, Chiaolong; Woods, Kristen Kruger; Moulaei, Tinoush; Hud, Nicholas V.; Williams, Loren Dean (GIT)

    2012-10-23

    Increasingly exact measurement of single crystal X-ray diffraction data offers detailed characterization of DNA conformation, hydration and electrostatics. However, instead of providing a more clear and unambiguous image of DNA, highly accurate diffraction data reveal polymorphism of the DNA atomic positions and conformation and hydration. Here we describe an accurate X-ray structure of B-DNA, painstakingly fit to a multistate model that contains multiple competing positions of most of the backbone and of entire base pairs. Two of ten base-pairs of CCAGGCCTGG are in multiple states distinguished primarily by differences in slide. Similarly, all the surrounding ions are seen to fractionally occupy discrete competing and overlapping sites. And finally, the vast majority of water molecules show strong evidence of multiple competing sites. Conventional resolution appears to give a false sense of homogeneity in conformation and interactions of DNA. In addition, conventional resolution yields an average structure that is not accurate, in that it is different from any of the multiple discrete structures observed at high resolution. Because base pair positional heterogeneity has not always been incorporated into model-building, even some high and ultrahigh-resolution structures of DNA do not indicate the full extent of conformational polymorphism.

  8. Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology

    International Nuclear Information System (INIS)

    Chemical shifts of nuclei in or attached to a protein backbone are exquisitely sensitive to their local environment. A computer program, SPARTA, is described that uses this correlation with local structure to predict protein backbone chemical shifts, given an input three-dimensional structure, by searching a newly generated database for triplets of adjacent residues that provide the best match in φ/ψ/χ1 torsion angles and sequence similarity to the query triplet of interest. The database contains 15N, 1HN, 1Hα, 13Cα, 13Cβ and 13C' chemical shifts for 200 proteins for which a high resolution X-ray (≤2.4 A) structure is available. The relative importance of the weighting factors for the φ/ψ/χ1 angles and sequence similarity was optimized empirically. The weighted, average secondary shifts of the central residues in the 20 best-matching triplets, after inclusion of nearest neighbor, ring current, and hydrogen bonding effects, are used to predict chemical shifts for the protein of known structure. Validation shows good agreement between the SPARTA-predicted and experimental shifts, with standard deviations of 2.52, 0.51, 0.27, 0.98, 1.07 and 1.08 ppm for 15N, 1HN, 1Hα, 13Cα, 13Cβ and 13C', respectively, including outliers

  9. RosettaRemodel: a generalized framework for flexible backbone protein design.

    Directory of Open Access Journals (Sweden)

    Po-Ssu Huang

    Full Text Available We describe RosettaRemodel, a generalized framework for flexible protein design that provides a versatile and convenient interface to the Rosetta modeling suite. RosettaRemodel employs a unified interface, called a blueprint, which allows detailed control over many aspects of flexible backbone protein design calculations. RosettaRemodel allows the construction and elaboration of customized protocols for a wide range of design problems ranging from loop insertion and deletion, disulfide engineering, domain assembly, loop remodeling, motif grafting, symmetrical units, to de novo structure modeling.

  10. Primerjava JavaScript ogrodij Angular, Backbone in Ember

    OpenAIRE

    Simin, Matija

    2016-01-01

    Diplomsko delo primerja tri JavaScript ogrodja za razvoj spletnih aplikacij, in sicer AngularJS, Ember.js in Backbone.js. V okviru dela smo primerjali njihovo implementacijo MVC arhitekturnega modela ali različice le-tega. Poleg implementacije MVC arhitekturnega modela smo primerjali njihove funkcionalnosti in lastnosti, kot so sistem predlog, implementacija usmerjevalnika, komunikacija s strežnikom, podatkovne povezave, prilagodljivosti, velikost in aktivnost skupnosti, kvaliteta obstoje...

  11. Comparison of JavaScript frameworks, Angular, Backbone, and Ember

    OpenAIRE

    Simin, Matija

    2016-01-01

    The thesis compares three JavaScript frameworks for developing web applications: AngularJS, Ember.js and Backbone.js. In the thesis we compared their implementation of the MVC design pattern and their subversions. Besides their implementation of MVC design pattern we compared their functionalities and features, such as templating system, routing implementation, communications with a server, data binding, adjustability, size and activity of the community, quality of existing documentation, pos...

  12. Backbone decomposition for continuous-state branching processes with immigration

    CERN Document Server

    Ren, A E Kyprianou Y-X

    2011-01-01

    In the spirit of Duqesne and Winkel (2007) and Berestycki et al. (2011) we show that supercritical continuous-state branching process with a general branching mechanism and general immigration mechanism is equal in law to a continuous-time Galton Watson process with immigration with Poissonian dressing. The result also characterises the limiting backbone decomposition which is predictable from the work on consistent growth of Galton-Watson trees with immigration in Cao and Winkel (2010).

  13. Extracting the multiscale backbone of complex weighted networks

    Science.gov (United States)

    Serrano, M. Ángeles; Boguñá, Marián; Vespignani, Alessandro

    2009-01-01

    A large number of complex systems find a natural abstraction in the form of weighted networks whose nodes represent the elements of the system and the weighted edges identify the presence of an interaction and its relative strength. In recent years, the study of an increasing number of large-scale networks has highlighted the statistical heterogeneity of their interaction pattern, with degree and weight distributions that vary over many orders of magnitude. These features, along with the large number of elements and links, make the extraction of the truly relevant connections forming the network's backbone a very challenging problem. More specifically, coarse-graining approaches and filtering techniques come into conflict with the multiscale nature of large-scale systems. Here, we define a filtering method that offers a practical procedure to extract the relevant connection backbone in complex multiscale networks, preserving the edges that represent statistically significant deviations with respect to a null model for the local assignment of weights to edges. An important aspect of the method is that it does not belittle small-scale interactions and operates at all scales defined by the weight distribution. We apply our method to real-world network instances and compare the obtained results with alternative backbone extraction techniques. PMID:19357301

  14. 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.

  15. 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.

  16. Reduced Dimensionality (4,3)D-hnCOCANH Experiment: An Efficient Backbone Assignment tool for NMR studies of Proteins

    CERN Document Server

    Kumar, Dinesh

    2013-01-01

    Sequence specific resonance assignment and secondary structure determination of proteins form the basis for variety of structural and functional proteomics studies by NMR. In this context, an efficient standalone method for rapid assignment of backbone (1H, 15N, 13Ca and 13C') resonances and secondary structure determination of proteins has been presented here. Compared to currently available strategies used for the purpose, the method employs only a single reduced dimensionality (RD) experiment -(4,3)D-hnCOCANH and exploits the linear combinations of backbone (13Ca and 13C') chemical shifts to achieve a dispersion relatively better compared to those of individual chemical shifts (see the text) for efficient and rapid data analysis. Further, the experiment leads to the spectrum with direct distinction of self (intra-residue) and sequential (inter-residue) carbon correlation peaks; these appear opposite in signs and therefore can easily be discriminated without using an additional complementary experiment. On ...

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

    DEFF Research Database (Denmark)

    Zong, Yu; Xu, Guandong; Jin, Pin;

    2011-01-01

    In social annotation systems, users label digital resources by using tags which are freely chosen textual descriptions. Tags are used to index, annotate and retrieve resource as an additional metadata of resource. Poor retrieval performance remains a major problem of most social tagging systems...

  18. Motion Structural Optimization Strategy for Rhombic Element Based Foldable Structure

    Directory of Open Access Journals (Sweden)

    Seung Hyun Jeong

    2015-02-01

    Full Text Available This research presents a new systematical design approach of foldable structure composed of several rhombic elements by applying genetic algorithm. As structural shapes represented by a foldable structure can be easily and dramatically morphed by manipulating rotational directions and angle of joints, the foldable structure has been used for various elementary structural members and engineering mechanisms. However a systematic design approach determining detail rotational angle and directions of unit cells for arbitrary shaped target areas has not been proposed yet. This research contributes to it by developing a new structural optimization method determining optimal angle and rotation directions to cover arbitrary shaped target areas of interest with aggregated rhombic elements. To achieve this purpose, we present an optimization formulation minimizing the sum of distances between each reference joint of an arbitrary shaped target area and its closest outer joints of foldable structure. To find out the outer joint set of a given foldable structure, an efficient geometric analysis method based on Delaunay triangulation is also developed and implemented. To show the validity and limitations of the present approach, several foldable structure design problems for two-dimensional arbitrary shaped target areas are solved with the present optimization procedure.

  19. 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.

  20. Silence is Golden with High Probability: Maintaining a Connected Backbone in Wireless Sensor Networks

    OpenAIRE

    Santi, Paolo; Simon, J?nos

    2003-01-01

    Reducing node energy consumption to extend network life- time is a vital requirement in wireless sensor networks. In this paper, we present and analyze the energy consumption of a class of cell-based energy conservation protocols. The goal of our protocols is to alternately turn off/on the transceivers of the nodes, while maintaining a connected backbone of active nodes. The protocols presented in this paper are shown to be optimal, in the sense that they extend the network lifetime by a fact...

  1. On the photostability of peptides after selective photoexcitation of the backbone: Prompt versus slow dissociation

    DEFF Research Database (Denmark)

    Byskov, Camilla Skinnerup; Jensen, Frank; Jørgensen, Thomas J D;

    2014-01-01

    , which is remote from the initial site of excitation. Hence loss of CE serves as direct proof that energy has reached the charge-site end, leaving the backbone intact. Our work demonstrates that excitation of tertiary amide moieties (proline linkages) results in both prompt dissociation and statistical...... present a protocol to disentangle slow and non-hazardous statistical dissociation from prompt cleavage of peptide bonds by 210 nm light based on experiments on protonated peptides isolated in vacuo and tagged by 18-crown-6 ether (CE). The weakest link in the system is between the charged site and CE...

  2. 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 load...

  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. Colloidal quantum dot lasers built on a passive two-dimensional photonic crystal backbone

    Science.gov (United States)

    Chang, Hojun; Min, Kyungtaek; Lee, Myungjae; Kang, Minsu; Park, Yeonsang; Cho, Kyung-Sang; Roh, Young-Geun; Woo Hwang, Sung; Jeon, Heonsu

    2016-03-01

    We report the room-temperature lasing action from two-dimensional photonic crystal (PC) structures composed of a passive Si3N4 backbone with an over-coat of CdSe/CdS/ZnS colloidal quantum dots (CQDs) for optical gain. When optically excited, devices lased in dual PC band-edge modes, with the modal dominance governed by the thickness of the CQD over-layer. The demonstrated laser platform should have an impact on future photonic integrated circuits as the on-chip coupling between active and passive components is readily achievable.We report the room-temperature lasing action from two-dimensional photonic crystal (PC) structures composed of a passive Si3N4 backbone with an over-coat of CdSe/CdS/ZnS colloidal quantum dots (CQDs) for optical gain. When optically excited, devices lased in dual PC band-edge modes, with the modal dominance governed by the thickness of the CQD over-layer. The demonstrated laser platform should have an impact on future photonic integrated circuits as the on-chip coupling between active and passive components is readily achievable. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr08544f

  5. Automated assignment of NMR chemical shifts based on a known structure and 4D spectra.

    Science.gov (United States)

    Trautwein, Matthias; Fredriksson, Kai; Möller, Heiko M; Exner, Thomas E

    2016-08-01

    Apart from their central role during 3D structure determination of proteins the backbone chemical shift assignment is the basis for a number of applications, like chemical shift perturbation mapping and studies on the dynamics of proteins. This assignment is not a trivial task even if a 3D protein structure is known and needs almost as much effort as the assignment for structure prediction if performed manually. We present here a new algorithm based solely on 4D [(1)H,(15)N]-HSQC-NOESY-[(1)H,(15)N]-HSQC spectra which is able to assign a large percentage of chemical shifts (73-82 %) unambiguously, demonstrated with proteins up to a size of 250 residues. For the remaining residues, a small number of possible assignments is filtered out. This is done by comparing distances in the 3D structure to restraints obtained from the peak volumes in the 4D spectrum. Using dead-end elimination, assignments are removed in which at least one of the restraints is violated. Including additional information from chemical shift predictions, a complete unambiguous assignment was obtained for Ubiquitin and 95 % of the residues were correctly assigned in the 251 residue-long N-terminal domain of enzyme I. The program including source code is available at https://github.com/thomasexner/4Dassign . PMID:27484442

  6. Structural choice based on knowledge discovery system

    Institute of Scientific and Technical Information of China (English)

    邢方亮; 王光远

    2002-01-01

    Structural choice is a significant decision having an important influence on structural function, socialeconomics, structural reliability and construction cost. A Case Based Reasoning system with its retrieval partconstructed with a KDD subsystem, is put forward to make a decision for a large scale engineering project. Atypical CBR system consists of four parts: case representation, case retriever, evaluation, and adaptation. Acase library is a set of parameterized excellent and successful structures. For a structural choice, the key pointis that the system must be able to detect the pattern classes hidden in the case library and classify the input pa-rameters into classes properly. That is done by using the KDD Data Mining algorithm based on Self-OrganizingFeature Maps ( SOFM), which makes the whole system more adaptive, self-organizing, self-learning and open.

  7. Unique optimal solution instance and computational complexity of backbone in the graph bi-partitioning problem

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    As an important tool for heuristic design of NP-hard problems, backbone analysis has become a hot spot in theoretical computer science in recent years. Due to the difficulty in the research on computational complexity of the backbone, many researchers analyzed the backbone by statistic ways. Aiming to increase the backbone size which is usually very small by the existing methods, the unique optimal solution instance construction (UOSIC) is proposed for the graph bi-partitioning problem (GBP). Also, we prove by using the UOSIC that it is NP-hard to obtain the backbone, i.e. no algorithm exists to obtain the backbone of a GBP in polynomial time under the assumption that P ( NP. Our work expands the research area of computational complexity of the backbone. And the UOSIC provides a new way for heuristic design of NP-hard problems.

  8. Resistance of Feynman diagrams and the percolation backbone dimension.

    Science.gov (United States)

    Janssen, H K; Stenull, O; Oerding, K

    1999-06-01

    We present an alternative view of Feynman diagrams for the field theory of random resistor networks, in which the diagrams are interpreted as being resistor networks themselves. This simplifies the field theory considerably as we demonstrate by calculating the fractal dimension D(B) of the percolation backbone to three loop order. Using renormalization group methods we obtain D(B)=2+epsilon/21-172epsilon(2)/9261+2epsilon(3)[-74 639+22 680zeta(3)]/4 084 101, where epsilon=6-d with d being the spatial dimension and zeta(3)=1.202 057... .

  9. A phylogenetic backbone for Bivalvia: an RNA-seq approach.

    Science.gov (United States)

    González, Vanessa L; Andrade, Sónia C S; Bieler, Rüdiger; Collins, Timothy M; Dunn, Casey W; Mikkelsen, Paula M; Taylor, John D; Giribet, Gonzalo

    2015-02-22

    Bivalves are an ancient and ubiquitous group of aquatic invertebrates with an estimated 10 000-20 000 living species. They are economically significant as a human food source, and ecologically important given their biomass and effects on communities. Their phylogenetic relationships have been studied for decades, and their unparalleled fossil record extends from the Cambrian to the Recent. Nevertheless, a robustly supported phylogeny of the deepest nodes, needed to fully exploit the bivalves as a model for testing macroevolutionary theories, is lacking. Here, we present the first phylogenomic approach for this important group of molluscs, including novel transcriptomic data for 31 bivalves obtained through an RNA-seq approach, and analyse these data with published genomes and transcriptomes of other bivalves plus outgroups. Our results provide a well-resolved, robust phylogenetic backbone for Bivalvia with all major lineages delineated, addressing long-standing questions about the monophyly of Protobranchia and Heterodonta, and resolving the position of particular groups such as Palaeoheterodonta, Archiheterodonta and Anomalodesmata. This now fully resolved backbone demonstrates that genomic approaches using hundreds of genes are feasible for resolving phylogenetic questions in bivalves and other animals.

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

    CERN Document Server

    Krokhotin, Andrey; Peng, Xubiao

    2012-01-01

    We construct an energy function that describes the crystallographic structure of spermwhale 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 non-linear Schrodinger equation. Likewise, ours supports solitons as local minimum energy configurations. We describe the 1ABS backbone in terms of 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 multisoliton solution to extensive numerical heating and cooling experiments, over a very wide range of temperatures. We concentrate in particular to temperatures above 300K and below the theta-point unfolding temperature, which is around 348K. We confirm that the...

  11. Increased Diels-Alderase activity through backbone remodeling guided by Foldit players.

    Science.gov (United States)

    Eiben, Christopher B; Siegel, Justin B; Bale, Jacob B; Cooper, Seth; Khatib, Firas; Shen, Betty W; Players, Foldit; Stoddard, Barry L; Popovic, Zoran; Baker, David

    2012-02-01

    Computational enzyme design holds promise for the production of renewable fuels, drugs and chemicals. De novo enzyme design has generated catalysts for several reactions, but with lower catalytic efficiencies than naturally occurring enzymes. Here we report the use of game-driven crowdsourcing to enhance the activity of a computationally designed enzyme through the functional remodeling of its structure. Players of the online game Foldit were challenged to remodel the backbone of a computationally designed bimolecular Diels-Alderase to enable additional interactions with substrates. Several iterations of design and characterization generated a 24-residue helix-turn-helix motif, including a 13-residue insertion, that increased enzyme activity >18-fold. X-ray crystallography showed that the large insertion adopts a helix-turn-helix structure positioned as in the Foldit model. These results demonstrate that human creativity can extend beyond the macroscopic challenges encountered in everyday life to molecular-scale design problems. PMID:22267011

  12. Structurally Diverse Polyamines: Solid-Phase Synthesis and Interaction with DNA.

    Science.gov (United States)

    Umezawa, Naoki; Horai, Yuhei; Imamura, Yuki; Kawakubo, Makoto; Nakahira, Mariko; Kato, Nobuki; Muramatsu, Akira; Yoshikawa, Yuko; Yoshikawa, Kenichi; Higuchi, Tsunehiko

    2015-08-17

    A versatile solid-phase approach based on peptide chemistry was used to construct four classes of structurally diverse polyamines with modified backbones: linear, partially constrained, branched, and cyclic. Their effects on DNA duplex stability and structure were examined. The polyamines showed distinct activities, thus highlighting the importance of polyamine backbone structure. Interestingly, the rank order of polyamine ability for DNA compaction was different to that for their effects on circular dichroism and melting temperature, thus indicating that these polyamines have distinct effects on secondary and higher-order structures of DNA.

  13. A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream

    Science.gov (United States)

    Moriarty, Nigel W.; Tronrud, Dale E.; Adams, Paul D.; Karplus, P. Andrew

    2016-01-01

    Chemical restraints are a fundamental part of crystallographic protein structure refinement. In response to mounting evidence that conventional restraints have shortcomings, it has previously been documented that using backbone restraints that depend on the protein backbone conformation helps to address these shortcomings and improves the performance of refinements [Moriarty et al. (2014 ▸), FEBS J. 281, 4061–4071]. It is important that these improvements be made available to all in the protein crystallography community. Toward this end, a change in the default geometry library used by Phenix is described here. Tests are presented showing that this change will not generate increased numbers of outliers during validation, or deposition in the Protein Data Bank, during the transition period in which some validation tools still use the conventional restraint libraries. PMID:26894545

  14. A Framework for Preliminary Design of Aircraft Structures Based on Process Information. Part 1

    Science.gov (United States)

    Rais-Rohani, Masoud

    1998-01-01

    This report discusses the general framework and development of a computational tool for preliminary design of aircraft structures based on process information. The described methodology is suitable for multidisciplinary design optimization (MDO) activities associated with integrated product and process development (IPPD). The framework consists of three parts: (1) product and process definitions; (2) engineering synthesis, and (3) optimization. The product and process definitions are part of input information provided by the design team. The backbone of the system is its ability to analyze a given structural design for performance as well as manufacturability and cost assessment. The system uses a database on material systems and manufacturing processes. Based on the identified set of design variables and an objective function, the system is capable of performing optimization subject to manufacturability, cost, and performance constraints. The accuracy of the manufacturability measures and cost models discussed here depend largely on the available data on specific methods of manufacture and assembly and associated labor requirements. As such, our focus in this research has been on the methodology itself and not so much on its accurate implementation in an industrial setting. A three-tier approach is presented for an IPPD-MDO based design of aircraft structures. The variable-complexity cost estimation methodology and an approach for integrating manufacturing cost assessment into design process are also discussed. This report is presented in two parts. In the first part, the design methodology is presented, and the computational design tool is described. In the second part, a prototype model of the preliminary design Tool for Aircraft Structures based on Process Information (TASPI) is described. Part two also contains an example problem that applies the methodology described here for evaluation of six different design concepts for a wing spar.

  15. 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.

  16. Constructing Path Efficient and Energy Aware Virtual Multicast Backbones in Static Ad Hoc Wireless Networks

    Directory of Open Access Journals (Sweden)

    Tamaghna Acharya

    2010-05-01

    Full Text Available For stationary wireless ad hoc networks, one of the key challenging issues in routing and multicasting isto conserve as much energy as possible without compromising path efficiency measured as end-to-enddelay. In this paper, we address the problem of path efficient and energy aware multicasting in staticwireless ad hoc networks. We propose a novel distributed scalable algorithm for finding a virtualmulticast backbone (VMB. Based on this VMB, we have further developed a multicasting scheme thatjointly improves path efficiency and energy conservation. By exploiting inherent broadcast advantage ofwireless communication and employing a more realistic energy consumption model for wirelesscommunication which not only depends on radio propagation losses but also on energy losses intransceiver circuitry, our simulation results show that the proposed VMB-based multicasting schemeoutperforms existing prominent tree based energy conserving, path efficient multicasting schemes.

  17. EM Structure Based and Vacuum Acceleration

    Energy Technology Data Exchange (ETDEWEB)

    Colby, E.R.; /SLAC

    2005-09-27

    The importance of particle acceleration may be judged from the number of applications which require some sort of accelerated beam. In addition to accelerator-based high energy physics research, non-academic applications include medical imaging and treatment, structural biology by x-ray diffraction, pulse radiography, cargo inspection, material processing, food and medical instrument sterilization, and so on. Many of these applications are already well served by existing technologies and will profit only marginally from developments in accelerator technology. Other applications are poorly served, such as structural biology, which is conducted at synchrotron radiation facilities, and medical treatment using proton accelerators, the machines for which are rare because they are complex and costly. Developments in very compact, high brightness and high gradient accelerators will change how accelerators are used for such applications, and potentially enable new ones. Physical and technical issues governing structure-based and vacuum acceleration of charged particles are reviewed, with emphasis on practical aspects.

  18. Bamboo-based Panels for Structural Applications

    Institute of Scientific and Technical Information of China (English)

    CHENXuhe; WANGZheng

    2005-01-01

    With technical assistance from INBAR and the Research Institute of Wood Industry of the Chinese Academy of Forestry, the construction of the Pingbian Primary School was completed in 2004,where bamboo plywood panels and laminated beams were used for the roof trusses, sheathing boards and wall panels. This is the first time that bamboo-based panels are used for structural applications.

  19. Vibrational Based Inspection of Civil Engineering Structures

    DEFF Research Database (Denmark)

    Rytter, Anders

    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...

  20. Narrative Structure in Inquiry-Based Learning

    Science.gov (United States)

    Kinsey, L. Christine; Moore, Teresa E.

    2015-01-01

    Our goal with this paper is three-fold. We want to increase awareness of inquiry-based learning by presenting the strategy we use to develop and implement lessons and activities. We describe our approach to structuring lessons in mathematics in a way that engages the students by using language and constructs with which they are familiar from other…

  1. Dolutegravir treatment response by baseline viral load and NRTI backbone in treatment-naïve HIV-infected individuals

    Directory of Open Access Journals (Sweden)

    C Small

    2012-11-01

    Full Text Available Background: In two 48-week studies in naïve subjects, dolutegravir with NRTI of choice has shown non-inferiority to raltegravir and, with ABC/3TC, superiority to Atripla. Factors that influenced choice of NRTIs included viral load, resistance and safety. Methods: We analysed response rates and time to virologic failure by NRTI backbone and baseline viral load in the pivotal DTG-naïve studies. SPRING-2 randomized participants to DTG 50 mg QD or RAL 400 mg BID, each in combination with investigator-selected NRTIs (TDF/FTC or ABC/3TC. SINGLE randomised participants to DTG 50 mg+ABC/3TC QD or TDF/FTC/EFV (Atripla QD. In SPRING-2, changes in serum creatinine were examined by INI and NRTI backbone. Results: The two studies randomized and treated 1655 subjects, of whom 249 (15% were female, 388 (23% non-white, 495 (30% had HIV-1 RNA >100,000 c/ml, and 224 (14% had CD4+ count <200 cells/mm3. Primary analyses demonstrated non-inferiority of DTG to RAL in SPRING-2 (Δ=2.5%; 95% CI:−2.2% to +7.1%, excluding −10%, and superiority of the DTG regimen in SINGLE (7.4%; +2.5% to +12.3%. In SPRING-2, response rates by NRTI backbone were comparable in each viral load stratum. In SINGLE, a 7% difference in response (favoring DTG+ABC/3TC was observed in each viral load stratum. Exploratory analyses examining time-to-virologic failure showed no difference in response rates between the NRTIs irrespective of baseline viral load or study. Resistance to INIs or NRTIs was not demonstrated in any subject on DTG-based therapy through 48 weeks. Withdrawals due to AEs on DTG-based regimen were few (2% in both studies. In SPRING-2, no significant differences were observed in serum creatinine change from baseline to Week 48 by NRTI backbones. Conclusions: In SPRING-2 and SINGLE, DTG was effective with both ABC/3TC and TDF/FTC, and in subjects with high and low viral load. DTG was well tolerated in both studies. Renal safety also was similar by NRTI backbone. DTG is a once

  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. Bioactivities of fish protein hydrolysates from defatted salmon backbones

    Directory of Open Access Journals (Sweden)

    Rasa Slizyte

    2016-09-01

    Full Text Available Bioactivities of bulk fish protein hydrolysates (FPH from defatted salmon backbones obtained with eight different commercial enzymes and their combinations were tested. All FPH showed antioxidative activity in vitro. DPPH scavenging activity increased, while iron chelating ability decreased with increasing time of hydrolysis. All FPH showed ACE inhibiting effect which depended on type of enzyme and increased with time of hydrolysis. The highest effect was found for FPH produced with Trypsin. Bromelain + Papain hydrolysates reduced the uptake of radiolabelled glucose into CaCo-2 cells, a model of human enterocytes, indicating a potential antidiabetic effect of FPH. FPH obtained by Trypsin, Bromelain + Papain and Protamex showed the highest ACE inhibitory, cellular glucose transporter (GLUT/SGLT inhibitory and in vitro antioxidative activities, respectively. Correlation was observed between the measured bioactivities, degree of hydrolysis and molecular weight profiles, supporting prolonged hydrolysis to obtain high bioactivities.

  4. Reconstruction of the Sunspot Group Number: the Backbone Method

    CERN Document Server

    Svalgaard, Leif

    2015-01-01

    We have reconstructed the sunspot group count, not by comparisons with other reconstructions and correcting those where they were deemed to be deficient, but by a re-assessment of original sources. The resulting series is a pure solar index and does not rely on input from other proxies, e.g. radionuclides, auroral sightings, or geomagnetic records. 'Backboning' the data sets, our chosen method, provides substance and rigidity by using long-time observers as a stiffness character. Solar activity, as defined by the Group Number, appears to reach and sustain for extended intervals of time the same level in each of the last three centuries since 1700 and the past several decades do not seem to have been exceptionally active, contrary to what is often claimed.

  5. The Prediction of Botulinum Toxin Structure Based on in Silico and in Vitro Analysis

    Science.gov (United States)

    Suzuki, Tomonori; Miyazaki, Satoru

    2011-01-01

    Many of biological system mediated through protein-protein interactions. Knowledge of protein-protein complex structure is required for understanding the function. The determination of huge size and flexible protein-protein complex structure by experimental studies remains difficult, costly and five-consuming, therefore computational prediction of protein structures by homolog modeling and docking studies is valuable method. In addition, MD simulation is also one of the most powerful methods allowing to see the real dynamics of proteins. Here, we predict protein-protein complex structure of botulinum toxin to analyze its property. These bioinformatics methods are useful to report the relation between the flexibility of backbone structure and the activity.

  6. STRUCTURAL EVOLUTION IN BIORENEWABLE SOY BASED POLYURETHANES

    Institute of Scientific and Technical Information of China (English)

    Deepa Puthanparambil; Casey Kimball; Shaw Ling Hsu; Zhiyong Ren

    2009-01-01

    Spectroscopic studies have revealed that the amount of polyureas formed and the kinetics of their formation in soy based polyurethane systems are considerably different from traditional systems employing ethylene oxide-propylene oxide (EO-PO) based polyols. The aggregation of polyureas was characterized by the hydrogen bonds formed utilizing FTIR spectroscopy. This study offered the opportunity to assign the previously undefined infrared features. The structural transformation is reflected in the segmental relaxation kinetics characterized by spin-spin diffusion most conveniently measured using low field NMR. The reaction kinetics and the products formed are directly related to the hydrophobic nature of the soy based polyols and its inability to disperse water.

  7. Backbone dynamics of the human CC-chemokine eotaxin

    Energy Technology Data Exchange (ETDEWEB)

    Ye Jiqing; Mayer, Kristen L.; Stone, Martin J. [Indiana University, Department of Chemistry (United States)

    1999-10-15

    Eotaxin is a CC chemokine with potent chemoattractant activity towards eosinophils. {sup 15}N NMR relaxation data have been used to characterize the backbone dynamics of recombinant human eotaxin. {sup 15}N longitudinal (R{sub 1}) and transverse (R{sub 2}) auto relaxation rates, heteronuclear {sup 1}H-{sup 15}N steady-state NOEs, and transverse cross-relaxation rates ({eta}{sub xy}) were obtained at 30 deg. C for all resolved backbone secondary amide groups using {sup 1} H-detected two-dimensional NMR experiments. Ratios of transverse auto and cross relaxation rates were used to identify NH groups influenced by slow conformational rearrangement. Relaxation data were fit to the extended model free dynamics formalism, yielding parameters describing axially symmetric molecular rotational diffusion and the internal dynamics of each NH group. The molecular rotational correlation time ({tau}{sub m}) is 5.09{+-}0.02 ns, indicating that eotaxin exists predominantly as a monomer under the conditions of the NMR study. The ratio of diffusion rates about unique and perpendicular axes (D{sub parallel}/D{sub perpendicular}) is 0.81{+-}0.02. Residues with large amplitudes of subnanosecond motion are clustered in the N-terminal region (residues 1-19), the C-terminus (residues 68-73) and the loop connecting the first two {beta}-strands (residues 30-37). N-terminal flexibility appears to be conserved throughout the chemokine family and may have implications for the mechanism of chemokine receptor activation. Residues exhibiting significant dynamics on the microsecond-millisecond time scale are located close to the two conserved disulfide bonds, suggesting that these motions may be coupled to disulfide bond isomerization.

  8. Synthesis, spectroscopic characterization and crystal structure of novel NNNN-donor μ-bis(bidentate) tetraaza acyclic Schiff base ligands

    Science.gov (United States)

    Habibi, Mohammad Hossein; Shojaee, Elahe; Nichol, Gary S.

    2012-12-01

    Novel NNNN-donor μ-bis(bidentate) tetraaza acyclic Schiff base ligands with different substituents (CF3, N(CH3)2 or OH groups) were synthesized by the condensation reaction of triethylenetetramine with 4-substituted benzaldehydes. Triethylenetetramine tris(4-trifluoromethylbenzylidene) (TTFMB), triethylenetetramine tris(4-dimethylaminobenzylidene) (TTDMB) and triethylenetetramine tris(2,4-dihydroxybenzylidene) (TTDHB) were formed as N4 donor ligands. The formation of a five-membered imidazolidine ring from the ethylenediamine backbone as a spacer-cumbridging unit gives rise to a new type of imidazolidine ligand. The structure of the TTFMB and TTDMB were determined by single crystal X-ray crystallography. The synthesized ligands have been characterized on the basis of the results of cyclic voltammetry (CV) and spectroscopic studies viz. FT-IR spectroscopy (FT-IR), mass spectroscopy (MS) and UV-Vis spectroscopy (UV-Vis).

  9. Efficiency of paramagnetism-based constraints to determine the spatial arrangement of {alpha}-helical secondary structure elements

    Energy Technology Data Exchange (ETDEWEB)

    Bertini, Ivano [University of Florence, CERM and Department of Chemistry (Italy)], E-mail: bertini@cerm.unifi.it; Longinetti, Marco [Dipartimento di Ingegneria Agraria e Forestale (Italy); Luchinat, Claudio; Parigi, Giacomo [University of Florence, CERM and Department of Agricultural Biotechnology (Italy); Sgheri, Luca [Istituto di Analisi Globale ed Applicazioni (CNR) (Italy)

    2002-02-15

    A computational approach has been developed to assess the power of paramagnetism-based backbone constraints with respect to the determination of the tertiary structure, once the secondary structure elements are known. This is part of the general assessment of paramagnetism-based constraints which are known to be relevant when used in conjunction with all classical constraints. The paramagnetism-based constraints here investigated are the pseudocontact shifts, the residual dipolar couplings due to self-orientation of the metalloprotein in high magnetic fields, and the cross correlation between dipolar relaxation and Curie relaxation. The relative constraints are generated by back-calculation from a known structure. The elements of secondary structure are supposed to be obtained from chemical shift index. The problem of the reciprocal orientation of the helices is addressed. It is shown that the correct fold can be obtained depending on the length of the {alpha}-helical stretches with respect to the length of the non helical segments connecting the {alpha}-helices. For example, the correct fold is straightforwardly obtained for the four-helix bundle protein cytochrome b{sub 562}, while the double EF-hand motif of calbindin D{sub 9k} is hardly obtained without ambiguity. In cases like calbindin D{sub 9k}, the availability of datasets from different metal ions is helpful, whereas less important is the location of the metal ion with respect to the secondary structure elements.

  10. Track Based Alignment of Composite Detector Structures

    CERN Document Server

    Karimäki, V; Schilling, F P

    2006-01-01

    An iterative algorithm for track based alignment is presented. The algorithm can be applied to rigid composite detector structures or to individual modules. The iterative process involves track reconstruction and alignment, in which the chi-2 function of the hit residuals of each alignable object is minimized. Six alignment parameters per structure or per module, three for location and three for orientation, can be computed. The method is computationally light and easily parallelizable. The performance of the method is demonstrated with simulated tracks in the CMS pixel detector and tracks reconstructed from experimental data recorded with a test beam setup.

  11. 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.

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

    International Nuclear Information System (INIS)

    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.

  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. Fluorous Peptide Nucleic Acids: PNA Analogues with Fluorine in Backbone (γ-CF2-apg-PNA) Enhance Cellular Uptake.

    Science.gov (United States)

    Ellipilli, Satheesh; Ganesh, Krishna N

    2015-09-18

    Fluorous PNA analogues possessing fluorine as inherent part of aminopropylglycine (apg) backbone (γ-CF2-apg PNA) have been synthesized and evaluated for biophysical and cell penetrating properties. These form duplexes of higher thermal stability with cRNA than cDNA, although destabilized compared to duplexes of standard aeg-PNA. Cellular uptake of the fluorinated γ-CF2-apg PNAs in NIH 3T3 and HeLa cells was 2-3-fold higher compared to that of nonfluorinated apg PNA, with NIH 3T3 cells showing better permeability compared to HeLa cells. The backbone fluorinated PNAs, which are first in this class, when combined with other chemical modifications may have potential for future PNA-based antisense agents. PMID:26322827

  15. Subpicosecond protein backbone changes detected during the green-absorbing proteorhodopsin primary photoreaction.

    Science.gov (United States)

    Amsden, Jason J; Kralj, Joel M; Chieffo, Logan R; Wang, Xihua; Erramilli, Shyamsunder; Spudich, Elena N; Spudich, John L; Ziegler, Lawrence D; Rothschild, Kenneth J

    2007-10-11

    Recent studies demonstrate that photoactive proteins can react within several picoseconds to photon absorption by their chromophores. Faster subpicosecond protein responses have been suggested to occur in rhodopsin-like proteins where retinal photoisomerization may impulsively drive structural changes in nearby protein groups. Here, we test this possibility by investigating the earliest protein structural changes occurring in proteorhodopsin (PR) using ultrafast transient infrared (TIR) spectroscopy with approximately 200 fs time resolution combined with nonperturbing isotope labeling. PR is a recently discovered microbial rhodopsin similar to bacteriorhodopsin (BR) found in marine proteobacteria and functions as a proton pump. Vibrational bands in the retinal fingerprint (1175-1215 cm(-1)) and ethylenic stretching (1500-1570 cm(-1)) regions characteristic of all-trans to 13-cis chromophore isomerization and formation of a red-shifted photointermediate appear with a 500-700 fs time constant after photoexcitation. Bands characteristic of partial return to the ground state evolve with a 2.0-3.5 ps time constant. In addition, a negative band appears at 1548 cm(-1) with a time constant of 500-700 fs, which on the basis of total-15N and retinal C15D (retinal with a deuterium on carbon 15) isotope labeling is assigned to an amide II peptide backbone mode that shifts to near 1538 cm(-1) concomitantly with chromophore isomerization. Our results demonstrate that one or more peptide backbone groups in PR respond with a time constant of 500-700 fs, almost coincident with the light-driven retinylidene chromophore isomerization. The protein changes we observe on a subpicosecond time scale may be involved in storage of the absorbed photon energy subsequently utilized for proton transport. PMID:17880126

  16. The Role of Backbone Hydrogen Bonds in the Transition State for Protein Folding of a PDZ Domain.

    Directory of Open Access Journals (Sweden)

    Søren W. Pedersen

    Full Text Available Backbone hydrogen bonds are important for the structure and stability of proteins. However, since conventional site-directed mutagenesis cannot be applied to perturb the backbone, the contribution of these hydrogen bonds in protein folding and stability has been assessed only for a very limited set of small proteins. We have here investigated effects of five amide-to-ester mutations in the backbone of a PDZ domain, a 90-residue globular protein domain, to probe the influence of hydrogen bonds in a β-sheet for folding and stability. The amide-to-ester mutation removes NH-mediated hydrogen bonds and destabilizes hydrogen bonds formed by the carbonyl oxygen. The overall stability of the PDZ domain generally decreased for all amide-to-ester mutants due to an increase in the unfolding rate constant. For this particular region of the PDZ domain, it is therefore clear that native hydrogen bonds are formed after crossing of the rate-limiting barrier for folding. Moreover, three of the five amide-to-ester mutants displayed an increase in the folding rate constant suggesting that the hydrogen bonds are involved in non-native interactions in the transition state for folding.

  17. 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...

  18. Electronic structure of Fe-based superconductors

    Indian Academy of Sciences (India)

    Kalobaran Maiti

    2015-06-01

    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 role of states in their electronic properties, which is significantly different from the cuprate superconductors. In this article, some of our studies of the electronic structure of these fascinating systems employing high-resolution photoemission spectroscopy is reviewed. The combined effect of electron correlation and covalency reveals an interesting scenario in their electronic structure. The contribution of ligand states at the Fermi level is found to be much more significant than indicated in earlier studies. Temperature evolution of the energy bands reveals the signature of transition akin to Lifshitz transition in these systems.

  19. Protein side-chain resonance assignment and NOE assignment using RDC-defined backbones without TOCSY data

    Energy Technology Data Exchange (ETDEWEB)

    Zeng Jianyang [Duke University, Department of Computer Science (United States); Zhou Pei [Duke University Medical Center, Department of Biochemistry (United States); Donald, Bruce Randall [Duke University, Department of Computer Science (United States)

    2011-08-15

    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

  20. (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. PMID:26154586

  1. Light weight cellular structures based on aluminium

    Energy Technology Data Exchange (ETDEWEB)

    Prakash, O. [Indian Inst. of Tech., Kanpur (India); Embury, J.D.; Sinclair, C. [McMaster Univ., Hamilton, ON (Canada); Sang, H. [Queen`s Univ., Kingston, ON (Canada); Silvetti, P. [Cordoba Univ. Nacional (Argentina). Facultad de Ciencias Exactas, Fisicas y Naturales

    1997-02-01

    An interesting form of lightweight material which has emerged in the past 2 decades is metallic foam. This paper deals with the basic concepts of making metallic foams and a detailed study of foams produced from Al-SiC. In addition, some aspects of cellular solids based on honeycomb structures are outlined including the concept of producing both two-phase foams and foams with composite walls.

  2. 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...

  3. 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 h

  4. Structure-Based Design of Ricin Inhibitors

    Directory of Open Access Journals (Sweden)

    Jon D. Robertus

    2011-10-01

    Full Text Available Ricin is a potent cytotoxin easily purified in large quantities. It presents a significant public health concern due to its potential use as a bioterrorism agent. For this reason, extensive efforts have been underway to develop antidotes against this deadly poison. The catalytic A subunit of the heterodimeric toxin has been biochemically and structurally well characterized, and is an attractive target for structure-based drug design. Aided by computer docking simulations, several ricin toxin A chain (RTA inhibitors have been identified; the most promising leads belonging to the pterin family. Development of these lead compounds into potent drug candidates is a challenging prospect for numerous reasons, including poor solubility of pterins, the large and highly polar secondary binding pocket of RTA, as well as the enzyme’s near perfect catalytic efficiency and tight binding affinity for its natural substrate, the eukaryotic ribosome. To date, the most potent RTA inhibitors developed using this approach are only modest inhibitors with apparent IC50 values in the 10−4 M range, leaving significant room for improvement. This review highlights the variety of techniques routinely employed in structure-based drug design projects, as well as the challenges faced in the design of RTA inhibitors.

  5. Data acquisition backbone core DABC release v1.0

    International Nuclear Information System (INIS)

    The new experiments at FAIR require new concepts of data acquisition systems for the distribution of self-triggered, time stamped data streams over high performance networks for event building. The Data Acquisition Backbone Core (DABC) is a general purpose software framework developed for the implementation of such data acquisition systems. A DABC application consists of functional components like data input, combiner, scheduler, event builder, filter, analysis and storage which can be configured at runtime. Application specific code including the support of all kinds of data channels (front-end systems) is implemented by C++ program plug-ins. DABC is also well suited as environment for various detector and readout components test beds. A set of DABC plug-ins has been developed for the FAIR experiment CBM (Compressed Baryonic Matter) at GSI. This DABC application is used as DAQ system for test beamtimes. Front-end boards equipped with n-XYTER ASICs and ADCs are connected to read-out controller boards (ROC). From there the data is sent over Ethernet (UDP), or over optics and PCIe interface cards into Linux PCs. DABC does the controlling, event building, archiving and data serving. The first release of DABC was published in 2009 and is available under GPL license.

  6. Solid state radiation chemistry of the DNA backbone

    International Nuclear Information System (INIS)

    The long term goal of this program is to determine the fundamental rules needed to predict the type and yield of damage produced in DNA due to direct effects of ionizing radiation. The focus is on damage to the sugar-phosphate backbone, damage that would lead to strand breaks. Model systems have been chosen that permit various aspects of this problem to be investigated. The emphasis will be on single crystals of monosaccharides, nucleosides, and nucleotides but will also include some powder work on polynucleotides. In these model systems, free radical products and reactions are observed by electron spin resonance (ESR) and electron nuclear double resonance (ENDOR) techniques. The information thus gained is used in constructing rules that predict what primary free radicals are formed in single crystals of model compounds and the reactions stemming from the primary radicals. The formulation of a set of rules that work in model systems will represent a major advance toward formulating a set of rules that predict the direct damage in DNA itself. In a broader context this program is part of the effort to understand and predict the effects of exposure to ionizing radiation received at low dose rates over long periods of time. Assessment of low dose effects requires a basic understanding of the action of radiation at the molecular level. By contributing to that basic understanding, this program will help solve the problems of risk assessment under low dose conditions. 5 refs., 3 figs

  7. Adaptive GOP structure based on motion coherence

    Science.gov (United States)

    Ma, Yanzhuo; Wan, Shuai; Chang, Yilin; Yang, Fuzheng; Wang, Xiaoyu

    2009-08-01

    Adaptive Group of Pictures (GOP) is helpful for increasing the efficiency of video encoding by taking account of characteristics of video content. This paper proposes a method for adaptive GOP structure selection for video encoding based on motion coherence, which extracts key frames according to motion acceleration, and assigns coding type for each key and non-key frame correspondingly. Motion deviation is then used instead of motion magnitude in the selection of the number of B frames. Experimental results show that the proposed method for adaptive GOP structure selection achieves performance gain of 0.2-1dB over the fixed GOP, and has the advantage of better transmission resilience. Moreover, this method can be used in real-time video coding due to its low complexity.

  8. 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.

  9. 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.

  10. Antigenic characterization of influenza viruses produced using synthetic DNA and novel backbones.

    Science.gov (United States)

    Suphaphiphat, Pirada; Whittaker, Lynne; De Souza, Ivna; Daniels, Rodney S; Dormitzer, Philip R; McCauley, John W; Settembre, Ethan C

    2016-07-12

    The global system for manufacturing seasonal influenza vaccines has been developed to respond to the natural evolution of influenza viruses, but the problem of antigenic mismatch continues to be a challenge in certain years. In some years, mismatches arise naturally due to the antigenic drift of circulating viruses after vaccine strain selection has already been made. In other years, antigenic differences between the vaccine virus and circulating viruses are introduced as part of the current system, which relies on the use of egg-adapted isolates as a starting material for candidate vaccine viruses (CVVs). Improving the current process for making vaccine viruses can provide great value. We have previously established a synthetic approach for rapidly generating influenza viruses in a vaccine-approved Madin Darby canine kidney (MDCK) cell line using novel, high-growth backbones that increase virus rescue efficiency and antigen yield. This technology also has the potential to produce viruses that maintain antigenic similarity to the intended reference viruses, depending on the hemagglutinin (HA) and neuraminidase (NA) sequences used for gene synthesis. To demonstrate this utility, we generated a panel of synthetic viruses using HA and NA sequences from recent isolates and showed by hemagglutination inhibition (HI) tests that all synthetic viruses were antigenically-like their conventional egg- or cell-propagated reference strains and there was no impact of the novel backbones on antigenicity. This synthetic approach can be used for the efficient production of CVVs that may be more representative of circulating viruses and may be used for both egg- and cell-based vaccine manufacturing platforms. When combined with mammalian cell culture technology for antigen production, synthetic viruses generated using HA and NA sequences from a non-egg-adapted prototype can help to reduce the potential impact of antigenic differences between vaccine virus and circulating viruses on

  11. Resistance issues with new nucleoside/nucleotide backbone options.

    Science.gov (United States)

    Wainberg, Mark A; Turner, Dan

    2004-09-01

    The nucleoside and nucleotide reverse transcriptase inhibitors (NRTIs/NtRTIs) remain an enduring feature of combination therapy. As NRTI/NtRTI options continue to expand, questions arise about how best to combine these agents to create effective dual NRTI/NtRTI backbones in antiretroviral regimens while avoiding treatment-emergent drug resistance. Clinicians must consider how NRTIs/NtRTIs such as tenofovir DF (TDF), abacavir (ABC), and emtricitabine (FTC), as well as new once-daily and coformulated NRTIs/NtRTIs, interact with older agents when combined in novel regimens and how sequencing the new NRTIs can preserve future treatment options. Resistance data from clinical trials have revealed important information on the patterns, prevalence, and effects of resistance seen among patients experiencing virologic failure. In recent years, the prevalence of some mutations such as M184V and Q151M has remained relatively constant, while the L74V mutation, the 69 insertions, and thymidine analogue mutations have decreased in prevalence. Other mutations such as K65R and Y115F, while still relatively uncommon, are increasing in prevalence. This increase may be due to the use of new treatment combinations that select for these mutations at a higher rate. Clinical trials suggest that new regimens containing TDF or ABC select for K65R and that this mutation is observed more frequently with TDF; in contrast, L74V is observed more frequently in ABC-containing regimens but is not commonly selected by TDF-containing regimens. Several lines of evidence are converging to suggest that the presence of zidovudine may decrease the risk of L74V and K65R in ABC- or TDF-containing regimens. This review summarizes the clinical implications of resistance profiles associated with new NRTI/NtRTI regimens in current use and in advanced clinical studies. PMID:15319668

  12. Conformation-specific spectroscopy of capped glutamine-containing peptides: role of a single glutamine residue on peptide backbone preferences.

    Science.gov (United States)

    Walsh, Patrick S; Dean, Jacob C; McBurney, Carl; Kang, Hyuk; Gellman, Samuel H; Zwier, Timothy S

    2016-04-28

    The conformational preferences of a series of short, aromatic-capped, glutamine-containing peptides have been studied under jet-cooled conditions in the gas phase. This work seeks a bottom-up understanding of the role played by glutamine residues in directing peptide structures that lead to neurodegenerative diseases. Resonant ion-dip infrared (RIDIR) spectroscopy is used to record single-conformation infrared spectra in the NH stretch, amide I and amide II regions. Comparison of the experimental spectra with the predictions of calculations carried out at the DFT M05-2X/6-31+G(d) level of theory lead to firm assignments for the H-bonding architectures of a total of eight conformers of four molecules, including three in Z-Gln-OH, one in Z-Gln-NHMe, three in Ac-Gln-NHBn, and one in Ac-Ala-Gln-NHBn. The Gln side chain engages actively in forming H-bonds with nearest-neighbor amide groups, forming C8 H-bonds to the C-terminal side, C9 H-bonds to the N-terminal side, and an amide-stacked geometry, all with an extended (C5) peptide backbone about the Gln residue. The Gln side chain also stabilizes an inverse γ-turn in the peptide backbone by forming a pair of H-bonds that bridge the γ-turn and stabilize it. Finally, the entire conformer population of Ac-Ala-Gln-NHBn is funneled into a single structure that incorporates the peptide backbone in a type I β-turn, stabilized by the Gln side chain forming a C7 H-bond to the central amide group in the β-turn not otherwise involved in a hydrogen bond. This β-turn backbone structure is nearly identical to that observed in a series of X-(AQ)-Y β-turns in the protein data bank, demonstrating that the gas-phase structure is robust to perturbations imposed by the crystalline protein environment.

  13. 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.

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

    Science.gov (United States)

    Pan, Chengqian; Shi, Yutong; Auckloo, Bibi Nazia; Chen, Xuegang; Chen, Chen-Tung Arthur; Tao, Xinyi; Wu, Bin

    2016-01-01

    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. PMID:27548192

  15. Interfacial Aspects of Polymer Based Photovoltaic Structures

    Science.gov (United States)

    Russell, Thomas

    2011-03-01

    Controlling thin film morphology is key in optimizing the efficiency of polymer-based photovoltaic (PV) devices. Poly(3- hexylthiophene) and [6,6]-penyl-C61 butyric acid methyl ester (P3HT:PCBM) based solar cell performance is dictated by nanostructure of the active layer, the interfaces between the active layer and the electrodes, and the P3HT chain orientation in the thin film. The above parameters were systematically studied by scanning transmission electron microscopy, scanning force microscopy, optical microscopy, grazing incident angle x- ray diffraction., dynamic secondary ion mass spectroscopy and near edge x-ray absorption fine structure analysis. The influence of thermal annealing on the morphology, interfaces and crystal structure was investigated in films that were either initially confined by two electrodes or confined by only one electrode. While the bulk morphology in these films were identical, significant differences in the concentration of components at the electrode interfaces were found, giving rise to a marked difference in performance. In addition, a model was established, based on the crystallization of the P3HTand the diffusion of the PCBM to describe the origins of the nanoscale morphology found in the active layer. The device performance parameters were quantitatively studied. In collaboration with D. Chen, H. Liu, Y. Gu and F. Lu at UMass Amherst, A. Nakahara at Kuraray Co., D. Wei at Carl Zeiss NTS LLC, D. Nordlund at SSRL and supported by the DOE-supported EFRC at the UMass Amherst (DE-PS02-08ER15944).

  16. Ruthenium-catalyzed olefin metathesis accelerated by the steric effect of the backbone substituent in cyclic (alkyl)(amino) carbenes.

    Science.gov (United States)

    Zhang, Jun; Song, Shangfei; Wang, Xiao; Jiao, Jiajun; Shi, Min

    2013-10-21

    Three ruthenium complexes bearing backbone-monosubstituted CAACs were prepared and displayed dramatic improvement in catalytic efficiency not only in RCM reaction but also in the ethenolysis of methyl oleate, compared to those bearing backbone-disubstituted CAACs.

  17. Ruthenium-catalyzed olefin metathesis accelerated by the steric effect of the backbone substituent in cyclic (alkyl)(amino) carbenes.

    Science.gov (United States)

    Zhang, Jun; Song, Shangfei; Wang, Xiao; Jiao, Jiajun; Shi, Min

    2013-10-21

    Three ruthenium complexes bearing backbone-monosubstituted CAACs were prepared and displayed dramatic improvement in catalytic efficiency not only in RCM reaction but also in the ethenolysis of methyl oleate, compared to those bearing backbone-disubstituted CAACs. PMID:24013192

  18. Folding a protein by discretizing its backbone torsional dynamics

    Science.gov (United States)

    Fernández, Ariel

    1999-05-01

    The aim of this work is to provide a coarse codification of local conformational constraints associated with each folding motif of a peptide chain in order to obtain a rough solution to the protein folding problem. This is accomplished by implementing a discretized version of the soft-mode dynamics on a personal computer (PC). Our algorithm mimics a parallel process as it evaluates concurrent folding possibilities by pattern recognition. It may be implemented in a PC as a sequence of perturbation-translation-renormalization (p-t-r) cycles performed on a matrix of local topological constraints (LTM). This requires suitable representational tools and a periodic quenching of the dynamics required for renormalization. We introduce a description of the peptide chain based on a local discrete variable the values of which label the basins of attraction of the Ramachandran map for each residue. Thus, the local variable indicates the basin in which the torsional coordinates of each residue lie at a given time. In addition, a coding of local topological constraints associated with each secondary and tertiary structural motif is introduced. Our treatment enables us to adopt a computation time step of 81 ps, a value far larger than hydrodynamic drag time scales. Folding pathways are resolved as transitions between patterns of locally encoded structural signals that change within the 10 μs-100 ms time scale range. These coarse folding pathways are generated by the periodic search for structural patterns in the time-evolving LTM. Each pattern is recorded as a contact matrix, an operation subject to a renormalization feedback loop. The validity of our approach is tested vis-a-vis experimentally-probed folding pathways eventually generating tertiary interactions in proteins which recover their active structure under in vitro renaturation conditions. As an illustration, we focus on determining significant folding intermediates and late kinetic bottlenecks that occur within the

  19. Pseudo 5D HN(C)N Experiment to Facilitate the Assignment of Backbone Resonances in Proteins Exhibiting High Backbone Shift Degeneracy

    CERN Document Server

    Kumar, Dinesh; Shukla, Vaibhav Kumar; Pandey, Himanshu; Arora, Ashish; Guleria, Anupam

    2014-01-01

    Assignment of protein backbone resonances is most routinely carried out using triple resonance three dimensional NMR experiments involving amide 1H and 15N resonances. However for intrinsically unstructured proteins, alpha-helical proteins or proteins containing several disordered fragments, the assignment becomes problematic because of high degree of backbone shift degeneracy. In this backdrop, a novel reduced dimensionality (RD) experiment -(5,3)D-hNCO-CANH- is presented to facilitate (and/or to validate) the sequential backbone resonance assignment in such proteins. The proposed 3D NMR experiment makes use of the modulated amide 15N chemical shifts (resulting from the joint sampling along both its indirect dimensions) to resolve the ambiguity involved in connecting the neighboring amide resonances (i.e. HiNi and Hi-1Ni-1) for overlapping amide NH peaks. The experiment -encoding 5D spectral information- leads to a conventional 3D spectrum with significantly reduced spectral crowding and complexity. The impr...

  20. Structured Debriefing in Simulation-Based Education.

    Science.gov (United States)

    Palaganas, Janice C; Fey, Mary; Simon, Robert

    2016-02-01

    Debriefing following a simulation event is a conversational period for reflection and feedback aimed at sustaining or improving future performance. It is considered by many simulation educators to be a critical activity for learning in simulation-based education. Deep learning can be achieved during debriefing and often depends on the facilitation skills of the debriefer as well as the learner's perceptions of a safe and supportive learning environment as created by the debriefer. On the other hand, poorly facilitated debriefings may create adverse learning, generate bad feelings, and may lead to a degradation of clinical performance, self-reflection, or harm to the educator-learner relationship. The use of a structure that recognizes logical and sequential phases during debriefing can assist simulation educators to achieve a deep level of learning. PMID:26909457

  1. Lagrangian based methods for coherent structure detection

    Energy Technology Data Exchange (ETDEWEB)

    Allshouse, Michael R., E-mail: mallshouse@chaos.utexas.edu [Center for Nonlinear Dynamics and Department of Physics, University of Texas at Austin, Austin, Texas 78712 (United States); Peacock, Thomas, E-mail: tomp@mit.edu [Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)

    2015-09-15

    There has been a proliferation in the development of Lagrangian analytical methods for detecting coherent structures in fluid flow transport, yielding a variety of qualitatively different approaches. We present a review of four approaches and demonstrate the utility of these methods via their application to the same sample analytic model, the canonical double-gyre flow, highlighting the pros and cons of each approach. Two of the methods, the geometric and probabilistic approaches, are well established and require velocity field data over the time interval of interest to identify particularly important material lines and surfaces, and influential regions, respectively. The other two approaches, implementing tools from cluster and braid theory, seek coherent structures based on limited trajectory data, attempting to partition the flow transport into distinct regions. All four of these approaches share the common trait that they are objective methods, meaning that their results do not depend on the frame of reference used. For each method, we also present a number of example applications ranging from blood flow and chemical reactions to ocean and atmospheric flows.

  2. 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.

  3. A structural model for Alzheimer's β-amyloid fibrils based on experimental constraints from solid state NMR

    Science.gov (United States)

    Petkova, Aneta T.; Ishii, Yoshitaka; Balbach, John J.; Antzutkin, Oleg N.; Leapman, Richard D.; Delaglio, Frank; Tycko, Robert

    2002-01-01

    We present a structural model for amyloid fibrils formed by the 40-residue β-amyloid peptide associated with Alzheimer's disease (Aβ1–40), based on a set of experimental constraints from solid state NMR spectroscopy. The model additionally incorporates the cross-β structural motif established by x-ray fiber diffraction and satisfies constraints on Aβ1–40 fibril dimensions and mass-per-length determined from electron microscopy. Approximately the first 10 residues of Aβ1–40 are structurally disordered in the fibrils. Residues 12–24 and 30–40 adopt β-strand conformations and form parallel β-sheets through intermolecular hydrogen bonding. Residues 25–29 contain a bend of the peptide backbone that brings the two β-sheets in contact through sidechain-sidechain interactions. A single cross-β unit is then a double-layered β-sheet structure with a hydrophobic core and one hydrophobic face. The only charged sidechains in the core are those of D23 and K28, which form salt bridges. Fibrils with minimum mass-per-length and diameter consist of two cross-β units with their hydrophobic faces juxtaposed. PMID:12481027

  4. 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.

  5. Aggregation tendencies in the p53 family are modulated by backbone hydrogen bonds.

    Science.gov (United States)

    Cino, Elio A; Soares, Iaci N; Pedrote, Murilo M; de Oliveira, Guilherme A P; Silva, Jerson L

    2016-01-01

    The p53 family of proteins is comprised of p53, p63 and p73. Because the p53 DNA binding domain (DBD) is naturally unstable and possesses an amyloidogenic sequence, it is prone to form amyloid fibrils, causing loss of functions. To develop p53 therapies, it is necessary to understand the molecular basis of p53 instability and aggregation. Light scattering, thioflavin T (ThT) and high hydrostatic pressure (HHP) assays showed that p53 DBD aggregates faster and to a greater extent than p63 and p73 DBDs, and was more susceptible to denaturation. The aggregation tendencies of p53, p63, and p73 DBDs were strongly correlated with their thermal stabilities. Molecular Dynamics (MD) simulations indicated specific regions of structural heterogeneity unique to p53, which may be promoted by elevated incidence of exposed backbone hydrogen bonds (BHBs). The results indicate regions of structural vulnerability in the p53 DBD, suggesting new targetable sites for modulating p53 stability and aggregation, a potential approach to cancer therapy. PMID:27600721

  6. Aggregation tendencies in the p53 family are modulated by backbone hydrogen bonds

    Science.gov (United States)

    Cino, Elio A.; Soares, Iaci N.; Pedrote, Murilo M.; de Oliveira, Guilherme A. P.; Silva, Jerson L.

    2016-01-01

    The p53 family of proteins is comprised of p53, p63 and p73. Because the p53 DNA binding domain (DBD) is naturally unstable and possesses an amyloidogenic sequence, it is prone to form amyloid fibrils, causing loss of functions. To develop p53 therapies, it is necessary to understand the molecular basis of p53 instability and aggregation. Light scattering, thioflavin T (ThT) and high hydrostatic pressure (HHP) assays showed that p53 DBD aggregates faster and to a greater extent than p63 and p73 DBDs, and was more susceptible to denaturation. The aggregation tendencies of p53, p63, and p73 DBDs were strongly correlated with their thermal stabilities. Molecular Dynamics (MD) simulations indicated specific regions of structural heterogeneity unique to p53, which may be promoted by elevated incidence of exposed backbone hydrogen bonds (BHBs). The results indicate regions of structural vulnerability in the p53 DBD, suggesting new targetable sites for modulating p53 stability and aggregation, a potential approach to cancer therapy. PMID:27600721

  7. Aggregation tendencies in the p53 family are modulated by backbone hydrogen bonds

    Science.gov (United States)

    Cino, Elio A.; Soares, Iaci N.; Pedrote, Murilo M.; de Oliveira, Guilherme A. P.; Silva, Jerson L.

    2016-09-01

    The p53 family of proteins is comprised of p53, p63 and p73. Because the p53 DNA binding domain (DBD) is naturally unstable and possesses an amyloidogenic sequence, it is prone to form amyloid fibrils, causing loss of functions. To develop p53 therapies, it is necessary to understand the molecular basis of p53 instability and aggregation. Light scattering, thioflavin T (ThT) and high hydrostatic pressure (HHP) assays showed that p53 DBD aggregates faster and to a greater extent than p63 and p73 DBDs, and was more susceptible to denaturation. The aggregation tendencies of p53, p63, and p73 DBDs were strongly correlated with their thermal stabilities. Molecular Dynamics (MD) simulations indicated specific regions of structural heterogeneity unique to p53, which may be promoted by elevated incidence of exposed backbone hydrogen bonds (BHBs). The results indicate regions of structural vulnerability in the p53 DBD, suggesting new targetable sites for modulating p53 stability and aggregation, a potential approach to cancer therapy.

  8. Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar-phosphate backbone and their comparison with modern density functional theory.

    Science.gov (United States)

    Mládek, Arnošt; Krepl, Miroslav; Svozil, Daniel; Cech, Petr; Otyepka, Michal; Banáš, Pavel; Zgarbová, Marie; Jurečka, Petr; Sponer, Jiří

    2013-05-21

    The DNA sugar-phosphate backbone has a substantial influence on the DNA structural dynamics. Structural biology and bioinformatics studies revealed that the DNA backbone in experimental structures samples a wide range of distinct conformational substates, known as rotameric DNA backbone conformational families. Their correct description is essential for methods used to model nucleic acids and is known to be the Achilles heel of force field computations. In this study we report the benchmark database of MP2 calculations extrapolated to the complete basis set of atomic orbitals with aug-cc-pVTZ and aug-cc-pVQZ basis sets, MP2(T,Q), augmented by ΔCCSD(T)/aug-cc-pVDZ corrections. The calculations are performed in the gas phase as well as using a COSMO solvent model. This study includes a complete set of 18 established and biochemically most important families of DNA backbone conformations and several other salient conformations that we identified in experimental structures. We utilize an electronically sufficiently complete DNA sugar-phosphate-sugar (SPS) backbone model system truncated to prevent undesired intramolecular interactions. The calculations are then compared with other QM methods. The BLYP and TPSS functionals supplemented with Grimme's D3(BJ) dispersion term provide the best tradeoff between computational demands and accuracy and can be recommended for preliminary conformational searches as well as calculations on large model systems. Among the tested methods, the best agreement with the benchmark database has been obtained for the double-hybrid DSD-BLYP functional in combination with a quadruple-ζ basis set, which is, however, computationally very demanding. The new hybrid density functionals PW6B95-D3 and MPW1B95-D3 yield outstanding results and even slightly outperform the computationally more demanding PWPB95 double-hybrid functional. B3LYP-D3 is somewhat less accurate compared to the other hybrids. Extrapolated MP2(D,T) calculations are not as

  9. A Distributed Virtual Backbone Formation for Wireless Ad Hoc and Sensor Networks

    Institute of Scientific and Technical Information of China (English)

    CAO Yong-tao; HE Chen; JIANG Ling-ge

    2007-01-01

    The virtual backbone is an approach for solving routing problems in wireless ad hoc and sensor networks. A connected dominating set (CDS) was proposed as a virtual backbone to improve the performance of wireless networks. The quality of a virtual backbone is measured not only by approximation factor, which is the ratio of its size to that of minimum CDS, but also time complexity and message complexity. In this paper, a distributed algorithm is presented to construct a minimum CDS for ad hoc and sensor networks. By destroying triangular loops in the virtual backbone, the proposed algorithm can effectively construct a CDS with smaller size. Moreover, our algorithm, which is fully localized, has a constant approximation ratio, linear message and time complexity, and low implementation complexity. The simulation results and theoretical analysis show that our algorithm has better efficiency and performance than conventional approaches.

  10. IMMUNOMODULATION OF SYNTHESIZED POLYMERS CONTAINING PHOSPHORUS IN THE BACKBONE —EFFECT ON THE PROLIFERATION OF LYMPHOCYTES

    Institute of Scientific and Technical Information of China (English)

    ZhuoRenxi; WangJun; 等

    1997-01-01

    The immunomodulation of several Charged synthetic polymers containing phosphorus in the backbone was studied in vitro through examining their inhibition or promotion effect on the proliferatioin of both T and B lymphocytes,It is found that polymers based on long chain alkyl ester of tyrosine exhibit immunomodulative activity.Negatively charged polymers show stimulative activity on LPS-induced B lymphocytes proliferation.Positively charged polymers exhibit inhibitory activity on both Con A-induced T lymphocytes and LPS-induced B lymplhyocytes proliferation.

  11. Semiconductor wire array structures, and solar cells and photodetectors based on such structures

    Science.gov (United States)

    Kelzenberg, Michael D.; Atwater, Harry A.; Briggs, Ryan M.; Boettcher, Shannon W.; Lewis, Nathan S.; Petykiewicz, Jan A.

    2014-08-19

    A structure comprising an array of semiconductor structures, an infill material between the semiconductor materials, and one or more light-trapping elements is described. Photoconverters and photoelectrochemical devices based on such structure also described.

  12. 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.

  13. Earthquake Analysis of Structure by Base Isolation Technique in SAP

    OpenAIRE

    T. Subramani; J. Jothi

    2014-01-01

    This paper presents an overview of the present state of base isolation techniques with special emphasis and a brief on other techniques developed world over for mitigating earthquake forces on the structures. The dynamic analysis procedure for isolated structures is briefly explained. The provisions of FEMA 450 for base isolated structures are highlighted. The effects of base isolation on structures located on soft soils and near active faults are given in brief. Simple case s...

  14. Pseudo 5D HN(C)N experiment to facilitate the assignment of backbone resonances in proteins exhibiting high backbone shift degeneracy

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Dinesh, E-mail: dineshcbmr@gmail.com [Centre of Biomedical Research (CBMR), SGPGIMS Campus, Raibareli Road, Lucknow 226014 (India); Raikwal, Nisha [Centre of Biomedical Research (CBMR), SGPGIMS Campus, Raibareli Road, Lucknow 226014 (India); Shukla, Vaibhav Kumar; Pandey, Himanshu; Arora, Ashish [Molecular and Structural Biology Division, CSIR, Central Drug Research Institute, Lucknow 226031 (India); Guleria, Anupam, E-mail: anuguleriaphy@gmail.com [Centre of Biomedical Research (CBMR), SGPGIMS Campus, Raibareli Road, Lucknow 226014 (India)

    2014-09-30

    Graphical abstract: - Highlights: • A reduced dimensionality experiment – referred as pseudo 5D HN(C)N- is presented. • Encodes highly resolved 5D spectral information in a 3D spectrum. • Superior in terms of peak dispersion. • Facilitates assignment of crowded HSQC spectra of moderately sized proteins. • Modulated {sup 15}N chemical shifts are used to break the amide shift degeneracy. - Abstract: Assignment of protein backbone resonances is most routinely carried out using triple resonance three-dimensional NMR experiments involving amide {sup 1}H/{sup 15}N resonances. However for intrinsically unstructured proteins, alpha-helical proteins or proteins containing several disordered fragments, the assignment becomes problematic because of high-degree of backbone shift degeneracy. In this backdrop, a novel reduced-dimensionality (RD) experiment –(5, 3)D-hNCO-CANH- is presented to facilitate/validate the sequential backbone resonance assignment in such proteins. The proposed 3D NMR experiment makes use of the modulated amide {sup 15}N chemical shifts (resulting from the joint sampling along both its indirect dimensions) to resolve the ambiguity involved in connecting the neighboring amide resonances (i.e. H{sub i}N{sub i} and H{sub i−1}N{sub i−1}) for overlapping amide-NH peaks. The experiment -in combination with routine triple resonance 3D-NMR experiments involving backbone amide ({sup 1}H/{sup 15}N) and carbon ({sup 13}C{sup α}/{sup 13}C′) chemical shifts- will serve as a powerful complementary tool to achieve the nearly complete assignment of protein backbone resonances in a time efficient manner.

  15. 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

    2014-08-01

    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.

  16. Noise assisted excitation energy transfer in a linear model of a selectivity filter backbone strand.

    Science.gov (United States)

    Bassereh, Hassan; Salari, Vahid; Shahbazi, Farhad

    2015-07-15

    In this paper, we investigate the effect of noise and disorder on the efficiency of excitation energy transfer (EET) in a N = 5 sites linear chain with 'static' dipole-dipole couplings. In fact, here, the disordered chain is a toy model for one strand of the selectivity filter backbone in ion channels. It has recently been discussed that the presence of quantum coherence in the selectivity filter is possible and can play a role in mediating ion-conduction and ion-selectivity in the selectivity filter. The question is 'how a quantum coherence can be effective in such structures while the environment of the channel is dephasing (i.e. noisy)?' Basically, we expect that the presence of the noise should have a destructive effect in the quantum transport. In fact, we show that such expectation is valid for ordered chains. However, our results indicate that introducing the dephasing in the disordered chains leads to the weakening of the localization effects, arising from the multiple back-scatterings due to the randomness, and then increases the efficiency of quantum energy transfer. Thus, the presence of noise is crucial for the enhancement of EET efficiency in disordered chains. We also show that the contribution of both classical and quantum mechanical effects are required to improve the speed of energy transfer along the chain. Our analysis may help for better understanding of fast and efficient functioning of the selectivity filters in ion channels.

  17. 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.

  18. Amino acid preference against beta sheet through allowing backbone hydration enabled by the presence of cation

    CERN Document Server

    Sharley, John N

    2016-01-01

    It is known that steric blocking by peptide sidechains of hydrogen bonding, HB, between water and peptide groups, PGs, in beta sheets accords with an amino acid intrinsic beta sheet preference. The present observations with Quantum Molecular Dynamics, QMD, simulation with quantum mechanical treatment of every water molecule solvating a beta sheet that would be transient in nature suggest that this steric blocking is not applicable in a hydrophobic region unless a cation is present, so that the amino acid beta sheet preference due to this steric blocking is only effective in the presence of a cation. We observed backbone hydration in a polyalanine and to a lesser extent polyvaline alpha helix without a cation being present, but a cation could increase the strength of these HBs. Parallel beta sheets have a greater tendency than antiparallel beta sheets of equivalent small size to retain regular structure in solvated QMD, and a 4 strand 4 inter-PG HB chain parallel beta sheet was used. Stability was reinforced b...

  19. Design, synthesis, and structure-property relationships of isoindigo-based conjugated polymers.

    Science.gov (United States)

    Lei, Ting; Wang, Jie-Yu; Pei, Jian

    2014-04-15

    Conjugated polymers have developed rapidly due to their promising applications in low-cost, lightweight, and flexible electronics. The development of the third-generation donor-acceptor (D-A) polymers greatly improved the device performance in organic solar cells (OSCs) and field-effect transistors (FETs). However, for further improvement of device performance, scientists need to develop new building blocks, in particular electron-deficient aromatics, and gain an in-depth understanding of the structure-property relationships. Recently, isoindigo has been used as a new acceptor of D-A conjugated polymers. An isomer of indigo, isoindigo is a less well-known dye and can be isolated as a by-product from certain biological processes. It has two lactam rings and exhibits strong electron-withdrawing character. This electron deficiency gives isoindigo-based polymers intriguing properties, such as broad absorption and high open circuit voltage in OSCs, as well as high mobility and good ambient stability in FETs. In this Account, we review our recent progress on the design, synthesis, and structure-property relationship study of isoindigo-based polymers for FETs. Starting with some discussion on carrier transport in polymer films, we provide some basic strategies towards high-performance polymer FETs. We discuss the stability issue of devices, the impediment of the alkyl side chains, and the choice of the donor part of conjugated polymers. We demonstrate that introducing the isoindigo core effectively lowers the HOMO levels of polymers and provides FETs with long-time stability. In addition, we have found that when we use inappropriate alkyl side chains or non-centrosymmetric donors, the device performance of isoindigo polymers suffers. To further improve device performance and ambient stability, we propose several design strategies, such as using farther branched alkyl chains, modulating polymer energy levels, and extending π-conjugated backbones. We have found that using

  20. 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.

  1. Reliability-Based Design of Coastal Structures

    DEFF Research Database (Denmark)

    Burcharth, H. F.

    1997-01-01

    The objective of this paper is to introduce the application of reliability theory for conceptual design and evaluation of coastal structures. It is without the scope to discuss the validity and quality of the various design formulae available for coastal structures. The contents of the paper is a....... Proceedings Conference of Port and Coastal Engineering in developing countries. Rio de Janeiro, Brazil, 1995.......The objective of this paper is to introduce the application of reliability theory for conceptual design and evaluation of coastal structures. It is without the scope to discuss the validity and quality of the various design formulae available for coastal structures. The contents of the paper...... 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...

  2. A revised interpretation of the wing base structure in Odonata

    OpenAIRE

    Ninomiya, Tomoya; Yoshizawa, Kazunori

    2009-01-01

    Homology of the wing base structure in the Odonata is highly controversial, and many different interpretations for this structure have been proposed to date. In extreme cases, two independent origins of the insect wings have been suggested based on comparative morphology between the odonate and other pterygote wing bases. Difficulties in establishing homology of the wing base structures between Odonata and other Pterygota are mainly due to their extreme differences in morphology and function....

  3. Floating structures (based on water activities)

    OpenAIRE

    Rodionovskaya Inna Serafi movna; Kocheryaev Stanislav Alexandrovich; Shakhova Marina Evgenevna

    2012-01-01

    The article briefly describes the types of structures that are widely spread worldwide, and many well-known projects that remain unimplemented. Particular attention is driven to the main features of floating structures and areas of their application. Despite the advances of the present-day technology, floating structures are only used in the travel industry and low-rise construction. The authors consider a substantial though yet unexplored potential of rivers, seas and lakes, a...

  4. Selective Acid Hydrolysis Condition for the Composition and Linkage with a Fructofuranosyl Backbone of a Polysaccharide from Angelica sinensis (Oliv) Diels

    Institute of Scientific and Technical Information of China (English)

    Gui Yun XU; Yang CHEN; Ru Xian CHEN

    2006-01-01

    A new polysaccharide was extracted and purified from the roots of Angelica sinensis (Oliv) Diels (ASD). Its composition and linkage was elucidated by selective hydrolysis and GC/MS analysis of its derivatives. The polysaccharide was made of→1) Fruf(2→and→6) GlCp (1→as its backbone with highly branched structure. To our best knowledge, this is the first report of the fructose residue in polysaccharides from the roots of the ASD.

  5. “少数民族高层次骨干人才计划”毕业生违约原因分析--基于理性选择制度主义的视角%The Cause of Contract Breaches by Graduates of Program of Training High-Caliber Backbone Personnel from the Ethnic Minorities:An Analysis Based on Rational Choice Institutionalism

    Institute of Scientific and Technical Information of China (English)

    潘健

    2015-01-01

    少数民族高层次骨干人才计划对于改善西部少数民族地区人才结构,提升人才水平具有重要的现实意义。然而,近年来,该计划毕业生违约现象日益突出,对政策的目标达成产生不利影响。文章借鉴理性选择制度主义的分析框架,通过政策文本梳理和对违约毕业生的深度访谈,对该计划就业政策实施过程中的制度、行动者、社会因素三方面进行深入分析。研究发现,制度规定功能性缺失、相关行动者利益冲突以及生源地经济发展状况社会因素是造成违约现象出现的主要原因。%The Program of Training High-Caliber Backbone Personnel from the Ethnic Minorities is of great significance to improve talent structure and talents’ capability. In recent years, however, the number of the graduates who breach contract seems to increase, which impinges the goal attainment of this policy. In this paper, institutions, actors and social factors in the executing process of the policy are analyzed by means of organizing policy discourse and interviewing defaulters on the basis of rational choice institutionalism. Research found that the main causes of this phenomenon are: functional deficiencies of the institution, conflicts of interest among relevant actors and social factors of the region that the students come from.

  6. 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.

  7. Modal Based Fatigue Monitoring of Steel Structures

    DEFF Research Database (Denmark)

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

    2005-01-01

    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...... by applying the mode shapes of the calibrated Finite Element model and strains are obtained using the shape functions for the actual elements. The technique has been applied on a model frame structure in the laboratory and on a wind loaded lattice pylon structure. In both cases the estimated stresses has been......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...

  8. Oxygen-aromatic contacts in intra-strand base pairs: analysis of high-resolution DNA crystal structures and quantum chemical calculations.

    Science.gov (United States)

    Jain, Alok; Krishna Deepak, R N V; Sankararamakrishnan, Ramasubbu

    2014-07-01

    Three-dimensional structures of biomolecules are stabilized by a large number of non-covalent interactions and some of them such as van der Waals, electrostatic and hydrogen bond interactions are well characterized. Delocalized π-electron clouds of aromatic residues are known to be involved in cation-π, CH-π, OH-π and π-π interactions. In proteins, many examples have been found in which the backbone carbonyl oxygen of one residue makes close contact with the aromatic center of aromatic residues. Quantum chemical calculations suggest that such contacts may provide stability to the protein secondary structures. In this study, we have systematically analyzed the experimentally determined high-resolution DNA crystal structures and identified 91 examples in which the aromatic center of one base is in close contact (interactions between the bases in base pairs with oxygen-aromatic contacts are energetically favorable. Decomposition of interaction energies indicates that dispersion forces are the major cause for energetically stable interaction in these base pairs. We speculate that oxygen-aromatic contacts in intra-strand base pairs in a DNA structure may have biological significance. PMID:24816369

  9. An approximate procedure for solving base-isolated structures

    International Nuclear Information System (INIS)

    Dynamic analysis of several shear type structures with base isolation indicates that the response of these structures follows their fundamental mode shape. Based on this observation, this paper uses an approximate procedure for computing the response of base-isolated structures. The procedure consists of modeling the structure and its base by a two-degree of freedom system, one representing the base and the other the structure. The response from the two-degree of freedom model and mode shapes of the structure are used to compute the response of the structure to earthquake excitation. The approximate procedure is simple, requires substantially less computational time than other methods, and gives results that are in excellent agreement with those from direct integration. Nonlinear properties and nonproportional damping are easily included in the model. Savings of approximately 54--77 percent in computational time result by using the approximate model

  10. Behavioural Stereotype as a Backbone Factor in Economic Security of an Enterprise

    Directory of Open Access Journals (Sweden)

    Ovcharenko Yevgen I.

    2013-11-01

    Full Text Available The article sets a problem of building a system of economic security of an enterprise with consideration of impossibility and inexpediency of such building on the hypothetical and logical mathematical basis. The task of ensuring functioning efficiency of such a system should be placed on the social element in the system – a human being, his or her consciousness, ability to solve problems intuitively, understanding and ensuring adaptability of the system to changes. A formal characteristic of the social element in the system is a behavioural stereotype and social role. Theoretical basis of building the system of economic security of an enterprise with a behavioural stereotype as a backbone factor is the theory of functional systems, which gives a possibility to consider understanding of behavioural acts in the functional system and behavioural stereotypes in the socio-economic system to be connected to such an extent that these two notions could be used for creation of the system of economic security of an enterprise. The article develops the author’s own model of the system of economic security of an enterprise in which the factor that stimulates the system elements to reflective and supraliminal expedient behaviour is a dominating motivation and starting afference of people, being part of these elements, which is fixed in certain behavioural stereotypes. Activity of each of the system elements depends on certain behavioural stereotypes on the basis of which the mechanisms of functioning of one or another element are based.

  11. Photoleucine Survives Backbone Cleavage by Electron Transfer Dissociation. A Near-UV Photodissociation and Infrared Multiphoton Dissociation Action Spectroscopy Study

    Science.gov (United States)

    Shaffer, Christopher J.; Martens, Jonathan; Marek, Aleš; Oomens, Jos; Tureček, František

    2016-07-01

    We report a combined experimental and computational study aimed at elucidating the structure of N-terminal fragment ions of the c type produced by electron transfer dissociation of photo-leucine (L*) peptide ions GL*GGKX. The c 4 ion from GL*GGK is found to retain an intact diazirine ring that undergoes selective photodissociation at 355 nm, followed by backbone cleavage. Infrared multiphoton dissociation action spectra point to the absence in the c 4 ion of a diazoalkane group that could be produced by thermal isomerization of vibrationally hot ions. The c 4 ion from ETD of GL*GGK is assigned an amide structure by a close match of the IRMPD action spectrum and calculated IR absorption. The energetics and kinetics of c 4 ion dissociations are discussed.

  12. 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...

  13. A fluorophosphate-based inverse Keggin structure

    Energy Technology Data Exchange (ETDEWEB)

    Fielden, John; Quasdorf, Kyle; Cronin, Leroy; Kogerler, Paul

    2012-07-17

    An unusual PFO(3)(2-)-templated "inverse Keggin" polyanion, [Mo(12)O(46)(PF)(4)](4-), has been isolated from the degradation reaction of an {Mo(132)}-type Keplerate to [PMo(12)O(40)](3-) by [Cu(MeCN)(4)](PF(6)) in acetonitrile. (31)P-NMR studies suggest a structure-directing role for [Cu(MeCN)(4)](+) in the formation of the highly unusual all-inorganic inverse Keggin structure.

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

    Energy Technology Data Exchange (ETDEWEB)

    Lopez del Amo, Juan-Miguel; Fink, Uwe; Reif, Bernd, E-mail: reif@tum.d [Leibniz-Institut fuer Molekulare Pharmakologie (FMP) (Germany)

    2010-12-15

    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 {alpha}-spectrin SH3 domain exchange rather slowly with the solvent (with exchange rates negligible within the individual {sup 15}N-T{sub 1} timescales). We observed chemical exchange for 6 residues with HDX exchange rates in the range from 0.2 to 5 s{sup -1}. Backbone amide {sup 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 W41{epsilon}. 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{sub 2}O is employed as a solvent for sample preparation. Due to the intrinsically long {sup 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.

  15. Combinatorics of RNA Secondary Structures with Base Triples.

    Science.gov (United States)

    Müller, Robert; Nebel, Markus E

    2015-07-01

    The structure of RNA has been the subject of intense research over the last decades due to its importance for the correct functioning of RNA molecules in biological processes. Hence, a large number of models for RNA folding and corresponding algorithms for structure prediction have been developed. However, previous models often only consider base pairs, although every base is capable of up to three edge-to-edge interactions with other bases. Recently, Höner zu Siederdissen et al. presented an extended model of RNA secondary structure, including base triples together with a folding algorithm-the first thermodynamics-based algorithm that allows the prediction of secondary structures with base triples. In this article, we investigate the search space processed by this new algorithm, that is, the combinatorics of extended RNA secondary structures with base triples. We present generalized definitions for structural motifs like hairpins, stems, bulges, or interior loops occurring in structures with base triples. Furthermore, we prove precise asymptotic results for the number of different structures (size of search space) and expectations for various parameters associated with structural motifs (typical shape of folding). Our analysis shows that the asymptotic number of secondary structures of size n increases exponentially to [Formula: see text] compared to the classic model by Stein and Waterman for which [Formula: see text] structures exist. A comparison with the classic model reveals large deviations in the expected structural appearance, too. The inclusion of base triples constitutes a significant refinement of the combinatorial model of RNA secondary structure, which, by our findings, is quantitatively characterized. Our results are of special theoretical interest, because a closer look at the numbers involved suggests that extended RNA secondary structures constitute a new combinatorial class not bijective with any other combinatorial objects studied so far.

  16. Structural Analysis Using Computer Based Methods

    Science.gov (United States)

    Dietz, Matthew R.

    2013-01-01

    The stiffness of a flex hose that will be used in the umbilical arms of the Space Launch Systems mobile launcher needed to be determined in order to properly qualify ground umbilical plate behavior during vehicle separation post T-0. This data is also necessary to properly size and design the motors used to retract the umbilical arms. Therefore an experiment was created to determine the stiffness of the hose. Before the test apparatus for the experiment could be built, the structure had to be analyzed to ensure it would not fail under given loading conditions. The design model was imported into the analysis software and optimized to decrease runtime while still providing accurate restlts and allow for seamless meshing. Areas exceeding the allowable stresses in the structure were located and modified before submitting the design for fabrication. In addition, a mock up of a deep space habitat and the support frame was designed and needed to be analyzed for structural integrity under different loading conditions. The load cases were provided by the customer and were applied to the structure after optimizing the geometry. Once again, weak points in the structure were located and recommended design changes were made to the customer and the process was repeated until the load conditions were met without exceeding the allowable stresses. After the stresses met the required factors of safety the designs were released for fabrication.

  17. Protein structure mining using a structural alphabet.

    Science.gov (United States)

    Tyagi, M; de Brevern, A G; Srinivasan, N; Offmann, B

    2008-05-01

    We present a comprehensive evaluation of a new structure mining method called PB-ALIGN. It is based on the encoding of protein structure as 1D sequence of a combination of 16 short structural motifs or protein blocks (PBs). PBs are short motifs capable of representing most of the local structural features of a protein backbone. Using derived PB substitution matrix and simple dynamic programming algorithm, PB sequences are aligned the same way amino acid sequences to yield structure alignment. PBs are short motifs capable of representing most of the local structural features of a protein backbone. Alignment of these local features as sequence of symbols enables fast detection of structural similarities between two proteins. Ability of the method to characterize and align regions beyond regular secondary structures, for example, N and C caps of helix and loops connecting regular structures, puts it a step ahead of existing methods, which strongly rely on secondary structure elements. PB-ALIGN achieved efficiency of 85% in extracting true fold from a large database of 7259 SCOP domains and was successful in 82% cases to identify true super-family members. On comparison to 13 existing structure comparison/mining methods, PB-ALIGN emerged as the best on general ability test dataset and was at par with methods like YAKUSA and CE on nontrivial test dataset. Furthermore, the proposed method performed well when compared to flexible structure alignment method like FATCAT and outperforms in processing speed (less than 45 s per database scan). This work also establishes a reliable cut-off value for the demarcation of similar folds. It finally shows that global alignment scores of unrelated structures using PBs follow an extreme value distribution. PB-ALIGN is freely available on web server called Protein Block Expert (PBE) at http://bioinformatics.univ-reunion.fr/PBE/.

  18. NMR study of oligonucleotides containing base pair mismatches and a human growth hormone peptide for the determination of solution structures

    International Nuclear Information System (INIS)

    Formation of unusual basepairs in DNA for random mutations in DNA was proposed in the sixties. These mismatches arise due to errors in replication, and from deamination of the 5-methylcytosine. The author's interest in studying mismatches and other oligonucleotides has been two fold. One is related to 31P chemical shifts and the backbone structure of oligonucleotides. He wanted to find out the significance of the dispersion of 31p chemical shifts in oligonucleotides. He wished to address whether this dispersion in 31P chemical shifts is related to global structural parameters of oligonucleotides like helix twist and whether he can prove the relationship between 31P chemical shifts and the backbone torsional angles epsilon and zeta. How does a mismatch affect 31P chemical shifts and the backbone torsional angle? The second interest is related to solving the three dimensional structure of these biopolymers by using NMR data (NOESY distances) and computer simulations. His major study of these mismatches has been in the assignments of the protons resonances and the phosphorus resonances by 2D NMR. He has also tried to answer the question about the relationships between 31P chemical shifts and global parameters for DNA such as the helix twist. He has made substantial progress in determination of J(H3'-P) coupling constants by 2D NMR and also in determining the relationship between the SIP chemical shifts and the backbone torsional angles by using the mismatch dodecamer sequences and the tetradecamer sequences. The 2D NMR data for the GG and GT mismatch have been used to determine three dimensional structures by using distance restrained molecular dynamics. The second project involved studying a 28 residue synthetic peptide by NMR

  19. Vanishing amplitude of backbone dynamics causes a true protein dynamical transition: H2 NMR studies on perdeuterated C-phycocyanin

    Science.gov (United States)

    Kämpf, Kerstin; Kremmling, Beke; Vogel, Michael

    2014-03-01

    Using a combination of H2 nuclear magnetic resonance (NMR) methods, we study internal rotational dynamics of the perdeuterated protein C-phycocyanin (CPC) in dry and hydrated states over broad temperature and dynamic ranges with high angular resolution. Separating H2 NMR signals from methyl deuterons, we show that basically all backbone deuterons exhibit highly restricted motion occurring on time scales faster than microseconds. The amplitude of this motion increases when a hydration shell exists, while it decreases upon cooling and vanishes near 175 K. We conclude that the vanishing of the highly restricted motion marks a dynamical transition, which is independent of the time window and of a fundamental importance. This conclusion is supported by results from experimental and computational studies of the proteins myoglobin and elastin. In particular, we argue based on findings in molecular dynamics simulations that the behavior of the highly restricted motion of proteins at the dynamical transition resembles that of a characteristic secondary relaxation of liquids at the glass transition, namely the nearly constant loss. Furthermore, H2 NMR studies on perdeuterated CPC reveal that, in addition to highly restricted motion, small fractions of backbone segments exhibit weakly restricted dynamics when temperature and hydration are sufficiently high.

  20. Risk based design of civil structures

    NARCIS (Netherlands)

    Van Gelder, P.; Roos, A.; Vrijling, H.

    2001-01-01

    The Art and Science of Model Building: A Bayesian Approach, by Prof. A. Der Kiureghian; The talk will describe a Bayesian approach to developing models, with special emphasis on limit-state models for reinforced concrete structures. The formulation can incorporate all kinds of information (theoretic

  1. Probing backbone hydrogen bonding in PDZ/ligand interactions by protein amide-to-ester mutations

    DEFF Research Database (Denmark)

    Pedersen, Søren W; Pedersen, Stine B; Anker, Louise;

    2014-01-01

    via backbone hydrogen bonds; however, little is known about the role of these hydrogen bonds due to experimental challenges with backbone mutations. Here we address this interaction by generating semisynthetic PDZ domains containing backbone amide-to-ester mutations and evaluating the importance...... of individual hydrogen bonds for ligand binding. We observe substantial and differential effects upon amide-to-ester mutation in PDZ2 of postsynaptic density protein 95 and other PDZ domains, suggesting that hydrogen bonding at the carboxylate-binding site contributes to both affinity and selectivity....... In particular, the hydrogen-bonding pattern is surprisingly different between the non-canonical and canonical interaction. Our data provide a detailed understanding of the role of hydrogen bonds in protein-protein interactions....

  2. 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...

  3. Using Excel To Study The Relation Between Protein Dihedral Angle Omega And Backbone Length

    Science.gov (United States)

    Shew, Christopher; Evans, Samari; Tao, Xiuping

    How to involve the uninitiated undergraduate students in computational biophysics research? We made use of Microsoft Excel to carry out calculations of bond lengths, bond angles and dihedral angles of proteins. Specifically, we studied protein backbone dihedral angle omega by examining how its distribution varies with the length of the backbone length. It turns out Excel is a respectable tool for this task. An ordinary current-day desktop or laptop can handle the calculations for midsized proteins in just seconds. Care has to be taken to enter the formulas for the spreadsheet column after column to minimize the computing load. Supported in part by NSF Grant #1238795.

  4. Topology Optimization in Damping Structure Based on ESO

    Institute of Scientific and Technical Information of China (English)

    GUO Zhong-ze; CHEN Yu-ze; HOU Qiang

    2008-01-01

    The damping material optimal placement for the structure with damping layer is studied based on evolutionary structural optimization (ESO) to maximize modal loss factors. A mathematical model is constructed with the objective function defined as the maximum of modal loss factors of the structure and design constraints function defined as volume fraction ofdamping material. The optimal placement is found. Several examples are presented for verification. The results demonstratethat the method based on ESO is effective in solving the topology optimization of the structure with uncon-strained damping layer and constrained damping layer. This optimization method suits for free and constrained damping structures.

  5. Identification of protein superfamily from structure- based sequence motif

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The structure-based sequence motif of the distant proteins in evolution, protein tyrosine phosphatases (PTP) Ⅰ and Ⅱ superfamilies, as an example, has been defined by the structural comparison, structure-based sequence alignment and analyses on substitution patterns of residues in common sequence conserved regions. And the phosphatases Ⅰ and Ⅱ can be correctly identified together by the structure-based PTP sequence motif from SWISS-PROT and TrEBML databases. The results show that the correct rates of identification are over 98%. This is the first time to identify PTP Ⅰ and Ⅱ together by this motif.

  6. 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....

  7. RM-structure alignment based statistical machine translation model

    Institute of Scientific and Technical Information of China (English)

    Sun Jiadong; Zhao Tiejun

    2008-01-01

    A novel model based on structure alignments is proposed for statistical machine translation in this paper.Meta-structure and sequence of meta-structure for a parse tree are defined.During the translation process, a parse tree is decomposed to deal with the structure divergence and the alignments can be constructed at different levels of recombination of meta-structure (RM).This method can perform the structure mapping across the sub-tree structure between languages.As a result, we get not only the translation for the target language, but sequence of meta-structure of its parse tree at the same time.Experiments show that the model in the framework of log-linear model has better generative ability and significantly outperforms Pharaoh, a phrase-based system.

  8. Integrated Data as backbone of e-Navigation

    OpenAIRE

    Michael Bergmann

    2013-01-01

    e-Navigation, a theme introduced but IMO to improve safety of navigation at sea, is starting to gain traction in various organizations. As the concept develops, the importance of data, both static as well as dynamic, is more and more realized. IALA and IHO, in their efforts to help making e-Navigation a reality, have agreed to propose the IHO GI Register (often known as S-100 Register) as the conceptual basis for the Common Maritime Data Structure (CMDS). Utilizing this common understanding o...

  9. ON THE STRUCTURES OF RAM-BASED CHINESE CHARACTER LIBRARIES

    Institute of Scientific and Technical Information of China (English)

    钱培德

    1991-01-01

    The Chinese character library is one of the important data structures in the Chinese information Processing system.The behavior of the whole system depends directly on the reasonableness of design for its structure.This paper expounds the structures of RAM-based Chinese character libraries,static and dynamic ,The paper offers a descriptive method for this behavior and inquires into some algorithms related to the structures mentioned above.

  10. 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

  11. 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.

  12. Binary Assembly of Au Nanoparticles with Controllable Two-dimensional Architecture Directed by Phosphate Backbone Modified Oligonucleotide

    Institute of Scientific and Technical Information of China (English)

    MA,Yu-Dan; GUO,Yi; LI,Jun; YANG,Wen-Sheng

    2008-01-01

    A three complementary strand oligonucleotide system was employed to assemble two different-sized,15 and 25 nm,Au nanoparticles into binary two-dimensional (2D) structures.First,two non-complementary strands of phosphate backbone modified oligonucleotides (PM oligo-DNA) were loaded on the surface of the 15 and 25 nm Au nanoparticles,respectively.Upon the addition of the third linker DNA,which was half complementary to each of the modified DNA,the An nanoparticles would be assembled to binary 2D aggregates.The number of the 15 nm Au nanoparticles around a 25 nm Au naoparticle can be readily controlled by the length of the DNA helix used.

  13. Backbone NxH compounds at high pressures.

    Science.gov (United States)

    Goncharov, Alexander F; Holtgrewe, Nicholas; Qian, Guangrui; Hu, Chaohao; Oganov, Artem R; Somayazulu, Maddury; Stavrou, Elissaios; Pickard, Chris J; Berlie, Adam; Yen, Fei; Mahmood, Mahmood; Lobanov, Sergey S; Konôpková, Zuzana; Prakapenka, Vitali B

    2015-06-01

    Optical and synchrotron x-ray diffraction diamond anvil cell experiments have been combined with first-principles theoretical structure predictions to investigate mixtures of N2 and H2 up to 55 GPa. Our experiments show the formation of structurally complex van der Waals compounds [see also D. K. Spaulding et al., Nat. Commun. 5, 5739 (2014)] above 10 GPa. However, we found that these NxH (0.5 < x < 1.5) compounds transform abruptly to new oligomeric materials through barochemistry above 47 GPa and photochemistry at pressures as low as 10 GPa. These oligomeric compounds can be recovered to ambient pressure at T < 130 K, whereas at room temperature, they can be metastable on pressure release down to 3.5 GPa. Extensive theoretical calculations show that such oligomeric materials become thermodynamically more stable in comparison to mixtures of N2, H2, and NH3 above approximately 40 GPa. Our results suggest new pathways for synthesis of environmentally benign high energy-density materials. These materials could also exist as alternative planetary ices.

  14. Backbone NxH compounds at high pressures

    Science.gov (United States)

    Goncharov, Alexander F.; Holtgrewe, Nicholas; Qian, Guangrui; Hu, Chaohao; Oganov, Artem R.; Somayazulu, Maddury; Stavrou, Elissaios; Pickard, Chris J.; Berlie, Adam; Yen, Fei; Mahmood, Mahmood; Lobanov, Sergey S.; Konôpková, Zuzana; Prakapenka, Vitali B.

    2015-06-01

    Optical and synchrotron x-ray diffraction diamond anvil cell experiments have been combined with first-principles theoretical structure predictions to investigate mixtures of N2 and H2 up to 55 GPa. Our experiments show the formation of structurally complex van der Waals compounds [see also D. K. Spaulding et al., Nat. Commun. 5, 5739 (2014)] above 10 GPa. However, we found that these NxH (0.5 < x < 1.5) compounds transform abruptly to new oligomeric materials through barochemistry above 47 GPa and photochemistry at pressures as low as 10 GPa. These oligomeric compounds can be recovered to ambient pressure at T < 130 K, whereas at room temperature, they can be metastable on pressure release down to 3.5 GPa. Extensive theoretical calculations show that such oligomeric materials become thermodynamically more stable in comparison to mixtures of N2, H2, and NH3 above approximately 40 GPa. Our results suggest new pathways for synthesis of environmentally benign high energy-density materials. These materials could also exist as alternative planetary ices.

  15. Beta-scission of alkoxyl radicals on peptides and proteins can give rise to backbone cleavage and loss of side-chains

    International Nuclear Information System (INIS)

    Full text: Exposure of proteins to radicals in the presence of O2 brings about multiple changes including side-chain oxidation, backbone fragmentation, cross-linking, unfolding, changes in hydrophobicity and conformation, altered susceptibility to proteolytic enzymes and formation of new reactive groups (e.g. hydroperoxides and 3,4-dihydroxyphenylalanine). All of these processes can result in loss of structural or enzymatic activity. The mechanisms that give rise to backbone cleavage are only partly understood. Whilst it is known that direct hydrogen atom abstraction at a-carbon sites gives backbone cleavages it has also been proposed that initial attack at side-chain sites might also give rise to backbone cleavage. In this study we have examined whether initial attack at the β- (C-3) position can give rise to α-carbon radicals (and hence backbone cleavage) via the formation, and subsequent β- scission, of C-3 alkoxyl radicals. This process has been observed previously with protected amino acids in organic solvents (J. Chem. Soc. Perkin Trans. 2, 1997, 503-507) but the occurrence of such reactions with proteins in aqueous solution has not been explored. Alkoxyl radicals were generated at the C-3 position of a variety of protected amino acids and small peptides by two methods: metal-ion catalysed decomposition of hydroperoxides formed as a result of γ-radiolysis in the presence of O2, and UV photolysis of nitrate esters. In most cases radicals have been detected by EPR spectroscopy using nitroso and nitrone spin traps, which can be assigned by comparison with literature data to α-carbon radicals; in some case assignments were confirmed by the generation of the putative species by other routes. With Ala peptide hydroperoxides and nitrate esters, and MNP as the spin trap, the major radical detected in each case has been assigned to the adduct of an α-carbon radical with partial structure - NH-.CH-C(O) - consistent with the rapid occurrence of the above reaction

  16. Synthesis and properties of polybenzazoles containing flexible methylene in backbone

    Institute of Scientific and Technical Information of China (English)

    Xiaohui XU; Xiaoyun LIU; Chengjun ZHOU; Qixin ZHUANG; Zhewen HAN

    2008-01-01

    A novel series of polybenzazoles with rigid-rod benzoxazole cycle and soft methylene segment was designed and synthesized via solution condensation poly-merizations from 4,6-diamino-l,3-benzenediol dipho-sphate, terephthalic acid and aliphatic dicarboxylic acid. The structures of polybenzazoles were characterized by means of FT-IR,1H NMR and Wide-angle X-ray diffrac-tion (WAXRD). All the polymers show excellent thermal stability and the TdS was above 471℃, The intrinsic vis-cosities [η] of the polymers ranged from 0.8 to 0.9. The UV-Vis absorption peaks of the polymers in MSA were blue-shifted from 429 nm for PBO to 291 nm for PBOC7, and the Stokes shifts in PL spectra enlarged.

  17. Building the backbone: the development and evolution of vertebral patterning.

    Science.gov (United States)

    Fleming, Angeleen; Kishida, Marcia G; Kimmel, Charles B; Keynes, Roger J

    2015-05-15

    The segmented vertebral column comprises a repeat series of vertebrae, each consisting of two key components: the vertebral body (or centrum) and the vertebral arches. Despite being a defining feature of the vertebrates, much remains to be understood about vertebral development and evolution. Particular controversy surrounds whether vertebral component structures are homologous across vertebrates, how somite and vertebral patterning are connected, and the developmental origin of vertebral bone-mineralizing cells. Here, we assemble evidence from ichthyologists, palaeontologists and developmental biologists to consider these issues. Vertebral arch elements were present in early stem vertebrates, whereas centra arose later. We argue that centra are homologous among jawed vertebrates, and review evidence in teleosts that the notochord plays an instructive role in segmental patterning, alongside the somites, and contributes to mineralization. By clarifying the evolutionary relationship between centra and arches, and their varying modes of skeletal mineralization, we can better appreciate the detailed mechanisms that regulate and diversify vertebral patterning.

  18. Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by guided-learning through a two-layer neural network.

    Science.gov (United States)

    Faraggi, Eshel; Xue, Bin; Zhou, Yaoqi

    2009-03-01

    This article attempts to increase the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins through improved learning. Most methods developed for improving the backpropagation algorithm of artificial neural networks are limited to small neural networks. Here, we introduce a guided-learning method suitable for networks of any size. The method employs a part of the weights for guiding and the other part for training and optimization. We demonstrate this technique by predicting residue solvent accessibility and real-value backbone torsion angles of proteins. In this application, the guiding factor is designed to satisfy the intuitive condition that for most residues, the contribution of a residue to the structural properties of another residue is smaller for greater separation in the protein-sequence distance between the two residues. We show that the guided-learning method makes a 2-4% reduction in 10-fold cross-validated mean absolute errors (MAE) for predicting residue solvent accessibility and backbone torsion angles, regardless of the size of database, the number of hidden layers and the size of input windows. This together with introduction of two-layer neural network with a bipolar activation function leads to a new method that has a MAE of 0.11 for residue solvent accessibility, 36 degrees for psi, and 22 degrees for phi. The method is available as a Real-SPINE 3.0 server in http://sparks.informatics.iupui.edu.

  19. Maximality-Based Structural Operational Semantics for Petri Nets

    Science.gov (United States)

    Saīdouni, Djamel Eddine; Belala, Nabil; Bouneb, Messaouda

    2009-03-01

    The goal of this work is to exploit an implementable model, namely the maximality-based labeled transition system, which permits to express true-concurrency in a natural way without splitting actions on their start and end events. One can do this by giving a maximality-based structural operational semantics for the model of Place/Transition Petri nets in terms of maximality-based labeled transition systems structures.

  20. 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.

  1. Viscous damping for base isolated structures

    Energy Technology Data Exchange (ETDEWEB)

    Lee, D. [Taylor Devices, Santa Monica, CA (United States). West Coast Division; Hussain, S. [Saif Hussain and Associates, Woodland Hills, CA (United States); Retamal, E. [Law Crandall, Northridge, CA (United States)

    1995-12-01

    Seismic Base Isolation can use elastomeric pads, sliding plates or inverted pendulums. Each method can include an energy dissipation means, but only as some kind of hysteretic damping. Hysteretic damping has limitations in terms of energy absorption and may tend to excite higher modes in some cases. It`s possible to avoid these problems with viscous dampers. Viscous damping adds energy dissipation through loads that are 900 out of phase with bending and shear loads so even with damping levels as high as 40% of critical adverse side effects tend to be minimal. This paper presents basic theory of viscous damping, and also describes a sample project. Viscous dampers being built for the new San Bernardino Medical Center reduce both deflections and loads by 50% compared with high damping elastomer base isolation bearings by themselves.

  2. Average-cost based robust structural control

    Science.gov (United States)

    Hagood, Nesbitt W.

    1993-01-01

    A method is presented for the synthesis of robust controllers for linear time invariant structural systems with parameterized uncertainty. The method involves minimizing quantities related to the quadratic cost (H2-norm) averaged over a set of systems described by real parameters such as natural frequencies and modal residues. Bounded average cost is shown to imply stability over the set of systems. Approximations for the exact average are derived and proposed as cost functionals. The properties of these approximate average cost functionals are established. The exact average and approximate average cost functionals are used to derive dynamic controllers which can provide stability robustness. The robustness properties of these controllers are demonstrated in illustrative numerical examples and tested in a simple SISO experiment on the MIT multi-point alignment testbed.

  3. Base pairing in RNA structures: A computational analysis of structural aspects and interaction energies

    Indian Academy of Sciences (India)

    Purshotam Sharma; Abhijit Mitra; Sitansh Sharma; Harjinder Singh

    2007-09-01

    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 geometries of base pairs have been calculated at the HF/6-31G∗∗ level. The structures and interaction energies of the base pairs in the crystal geometry are compared with those obtained after optimization of the base pairs. We find that the base pairs become more planar on full optimization. No change in the hydrogen bonding pattern is seen. It is expected that the inclusion of appropriate considerations of many of these aspects of RNA base pairing would significantly improve the accuracy of RNA secondary structure prediction.

  4. Vibration based fault detection techniques for mechanical structures

    International Nuclear Information System (INIS)

    Fault detection techniques for mechanical structures and their application are becoming more important in recent years in the field of structure health monitoring. The intention of this paper is to present available state of the art methods that could be implemented in mechanical structures. Global based methods that contribute on detection, isolation and analysis of fault from changes in vibration characteristics of the structure are presented. Techniques are based on the idea that modal frequencies, mode shapes and modal damping as model properties of the structure can be determine as function of physical properties. In addition, if a fault appears in mechanical structure, this can be recognized as changes in the physical properties, which leads to cause changes in the modal properties of the structure. (Author)

  5. The Zurich Tradition: Backbone of the Wolf Number Series (Invited)

    Science.gov (United States)

    Friedli, T. K.

    2013-12-01

    The Wolf Series of Sunspot Relative Numbers is divided into a more recent part starting from 1849 up to present which is based on dedicated visual observations and into a reconstructed part reaching back to the mythological ages of Galileo, Harriot and Scheiner which is based solely on indirect countings made from drawings or texts from various archives. The Zurich tradition consists of a framework of rules and prerequisites concerning the quality and power of the instrumentation, the observation and counting techniques, the methods for calibration and preservation of scale and the construction of a long-term record. This framework guarantees the homogeneity of the series and the preservation of the original scale. In the modern part of the series up to 1980, the published Wolf numbers are based in over 90% of the days on calibrated visual observations of the original Fraunhofer refractor. The long term preservation of the original scale is thus mainly determined by the quality and validity of the calibration from one generation of standard observers to the next and on the internal consistency of the individual observing and counting methods of each standard observer. Since 1996 the historical standard refractor of Rudolf Wolf, in succession of the Zurich observers, has been used by the author for the daily determination of the sunspot relative number. With the aid of a small network of keen amateur astronomers of the Rudolf Wolf Gesellschaft these observations could be calibrated to the former Zurich scale. This results in an extension of the original Zurich series which is independent from the official one by SIDC or from the one by AAVSO. The main lesson learned from this exercise is that calibration functions reduce to simple proportionality factors as long as the calculations are made within a proper statistical regression framework over a sufficiently long evaluation period covering both maximum and minimum activity phases. Based on the original observations

  6. An in vitro recombination-based reverse genetic system for rapid mutagenesis of structural genes of the Japanese encephalitis virus

    Institute of Scientific and Technical Information of China (English)

    Ruikun; Du; Manli; Wang; Zhihong; Hu; Hualin; Wang; Fei; Deng

    2015-01-01

    Japanese encephalitis virus(JEV) is one of the most common pathogens of severe viral encephalitis, which is a severe threat to human health. Despite instability of the JEV genome in bacteria, many strategies have been developed to establish molecular clone systems of JEV, providing convenient tools for studying the virus life cycle and virus–host interactions. In this study, we adapted an In-Fusion enzyme-based in vitro recombination method to construct a reverse genetic system of JEV, thereby providing a rapid approach to introduce mutations into the structural genes. A truncated genome without the structural genes was constructed as the backbone, and the complementary segment containing the structural genes was recombined in vitro, which was then transfected directly into virus-permissive cells. The progeny of the infectious virus was successfully detected in the supernatant of the transfected cells, and showed an identical phenotype to its parental virus. To provide a proof-of-principle, the 12 conserved cysteine residues in the envelope(E) protein of JEV were respectively mutated using this approach, and all mutations resulted in a complete failure to generate infectious virus. However, a leucine-tophenylanine mutation at amino acid 107 of the E protein did not interfere with the production of the infectious virus. These results suggested that all 12 cysteines in the E protein are essential for the JEV life cycle. In summary, a novel reverse genetic system of JEV was established for rapidly introducing mutations into structural genes, which will serve as a useful tool for functional studies.

  7. Purification, crystallization and halide phasing of a Streptococcus agalactiae backbone pilin GBS80 fragment

    OpenAIRE

    Vengadesan, Krishnan; Ma, Xin; Dwivedi, Prabhat; Ton-That, Hung; Narayana, Sthanam V. L

    2010-01-01

    The C-terminal fragment of Streptococcus agalactiae (group B streptococcus) major (backbone) pilin GBS80 was purified and crystallized in two different space groups. Single-wavelength anomalous dispersion (SAD) data collected to 2.0 Å resolution on a iodide (NaI) derivative crystal using the home source were used to obtain initial phases.

  8. Analysis of components of conserved "backbone sequences" among genomes of Shigella spp. strains

    Institute of Scientific and Technical Information of China (English)

    LIU Hong; PENG Junping; YANG Jian; SUN Lilian; CHEN Shuxia; Jin Qi

    2004-01-01

    Difference in the genomic compositions of prokaryotes is the basis of the diversity in their biological characters. However, besides their flora- or strain-specific genes, those floras with closer relationship in the evolution also have conserved "backbone sequences", which reveal the marks of their origin and evolution, and these "backbone sequences" are just the basis of their elementary living abilities and common biological properties. Shigella is very closely related to E. coli in the origin and evolution, and may turn out to belong to the same genus. In this study, a microarray containing E. coli K-12 whole genome and Sf301 specific ORFs is used to investigate the genomic components of four Shigella strains. The results indicate that 16%-22% K-12 ORFs sequences are not detected in the genome of Shigella strains while the genome of Shigella contains at least 2800 conserved ORFs, which compose the common "backbone sequences". Advanced analysis indicated that the "backbone sequences" are the essential components in maintaining the normal physiological activities of intestinal bacteria. Furthermore, only 20% Sf301-specific ORFs exist in other strains simultaneously, which demonstrate the great genome heterogeneity and the genetic diversity among the strains.

  9. 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...

  10. 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...

  11. Synthesis and characterization of multifunctional copolyimide incorporating triarylamine and NLO chromophore in backbone

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Presents the synthesis of Copolyimide containing triarylamine andNLO chromophore in backbone by azo coupling of 4-nitrobenzenediazonium tetrafloroborate to copoly(amic acid) in organic solvent and characterized by IR and UV-Vis spectra, which had high glass transition temperatrue and big second-order nonlinear optical coefficient x(2).

  12. 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.

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

    Directory of Open Access Journals (Sweden)

    Kotelevskiy V.I.

    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.

  14. Interconnection and Competition Among Asymmetric Networks in the Internet Backbone Market

    NARCIS (Netherlands)

    Jahn, E.; Prüfer, J.

    2006-01-01

    We examine the interrelation between interconnection and competition in the internet backbone market.Networks asymmetric in size choose among different interconnection regimes and compete for end-users.We show that a direct interconnection regime, Peering, softens competition compared to indirect in

  15. Integrated Data as backbone of e-Navigation

    Directory of Open Access Journals (Sweden)

    Michael Bergmann

    2013-09-01

    Full Text Available e-Navigation, a theme introduced but IMO to improve safety of navigation at sea, is starting to gain traction in various organizations. As the concept develops, the importance of data, both static as well as dynamic, is more and more realized. IALA and IHO, in their efforts to help making e-Navigation a reality, have agreed to propose the IHO GI Register (often known as S-100 Register as the conceptual basis for the Common Maritime Data Structure (CMDS. Utilizing this common understanding of key players in e-Navigation arena, the IMO e-Navigation Correspondence Group has firmed up the overarching architecture, enabling a series to test beds proving the concept of integration of various data streams to enable improved communication between the stakeholders on shore or at sea. The integration of pre-composed, expert generated navigational data with real time and semi real-time data like Virtual AtoNs, Tide Gages Data or MSI transmission from VTS into a single e-Navigation display, if correctly developed, implemented and executed, will be the enabler of increased situational awareness.

  16. Vibration-based localisation of structural deterioration in frame-like civil engineering structures

    DEFF Research Database (Denmark)

    Ulriksen, Martin Dalgaard; Damkilde, Lars

    2016-01-01

    , these vibrations can potentially lead to an evident risk of structural deterioration. In order to ensure the safety of the structures, it is thus paramount that the potential structural deterioration can be identified before it becomes critical from a structural integrity point of view. One way of facilitating...... such identification is by use of structural health monitoring (SHM) techniques, which enable remote, typically through pre-installed sensors, diagnosing of the structural health. In the present paper, it is examined whether a vibration-based SHM approach proposed by the authors—and previously applied successfully...

  17. Dissimilarity-based classification of anatomical tree structures

    DEFF Research Database (Denmark)

    Sørensen, Lauge Emil Borch Laurs; 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 betw...

  18. 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.

  19. A data base for aging of structural materials

    International Nuclear Information System (INIS)

    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)

  20. A data base for aging of structural materials

    International Nuclear Information System (INIS)

    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

  1. Ultrafast vibrational dynamics of the DNA backbone at different hydration levels mapped by two-dimensional infrared spectroscopy.

    Science.gov (United States)

    Guchhait, Biswajit; Liu, Yingliang; Siebert, Torsten; Elsaesser, Thomas

    2016-07-01

    DNA oligomers are studied at 0% and 92% relative humidity, corresponding to N  20 water molecules per base pair. Two-dimensional (2D) infrared spectroscopy of DNA backbone modes between 920 and 1120 cm(-1) maps fluctuating interactions at the DNA surface. At both hydration levels, a frequency fluctuation correlation function with a 300 fs decay and a slow decay beyond 10 ps is derived from the 2D lineshapes. The fast component reflects motions of DNA helix, counterions, and water shell. Its higher amplitude at high hydration level reveals a significant contribution of water to the fluctuating forces. The slow component reflects disorder-induced inhomogeneous broadening. PMID:26798841

  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. 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

  4. Industrial Utilization of Lignin Based on its Structure and Capability

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Chemical modification and industrial utilization of lignin based on its structure were reviewed in this paper. And its economic value and significance for the society and environmental protection were also evaluated.

  5. Knowledge-Based Optimization of Molecular Geometries Using Crystal Structures.

    Science.gov (United States)

    Cole, Jason C; Groom, Colin R; Korb, Oliver; McCabe, Patrick; Shields, Gregory P

    2016-04-25

    This paper describes a novel way to use the structural information contained in the Cambridge Structural Database (CSD) to drive geometry optimization of organic molecules. We describe how CSD structural information is transformed into objective functions for gradient-based optimization to provide good quality geometries for a large variety of organic molecules. Performance is assessed by minimizing different sets of organic molecules reporting RMSD movements for bond lengths, valence angles, torsion angles, and heavy atom positions. PMID:26977906

  6. Deep Structured Energy Based Models for Anomaly Detection

    OpenAIRE

    Zhai, Shuangfei; Cheng, Yu; Lu, Weining; Zhang, Zhongfei

    2016-01-01

    In this paper, we attack the anomaly detection problem by directly modeling the data distribution with deep architectures. We propose deep structured energy based models (DSEBMs), where the energy function is the output of a deterministic deep neural network with structure. We develop novel model architectures to integrate EBMs with different types of data such as static data, sequential data, and spatial data, and apply appropriate model architectures to adapt to the data structure. Our trai...

  7. Graph-based linear scaling electronic structure theory.

    Science.gov (United States)

    Niklasson, Anders M N; Mniszewski, Susan M; Negre, Christian F A; Cawkwell, Marc J; Swart, Pieter J; Mohd-Yusof, Jamal; Germann, Timothy C; Wall, Michael E; Bock, Nicolas; Rubensson, Emanuel H; Djidjev, Hristo

    2016-06-21

    We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations. PMID:27334148

  8. Structural Optimization of Machine Gun Based on Dynamic Stability Concept

    Institute of Scientific and Technical Information of China (English)

    LI Yong-jian; WANG Rui-lin; ZHANG Ben-jun

    2008-01-01

    Improving the firing accuracy is a final goal of structural optimization of machine guns. The main factors which affect the dispersion accuracy of machine gun are analyzed. Based on the concept of dynamic stability, a structural optimization model is built up, and the sensitivity of dispersion accuracy to design variables is analyzed. The optimization results of a type of machine gun show that the method is valid, feasible, and can be used as a guide to the structural optimization of other automatic weapons.

  9. Graph-based linear scaling electronic structure theory

    CERN Document Server

    Niklasson, Anders M N; Negre, Christian F A; Cawkwell, Marc J; Swart, Pieter J; Mohd-Yusof, Jamal; Germann, Timothy C; Wall, Michael E; Bock, Nicolas; Djidjev, Hristo

    2016-01-01

    We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.

  10. 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...

  11. Economic structure and performance of forest-based industries

    International Nuclear Information System (INIS)

    This paper reports on the economic structure, conduct, and performance of industries dependent on the nation's forests that are topics of special importance for research. A major challenge to research involving industrial organization of forest-based industries is to link descriptions of structure, conduct, and industrial performance in ways that facilitate public and private policy making. Not to be overlooked is the need to continue efforts to monitor changes in structure and conduct dimensions at the national level and to conduct baseline studies of industry structure-conduct-performance at regional, state, and local levels. Specifically needed is research that will improve understanding of restructuring within the wood-based industry; definitions of the wood-based industry and segments thereof; linkages between structure and regional economic development; timberland as a managerial and economic variable; structural consequences of technological innovations; corporate strategies as related to performance; structural dimensions in an international setting; and structure and performance of nonwood-based forest industries. Economics research focused in such directions will go far toward improving the manner in which the nation's many forest industries organize and conduct their activities

  12. 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...... analysis based on tree{structured graphical models is a simple nonlinear method competitive with, and sometimes superior to, other well{known linear methods like those assuming mutual independence between variables and linear logistic regression....

  13. Polymer composite material structures comprising carbon based conductive loads

    OpenAIRE

    Jérôme, Robert; Pagnoulle, Christophe; Detrembleur, Christophe; Thomassin, Jean-Michel; Huynen, Isabelle; Bailly, Christian; Bednarz, Luikasz; Daussin, Raphaël; Saib, Aimad; Baudouin, Anne-Christine; Laloyaux, Xavier

    2007-01-01

    The present invention provides a polymer composite material structure comprising at least one layer of a foamed polymer composite material comprising a foamed polymer matrix and 0.1 wt % to 6 wt % carbon based conductive loads, such as e.g. carbon nanotubes, dispersed in the foamed polymer matrix. The polymer composite material structure according to embodiments of the present invention shows good shielding and absorbing properties notwithstanding the low amount of carbon based conductive loa...

  14. Polymer composite material structures comprising carbon based conductive loads

    OpenAIRE

    Jérôme, Robert; Pagnoulle, Christophe; Detrembleur, Christophe; Thomassin, Jean-Michel; Huynen, Isabelle; Bailly, Christian; Bednarz, Lucasz; Daussin, Raphaël; Saib, Aimad

    2006-01-01

    The present invention provides a polymer composite material structure comprising at least one layer of a foamed polymer composite material comprising a foamed polymer matrix and 0.1 to 6 wt% carbon based conductive loads, such as e.g. carbon nanotubes, dispersed in the foamed polymer matrix. The polymer composite material structure according to embodiments of the present invention shows good shielding and absorbing properties notwithstanding the low amount of carbon based conductive loads. Th...

  15. Base Stress of the Opened Bottom Cylinder Structures

    Institute of Scientific and Technical Information of China (English)

    刘建起; 孟晓娟

    2004-01-01

    The base stress of the opened bottom cylinder structure differs greatly from that of the structure with a closed bottom. By investigating the inner soil pressure on the cylinder wall and the base stress of the cylinder base, which were obtained from the model experiments, the interactions among the filler inside the cylinder,subsoil and cylinder are analyzed. The adjusting mechanism of frictional resistance between the inner filler and the wall of the cylinder during the overturning of the cylinder is discussed. Based on the experimental study, a method for calculating the base stress of the opened bottom cylinder structure is proposed. Meanwhile, the formulas for calculating the effective anti-overturning ratio of the opened bottom cylinder are derived.

  16. Structures and photoelectric properties of five benzotrithiophene isomers-based donor-acceptor copolymers

    Science.gov (United States)

    Cheng, Na; Ma, Yuchen; Liu, Yongjun; Zhang, Changqiao; Liu, Chengbu

    2016-04-01

    In this paper, we have investigated the structures, electronic and optical properties of five conjugated copolymers (BTT1-BTz, BTT2-BTz, BTT3-BTz, BTT4-BTz and BTT5-BTz) featuring benzotrithiophene (BTT) isomers as donor units and benzothiadiazole (BTz) as acceptor units, linked through thiophene spacers, employing many-body perturbation theory (MBPT). We have explored the isomer effects by configuration of the sulfur atoms in BTT units, aimed to get insight into how the structural modifications to the conjugated backbone can influence the molecular structures and electronic properties of conjugated polymers. Using the trimer as the computational model, the calculated low and high energy absorption bands (660 and 413 nm) for BTT1-BTz agree well with the experimental ones (645 and 430 nm) with a small offset of ~ 15 nm. On the basis of our calculations, it is found that the backbones of these polymers display different coplanarities, with the dihedral angles between the two neighboring rings varying from 12.3° to 79.0°. Importantly, both BTT1-BTz and BTT2-BTz exhibit intense adsorption around 660 and 623 nm, indicating their promising application in solar cells, whereas BTT3-BTz and BTT4-BTz display the intense adsorption at 569 and 551 nm, which are also usable in the tandem solar cells. BTT5-BTz has narrow and weak adsorption in the visible and infrared region, implying it is not conducive to the sunlight absorption. The blue shift of about 150 nm from BTT1-BTz to BTT5-BTz is suggested to be originated from the shorter effective conjugation lengths.

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

    Institute of Scientific and Technical Information of China (English)

    信赢

    2003-01-01

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

  18. Theoretical study on the structures of ethanolamine and its water complexes using the Hamiltonian algorithm

    Science.gov (United States)

    Teramae, Hiroyuki; Maruo, Yasuko Y.

    2015-12-01

    We try to optimize the structures of monoethanolamine (MEA), MEA dimer, MEA + two water molecules, and MEA dimer + four water molecules as the model of MEA in aqueous solutions using the Hamiltonian algorithm. We found the most stable MEA backbones are all gauche structures. The MEA in aqueous solution seems to exist as dimer or larger aggregates. As the base, the water molecule would be more important than another MEA because of the hydrogen bond networks.

  19. Aircraft detection based on probability model of structural elements

    Science.gov (United States)

    Chen, Long; Jiang, Zhiguo

    2014-11-01

    Detecting aircrafts is important in the field of remote sensing. In past decades, researchers used various approaches to detect aircrafts based on classifiers for overall aircrafts. However, with the development of high-resolution images, the internal structures of aircrafts should also be taken into consideration now. To address this issue, a novel aircrafts detection method for satellite images based on probabilistic topic model is presented. We model aircrafts as the connected structural elements rather than features. The proposed method contains two major steps: 1) Use Cascade-Adaboost classier to identify the structural elements of aircraft firstly. 2) Connect these structural elements to aircrafts, where the relationships between elements are estimated by hierarchical topic model. The model places strict spatial constraints on structural elements which can identify differences between similar features. The experimental results demonstrate the effectiveness of the approach.

  20. Gradient-based optimization in nonlinear structural dynamics

    DEFF Research Database (Denmark)

    Dou, Suguang

    , and optimization of nonlinear structural dynamics. In the modelling, nonlinear finite elements are used. In the analysis, nonlinear frequency response and nonlinear normal modes are calculated based on a harmonic balance method with higher-order harmonics. In the characterization, nonlinear modal coupling......, 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...... 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...

  1. 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.

  2. Evaluation Method of Web Site Based on Web Structure Mining

    Institute of Scientific and Technical Information of China (English)

    LiJun-e; ZhouDong-ru

    2003-01-01

    The structure of Web site became more complex than before. During the design period of a Web site, the lack of model and method results in improper Web structure,which depend on the designer's experience. From the point of view of software engineering, every period in the software life must be evaluated before starting the next period's work. It is very important and essential to search relevant methods for evaluating Web structure before the site is completed. In this work, after studying the related work about the Web structure mining and analyzing the major structure mining methods (Page-rank and Hub/Authority), a method based on the Page-rank for Web structure evaluation in design stage is proposed. A Web structure modeling language WSML is designed, and the implement strategies for evaluating system of the Web site structure are given out. Web structure mining has being used mainly in search engines before. It is the first time to employ the Web structure mining technology to evaluate a Web structure in the design period of a Web site. It contributes to the formalization of the design documents for Web site and the improving of software engineering for large scale Web site, and the evaluating system is a practical tool for Web site construction.

  3. Health monitoring of aeronautical structures based on vibrations measurements

    Science.gov (United States)

    Bovio, Igor; Lecce, Leonardo

    2006-03-01

    Purpose of the paper is to present an innovative application inside the Non Destructive Testing field based on vibrations measurements, developed by the authors during the last three years, and already tested for analysing damage of many structural elements. The proposed new method is based on the acquisition and comparison of Frequency Response Functions (FRFs) of the monitored structure before and after an occurred damage. Structural damage modify the dynamical behaviour of the structure such as mass, stiffened and damping, and consequently the FRFs of the damaged structure in comparison with the FRFs of the sound structure, making possible to identify, to localize and quantify a structural damage. The activities, presented in the paper, mostly focused on a new FRFs processing technique based on the determining of a representative "Damage Index" for identifying and analysing damage both on real scale aeronautical structural components, like large-scale fuselage reinforced panels, and on aeronautical composite panels. Besides it has been carried out a dedicated neural network algorithm aiming at obtaining a "recognition-based learning"; this kind of learning methodology permits to train the neural network in order to let it recognises only "positive" examples discarding as a consequence the "negative" ones. Within the structural NDT a "positive" example means "healthy" state of the analysed structural component and, obviously, a "negative" one means a "damaged" or perturbed state. From an architectural point of view piezoceramic patches have been tested as actuators and sensors. Besides it has been used a laser-scanning vibrometer system to validate the behaviour of the piezoceramic patches.

  4. Spectral analysis based on compressive sensing in nanophotonic structures.

    Science.gov (United States)

    Wang, Zhu; Yu, Zongfu

    2014-10-20

    A method of spectral sensing based on compressive sensing is shown to have the potential to achieve high resolution in a compact device size. The random bases used in compressive sensing are created by the optical response of a set of different nanophotonic structures, such as photonic crystal slabs. The complex interferences in these nanostructures offer diverse spectral features suitable for compressive sensing.

  5. 基于噻吩和亚苯基合成的新物质的结构和电子性质%Structural and Electronic Properties of New Materials Based on Thiophene and Phenylene

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Theoretical study on the geometries and electronic properties of new conjugated compounds based on thiophene and phenylene was carried out. The theoretical ground-state geometries and electronic structures of the studied molecules were obtained using the density functional theory (DFT) method at B3LYP level with 6-31G(d) basis set. The electronic properties were determined by ZINDO/s, CIS/3-21G(d), and TD//B3LYP/3-21G(d) calculations performed on the B3LYP/6-31(d) optimized geometries. The effects of the ring structure and the substituents on the geometries and electronic properties of these materials were discussed. The results of this study indicate how the electronic properties can be tuned by the backbone ring or side group and suggest these compounds as good candidates for opro-electronic applications.

  6. Photo-excited terahertz switch based on composite metamaterial structure

    Science.gov (United States)

    Wang, Guocui; Zhang, Jianna; Zhang, Bo; He, Ting; He, Yanan; Shen, Jingling

    2016-09-01

    A photo-excited terahertz switch based on a composite metamaterial structure was designed by integration of photoconductive silicon into the gaps of split-ring resonators. The conductivity of the silicon that was used to fill the gaps in the split-ring resonators was tuned dynamically as a function of the incident pump power using laser excitation, leading to a change in the composite metamaterial structure's properties. We studied the transmission characteristics of the composite metamaterial structure for various silicon conductivities, and the results indicated that this type of composite metamaterial structure could be used as a resonance frequency tunable terahertz metamaterial switch. We also designed other structures by filling different gaps with silicon, and proved that these structures could be used as terahertz metamaterial switches can change the working mode from a single frequency to multiple frequencies.

  7. Earthquake Damage Assessment for RC Structures Based on Fuzzy Sets

    Directory of Open Access Journals (Sweden)

    Haoxiang He

    2013-01-01

    Full Text Available A global damage index based on multiple linear force-deformation curves in pushover analysis is presented to evaluate the integrated damage of reinforced concrete structure. The modified coefficient is provided considering the cyclic load and hysteresis energy. The number of inelastic cycles and the coefficient of hysteresis energy concentration are also introduced as damage indices. Hence, multiple damage indices about displacement and energy for performance-based design are considered. The relation of multiple damage indices or factors and the fuzzy damage set is presented by comprehensive fuzzy evaluation; hence, a performance-based multiple fuzzy seismic damage-assessment method for reinforced concrete frame structures is established. The method can be accomplished based on pushover analysis, code spectrum, and capacity spectrum method. The fuzzy seismic damage-assessment method is verified through nonlinear analysis four different structures and the corresponding results and assessment conclusions are accurate.

  8. New nucleoside/nucleotide backbone options: a review of recent studies.

    Science.gov (United States)

    Ruane, Peter J; DeJesus, Edwin

    2004-09-01

    The nucleoside/nucleotide reverse transcriptase inhibitor (NRTI/NtRTI) class continues to serve as an important component of the standard of care for HIV infection. Combinations of dual NRTIs/NtRTIs with protease inhibitors (PIs) or nonnucleoside reverse transcriptase inhibitors (NNRTIs) remain the most commonly used regimens in clinical practice. In recent years, clinical outcomes data on previously novel NRTI/NtRTI backbone combinations have provided clinicians with new options to address potency, tolerability, and convenience of antiretroviral therapy. However, the tolerability, drug-drug interactions, and resistance profiles of specific regimens using new NRTI/NtRTI combinations must be weighed against the needs and preferences of individual patients. This review summarizes recent efficacy and safety data on emerging NRTI/NtRTI combination backbones, including tenofovir DF (TDF) with lamivudine (3TC), abacavir with 3TC, didanosine (ddI) with 3TC, ddI with emtricitabine (FTC), and TDF with FTC. PMID:15319666

  9. 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.

  10. Extended Kalman filter based structural damage detection for MR damper controlled structures

    Science.gov (United States)

    Jin, Chenhao; Jang, Shinae; Sun, Xiaorong; Jiang, Zhaoshuo; Christenson, Richard

    2016-04-01

    The Magneto-rheological (MR) dampers have been widely used in many building and bridge structures against earthquake and wind loadings due to its advantages including mechanical simplicity, high dynamic range, low power requirements, large force capacity, and robustness. However, research about structural damage detection methods for MR damper controlled structures is limited. This paper aims to develop a real-time structural damage detection method for MR damper controlled structures. A novel state space model of MR damper controlled structure is first built by combining the structure's equation of motion and MR damper's hyperbolic tangent model. In this way, the state parameters of both the structure and MR damper are added in the state vector of the state space model. Extended Kalman filter is then used to provide prediction for state variables from measurement data. The two techniques are synergistically combined to identify parameters and track the changes of both structure and MR damper in real time. The proposed method is tested using response data of a three-floor MR damper controlled linear building structure under earthquake excitation. The testing results show that the adaptive extended Kalman filter based approach is capable to estimate not only structural parameters such as stiffness and damping of each floor, but also the parameters of MR damper, so that more insights and understanding of the damage can be obtained. The developed method also demonstrates high damage detection accuracy and light computation, as well as the potential to implement in a structural health monitoring system.

  11. Integrating the university medical center. Phase one: providing an information backbone.

    OpenAIRE

    Berry, S J; Reber, E.; Offeman, W. E.

    1991-01-01

    UCLA School of Medicine represents a diverse computing community where the creation of each individual network has been driven by applications, price/performance and functionality. Indeed, the ability to connect to other computers has had no bearing on selection. Yet, there exists a need to seamlessly connect the individual networks to other minicomputers, mainframes and remote computers. We have created a school wide backbone network that will enable an individual from a single workstation t...

  12. Power consumption evaluation of circuit-switched versus packet-switched optical backbone networks

    OpenAIRE

    Van Heddeghem W.; Lannoo B.; Colle D.; Pickavet M.; Musumeci F.; Pattavina A.; Idzikowski F.

    2013-01-01

    While telecommunication networks have historically been dominated by a circuit-switched paradigm, the last decades have seen a clear trend towards packet-switched networks. In this paper we evaluate how both paradigms perform in optical backbone networks from a power consumption point of view, and whether the general agreement of circuit switching being more power-efficient holds. We consider artificially generated topologies of various sizes, mesh degrees and not yet previously explored in t...

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

    OpenAIRE

    Olson, Randal S.; Neal, Zachary P.

    2013-01-01

    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 o...

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

    Institute of Scientific and Technical Information of China (English)

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

    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-Tc 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 Fe2Pn2 (Pn =P,As,Sb) or Fe2Ch2 (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 K0.8Fe1.6+xSe2 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.

  15. An Analytic Method for the Kinematics and Dynamics of a Multiple-Backbone Continuum Robot

    Directory of Open Access Journals (Sweden)

    Bin He

    2013-01-01

    Full Text Available Continuum robots have been the subject of extensive research due to their potential use in a wide range of applications. In this paper, we propose a new continuum robot with three backbones, and provide a unified analytic method for the kinematics and dynamics of a multiple‐backbone continuum robot. The robot achieves actuation by independently pulling three backbones to carry out a bending motion of two‐degrees‐of‐freedom (DoF. A three‐dimensional CAD model of the robot is built and the kinematical equation is established on the basis of the Euler‐Bernoulli beam. The dynamical model of the continuum robot is constructed by using the Lagrange method. The simulation and the experiment’s validation results show the continuum robot can exactly bend into pre‐set angles in the two‐dimensional space (the maximum error is less than 5% of the robot length and can make a circular motion in three‐dimensional space. The results demonstrate that the proposed analytic method for the kinematics and dynamics of a continuum robot is feasible.

  16. A neighboring structure reconstructed matching algorithm based on LARK features

    Science.gov (United States)

    Xue, Taobei; Han, Jing; Zhang, Yi; Bai, Lianfa

    2015-11-01

    Aimed at the low contrast ratio and high noise of infrared images, and the randomness and ambient occlusion of its objects, this paper presents a neighboring structure reconstructed matching (NSRM) algorithm based on LARK features. The neighboring structure relationships of local window are considered based on a non-negative linear reconstruction method to build a neighboring structure relationship matrix. Then the LARK feature matrix and the NSRM matrix are processed separately to get two different similarity images. By fusing and analyzing the two similarity images, those infrared objects are detected and marked by the non-maximum suppression. The NSRM approach is extended to detect infrared objects with incompact structure. High performance is demonstrated on infrared body set, indicating a lower false detecting rate than conventional methods in complex natural scenes.

  17. Integrated Reliability-Based Optimal Design of Structures

    DEFF Research Database (Denmark)

    Sørensen, John Dalsgaard; Thoft-Christensen, Palle

    1987-01-01

    value. The reliability can be measured from an element and/or a systems point of view. A number of methods to solve reliability-based optimization problems has been suggested, see e.g. Frangopol [I]. Murotsu et al. (2], Thoft-Christensen & Sørensen (3] and Sørensen (4). For structures where......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......-based optimal design is discussed. Next, an optimal inspection and repair strategy for existing structural systems is presented. An optimization problem is formulated , where the objective is to minimize the expected total future cost of inspection and repair subject to the constraint that the reliability...

  18. Oxidation resistance coating for niobium base structural composites

    International Nuclear Information System (INIS)

    Oxidation behavior of Al-rich Mo(Si,Al)2 base alloys, which is a candidate material for the oxidation resistance coating on Nb base structural composites, were investigated by thermogravimetry. The Mo(Si,Al)2 base alloys containing Mo5(Si,Al)3 up to about 10 vol% exhibits excellent oxidation resistance at temperatures ranging from 780 to 1580 K, particularly at 1580 K due to continuous Al2O3 layer development. To evaluate the applicability of the Mo(Si,Al)2 base coating, plasma spraying on Nb base composites were undertaken. However, interface reaction layer was found to form during the following heat treatment. Preparation of Mo(Si,Al)2/Al2O3/Nb layered structures via powder metallurgical process was attempted to preclude diffusion reaction between coating and substrate. (orig.)

  19. Reliability based robustness of timber structures through NDT data updating

    OpenAIRE

    Sousa, Hélder S.; Sorensen, John D.; Kirkegaard, Poul H.; Lourenço, Paulo B.; Branco, Jorge M.

    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. These methods are suitable to be used for parameter estimation and also allow updating model uncertainties. From the updated model, decisions upon the life-cycle reliability of existing structures may be taken and mai...

  20. Medical Images Fusion with Patch Based Structure Tensor

    OpenAIRE

    Luo, Fen; Sun, Jiangfeng; Hou, Shouming

    2015-01-01

    Nowadays medical imaging has played an important role in clinical use, which provide important clues for medical diagnosis. In medical image fusion, the extraction of some fine details and description is critical. To solve this problem, a modified structure tensor by considering similarity between two patches is proposed. The patch based filter can suppress noise and add the robustness of the eigen-values of the structure tensor by allowing the use of more information of far away pixels. Afte...

  1. A fingerprint based metric for measuring similarities of crystalline structures

    OpenAIRE

    Zhu, Li; Amsler, Maximilian; Fuhrer, Tobias; Schaefer, Bastian; Faraji, Somayeh; Rostami, Samare; Ghasemi, S. Alireza; Sadeghi, Ali; Grauzinyte, Migle; Wolverton, Christopher; Goedecker, Stefan

    2015-01-01

    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 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 allow to define configurati...

  2. Nominal and Structural Subtyping in Component-Based Programming

    DEFF Research Database (Denmark)

    Ostermann, Klaus

    2007-01-01

    type. We analyze structural and different flavors of nominal subtyping from the perspective of component-based programming, where issues such as blame assignment and modular extensibility are important. Our analysis puts various existing subtyping mechanisms into a common frame of reference...... and delineates the frontiers of the subtyping design space. In addition, we propose a new subtyping definition in one particularly interesting corner of the design space which combines the safety of nominal subtyping with the flexibility of structural subtyping....

  3. Miniature Microwave Bandpass Filter Based on EBG Structures

    OpenAIRE

    Zhurbenko, Vitaliy; Krozer, Viktor; Meincke, Peter

    2006-01-01

    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 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. Measu...

  4. Research on Web-Based Product Structure and Configuration Management

    Institute of Scientific and Technical Information of China (English)

    CHENJi-zhong; TIANLing; XUXiao-hui

    2004-01-01

    An enhanced system architecture of Web-based product structure and configuration management system along with its, functions are is presented. The key techniques, such as construction of object models of product structure and product configuration, hybrid approach method in product configuration management, sharing and integration of heterogeneous product data, integration with other sub-systems, are discussed too. A prototype system is developed by J2EE technology.

  5. Structured Interleaver Design Based on Two Interleaving Distances

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Based on the analysis of codeword Hamming distances, two parameters, i.e. self-interleaving distance and cross-interleaving distance, are proposed herein. To make these two distances as large as possible, a method to evaluate the efficiency of an interleaver produced and a new type of structured interleaver is proposed. Simulations show that turbo codes with the new type of structured interleaver can obtain a better performance compared with a random interleaver or a block interleaver.

  6. Solution Structure and Backbone Dynamics of Human Liver Fatty Acid Binding Protein: Fatty Acid Binding Revisited

    OpenAIRE

    Cai, Jun; Lücke, Christian; Chen, Zhongjing; Qiao, Ye; Klimtchuk, Elena; Hamilton, James A.

    2012-01-01

    Liver fatty acid binding protein (L-FABP), a cytosolic protein most abundant in liver, is associated with intracellular transport of fatty acids, nuclear signaling, and regulation of intracellular lipolysis. Among the members of the intracellular lipid binding protein family, L-FABP is of particular interest as it can i), bind two fatty acid molecules simultaneously and ii), accommodate a variety of bulkier physiological ligands such as bilirubin and fatty acyl CoA. To better understand the p...

  7. 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...

  8. Gradient-based adaptation of continuous dynamic model structures

    Science.gov (United States)

    La Cava, William G.; Danai, Kourosh

    2016-01-01

    A gradient-based method of symbolic adaptation is introduced for a class of continuous dynamic models. The proposed model structure adaptation method starts with the first-principles model of the system and adapts its structure after adjusting its individual components in symbolic form. A key contribution of this work is its introduction of the model's parameter sensitivity as the measure of symbolic changes to the model. This measure, which is essential to defining the structural sensitivity of the model, not only accommodates algebraic evaluation of candidate models in lieu of more computationally expensive simulation-based evaluation, but also makes possible the implementation of gradient-based optimisation in symbolic adaptation. The proposed method is applied to models of several virtual and real-world systems that demonstrate its potential utility.

  9. An RNA secondary structure prediction method based on minimum and suboptimal free energy structures.

    Science.gov (United States)

    Fu, Haoyue; Yang, Lianping; Zhang, Xiangde

    2015-09-01

    The function of an RNA-molecule is mainly determined by its tertiary structures. And its secondary structure is an important determinant of its tertiary structure. The comparative methods usually give better results than the single-sequence methods. Based on minimum and suboptimal free energy structures, the paper presents a novel method for predicting conserved secondary structure of a group of related RNAs. In the method, the information from the known RNA structures is used as training data in a SVM (Support Vector Machine) classifier. Our method has been tested on the benchmark dataset given by Puton et al. The results show that the average sensitivity of our method is higher than that of other comparative methods such as CentroidAlifold, MXScrana, RNAalifold, and TurboFold. PMID:26100179

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

    International Nuclear Information System (INIS)

    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

  11. Tl-based high temperature superconducting cuprates: structure and properties

    International Nuclear Information System (INIS)

    The structure and properties of the Tl-based high temperature superconducting cuprates are reviewed. The single Tl-O layered phases Tl(Sr/Ba)2Ca2Cu3O9 stabilized by substitution of Pb or Bi in the Tl site are being developed for technological applications, because of their high Tc, excellent magnetic flux pinning and minimal weak-link behavior. Some of the factors that affect the high temperature superconducting properties, including substitutions, electronic structure, oxygen nonstoichiometry and defects are discussed in relation to the structure. (orig.)

  12. Method for Real-Time Model Based Structural Anomaly Detection

    Science.gov (United States)

    Smith, Timothy A. (Inventor); Urnes, James M., Sr. (Inventor); Reichenbach, Eric Y. (Inventor)

    2015-01-01

    A system and methods for real-time model based vehicle structural anomaly detection are disclosed. A real-time measurement corresponding to a location on a vehicle structure during an operation of the vehicle is received, and the real-time measurement is compared to expected operation data for the location to provide a modeling error signal. A statistical significance of the modeling error signal to provide an error significance is calculated, and a persistence of the error significance is determined. A structural anomaly is indicated, if the persistence exceeds a persistence threshold value.

  13. 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

  14. Inorganic backbone ionomers: Design and dielectric response of single-ion conducting polymers

    Science.gov (United States)

    Bartels, Joshua

    Ion-conducting polymers were studied primarily through the use of dielectric spectroscopy. The conclusions drawn from ion conduction models of the dielectric data are corroborated by additional independent experiments, including x-ray scattering, calorimetry, prism coupling, and DFT calculations. The broad concern of this dissertation is to understand and clarify a path forward in ion conducting polymer research. This is achieved by considering low-Tg ionomers and the advantages imparted by siloxane and phosphazene backbones. The most successful dielectric spectroscopy model for the materials studied is the electrode polarization model (EP), whereas other models, such as the Dyre random barrier model, fail to describe the experimental results. Seven nonionic ether oxygen (EO) containing polymers were studied in order to observe the effect that backbone chemistry has on dipole motion. Conventional carboncarbon backbone EO-containing polymers show no distinct advantage over similar EO-pendant polysiloxane or polyphosphazene systems. The mobility and effective backbone Tg imparted by the inorganic backbones are comparable. A short EO pendant results in a lower static dielectric constant due to restricted motion of dipoles close to the chain. The flexibility and chemical versatility of inorganic backbone polymers motivates further study of two ionomer systems. A polypohosphazene iodide conducting system was characterized by dielectric spectroscopy and x-ray scattering. Two end "tail" functionalization of the ammonium ion were used, a tail with two EOs and an alkyl tail of six carbons. This functional group plays an important role in ion dynamics and can wrap around the ion and self-solvate when EOs are present. The iodide-ammonium ionomers are observed to have unusually large high-frequency dielectric constants due to atomic polarization of ions. The strength of the atomic polarization scales with ion content. The aggregation state of ions is able to be determined from

  15. Structural segmentation for multimedia content-based information retrieval

    Science.gov (United States)

    Carli, Marco; Degli Esposti, Alberto; Micarelli, Alessandro; Neri, Alessandro

    2001-12-01

    In this contribution we propose a novel semantic-based architecture to manage multimedia data. We propose an innovatory approach, introducing an abstraction level to study the relationships among the low level attributes, as color, motion, in a systematic way, before the visual image content estimation. Aim of this analysis is to unify the descriptors information and to gather them into structures that we call over-regions, which represent particular configurations of the objects to be recognized. This step will allow for the higher abstraction level effective object-based or event-based image recognition. The case-based reasoning paradigm is used in our approach for the high level analysis.

  16. Structure-Based Search for New Inhibitors of Cholinesterases

    Directory of Open Access Journals (Sweden)

    Barbara Malawska

    2013-03-01

    Full Text Available Cholinesterases are important biological targets responsible for regulation of cholinergic transmission, and their inhibitors are used for the treatment of Alzheimer’s disease. To design new cholinesterase inhibitors, of different structure-based design strategies was followed, including the modification of compounds from a previously developed library and a fragment-based design approach. This led to the selection of heterodimeric structures as potential inhibitors. Synthesis and biological evaluation of selected candidates confirmed that the designed compounds were acetylcholinesterase inhibitors with IC50 values in the mid-nanomolar to low micromolar range, and some of them were also butyrylcholinesterase inhibitors.

  17. 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......, 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 the structural design of WECs based on a reliability-based optimization problem...

  18. Evaluation Method of Web Site Structure Based on Web Structure Mining

    Institute of Scientific and Technical Information of China (English)

    Li Jun-e; Zhou Dong-ru

    2003-01-01

    The structure of Web site hecarne more complex titan before. During the design period of a Web site, the lack of model and method results in improper Web structure,which depend on the designer's experience. From the point of view of software engineering, every period in the software life must be evaluated before starting the next period's work. It is very important and essential to search relevant methods for evaluating Web structure before the site is completed. In this work, after studying the related work about the Web struc lure mining and analyzing the major structure mining methods (Page-rank and Hub/Authority), a method based on the Page-rank for Web structure evaluation in design stage is proposecL A Web structure modeling language WSML is designed, and the implement strategies for evaluating system of the Web site structure are given out. Web structure mining has being used mainly in search engines before. It is the first time to employ the Web structure mining technology to evaluate a Web structure in the design period of a Web site. It contributes to the formalization of the design documents for Web site and the improving of software engineering for large scale Web site, and the evaluating system is a practical tool for Web site construction.

  19. 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.

  20. A velocity-based seismic control for base-isolated building structures

    OpenAIRE

    Pozo Montero, Francesc; Acho Zuppa, Leonardo; Rodellar Benedé, José; Rossell Garriga, Josep Maria

    2009-01-01

    Passive, active and semi-active control have been extensively considered to improve the protection of base-isolated structures against earthquakes. This paper presents a strategy to apply control forces to the base of an isolated structure to enhance the performance of purely passive devices. The main feature is the simplicity in formulation, design and implementation. It is formulated as a static nonlinear function depending only on the base velocity. This function ensures energy dissi...

  1. Improving structural similarity based virtual screening using background knowledge

    OpenAIRE

    Girschick, Tobias; Puchbauer, Lucia; Kramer, Stefan

    2013-01-01

    Background Virtual screening in the form of similarity rankings is often applied in the early drug discovery process to rank and prioritize compounds from a database. This similarity ranking can be achieved with structural similarity measures. However, their general nature can lead to insufficient performance in some application cases. In this paper, we provide a link between ranking-based virtual screening and fragment-based data mining methods. The inclusion of binding-relevant background k...

  2. Synthesis of novel cationic lipids with fully or partially non-scissile linkages between the hydrocarbon chains and pseudoglyceryl backbone

    Indian Academy of Sciences (India)

    Santanu Bhattacharya; Saubhik Haldar

    2002-06-01

    Five novel cationic lipids with fully or partially non-scissile linkage regions between the pseudoglyceryl backbone and the hydrocarbon chains have been synthesized. The membrane-forming properties of these new lipids are briefly presented.

  3. Membrane adsorption and binding, cellular uptake and cytotoxicity of cell-penetrating peptidomimetics with α-peptide/β-peptoid backbone

    DEFF Research Database (Denmark)

    Jing, Xiaona; Yang, Mingjun; Kasimova, Marina Robertovna;

    2012-01-01

    Cell-penetrating peptides (CPPs) provide a promising approach for enhancing intracellular delivery of therapeutic biomacromolecules by increasing transport through membrane barriers. Here, proteolytically stable cell-penetrating peptidomimetics with α-peptide/β-peptoid backbone were studied...

  4. Structure-based design of combinatorial mutagenesis libraries.

    Science.gov (United States)

    Verma, Deeptak; Grigoryan, Gevorg; Bailey-Kellogg, Chris

    2015-05-01

    The development of protein variants with improved properties (thermostability, binding affinity, catalytic activity, etc.) has greatly benefited from the application of high-throughput screens evaluating large, diverse combinatorial libraries. At the same time, since only a very limited portion of sequence space can be experimentally constructed and tested, an attractive possibility is to use computational protein design to focus libraries on a productive portion of the space. We present a general-purpose method, called "Structure-based Optimization of Combinatorial Mutagenesis" (SOCoM), which can optimize arbitrarily large combinatorial mutagenesis libraries directly based on structural energies of their constituents. SOCoM chooses both positions and substitutions, employing a combinatorial optimization framework based on library-averaged energy potentials in order to avoid explicitly modeling every variant in every possible library. In case study applications to green fluorescent protein, β-lactamase, and lipase A, SOCoM optimizes relatively small, focused libraries whose variants achieve energies comparable to or better than previous library design efforts, as well as larger libraries (previously not designable by structure-based methods) whose variants cover greater diversity while still maintaining substantially better energies than would be achieved by representative random library approaches. By allowing the creation of large-scale combinatorial libraries based on structural calculations, SOCoM promises to increase the scope of applicability of computational protein design and improve the hit rate of discovering beneficial variants. While designs presented here focus on variant stability (predicted by total energy), SOCoM can readily incorporate other structure-based assessments, such as the energy gap between alternative conformational or bound states.

  5. Density-Based and Transport-Based Core-Periphery Structures in Networks

    CERN Document Server

    Lee, Sang Hoon; Porter, Mason A

    2013-01-01

    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 transportation. 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 this new diagnostic i...

  6. Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes.

    Directory of Open Access Journals (Sweden)

    Christopher A Lavender

    2015-05-01

    Full Text Available 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.

  7. Crystal chemistry and structural design of iron-based superconductors

    Institute of Scientific and Technical Information of China (English)

    Jiang Hao; Sun Yun-Lei; Xu Zhu-An; Cao Guang-Han

    2013-01-01

    The second class of high-temperature superconductors (HTSCs),iron-based pnictides and chalcogenides,necessarily contain Fe2X2 (“X” refers to a pnictogen or a chalcogen element) layers,just like the first class of HTSCs which possess the essential CuO2 sheets.So far,dozens of iron-based HTSCs,classified into nine groups,have been discovered.In this article,the crystal-chemistry aspects of the known iron-based superconductors are reviewed and summarized by employing “hard and soft acids and bases (HSAB)” concept.Based on these understandings,we propose an alternative route to exploring new iron-based superconductors via rational structural design.

  8. Knowledge-based System Prototype in Structural Component Design Based on FM

    Institute of Scientific and Technical Information of China (English)

    JIANG; Tao; LI; Qing-fen; LI; Ming; FU; Wei

    2002-01-01

    A knowledge-based system in structural component design based on fracture mechanics is developed in this paper. The system consists of several functional parts: a general inference engine, a set of knowledge bases and data-bases, an interpretation engine, a bases administration system and the interface. It can simulate a human expert to make analysis and design scheme mainly for four kinds of typical structural components widely used in shipbuilding industry: pressure vessels, huge rotation constructions, pump-rod and welded structures. It is an open system which may be broadened and perfected to cover a wider range of engineering application through the modification and enlargement of knowledge bases and data-bases. It has a natural and friendly interface that may be easily operated. An on-line help service is also provided.

  9. 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...

  10. Synthesis and Crystal Structures of Schiff Bases Bearing Ferrocenylphenyl Groups

    Institute of Scientific and Technical Information of China (English)

    Yan XU; Yong FU; Mao Ping SONG; Yang Jie WU

    2005-01-01

    The Schiff bases bearing ferrocenylphenyl and diferrocenylphenyl groups were synthesized by the reactions of m-ferrocenylaniline with salicylaldehyde or 1, 4-bis (2'-formylphenyl)-1, 4-dioxabutane. The title compounds were characterized by elemental analysis, IR, 1H NMR and X-ray structural determination.

  11. Easy and unambiguous sequential assignments of intrinsically disordered proteins by correlating the backbone {sup 15}N or {sup 13}C′ chemical shifts of multiple contiguous residues in highly resolved 3D spectra

    Energy Technology Data Exchange (ETDEWEB)

    Yoshimura, Yuichi; Kulminskaya, Natalia V.; Mulder, Frans A. A., E-mail: fmulder@chem.au.dk [Aarhus University, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO) (Denmark)

    2015-02-15

    Sequential resonance assignment strategies are typically based on matching one or two chemical shifts of adjacent residues. However, resonance overlap often leads to ambiguity in resonance assignments in particular for intrinsically disordered proteins. We investigated the potential of establishing connectivity through the three-bond couplings between sequentially adjoining backbone carbonyl carbon nuclei, combined with semi-constant time chemical shift evolution, for resonance assignments of small folded and larger unfolded proteins. Extended sequential connectivity strongly lifts chemical shift degeneracy of the backbone nuclei in disordered proteins. We show here that 3D (H)N(COCO)NH and (HN)CO(CO)NH experiments with relaxation-optimized multiple pulse mixing correlate up to seven adjacent backbone amide nitrogen or carbonyl carbon nuclei, respectively, and connections across proline residues are also obtained straightforwardly. Multiple, recurrent long-range correlations with ultra-high resolution allow backbone {sup 1}H{sup N}, {sup 15}N{sup H}, and {sup 13}C′ resonance assignments to be completed from a single pair of 3D experiments.

  12. 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...

  13. 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.

  14. A fingerprint based metric for measuring similarities of crystalline structures

    International Nuclear Information System (INIS)

    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

  15. Optimization of multi-constrained structures based on optimality criteria

    Science.gov (United States)

    Rizzi, P.

    1976-01-01

    A weight-reduction algorithm is developed for the optimal design of structures subject to several multibehavioral inequality constraints. The structural weight is considered to depend linearly on the design variables. The algorithm incorporates a simple recursion formula derived from the Kuhn-Tucker necessary conditions for optimality, associated with a procedure to delete nonactive constraints based on the Gauss-Seidel iterative method for linear systems. A number of example problems is studied, including typical truss structures and simplified wings subject to static loads and with constraints imposed on stresses and displacements. For one of the latter structures, constraints on the fundamental natural frequency and flutter speed are also imposed. The results obtained show that the method is fast, efficient, and general when compared to other competing techniques. Extensions to the generality of the method to include equality constraints and nonlinear merit functions is discussed.

  16. Technology of structure damage monitoring based on multi-agent

    Institute of Scientific and Technical Information of China (English)

    Hongbing Sun; Shenfang Yuan; Xia Zhao; Hengbao Zhou; Dong Liang

    2010-01-01

    The health monitoring for large-scale structures need to resolve a large number of difficulties,such as the data transmission and distributing information handling.To solve these problems,the technology of multi-agent is a good candidate to be used in the field of structural health monitoring.A structural health monitoring system architecture based on multi-agent technology is proposed.The measurement system for aircraft airfoil is designed with FBG,strain gage,and corresponding signal processing circuit.The experiment to determine the location of the concentrate loading on the structure is carried on with the system combined with technologies of pattern recognition and multi-agent.The results show that the system can locate the concentrate loading of the aircraft airfoil at the accuracy of 91.2%.

  17. A fingerprint based metric for measuring similarities of crystalline structures

    CERN Document Server

    Zhu, Li; Fuhrer, Tobias; Schaefer, Bastian; Faraji, Somayeh; Rostami, Samara; Ghasemi, S Alireza; Sadeghi, Ali; Grauzinyte, Migle; Wolverton, Christopher; Goedecker, Stefan

    2015-01-01

    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 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 allow to 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 is an useful tool within various energy landscape exploration schemes, such as minima hopping, random search, swarm intelligence algorithms and high-throughput screenings.

  18. 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.

  19. Backbone conformational flexibility of the lipid modified membrane anchor of the human N-Ras protein investigated by solid-state NMR and molecular dynamics simulation.

    Science.gov (United States)

    Vogel, Alexander; Reuther, Guido; Roark, Matthew B; Tan, Kui-Thong; Waldmann, Herbert; Feller, Scott E; Huster, Daniel

    2010-02-01

    The lipid modified human N-Ras protein, implicated in human cancer development, is of particular interest due to its membrane anchor that determines the activity and subcellular location of the protein. Previous solid-state NMR investigations indicated that this membrane anchor is highly dynamic, which may be indicative of backbone conformational flexibility. This article aims to address if a dynamic exchange between three structural models exist that had been determined previously. We applied a combination of solid-state nuclear magnetic resonance (NMR) methods and replica exchange molecular dynamics (MD) simulations using a Ras peptide that represents the terminal seven amino acids of the human N-Ras protein. Analysis of correlations between the conformations of individual amino acids revealed that Cys 181 and Met 182 undergo collective conformational exchange. Two major structures constituting about 60% of all conformations could be identified. The two conformations found in the simulation are in rapid exchange, which gives rise to low backbone order parameters and nuclear spin relaxation as measured by experimental NMR methods. These parameters were also determined from two 300 ns conventional MD simulations, providing very good agreement with the experimental data. PMID:19819220

  20. Rock burst prevention based on dissipative structure theory

    Institute of Scientific and Technical Information of China (English)

    Song Dazhao; Wang Enyuan; Li Nan; Jin Mingyue; Xue Shipeng

    2012-01-01

    Dynamic collapses of deeply mined coal rocks are severe.In order to explore new ideas for rock burst prevention,the relationship between entropy equations and dissipative structure was studied,and a concept-rock burst activity system (RAS) was proposed and its entropy was analyzed.The energy features of RAS were analyzed,and the relationship between electromagnetic radiation (EMR) intensity E and dissipated energy Ud was initially established.We suggest that rock burst normally happens only when d,S<< -des in RAS:RAS is the dissipative structure before collapse,and after which it become a new orderly structure,i.e.,a "dead",a statically orderly structure.We advanced that the effective way to prevent rock burst is to introduce entropy to the system for it keeps the system away from the dissipative structure.E and Ud of RAS are positively related,which is used as a bridge between dissipative structure theory and rock burst prevention engineering applications.Based on this.and using the data of rock burst prevention for working face No.250205up of Yanbei coal mine,an engineering verification for the dissipative structure of RAS was carried out,which showed good results.

  1. The influence of DNA binding on the backbone dynamics of the yeast cell-cycle protein Mbp1

    International Nuclear Information System (INIS)

    Mbp1 is a transcription factor involved in the regulation of the cell cycle in yeast. The N-terminus of this protein contains a DNA binding domain that includes a winged helix-turn-helix motif. The C-terminal 24 residues of this domain (the 'tail') are disordered in the crystal state, but are important for DNA binding. We have measured 15N NMR relaxation rates at 11.75 and 14.1 T to determine the dynamics of the free protein and in its complex with a specific DNA duplex. The dynamics data were quantitatively analysed using both spectral density mapping and the Lipari-Szabo formalism including the effects of chemical exchange and rotational anisotropy. A detailed analysis has been made of the effect of anisotropy, exchange and experimental precision on the recovered motional parameters. The backbone NH relaxation is affected by motions on a variety of time scales from millisecond to tens of picoseconds. The relaxation data show a structured core of 100 residues corresponding to that observed in the crystal state. Within the core of the protein, two regions on either side of the putative recognition helix (helix B) show slow (ca. 0.2 ms) conformational exchange dynamics that are quenched upon DNA binding. The C-terminal 24 residues are generally more dynamic than in the core. However, in the free protein, a stretch of ∼8 residues in the middle of the tail show relaxation behaviour similar to that in the core, indicating a structured region. NOEs between Ala 114 in this structured part of the tail and residues in the N-terminal beta strand of the core of the protein demonstrate that the tail folds back onto the core of the protein. In the complex with DNA, the structured part of the tail extends by ca. 3 residues. These data provide a framework for understanding the biochemical data on the mechanism and specificity of DNA binding

  2. 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

    2016-01-01

    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. PMID:27598112

  3. 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.

  4. Wireless system for structural health monitoring based on Lamb waves

    Science.gov (United States)

    Lieske, U.; Dietrich, A.; Schubert, L.; Frankenstein, B.

    2012-04-01

    Structural health monitoring systems are increasingly used for comprehensive fatigue tests and surveillance of large scale structures. In this paper we describe the development and validation of a wireless system for SHM application based on Lamb-waves. The system is based on a wireless sensor network and focuses especially on low power measurement, signal processing and communication. The sensor nodes were realized by compact, sensor near signal processing structures containing components for analog preprocessing of acoustic signals, their digitization and network communication. The core component is a digital microprocessor ARM Cortex-M3 von STMicroelectronics, which performs the basic algorithms necessary for data acquisition synchronization and filtering. The system provides network discovery and multi-hop and self-healing mechanisms. If the distance between two communicating devices is too big for direct radio transmission, packets are routed over intermediate devices automatically. The system represents a low-power and low-cost active structural health monitoring solution. As a first application, the system was installed on a CFRP structure.

  5. Dynamic Resource Allocation and QoS Control Capabilities of the Japanese Academic Backbone Network

    Directory of Open Access Journals (Sweden)

    Michihiro Aoki

    2010-08-01

    Full Text Available Dynamic resource control capabilities have become increasingly important for academic networks that must support big scientific research projects at the same time as less data intensive research and educational activities. This paper describes the dynamic resource allocation and QoS control capabilities of the Japanese academic backbone network, called SINET3, which supports a variety of academic applications with a wide range of network services. The article describes the network architecture, networking technologies, resource allocation, QoS control, and layer-1 bandwidth on-demand services. It also details typical services developed for scientific research, including the user interface, resource control, and management functions, and includes performance evaluations.

  6. 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...... to the synthetic biology community....

  7. Synthesis of Aminophosphine Ligands with Binaphthyl Backbones for Silver(I)-catalyzed Enantioselective Allylation of Benzaldehyde

    Institute of Scientific and Technical Information of China (English)

    WANG,Yi(王以); JI,Bao-Ming(吉保明); DING,Kui-Ling(丁奎岭)

    2002-01-01

    A series of aminophosphine ligands was synthesized from 2amino-2′-hydroxy-1,1′-binaphthyl (NOBIN). Their asymmetric induction efficiency was examined for silver(I)catalyzed enantioselective allylation reaction of benzaldehyde with allyltributyltin.Under the optimized reaction conditions,quantitative yield as well as moderate ee value (54.5% ee)of product was achieved by the catalysis with silver(I)/3 complex. The effects of the binaphthyl backbone and the substituted situated at chelating N, Patoms on enantioselectivity of the reaction were also discussed.

  8. Capacitance-based damage detection sensing for aerospace structural composites

    Science.gov (United States)

    Bahrami, P.; Yamamoto, N.; Chen, Y.; Manohara, H.

    2014-04-01

    Damage detection technology needs improvement for aerospace engineering application because detection within complex composite structures is difficult yet critical to avoid catastrophic failure. Damage detection is challenging in aerospace structures because not all the damage detection technology can cover the various defect types (delamination, fiber fracture, matrix crack etc.), or conditions (visibility, crack length size, etc.). These defect states are expected to become even more complex with future introduction of novel composites including nano-/microparticle reinforcement. Currently, non-destructive evaluation (NDE) methods with X-ray, ultrasound, or eddy current have good resolutions (analysis currently requires excessive wiring and complex signal analysis. Here, we present a capacitance sensor-based, structural defect detection technology with improved sensing capability. Thin dielectric polymer layer is integrated as part of the structure; the defect in the structure directly alters the sensing layer's capacitance, allowing full-coverage sensing capability independent of defect size, orientation or location. In this work, capacitance-based sensing capability was experimentally demonstrated with a 2D sensing layer consisting of a dielectric layer sandwiched by electrodes. These sensing layers were applied on substrate surfaces. Surface indentation damage (~1mm diameter) and its location were detected through measured capacitance changes: 1 to 250 % depending on the substrates. The damage detection sensors are light weight, and they can be conformably coated and can be part of the composite structure. Therefore it is suitable for aerospace structures such as cryogenic tanks and rocket fairings for example. The sensors can also be operating in space and harsh environment such as high temperature and vacuum.

  9. Prediction of eukaryotic gene structures based on multilevel optimization

    Institute of Scientific and Technical Information of China (English)

    ZHOU Yanhong; YANG Lei; WANG Hui; LU Feng; WAN Honghui

    2004-01-01

    Computational gene structure prediction, which is valuable for finding new genes and understanding the composition of genomes, plays a very important role in various kinds of genome projects. For eukaryotic gene structures, however, the prediction accuracy of existing methods is still limited. This paper presents a method of predicting eukaryotic gene structures based on multilevel optimization. The complicated problem of predicting gene structure in eukaryotic DNA sequence containing multiple genes can be decomposed into a series of sub-problems at several levels with decreasing complexity, including the gene level (single-exon gene, multi-exon gene), the element level (exon, intron, etc.), and the feature level (functional site signals, codon usage preference, etc.). On the basis of this decomposition, a multilevel model for the prediction of complex gene structures is created by a multilevel optimization process, in which the models dealing with sub-problems at low complexity level are first optimized respectively, and then optimally combined together to form models for those sub-problems at higher complexity level. Based on the multilevel model, a dynamic programming algorithm is designed to search for optimal gene structures from DNA sequences, and a new program GeneKey (1.0) for the prediction of eukaryotic gene structures is developed. Testing results with widely used datasets demonstrate that the prediction accuracies of GeneKey (1.0) at the nucleotide level, exon level and gene level are all higher than that of the well known program GENSCAN. A web server of GeneKey(1.0) is available at http://infosci.hust.edu.cn

  10. High efficiency tantalum-based ceramic composite structures

    Science.gov (United States)

    Stewart, David A. (Inventor); Leiser, Daniel B. (Inventor); DiFiore, Robert R. (Inventor); Katvala, Victor W. (Inventor)

    2010-01-01

    Tantalum-based ceramics are suitable for use in thermal protection systems. These composite structures have high efficiency surfaces (low catalytic efficiency and high emittance), thereby reducing heat flux to a spacecraft during planetary re-entry. These ceramics contain tantalum disilicide, molybdenum disilicide and borosilicate glass. The components are milled, along with a processing aid, then applied to a surface of a porous substrate, such as a fibrous silica or carbon substrate. Following application, the coating is then sintered on the substrate. The composite structure is substantially impervious to hot gas penetration and capable of surviving high heat fluxes at temperatures approaching 3000.degree. F. and above.

  11. Miniature Microwave Bandpass Filter Based on EBG Structures

    DEFF Research Database (Denmark)

    Zhurbenko, Vitaliy; Krozer, Viktor; Meincke, Peter

    2006-01-01

    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...... 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...... characteristics in comparison to existing SIH filter design....

  12. 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.

  13. Direct Formation of the C5′-Radical in the Sugar-Phosphate Backbone of DNA by High Energy Radiation

    Science.gov (United States)

    Adhikary, Amitava; Becker, David; Palmer, Brian J.; Heizer, Alicia N.; Sevilla, Michael D.

    2012-01-01

    Neutral sugar radicals formed in DNA sugar-phosphate backbone are well-established as precursors of biologically important damage such as DNA-strand scission and crosslinking. In this work, we present electron spin resonance (ESR) evidence showing that the sugar radical at C5′ (C5′•) is one of the most abundant (ca. 30%) sugar radicals formed by γ- and Ar ion-beam irradiated hydrated DNA samples. Taking dimethyl phosphate as a model of sugar-phosphate backbone, ESR and theoretical (DFT) studies of γ-irradiated dimethyl phosphate were carried out. CH3OP(O2−)OCH2• is formed via deprotonation from the methyl group of directly ionized dimethyl phosphate at 77 K. Formation of CH3OP(O2−)OCH2• is independent of dimethyl phosphate concentration (neat or in aqueous solution) or pH. ESR spectra of C5′• found in DNA and of CH3OP(O2−)OCH2• do not show an observable β-phosphorous hyperfine coupling (HFC). Further, C5′• found in DNA does not show a significant C4′-H β–proton HFC. Applying the DFT/B3LYP/6-31G(d) method, a study of conformational dependence of the phosphorous HFC in CH3OP(O2−)OCH2• shows that in its minimum energy conformation, CH3OP(O2−)OCH2• has a negligible β-phosphorous HFC. Based on these results, formation of radiation-induced C5′• is proposed to occur via a very rapid deprotonation from the directly ionized sugar-phosphate backbone and rate of this deprotonation must be faster than that of energetically downhill transfer of the unpaired spin (hole) from ionized sugar-phosphate backbone to the DNA bases. Moreover, C5′• in irradiated DNA is found to be in a conformation that does not exhibit β proton or β phosphorous HFCs. PMID:22553971

  14. A CADASTRAL SPATIAL DATA STORAGE STRUCTURE BASED ON RELATIONAL DATABASE

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    This paper presents a cadastral spatial data storage structure based on relational database,the method and the procedure to realize it.The paper consists of three parts.In the first part,some existing problems in some de veloped cadastral management systems are discussed.These problems are the fo llowing four.1) The security of cadastral spatial data is difficult to be assure d.2) It is difficult to varify cadastral data and the integrality of cadastral d ata is diffi cult to be kept.3) To transmit and share cadastral data is difficult.4) The effi ciency of data access is low.In the second part,t he feasibility of using relational database to store spatial data is analyzed an d a new cadastral spatial data storage structure is presented.At the same time, the related table structures and field descriptions are given,and then the merits and demerits of this storage structure are analyzed in detail.In th e last part,through a real example,the detailed methods to make the new storag e structure a reality are given.Moreover,some involving key techniques of the ne w storage structure are discussed.These techniques are:1) the application of database transaction,2) the application of database trigger,3) and the appl ication of secure recovery of database.

  15. Perspectives for the structure-based design of acetylcholinesterase reactivators.

    Science.gov (United States)

    Ochoa, Rodrigo; Rodriguez, Carlos A; Zuluaga, Andres F

    2016-07-01

    Rational design of active molecules through structure-based methods has been gaining adepts during the last decades due to the wider availability of protein structures, most of them conjugated with relevant ligands. Acetylcholinesterase (AChE) is a molecular target with a considerable amount of data related to its sequence and 3-dimensional structure. In addition, there are structural insights about the mechanism of action of the natural substrate and drugs used in Alzheimer's disease, organophosphorus compounds, among others. We looked for AChE structural data useful for in silico design of potential interacting molecules. In particular, we focused on information regarding the design of ligands aimed to reactivate AChE catalytic activity. The structures of 178 AChE were annotated and categorized on different subsets according to the nature of the ligand, source organisms and experimental details. We compared sequence homology among the active site from Torpedo californica, Mus musculus and Homo sapiens with the latter two species having the closest relationship (88.9% identity). In addition, the mechanism of organophosphorus binding and the design of effective reactivators are reviewed. A curated data collection obtained with information from several sources was included for researchers working on the field. Finally, a molecular dynamics simulation with human AChE indicated that the catalytic pocket volume stabilizes around 600 Å(3), providing additional clues for drug design. PMID:27450771

  16. 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…

  17. Impairment assessment of orthogonal frequency division multiplexing over dispersion-managed links in backbone and backhaul networks

    Science.gov (United States)

    Tamilarasan, Ilavarasan; Saminathan, Brindha; Murugappan, Meenakshi

    2016-04-01

    The past decade has seen the phenomenal usage of orthogonal frequency division multiplexing (OFDM) in the wired as well as wireless communication domains, and it is also proposed in the literature as a future proof technique for the implementation of flexible resource allocation in cognitive optical networks. Fiber impairment assessment and adaptive compensation becomes critical in such implementations. A comprehensive analytical model for impairments in OFDM-based fiber links is developed. The proposed model includes the combined impact of laser phase fluctuations, fiber dispersion, self phase modulation, cross phase modulation, four-wave mixing, the nonlinear phase noise due to the interaction of amplified spontaneous emission with fiber nonlinearities, and the photodetector noises. The bit error rate expression for the proposed model is derived based on error vector magnitude estimation. The performance analysis of the proposed model is presented and compared for dispersion compensated and uncompensated backbone/backhaul links. The results suggest that OFDM would perform better for uncompensated links than the compensated links due to the negligible FWM effects and there is a need for flexible compensation. The proposed model can be employed in cognitive optical networks for accurate assessment of fiber-related impairments.

  18. 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. PMID:27335085

  19. Insight into a molecular interaction force supporting peptide backbones and its implication to protein loops and folding.

    Science.gov (United States)

    Du, Qi-Shi; Chen, Dong; Xie, Neng-Zhong; Huang, Ri-Bo; Chou, Kuo-Chen

    2015-09-01

    Although not being classified as the most fundamental protein structural elements like α-helices and β-strands, the loop segment may play considerable roles for protein stability, flexibility, and dynamic activity. Meanwhile, the protein loop is also quite elusive; i.e. its interactions with the other parts of protein as well as its own shape-maintaining forces have still remained as a puzzle or at least not quite clear yet. Here, we report a molecular force, the so-called polar hydrogen-π interaction (Hp-π), which may play an important role in supporting the backbones of protein loops. By conducting the potential energy surface scanning calculations on the quasi π-plane of peptide bond unit, we have observed the following intriguing phenomena: (1) when the polar hydrogen atom of a peptide unit is perpendicularly pointing to the π-plane of other peptide bond units, a remarkable Hp-π interaction occurs; (2) the interaction is distance and orientation dependent, acting in a broad space, and belonging to the 'point-to-plane' one. The molecular force reported here may provide useful interaction concepts and insights into better understanding the loop's unique stability and flexibility feature, as well as the driving force of the protein global folding. PMID:25375237

  20. 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.

  1. 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).

  2. Vaccines based on structure-based design provide protection against infectious diseases.

    Science.gov (United States)

    Thomas, Sunil; Luxon, Bruce A

    2013-11-01

    Vaccines elicit immune responses, provide protection against microorganisms and are considered as one of the most successful medical interventions against infectious diseases. Vaccines can be produced using attenuated virus or bacteria, recombinant proteins, bacterial polysaccharides, carbohydrates or plasmid DNA. Conventional vaccines rely on the induction of immune responses against antigenic proteins to be effective. The genetic diversity of microorganisms, coupled with the high degree of sequence variability in antigenic proteins, presents a challenge to developing broadly effective conventional vaccines. The observation that whole protein antigens are not necessarily essential for inducing immunity has led to the emergence of a new branch of vaccine design termed 'structural vaccinology'. Structure-based vaccines are designed on the rationale that protective epitopes should be sufficient to induce immune responses and provide protection against pathogens. Recent studies demonstrated that designing structure-based vaccine candidates with multiple epitopes induce a higher immune response. As yet there are no commercial vaccines available based on structure-based design and most of the structure-based vaccine candidates are in the preclinical stages of development. This review focuses on recent advances in structure-based vaccine candidates and their application in providing protection against infectious diseases.

  3. 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.

  4. 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

  5. Medical Images Fusion with Patch Based Structure Tensor.

    Science.gov (United States)

    Luo, Fen; Sun, Jiangfeng; Hou, Shouming

    2015-01-01

    Nowadays medical imaging has played an important role in clinical use, which provide important clues for medical diagnosis. In medical image fusion, the extraction of some fine details and description is critical. To solve this problem, a modified structure tensor by considering similarity between two patches is proposed. The patch based filter can suppress noise and add the robustness of the eigen-values of the structure tensor by allowing the use of more information of far away pixels. After defining the new structure tensor, we apply it into medical image fusion with a multi-resolution wavelet theory. The features are extracted and described by the eigen-values of two multi-modality source data. To test the performance of the proposed scheme, the CT and MR images are used as input source images for medical image fusion. The experimental results show that the proposed method can produce better results compared to some related approaches. PMID:26628927

  6. Healing Temperature of Hybrid Structures Based on Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    赵中伟; 陈志华; 刘红波

    2016-01-01

    The healing temperature of suspen-dome with stacked arches(SDSA)and arch-supported single-layer lattice shell structures was investigated based on the genetic algorithm. The temperature field of arch under solar radiation was derived by FLUENT to investigate the influence of solar radiation on the determination of the healing temperature. Moreover, a multi-scale model was established to apply the complex temperature field under solar radiation. The change in the mechanical response of these two kinds of structures with the healing temperature was discussed. It can be concluded that solar radiation has great influence on the healing temperature, and the genetic algorithm can be effectively used in the optimization of the healing temperature for hybrid structures.

  7. A permalloy zigzag structure based magnetic bio-sensor

    Science.gov (United States)

    Ger, Tzong-Rong; Xu, You-Ren; Huang, Hao-Ting; Wei, Zung-Hang

    2012-04-01

    A magnetic fluid consisting of Fe3O4 magnetic nanoparticles is embedded inside cells by intracellular uptake. A micro-fabricated magnetic zigzag-shaped surface structure is studied for use as a biosensor. We have developed a MOKE magnetometer based methodology to measure the different hysteresis loop signals between cells with and without being placed on zigzag sensors. Adding the magnetic cells on the structure decreases the coercivity from the magneto-optical Kerr effect (MOKE) signal of zigzag magnetic thin films because of the magnetic properties of superparamagnetic nanoparticles. The magnetoresistance measurement observed is that the switching fields of the zigzag structure with magnetic cells are significantly increased compared to the case without cells in the hard axis of the external field applied.

  8. AGENT based structural static and dynamic collaborative optimization

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    A static and dynamic collaborative optimization mode for complex machine system and itsontology project relationship are put forward, on which an agent-based structural static and dynamiccollaborative optimization system is constructed as two agent colonies: optimization agent colony andfinite element analysis colony. And a two-level solving strategy as well as the necessity and possibilityfor handing with finite element analysis model in multi-level mode is discussed. Furthermore, the coop-eration of all FEA agents for optimal design of complicated structural is studied in detail. Structural stat-ic and dynamic collaborative optimization of hydraulic excavator working equimpent is taken as an ex-ample to show that the system is reliable.

  9. Optimization of Land Use Structure Based on Ecological GREEN Equivalent

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Optimization of land use structure consists of economic and social and ecological optimization.Applying the minds of system engineering and principles of ecology,this paper presents such thoughts:the optimal forest-coverage rate calculated according to the reality of a district is set as main standard of ecological rationality in the district;through considering the value of ecosystem services of the land with GREEN equivalent (mainly cultivated land and grassland)and based on the rule,GREEN equivalent,this paper introduces the area conversion between woodland and cultivated land,also between woodland and grassland;this paper establishes a multi-dimension controlling model of optimization of land use structure.In addition,a multi-objective linear programming model for optimization of land use structure is designed.In the end,this paper tests and verifies this theory of ecological optimization,taking Qionghai city in Hainan Province as an example.

  10. Scalable, ultra-resistant structural colors based on network metamaterials

    CERN Document Server

    Galinski, Henning; Dong, Hao; Gongora, Juan S Totero; Favaro, Grégory; Döbeli, Max; Spolenak, Ralph; Fratalocchi, Andrea; Capasso, Federico

    2016-01-01

    Structural colours 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 realise robust colours with a scalable fabrication technique is still lacking, hampering the realisation of practical applications with this platform. Here we develop a new approach based on large scale network metamaterials, which combine dealloyed subwavelength structures at the nanoscale with loss-less, ultra-thin dielectrics coatings. By using theory and experiments, we show how sub-wavelength dielectric coatings control a mechanism of resonant light coupling with epsilon-near-zero (ENZ) regions generated in the metallic network, manifesting the formation of highly saturated structural colours that cover a wide portion of the spectrum. Ellipsometry measurements report the efficient observation of these colours even at angles of $70$ degrees. The network-like architecture of these nanoma...

  11. Disaster mitigation based on smart structures/materials

    Science.gov (United States)

    Asanuma, H.; Su, J.; Shahinpoor, M.; Felli, F.; Paolozzi, A.; Nejhad, M.; Hihara, L.; Aimmanee, S.; Furuya, Y.; Adachi, K.; Yanaseko, T.

    2016-04-01

    The concept "Disaster Mitigation and Sustainable Engineering" is introduced comprehensively and several examples are shown in this paper. It is emphasized that it can be effectively realized in the field "smart materials and structural systems." As serious disasters may not occur for a long period of time, and the structures for disaster mitigation suffer from vast amount of maintenance cost etc., they are better to be used daily. Their compactness and deploying function are also very useful. In order to demonstrate the concept, two examples having been experimentally tried are introduced, that is, artificial forests and deployable structure based on honeycomb to be used against flooding. Other examples and products in the world are also introduced and future directions are discussed.

  12. Structure formation and properties of molybdenum-base powder composites

    Energy Technology Data Exchange (ETDEWEB)

    Minakova, R.V.; Kresanova, A.P.; Lesnik, N.D.; Malyshenko, A.A.; Antonov, S.O.

    1988-07-01

    The purpose of this work was to investigate physicochemical conditions of formation and features of structure formation of molybdenum-base composites and, in particular, to study the adhesion characteristics and features of contact interaction in Mo-Cu-Ni(Co) systems, to investigate the distribution of the basic elements and impurities, the phase composition, the structure, and certain properties of the materials and parts. A combination of methods was used including x-ray spectral microanalysis, Auger spectroscopy, x-ray diffraction phase and structure analysis, microhardness and hot hardness methods, scanning electron microscopy, and metallography by optical microscopy. The influence of hot hardness of the composite was selected as the criterion of evaluation and it was found that increases in hot hardness and in high-temperature oxidation increased the life and service properties of electrodes used for spot welding and brazing in production.

  13. NEW APPROACH FOR IMAGE REPRESENTATION BASED ON GEOMETRIC STRUCTURAL CONTENTS

    Institute of Scientific and Technical Information of China (English)

    Jia Xiaomeng; Wang Guoyu

    2003-01-01

    This paper presents a novel approach for representation of image contents based on edge structural features. Edge detection is carried out for an image in the pre-processing stage.For feature representation, edge pixels are grouped into a set of segments through geometrical partitioning of the whole edge image. Then the invariant feature vector is computed for each edge-pixel segment. Thereby the image is represented with a set of spatially distributed feature vectors, each of which describes the local pattern of edge structures. Matching of two images can be achieved by the correspondence of two sets of feature vectors. Without the difficulty of image segmentation and object extraction due to the complexity of the real world images, the proposed approach provides a simple and flexible description for the image with complex scene, in terms of structural features of the image content. Experiments with real images illustrate the effectiveness of this new method.

  14. Noise analysis for sensitivity-based structural damage detection

    Institute of Scientific and Technical Information of China (English)

    YIN Tao; ZHU Hong-ping; YU Ling

    2007-01-01

    As vibration-based structural damage detection methods are easily affected by environmental noise, a new statistic-based noise analysis method is proposed together with the Monte Carlo technique to investigate the influence of experimental noise of modal data on sensitivity-based damage detection methods. Different from the commonly used random perturbation technique, the proposed technique is deduced directly by Moore-Penrose generalized inverse of the sensitivity matrix, which does not only make the analysis process more efficient but also can analyze the influence of noise on both frequencies and mode shapes for three commonly used sensitivity-based damage detection methods in a similar way. A one-story portal frame is adopted to evaluate the efficiency of the proposed noise analysis technique.

  15. Machine Translation Based on Translation Corresponding Tree Structure

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    A representation schema called translation corresponding tree (TCT) has been applied to a Portuguese to Chinese example-based machine translation system. The translation examples are annotated by the representation of the TCT structure. Each TCT describes not only the syntactic structure of the source sentence (i.e., Portuguese in our system) but also the translation correspondences (i.e., Chinese translation). In addition, the TCT nodes describe the corresponding linguistic relationships between the source and target languages. The translation examples can be effectively represented with this annotation schema and organized in the bilingual knowledge database or example base. In the real machine translation process, the target language is synthesized with higher quality by referring to the TCT translation information.

  16. Structure-Based Virtual Screening of Commercially Available Compound Libraries.

    Science.gov (United States)

    Kireev, Dmitri

    2016-01-01

    Virtual screening (VS) is an efficient hit-finding tool. Its distinctive strength is that it allows one to screen compound libraries that are not available in the lab. Moreover, structure-based (SB) VS also enables an understanding of how the hit compounds bind the protein target, thus laying ground work for the rational hit-to-lead progression. SBVS requires a very limited experimental effort and is particularly well suited for academic labs and small biotech companies that, unlike pharmaceutical companies, do not have physical access to quality small-molecule libraries. Here, we describe SBVS of commercial compound libraries for Mer kinase inhibitors. The screening protocol relies on the docking algorithm Glide complemented by a post-docking filter based on structural protein-ligand interaction fingerprints (SPLIF). PMID:27316988

  17. Structuring User Involvement in Panel-Based Living Labs

    Directory of Open Access Journals (Sweden)

    Lieven De Marez

    2012-09-01

    Full Text Available A shift towards open innovation approaches with systematic user involvement has occurred within media and ICT. One of the emerging frameworks structuring these initiatives is the "living lab" approach. Despite the growing evidence of the beneficial nature of customer involvement in product development, research into specific user characteristics for innovation is still scarce, particularly in living labs, with the notable exception of literature on lead users. Especially within the context of living labs for ICT and media innovation, an application of the lead-user framework looks promising as a way to structure and facilitate user involvement. This article is based on the experiences of three Flemish living lab initiatives with a panel-based approach and provides a customer characteristics framework that guides user involvement in living labs.

  18. Structure-Based Virtual Screening of Commercially Available Compound Libraries.

    Science.gov (United States)

    Kireev, Dmitri

    2016-01-01

    Virtual screening (VS) is an efficient hit-finding tool. Its distinctive strength is that it allows one to screen compound libraries that are not available in the lab. Moreover, structure-based (SB) VS also enables an understanding of how the hit compounds bind the protein target, thus laying ground work for the rational hit-to-lead progression. SBVS requires a very limited experimental effort and is particularly well suited for academic labs and small biotech companies that, unlike pharmaceutical companies, do not have physical access to quality small-molecule libraries. Here, we describe SBVS of commercial compound libraries for Mer kinase inhibitors. The screening protocol relies on the docking algorithm Glide complemented by a post-docking filter based on structural protein-ligand interaction fingerprints (SPLIF).

  19. Comparison of backbone dynamics of the type III antifreeze protein and antifreeze-like domain of human sialic acid synthase

    International Nuclear Information System (INIS)

    Antifreeze proteins (AFPs) are found in a variety of cold-adapted (psychrophilic) organisms to promote survival at subzero temperatures by binding to ice crystals and decreasing the freezing temperature of body fluids. The type III AFPs are small globular proteins that consist of one α-helix, three 310-helices, and two β-strands. Sialic acids play important roles in a variety of biological functions, such as development, recognition, and cell adhesion and are synthesized by conserved enzymatic pathways that include sialic acid synthase (SAS). SAS consists of an N-terminal catalytic domain and a C-terminal antifreeze-like (AFL) domain, which is similar to the type III AFPs. Despite having very similar structures, AFL and the type III AFPs exhibit very different temperature-dependent stability and activity. In this study, we have performed backbone dynamics analyses of a type III AFP (HPLC12 isoform) and the AFL domain of human SAS (hAFL) at various temperatures. We also characterized the structural/dynamic properties of the ice-binding surfaces by analyzing the temperature gradient of the amide proton chemical shift and its correlation with chemical shift deviation from random coil. The dynamic properties of the two proteins were very different from each other. While HPLC12 was mostly rigid with a few residues exhibiting slow motions, hAFL showed fast internal motions at low temperature. Our results provide insight into the molecular basis of thermostability and structural flexibility in homologous psychrophilic HPLC12 and mesophilic hAFL proteins

  20. Comparison of backbone dynamics of the type III antifreeze protein and antifreeze-like domain of human sialic acid synthase

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Yong-Geun [Gyeongsang National University, Department of Chemistry and Research Institute of Natural Science (Korea, Republic of); Park, Chin-Ju [Gwangju Institute of Science and Technology, Division of Liberal Arts and Sciences and Department of Chemistry (Korea, Republic of); Kim, Hee-Eun; Seo, Yeo-Jin; Lee, Ae-Ree; Choi, Seo-Ree; Lee, Shim Sung; Lee, Joon-Hwa, E-mail: joonhwa@gnu.ac.kr [Gyeongsang National University, Department of Chemistry and Research Institute of Natural Science (Korea, Republic of)

    2015-02-15

    Antifreeze proteins (AFPs) are found in a variety of cold-adapted (psychrophilic) organisms to promote survival at subzero temperatures by binding to ice crystals and decreasing the freezing temperature of body fluids. The type III AFPs are small globular proteins that consist of one α-helix, three 3{sub 10}-helices, and two β-strands. Sialic acids play important roles in a variety of biological functions, such as development, recognition, and cell adhesion and are synthesized by conserved enzymatic pathways that include sialic acid synthase (SAS). SAS consists of an N-terminal catalytic domain and a C-terminal antifreeze-like (AFL) domain, which is similar to the type III AFPs. Despite having very similar structures, AFL and the type III AFPs exhibit very different temperature-dependent stability and activity. In this study, we have performed backbone dynamics analyses of a type III AFP (HPLC12 isoform) and the AFL domain of human SAS (hAFL) at various temperatures. We also characterized the structural/dynamic properties of the ice-binding surfaces by analyzing the temperature gradient of the amide proton chemical shift and its correlation with chemical shift deviation from random coil. The dynamic properties of the two proteins were very different from each other. While HPLC12 was mostly rigid with a few residues exhibiting slow motions, hAFL showed fast internal motions at low temperature. Our results provide insight into the molecular basis of thermostability and structural flexibility in homologous psychrophilic HPLC12 and mesophilic hAFL proteins.

  1. Guidance for structuring team-based incentives in healthcare.

    Science.gov (United States)

    Blumenthal, Daniel M; Song, Zirui; Jena, Anupam B; Ferris, Timothy G

    2013-02-01

    New payment methods designed to incentivize more efficient care delivery are accelerating the movement of healthcare providers into organized provider groups. More efficient healthcare delivery requires explicit structuring of care delivery processes around teams of clinicians working toward common patient care goals. Provider organizations accepting new payment methods will need to design and implement compensation systems that provide incentives for team-based care. While lessons from studies performed both outside and inside healthcare provide some guidance on designing and implementing team-based incentives, organized delivery systems face several significant barriers to accomplishing this. PMID:23448116

  2. Schiff base functionalized Organopropylsilatranes: Synthesis and structural characterization

    Indian Academy of Sciences (India)

    Gurjaspreet Singh; Promila; Amandeep Saroa; Jandeep Singh; Raj Pal Sharm; V Ferretti

    2016-02-01

    Synthesis of Schiff bases linked to organopropylsilatranes were performed by condensation reaction of post-functionalized silatranes such as aminopropylsilatrane (4), aminopropyl-3,7,10-trimethylsilatrane (5) and N-substituted aminopropylsilatrane (10) with two different aldehydes viz. pyrrole-2-carboxaldehyde and 2-hydroxy-1-napthaldehyde. The resulting Schiff base substituted silatranes were well characterized by elemental analysis, spectroscopic studies [IR, (1H, 13C) NMR, and MS]. The structures of two silatranes were confirmed by single crystal X-ray diffraction analysis.

  3. Structural design systems using knowledge-based techniques

    International Nuclear Information System (INIS)

    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

  4. 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.

  5. Atomic structures of Zr-based metallic glasses

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The atomic structures of Zr-Ni and Zr-Ti-Al-Cu-Ni metallic glasses were investigated by using classical molecular dynamic (MD),reverse Monte Carlo (RMC),ab initio MD (AIMD) simulations and high resolution transmission electron microscopy (HRTEM) techniques. We focused on the short-range order (SRO) and medium-range order (MRO) in the glassy structure. It is shown that there are icosahedral,FCC-and BCC-type SROs in the Zr-based metallic glasses. A structural model,characterized by imperfect ordered packing (IOP),was proposed based on the MD simulation and confirmed by the HRTEM observation. Furthermore,the evolution from IOP to nanocrystal during the crystallization of metallic glasses was also ex-plored. It is found that the growth from IOP to nanocrystal proceeds through three distinct stages: the formation of quasi-ordered structure with one-dimensional (1D) periodicity,then 2D periodicity,and finally the formation of 3D nanocrystals. It is also noted that these three growth steps are crosslinked.

  6. Atomic structures of Zr-based metallic glasses

    Institute of Scientific and Technical Information of China (English)

    HUI XiDong; LIU Xiongdun; GAO Rui; HOU HuaiYu; FANG HuaZhi; LIU ZiKui; CHEN GuoLiang

    2008-01-01

    The atomic structures of Zr-Ni and Zr-Ti-Al-Cu-Ni metallic glasses were investigated by using classical molecular dynamic (MD), reverse Monte Carlo (RMC), ab initio MD (AIMD) simulations and high resolution transmission electron microscopy (HRTEM) techniques. We focused on the short-range order (SRO) and medium-range order (MRO) in the glassy structure. It is shown that there are icosahedral, FCC- and BCC-type SROs in the Zr-based metallic glasses. A structural model, characterized by imperfect ordered packing (IOP), was proposed based on the MD simulation and confirmed by the HRTEM observation. Furthermore, the evolution from lOP to nanocrystal during the crystallization of metallic glasses was also ex-plored. It is found that the growth from IOP to nanocrystal proceeds through three distinct stages: the formation of quasi-ordered structure with one-dimensional (1 D) periodicity, then 2D periodicity, and finally the formation of 3D nanocrystals. It is also noted that these three growth steps are crosslinked.

  7. 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.

  8. Microscopic structure and properties of wood-based foaming composites

    Institute of Scientific and Technical Information of China (English)

    Zheng WANG; Li GAO; Guilan ZHANG; Liang CHANG

    2008-01-01

    In order to reduce the density of wood-based composites without causing a deterioration of their mech-anical properties, we studied the process of manufacturing wood-based composites. A combination of polymer foaming technology and flat hot-pressing technology was used. The microscopic structure of the various wood-based composites was analyzed with a scanning electron microscope (SEM). Modulus of rupture (MOR), modulus of elasticity (MOE), impact strength, and thickness expansion rate of water sorption (TS) were all measured. The results showed that fibers loosely inter-weave, and fibers had been connected by micropore. They also showed that spaces between fibers had big micropore structure. MOR, MOE and impact strength were the high-est among three levels of ratio. When the total content of resin and foaming agent were 20% by weight, TS was higher. A hot-pressing temperature of 120℃ was optimal. At the low temperatures of 80℃, the foaming process was uncompleted. At a higher temperature, micropores burst at a certain pressure. Based on the variance analysis and maximum difference analysis, a significance test shows that the optimum conditions for the total content of resin and foaming agent is 20% by weight, with a hot pressing temperature of 120℃ for 15 min. Under these conditions, the properties of wood-based foaming composites all achieved the industry standard.

  9. 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.

  10. An Optimized microRNA Backbone for Effective Single-Copy RNAi

    Directory of Open Access Journals (Sweden)

    Christof Fellmann

    2013-12-01

    Full Text Available Short hairpin RNA (shRNA technology enables stable and regulated gene repression. For establishing experimentally versatile RNAi tools and minimizing toxicities, synthetic shRNAs can be embedded into endogenous microRNA contexts. However, due to our incomplete understanding of microRNA biogenesis, such “shRNAmirs” often fail to trigger potent knockdown, especially when expressed from a single genomic copy. Following recent advances in design of synthetic shRNAmir stems, here we take a systematic approach to optimize the experimental miR-30 backbone. Among several favorable features, we identify a conserved element 3′ of the basal stem as critically required for optimal shRNAmir processing and implement it in an optimized backbone termed “miR-E”, which strongly increases mature shRNA levels and knockdown efficacy. Existing miR-30 reagents can be easily converted to miR-E, and its combination with up-to-date design rules establishes a validated and accessible platform for generating effective single-copy shRNA libraries that will facilitate the functional annotation of the genome.

  11. An optimized microRNA backbone for effective single-copy RNAi.

    Science.gov (United States)

    Fellmann, Christof; Hoffmann, Thomas; Sridhar, Vaishali; Hopfgartner, Barbara; Muhar, Matthias; Roth, Mareike; Lai, Dan Yu; Barbosa, Inês A M; Kwon, Jung Shick; Guan, Yuanzhe; Sinha, Nishi; Zuber, Johannes

    2013-12-26

    Short hairpin RNA (shRNA) technology enables stable and regulated gene repression. For establishing experimentally versatile RNAi tools and minimizing toxicities, synthetic shRNAs can be embedded into endogenous microRNA contexts. However, due to our incomplete understanding of microRNA biogenesis, such "shRNAmirs" often fail to trigger potent knockdown, especially when expressed from a single genomic copy. Following recent advances in design of synthetic shRNAmir stems, here we take a systematic approach to optimize the experimental miR-30 backbone. Among several favorable features, we identify a conserved element 3' of the basal stem as critically required for optimal shRNAmir processing and implement it in an optimized backbone termed "miR-E", which strongly increases mature shRNA levels and knockdown efficacy. Existing miR-30 reagents can be easily converted to miR-E, and its combination with up-to-date design rules establishes a validated and accessible platform for generating effective single-copy shRNA libraries that will facilitate the functional annotation of the genome. PMID:24332856

  12. 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%.

  13. Structuring from nanoparticles in oil-based ferrofluids

    OpenAIRE

    Z. Rozynek; Jozefczak, A.; Knudsen, K. D.; Skumiel, A.; Hornowski, T.; Fossum, J. O.; Timko, M.; Kopcansky, P.; Koneracka, M.

    2011-01-01

    The effect of magnetic field on the structure formation in an oil-based magnetic fluid with various concentrations of magnetite particles was studied. The evaluation of the experimental data obtained from small-angle X-ray scattering and ultrasonic attenuation indicates the formation of chain-like aggregates composed of magnetite particles. The experimental data obtained from ultrasonic spectroscopy fit well with the recent theoretical model by Shliomis, Mond and Morozov but only for a dilute...

  14. Electronic structure of ternary hydrides based on light elements

    Energy Technology Data Exchange (ETDEWEB)

    Orgaz, E. [Departamento de Fisica y Quimica Teorica, Facultad de Quimica, Universidad Nacional Autonoma de Mexico, CP 04510 Coyoacan, Mexico, D.F. (Mexico)]. E-mail: orgaz@eros.pquim.unam.mx; Membrillo, A. [Departamento de Fisica y Quimica Teorica, Facultad de Quimica, Universidad Nacional Autonoma de Mexico, CP 04510 Coyoacan, Mexico, D.F. (Mexico); Castaneda, R. [Departamento de Fisica y Quimica Teorica, Facultad de Quimica, Universidad Nacional Autonoma de Mexico, CP 04510 Coyoacan, Mexico, D.F. (Mexico); Aburto, A. [Departamento de Fisica, Facultad de Ciencias, Universidad Nacional Autonoma de Mexico, CP 04510 Coyoacan, Mexico, D.F. (Mexico)

    2005-12-08

    Ternary hydrides based on light elements are interesting owing to the high available energy density. In this work we focused into the electronic structure of a series of known systems having the general formula AMH{sub 4}(A=Li,Na,M=B,Al). We computed the energy bands and the total and partial density of states using the linear-augmented plane waves method. In this report, we discuss the chemical bonding in this series of complex hydrides.

  15. Computational structure-based redesign of enzyme activity

    OpenAIRE

    Chen, Cheng-Yu; Georgiev, Ivelin; Anderson, Amy C.; Donald, Bruce R.

    2009-01-01

    We report a computational, structure-based redesign of the phenylalanine adenylation domain of the nonribosomal peptide synthetase enzyme gramicidin S synthetase A (GrsA-PheA) for a set of noncognate substrates for which the wild-type enzyme has little or virtually no specificity. Experimental validation of a set of top-ranked computationally predicted enzyme mutants shows significant improvement in the specificity for the target substrates. We further present enhancements to the methodology ...

  16. Tests for Cointegration with Structural Breaks Based on Subsamples

    OpenAIRE

    James Davidson; Andrea Monticini

    2007-01-01

    This paper considers tests for cointegration with allowance for structural breaks, using the extrema of residual-based tests over subsamples of the data. One motivation for the approach is to formalize the practice of data snooping by practitioners, who may examine subsamples after failing to find a predicted cointegrating relationship. Valid critical values for such multiple testing situations may be useful. The methods also have the advantage of not imposing a form for the alternative hypot...

  17. Resonantly enhanced thermal emitters based on nanophotonic structures

    OpenAIRE

    O'Regan, Bryan J.

    2015-01-01

    The manipulation of photons, especially the control of spontaneous emission, has become a core area of photonics research in the 21st century. One of the key challenges is the control of the broadband emission profile of thermal emitters. Recently, attention has focused on resonant nanophotonic structures to control the thermal emission with most of the work concentrating on the mid-infrared wavelength range and/or based on metallic nanostructures. However, the realisation of a high temperatu...

  18. SENSITIVITY ANALYSIS BASED ON LANCZOS ALGORITHM IN STRUCTURAL DYNAMICS

    Institute of Scientific and Technical Information of China (English)

    李书; 王波; 胡继忠

    2003-01-01

    The sensitivity calculating formulas in structural dynamics was developed byutilizing the mathematical theorem and new definitions of sensitivities. So the singularityproblem of sensitivity with repeated eigenvalues is solved completely. To improve thecomputational efficiency, the reduction system is obtained based on Lanczos vectors. Afterincorporating the mathematical theory with the Lanczos algorithm, the approximatesensitivity solution can be obtained. A numerical example is presented to illustrate theperformance of the method.

  19. Guidance for Structuring Team-Based Incentives in Health Care

    OpenAIRE

    Blumenthal, Daniel M.; Song, Zirui; Jena, Anupam B.; Ferris, Timothy

    2013-01-01

    New payment methods designed to incentivize more efficient care delivery are accelerating the movement of health care providers into organized provider groups. More efficient health care delivery requires explicit structuring of care delivery processes around teams of clinicians working toward common patient care goals. Provider organizations accepting new payment methods will need to design and implement compensation systems that provide incentives for team-based care. While lessons from stu...

  20. Ultrafast lasers based on quantum dot structures physics and devices

    CERN Document Server

    Rafailov, Edik U; Avrutin, Eugene A

    2011-01-01

    In this monograph, the authors address the physics and engineering together with the latest achievements of efficient and compact ultrafast lasers based on novel quantum-dot structures and devices. Their approach encompasses a broad range of laser systems, while taking into consideration not only the physical and experimental aspects but also the much needed modeling tools, thus providing a holistic understanding of this hot topic.

  1. Ultrasound Image Enhancement Using Structure-Based Filtering

    Directory of Open Access Journals (Sweden)

    Shyh-Kuang Ueng

    2014-01-01

    the diffusion tensor of intensity is computed at each pixel at first. Then the eigensystem of the diffusion tensor is calculated and employed to detect and classify the underlying structure. Based on the classification result, a feasible filter is selected to suppress speckles and enhance features. Test results show that the proposed despeckle method reduces speckles in uniform areas and enhances tissue boundaries and spots.

  2. Crosscumulants Based Approaches for the Structure Identification of Volterra Models

    Institute of Scientific and Technical Information of China (English)

    Houda Mathlouthi; Kamel Abederrahim; Faouzi Msahli; Gerard Favier

    2009-01-01

    In this paper, we address the problem of structure identification of Volterra models. It consists in estimating the model order and the memory lcngth of each kernel. Two methods based on input-output crosscumulants arc developed. The first one uses zero mean independent and identically distributed Ganssian input, and the second one concerns a symmetric input sequence. Simulations are performed on six models having different orders and kernel memory lengths to demonstrate the advantages of the proposed methods.

  3. Significant Role of DNA Backbone in Mediating the Transition Origin of Electronic Excitations of B-DNA - Implication from Long Range Corrected TDDFT and Quantified NTO Analysis

    CERN Document Server

    Li, Jian-Hao; Guo, Guang-Yu; Hayashi, Michitoshi

    2011-01-01

    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 biomolecule B-DNA are then studied as examples, where the model systems have been constructed extracting from the perfect or a 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, di-Thy) and a surrounding physical/chemical environment of interest (e.g. backbone, adjacent stacking nucleobases) and examine how the excitation properties of the core vary in response to the environment. We find that the orbitals contributed from DNA backbone and surrounding nucleobases often participate in a transition of Thy-related excitations affecting their composition, abso...

  4. Image-based surface matching algorithm oriented to structural biology.

    Science.gov (United States)

    Merelli, Ivan; Cozzi, Paolo; D'Agostino, Daniele; Clematis, Andrea; Milanesi, Luciano

    2011-01-01

    Emerging technologies for structure matching based on surface descriptions have demonstrated their effectiveness in many research fields. In particular, they can be successfully applied to in silico studies of structural biology. Protein activities, in fact, are related to the external characteristics of these macromolecules and the ability to match surfaces can be important to infer information about their possible functions and interactions. In this work, we present a surface-matching algorithm, based on encoding the outer morphology of proteins in images of local description, which allows us to establish point-to-point correlations among macromolecular surfaces using image-processing functions. Discarding methods relying on biological analysis of atomic structures and expensive computational approaches based on energetic studies, this algorithm can successfully be used for macromolecular recognition by employing local surface features. Results demonstrate that the proposed algorithm can be employed both to identify surface similarities in context of macromolecular functional analysis and to screen possible protein interactions to predict pairing capability. PMID:21566253

  5. Development of cyber-based autonomous structural integrity assessment system for building structures

    Science.gov (United States)

    Kurata, M.; Fujita, K.; Li, X.; Yamazaki, T.; Yamaguchi, M.

    2013-04-01

    For the application of structural health monitoring (SHM) system to the post-earthquake damage screening of building structures, an immediate evaluation of the degree of damage in primary structural components is a challenging task. To increase the resolution in damage detection above a certain level to detect damage in individual components, a SHM requires the use of a dense array of sensors deployed to building structures. In order to deal with a large amount of data acquired by the sensing network and to distribute quick safety alerts on the condition of earthquake-affected buildings, a SHM system that is connected with a cyberinfrastructure specifically designed for the autonomous structural integrity assessment of buildings is developed. In the system, big data transferred from a dense sensing network is automatically stored and processed to extract damage features using a PostgresSQL relational database and embedded local damage detection algorithms. In a benchmark study, the schema of the SHM system is specifically designed to function with a built-in local damage detection algorithm that needs a comparative study of current dataset with past reference dataset. To visualize the results of the damage detection analysis, a PHP-based web-viewer is also designed for the SHM system. Finally, the performance of the developed cyber-based SHM system is evaluated through a series of the damage detection tests on a 5-story steel testbed frame that can replicate damage in beams and columns.

  6. 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.

  7. Aircraft wing structural design optimization based on automated finite element modelling and ground structure approach

    Science.gov (United States)

    Yang, Weizhu; Yue, Zhufeng; Li, Lei; Wang, Peiyan

    2016-01-01

    An optimization procedure combining an automated finite element modelling (AFEM) technique with a ground structure approach (GSA) is proposed for structural layout and sizing design of aircraft wings. The AFEM technique, based on CATIA VBA scripting and PCL programming, is used to generate models automatically considering the arrangement of inner systems. GSA is used for local structural topology optimization. The design procedure is applied to a high-aspect-ratio wing. The arrangement of the integral fuel tank, landing gear and control surfaces is considered. For the landing gear region, a non-conventional initial structural layout is adopted. The positions of components, the number of ribs and local topology in the wing box and landing gear region are optimized to obtain a minimum structural weight. Constraints include tank volume, strength, buckling and aeroelastic parameters. The results show that the combined approach leads to a greater weight saving, i.e. 26.5%, compared with three additional optimizations based on individual design approaches.

  8. Structuring from nanoparticles in oil-based ferrofluids.

    Science.gov (United States)

    Rozynek, Z; Józefczak, A; Knudsen, K D; Skumiel, A; Hornowski, T; Fossum, J O; Timko, M; Kopčanský, P; Koneracká, M

    2011-03-01

    The effect of magnetic field on the structure formation in an oil-based magnetic fluid with various concentrations of magnetite particles was studied. The evaluation of the experimental data obtained from small-angle X-ray scattering and ultrasonic attenuation indicates the formation of chain-like aggregates composed of magnetite particles. The experimental data obtained from ultrasonic spectroscopy fit well with the recent theoretical model by Shliomis, Mond and Morozov but only for a diluted magnetic fluid. In this model it is assumed that a dimer is the main building block of a B -field-induced chain-like structure, thus the estimation of the nematic order parameter does not depend on the actual length of the structure. The scattering method used reveals information about the aggregated structure size and relative changes in the degree of anisotropy in qualitative terms. The coupling constant [Formula: see text] , concentrations [Formula: see text] , average particle size d and its polydispersity [Formula: see text] were initially obtained using the vibrating sample magnetometry and these results were further confirmed by rheometry and scattering methods. Both the particles' orientational distribution and the nematic order parameter S were inferred from the ultrasonic measurements. The investigation of SAXS patterns reveals the orientation and sizes of aggregated structures under application of different magnetic-field strengths. In addition, the magnetic-field-dependent yield stress was measured, and a relationship between the yield stress and magnetic-field strength up to 0.5 T was established. PMID:21416265

  9. Crack width monitoring of concrete structures based on smart film

    International Nuclear Information System (INIS)

    Due to its direct link to structural security, crack width is thought to be one of the most important parameters reflecting damage conditions of concrete structures. However, the width problem is difficult to solve with the existing structural health monitoring methods. In this paper, crack width monitoring by means of adhering enameled copper wires with different ultimate strains on the surface of structures is proposed, based on smart film crack monitoring put forward by the present authors. The basic idea of the proposed method is related to a proportional relationship between the crack width and ultimate strain of the broken wire. Namely, when a certain width of crack passes through the wire, some low ultimate strain wires will be broken and higher ultimate strain wires may stay non-broken until the crack extends to a larger scale. Detection of the copper wire condition as broken or non-broken may indicate the width of the structural crack. Thereafter, a multi-layered stress transfer model and specimen experiment are performed to quantify the relationship. A practical smart film is then redesigned with this idea and applied to Chongqing Jiangjin Yangtze River Bridge. (paper)

  10. Crack width monitoring of concrete structures based on smart film

    Science.gov (United States)

    Zhang, Benniu; Wang, Shuliang; Li, Xingxing; Zhang, Xu; Yang, Guang; Qiu, Minfeng

    2014-04-01

    Due to its direct link to structural security, crack width is thought to be one of the most important parameters reflecting damage conditions of concrete structures. However, the width problem is difficult to solve with the existing structural health monitoring methods. In this paper, crack width monitoring by means of adhering enameled copper wires with different ultimate strains on the surface of structures is proposed, based on smart film crack monitoring put forward by the present authors. The basic idea of the proposed method is related to a proportional relationship between the crack width and ultimate strain of the broken wire. Namely, when a certain width of crack passes through the wire, some low ultimate strain wires will be broken and higher ultimate strain wires may stay non-broken until the crack extends to a larger scale. Detection of the copper wire condition as broken or non-broken may indicate the width of the structural crack. Thereafter, a multi-layered stress transfer model and specimen experiment are performed to quantify the relationship. A practical smart film is then redesigned with this idea and applied to Chongqing Jiangjin Yangtze River Bridge.

  11. Reliability-Based Optimal Design for Very Large Floating Structure

    Institute of Scientific and Technical Information of China (English)

    ZHANG Shu-hua(张淑华); FUJIKUBO Masahiko

    2003-01-01

    Costs and losses induced by possible future extreme environmental conditions and difficulties in repairing post-yielding damage strongly suggest the need for proper consideration in design rather than just life loss prevention. This can be addressed through the development of design methodology that balances the initial cost of the very large floating structure (VLFS) against the expected potential losses resulting from future extreme wave-induced structural damage. Here, the development of a methodology for determining optimal, cost-effective design will be presented and applied to a VLFS located in the Tokyo bay. Optimal design criteria are determined based on the total expected life-cycle cost and acceptable damage probability and curvature of the structure, and a set of sizes of the structure are obtained. The methodology and applications require expressions of the initial cost and the expected life-cycle damage cost as functions of the optimal design variables. This study includes the methodology, total life-cycle cost function, structural damage modeling, and reliability analysis.

  12. Computational challenges of structure-based approaches applied to HIV.

    Science.gov (United States)

    Forli, Stefano; Olson, Arthur J

    2015-01-01

    Here, we review some of the opportunities and challenges that we face in computational modeling of HIV therapeutic targets and structural biology, both in terms of methodology development and structure-based drug design (SBDD). Computational methods have provided fundamental support to HIV research since the initial structural studies, helping to unravel details of HIV biology. Computational models have proved to be a powerful tool to analyze and understand the impact of mutations and to overcome their structural and functional influence in drug resistance. With the availability of structural data, in silico experiments have been instrumental in exploiting and improving interactions between drugs and viral targets, such as HIV protease, reverse transcriptase, and integrase. Issues such as viral target dynamics and mutational variability, as well as the role of water and estimates of binding free energy in characterizing ligand interactions, are areas of active computational research. Ever-increasing computational resources and theoretical and algorithmic advances have played a significant role in progress to date, and we envision a continually expanding role for computational methods in our understanding of HIV biology and SBDD in the future.

  13. Locate damage based on change in structural shape for civil space structures

    Science.gov (United States)

    Yan, Guirong; Yu, Jianxin; Zhao, Yi; Feng, Ruoqiang

    2016-04-01

    Recent years have witnessed a number of collapses of civil space structures, which have severely jeopardized the safety of the general public. Therefore, it is imperative to propose an approach that can localize damage to exact members at an early stage for space structures. Then, the obtained damage location results can be used by the maintenance/repair crew for taking timely actions. For most space structures, the member configuration possesses a regular pattern. For this type of structure, before damage occurs, the regular pattern in the member configuration is maintained. After damage occurs, the regular pattern around the damaged member will be destroyed. In this study, the proposed approach to locate damage is based on the change in the status of regularity of member configuration. Herein the difference in an angle of the triangular shape in the related region of a space structure is used to indicate whether the regularity of member configuration is maintained. To validate the proposed approach, a reticulated shell space structure will be investigated.

  14. Structured Language Requirement Elicitation Using Case Base Reasoning

    Directory of Open Access Journals (Sweden)

    Marryam Murtaza

    2013-12-01

    Full Text Available Requirement elicitation is very difficult process in highly challenging and business based software as well as in real time software. Common problems associated with these types of software are rapidly changing the requirements and understanding the language of the layman person. In this study, a framework for requirement elicitation by using knowledge based system is proposed, which is very helpful for knowledge documentation, intelligent decision support, self-learning and more specifically it is very helpful for case based reasoning and explanation. Basically in this method requirements are gathered from Artificial Intelligence (AI expert system from various sources e.g., via interviews, scenarios or use cases. Then, these are converted into structured natural language using ontology and this new problem/case is put forward to Case Based Reasoning (CBR. CBR based on its previous information having similar requirements combines with new case and suggests a proposed solution. Based on this solution a prototype is developed and delivered to customer. The use of case-based reasoning in requirements elicitation process has greatly reduced the burden and saved time of requirement analyst and results in an effective solution for handling complex or vague requirements during the elicitation process.

  15. 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

  16. Adaptive base-isolation of civil structures using variable amplification

    Institute of Scientific and Technical Information of China (English)

    Kenneth K. Walsh; Makola M. Abdullah

    2006-01-01

    Semi-active dampers are used in base-isolation to reduce the seismic response of civil engineering structures.In the present study, a new semi-active damping system using variable amplification will be investigated for adaptive baseisolation. It uses a novel variable amplification device (VAD) connected in series with a passive damper. The VAD is capable of producing multiple amplification factors, each corresponding to a different amplification state. Forces from the damper are amplified to the structure according to the current amplification state, which is selected via a semi-active control algorithm specifically tailored to the system's unique damping characteristics. To demonstrate the effectiveness of the VAD-damper system for adaptive base-isolation, numerical simulations are conducted for three and seven-story base-isolated buildings subject to both far and near-field ground motions. The results indicate that the system can achieve significant reductions in response compared to the base-isolated buildings with no damper. The proposed system is also found to perform well compared to a typical semi-active damper.

  17. Advanced instrumentation for acousto-ultrasonic based structural health monitoring

    Science.gov (United States)

    Smithard, Joel; Galea, Steve; van der Velden, Stephen; Powlesland, Ian; Jung, George; Rajic, Nik

    2016-04-01

    Structural health monitoring (SHM) systems using structurally-integrated sensors potentially allow the ability to inspect for damage in aircraft structures on-demand and could provide a basis for the development of condition-based maintenance approaches for airframes. These systems potentially offer both substantial cost savings and performance improvements over conventional nondestructive inspection (NDI). Acousto-ultrasonics (AU), using structurallyintegrated piezoelectric transducers, offers a promising basis for broad-field damage detection in aircraft structures. For these systems to be successfully applied in the field the hardware for AU excitation and interrogation needs to be easy to use, compact, portable, light and, electrically and mechanically robust. Highly flexible and inexpensive instrumentation for basic background laboratory investigations is also required to allow researchers to tackle the numerous scientific and engineering issues associated with AU based SHM. The Australian Defence Science and Technology Group (DST Group) has developed the Acousto Ultrasonic Structural health monitoring Array Module (AUSAM+), a compact device for AU excitation and interrogation. The module, which has the footprint of a typical current generation smart phone, provides autonomous control of four send and receive piezoelectric elements, which can operate in pitch-catch or pulse-echo modes and can undertake electro-mechanical impedance measurements for transducer and structural diagnostics. Modules are designed to operate synchronously with other units, via an optical link, to accommodate larger transducer arrays. The module also caters for fibre optic sensing of acoustic waves with four intensity-based optical inputs. Temperature and electrical resistance strain gauge inputs as well as external triggering functionality are also provided. The development of a Matlab hardware object allows users to easily access the full hardware functionality of the device and

  18. 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

  19. 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

  20. 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.