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Sample records for helix structure dynamics

  1. Correlation of bistranded clustered abasic DNA lesion processing with structural and dynamic DNA helix distortion

    Science.gov (United States)

    Bignon, Emmanuelle; Gattuso, Hugo; Morell, Christophe; Dehez, François; Georgakilas, Alexandros G.; Monari, Antonio; Dumont, Elise

    2016-01-01

    Clustered apurinic/apyrimidinic (AP; abasic) DNA lesions produced by ionizing radiation are by far more cytotoxic than isolated AP lesion entities. The structure and dynamics of a series of seven 23-bp oligonucleotides featuring simple bistranded clustered damage sites, comprising of two AP sites, zero, one, three or five bases 3′ or 5′ apart from each other, were investigated through 400 ns explicit solvent molecular dynamics simulations. They provide representative structures of synthetically engineered multiply damage sites-containing oligonucleotides whose repair was investigated experimentally (Nucl. Acids Res. 2004, 32:5609-5620; Nucl. Acids Res. 2002, 30: 2800–2808). The inspection of extrahelical positioning of the AP sites, bulge and non Watson–Crick hydrogen bonding corroborates the experimental measurements of repair efficiencies by bacterial or human AP endonucleases Nfo and APE1, respectively. This study provides unprecedented knowledge into the structure and dynamics of clustered abasic DNA lesions, notably rationalizing the non-symmetry with respect to 3′ to 5′ position. In addition, it provides strong mechanistic insights and basis for future studies on the effects of clustered DNA damage on the recognition and processing of these lesions by bacterial or human DNA repair enzymes specialized in the processing of such lesions. PMID:27587587

  2. Nucleic acid helix structure determination from NMR proton chemical shifts

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    Werf, Ramon M. van der; Tessari, Marco; Wijmenga, Sybren S., E-mail: S.Wijmenga@science.ru.nl [Radboud University Nijmegen, Department of Biophysical Chemistry, Institute of Molecules and Materials (Netherlands)

    2013-06-15

    We present a method for de novo derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole source of experimental restraints. The method is called chemical shift de novo structure derivation protocol employing singular value decomposition (CHEOPS) and uses iterative singular value decomposition to optimize the structure in helix parameter space. The correct performance of CHEOPS and its range of application are established via an extensive set of structure derivations using either simulated or experimental chemical shifts as input. The simulated input data are used to assess in a defined manner the effect of errors or limitations in the input data on the derived structures. We find that the RNA helix parameters can be determined with high accuracy. We finally demonstrate via three deposited RNA structures that experimental proton chemical shifts suffice to derive RNA helix structures with high precision and accuracy. CHEOPS provides, subject to further development, new directions for high-resolution NMR structure determination of nucleic acids.

  3. Recognition and Binding of a Helix-Loop-Helix Peptide to Carbonic Anhydrase Occurs via Partly Folded Intermediate Structures

    Science.gov (United States)

    Lignell, Martin; Becker, Hans-Christian

    2010-01-01

    Abstract We have studied the association of a helix-loop-helix peptide scaffold carrying a benzenesulfonamide ligand to carbonic anhydrase using steady-state and time-resolved fluorescence spectroscopy. The helix-loop-helix peptide, developed for biosensing applications, is labeled with the fluorescent probe dansyl, which serves as a polarity-sensitive reporter of the binding event. Using maximum entropy analysis of the fluorescence lifetime of dansyl at 1:1 stoichiometry reveals three characteristic fluorescence lifetime groups, interpreted as differently interacting peptide/protein structures. We characterize these peptide/protein complexes as mostly bound but unfolded, bound and partly folded, and strongly bound and folded. Furthermore, analysis of the fluorescence anisotropy decay resulted in three different dansyl rotational correlation times, namely 0.18, 1.2, and 23 ns. Using the amplitudes of these times, we can correlate the lifetime groups with the corresponding fluorescence anisotropy component. The 23-ns rotational correlation time, which appears with the same amplitude as a 17-ns fluorescence lifetime, shows that the dansyl fluorophore follows the rotational diffusion of carbonic anhydrase when it is a part of the folded peptide/protein complex. A partly folded and partly hydrated interfacial structure is manifested in an 8-ns dansyl fluorescence lifetime and a 1.2-ns rotational correlation time. This structure, we believe, is similar to a molten-globule-like interfacial structure, which allows segmental movement and has a higher degree of solvent exposure of dansyl. Indirect excitation of dansyl on the helix-loop-helix peptide through Förster energy transfer from one or several tryptophans in the carbonic anhydrase shows that the helix-loop-helix scaffold binds to a tryptophan-rich domain of the carbonic anhydrase. We conclude that binding of the peptide to carbonic anhydrase involves a transition from a disordered to an ordered structure of the

  4. Generating structured light with phase helix and intensity helix using reflection-enhanced plasmonic metasurface at 2 μm

    Science.gov (United States)

    Zhao, Yifan; Du, Jing; Zhang, Jinrun; Shen, Li; Wang, Jian

    2018-04-01

    Mid-infrared (2-20 μm) light has been attracting great attention in many areas of science and technology. Beyond the extended wavelength range from visible and near-infrared to mid-infrared, shaping spatial structures may add opportunities to grooming applications of mid-infrared photonics. Here, we design and fabricate a reflection-enhanced plasmonic metasurface and demonstrate efficient generation of structured light with the phase helix and intensity helix at 2 μm. This work includes two distinct aspects. First, structured light (phase helix, intensity helix) generation at 2 μm, which is far beyond the ability of conventional spatial light modulators, is enabled by the metasurface with sub-wavelength engineered structures. Second, the self-referenced intensity helix against environmental noise is generated without using a spatially separated light. The demonstrations may open up advanced perspectives to structured light applications at 2 μm, such as phase helix for communications and non-communications (imaging, sensing) and intensity helix for enhanced microscopy and advanced metrology.

  5. One Peptide Reveals the Two Faces of α-Helix Unfolding-Folding Dynamics.

    Science.gov (United States)

    Jesus, Catarina S H; Cruz, Pedro F; Arnaut, Luis G; Brito, Rui M M; Serpa, Carlos

    2018-04-12

    The understanding of fast folding dynamics of single α-helices comes mostly from studies on rationally designed peptides displaying sequences with high helical propensity. The folding/unfolding dynamics and energetics of α-helix conformations in naturally occurring peptides remains largely unexplored. Here we report the study of a protein fragment analogue of the C-peptide from bovine pancreatic ribonuclease-A, RN80, a 13-amino acid residue peptide that adopts a highly populated helical conformation in aqueous solution. 1 H NMR and CD structural studies of RN80 showed that α-helix formation displays a pH-dependent bell-shaped curve, with a maximum near pH 5, and a large decrease in helical content in alkaline pH. The main forces stabilizing this short α-helix were identified as a salt bridge formed between Glu-2 and Arg-10 and the cation-π interaction involving Tyr-8 and His-12. Thus, deprotonation of Glu-2 or protonation of His-12 are essential for the RN80 α-helix stability. In the present study, RN80 folding and unfolding were triggered by laser-induced pH jumps and detected by time-resolved photoacoustic calorimetry (PAC). The photoacid proton release, amino acid residue protonation, and unfolding/folding events occur at different time scales and were clearly distinguished using time-resolved PAC. The partial unfolding of the RN80 α-helix, due to protonation of Glu-2 and consequent breaking of the stabilizing salt bridge between Glu-2 and Arg-10, is characterized by a concentration-independent volume expansion in the sub-microsecond time range (0.8 mL mol -1 , 369 ns). This small volume expansion reports the cost of peptide backbone rehydration upon disruption of a solvent-exposed salt bridge, as well as backbone intrinsic expansion. On the other hand, RN80 α-helix folding triggered by His-12 protonation and subsequent formation of a cation-π interaction leads to a microsecond volume contraction (-6.0 mL mol -1 , ∼1.7 μs). The essential role of two

  6. Structure of the membrane anchor of pestivirus glycoprotein E(rns, a long tilted amphipathic helix.

    Directory of Open Access Journals (Sweden)

    Daniel Aberle

    2014-02-01

    Full Text Available E(rns is an essential virion glycoprotein with RNase activity that suppresses host cellular innate immune responses upon being partially secreted from the infected cells. Its unusual C-terminus plays multiple roles, as the amphiphilic helix acts as a membrane anchor, as a signal peptidase cleavage site, and as a retention/secretion signal. We analyzed the structure and membrane binding properties of this sequence to gain a better understanding of the underlying mechanisms. CD spectroscopy in different setups, as well as Monte Carlo and molecular dynamics simulations confirmed the helical folding and showed that the helix is accommodated in the amphiphilic region of the lipid bilayer with a slight tilt rather than lying parallel to the surface. This model was confirmed by NMR analyses that also identified a central stretch of 15 residues within the helix that is fully shielded from the aqueous layer, which is C-terminally followed by a putative hairpin structure. These findings explain the strong membrane binding of the protein and provide clues to establishing the E(rns membrane contact, processing and secretion.

  7. Structure of the Membrane Anchor of Pestivirus Glycoprotein Erns, a Long Tilted Amphipathic Helix

    Science.gov (United States)

    Aberle, Daniel; Muhle-Goll, Claudia; Bürck, Jochen; Wolf, Moritz; Reißer, Sabine; Luy, Burkhard; Wenzel, Wolfgang; Ulrich, Anne S.; Meyers, Gregor

    2014-01-01

    Erns is an essential virion glycoprotein with RNase activity that suppresses host cellular innate immune responses upon being partially secreted from the infected cells. Its unusual C-terminus plays multiple roles, as the amphiphilic helix acts as a membrane anchor, as a signal peptidase cleavage site, and as a retention/secretion signal. We analyzed the structure and membrane binding properties of this sequence to gain a better understanding of the underlying mechanisms. CD spectroscopy in different setups, as well as Monte Carlo and molecular dynamics simulations confirmed the helical folding and showed that the helix is accommodated in the amphiphilic region of the lipid bilayer with a slight tilt rather than lying parallel to the surface. This model was confirmed by NMR analyses that also identified a central stretch of 15 residues within the helix that is fully shielded from the aqueous layer, which is C-terminally followed by a putative hairpin structure. These findings explain the strong membrane binding of the protein and provide clues to establishing the Erns membrane contact, processing and secretion. PMID:24586172

  8. Structure of the membrane anchor of pestivirus glycoprotein E(rns), a long tilted amphipathic helix.

    Science.gov (United States)

    Aberle, Daniel; Muhle-Goll, Claudia; Bürck, Jochen; Wolf, Moritz; Reißer, Sabine; Luy, Burkhard; Wenzel, Wolfgang; Ulrich, Anne S; Meyers, Gregor

    2014-02-01

    E(rns) is an essential virion glycoprotein with RNase activity that suppresses host cellular innate immune responses upon being partially secreted from the infected cells. Its unusual C-terminus plays multiple roles, as the amphiphilic helix acts as a membrane anchor, as a signal peptidase cleavage site, and as a retention/secretion signal. We analyzed the structure and membrane binding properties of this sequence to gain a better understanding of the underlying mechanisms. CD spectroscopy in different setups, as well as Monte Carlo and molecular dynamics simulations confirmed the helical folding and showed that the helix is accommodated in the amphiphilic region of the lipid bilayer with a slight tilt rather than lying parallel to the surface. This model was confirmed by NMR analyses that also identified a central stretch of 15 residues within the helix that is fully shielded from the aqueous layer, which is C-terminally followed by a putative hairpin structure. These findings explain the strong membrane binding of the protein and provide clues to establishing the E(rns) membrane contact, processing and secretion.

  9. Nuclear receptor ligand-binding domains: reduction of helix H12 dynamics to favour crystallization

    Energy Technology Data Exchange (ETDEWEB)

    Nahoum, Virginie; Lipski, Alexandra; Quillard, Fabien; Guichou, Jean-François [INSERM, U554, 34090 Montpellier (France); Université de Montpellier, CNRS, UMR5048, Centre de Biochimie Structurale (CBS), 34090 Montpellier (France); Boublik, Yvan [CNRS, UMR5237, Centre de Recherche de Biochimie Macromoléculaire (CRBM), 34293 Montpellier (France); Pérez, Efrèn [Universidade de Vigo, Departamento de Quimica Organica, Facultad de Química, 36310 Vigo (Spain); Germain, Pierre [Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), BP 10142, 67404 Illkirch CEDEX (France); Lera, Angel R. de [Universidade de Vigo, Departamento de Quimica Organica, Facultad de Química, 36310 Vigo (Spain); Bourguet, William, E-mail: bourguet@cbs.cnrs.fr [INSERM, U554, 34090 Montpellier (France); Université de Montpellier, CNRS, UMR5048, Centre de Biochimie Structurale (CBS), 34090 Montpellier (France)

    2008-07-01

    Attempts have been made to crystallize the ligand-binding domain of the human retinoid X receptor in complex with a variety of newly synthesized ligands. An inverse correlation was observed between the ‘crystallizability’ and the structural dynamics of the various receptor–ligand complexes. Crystallization trials of the human retinoid X receptor α ligand-binding domain (RXRα LBD) in complex with various ligands have been carried out. Using fluorescence anisotropy, it has been found that when compared with agonists these small-molecule effectors enhance the dynamics of the RXRα LBD C-terminal helix H12. In some cases, the mobility of this helix could be dramatically reduced by the addition of a 13-residue co-activator fragment (CoA). In keeping with these observations, crystals have been obtained of the corresponding ternary RXRα LBD–ligand–CoA complexes. In contrast, attempts to crystallize complexes with a highly mobile H12 remained unsuccessful. These experimental observations substantiate the previously recognized role of co-regulator fragments in facilitating the crystallization of nuclear receptor LBDs.

  10. Observation of helix associations for insertion of a retinal molecule and distortions of helix structures in bacteriorhodopsin

    Science.gov (United States)

    Urano, Ryo; Okamoto, Yuko

    2015-12-01

    We applied a newly proposed prediction method for membrane protein structures to bacteriorhodopsin that has distorted transmembrane helices in the native structure. This method uses an implicit membrane model, which restricts sampling space during folding in a membrane region, and includes helix bending. Replica-exchange simulations were performed with seven transmembrane helices only without a retinal molecule. Obtained structures were classified into clusters of similar structures, which correspond to local-minimum free energy states. The two lowest free energy states corresponded to a native-like structure with the correct empty space for retinal and a structure with this empty space filled with a helix. Previous experiments of bacteriorhodopsin suggested that association of transmembrane helices enables them to make a room for insertion of a retinal. Our results are consistent with these results. Moreover, distortions of helices in the native-like structures were successfully reproduced. In the distortions, whereas the locations of kinks for all helices were similar to those of Protein Data Bank's data, the amount of bends was more similar for helices away from the retinal than for those close to the retinal in the native structure. This suggests a hypothesis that the amino-acid sequence specifies the location of kinks in transmembrane helices and that the amount of distortions depends on the interactions with the surrounding molecules such as neighboring helices, lipids, and retinal.

  11. Structure of bacteriophage [phi]29 head fibers has a supercoiled triple repeating helix-turn-helix motif

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    Xiang, Ye; Rossmann, Michael G. (Purdue)

    2011-12-22

    The tailed bacteriophage {phi}29 capsid is decorated with 55 fibers attached to quasi-3-fold symmetry positions. Each fiber is a homotrimer of gene product 8.5 (gp8.5) and consists of two major structural parts, a pseudohexagonal base and a protruding fibrous portion that is about 110 {angstrom} in length. The crystal structure of the C-terminal fibrous portion (residues 112-280) has been determined to a resolution of 1.6 {angstrom}. The structure is about 150 {angstrom} long and shows three distinct structural domains designated as head, neck, and stem. The stem region is a unique three-stranded helix-turn-helix supercoil that has not previously been described. When fitted into a cryoelectron microscope reconstruction of the virus, the head structure corresponded to a disconnected density at the distal end of the fiber and the neck structure was located in weak density connecting it to the fiber. Thin section studies of Bacillus subtilis cells infected with fibered or fiberless {phi}29 suggest that the fibers might enhance the attachment of the virions onto the host cell wall.

  12. Right- and left-handed three-helix proteins. I. Experimental and simulation analysis of differences in folding and structure.

    Science.gov (United States)

    Glyakina, Anna V; Pereyaslavets, Leonid B; Galzitskaya, Oxana V

    2013-09-01

    Despite the large number of publications on three-helix protein folding, there is no study devoted to the influence of handedness on the rate of three-helix protein folding. From the experimental studies, we make a conclusion that the left-handed three-helix proteins fold faster than the right-handed ones. What may explain this difference? An important question arising in this paper is whether the modeling of protein folding can catch the difference between the protein folding rates of proteins with similar structures but with different folding mechanisms. To answer this question, the folding of eight three-helix proteins (four right-handed and four left-handed), which are similar in size, was modeled using the Monte Carlo and dynamic programming methods. The studies allowed us to determine the orders of folding of the secondary-structure elements in these domains and amino acid residues which are important for the folding. The obtained data are in good correlation with each other and with the experimental data. Structural analysis of these proteins demonstrated that the left-handed domains have a lesser number of contacts per residue and a smaller radius of cross section than the right-handed domains. This may be one of the explanations of the observed fact. The same tendency is observed for the large dataset consisting of 332 three-helix proteins (238 right- and 94 left-handed). From our analysis, we found that the left-handed three-helix proteins have some less-dense packing that should result in faster folding for some proteins as compared to the case of right-handed proteins. Copyright © 2013 Wiley Periodicals, Inc.

  13. Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides.

    Science.gov (United States)

    Best, Robert B; Hummer, Gerhard

    2009-07-02

    Obtaining the correct balance of secondary structure propensities is a central priority in protein force-field development. Given that current force fields differ significantly in their alpha-helical propensities, a correction to match experimental results would be highly desirable. We have determined simple backbone energy corrections for two force fields to reproduce the fraction of helix measured in short peptides at 300 K. As validation, we show that the optimized force fields produce results in excellent agreement with nuclear magnetic resonance experiments for folded proteins and short peptides not used in the optimization. However, despite the agreement at ambient conditions, the dependence of the helix content on temperature is too weak, a problem shared with other force fields. A fit of the Lifson-Roig helix-coil theory shows that both the enthalpy and entropy of helix formation are too small: the helix extension parameter w agrees well with experiment, but its entropic and enthalpic components are both only about half the respective experimental estimates. Our structural and thermodynamic analyses point toward the physical origins of these shortcomings in current force fields, and suggest ways to address them in future force-field development.

  14. The close-packed triple helix as a possible new structural motif for collagen

    DEFF Research Database (Denmark)

    Bohr, Jakob; Olsen, Kasper

    2010-01-01

    that close packing form the underlying principle behind the structure of collagen, and the implications of this suggestion are considered. Further, it is shown that the unique zero-twist structure with no strain-twist coupling is practically identical to the close-packed triple helix. Some...

  15. Defining the structural requirements for a helix in 23 S ribosomal RNA that confers erythromycin resistance

    DEFF Research Database (Denmark)

    Douthwaite, S; Powers, T; Lee, J Y

    1989-01-01

    The helix spanning nucleotides 1198 to 1247 (helix 1200-1250) in Escherichia coli 23 S ribosomal RNA (rRNA) is functionally important in protein synthesis, and deletions in this region confer erythromycin resistance. In order to define the structural requirements for resistance, we have dissected...... deletion mutants show a sensitive phenotype. Deletions that extend into the base-pairing between GCC1208 and GGU1240 result in non-functional 23 S RNAs, which consequently do not confer resistance. A number of phylogenetically conserved nucleotides have been shown to be non-essential for 23 S RNA function....... However, removal of either these or non-conserved nucleotides from helix 1200-1250 measurably reduces the efficiency of 23 S RNA in forming functional ribosomes. We have used chemical probing and a modified primer extension method to investigate erythromycin binding to wild-type and resistant ribosomes...

  16. The triple helix of collagens - an ancient protein structure that enabled animal multicellularity and tissue evolution.

    Science.gov (United States)

    Fidler, Aaron L; Boudko, Sergei P; Rokas, Antonis; Hudson, Billy G

    2018-04-09

    The cellular microenvironment, characterized by an extracellular matrix (ECM), played an essential role in the transition from unicellularity to multicellularity in animals (metazoans), and in the subsequent evolution of diverse animal tissues and organs. A major ECM component are members of the collagen superfamily -comprising 28 types in vertebrates - that exist in diverse supramolecular assemblies ranging from networks to fibrils. Each assembly is characterized by a hallmark feature, a protein structure called a triple helix. A current gap in knowledge is understanding the mechanisms of how the triple helix encodes and utilizes information in building scaffolds on the outside of cells. Type IV collagen, recently revealed as the evolutionarily most ancient member of the collagen superfamily, serves as an archetype for a fresh view of fundamental structural features of a triple helix that underlie the diversity of biological activities of collagens. In this Opinion, we argue that the triple helix is a protein structure of fundamental importance in building the extracellular matrix, which enabled animal multicellularity and tissue evolution. © 2018. Published by The Company of Biologists Ltd.

  17. What can triple helix frameworks offer to the analysis of eco-innovation dynamics? Theoretical and methodological considerations

    DEFF Research Database (Denmark)

    Yang, Yan; Holgaard, Jette Egelund; Remmen, Arne

    2012-01-01

    stakeholder groups are interacting in this connection. Taking the triple helix as the theoretical departure point, this paper discusses the opportunities offered by these triple helix frameworks for analyzing eco-innovation dynamics from both theoretical and practical perspectives. It adds to the debate about......Bringing environmental concerns into focus of innovation processes will in several cases also expand the numbers of actors involved. Eco-innovation and triple helix are often frameworks applied to analyse how environmental concerns are integrated in the innovation processes and how different...

  18. Shielded helix traveling wave cathode ray tube deflection structure

    Science.gov (United States)

    Norris, N.J.; Hudson, C.L.

    1992-12-15

    Various embodiments of a helical coil deflection structure of a CRT are described and illustrated which provide shielding between adjacent turns of the coil on either three or four sides of each turn in the coil. Threaded members formed with either male or female threads and having the same pitch as the deflection coil are utilized for shielding the deflection coil with each turn of the helical coil placed between adjacent threads which act to shield each coil turn from adjacent turns and to confine the field generated by the coil to prevent or inhibit cross-coupling between adjacent turns of the coil to thereby prevent generation of fast fields which might otherwise deflect the beam out of time synchronization with the electron beam pulse. 13 figs.

  19. Structural Dynamics

    International Nuclear Information System (INIS)

    Kim, Du Gi

    2005-08-01

    This book introduces summary of structural dynamics, the reason of learning of structural dynamics, single-degree of freedom system, simple harmonic vibration and application, numerical analysis method, such as time domain and frequency domain and nonlinear system, multi-degree of freedom system random vibration over discrete distribution, continuous distribution and extreme value distribution, circumstance vibration, earth quake vibration, including input earthquake, and earthquake-resistant design and capacity spectrum method, wind oscillation wave vibration, vibration control and maintenance control.

  20. Structural plasticity of the N-terminal capping helix of the TPR domain of kinesin light chain.

    Directory of Open Access Journals (Sweden)

    The Quyen Nguyen

    Full Text Available Kinesin1 plays a major role in neuronal transport by recruiting many different cargos through its kinesin light chain (KLC. Various structurally unrelated cargos interact with the conserved tetratricopeptide repeat (TPR domain of KLC. The N-terminal capping helix of the TPR domain exhibits an atypical sequence and structural features that may contribute to the versatility of the TPR domain to bind different cargos. We determined crystal structures of the TPR domain of both KLC1 and KLC2 encompassing the N-terminal capping helix and show that this helix exhibits two distinct and defined orientations relative to the rest of the TPR domain. Such a difference in orientation gives rise, at the N-terminal part of the groove, to the formation of one hydrophobic pocket, as well as to electrostatic variations at the groove surface. We present a comprehensive structural analysis of available KLC1/2-TPR domain structures that highlights that ligand binding into the groove can be specific of one or the other N-terminal capping helix orientations. Further, structural analysis reveals that the N-terminal capping helix is always involved in crystal packing contacts, especially in a TPR1:TPR1' contact which highlights its propensity to be a protein-protein interaction site. Together, these results underline that the structural plasticity of the N-terminal capping helix might represent a structural determinant for TPR domain structural versatility in cargo binding.

  1. Steady-state configurations and dynamics of the MreB helix within bacteria

    Science.gov (United States)

    Rutenberg, Andrew; Allard, Jun

    2007-03-01

    We present a quantitative model of the actin-like MreB cytoskeleton that is present in many prokaryotes. Individual MreB polymers are bundled into a supra-molecular array to make up helical cables. The cell wall imposes constraint forces through a global elasticity model. With variational techniques and stochastic simulations we obtain relationships between observable quantities such as the pitch of the helix, the total abundance of MreB molecules, and the thickness of the MreB cables. We address changes expected with slow cell growth, as well as turnover dynamics that are relevant to FRAP studies. We also address polarized macromolecular trafficking along the MreB cables without motor proteins.

  2. Structural dynamics

    CERN Document Server

    Strømmen, Einar N

    2014-01-01

    This book introduces to the theory of structural dynamics, with focus on civil engineering structures that may be described by line-like beam or beam-column type of systems, or by a system of rectangular plates. Throughout this book the mathematical presentation contains a classical analytical description as well as a description in a discrete finite element format, covering the mathematical development from basic assumptions to the final equations ready for practical dynamic response predictions. Solutions are presented in time domain as well as in frequency domain. Structural Dynamics starts off at a basic level and step by step brings the reader up to a level where the necessary safety considerations to wind or horizontal ground motion induced dynamic design problems can be performed. The special theory of the tuned mass damper has been given a comprehensive treatment, as this is a theory not fully covered elsewhere. For the same reason a chapter on the problem of moving loads on beams has been included.

  3. Structural and functional aspects of winged-helix domains at the core of transcription initiation complexes.

    Science.gov (United States)

    Teichmann, Martin; Dumay-Odelot, Hélène; Fribourg, Sébastien

    2012-01-01

    The winged helix (WH) domain is found in core components of transcription systems in eukaryotes and prokaryotes. It represents a sub-class of the helix-turn-helix motif. The WH domain participates in establishing protein-DNA and protein-protein-interactions. Here, we discuss possible explanations for the enrichment of this motif in transcription systems.

  4. Conservation of Three-Dimensional Helix-Loop-Helix Structure through the Vertebrate Lineage Reopens the Cold Case of Gonadotropin-Releasing Hormone-Associated Peptide.

    Science.gov (United States)

    Pérez Sirkin, Daniela I; Lafont, Anne-Gaëlle; Kamech, Nédia; Somoza, Gustavo M; Vissio, Paula G; Dufour, Sylvie

    2017-01-01

    GnRH-associated peptide (GAP) is the C-terminal portion of the gonadotropin-releasing hormone (GnRH) preprohormone. Although it was reported in mammals that GAP may act as a prolactin-inhibiting factor and can be co-secreted with GnRH into the hypophyseal portal blood, GAP has been practically out of the research circuit for about 20 years. Comparative studies highlighted the low conservation of GAP primary amino acid sequences among vertebrates, contributing to consider that this peptide only participates in the folding or carrying process of GnRH. Considering that the three-dimensional (3D) structure of a protein may define its function, the aim of this study was to evaluate if GAP sequences and 3D structures are conserved in the vertebrate lineage. GAP sequences from various vertebrates were retrieved from databases. Analysis of primary amino acid sequence identity and similarity, molecular phylogeny, and prediction of 3D structures were performed. Amino acid sequence comparison and phylogeny analyses confirmed the large variation of GAP sequences throughout vertebrate radiation. In contrast, prediction of the 3D structure revealed a striking conservation of the 3D structure of GAP1 (GAP associated with the hypophysiotropic type 1 GnRH), despite low amino acid sequence conservation. This GAP1 peptide presented a typical helix-loop-helix (HLH) structure in all the vertebrate species analyzed. This HLH structure could also be predicted for GAP2 in some but not all vertebrate species and in none of the GAP3 analyzed. These results allowed us to infer that selective pressures have maintained GAP1 HLH structure throughout the vertebrate lineage. The conservation of the HLH motif, known to confer biological activity to various proteins, suggests that GAP1 peptides may exert some hypophysiotropic biological functions across vertebrate radiation.

  5. Conservation of Three-Dimensional Helix-Loop-Helix Structure through the Vertebrate Lineage Reopens the Cold Case of Gonadotropin-Releasing Hormone-Associated Peptide

    Directory of Open Access Journals (Sweden)

    Daniela I. Pérez Sirkin

    2017-08-01

    Full Text Available GnRH-associated peptide (GAP is the C-terminal portion of the gonadotropin-releasing hormone (GnRH preprohormone. Although it was reported in mammals that GAP may act as a prolactin-inhibiting factor and can be co-secreted with GnRH into the hypophyseal portal blood, GAP has been practically out of the research circuit for about 20 years. Comparative studies highlighted the low conservation of GAP primary amino acid sequences among vertebrates, contributing to consider that this peptide only participates in the folding or carrying process of GnRH. Considering that the three-dimensional (3D structure of a protein may define its function, the aim of this study was to evaluate if GAP sequences and 3D structures are conserved in the vertebrate lineage. GAP sequences from various vertebrates were retrieved from databases. Analysis of primary amino acid sequence identity and similarity, molecular phylogeny, and prediction of 3D structures were performed. Amino acid sequence comparison and phylogeny analyses confirmed the large variation of GAP sequences throughout vertebrate radiation. In contrast, prediction of the 3D structure revealed a striking conservation of the 3D structure of GAP1 (GAP associated with the hypophysiotropic type 1 GnRH, despite low amino acid sequence conservation. This GAP1 peptide presented a typical helix-loop-helix (HLH structure in all the vertebrate species analyzed. This HLH structure could also be predicted for GAP2 in some but not all vertebrate species and in none of the GAP3 analyzed. These results allowed us to infer that selective pressures have maintained GAP1 HLH structure throughout the vertebrate lineage. The conservation of the HLH motif, known to confer biological activity to various proteins, suggests that GAP1 peptides may exert some hypophysiotropic biological functions across vertebrate radiation.

  6. Coherent helix vacancy phonon and its ultrafast dynamics waning in topological Dirac semimetal C d3A s2

    Science.gov (United States)

    Sun, Fei; Wu, Q.; Wu, Y. L.; Zhao, H.; Yi, C. J.; Tian, Y. C.; Liu, H. W.; Shi, Y. G.; Ding, H.; Dai, X.; Richard, P.; Zhao, Jimin

    2017-06-01

    We report an ultrafast lattice dynamics investigation of the topological Dirac semimetal C d3A s2 . A coherent phonon beating among three evenly spaced A1 g optical phonon modes (of frequencies 1.80, 1.96, and 2.11 THz, respectively) is unambiguously observed. The two side modes originate from the counter helixes composing Cd vacancies. Significantly, such helix vacancy-induced phonon (HVP) modes experience prominent extra waning in their ultrafast dynamics as temperature increases, which is immune to the central mode. Above 200 K, the HVP becomes inactive, which may potentially affect the topological properties. Our results in the lattice degree of freedom suggest the indispensable role of temperature in considering topological properties of such quantum materials.

  7. Comparative Study on the Adaptation and Growth Dynamics of the Helix pomatia and Helix aspersa Muller Terrestrial Snails Under Different Feeding Regimes

    Directory of Open Access Journals (Sweden)

    Adrian Toader-Williams

    2010-05-01

    Full Text Available We used Helix pomatia and Helix aspersa species and measure their growth as the snails were approaching the hibernation season. Helix pomatia 2yo shown a decrease in weight while being raised in enclosed parcels of 4sqm the younger Helix pomatia 1yo as well as Helix aspersa Muller demonstrated the ability to adapt relatively fast to the same conditions. We established 5 experimental lots in a Helix pomatia farm, GPS coordinates N46.606040 E23.599950. Control lot contained Taraxacum officinales, Sonchus oleraceus, Equisetum arvense and Atriplex hortensis, wild flora found within the farm. The other lots contained the same plants as the control lot plus different combinations of imported plants from other areals. The H. pomatia 2yo weight decreased in the control lot by a mean of -3.86% while H. aspersa 1yo marked an increase of +16.89% in the same lot during the same period. The lot containing lupinus polyphyllus delivered snails with weight gain of +24.66% for H. pomatia 2yo and an increase of only +1.98% for H. aspersa 1yo. As a contrast, H. pomatia 2yo gained only +7.72% while H. aspersa 1yo gained +28.89%, in the lot containing Lavanda officinalis, Foeniculum vulgare and Hyssopus officinalis among the other plants.

  8. Glass-like dynamics of the strain-induced coil/helix transition on a permanent polymer network.

    Science.gov (United States)

    Ronsin, O; Caroli, C; Baumberger, T

    2016-02-14

    We study the stress response to a step strain of covalently bonded gelatin gels in the temperature range where triple helix reversible crosslink formation is prohibited. We observe slow stress relaxation towards a T-dependent finite asymptotic level. We show that this is assignable to the strain-induced coil → helix transition, previously evidenced by Courty et al. [Proc. Natl. Acad. Sci. U. S. A. 102, 13457 (2005)], of a fraction of the polymer strands. Relaxation proceeds, in a first stage, according to a stretched exponential dynamics, then crosses over to a terminal simple exponential decay. The respective characteristic times τK and τf exhibit an Arrhenius-like T-dependence with an associated energy E incompatibly larger than the activation barrier height for the isomerisation process which sets the clock for an elementary coil → helix transformation event. We tentatively assign this glass-like slowing down of the dynamics to the long-range couplings due to the mechanical noise generated by the local elementary events in this random elastic medium.

  9. Structural Variation and Uniformity among Tetraloop-Receptor Interactions and Other Loop-Helix Interactions in RNA Crystal Structures

    Science.gov (United States)

    Wu, Li; Chai, Dinggeng; Fraser, Marie E.; Zimmerly, Steven

    2012-01-01

    Tetraloop-receptor interactions are prevalent structural units in RNAs, and include the GAAA/11-nt and GNRA-minor groove interactions. In this study, we have compiled a set of 78 nonredundant loop-helix interactions from X-ray crystal structures, and examined them for the extent of their sequence and structural variation. Of the 78 interactions in the set, only four were classical GAAA/11-nt motifs, while over half (48) were GNRA-minor groove interactions. The GNRA-minor groove interactions were not a homogeneous set, but were divided into five subclasses. The most predominant subclass is characterized by two triple base pair interactions in the minor groove, flanked by two ribose zipper contacts. This geometry may be considered the “standard” GNRA-minor groove interaction, while the other four subclasses are alternative ways to form interfaces between a minor groove and tetraloop. The remaining 26 structures in the set of 78 have loops interacting with mostly idiosyncratic receptors. Among the entire set, a number of sequence-structure correlations can be identified, which may be used as initial hypotheses in predicting three-dimensional structures from primary sequences. Conversely, other sequence patterns are not predictive; for example, GAAA loop sequences and GG/CC receptors bind to each other with three distinct geometries. Finally, we observe an example of structural evolution in group II introns, in which loop-receptor motifs are substituted for each other while maintaining the larger three-dimensional geometry. Overall, the study gives a more complete view of RNA loop-helix interactions that exist in nature. PMID:23152878

  10. Structural Dynamics

    DEFF Research Database (Denmark)

    Nielsen, Søren R.K.

    The present textbook has been written for a course on stochastic vibration theory that is being given on the 9th semester at Aalborg University for M.Sc. students in structural engineering.......The present textbook has been written for a course on stochastic vibration theory that is being given on the 9th semester at Aalborg University for M.Sc. students in structural engineering....

  11. Structure, stability, and thermodynamics of a short intermolecular purine-purine-pyrimidine triple helix

    International Nuclear Information System (INIS)

    Pilch, D.S.; Shafer, R.H.; Levenson, C.

    1991-01-01

    The authors have investigated the structure and physical chemistry of the d(C 3 T 4 C 3 )·2[d(G 3 A 4 G 3 )] triple helix by polyacrylamide gel electrophoresis (PAGE), 1 H NMR, and ultraviolet (UV) absorption spectroscopy. The triplex was stabilized with MgCl 2 at neutral pH. PAGE studies verify the stoichiometry of the strands comprising the triplex and indicate that the orientation of the third strand in purine-purine-pyrimidine (pur-pur-pyr) triplexes is antiparallel with respect to the purine strand of the underlying duplex. Imino proton NMR spectra provide evidence for the existence of new purine-purine (pur·pur) hydrogen bonds, in addition to those of the Watson-Crick (W-C) base pairs, in the triplex structure. These new hydrogen bonds are likely to correspond to the interaction between third-strand guanine NH1 imino protons and the N7 atoms of guanine residues on the puring strand of the underlying duplex. Thermal denaturation of the triplex proceeds to single strands in one step, under the conditions used in this study. Binding of the third strand appears to enhance the thermal stability of the duplex by 1-3 C, depending on the DNA concentration. This marked enhancement in stability, coupled with the lack of an acidic pH requirement, suggests that pur-pur-pyr triplexes are appealing choices for use in applications involving oligonucleotide targeting of duplex DNA in vitro and in vivo

  12. Sensitivity of immune response quality to influenza helix 190 antigen structure displayed on a modular virus-like particle.

    Science.gov (United States)

    Anggraeni, Melisa R; Connors, Natalie K; Wu, Yang; Chuan, Yap P; Lua, Linda H L; Middelberg, Anton P J

    2013-09-13

    Biomolecular engineering enables synthesis of improved proteins through synergistic fusion of modules from unrelated biomolecules. Modularization of peptide antigen from an unrelated pathogen for presentation on a modular virus-like particle (VLP) represents a new and promising approach to synthesize safe and efficacious vaccines. Addressing a key knowledge gap in modular VLP engineering, this study investigates the underlying fundamentals affecting the ability of induced antibodies to recognize the native pathogen. Specifically, this quality of immune response is correlated to the peptide antigen module structure. We modularized a helical peptide antigen element, helix 190 (H190) from the influenza hemagglutinin (HA) receptor binding region, for presentation on murine polyomavirus VLP, using two strategies aimed to promote H190 helicity on the VLP. In the first strategy, H190 was flanked by GCN4 structure-promoting elements within the antigen module; in the second, dual H190 copies were arrayed as tandem repeats in the module. Molecular dynamics simulation predicted that tandem repeat arraying would minimize secondary structural deviation of modularized H190 from its native conformation. In vivo testing supported this finding, showing that although both modularization strategies conferred high H190-specific immunogenicity, tandem repeat arraying of H190 led to a strikingly higher immune response quality, as measured by ability to generate antibodies recognizing a recombinant HA domain and split influenza virion. These findings provide new insights into the rational engineering of VLP vaccines, and could ultimately enable safe and efficacious vaccine design as an alternative to conventional approaches necessitating pathogen cultivation. Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. Double helix vortex breakdown in a turbulent swirling annular jet flow

    NARCIS (Netherlands)

    Vanierschot, M.; Perçin, M.; van Oudheusden, B.W.

    2018-01-01

    In this paper, we report on the structure and dynamics of double helix vortex breakdown in a turbulent annular swirling jet. Double helix breakdown has been reported previously for the laminar flow regime, but this structure has rarely been observed in turbulent flow. The flow field is

  14. The basic helix-loop-helix region of the transcriptional repressor hairy and enhancer of split 1 is preorganized to bind DNA

    NARCIS (Netherlands)

    Popovic, Matija; Wienk, Hans; Coglievina, Maristella; Boelens, Rolf; Pongor, Sándor; Pintar, Alessandro

    2014-01-01

    Hairy and enhancer of split 1, one of the main downstream effectors in Notch signaling, is a transcriptional repressor of the basic helix-loop-helix (bHLH) family. Using nuclear magnetic resonance methods, we have determined the structure and dynamics of a recombinant protein, H1H, which includes an

  15. Modulating immunogenic properties of HIV-1 gp41 membrane-proximal external region by destabilizing six-helix bundle structure

    Energy Technology Data Exchange (ETDEWEB)

    Banerjee, Saikat; Shi, Heliang; Habte, Habtom H.; Qin, Yali; Cho, Michael W., E-mail: mcho@iastate.edu

    2016-03-15

    The C-terminal alpha-helix of gp41 membrane-proximal external region (MPER; {sup 671}NWFDITNWLWYIK{sup 683}) encompassing 4E10/10E8 epitopes is an attractive target for HIV-1 vaccine development. We previously reported that gp41-HR1-54Q, a trimeric protein comprised of the MPER in the context of a stable six-helix bundle (6HB), induced strong immune responses against the helix, but antibodies were directed primarily against the non-neutralizing face of the helix. To better target 4E10/10E8 epitopes, we generated four putative fusion intermediates by introducing double point mutations or deletions in the heptad repeat region 1 (HR1) that destabilize 6HB in varying degrees. One variant, HR1-∆10-54K, elicited antibodies in rabbits that targeted W672, I675 and L679, which are critical for 4E10/10E8 recognition. Overall, the results demonstrated that altering structural parameters of 6HB can influence immunogenic properties of the MPER and antibody targeting. Further exploration of this strategy could allow development of immunogens that could lead to induction of 4E10/10E8-like antibodies. - Highlights: • Four gp41 MPER-based immunogens that resemble fusion intermediates were generated. • C-terminal region of MPER that contains 4E10/10E8 epitopes was highly immunogenic. • Altering 6HB structure can influence immunogenic properties of the MPER. • Induced antibodies targeted multiple residues critical for 4E10/10E8 binding. • Development of immunogens based on fusion intermediates is a promising strategy.

  16. Loop-to-helix transition in the structure of multidrug regulator AcrR at the entrance of the drug-binding cavity

    Energy Technology Data Exchange (ETDEWEB)

    Manjasetty, Babu A.; Halavaty, Andrei S.; Luan, Chi-Hao; Osipiuk, Jerzy; Mulligan, Rory; Kwon, Keehwan; Anderson, Wayne F.; Joachimiak, Andrzej

    2016-04-01

    Multidrug transcription regulator AcrR from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 belongs to the tetracycline repressor family, one of the largest groups of bacterial transcription factors. The crystal structure of dimeric AcrR was determined and refined to 1.56 Å resolution. The tertiary and quaternary structures of AcrR are similar to those of its homologs. The multidrug binding site was identified based on structural alignment with homologous proteins and has a di(hydroxyethyl)ether molecule bound. Residues from helices a4 and a7 shape the entry into this binding site. The structure of AcrR reveals that the extended helical conformation of helix a4 is stabilized by the hydrogen bond between Glu67 (helix a4) and Gln130 (helix a7). Based on the structural comparison with the closest homolog structure, the Escherichia coli AcrR, we propose that this hydrogen bond is responsible for control of the loop-to-helix transition within helix a4. This local conformational switch of helix a4 may be a key step in accessing the multidrug binding site and securing ligands at the binding site. Solution smallmolecule binding studies suggest that AcrR binds ligands with their core chemical structure resembling the tetracyclic ring of cholesterol.

  17. Loop-to-helix transition in the structure of multidrug regulator AcrR at the entrance of the drug-binding cavity.

    Science.gov (United States)

    Manjasetty, Babu A; Halavaty, Andrei S; Luan, Chi-Hao; Osipiuk, Jerzy; Mulligan, Rory; Kwon, Keehwan; Anderson, Wayne F; Joachimiak, Andrzej

    2016-04-01

    Multidrug transcription regulator AcrR from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 belongs to the tetracycline repressor family, one of the largest groups of bacterial transcription factors. The crystal structure of dimeric AcrR was determined and refined to 1.56Å resolution. The tertiary and quaternary structures of AcrR are similar to those of its homologs. The multidrug binding site was identified based on structural alignment with homologous proteins and has a di(hydroxyethyl)ether molecule bound. Residues from helices α4 and α7 shape the entry into this binding site. The structure of AcrR reveals that the extended helical conformation of helix α4 is stabilized by the hydrogen bond between Glu67 (helix α4) and Gln130 (helix α7). Based on the structural comparison with the closest homolog structure, the Escherichia coli AcrR, we propose that this hydrogen bond is responsible for control of the loop-to-helix transition within helix α4. This local conformational switch of helix α4 may be a key step in accessing the multidrug binding site and securing ligands at the binding site. Solution small-molecule binding studies suggest that AcrR binds ligands with their core chemical structure resembling the tetracyclic ring of cholesterol. Copyright © 2016. Published by Elsevier Inc.

  18. Fundamentals of structural dynamics

    CERN Document Server

    Craig, Roy R

    2006-01-01

    From theory and fundamentals to the latest advances in computational and experimental modal analysis, this is the definitive, updated reference on structural dynamics.This edition updates Professor Craig's classic introduction to structural dynamics, which has been an invaluable resource for practicing engineers and a textbook for undergraduate and graduate courses in vibrations and/or structural dynamics. Along with comprehensive coverage of structural dynamics fundamentals, finite-element-based computational methods, and dynamic testing methods, this Second Edition includes new and e

  19. Structural factors involved in the recognition of helix distortions in uv-damaged DNA by model peptides

    Energy Technology Data Exchange (ETDEWEB)

    Lang, H; Zimmer, C [Akademie der Wissenschaften der DDR, Jena. Forschungszentrum fuer Molekularbiologie und Medizin

    1977-02-28

    On the basis of our previous and present results concerning conformational changes of DNA after uv-irradiation some conclusions on the structure of DNA double helix in uv-damaged regions were drawn. From the results it appears that local distortions like denaturation or premelting should be excluded. Furthermore it was shown that the thymine dimerization strongly depends on the adjacent nucleic acid bases. By means of a strong binding effect of the oligopeptide netropsin to DNA irradiated at low uv-doses it is concluded that such local distortions in DNA together with a specific sequence-dependent variation of the conformation could act as recognition sites for endonucleases.

  20. Structure, Reactivity and Dynamics

    Indian Academy of Sciences (India)

    Understanding structure, reactivity and dynamics is the core issue in chemical ... functional theory (DFT) calculations, molecular dynamics (MD) simulations, light- ... between water and protein oxygen atoms, the superionic conductors which ...

  1. Mechanical unfolding reveals stable 3-helix intermediates in talin and α-catenin.

    Directory of Open Access Journals (Sweden)

    Vasyl V Mykuliak

    2018-04-01

    Full Text Available Mechanical stability is a key feature in the regulation of structural scaffolding proteins and their functions. Despite the abundance of α-helical structures among the human proteome and their undisputed importance in health and disease, the fundamental principles of their behavior under mechanical load are poorly understood. Talin and α-catenin are two key molecules in focal adhesions and adherens junctions, respectively. In this study, we used a combination of atomistic steered molecular dynamics (SMD simulations, polyprotein engineering, and single-molecule atomic force microscopy (smAFM to investigate unfolding of these proteins. SMD simulations revealed that talin rod α-helix bundles as well as α-catenin α-helix domains unfold through stable 3-helix intermediates. While the 5-helix bundles were found to be mechanically stable, a second stable conformation corresponding to the 3-helix state was revealed. Mechanically weaker 4-helix bundles easily unfolded into a stable 3-helix conformation. The results of smAFM experiments were in agreement with the findings of the computational simulations. The disulfide clamp mutants, designed to protect the stable state, support the 3-helix intermediate model in both experimental and computational setups. As a result, multiple discrete unfolding intermediate states in the talin and α-catenin unfolding pathway were discovered. Better understanding of the mechanical unfolding mechanism of α-helix proteins is a key step towards comprehensive models describing the mechanoregulation of proteins.

  2. Structural Dynamics Laboratory (SDL)

    Data.gov (United States)

    Federal Laboratory Consortium — Structural dynamic testing is performed to verify the survivability of a component or assembly when exposed to vibration stress screening, or a controlled simulation...

  3. The structure and dynamic properties of the complete histidine phosphotransfer domain of the chemotaxis specific histidine autokinase CheA from Thermotoga maritima

    International Nuclear Information System (INIS)

    Vu, Anh; Hamel, Damon J.; Zhou Hongjun; Dahlquist, Frederick W.

    2011-01-01

    The bacterial histidine autokinase CheA contains a histidine phosphotransfer (Hpt) domain that accepts a phosphate from the catalytic domain and donates the phosphate to either target response regulator protein, CheY or CheB. The Hpt domain forms a helix-bundle structure with a conserved four-helix bundle motif and a variable fifth helix. Observation of two nearly equally populated conformations in the crystal structure of a Hpt domain fragment of CheA from Thermotoga maritima containing only the first four helices suggests more mobility in a tightly packed helix bundle structure than previously thought. In order to examine how the structures of Hpt domain homologs may differ from each other particularly in the conformation of the last helix, and whether an alternative conformation exists in the intact Hpt domain in solution, we have solved a high-resolution, solution structure of the CheA Hpt from T. maritima and characterized the backbone dynamics of this protein. The structure contains a four-helix bundle characteristic of histidine phosphotransfer domains. The position and orientation of the fifth helix resembles those in known Hpt domain crystal and solution structures in other histidine kinases. The alternative conformation that was reported in the crystal structure of the CheA Hpt from T. maritima missing the fifth helix is not detected in the solution structure, suggesting a role for the fifth helix in providing stabilizing forces to the overall structure.

  4. Basic structural dynamics

    CERN Document Server

    Anderson, James C

    2012-01-01

    A concise introduction to structural dynamics and earthquake engineering Basic Structural Dynamics serves as a fundamental introduction to the topic of structural dynamics. Covering single and multiple-degree-of-freedom systems while providing an introduction to earthquake engineering, the book keeps the coverage succinct and on topic at a level that is appropriate for undergraduate and graduate students. Through dozens of worked examples based on actual structures, it also introduces readers to MATLAB, a powerful software for solving both simple and complex structural d

  5. Structural Dynamics, Vol. 9

    DEFF Research Database (Denmark)

    Nielsen, Søren R.K.

    This book has been prepared for the course on Computational Dynamics given at the 8th semester at the structural program in civil engineering at Aalborg University.......This book has been prepared for the course on Computational Dynamics given at the 8th semester at the structural program in civil engineering at Aalborg University....

  6. Nonlinear dynamics of structures

    CERN Document Server

    Oller, Sergio

    2014-01-01

    This book lays the foundation of knowledge that will allow a better understanding of nonlinear phenomena that occur in structural dynamics.   This work is intended for graduate engineering students who want to expand their knowledge on the dynamic behavior of structures, specifically in the nonlinear field, by presenting the basis of dynamic balance in non‐linear behavior structures due to the material and kinematics mechanical effects.   Particularly, this publication shows the solution of the equation of dynamic equilibrium for structure with nonlinear time‐independent materials (plasticity, damage and frequencies evolution), as well as those time dependent non‐linear behavior materials (viscoelasticity and viscoplasticity). The convergence conditions for the non‐linear dynamic structure solution  are studied, and the theoretical concepts and its programming algorithms are presented.  

  7. Reaction Path Averaging: Characterizing the Structural Response of the DNA Double Helix to Electron Transfer

    Czech Academy of Sciences Publication Activity Database

    Kolář, Michal H.; Kubař, T.

    2017-01-01

    Roč. 121, č. 7 (2017), s. 1520-1532 ISSN 1520-6106 Institutional support: RVO:61388963 Keywords : excited-state dynamics * excitation energy transfer * solvation dynamics Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 3.177, year: 2016

  8. The structure of Plasmodium vivax phosphatidylethanolamine-binding protein suggests a functional motif containing a left-handed helix

    International Nuclear Information System (INIS)

    Arakaki, Tracy; Neely, Helen; Boni, Erica; Mueller, Natasha; Buckner, Frederick S.; Van Voorhis, Wesley C.; Lauricella, Angela; DeTitta, George; Luft, Joseph; Hol, Wim G. J.; Merritt, Ethan A.

    2007-01-01

    The crystal structure of a phosphatidylethanolamine-binding protein from P. vivax, a homolog of Raf-kinase inhibitor protein (RKIP), has been solved to a resolution of 1.3 Å. The inferred interaction surface near the anion-binding site is found to include a distinctive left-handed α-helix. The structure of a putative Raf kinase inhibitor protein (RKIP) homolog from the eukaryotic parasite Plasmodium vivax has been studied to a resolution of 1.3 Å using multiple-wavelength anomalous diffraction at the Se K edge. This protozoan protein is topologically similar to previously studied members of the phosphatidylethanolamine-binding protein (PEBP) sequence family, but exhibits a distinctive left-handed α-helical region at one side of the canonical phospholipid-binding site. Re-examination of previously determined PEBP structures suggests that the P. vivax protein and yeast carboxypeptidase Y inhibitor may represent a structurally distinct subfamily of the diverse PEBP-sequence family

  9. Defining the transmembrane helix of M2 protein from influenza A by molecular dynamics simulations in a lipid bilayer

    NARCIS (Netherlands)

    Forrest, LR; Tieleman, DP; Sansom, MSP

    Integral membrane proteins containing at least one transmembrane (TM) alpha-helix are believed to account for between 20% and 30% of most genomes. There are several algorithms that accurately predict the number and position of TM helices within,a membrane protein sequence. However, these methods

  10. Dynamic term structure models

    DEFF Research Database (Denmark)

    Andreasen, Martin Møller; Meldrum, Andrew

    This paper studies whether dynamic term structure models for US nominal bond yields should enforce the zero lower bound by a quadratic policy rate or a shadow rate specification. We address the question by estimating quadratic term structure models (QTSMs) and shadow rate models with at most four...

  11. Structures of two Arabidopsis thaliana major latex proteins represent novel helix-grip folds

    Energy Technology Data Exchange (ETDEWEB)

    Lytle, Betsy L.; Song, Jikui; de la Cruz, Norberto B.; Peterson, Francis C.; Johnson, Kenneth A.; Bingman, Craig A.; Phillips, Jr., George N.; Volkman, Brian F.; (MCW); (UW)

    2009-06-02

    Here we report the first structures of two major latex proteins (MLPs) which display unique structural differences from the canonical Bet v 1 fold described earlier. MLP28 (SwissProt/TrEMBL ID Q9SSK9), the product of gene At1g70830.1, and the At1g24000.1 gene product (Swiss- Prot/TrEMBL ID P0C0B0), proteins which share 32% sequence identity, were independently selected as foldspace targets by the Center for Eukaryotic Structural Genomics. The structure of a single domain (residues 17-173) of MLP28 was solved by NMR spectroscopy, while the full-length At1g24000.1 structure was determined by X-ray crystallography. MLP28 displays greater than 30% sequence identity to at least eight MLPs from other species. For example, the MLP28 sequence shares 64% identity to peach Pp-MLP119 and 55% identity to cucumber Csf2.20 In contrast, the At1g24000.1 sequence is highly divergent (see Fig. 1), containing a gap of 33 amino acids when compared with all other known MLPs. Even when the gap is excluded, the sequence identity with MLPs from other species is less than 30%. Unlike some of the MLPs from other species, none of the A. thaliana MLPs have been characterized biochemically. We show by NMR chemical shift mapping that At1g24000.1 binds progesterone, demonstrating that despite its sequence dissimilarity, the hydrophobic binding pocket is conserved and, therefore, may play a role in its biological function and that of the MLP family in general.

  12. Structural dynamics in FBR

    International Nuclear Information System (INIS)

    Bhoje, S.B.

    2003-01-01

    In view of thin walled large diameter shell structures with associated fluid effects, structural dynamics problems are very critical in a fast breeder reactor. Structural characteristics and consequent structural dynamics problems in typical pool type Fast Breeder Reactor are highlighted. A few important structural dynamics problems are pump induced as well as flow induced vibrations, seismic excitations, pressure transients in the intermediate heat exchangers and pipings due to a large sodium water reaction in the steam generator, and core disruptive accident loadings. The vibration problems which call for identification of excitation forces, formulation of special governing equations and detailed analysis with fluid structure interaction and sloshing effects, particularly for the components such as PSP, inner vessel, CP, CSRDM and TB are elaborated. Seismic design issues are presented in a comprehensive way. Other transient loadings which are specific to FBR, resulting from sodium-water reaction and core disruptive accident are highlighted. A few important results of theoretical as well as experimental works carried out for 500 MWe Prototype Fast Breeder Reactor (PFBR), in the domain of structural dynamics are presented. (author)

  13. Double helix vortex breakdown in a turbulent swirling annular jet flow

    Science.gov (United States)

    Vanierschot, M.; Percin, M.; van Oudheusden, B. W.

    2018-03-01

    In this paper, we report on the structure and dynamics of double helix vortex breakdown in a turbulent annular swirling jet. Double helix breakdown has been reported previously for the laminar flow regime, but this structure has rarely been observed in turbulent flow. The flow field is investigated experimentally by means of time-resolved tomographic particle image velocimetry. Notwithstanding the axisymmetric nature of the time-averaged flow, analysis of the instantaneous three-dimensional (3D) vortical structures shows the existence of a vortex core along the central axis which breaks up into a double helix downstream. The winding sense of this double helix is opposite to the swirl direction (m =-2 ) and it is wrapped around a central vortex breakdown bubble. This structure is quite different from double helix breakdown found in laminar flows where the helix is formed in the wake of the bubble and not upstream. The double helix precesses around the central axis of the jet with a precessing frequency corresponding to a Strouhal number of 0.27.

  14. Triple Helix going abroad?

    DEFF Research Database (Denmark)

    Sørensen, Olav Jull; Hu, Yimei

    2014-01-01

    The aim of the article is to explore to what extent the Tripple helix is being internationalized. Each of the helixes have their own internationalization rationale but the article show by small example that the helix itself is being internationalized and integrated with the host country tripple h...

  15. Dynamics of structures

    CERN Document Server

    Paultre, Patrick

    2013-01-01

    This book covers structural dynamics from a theoretical and algorithmic approach. It covers systems with both single and multiple degrees-of-freedom. Numerous case studies are given to provide the reader with a deeper insight into the practicalities of the area, and the solutions to these case studies are given in terms of real-time and frequency in both geometric and modal spaces. Emphasis is also given to the subject of seismic loading. The text is based on many lectures on the subject of structural dynamics given at numerous institutions and thus will be an accessible and practical aid to

  16. Structural studies of polypeptides: Mechanism of immunoglobin catalysis and helix propagation in hybrid sequence, disulfide containing peptides

    Energy Technology Data Exchange (ETDEWEB)

    Storrs, Richard Wood [Univ. of California, Berkeley, CA (United States)

    1992-08-01

    Catalytic immunoglobin fragments were studied Nuclear Magnetic Resonance spectroscopy to identify amino acid residues responsible for the catalytic activity. Small, hybrid sequence peptides were analyzed for helix propagation following covalent initiation and for activity related to the protein from which the helical sequence was derived. Hydrolysis of p-nitrophenyl carbonates and esters by specific immunoglobins is thought to involve charge complementarity. The pK of the transition state analog P-nitrophenyl phosphate bound to the immunoglobin fragment was determined by 31P-NMR to verify the juxtaposition of a positively charged amino acid to the binding/catalytic site. Optical studies of immunoglobin mediated photoreversal of cis, syn cyclobutane thymine dimers implicated tryptophan as the photosensitizing chromophore. Research shows the chemical environment of a single tryptophan residue is altered upon binding of the thymine dimer. This tryptophan residue was localized to within 20 Å of the binding site through the use of a nitroxide paramagnetic species covalently attached to the thymine dimer. A hybrid sequence peptide was synthesized based on the bee venom peptide apamin in which the helical residues of apamin were replaced with those from the recognition helix of the bacteriophage 434 repressor protein. Oxidation of the disufide bonds occured uniformly in the proper 1-11, 3-15 orientation, stabilizing the 434 sequence in an α-helix. The glycine residue stopped helix propagation. Helix propagation in 2,2,2-trifluoroethanol mixtures was investigated in a second hybrid sequence peptide using the apamin-derived disulfide scaffold and the S-peptide sequence. The helix-stop signal previously observed was not observed in the NMR NOESY spectrum. Helical connectivities were seen throughout the S-peptide sequence. The apamin/S-peptide hybrid binded to the S-protein (residues 21-166 of ribonuclease A) and reconstituted enzymatic activity.

  17. Structural studies of polypeptides: Mechanism of immunoglobin catalysis and helix propagation in hybrid sequence, disulfide containing peptides

    Energy Technology Data Exchange (ETDEWEB)

    Storrs, R.W.

    1992-08-01

    Catalytic immunoglobin fragments were studied Nuclear Magnetic Resonance spectroscopy to identify amino acid residues responsible for the catalytic activity. Small, hybrid sequence peptides were analyzed for helix propagation following covalent initiation and for activity related to the protein from which the helical sequence was derived. Hydrolysis of p-nitrophenyl carbonates and esters by specific immunoglobins is thought to involve charge complementarity. The pK of the transition state analog P-nitrophenyl phosphate bound to the immunoglobin fragment was determined by [sup 31]P-NMR to verify the juxtaposition of a positively charged amino acid to the binding/catalytic site. Optical studies of immunoglobin mediated photoreversal of cis, syn cyclobutane thymine dimers implicated tryptophan as the photosensitizing chromophore. Research shows the chemical environment of a single tryptophan residue is altered upon binding of the thymine dimer. This tryptophan residue was localized to within 20 [Angstrom] of the binding site through the use of a nitroxide paramagnetic species covalently attached to the thymine dimer. A hybrid sequence peptide was synthesized based on the bee venom peptide apamin in which the helical residues of apamin were replaced with those from the recognition helix of the bacteriophage 434 repressor protein. Oxidation of the disufide bonds occured uniformly in the proper 1-11, 3-15 orientation, stabilizing the 434 sequence in an [alpha]-helix. The glycine residue stopped helix propagation. Helix propagation in 2,2,2-trifluoroethanol mixtures was investigated in a second hybrid sequence peptide using the apamin-derived disulfide scaffold and the S-peptide sequence. The helix-stop signal previously observed was not observed in the NMR NOESY spectrum. Helical connectivities were seen throughout the S-peptide sequence. The apamin/S-peptide hybrid binded to the S-protein (residues 21-166 of ribonuclease A) and reconstituted enzymatic activity.

  18. Proteins with Novel Structure, Function and Dynamics

    Science.gov (United States)

    Pohorille, Andrew

    2014-01-01

    Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828-831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81-83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha-helix or beta-sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.

  19. Dynamic Data Structures

    DEFF Research Database (Denmark)

    Kejlberg-Rasmussen, Casper

    statements about our data structure, which are based on the structure of the underlying problem, that we are trying to solve. We can rely on the properties of the invariants when performing queries, and in return we need to ensure that the invariants remain true after we perform updates. When designing data......In this thesis I will address three dynamic data structure problems using the concept of invariants. The first problem is maintaining a dynamically changing set of keys – a dictionary – where the queries we can ask are: does it contain a given key? and what is the preceding (or succeeding) key...... to a given key? The updates we can do are: inserting a new key or deleting a given key. Our dictionary has the working set property, which means that the running time of a query depends on the query distribution. Specifically the time to search for a key depends on when we last searched for it. Our data...

  20. Effect of secondary structure on the potential of mean force for poly-L-lysine in the alpha-Helix and beta-sheet conformations

    Energy Technology Data Exchange (ETDEWEB)

    Grigsby, J.J.; Blanch, H.W.; Prausnitz, J.M.

    2001-10-30

    Because poly-L-lysine (PLL) can exist in the {alpha}-helix or {beta}-sheet conformation depending on solution preparation and solution conditions, PLL is a suitable candidate to probe the dependence of protein interactions on secondary structure. The osmotic second virial coefficient and weight-average molecular weight are reported from low-angle laser-light scattering measurements for PLL as a function of NaCl concentration, pH, and {alpha}-helix or {beta}-sheet content. Interactions between PLL molecules become more attractive as salt concentration increases due to screening of PLL charge by salt ions and at low salt concentration become more attractive as pH increases due to decreased net charge on PLL. The experimental results show that interactions are stronger for the {beta}-sheet conformation than for the {alpha}-helix conformation. A spherically-symmetric model for the potential of mean force is used to account for specific interactions not described by DLVO theory and to show how differences in secondary structure affect PLL interactions.

  1. Teaching helix and problems connected with helix using GeoGebra

    Science.gov (United States)

    Bímová, Daniela

    2017-12-01

    The contribution presents the dynamic applets created in GeoGebra that show the origin and main properties of a helix and it also presents some constructive problems connected with the helix. There are created the step by step algorithms of some constructions in the chosen applets. Three-dimensional applets include illustrative helix samples and spatial animations that help students better see problems concerning the helix spatially. There is mentioned the website in the contribution on which there is situated GeoGebra book dedicated to the topic "Helix" and containing the mentioned applets. The created applets and materials of the GeoGebra book "Helix" help in teaching and studying the course Constructive Geometry determined for the students of the Faculty of Mechanical Engineering of the Technical University of Liberec.

  2. On the helix equation

    Directory of Open Access Journals (Sweden)

    Taouil Hajer

    2012-08-01

    Full Text Available This paper is devoted to the helices processes, i.e. the solutions H : ℝ × Ω → ℝd, (t, ω ↦ H(t, ω of the helix equation egin{eqnarray} H(0,o=0; quad H(s+t,o= H(s,Phi(t,o +H(t,oonumber end{eqnarray} H ( 0 ,ω = 0 ;   H ( s + t,ω = H ( s, Φ ( t,ω + H ( t,ω where Φ : ℝ × Ω → Ω, (t, ω ↦ Φ(t, ω is a dynamical system on a measurable space (Ω, ℱ. More precisely, we investigate dominated solutions and non differentiable solutions of the helix equation. For the last case, the Wiener helix plays a fundamental role. Moreover, some relations with the cocycle equation defined by Φ, are investigated. Ce papier est consacré aux hélices, c’est-à-dire les solutions H : ℝ × Ω → ℝd, (t, ω ↦ H(t, ω de l’équation fonctionnelle egin{eqnarray} H(0,o=0; quad H(s+t,o= H(s,Phi(t,o +H(t,o onumber end{eqnarray} H ( 0 ,ω = 0 ;   H ( s + t,ω = H ( s, Φ ( t,ω + H ( t,ω où Φ : ℝ × Ω → Ω, (t, ω ↦ Φ(t, ω est un système dynamique défini sur un espace mesurable (Ω, ℱ. Plus présisément, nous déterminons d’abord les hélices dominées puis nous caractérisons les hélices non différentiables. Dans ce dernier cas, l’hélice de Wiener joue un rôle important. Nous précisons aussi quelques relations des hélices avec les cocycles définis par Φ.

  3. Field control of anisotropic spin transport and spin helix dynamics in a modulation-doped GaAs quantum well

    Science.gov (United States)

    Anghel, S.; Passmann, F.; Singh, A.; Ruppert, C.; Poshakinskiy, A. V.; Tarasenko, S. A.; Moore, J. N.; Yusa, G.; Mano, T.; Noda, T.; Li, X.; Bristow, A. D.; Betz, M.

    2018-03-01

    Electron spin transport and dynamics are investigated in a single, high-mobility, modulation-doped, GaAs quantum well using ultrafast two-color Kerr-rotation microspectroscopy, supported by qualitative kinetic theory simulations of spin diffusion and transport. Evolution of the spins is governed by the Dresselhaus bulk and Rashba structural inversion asymmetries, which manifest as an effective magnetic field that can be extracted directly from the experimental coherent spin precession. A spin-precession length λSOI is defined as one complete precession in the effective magnetic field. It is observed that application of (i) an out-of-plane electric field changes the spin decay time and λSOI through the Rashba component of the spin-orbit coupling, (ii) an in-plane magnetic field allows for extraction of the Dresselhaus and Rashba parameters, and (iii) an in-plane electric field markedly modifies both the λSOI and diffusion coefficient.

  4. Spatial attributes of the four-helix bundle group of bacteriocins – The high-resolution structure of BacSp222 in solution

    KAUST Repository

    Nowakowski, Michał

    2017-11-01

    BacSp222 is a multifunctional bacteriocin produced by Staphylococcus pseudintermedius strain 222, an opportunistic pathogen of domestic animals. At micromolar concentrations, BacSp222 kills Gram-positive bacteria and is cytotoxic toward mammalian cells, while at nanomolar doses, it acts as an immunomodulatory factor, enhancing nitric oxide release in macrophage-like cell lines. The bacteriocin is a cationic, N-terminally formylated, 50-amino-acid-long linear peptide that is rich in tryptophan residues.In this study, the solution structure of BacSp222 was determined and compared to the currently known structures of similar bacteriocins. BacSp222 was isolated from a liquid culture medium in a uniformly 13C- and 15N-labeled form, and NMR data were collected. The structure was calculated based on NMR-derived constraints and consists of a rigid and tightly packed globular bundle of four alpha-helices separated by three short turns.Although the amino acid sequence of BacSp222 has no significant similarity to any known peptide or protein, a 3D structure similarity search indicates a close relation to other four-helix bundle-motif bacteriocins, such as aureocin A53, lacticin Q and enterocins 7A/7B. Assuming similar functions, biology, structure and physicochemical properties, we propose to distinguish the four-helix bundle bacteriocins as a new Type A in subclass IId of bacteriocins, containing linear, non-pediocin-like peptides.

  5. Helix-Hopes on Finite Hyperfields

    Directory of Open Access Journals (Sweden)

    Thomas Vougiouklis

    2016-12-01

    Full Text Available Hyperstructure theory can overcome restrictions which ordinary algebraic structures have. A hyperproduct on non-square ordinary matrices can be defined by using the so called helix-hyperoperations. We study the helix-hyperstructures on the representations using ordinary fields. The related theory can be faced by defining the hyperproduct on the set of non square matrices. The main tools of the Hyperstructure Theory are the fundamental relations which connect the largest class of hyperstructures, the Hv-structures, with the corresponding classical ones. We focus on finite dimensional helix-hyperstructures and on small Hv-fields, as well.

  6. Membrane-Dependent Effects of a Cytoplasmic Helix on the Structure and Drug Binding of the Influenza Virus M2 Protein

    Science.gov (United States)

    Cady, Sarah; Wang, Tuo; Hong, Mei

    2011-01-01

    The influenza A M2 protein forms a proton channel for virus infection and also mediates virus assembly and budding. The minimum protein length that encodes both functions contains the transmembrane (TM) domain (roughly residues 22 to 46) for the amantadine-sensitive proton-channel activity and an amphipathic cytoplasmic helix (roughly residues 45 to 62) for curvature induction and virus budding. However, structural studies involving the TM domain with or without the amphipathic helix differed on the drug-binding site. Here we use solid-state NMR spectroscopy to determine the amantadine binding site in the cytoplasmic-helix-containing M2(21–61). 13C-2H distance measurements of 13C-labeled protein and 2H-labeled amantadine showed that in DMPC bilayers, the first equivalent of drug bound S31 inside the M2(21–61) pore, similar to the behavior of M2TM in DMPC bilayers. The non-specific surface site of D44 observed in M2TM is disfavored in the longer peptide. Thus, the pharmacologically relevant drug-binding site in the fully functional M2(21–61) is S31 in the TM pore. Interestingly, when M2(21–61) was reconstituted into a virus-mimetic membrane containing 30% cholesterol, no chemical shift perturbation was observed for pore-lining residues, while M2TM in the same membrane exhibited drug-induced chemical shift changes. Reduction of the cholesterol level and the use of unsaturated phospholipids shifted the conformational equilibrium of M2TM fully to the bound state, but did not rescue drug binding to M2(21–61). These results suggest that the amphipathic helix, together with cholesterol, modulates the ability of the TM helices to bind amantadine. Thus, the M2 protein interacts with the lipid membrane and small-molecule inhibitors in a complex fashion, and a careful examination of the environmental dependence of the protein conformation is required to fully understand the structure-function relation of this protein. PMID:21661724

  7. Protein Secondary Structures (α-helix and β-sheet) at a Cellular Level and Protein Fractions in Relation to Rumen Degradation Behaviours of Protein: A New Approach

    International Nuclear Information System (INIS)

    Yu, P.

    2007-01-01

    Studying the secondary structure of proteins leads to an understanding of the components that make up a whole protein, and such an understanding of the structure of the whole protein is often vital to understanding its digestive behaviour and nutritive value in animals. The main protein secondary structures are the α-helix and β-sheet. The percentage of these two structures in protein secondary structures influences protein nutritive value, quality and digestive behaviour. A high percentage of β-sheet structure may partly cause a low access to gastrointestinal digestive enzymes, which results in a low protein value. The objectives of the present study were to use advanced synchrotron-based Fourier transform IR (S-FTIR) microspectroscopy as a new approach to reveal the molecular chemistry of the protein secondary structures of feed tissues affected by heat-processing within intact tissue at a cellular level, and to quantify protein secondary structures using multicomponent peak modelling Gaussian and Lorentzian methods, in relation to protein digestive behaviours and nutritive value in the rumen, which was determined using the Cornell Net Carbohydrate Protein System. The synchrotron-based molecular chemistry research experiment was performed at the National Synchrotron Light Source at Brookhaven National Laboratory, US Department of Energy. The results showed that, with S-FTIR microspectroscopy, the molecular chemistry, ultrastructural chemical make-up and nutritive characteristics could be revealed at a high ultraspatial resolution (∼10 μm). S-FTIR microspectroscopy revealed that the secondary structure of protein differed between raw and roasted golden flaxseeds in terms of the percentages and ratio of α-helixes and β-sheets in the mid-IR range at the cellular level. By using multicomponent peak modelling, the results show that the roasting reduced (P <0.05) the percentage of α-helixes (from 47.1% to 36.1%: S-FTIR absorption intensity), increased the

  8. Protein Secondary Structures (alpha-helix and beta-sheet) at a Cellular Levle and Protein Fractions in Relation to Rumen Degradation Behaviours of Protein: A New Approach

    Energy Technology Data Exchange (ETDEWEB)

    Yu,P.

    2007-01-01

    Studying the secondary structure of proteins leads to an understanding of the components that make up a whole protein, and such an understanding of the structure of the whole protein is often vital to understanding its digestive behaviour and nutritive value in animals. The main protein secondary structures are the {alpha}-helix and {beta}-sheet. The percentage of these two structures in protein secondary structures influences protein nutritive value, quality and digestive behaviour. A high percentage of {beta}-sheet structure may partly cause a low access to gastrointestinal digestive enzymes, which results in a low protein value. The objectives of the present study were to use advanced synchrotron-based Fourier transform IR (S-FTIR) microspectroscopy as a new approach to reveal the molecular chemistry of the protein secondary structures of feed tissues affected by heat-processing within intact tissue at a cellular level, and to quantify protein secondary structures using multicomponent peak modelling Gaussian and Lorentzian methods, in relation to protein digestive behaviours and nutritive value in the rumen, which was determined using the Cornell Net Carbohydrate Protein System. The synchrotron-based molecular chemistry research experiment was performed at the National Synchrotron Light Source at Brookhaven National Laboratory, US Department of Energy. The results showed that, with S-FTIR microspectroscopy, the molecular chemistry, ultrastructural chemical make-up and nutritive characteristics could be revealed at a high ultraspatial resolution ({approx}10 {mu}m). S-FTIR microspectroscopy revealed that the secondary structure of protein differed between raw and roasted golden flaxseeds in terms of the percentages and ratio of {alpha}-helixes and {beta}-sheets in the mid-IR range at the cellular level. By using multicomponent peak modelling, the results show that the roasting reduced (P <0.05) the percentage of {alpha}-helixes (from 47.1% to 36.1%: S

  9. Nuclear Knowledge Innovations Assimilation: The Impact of Organizational Knowledge Frames and Triple Helix Dynamics of Knowledge Base

    International Nuclear Information System (INIS)

    Hossain, M. D.; Sultana, T.

    2016-01-01

    Full text: Previous research did not investigate the impact of the TH dynamics of knowledge innovations on the nuclear knowledge innovations adoption/assimilation in the organizational context. Hence, the recommendation of R&D policy reformulation seems too broad. These gaps are the prime motivators for the research. In the organizational context, we posit that TH dynamics of knowledge base innovation serves as complements to managers’ knowledge frames related to a technology innovation. We examine interactions between three knowledge frames—integration frame, opportunism frame, and policy knowledge frame, and two TH dynamics of knowledge innovations—bilateral TH dynamics of knowledge innovations and trilateral TH dynamics of knowledge innovations, and their relationship with the assimilation of nuclear knowledge innovations. We aim to research on the issues of the dynamics of knowledge base of innovations involving TH collaborations (university, industry and government) in Bangladesh as a new build nuclear project. As a result, we can find out the impact of TH collaborations on organizational nuclear knowledge innovations management as well as core institutional problems of the knowledge base of innovation systems in terms of R&D policy. Finally, findings identify lack in production of nuclear knowledge innovations and concrete recommendation of R&D policy reformulation. (author

  10. Distributed Dynamic Condition Response Structures

    DEFF Research Database (Denmark)

    Hildebrandt, Thomas; Mukkamala, Raghava Rao

    We present distributed dynamic condition response structures as a declarative process model inspired by the workflow language employed by our industrial partner and conservatively generalizing labelled event structures. The model adds to event structures the possibility to 1) finitely specify...... as a labelled transition system. Exploration of the relationship between dynamic condition response structures and traditional models for concurrency, application to more complex scenarios, and further extensions of the model is left to future work....

  11. Structural dynamic modification

    Indian Academy of Sciences (India)

    and stiffness matrices) andaor modal parameters, in order to acquire some ... For the above reasons, another modification approach is presented here ... The data necessary to solve the direct problem are dynamic behaviour of the original.

  12. Dynamic testing of cable structures

    Directory of Open Access Journals (Sweden)

    Caetano Elsa

    2015-01-01

    Full Text Available The paper discusses the role of dynamic testing in the study of cable structures. In this context, the identification of cable force based on vibration measurements is discussed. Vibration and damping assessment are then introduced as the focus of dynamic monitoring systems, and particular aspects of the structural behaviour under environmental loads are analysed. Diverse application results are presented to support the discussion centred on cable-stayed bridges, roof structures, a guyed mast and a transmission line.

  13. Designing cooperatively folded abiotic uni- and multimolecular helix bundles

    Science.gov (United States)

    de, Soumen; Chi, Bo; Granier, Thierry; Qi, Ting; Maurizot, Victor; Huc, Ivan

    2018-01-01

    Abiotic foldamers, that is foldamers that have backbones chemically remote from peptidic and nucleotidic skeletons, may give access to shapes and functions different to those of peptides and nucleotides. However, design methodologies towards abiotic tertiary and quaternary structures are yet to be developed. Here we report rationally designed interactional patterns to guide the folding and assembly of abiotic helix bundles. Computational design facilitated the introduction of hydrogen-bonding functionalities at defined locations on the aromatic amide backbones that promote cooperative folding into helix-turn-helix motifs in organic solvents. The hydrogen-bond-directed aggregation of helices not linked by a turn unit produced several thermodynamically and kinetically stable homochiral dimeric and trimeric bundles with structures that are distinct from the designed helix-turn-helix. Relative helix orientation within the bundles may be changed from parallel to tilted on subtle solvent variations. Altogether, these results prefigure the richness and uniqueness of abiotic tertiary structure behaviour.

  14. Double-helix stellarator

    International Nuclear Information System (INIS)

    Moroz, P.E.

    1997-09-01

    A new stellarator configuration, the Double-Helix Stellarator (DHS), is introduced. This novel configuration features a double-helix center post as the only helical element of the stellarator coil system. The DHS configuration has many unique characteristics. One of them is the extreme low plasma aspect ratio, A ∼ 1--1.2. Other advantages include a high enclosed volume, appreciable rotational transform, and a possibility of extreme-high-β MHD equilibria. Moreover, the DHS features improved transport characteristics caused by the absence of the magnetic field ripple on the outboard of the torus. Compactness, simplicity and modularity of the coil system add to the DHS advantages for fusion applications

  15. Structural dynamic modifications via models

    Indian Academy of Sciences (India)

    The study shows that as many as half of the matrix ... the dynamicist's analytical modelling skill which would appear both in the numerator as. Figure 2. ..... Brandon J A 1990 Strategies for structural dynamic modification (New York: John Wiley).

  16. Dynamics test on structures

    International Nuclear Information System (INIS)

    De Canio, G.; Ranieri, N.

    2009-01-01

    Shake table tests allow to assess the effectiveness of technologies for structures protection from natural events such as earthquakes. The article summarizes the remarkable results of the most significant projects. [it

  17. Structural Dynamics, Vol. 3

    DEFF Research Database (Denmark)

    Nielsen, Søren R.K.

    The present textbook has been written for a course on stochastic vibration theory that is being given on the 9th semester at Aalborg University for M.Sc. students in structural engineering.......The present textbook has been written for a course on stochastic vibration theory that is being given on the 9th semester at Aalborg University for M.Sc. students in structural engineering....

  18. Dynamic Data Structures

    DEFF Research Database (Denmark)

    Tsakalidis, Konstantinos

    multi-versioned indexing database. We first present a generic method for making data structures fully persistent in external memory. This method can render any database multi-versioned, as long as its implementation abides by our assumptions. We obtain the result by presenting an implementation of B...

  19. Lysine as helix C-capping residue in a synthetic peptide.

    Science.gov (United States)

    Esposito, G; Dhanapal, B; Dumy, P; Varma, V; Mutter, M; Bodenhausen, G

    1997-01-01

    The structure of the synthetic peptide CH3CO(Leu-Ser-Leu-Leu-Leu-Ser-Leu)3Lys-NH2 in trifluoroethanol/water 60/40 (volume ratio) was characterized by two-dimensional nmr spectroscopy. The peptide, closely related to the amphiphilic helix models designed by W. F. De-Grado and co-workers to mimic protein ion channels [(1988) Science, Vol. 240, p. 1177-1181], folds into a regular helix spanning residues 1-20. Evidence for a helix C-terminal capping conformation, involving the terminal lysine residue, was observed from Overhauser effects and checked for consistency by restrained molecular dynamics simulations. The side-chain amino group of Lys22 forms a hydrogen bond with the carbonyl of Leu18, and the distorted helical geometry of the terminal dipeptide allows the inclusion of a water bridge between the backbone NH of the Lys22 residue and the carbonyls of Leu19 and Ser20.

  20. Foams structure and dynamics

    CERN Document Server

    Cantat, Isabelle; Graner, François; Pitois, Olivier; Höhler, Reinard; Elias, Florence; Saint-Jalmes, Arnaud; Rouyer, Florence

    2013-01-01

    This book is the first to provide a thorough description of all aspects of the physico-chemical properties of foams. It sets out what is known about their structure, their stability, and their rheology. Engineers, researchers and students will find descriptions of all the key concepts, illustrated by numerous applications, as well as experiments and exercises for the reader. A solutions manual for lecturers is available via the publisher's web site.

  1. Solution NMR and molecular dynamics reveal a persistent alpha helix within the dynamic region of PsbQ from photosystem II of higher plants

    Czech Academy of Sciences Publication Activity Database

    Rathner, P.; Rathner, A.; Horničáková, M.; Wohlschlager, Ch.; Chandra, K.; Kohoutová, Jaroslava; Ettrich, Rüdiger; Wimmer, R.; Müller, N.

    2015-01-01

    Roč. 83, č. 9 (2015), s. 1677-1686 ISSN 0887-3585 Institutional support: RVO:61388971 Keywords : dynamic N-terminus * extrinsic photosynthetic protein * hydrogen bond dynamics Subject RIV: EE - Microbiology, Virology Impact factor: 2.499, year: 2015

  2. Lasing thresholds of helical photonic structures with different positions of a single light-amplifying helix turn

    Energy Technology Data Exchange (ETDEWEB)

    Blinov, L M; Palto, S P [A.V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Moscow, Russian Federaion (Russian Federation)

    2013-09-30

    Numerical simulation is used to assess the lasing threshold of helical structures of cholesteric liquid crystals (CLCs) in which only one turn amplifies light. This turn is located either in the centre of symmetric structures of various sizes or in an arbitrary place in asymmetric structures of preset size. In all cases, we find singularities in light amplification by a one-dimensional CLC structure for the most important band-edge modes (m1, m2 and m3) and plot the threshold gain coefficient k{sub th} against the position of the amplifying turn. For the symmetric structures, the lasing threshold of the m1 mode is shown to vary linearly with the inverse of the square of the cavity length. Moreover, modes with a lower density of photonic states (DOS) in the cavity may have a lower lasing threshold. This can be accounted for by the dependence of the density of photonic states on the position of the amplifying turn and, accordingly, by the nonuniform electromagnetic field intensity distribution along the cavity for different modes. In the asymmetric structures, the same field energy distribution is responsible for a correlation between k{sub th} and DOS curves. (lasers)

  3. Coherent structures and dynamical systems

    Science.gov (United States)

    Jimenez, Javier

    1987-01-01

    Any flow of a viscous fluid has a finite number of degrees of freedom, and can therefore be seen as a dynamical system. A coherent structure can be thought of as a lower dimensional manifold in whose neighborhood the dynamical system spends a substantial fraction of its time. If such a manifold exists, and if its dimensionality is substantially lower that that of the full flow, it is conceivable that the flow could be described in terms of the reduced set of degrees of freedom, and that such a description would be simpler than one in which the existence of structure was not recognized. Several examples are briefly summarized.

  4. Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix.

    Science.gov (United States)

    Pley, H W; Flaherty, K M; McKay, D B

    1994-11-03

    In large structured RNAs, RNA hairpins in which the strands of the duplex stem are connected by a tetraloop of the consensus sequence 5'-GNRA (where N is any nucleotide, and R is either G or A) are unusually frequent. In group I introns there is a covariation in sequence between nucleotides in the third and fourth positions of the loop with specific distant base pairs in putative RNA duplex stems: GNAA loops correlate with successive 5'-C-C.G-C base pairs in stems, whereas GNGA loops correlate with 5'-C-U.G-A. This has led to the suggestion that GNRA tetraloops may be involved in specific long-range tertiary interactions, with each A in position 3 or 4 of the loop interacting with a C-G base pair in the duplex, and G in position 3 interacting with a U-A base pair. This idea is supported experimentally for the GAAA loop of the P5b extension of the group I intron of Tetrahymena thermophila and the L9 GUGA terminal loop of the td intron of bacteriophage T4 (ref. 4). NMR has revealed the overall structure of the tetraloop for 12-nucleotide hairpins with GCAA and GAAA loops and models have been proposed for the interaction of GNRA tetraloops with base pairs in the minor groove of A-form RNA. Here we describe the crystal structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. The interactions we observe correlate with the specificity of GNRA tetraloops inferred from phylogenetic studies, suggesting that this complex is a legitimate model for intramolecular tertiary interactions mediated by GNRA tetraloops in large structured RNAs.

  5. DNA-like double helix formed by peptide nucleic acid

    DEFF Research Database (Denmark)

    Wittung, P; Nielsen, Peter E.; Buchardt, O

    1994-01-01

    Although the importance of the nucleobases in the DNA double helix is well understood, the evolutionary significance of the deoxyribose phosphate backbone and the contribution of this chemical entity to the overall helical structure and stability of the double helix is not so clear. Peptide nucleic...

  6. Relating structure and dynamics in organisation models

    NARCIS (Netherlands)

    Jonkers, C.M.; Treur, J.

    2002-01-01

    To understand how an organisational structure relates to dynamics is an interesting fundamental challenge in the area of social modelling. Specifications of organisational structure usually have a diagrammatic form that abstracts from more detailed dynamics. Dynamic properties of agent systems,

  7. Noncanonical structures and their thermodynamics of DNA and RNA under molecular crowding: beyond the Watson-Crick double helix.

    Science.gov (United States)

    Sugimoto, Naoki

    2014-01-01

    How does molecular crowding affect the stability of nucleic acid structures inside cells? Water is the major solvent component in living cells, and the properties of water in the highly crowded media inside cells differ from that in buffered solution. As it is difficult to measure the thermodynamic behavior of nucleic acids in cells directly and quantitatively, we recently developed a cell-mimicking system using cosolutes as crowding reagents. The influences of molecular crowding on the structures and thermodynamics of various nucleic acid sequences have been reported. In this chapter, we discuss how the structures and thermodynamic properties of nucleic acids differ under various conditions such as highly crowded environments, compartment environments, and in the presence of ionic liquids, and the major determinants of the crowding effects on nucleic acids are discussed. The effects of molecular crowding on the activities of ribozymes and riboswitches on noncanonical structures of DNA- and RNA-like quadruplexes that play important roles in transcription and translation are also described. © 2014 Elsevier Inc. All rights reserved.

  8. Static and Dynamic Membrane Structures

    Directory of Open Access Journals (Sweden)

    Sergiu Ivanov

    2012-10-01

    Full Text Available While originally P systems were defined to contain multiset rewriting rules, it turned out that considering different types of rules may produce important results, such as increasing the computational power of the rules. This paper focuses on factoring out the concept of a membrane structure out of various P system models with the goal of providing useful formalisations. Both static and dynamic membrane structures are considered.

  9. FMRFamide receptors of Helix aspersa

    International Nuclear Information System (INIS)

    Payza, K.

    1988-01-01

    A receptor binding assay and an isolated heart bioassay were used to identify and characterize the FMRFamide receptors in Helix. In the heart bioassay, FMRFamide increased myocardial contraction force. A potent FMRFamide analog, desaminoTyr-Phe-norLeu-arg-Phe-amide (daYFnLRFamide), was used as a radioiodinated receptor ligand. The high affinity binding of 125 I-daYFnLRFamide at 0 degree C to Helix brain membranes was reversible, saturable, pH-dependent and specific, with a K D of 13-14 nM. A lower affinity (245 nM) site was also observed. Radioligand binding sites were also identified in the heart, male reproductive organs and digestive organs. The structure-activity relations (SAR) of cardiostimulation correlated with the specificity of 125 I-daYFnLRFamide binding to brain and heart receptors. The SAR were similar to those of other molluscan FMRFamide bioassays, except that they showed a marked preference for some analogs with blocked amino-terminals

  10. Structural system identification: Structural dynamics model validation

    Energy Technology Data Exchange (ETDEWEB)

    Red-Horse, J.R.

    1997-04-01

    Structural system identification is concerned with the development of systematic procedures and tools for developing predictive analytical models based on a physical structure`s dynamic response characteristics. It is a multidisciplinary process that involves the ability (1) to define high fidelity physics-based analysis models, (2) to acquire accurate test-derived information for physical specimens using diagnostic experiments, (3) to validate the numerical simulation model by reconciling differences that inevitably exist between the analysis model and the experimental data, and (4) to quantify uncertainties in the final system models and subsequent numerical simulations. The goal of this project was to develop structural system identification techniques and software suitable for both research and production applications in code and model validation.

  11. Analysis of Nonlinear Dynamic Structures

    African Journals Online (AJOL)

    Bheema

    work a two degrees of freedom nonlinear system with zero memory was ... FRF is the most widely used method in structural dynamics which gives information about the ..... 3.6, which is the waterfall diagram of the same response, as well.

  12. Different secondary structure elements as scaffolds for protein folding transition states of two homologous four-helix bundles.

    Science.gov (United States)

    Teilum, Kaare; Thormann, Thorsten; Caterer, Nigel R; Poulsen, Heidi I; Jensen, Peter H; Knudsen, Jens; Kragelund, Birthe B; Poulsen, Flemming M

    2005-04-01

    Comparison of the folding processes for homologue proteins can provide valuable information about details in the interactions leading to the formation of the folding transition state. Here the folding kinetics of 18 variants of yACBP and 3 variants of bACBP have been studied by Phi-value analysis. In combination with Phi-values from previous work, detailed insight into the transition states for folding of both yACBP and bACBP has been obtained. Of the 16 sequence positions that have been studied in both yACBP and bACBP, 5 (V12, I/L27, Y73, V77, and L80) have high Phi-values and appear to be important for the transition state formation in both homologues. Y31, A34, and A69 have high Phi-values only in yACBP, while F5, A9, and I74 have high Phi-values only in bACBP. Thus, additional interactions between helices A2 and A4 appear to be important for the transition state of yACBP, whereas additional interactions between helices A1 and A4 appear to be important for the transition state of bACBP. To examine whether these differences could be assigned to different packing of the residues in the native state, a solution structure of yACBP was determined by NMR. Small changes in the packing of the hydrophobic side-chains, which strengthen the interactions between helices A2 and A4, are observed in yACBP relative to bACBP. It is suggested that different structure elements serve as scaffolds for the folding of the 2 ACBP homologues. (c) 2005 Wiley-Liss, Inc.

  13. Efficient Fatigue Analysis of Helix Elements in Umbilicals and Flexible Risers: Theory and Applications

    Directory of Open Access Journals (Sweden)

    Geir Skeie

    2012-01-01

    Full Text Available Fatigue analysis of structural components such as helix tensile armors and steel tubes is a critical design issue for dynamic umbilicals and flexible pipes. The basis for assessment of fatigue damage of such elements is the long-term stress cycle distribution at critical locations on the helix elements caused by long-term environmental loading on the system. The long-term stress cycle distribution will hence require global dynamic time domain analysis followed by a detailed cross-sectional analysis in a large number of irregular sea states. An overall computational consistent and efficient fatigue analysis scheme is outlined with due regard of the cross-sectional analysis technique required for fatigue stress calculation with particular attention to the helix elements. The global cross-section is exposed to pure bending, tensile, torsion, and pressure loading. The state of the different cross-section elements is based on the global response. Special emphasis is placed on assessment of friction stresses caused by the stick-slip behavior of helix elements in bending that are of special importance for fatigue life assessments. The described cross-sectional analysis techniques are based on an extensive literature survey and are hence considered to represent industry consensus. The performance of the described calculation scheme is illustrated by case studies.

  14. Dynamic Soil-Structure-Interaction

    DEFF Research Database (Denmark)

    Kellezi, Lindita

    1998-01-01

    The aim of this thesis is to investigate and develop alternative methods of analyzing problems in dynamic soil-structure-interaction. The main focus is the major difficulty posed by such an analysis - the phenomenon of waves which radiate outward from the excited structures towards infinity....... In numerical calculations, only a finite region of the foundation metium is analyzed and something is done to prevent the outgoing radiating waves to reflect from the regions's boundary. The prosent work concerns itself with the study of such effects, using the finite element method, and artificial...... transmitting boundary at the edges of the computational mesh. To start with, an investigation of the main effects of the interaction phenomena is carried out employing a widely used model, considering dynamic stiffness of the unbounded soil as frequency independent. Then a complete description...

  15. Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A.

    Science.gov (United States)

    Sathyamoorthy, Bharathwaj; Shi, Honglue; Zhou, Huiqing; Xue, Yi; Rangadurai, Atul; Merriman, Dawn K; Al-Hashimi, Hashim M

    2017-05-19

    In the canonical DNA double helix, Watson-Crick (WC) base pairs (bps) exist in dynamic equilibrium with sparsely populated (∼0.02-0.4%) and short-lived (lifetimes ∼0.2-2.5 ms) Hoogsteen (HG) bps. To gain insights into transient HG bps, we used solution-state nuclear magnetic resonance spectroscopy, including measurements of residual dipolar couplings and molecular dynamics simulations, to examine how a single HG bp trapped using the N1-methylated adenine (m1A) lesion affects the structural and dynamic properties of two duplexes. The solution structure and dynamic ensembles of the duplexes reveals that in both cases, m1A forms a m1A•T HG bp, which is accompanied by local and global structural and dynamic perturbations in the double helix. These include a bias toward the BI backbone conformation; sugar repuckering, major-groove directed kinking (∼9°); and local melting of neighboring WC bps. These results provide atomic insights into WC/HG breathing dynamics in unmodified DNA duplexes as well as identify structural and dynamic signatures that could play roles in m1A recognition and repair. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. Insights into Watson–Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A

    Science.gov (United States)

    Sathyamoorthy, Bharathwaj; Shi, Honglue; Zhou, Huiqing; Xue, Yi; Rangadurai, Atul; Merriman, Dawn K.

    2017-01-01

    Abstract In the canonical DNA double helix, Watson–Crick (WC) base pairs (bps) exist in dynamic equilibrium with sparsely populated (∼0.02–0.4%) and short-lived (lifetimes ∼0.2–2.5 ms) Hoogsteen (HG) bps. To gain insights into transient HG bps, we used solution-state nuclear magnetic resonance spectroscopy, including measurements of residual dipolar couplings and molecular dynamics simulations, to examine how a single HG bp trapped using the N1-methylated adenine (m1A) lesion affects the structural and dynamic properties of two duplexes. The solution structure and dynamic ensembles of the duplexes reveals that in both cases, m1A forms a m1A•T HG bp, which is accompanied by local and global structural and dynamic perturbations in the double helix. These include a bias toward the BI backbone conformation; sugar repuckering, major-groove directed kinking (∼9°); and local melting of neighboring WC bps. These results provide atomic insights into WC/HG breathing dynamics in unmodified DNA duplexes as well as identify structural and dynamic signatures that could play roles in m1A recognition and repair. PMID:28369571

  17. Three-dimensional structure and dynamics of wine tannin-saliva protein complexes. A multitechnique approach.

    Science.gov (United States)

    Simon, Cécile; Barathieu, Karine; Laguerre, Michel; Schmitter, Jean-Marie; Fouquet, Eric; Pianet, Isabelle; Dufourc, Erick J

    2003-09-09

    The interactions between the B3 (catechin-4alpha,8-catechin) red wine tannin and the human salivary protein fragment IB7(14) (SPPGKPQGPPPQGG) were monitored by (1)H magic angle spinning NMR, circular dichroism, electrospray ionization mass spectrometry, and molecular modeling. It is found that the secondary structure of IB7(14) is made of a type II helix (collagen helix) and random coil. The central glycine 8 appears to act as a flexible rotula separating two helix II regions. Three tannin molecules tightly complex the peptide, without modifying its secondary structure, but seem to reduce its conformational dynamics. The binding dissociation constant is in the millimolar range. B3 tannins with a "tweezers" conformation bind to the hydrophilic side of the saliva peptide, suggesting that the principal driving forces toward association are governed by hydrogen bonding between the carbonyl functions of proline residues and both the phenol and catechol OH groups. These findings are further discussed in the frame of an astringency phenomenon.

  18. Dynamics of Quantum Causal Structures

    Science.gov (United States)

    Castro-Ruiz, Esteban; Giacomini, Flaminia; Brukner, Časlav

    2018-01-01

    It was recently suggested that causal structures are both dynamical, because of general relativity, and indefinite, because of quantum theory. The process matrix formalism furnishes a framework for quantum mechanics on indefinite causal structures, where the order between operations of local laboratories is not definite (e.g., one cannot say whether operation in laboratory A occurs before or after operation in laboratory B ). Here, we develop a framework for "dynamics of causal structures," i.e., for transformations of process matrices into process matrices. We show that, under continuous and reversible transformations, the causal order between operations is always preserved. However, the causal order between a subset of operations can be changed under continuous yet nonreversible transformations. An explicit example is that of the quantum switch, where a party in the past affects the causal order of operations of future parties, leading to a transition from a channel from A to B , via superposition of causal orders, to a channel from B to A . We generalize our framework to construct a hierarchy of quantum maps based on transformations of process matrices and transformations thereof.

  19. Dynamics of Quantum Causal Structures

    Directory of Open Access Journals (Sweden)

    Esteban Castro-Ruiz

    2018-03-01

    Full Text Available It was recently suggested that causal structures are both dynamical, because of general relativity, and indefinite, because of quantum theory. The process matrix formalism furnishes a framework for quantum mechanics on indefinite causal structures, where the order between operations of local laboratories is not definite (e.g., one cannot say whether operation in laboratory A occurs before or after operation in laboratory B. Here, we develop a framework for “dynamics of causal structures,” i.e., for transformations of process matrices into process matrices. We show that, under continuous and reversible transformations, the causal order between operations is always preserved. However, the causal order between a subset of operations can be changed under continuous yet nonreversible transformations. An explicit example is that of the quantum switch, where a party in the past affects the causal order of operations of future parties, leading to a transition from a channel from A to B, via superposition of causal orders, to a channel from B to A. We generalize our framework to construct a hierarchy of quantum maps based on transformations of process matrices and transformations thereof.

  20. Controlling chirality with helix inversion in cholesteric liquid crystals

    NARCIS (Netherlands)

    Katsonis, Nathalie Hélène; Lacaze, E.; Ferrarini, A.

    2012-01-01

    The helical organization of cholesteric liquid crystals is omnipresent in living matter. Achieving control over the structure of the cholesteric helix consequently holds great potential for developing stimuli-responsive materials matching the level of sophistication of biological systems. In

  1. Structure and dynamics of solutions

    CERN Document Server

    Ohtaki, H

    2013-01-01

    Recent advances in the study of structural and dynamic properties of solutions have provided a molecular picture of solute-solvent interactions. Although the study of thermodynamic as well as electronic properties of solutions have played a role in the development of research on the rate and mechanism of chemical reactions, such macroscopic and microscopic properties are insufficient for a deeper understanding of fast chemical and biological reactions. In order to fill the gap between the two extremes, it is necessary to know how molecules are arranged in solution and how they change their pos

  2. Sierra Structural Dynamics Theory Manual

    Energy Technology Data Exchange (ETDEWEB)

    Reese, Garth M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-10-19

    Sierra/SD provides a massively parallel implementation of structural dynamics finite element analysis, required for high fidelity, validated models used in modal, vibration, static and shock analysis of structural systems. This manual describes the theory behind many of the constructs in Sierra/SD. For a more detailed description of how to use Sierra/SD , we refer the reader to Sierra/SD, User's Notes . Many of the constructs in Sierra/SD are pulled directly from published material. Where possible, these materials are referenced herein. However, certain functions in Sierra/SD are specific to our implementation. We try to be far more complete in those areas. The theory manual was developed from several sources including general notes, a programmer notes manual, the user's notes and of course the material in the open literature. This page intentionally left blank.

  3. Dynamic analysis of embedded structures

    International Nuclear Information System (INIS)

    Kausel, E.; Whitman, R.V.; Morray, J.P.

    1977-01-01

    The paper presents simplified rules to account for embeddment and soil layering in the soil-structure interaction problem, to be used in dynamic analysis. The relationship between the spring method, and a direct solution (in which both soil and structure are modeled with finite elements and linear members) is first presented. It is shown that for consistency of the results with the two solution methods the spring method should be performed in the following three steps: 1. Determination of the motion of the massless foundation (having the same shape as the actual one) when subjected to the same input motion as the direct solution. 2. Determination of the frequency dependent subgrade stiffness for the relevant degrees of freedom. 3. Computations of the response of the real structure supported on frequency dependent soil springs and subjected at the base of these springs to the motion computed in step 1. The first two steps require, in general, finite element methods, which would make the procedure not attractive. It is shown in the paper, however, that excellent approximations can be obtained, on the basis of 1-dimensional wave propagation theory for the solution of step 1, and correction factors modifying for embeddment the corresponding springs of a surface footing on a layered stratum, for the solution of step 2. (Auth.)

  4. Unfolding four-helix bundles

    Science.gov (United States)

    Gray, Harry B.; Winkler, Jay R.; Kozak, John J.

    2011-03-01

    A geometrical model has been developed to describe the early stages of unfolding of cytochromes c‧ and c-b562 . Calculations are based on a step-wise extension of the polypeptide chain subject to the constraint that the spatial relationship among the residues of each triplet is fixed by the native-state crystallographic data. The response of each protein to these structural perturbations allows the evolution of each of the four helices in these two proteins to be differentiated. It is found that the two external helices in c‧ unfold before its two internal helices, whereas exactly the opposite behaviour is demonstrated by c-b562 . Each of these cytochromes has an extended, internal, non-helical ('turning') region that initially lags behind the most labile helix but then, at a certain stage (identified for each cytochrome), unravels before any of the four helices present in the native structure. It is believed that these predictions will be useful in guiding future experimental studies on the unfolding of these two cytochromes.

  5. Dynamic buckling of inelastic structures

    International Nuclear Information System (INIS)

    Pegon, P.; Guelin, P.

    1983-01-01

    The aim of this paper is to provide research engineers with a method of approach, qualitative feature and order of magnitude of the relevant parameters in the field of dynamic buckling of structures exhibiting constitutive irreversibility and geometrical, constitutive or loading imperfections. It is difficult to adjust some of the classical analysis of the quasi-static elastic case. There remain also some difficulties in justifying the choice of constitutive schemes and in dealing with general kinematic formulation. Moreover, the interpretation of dynamical experimental data is not an easy matter. Consequently, the attempts described here use a simple symbolic model including all essential physical aspects. This symbolic model, of discrete character, is an n-hinged strut with masses located at each n+1 joint. The constitutive properties of the strut and hinge are defined using the same method: a dash-pot is in parallel with a two fold element (spring and friction-slider in series). The intrinsic restrictions are: the two dimensionality assumption, however no additional hypothesis are made concerning the kinematic of the constitutive elements; the use of simple sources of intrinsic dissipation. The relevant question of the longitudinal-transverse coupling effects is studied. Then, after various validation, we verify that a Lagrange resolution of this n+1 body problem gives physical relevant qualitative results concerning rods and cylindrical shells subjected to impact loading. (orig./RW)

  6. Relating structure and dynamics in organisation models

    NARCIS (Netherlands)

    Jonker, C.M.; Treur, J.

    2003-01-01

    To understand how an organisational structure relates to dynamics is an interesting fundamental challenge in the area of social modelling. Specifications of organisational structure usually have a diagrammatic form that abstracts from more detailed dynamics. Dynamic properties of agent systems, on

  7. Langevin dynamics for ramified structures

    Science.gov (United States)

    Méndez, Vicenç; Iomin, Alexander; Horsthemke, Werner; Campos, Daniel

    2017-06-01

    We propose a generalized Langevin formalism to describe transport in combs and similar ramified structures. Our approach consists of a Langevin equation without drift for the motion along the backbone. The motion along the secondary branches may be described either by a Langevin equation or by other types of random processes. The mean square displacement (MSD) along the backbone characterizes the transport through the ramified structure. We derive a general analytical expression for this observable in terms of the probability distribution function of the motion along the secondary branches. We apply our result to various types of motion along the secondary branches of finite or infinite length, such as subdiffusion, superdiffusion, and Langevin dynamics with colored Gaussian noise and with non-Gaussian white noise. Monte Carlo simulations show excellent agreement with the analytical results. The MSD for the case of Gaussian noise is shown to be independent of the noise color. We conclude by generalizing our analytical expression for the MSD to the case where each secondary branch is n dimensional.

  8. Hydrated and Dehydrated Tertiary Interactions–Opening and Closing–of a Four-Helix Bundle Peptide

    Science.gov (United States)

    Lignell, Martin; Tegler, Lotta T.; Becker, Hans-Christian

    2009-01-01

    Abstract The structural heterogeneity and thermal denaturation of a dansyl-labeled four-helix bundle homodimeric peptide was studied with steady-state and time-resolved fluorescence spectroscopy and with circular dichroism (CD). At room temperature the fluorescence decay of the polarity-sensitive dansyl, located in the hydrophobic core region, can be described by a broad distribution of fluorescence lifetimes, reflecting the heterogeneous microenvironment. However, the lifetime distribution is nearly bimodal, which we ascribe to the presence of two major conformational subgroups. Since the fluorescence lifetime reflects the water content of the four-helix bundle conformations, we can use the lifetime analysis to monitor the change in hydration state of the hydrophobic core of the four-helix bundle. Increasing the temperature from 9°C to 23°C leads to an increased population of molten-globule-like conformations with a less ordered helical backbone structure. The fluorescence emission maximum remains constant in this temperature interval, and the hydrophobic core is not strongly affected. Above 30°C the structural dynamics involve transient openings of the four-helix bundle structure, as evidenced by the emergence of a water-quenched component and less negative CD. Above 60°C the homodimer starts to dissociate, as shown by the increasing loss of CD and narrow, short-lived fluorescence lifetime distributions. PMID:19619472

  9. Modeling of arylamide helix mimetics in the p53 peptide binding site of hDM2 suggests parallel and anti-parallel conformations are both stable.

    Directory of Open Access Journals (Sweden)

    Jonathan C Fuller

    Full Text Available The design of novel α-helix mimetic inhibitors of protein-protein interactions is of interest to pharmaceuticals and chemical genetics researchers as these inhibitors provide a chemical scaffold presenting side chains in the same geometry as an α-helix. This conformational arrangement allows the design of high affinity inhibitors mimicking known peptide sequences binding specific protein substrates. We show that GAFF and AutoDock potentials do not properly capture the conformational preferences of α-helix mimetics based on arylamide oligomers and identify alternate parameters matching solution NMR data and suitable for molecular dynamics simulation of arylamide compounds. Results from both docking and molecular dynamics simulations are consistent with the arylamides binding in the p53 peptide binding pocket. Simulations of arylamides in the p53 binding pocket of hDM2 are consistent with binding, exhibiting similar structural dynamics in the pocket as simulations of known hDM2 binders Nutlin-2 and a benzodiazepinedione compound. Arylamide conformations converge towards the same region of the binding pocket on the 20 ns time scale, and most, though not all dihedrals in the binding pocket are well sampled on this timescale. We show that there are two putative classes of binding modes for arylamide compounds supported equally by the modeling evidence. In the first, the arylamide compound lies parallel to the observed p53 helix. In the second class, not previously identified or proposed, the arylamide compound lies anti-parallel to the p53 helix.

  10. Structural Dynamics Control Allosteric Activation of Cytohesin Family Arf GTPase Exchange Factors

    Energy Technology Data Exchange (ETDEWEB)

    Malaby, Andrew W.; Das, Sanchaita; Chakravarthy, Srinivas; Irving, Thomas C.; Bilsel, Osman; Lambright, David G.

    2018-01-01

    Membrane dynamic processes including vesicle biogenesis depend on Arf guanosine triphosphatase (GTPase) activation by guanine nucleotide exchange factors (GEFs) containing a catalytic Sec7 domain and a membrane-targeting module such as a pleckstrin homology (PH) domain. The catalytic output of cytohesin family Arf GEFs is controlled by autoinhibitory interactions that impede accessibility of the exchange site in the Sec7 domain. These restraints can be relieved through activator Arf-GTP binding to an allosteric site comprising the PH domain and proximal autoinhibitory elements (Sec7-PH linker and C-terminal helix). Small-angle X-ray scattering and negative-stain electron microscopy were used to investigate the structural organization and conformational dynamics of cytohesin-3 (Grp1) in autoinhibited and active states. The results support a model in which hinge dynamics in the autoinhibited state expose the activator site for Arf-GTP binding, while subsequent C-terminal helix unlatching and repositioning unleash conformational entropy in the Sec7-PH linker to drive exposure of the exchange site.

  11. A Classification of Basic Helix-Loop-Helix Transcription Factors of Soybean

    Directory of Open Access Journals (Sweden)

    Karen A. Hudson

    2015-01-01

    Full Text Available The complete genome sequence of soybean allows an unprecedented opportunity for the discovery of the genes controlling important traits. In particular, the potential functions of regulatory genes are a priority for analysis. The basic helix-loop-helix (bHLH family of transcription factors is known to be involved in controlling a wide range of systems critical for crop adaptation and quality, including photosynthesis, light signalling, pigment biosynthesis, and seed pod development. Using a hidden Markov model search algorithm, 319 genes with basic helix-loop-helix transcription factor domains were identified within the soybean genome sequence. These were classified with respect to their predicted DNA binding potential, intron/exon structure, and the phylogeny of the bHLH domain. Evidence is presented that the vast majority (281 of these 319 soybean bHLH genes are expressed at the mRNA level. Of these soybean bHLH genes, 67% were found to exist in two or more homeologous copies. This dataset provides a framework for future studies on bHLH gene function in soybean. The challenge for future research remains to define functions for the bHLH factors encoded in the soybean genome, which may allow greater flexibility for genetic selection of growth and environmental adaptation in this widely grown crop.

  12. Dynamic analysis and design of offshore structures

    CERN Document Server

    Chandrasekaran, Srinivasan

    2015-01-01

    This book  attempts to provide readers with an overall idea of various types of offshore platform geometries. It covers the various environmental loads encountered by these structures, a detailed description of the fundamentals of structural dynamics in a class-room style, estimate of damping in offshore structures and their applications in the preliminary analysis and design. Basic concepts of structural dynamics are emphasized through simple illustrative examples and exercises. Design methodologies and guidelines, which are FORM based concepts are explained through a few applied example structures. Each chapter also has tutorials and exercises for self-learning. A dedicated chapter on stochastic dynamics will help the students to extend the basic concepts of structural dynamics to this advanced domain of research. Hydrodynamic response of offshore structures with perforated members is one of the recent research applications, which is found to be one of the effective manner of retrofitting offshore structur...

  13. Relating the variation of secondary structure of gelatin at fish oil-water interface to adsorption kinetics, dynamic interfacial tension and emulsion stability.

    Science.gov (United States)

    Liu, Huihua; Wang, Bo; Barrow, Colin J; Adhikari, Benu

    2014-01-15

    The objectives of this study were to quantify the relationship between secondary structure of gelatin and its adsorption at the fish-oil/water interface and to quantify the implication of the adsorption on the dynamic interfacial tension (DST) and emulsion stability. The surface hydrophobicity of the gelatin solutions decreased when the pH increased from 4.0 to 6.0, while opposite tend was observed in the viscosity of the solution. The DST values decreased as the pH increased from 4.0 to 6.0, indicating that higher positive charges (measured trough zeta potential) in the gelatin solution tended to result in higher DST values. The adsorption kinetics of the gelatin solution was examined through the calculated diffusion coefficients (Deff). The addition of acid promoted the random coil and β-turn structures at the expense of α-helical structure. The addition of NaOH decreased the β-turn and increased the α-helix and random coil. The decrease in the random coil and triple helix structures in the gelatin solution resulted into increased Deff values. The highest diffusion coefficients, the highest emulsion stability and the lowest amount of random coil and triple helix structures were observed at pH=4.8. The lowest amount of random coil and triple helix structures in the interfacial protein layer correlated with the highest stability of the emulsion (highest ESI value). The lower amount of random coil and triple helix structures allowed higher coverage of the oil-water interface by relatively highly ordered secondary structure of gelatin. Copyright © 2013 Elsevier Ltd. All rights reserved.

  14. Motion Tree Delineates Hierarchical Structure of Protein Dynamics Observed in Molecular Dynamics Simulation.

    Directory of Open Access Journals (Sweden)

    Kei Moritsugu

    Full Text Available Molecular dynamics (MD simulations of proteins provide important information to understand their functional mechanisms, which are, however, likely to be hidden behind their complicated motions with a wide range of spatial and temporal scales. A straightforward and intuitive analysis of protein dynamics observed in MD simulation trajectories is therefore of growing significance with the large increase in both the simulation time and system size. In this study, we propose a novel description of protein motions based on the hierarchical clustering of fluctuations in the inter-atomic distances calculated from an MD trajectory, which constructs a single tree diagram, named a "Motion Tree", to determine a set of rigid-domain pairs hierarchically along with associated inter-domain fluctuations. The method was first applied to the MD trajectory of substrate-free adenylate kinase to clarify the usefulness of the Motion Tree, which illustrated a clear-cut dynamics picture of the inter-domain motions involving the ATP/AMP lid and the core domain together with the associated amplitudes and correlations. The comparison of two Motion Trees calculated from MD simulations of ligand-free and -bound glutamine binding proteins clarified changes in inherent dynamics upon ligand binding appeared in both large domains and a small loop that stabilized ligand molecule. Another application to a huge protein, a multidrug ATP binding cassette (ABC transporter, captured significant increases of fluctuations upon binding a drug molecule observed in both large scale inter-subunit motions and a motion localized at a transmembrane helix, which may be a trigger to the subsequent structural change from inward-open to outward-open states to transport the drug molecule. These applications demonstrated the capabilities of Motion Trees to provide an at-a-glance view of various sizes of functional motions inherent in the complicated MD trajectory.

  15. Structural and dynamical properties of Yukawa balls

    International Nuclear Information System (INIS)

    Block, D; Kroll, M; Arp, O; Piel, A; Kaeding, S; Ivanov, Y; Melzer, A; Henning, C; Baumgartner, H; Ludwig, P; Bonitz, M

    2007-01-01

    To study the structural and dynamical properties of finite 3D dust clouds (Yukawa balls) new diagnostic tools have been developed. This contribution describes the progress towards 3D diagnostics for measuring the particle positions. It is shown that these diagnostics are capable of investigating the structural and dynamical properties of Yukawa balls and gaining insight into their basic construction principles

  16. Structural biology by NMR: structure, dynamics, and interactions.

    Directory of Open Access Journals (Sweden)

    Phineus R L Markwick

    2008-09-01

    Full Text Available The function of bio-macromolecules is determined by both their 3D structure and conformational dynamics. These molecules are inherently flexible systems displaying a broad range of dynamics on time-scales from picoseconds to seconds. Nuclear Magnetic Resonance (NMR spectroscopy has emerged as the method of choice for studying both protein structure and dynamics in solution. Typically, NMR experiments are sensitive both to structural features and to dynamics, and hence the measured data contain information on both. Despite major progress in both experimental approaches and computational methods, obtaining a consistent view of structure and dynamics from experimental NMR data remains a challenge. Molecular dynamics simulations have emerged as an indispensable tool in the analysis of NMR data.

  17. Structural stability of nonlinear population dynamics.

    Science.gov (United States)

    Cenci, Simone; Saavedra, Serguei

    2018-01-01

    In population dynamics, the concept of structural stability has been used to quantify the tolerance of a system to environmental perturbations. Yet, measuring the structural stability of nonlinear dynamical systems remains a challenging task. Focusing on the classic Lotka-Volterra dynamics, because of the linearity of the functional response, it has been possible to measure the conditions compatible with a structurally stable system. However, the functional response of biological communities is not always well approximated by deterministic linear functions. Thus, it is unclear the extent to which this linear approach can be generalized to other population dynamics models. Here, we show that the same approach used to investigate the classic Lotka-Volterra dynamics, which is called the structural approach, can be applied to a much larger class of nonlinear models. This class covers a large number of nonlinear functional responses that have been intensively investigated both theoretically and experimentally. We also investigate the applicability of the structural approach to stochastic dynamical systems and we provide a measure of structural stability for finite populations. Overall, we show that the structural approach can provide reliable and tractable information about the qualitative behavior of many nonlinear dynamical systems.

  18. Structural stability of nonlinear population dynamics

    Science.gov (United States)

    Cenci, Simone; Saavedra, Serguei

    2018-01-01

    In population dynamics, the concept of structural stability has been used to quantify the tolerance of a system to environmental perturbations. Yet, measuring the structural stability of nonlinear dynamical systems remains a challenging task. Focusing on the classic Lotka-Volterra dynamics, because of the linearity of the functional response, it has been possible to measure the conditions compatible with a structurally stable system. However, the functional response of biological communities is not always well approximated by deterministic linear functions. Thus, it is unclear the extent to which this linear approach can be generalized to other population dynamics models. Here, we show that the same approach used to investigate the classic Lotka-Volterra dynamics, which is called the structural approach, can be applied to a much larger class of nonlinear models. This class covers a large number of nonlinear functional responses that have been intensively investigated both theoretically and experimentally. We also investigate the applicability of the structural approach to stochastic dynamical systems and we provide a measure of structural stability for finite populations. Overall, we show that the structural approach can provide reliable and tractable information about the qualitative behavior of many nonlinear dynamical systems.

  19. Triple Helix - in Action?

    DEFF Research Database (Denmark)

    Helms, Niels Henrik; Tellerup, Susanne

    This paper presents a project i-Space about learning and playful applications, which could also document performance. The target group is mentally impaired citizens. The project is used as reference to a discussion on structures within innovation processes. This discussion leads to a discussion o...... of the user as a sense-making category in multi-disciplinary settings....

  20. POSTER : Identifying dynamic data structures in Malware

    NARCIS (Netherlands)

    Rupprecht, Thomas; Chen, Xi; White, David H.; Mühlberg, Jan Tobias; Bos, Herbert; Lüttgen, Gerald

    2016-01-01

    As the complexity of malware grows, so does the necessity of employing program structuring mechanisms during development. While control ow structuring is often obfuscated, the dynamic data structures employed by the program are typically untouched. We report on work in progress that exploits this

  1. Dynamic analysis program for frame structure

    International Nuclear Information System (INIS)

    Ando, Kozo; Chiba, Toshio

    1975-01-01

    A general purpose computer program named ISTRAN/FD (Isub(HI) STRucture ANalysis/Frame structure, Dynamic analysis) has been developed for dynamic analysis of three-dimensional frame structures. This program has functions of free vibration analysis, seismic response analysis, graphic display by plotter and CRT, etc. This paper introduces ISTRAN/FD; examples of its application are shown with various problems : idealization of the cantilever, dynamic analysis of the main tower of the suspension bridge, three-dimensional vibration in the plate girder bridge, seismic response in the boiler steel structure, and dynamic properties of the underground LNG tank. In this last example, solid elements, in addition to beam elements, are especially used for the analysis. (auth.)

  2. Structural Dynamic Behavior of Wind Turbines

    Science.gov (United States)

    Thresher, Robert W.; Mirandy, Louis P.; Carne, Thomas G.; Lobitz, Donald W.; James, George H. III

    2009-01-01

    The structural dynamicist s areas of responsibility require interaction with most other members of the wind turbine project team. These responsibilities are to predict structural loads and deflections that will occur over the lifetime of the machine, ensure favorable dynamic responses through appropriate design and operational procedures, evaluate potential design improvements for their impact on dynamic loads and stability, and correlate load and control test data with design predictions. Load prediction has been a major concern in wind turbine designs to date, and it is perhaps the single most important task faced by the structural dynamics engineer. However, even if we were able to predict all loads perfectly, this in itself would not lead to an economic system. Reduction of dynamic loads, not merely a "design to loads" policy, is required to achieve a cost-effective design. The two processes of load prediction and structural design are highly interactive: loads and deflections must be known before designers and stress analysts can perform structural sizing, which in turn influences the loads through changes in stiffness and mass. Structural design identifies "hot spots" (local areas of high stress) that would benefit most from dynamic load alleviation. Convergence of this cycle leads to a turbine structure that is neither under-designed (which may result in structural failure), nor over-designed (which will lead to excessive weight and cost).

  3. Dynamics and acceleration in linear structures

    International Nuclear Information System (INIS)

    Le Duff, J.

    1985-06-01

    Basic methods of linear acceleration are reviewed. Both cases of non relativistic and ultra relativistic particles are considered. Induction linac, radiofrequency quadrupole are mentioned. Fundamental parameters of accelerating structures are recalled; they are transit time factor, shunt impedance, quality factor and stored energy, phase velocity and group velocity, filling time, space harmonics in loaded waveguides. Energy gain in linear accelerating structures is considered through standing wave structures and travelling wave structures. Then particle dynamics in linear accelerators is studied: longitudinal motion, transverse motion and dynamics in RFQ

  4. Use of 1–4 interaction scaling factors to control the conformational equilibrium between α-helix and β-strand

    Energy Technology Data Exchange (ETDEWEB)

    Pang, Yuan-Ping, E-mail: pang@mayo.edu

    2015-02-06

    Highlights: • 1–4 interaction scaling factors are used to adjust conformational energy. • This article reports the effects of these factors on protein conformations. • Reducing these factors changes a helix to a strand in molecular dynamics simulation. • Increasing these factors causes the reverse conformational change. • These factors control the conformational equilibrium between helix and strand. - Abstract: 1–4 interaction scaling factors are used in AMBER forcefields to reduce the exaggeration of short-range repulsion caused by the 6–12 Lennard-Jones potential and a nonpolarizable charge model and to obtain better agreements of small-molecule conformational energies with experimental data. However, the effects of these scaling factors on protein secondary structure conformations have not been investigated until now. This article reports the finding that the 1–4 interactions among the protein backbone atoms separated by three consecutive covalent bonds are more repulsive in the α-helix conformation than in two β-strand conformations. Therefore, the 1–4 interaction scaling factors of protein backbone torsions ϕ and ψ control the conformational equilibrium between α-helix and β-strand. Molecular dynamics simulations confirm that reducing the ϕ and ψ scaling factors readily converts the α-helix conformation of AcO-(AAQAA){sub 3}-NH{sub 2} to a β-strand conformation, and the reverse occurs when these scaling factors are increased. These results suggest that the ϕ and ψ scaling factors can be used to generate the α-helix or β-strand conformation in situ and to control the propensities of a forcefield for adopting secondary structure elements.

  5. Use of 1–4 interaction scaling factors to control the conformational equilibrium between α-helix and β-strand

    International Nuclear Information System (INIS)

    Pang, Yuan-Ping

    2015-01-01

    Highlights: • 1–4 interaction scaling factors are used to adjust conformational energy. • This article reports the effects of these factors on protein conformations. • Reducing these factors changes a helix to a strand in molecular dynamics simulation. • Increasing these factors causes the reverse conformational change. • These factors control the conformational equilibrium between helix and strand. - Abstract: 1–4 interaction scaling factors are used in AMBER forcefields to reduce the exaggeration of short-range repulsion caused by the 6–12 Lennard-Jones potential and a nonpolarizable charge model and to obtain better agreements of small-molecule conformational energies with experimental data. However, the effects of these scaling factors on protein secondary structure conformations have not been investigated until now. This article reports the finding that the 1–4 interactions among the protein backbone atoms separated by three consecutive covalent bonds are more repulsive in the α-helix conformation than in two β-strand conformations. Therefore, the 1–4 interaction scaling factors of protein backbone torsions ϕ and ψ control the conformational equilibrium between α-helix and β-strand. Molecular dynamics simulations confirm that reducing the ϕ and ψ scaling factors readily converts the α-helix conformation of AcO-(AAQAA) 3 -NH 2 to a β-strand conformation, and the reverse occurs when these scaling factors are increased. These results suggest that the ϕ and ψ scaling factors can be used to generate the α-helix or β-strand conformation in situ and to control the propensities of a forcefield for adopting secondary structure elements

  6. 31st IMAC Conference on Structural Dynamics

    CERN Document Server

    Adams, Douglas; Carrella, Alex; Mayes, Randy; Rixen, Daniel; Allen, Matt; Cunha, Alvaro; Catbas, Fikret; Pakzad, Shamim; Racic, Vitomir; Pavic, Aleksandar; Reynolds, Paul; Simmermacher, Todd; Cogan, Scott; Moaveni, Babak; Papadimitriou, Costas; Allemang, Randall; Clerck, James; Niezrecki, Christopher; Wicks, Alfred

    2013-01-01

    Topics in Nonlinear Dynamics, Volume 1: Proceedings of the 31st IMAC, A Conference and Exposition on Structural Dynamics, 2013, the first volume of seven from the Conference, brings together contributions to this important area of research and engineering. The collection presents early findings and case studies on fundamental and applied aspects of Structural Dynamics, including papers on:   Nonlinear Oscillations Nonlinearities In Practice Nonlinear System Identification: Methods Nonlinear System Identification: Friction & Contact Nonlinear Modal Analysis Nonlinear Modeling & Simulation Nonlinear Vibration Absorbers Constructive Utilization of Nonlinearity.

  7. Collagenolytic Matrix Metalloproteinase Structure-Function Relationships: Insights From Molecular Dynamics Studies.

    Science.gov (United States)

    Karabencheva-Christova, Tatyana G; Christov, Christo Z; Fields, Gregg B

    2017-01-01

    Several members of the zinc-dependent matrix metalloproteinase (MMP) family catalyze collagen degradation. Experimental data reveal a collaboration between different MMP domains in order to achieve efficient collagenolysis. Molecular dynamics (MD) simulations have been utilized to provide atomistic details of the collagenolytic process. The triple-helical structure of collagen exhibits local regions of flexibility, with modulation of interchain salt bridges and water bridges contributing to accessibility of individual chains by the enzyme. In turn, the hemopexin-like (HPX) domain of the MMP initially binds the triple helix and facilitates the presentation of individual strands to active site in the catalytic (CAT) domain. Extensive positive and negative correlated motions are observed between the CAT and HPX domains when collagen is bound. Ultimately, the MD simulation studies have complemented structural (NMR spectroscopy, X-ray crystallography) and kinetic analyses to provide a more detailed mechanistic view of MMP-catalyzed collagenolysis. © 2017 Elsevier Inc. All rights reserved.

  8. Network structure shapes spontaneous functional connectivity dynamics.

    Science.gov (United States)

    Shen, Kelly; Hutchison, R Matthew; Bezgin, Gleb; Everling, Stefan; McIntosh, Anthony R

    2015-04-08

    The structural organization of the brain constrains the range of interactions between different regions and shapes ongoing information processing. Therefore, it is expected that large-scale dynamic functional connectivity (FC) patterns, a surrogate measure of coordination between brain regions, will be closely tied to the fiber pathways that form the underlying structural network. Here, we empirically examined the influence of network structure on FC dynamics by comparing resting-state FC (rsFC) obtained using BOLD-fMRI in macaques (Macaca fascicularis) to structural connectivity derived from macaque axonal tract tracing studies. Consistent with predictions from simulation studies, the correspondence between rsFC and structural connectivity increased as the sample duration increased. Regions with reciprocal structural connections showed the most stable rsFC across time. The data suggest that the transient nature of FC is in part dependent on direct underlying structural connections, but also that dynamic coordination can occur via polysynaptic pathways. Temporal stability was found to be dependent on structural topology, with functional connections within the rich-club core exhibiting the greatest stability over time. We discuss these findings in light of highly variable functional hubs. The results further elucidate how large-scale dynamic functional coordination exists within a fixed structural architecture. Copyright © 2015 the authors 0270-6474/15/355579-10$15.00/0.

  9. Dynamic response of structures with uncertain parameters

    International Nuclear Information System (INIS)

    Cai, Z H; Liu, Y; Yang, Y

    2010-01-01

    In this paper, an interval method for the dynamic response of structures with uncertain parameters is presented. In the presented method, the structural physical and geometric parameters and loads can be considered as interval variables. The structural stiffness matrix, mass matrix and loading vectors are described as the sum of two parts corresponding to the deterministic matrix and the uncertainty of the interval parameters. The interval problem is then transformed into approximate deterministic one. The Laplace transform is used to transform the equations of the dynamic system into linear algebra equations. The Maclaurin series expansion is applied on the modified dynamic equation in order to deal with the linear algebra equations. Numerical examples are studied by the presented interval method for the cases with and without damping. The upper bound and lower bound of the dynamic responses of the examples are compared, and it shows that the presented method is effective.

  10. Design optimization applied in structural dynamics

    NARCIS (Netherlands)

    Akcay-Perdahcioglu, Didem; de Boer, Andries; van der Hoogt, Peter; Tiskarna, T

    2007-01-01

    This paper introduces the design optimization strategies, especially for structures which have dynamic constraints. Design optimization involves first the modeling and then the optimization of the problem. Utilizing the Finite Element (FE) model of a structure directly in an optimization process

  11. Dynamical structure of space and time

    International Nuclear Information System (INIS)

    Sannikov-Proskuryakov, S.S.

    2000-01-01

    A mathematically correct solution of the problem of ultraviolet divergences requires a radical change of our ideas on space and matter. We show that the space is a discontinuum in small which is the carrier of a new dynamical structure. Taking into account this structure, a new theory of elementary particles can be suggested

  12. IFITM3 requires an amphipathic helix for antiviral activity.

    Science.gov (United States)

    Chesarino, Nicholas M; Compton, Alex A; McMichael, Temet M; Kenney, Adam D; Zhang, Lizhi; Soewarna, Victoria; Davis, Matthew; Schwartz, Olivier; Yount, Jacob S

    2017-10-01

    Interferon-induced transmembrane protein 3 (IFITM3) is a cellular factor that blocks virus fusion with cell membranes. IFITM3 has been suggested to alter membrane curvature and fluidity, though its exact mechanism of action is unclear. Using a bioinformatic approach, we predict IFITM3 secondary structures and identify a highly conserved, short amphipathic helix within a hydrophobic region of IFITM3 previously thought to be a transmembrane domain. Consistent with the known ability of amphipathic helices to alter membrane properties, we show that this helix and its amphipathicity are required for the IFITM3-dependent inhibition of influenza virus, Zika virus, vesicular stomatitis virus, Ebola virus, and human immunodeficiency virus infections. The homologous amphipathic helix within IFITM1 is also required for the inhibition of infection, indicating that IFITM proteins possess a conserved mechanism of antiviral action. We further demonstrate that the amphipathic helix of IFITM3 is required to block influenza virus hemagglutinin-mediated membrane fusion. Overall, our results provide evidence that IFITM proteins utilize an amphipathic helix for inhibiting virus fusion. © 2017 The Authors.

  13. Has globalization strengthened South Korea’s national research system? National and international dynamics of the Triple Helix of scientific co-authorship relationships in South Korea

    NARCIS (Netherlands)

    Kwon, K.-S.; Park, H.W.; So, M.; Leydesdorff, L.

    2012-01-01

    We trace the structural patterns of co-authorship between Korean researchers at three institutional types (university, government, and industry) and their international partners in terms of the mutual information generated in these relations. Data were collected from the Web of Science during the

  14. The Structure and Dynamics of GRB Jets

    Energy Technology Data Exchange (ETDEWEB)

    Granot, Jonathan; /KIPAC, Menlo Park

    2006-10-25

    There are several lines of evidence which suggest that the relativistic outflows in gamma-ray bursts (GRBs) are collimated into narrow jets. The jet structure has important implications for the true energy release and the event rate of GRBs, and can constrain the mechanism responsible for the acceleration and collimation of the jet. Nevertheless, the jet structure and its dynamics as it sweeps up the external medium and decelerates, are not well understood. In this review I discuss our current understanding of GRB jets, stressing their structure and dynamics.

  15. S-Nitrosylation Induces Structural and Dynamical Changes in a Rhodanese Family Protein.

    Science.gov (United States)

    Eichmann, Cédric; Tzitzilonis, Christos; Nakamura, Tomohiro; Kwiatkowski, Witek; Maslennikov, Innokentiy; Choe, Senyon; Lipton, Stuart A; Riek, Roland

    2016-09-25

    S-Nitrosylation is well established as an important post-translational regulator in protein function and signaling. However, relatively little is known about its structural and dynamical consequences. We have investigated the effects of S-nitrosylation on the rhodanese domain of the Escherichia coli integral membrane protein YgaP by NMR, X-ray crystallography, and mass spectrometry. The results show that the active cysteine in the rhodanese domain of YgaP is subjected to two competing modifications: S-nitrosylation and S-sulfhydration, which are naturally occurring in vivo. It has been observed that in addition to inhibition of the sulfur transfer activity, S-nitrosylation of the active site residue Cys63 causes an increase in slow motion and a displacement of helix 5 due to a weakening of the interaction between the active site and the helix dipole. These findings provide an example of how nitrosative stress can exert action at the atomic level. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Modeling and identification in structural dynamics

    OpenAIRE

    Jayakumar, Paramsothy

    1987-01-01

    Analytical modeling of structures subjected to ground motions is an important aspect of fully dynamic earthquake-resistant design. In general, linear models are only sufficient to represent structural responses resulting from earthquake motions of small amplitudes. However, the response of structures during strong ground motions is highly nonlinear and hysteretic. System identification is an effective tool for developing analytical models from experimental data. Testing of full-scale prot...

  17. Dynamic Response of a Floating Bridge Structure

    OpenAIRE

    Viuff, Thomas; Leira, Bernt Johan; Øiseth, Ole; Xiang, Xu

    2016-01-01

    A theoretical overview of the stochastic dynamic analysis of a floating bridge structure is presented. Emphasis is on the wave-induced response and the waves on the sea surface are idealized as a zero mean stationary Gaussian process. The first-order wave load processes are derived using linear potential theory and the structural idealization is based on the Finite Element Method. A frequency response calculation is presented for a simplified floating bridge structure example emphasising the ...

  18. About the dynamics of structural phase transitions

    International Nuclear Information System (INIS)

    Medeiros, J.T.N.

    1975-01-01

    The dynamics of structural phase transitions with a fourth order interaction between the soft phonon fields is studied in the 1/n approximation, using many body methods at finite temperatures. Two limits are considered: high transition temperature T sub(c) (classical limit) and T sub(c) = 0 (quantum limit). The dynamical contribution to the critical coefficient eta of the correlation function is calculated in these limits. It is found that there is no dynamical contribution to eta in the classical limit, whereas in the quantum limit eta is non-zero only for dimensions of the system d [pt

  19. Simultaneous determination of protein structure and dynamics

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Best, Robert B.; DePristo, M. A.

    2005-01-01

    at the atomic level about the structural and dynamical features of proteins-with the ability of molecular dynamics simulations to explore a wide range of protein conformations. We illustrate the method for human ubiquitin in solution and find that there is considerable conformational heterogeneity throughout......We present a protocol for the experimental determination of ensembles of protein conformations that represent simultaneously the native structure and its associated dynamics. The procedure combines the strengths of nuclear magnetic resonance spectroscopy-for obtaining experimental information...... the protein structure. The interior atoms of the protein are tightly packed in each individual conformation that contributes to the ensemble but their overall behaviour can be described as having a significant degree of liquid-like character. The protocol is completely general and should lead to significant...

  20. Unifying dynamical and structural stability of equilibria

    Science.gov (United States)

    Arnoldi, Jean-François; Haegeman, Bart

    2016-09-01

    We exhibit a fundamental relationship between measures of dynamical and structural stability of linear dynamical systems-e.g. linearized models in the vicinity of equilibria. We show that dynamical stability, quantified via the response to external perturbations (i.e. perturbation of dynamical variables), coincides with the minimal internal perturbation (i.e. perturbations of interactions between variables) able to render the system unstable. First, by reformulating a result of control theory, we explain that harmonic external perturbations reflect the spectral sensitivity of the Jacobian matrix at the equilibrium, with respect to constant changes of its coefficients. However, for this equivalence to hold, imaginary changes of the Jacobian's coefficients have to be allowed. The connection with dynamical stability is thus lost for real dynamical systems. We show that this issue can be avoided, thus recovering the fundamental link between dynamical and structural stability, by considering stochastic noise as external and internal perturbations. More precisely, we demonstrate that a linear system's response to white-noise perturbations directly reflects the intensity of internal white-noise disturbance that it can accommodate before becoming stochastically unstable.

  1. Structure and Dynamics of Negative Ions

    International Nuclear Information System (INIS)

    None

    2000-01-01

    This report describes progress made during the final three-year grant period 1997-2000. During this period, we experimentally investigated the structure and dynamics of negative ions by detaching the outermost electron in controlled processes induced by photon-, electron- and heavy particle-impact. In this manner we studied, at a fundamental level, the role of electron correlation in the structure and dynamics of simple, few-particle atomic systems. Our measurements have provided sensitive tests of the ability of theory to go beyond the independent electron model

  2. Structural dynamics of electronic and photonic systems

    CERN Document Server

    Suhir, Ephraim; Steinberg, David S

    2011-01-01

    The proposed book will offer comprehensive and versatile methodologies and recommendations on how to determine dynamic characteristics of typical micro- and opto-electronic structural elements (printed circuit boards, solder joints, heavy devices, etc.) and how to design a viable and reliable structure that would be able to withstand high-level dynamic loading. Particular attention will be given to portable devices and systems designed for operation in harsh environments (such as automotive, aerospace, military, etc.)  In-depth discussion from a mechanical engineer's viewpoint will be conducte

  3. Multiple helix ecosystems for sustainable competitiveness

    CERN Document Server

    Ferreira, João; Farinha, Luís; Fernandes, Nuno

    2016-01-01

    This book discusses the main issues, challenges, opportunities, and trends involving the interactions between academia, industry, government and society. Specifically, it aims to explore how these interactions enhance the ways in which companies deliver products and services in order to achieve sustainable competitiveness in the marketplace. Sustainable competitiveness has been widely discussed by academics and practitioners, considering the importance of protecting the environment while sustaining the economic goals of organizations. The Quintuple Helix innovation model is a framework for facilitating knowledge, innovation and sustainable competitive advantage. It embeds the Triple and the Quadruple Helix models by adding a fifth helix, the “natural environment.” The Triple Helix model focuses on the university-industry-government triad, while the Quadruple adds civil society (the media- and culture-driven public) as a fourth helix. The Quintuple Helix model facilitates research, public policy, and pract...

  4. Chemical structure and dynamics: Annual report 1993

    Energy Technology Data Exchange (ETDEWEB)

    Colson, S.D.

    1994-07-01

    The Chemical Structure and Dynamics program responds to the need for a fundamental, molecular-level understanding of chemistry at the wide variety of environmentally-important interfaces. The research program is built around the established relationship between structure, thermodynamics, and kinetics. This research effort continues to evolve into a program of rigorous studies of fundamental molecular processes in model systems (e.g., well-characterized surfaces, single-component solutions, clusters, and biological molecules), and studies of complex systems found in the environment. Experimental studies of molecular and supramolecular structures and thermodynamics are key to understanding the nature of matter, and lead to direct comparison with computational results. Kinetic and mechanistic measurements, combined with real-time dynamics measurements of atomic and molecular motions during chemical reactions, provide for a molecular-level description of chemical reactions. The anticipated results of this work are the achievement of a quantitative understanding of chemical processes at complex interfaces, the development of new techniques for the detection and measurement of species at such interfaces, and the interpretation and extrapolation of the observations in terms of models of interfacial chemistry. The Chemical Structure and Dynamics research program includes five areas described in detail in this report: Reaction mechanisms at solid interfaces; Solution and solution interfaces; Structure and dynamics of biological systems; Analytical methods development; and atmospheric chemistry. Extended abstracts are presented for 23 studies.

  5. Multiscale structure in eco-evolutionary dynamics

    Science.gov (United States)

    Stacey, Blake C.

    In a complex system, the individual components are neither so tightly coupled or correlated that they can all be treated as a single unit, nor so uncorrelated that they can be approximated as independent entities. Instead, patterns of interdependency lead to structure at multiple scales of organization. Evolution excels at producing such complex structures. In turn, the existence of these complex interrelationships within a biological system affects the evolutionary dynamics of that system. I present a mathematical formalism for multiscale structure, grounded in information theory, which makes these intuitions quantitative, and I show how dynamics defined in terms of population genetics or evolutionary game theory can lead to multiscale organization. For complex systems, "more is different," and I address this from several perspectives. Spatial host--consumer models demonstrate the importance of the structures which can arise due to dynamical pattern formation. Evolutionary game theory reveals the novel effects which can result from multiplayer games, nonlinear payoffs and ecological stochasticity. Replicator dynamics in an environment with mesoscale structure relates to generalized conditionalization rules in probability theory. The idea of natural selection "acting at multiple levels" has been mathematized in a variety of ways, not all of which are equivalent. We will face down the confusion, using the experience developed over the course of this thesis to clarify the situation.

  6. Structure and dynamics of the solar chromosphere

    NARCIS (Netherlands)

    Krijger, Johannes Mattheus

    2002-01-01

    The thesis "Structure and dynamics of the solar chromosphere" of J.M. Krijger is a study on the behavior of the solar chromosphere, the thin layer just above the solar surface (photosphere) visible in purple red light during a total solar eclipse. The most important result of this thesis is that the

  7. Natural Poisson structures of nonlinear plasma dynamics

    International Nuclear Information System (INIS)

    Kaufman, A.N.

    1982-01-01

    Hamiltonian field theories, for models of nonlinear plasma dynamics, require a Poisson bracket structure for functionals of the field variables. These are presented, applied, and derived for several sets of field variables: coherent waves, incoherent waves, particle distributions, and multifluid electrodynamics. Parametric coupling of waves and plasma yields concise expressions for ponderomotive effects (in kinetic and fluid models) and for induced scattering. (Auth.)

  8. Natural Poisson structures of nonlinear plasma dynamics

    International Nuclear Information System (INIS)

    Kaufman, A.N.

    1982-06-01

    Hamiltonian field theories, for models of nonlinear plasma dynamics, require a Poisson bracket structure for functionals of the field variables. These are presented, applied, and derived for several sets of field variables: coherent waves, incoherent waves, particle distributions, and multifluid electrodynamics. Parametric coupling of waves and plasma yields concise expressions for ponderomotive effects (in kinetic and fluid models) and for induced scattering

  9. Structural dynamic modification using additive damping

    Indian Academy of Sciences (India)

    elements, FEM and perturbation methods for reanalysis or structural dynamic modification ... to a system changes its mass, stiffness and damping. Thus ... due to the phase difference between stress ' and strain or 'a И E1 З iE2 for direct strain.

  10. Structure of the TPR domain of AIP: lack of client protein interaction with the C-terminal α-7 helix of the TPR domain of AIP is sufficient for pituitary adenoma predisposition.

    Directory of Open Access Journals (Sweden)

    Rhodri M L Morgan

    Full Text Available Mutations of the aryl hydrocarbon receptor interacting protein (AIP have been associated with familial isolated pituitary adenomas predisposing to young-onset acromegaly and gigantism. The precise tumorigenic mechanism is not well understood as AIP interacts with a large number of independent proteins as well as three chaperone systems, HSP90, HSP70 and TOMM20. We have determined the structure of the TPR domain of AIP at high resolution, which has allowed a detailed analysis of how disease-associated mutations impact on the structural integrity of the TPR domain. A subset of C-terminal α-7 helix (Cα-7h mutations, R304* (nonsense mutation, R304Q, Q307* and R325Q, a known site for AhR and PDE4A5 client-protein interaction, occur beyond those that interact with the conserved MEEVD and EDDVE sequences of HSP90 and TOMM20. These C-terminal AIP mutations appear to only disrupt client-protein binding to the Cα-7h, while chaperone binding remains unaffected, suggesting that failure of client-protein interaction with the Cα-7h is sufficient to predispose to pituitary adenoma. We have also identified a molecular switch in the AIP TPR-domain that allows recognition of both the conserved HSP90 motif, MEEVD, and the equivalent sequence (EDDVE of TOMM20.

  11. Component mode synthesis in structural dynamics

    International Nuclear Information System (INIS)

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

    1993-01-01

    In seismic analysis of Nuclear Reactor Structures and equipments eigen solution requires large computer time. Component mode synthesis is an efficient technique with which one can evaluate dynamic characteristics of a large structure with minimum computer time. Due to this reason it is possible to do a coupled analysis of structure and equipment which takes into account the interaction effects. Basically in this the method large size structure is divided into small substructures and dynamic characteristics of individual substructure are determined. The dynamic characteristics of entire structure are evaluated by synthesising the individual substructure characteristics. Component mode synthesis has been applied in this paper to the analysis of a tall heavy water upgrading tower. Use of fixed interface normal modes, constrained modes, attachment modes in the component mode synthesis using energy principle and using Ritz vectors have been discussed. The validity of this method is established by solving fixed-fixed beam and comparing the results obtained by conventional and classical method. The eigen value problem has been solved using simultaneous iteration method. (author)

  12. The dynamical conductance of graphene tunnelling structures

    International Nuclear Information System (INIS)

    Zhang Huan; Chan, K S; Lin Zijing

    2011-01-01

    The dynamical conductances of graphene tunnelling structures were numerically calculated using the scattering matrix method with the interaction effect included in a phenomenological approach. The overall single-barrier dynamical conductance is capacitative. Transmission resonances in the single-barrier structure lead to dips in the capacitative imaginary part of the response. This is different from the ac responses of typical semiconductor nanostructures, where transmission resonances usually lead to inductive peaks. The features of the dips depend on the Fermi energy. When the Fermi energy is below half of the barrier height, the dips are sharper. When the Fermi energy is higher than half of the barrier height, the dips are broader. Inductive behaviours can be observed in a double-barrier structure due to the resonances formed by reflection between the two barriers.

  13. The dynamical conductance of graphene tunnelling structures.

    Science.gov (United States)

    Zhang, Huan; Chan, K S; Lin, Zijing

    2011-12-16

    The dynamical conductances of graphene tunnelling structures were numerically calculated using the scattering matrix method with the interaction effect included in a phenomenological approach. The overall single-barrier dynamical conductance is capacitative. Transmission resonances in the single-barrier structure lead to dips in the capacitative imaginary part of the response. This is different from the ac responses of typical semiconductor nanostructures, where transmission resonances usually lead to inductive peaks. The features of the dips depend on the Fermi energy. When the Fermi energy is below half of the barrier height, the dips are sharper. When the Fermi energy is higher than half of the barrier height, the dips are broader. Inductive behaviours can be observed in a double-barrier structure due to the resonances formed by reflection between the two barriers.

  14. Dynamic structural disorder in supported nanoscale catalysts

    International Nuclear Information System (INIS)

    Rehr, J. J.; Vila, F. D.

    2014-01-01

    We investigate the origin and physical effects of “dynamic structural disorder” (DSD) in supported nano-scale catalysts. DSD refers to the intrinsic fluctuating, inhomogeneous structure of such nano-scale systems. In contrast to bulk materials, nano-scale systems exhibit substantial fluctuations in structure, charge, temperature, and other quantities, as well as large surface effects. The DSD is driven largely by the stochastic librational motion of the center of mass and fluxional bonding at the nanoparticle surface due to thermal coupling with the substrate. Our approach for calculating and understanding DSD is based on a combination of real-time density functional theory/molecular dynamics simulations, transient coupled-oscillator models, and statistical mechanics. This approach treats thermal and dynamic effects over multiple time-scales, and includes bond-stretching and -bending vibrations, and transient tethering to the substrate at longer ps time-scales. Potential effects on the catalytic properties of these clusters are briefly explored. Model calculations of molecule-cluster interactions and molecular dissociation reaction paths are presented in which the reactant molecules are adsorbed on the surface of dynamically sampled clusters. This model suggests that DSD can affect both the prefactors and distribution of energy barriers in reaction rates, and thus can significantly affect catalytic activity at the nano-scale

  15. Dynamic structural disorder in supported nanoscale catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Rehr, J. J.; Vila, F. D. [Department of Physics, University of Washington, Seattle, Washington 98195 (United States)

    2014-04-07

    We investigate the origin and physical effects of “dynamic structural disorder” (DSD) in supported nano-scale catalysts. DSD refers to the intrinsic fluctuating, inhomogeneous structure of such nano-scale systems. In contrast to bulk materials, nano-scale systems exhibit substantial fluctuations in structure, charge, temperature, and other quantities, as well as large surface effects. The DSD is driven largely by the stochastic librational motion of the center of mass and fluxional bonding at the nanoparticle surface due to thermal coupling with the substrate. Our approach for calculating and understanding DSD is based on a combination of real-time density functional theory/molecular dynamics simulations, transient coupled-oscillator models, and statistical mechanics. This approach treats thermal and dynamic effects over multiple time-scales, and includes bond-stretching and -bending vibrations, and transient tethering to the substrate at longer ps time-scales. Potential effects on the catalytic properties of these clusters are briefly explored. Model calculations of molecule-cluster interactions and molecular dissociation reaction paths are presented in which the reactant molecules are adsorbed on the surface of dynamically sampled clusters. This model suggests that DSD can affect both the prefactors and distribution of energy barriers in reaction rates, and thus can significantly affect catalytic activity at the nano-scale.

  16. Mode conversions by a discontinuous junction of two helix loaded waveguides

    International Nuclear Information System (INIS)

    Choe, J.Y.; Ahn, S.; Ganquly, A.K.; Uhm, H.S.

    1983-01-01

    For various reasons, it is desirable to vary the primary propagating mode from one section of the waveguide to another. We choose the base structure to be the sheath helix loaded waveguide. Specifically, we join two physically different helix loaded waveguides axisymmetrically, thereby providing the required discontinuities at the junction (Z = 0). The helix loaded waveguide is more advantageous to the simple waveguide in that the helix mode that exists uniquely in the helix waveguide in addition to the usual fast wave hybrid modes, is without cutoff and thus behaves like a transmission line. In order to obtain the mode conversion rates, we expand the waves in the both sides of the junction with its own eigenmodes including the evanescent modes, and by matching fields at the junction (Z = 0) obtain the matrix equation for the coefficients for the eigenmodes in both sides. By choosing the propagating incident wave (Z = 0) the resulting outgoing waves in the other end (Z > 0) will be computed from the matrix equation. A computer program is devised to solve the suitably truncated matrix equation, and the numerical examples for the mode conversion rates with the parameter variations will be presented. The relevant physical parameters to yield discontinuities at the junction are the radii of the outer conductor and the helix wire and the pitch angle of the helix. Special emphases are on the conversion rates from the helix mode (Z 0) for the application to the tapered gyrotron amplifier

  17. Dynamics and structure of stretched flames

    Energy Technology Data Exchange (ETDEWEB)

    Law, C.K. [Princeton Univ., NJ (United States)

    1993-12-01

    This program aims to gain fundamental understanding on the structure, geometry, and dynamics of laminar premixed flames, and relate these understanding to the practical issues of flame extinction and stabilization. The underlying fundamental interest here is the recent recognition that the response of premixed flames can be profoundly affected by flame stretch, as manifested by flow nonuniformity, flame curvature, and flame/flow unsteadiness. As such, many of the existing understanding on the behavior of premixed flames need to be qualitatively revised. The research program consists of three major thrusts: (1) detailed experimental and computational mapping of the structure of aerodynamically-strained planar flames, with emphasis on the effects of heat loss, nonequidiffusion, and finite residence time on the flame thickness, extent of incomplete reaction, and the state of extinction. (2) Analytical study of the geometry and dynamics of stretch-affected wrinkled flame sheets in simple configurations, as exemplified by the Bunsen flame and the spatially-periodic flame, with emphasis on the effects of nonlinear stretch, the phenomena of flame cusping, smoothing, and tip opening, and their implications on the structure and burning rate of turbulent flames. (3) Stabilization and blowoff of two-dimensional inverted premixed and stabilization and determining the criteria governing flame blowoff. The research is synergistically conducted through the use of laser-based diagnostics, computational simulation of the flame structure with detailed chemistry and transport, and mathematical analysis of the flame dynamics.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2018-01-02

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

  19. Spatial attributes of the four-helix bundle group of bacteriocins – The high-resolution structure of BacSp222 in solution

    KAUST Repository

    Nowakowski, Michał; Jaremko, Łukasz; Wladyka, Benedykt; Dubin, Grzegorz; Ejchart, Andrzej; Mak, Paweł

    2017-01-01

    collected. The structure was calculated based on NMR-derived constraints and consists of a rigid and tightly packed globular bundle of four alpha-helices separated by three short turns.Although the amino acid sequence of BacSp222 has no significant

  20. Chemical structure and dynamics. Annual report 1995

    Energy Technology Data Exchange (ETDEWEB)

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

    1996-05-01

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

  1. Chemical structure and dynamics: Annual report 1996

    International Nuclear Information System (INIS)

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

    1997-03-01

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

  2. Annual Report 2000. Chemical Structure and Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Colson, Steven D.; McDowell, Robin S.

    2001-04-15

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

  3. Chemical structure and dynamics: Annual report 1996

    Energy Technology Data Exchange (ETDEWEB)

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

    1997-03-01

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

  4. On R factors for dynamic structure crystallography

    DEFF Research Database (Denmark)

    Coppens, Philip; Kaminski, Radoslaw; Schmøkel, Mette Stokkebro

    2010-01-01

    In studies of dynamic changes in crystals in which induced metastable species may have lifetimes of microseconds or less, refinements are most sensitive if based on the changes induced in the measured intensities. Agreement factors appropriate for such refinements, based on the ratios of the inte...... of the intensities before and after the external perturbation is applied, are discussed and compared with R factors commonly applied in static structure crystallography....

  5. Feature Extraction for Structural Dynamics Model Validation

    Energy Technology Data Exchange (ETDEWEB)

    Farrar, Charles [Los Alamos National Laboratory; Nishio, Mayuko [Yokohama University; Hemez, Francois [Los Alamos National Laboratory; Stull, Chris [Los Alamos National Laboratory; Park, Gyuhae [Chonnam Univesity; Cornwell, Phil [Rose-Hulman Institute of Technology; Figueiredo, Eloi [Universidade Lusófona; Luscher, D. J. [Los Alamos National Laboratory; Worden, Keith [University of Sheffield

    2016-01-13

    As structural dynamics becomes increasingly non-modal, stochastic and nonlinear, finite element model-updating technology must adopt the broader notions of model validation and uncertainty quantification. For example, particular re-sampling procedures must be implemented to propagate uncertainty through a forward calculation, and non-modal features must be defined to analyze nonlinear data sets. The latter topic is the focus of this report, but first, some more general comments regarding the concept of model validation will be discussed.

  6. Design and synthesis of DNA four-helix bundles

    Energy Technology Data Exchange (ETDEWEB)

    Rangnekar, Abhijit; Gothelf, Kurt V [Department of Chemistry, Centre for DNA Nanotechnology (CDNA) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C (Denmark); LaBean, Thomas H, E-mail: kvg@chem.au.dk, E-mail: thl@cs.duke.edu [Department of Chemistry, Duke University, Durham, NC 27708 (United States)

    2011-06-10

    The field of DNA nanotechnology has evolved significantly in the past decade. Researchers have succeeded in synthesizing tile-based structures and using them to form periodic lattices in one, two and three dimensions. Origami-based structures have also been used to create nanoscale structures in two and three dimensions. Design and construction of DNA bundles with fixed circumference has added a new dimension to the field. Here we report the design and synthesis of a DNA four-helix bundle. It was found to be extremely rigid and stable. When several such bundles were assembled using appropriate sticky-ends, they formed micrometre-long filaments. However, when creation of two-dimensional sheet-like arrays of the four-helix bundles was attempted, nanoscale rings were observed instead. The exact reason behind the nanoring formation is yet to be ascertained, but it provides an exciting prospect for making programmable circular nanostructures using DNA.

  7. Design and synthesis of DNA four-helix bundles

    International Nuclear Information System (INIS)

    Rangnekar, Abhijit; Gothelf, Kurt V; LaBean, Thomas H

    2011-01-01

    The field of DNA nanotechnology has evolved significantly in the past decade. Researchers have succeeded in synthesizing tile-based structures and using them to form periodic lattices in one, two and three dimensions. Origami-based structures have also been used to create nanoscale structures in two and three dimensions. Design and construction of DNA bundles with fixed circumference has added a new dimension to the field. Here we report the design and synthesis of a DNA four-helix bundle. It was found to be extremely rigid and stable. When several such bundles were assembled using appropriate sticky-ends, they formed micrometre-long filaments. However, when creation of two-dimensional sheet-like arrays of the four-helix bundles was attempted, nanoscale rings were observed instead. The exact reason behind the nanoring formation is yet to be ascertained, but it provides an exciting prospect for making programmable circular nanostructures using DNA.

  8. Handbook on dynamics of jointed structures.

    Energy Technology Data Exchange (ETDEWEB)

    Ames, Nicoli M.; Lauffer, James P.; Jew, Michael D.; Segalman, Daniel Joseph; Gregory, Danny Lynn; Starr, Michael James; Resor, Brian Ray

    2009-07-01

    The problem of understanding and modeling the complicated physics underlying the action and response of the interfaces in typical structures under dynamic loading conditions has occupied researchers for many decades. This handbook presents an integrated approach to the goal of dynamic modeling of typical jointed structures, beginning with a mathematical assessment of experimental or simulation data, development of constitutive models to account for load histories to deformation, establishment of kinematic models coupling to the continuum models, and application of finite element analysis leading to dynamic structural simulation. In addition, formulations are discussed to mitigate the very short simulation time steps that appear to be required in numerical simulation for problems such as this. This handbook satisfies the commitment to DOE that Sandia will develop the technical content and write a Joints Handbook. The content will include: (1) Methods for characterizing the nonlinear stiffness and energy dissipation for typical joints used in mechanical systems and components. (2) The methodology will include practical guidance on experiments, and reduced order models that can be used to characterize joint behavior. (3) Examples for typical bolted and screw joints will be provided.

  9. Structural dynamic analysis of turbine blade

    Science.gov (United States)

    Antony, A. Daniel; Gopalsamy, M.; Viswanadh, Chaparala B. V.; Krishnaraj, R.

    2017-10-01

    In any gas turbine design cycle, blade design is a crucial element which needs maximum attention to meet the aerodynamic performance, structural safety margins, manufacturing feasibility, material availability etc. In present day gas turbine engines, most of the failures occur during engine development test and in-service, in rotor and stator blades due to fatigue and resonance failures. To address this issue, an extensive structural dynamic analysis is carried out to predict the natural frequencies and mode shapes using FE methods. Using the dynamics characteristics, the Campbell diagram is constructed to study the possibility of resonance at various operating speeds. In this work, the feasibility of using composite material in place of titanium alloy from the structural dynamics point of view. This is being attempted in a Low-pressure compressor where the temperatures are relatively low and fixed with the casings. The analysis will be carried out using FE method for different composite material with different lamina orientations chosen through the survey. This study will focus on the sensitivity of blade mode shapes to different laminae orientations, which will be used to alter the natural frequency and tailor the mode shapes. Campbell diagrams of existing titanium alloy are compared with the composite materials with different laminae at all critical operating conditions. The existing manufacturing methods and the proven techniques for blade profiles will also be discussed in this report.

  10. DYNAMIC CINEMATIC TO A STRUCTURE 2R

    Directory of Open Access Journals (Sweden)

    Florian Ion Tiberiu Petrescu

    2016-06-01

    Full Text Available Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4 Flat structures 2R can solve all the problems posed by all the robotic anthropomorphic structures. The study of the anthropomorphic robots by the use of a flat structure 2R is a much easier method than classical used spatial methods. The paper outlines a method for the determination of dynamic to a robotic structure 2R balanced. 2R plane structures are used in practice only in the form balanced, for which in this paper will be made, initial, the total balance, and then the study cinematico-dynamic will only develop on the model already balanced. Dynamic relations presented then briefly without deduction will be explained and discussed with regard to their application. On the basis of the model presented and following calculations performed can be chosen correctly the two electric motors in the actuator. /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;}

  11. Crosslinked Aspartic Acids as Helix-Nucleating Templates.

    Science.gov (United States)

    Zhao, Hui; Liu, Qi-Song; Geng, Hao; Tian, Yuan; Cheng, Min; Jiang, Yan-Hong; Xie, Ming-Sheng; Niu, Xiao-Gang; Jiang, Fan; Zhang, Ya-Ou; Lao, Yuan-Zhi; Wu, Yun-Dong; Xu, Nai-Han; Li, Zi-Gang

    2016-09-19

    Described is a facile helix-nucleating template based on a tethered aspartic acid at the N-terminus [terminal aspartic acid (TD)]. The nucleating effect of the template is subtly influenced by the substituent at the end of the side-chain-end tether as indicated by circular dichroism, nuclear magnetic resonance, and molecular dynamics simulations. Unlike most nucleating strategies, the N-terminal amine is preserved, thus enabling further modification. Peptidomimetic estrogen receptor modulators (PERMs) constructed using this strategy show improved therapeutic properties. The current strategy can be regarded as a good complement to existing helix-stabilizing methods. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. A genome-wide survey on basic helix-loop-helix transcription factors in giant panda.

    Directory of Open Access Journals (Sweden)

    Chunwang Dang

    Full Text Available The giant panda (Ailuropoda melanoleuca is a critically endangered mammalian species. Studies on functions of regulatory proteins involved in developmental processes would facilitate understanding of specific behavior in giant panda. The basic helix-loop-helix (bHLH proteins play essential roles in a wide range of developmental processes in higher organisms. bHLH family members have been identified in over 20 organisms, including fruit fly, zebrafish, mouse and human. Our present study identified 107 bHLH family members being encoded in giant panda genome. Phylogenetic analyses revealed that they belong to 44 bHLH families with 46, 25, 15, 4, 11 and 3 members in group A, B, C, D, E and F, respectively, while the remaining 3 members were assigned into "orphan". Compared to mouse, the giant panda does not encode seven bHLH proteins namely Beta3a, Mesp2, Sclerax, S-Myc, Hes5 (or Hes6, EBF4 and Orphan 1. These results provide useful background information for future studies on structure and function of bHLH proteins in the regulation of giant panda development.

  13. Hydroxyproline Ring Pucker Causes Frustration of Helix Parameters in the Collagen Triple Helix

    Science.gov (United States)

    Ying Chow, W.; Bihan, Dominique; Forman, Chris J.; Slatter, David A.; Reid, David G.; Wales, David J.; Farndale, Richard W.; Duer, Melinda J.

    2015-07-01

    Collagens, the most abundant proteins in mammals, are defined by their triple-helical structures and distinctive Gly-Xaa-Yaa repeating sequence, where Xaa is often proline and Yaa, hydroxyproline (Hyp/O). It is known that hydroxyproline in the Yaa position stabilises the triple helix, and that lack of proline hydroxylation in vivo leads to dysfunctional collagen extracellular matrix assembly, due to a range of factors such as a change in hydration properties. In addition, we note that in model peptides, when Yaa is unmodified proline, the Xaa proline has a strong propensity to adopt an endo ring conformation, whilst when Yaa is hydroxyproline, the Xaa proline adopts a range of endo and exo conformations. Here we use a combination of solid-state NMR spectroscopy and potential energy landscape modelling of synthetic triple-helical collagen peptides to understand this effect. We show that hydroxylation of the Yaa proline causes the Xaa proline ring conformation to become metastable, which in turn confers flexibility on the triple helix.

  14. Dynamic Failure of Composite and Sandwich Structures

    CERN Document Server

    Abrate, Serge; Rajapakse, Yapa D S

    2013-01-01

    This book presents a broad view of the current state of the art regarding the dynamic response of composite and sandwich structures subjected to impacts and explosions. Each chapter combines a thorough assessment of the literature with original contributions made by the authors.  The first section deals with fluid-structure interactions in marine structures.  The first chapter focuses on hull slamming and particularly cases in which the deformation of the structure affects the motion of the fluid during the water entry of flexible hulls. Chapter 2 presents an extensive series of tests underwater and in the air to determine the effects of explosions on composite and sandwich structures.  Full-scale structures were subjected to significant explosive charges, and such results are extremely rare in the open literature.  Chapter 3 describes a simple geometrical theory of diffraction for describing the interaction of an underwater blast wave with submerged structures. The second section addresses the problem of...

  15. Dynamic analysis of the BPX machine structure

    International Nuclear Information System (INIS)

    Dahlgen, F.; Citrolo, J.; Knutson, D.; Kalish, M.

    1992-01-01

    A preliminary analysis of the response of the BPX machine structure to a seismic input was performed. MSC/NASTRAN 5 , a general purpose XXX element computer code, has been used. The purpose of this paper is to assess the probable range of seismically induced stresses and deflections in the machine substructure which connects the machine to the test cell floor, with particular emphasis on the shear pins which will be used to attach the TF coil modules to the machine substructure (for a more detailed description of the shear pins and structure see ref. 4 in these proceedings). The model was developed with sufficient detail to be used subsequently to investigate the transient response to various dynamic loading conditions imposed on the structure by the PF, TF, and Vacuum Vessel, during normal and off-normal operations. The model does not include the mass and stiffness of the building or the building-soil interaction and as such can only be considered an interim assessment of the dynamic response of the machine to the S.S.E.(this is the Safe Shutdown Earthquake which is also the Design XXX Earthquake for all major structural components)

  16. Structured population dynamics: continuous size and discontinuous stage structures.

    Science.gov (United States)

    Buffoni, Giuseppe; Pasquali, Sara

    2007-04-01

    A nonlinear stochastic model for the dynamics of a population with either a continuous size structure or a discontinuous stage structure is formulated in the Eulerian formalism. It takes into account dispersion effects due to stochastic variability of the development process of the individuals. The discrete equations of the numerical approximation are derived, and an analysis of the existence and stability of the equilibrium states is performed. An application to a copepod population is illustrated; numerical results of Eulerian and Lagrangian models are compared.

  17. 30th IMAC, A Conference on Structural Dynamics

    CERN Document Server

    Catbas, FN; Mayes, R; Rixen, D; Griffith, DT; Allemang, R; Clerck, J; Klerk, D; Simmermacher, T; Cogan, S; Chauhan, S; Cunha, A; Racic, V; Reynolds, P; Salyards, K; Adams, D; Kerschen, G; Carrella, A; Voormeeren, SN; Allen, MS; Horta, LG; Barthorpe, R; Niezrecki, C; Blough, JR; Vol.1 Topics on the Dynamics of Civil Structures; Vol.2 Topics in Experimental Dynamics Substructuring and Wind Turbine Dynamics; Vol.3 Topics in Nonlinear Dynamics; Vol.4 Topics in Model Validation and Uncertainty Quantification; Vol.5 Topics in Modal Analysis I; Vol.6 Topics in Modal Analysis II

    2012-01-01

    Topics on the Dynamics of Civil Structures, Volume 1, Proceedings of the 30th IMAC, A Conference and Exposition on Structural Dynamics, 2012, the first volume of six from the Conference, brings together 45 contributions to this important area of research and engineering. The collection presents early findings and case studies on fundamental and applied aspects of Structural Dynamics, including papers on: Human Induced Vibrations Bridge Dynamics Operational Modal Analysis Experimental Techniques and Modeling for Civil Structures System Identification for Civil Structures Method and Technologies for Bridge Monitoring Damage Detection for Civil Structures Structural Modeling Vibration Control Method and Approaches for Civil Structures Modal Testing of Civil Structures.

  18. Effect of TFE on the Helical Content of AK17 and HAL-1 Peptides: Theoretical Insights into the Mechanism of Helix Stabilization.

    Science.gov (United States)

    Vymětal, Jiří; Bednárová, Lucie; Vondrášek, Jiří

    2016-02-18

    Fluorinated alcohols such as 2,2,2-trifluoroethanol (TFE) are among the most frequently used cosolvents in experiment studies of peptides. They have significant effects on secondary structure and a particularly strong promotion of α-helix is induced by TFE. In this study we validated recently proposed force field parameters for TFE in molecular dynamics simulations with two model peptides-alanine-rich AK-17 and antimicrobial peptide halictine-1 (HAL-1). In the case of HAL-1, we characterized the effect of TFE on this peptide experimentally by ECD spectroscopy. Our TFE model in question reproduced the helix-promoting effect of TFE and provided insight into the mechanisms of TFE action on peptides. Our simulations confirmed the preferential interaction of TFE molecules with α-helices, although the TFE molecules accumulate in the vicinity of the peptides in various conformations. Moreover, we observed a significant effect of TFE on the thermodynamics of the helix-coil transition and a change in local conformational preferences in the unfolded (coil) state induced by TFE. In addition, our simulation-based analysis suggests that different mechanisms participate in helix stabilization in both model peptides in water and TFE solution. Our results thus support the picture of complex TFE action on peptides that is further diversified by the identity and intrinsic properties of the peptide.

  19. Structural optimization for nonlinear dynamic response

    DEFF Research Database (Denmark)

    Dou, Suguang; Strachan, B. Scott; Shaw, Steven W.

    2015-01-01

    by a single vibrating mode, or by a pair of internally resonant modes. The approach combines techniques from nonlinear dynamics, computational mechanics and optimization, and it allows one to relate the geometric and material properties of structural elements to terms in the normal form for a given resonance......Much is known about the nonlinear resonant response of mechanical systems, but methods for the systematic design of structures that optimize aspects of these responses have received little attention. Progress in this area is particularly important in the area of micro-systems, where nonlinear...... resonant behaviour is being used for a variety of applications in sensing and signal conditioning. In this work, we describe a computational method that provides a systematic means for manipulating and optimizing features of nonlinear resonant responses of mechanical structures that are described...

  20. Dynamics of Correlation Structure in Stock Market

    Directory of Open Access Journals (Sweden)

    Maman Abdurachman Djauhari

    2014-01-01

    Full Text Available In this paper a correction factor for Jennrich’s statistic is introduced in order to be able not only to test the stability of correlation structure, but also to identify the time windows where the instability occurs. If Jennrich’s statistic is only to test the stability of correlation structure along predetermined non-overlapping time windows, the corrected statistic provides us with the history of correlation structure dynamics from time window to time window. A graphical representation will be provided to visualize that history. This information is necessary to make further analysis about, for example, the change of topological properties of minimal spanning tree. An example using NYSE data will illustrate its advantages.

  1. Calculating evolutionary dynamics in structured populations.

    Directory of Open Access Journals (Sweden)

    Charles G Nathanson

    2009-12-01

    Full Text Available Evolution is shaping the world around us. At the core of every evolutionary process is a population of reproducing individuals. The outcome of an evolutionary process depends on population structure. Here we provide a general formula for calculating evolutionary dynamics in a wide class of structured populations. This class includes the recently introduced "games in phenotype space" and "evolutionary set theory." There can be local interactions for determining the relative fitness of individuals, but we require global updating, which means all individuals compete uniformly for reproduction. We study the competition of two strategies in the context of an evolutionary game and determine which strategy is favored in the limit of weak selection. We derive an intuitive formula for the structure coefficient, sigma, and provide a method for efficient numerical calculation.

  2. The structural dynamics of social class.

    Science.gov (United States)

    Kraus, Michael W; Park, Jun Won

    2017-12-01

    Individual agency accounts of social class persist in society and even in psychological science despite clear evidence for the role of social structures. This article argues that social class is defined by the structural dynamics of society. Specifically, access to powerful networks, groups, and institutions, and inequalities in wealth and other economic resources shape proximal social environments that influence how individuals express their internal states and motivations. An account of social class that highlights the means by which structures shape and are shaped by individuals guides our understanding of how people move up or down in the social class hierarchy, and provides a framework for interpreting neuroscience studies, experimental paradigms, and approaches that attempt to intervene on social class disparities. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Dynamic sign structures in visual art and music

    DEFF Research Database (Denmark)

    Zeller, Jörg

    2006-01-01

    Seemingly static meaning carriers in visual art are considered as aspects of holistic dynamical sign structures.......Seemingly static meaning carriers in visual art are considered as aspects of holistic dynamical sign structures....

  4. Dynamics of a structured neuron population

    International Nuclear Information System (INIS)

    Pakdaman, Khashayar; Salort, Delphine; Perthame, Benoît

    2010-01-01

    We study the dynamics of assemblies of interacting neurons. For large fully connected networks, the dynamics of the system can be described by a partial differential equation reminiscent of age-structure models used in mathematical ecology, where the 'age' of a neuron represents the time elapsed since its last discharge. The nonlinearity arises from the connectivity J of the network. We prove some mathematical properties of the model that are directly related to qualitative properties. On the one hand, we prove that it is well-posed and that it admits stationary states which, depending upon the connectivity, can be unique or not. On the other hand, we study the long time behaviour of solutions; both for small and large J, we prove the relaxation to the steady state describing asynchronous firing of the neurons. In the middle range, numerical experiments show that periodic solutions appear expressing re-synchronization of the network and asynchronous firing

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

    Science.gov (United States)

    Mansbach, Rachael A; Ferguson, Andrew L

    2015-03-14

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

  6. A supramolecular ''Double-cable'' structure with a 129{sub 44} helix in a columnar porphyrin-C{sub 60} dyad and its application in polymer solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Chien-Lung [College of Polymer Science and Polymer Engineering, The University of Akron, Akron, OH (United States); Department of Applied Chemistry, National Chiao Tung University, Hsinchu, Taiwan (China); Zhang, Wen-Bin; Sun, Hao-Jan; Van Horn, Ryan M.; Kulkarni, Rahul R.; Tsai, Chi-Chun; Gong, Xiong; Cheng, Stephen Z.D. [College of Polymer Science and Polymer Engineering, The University of Akron, Akron, OH (United States); Hsu, Chain-Shu [Department of Applied Chemistry, National Chiao Tung University, Hsinchu, Taiwan (China); Lotz, Bernard [Institut Charles Sadron, Strasbourg (France)

    2012-11-15

    A novel porphyrin-C{sub 60} dyad (PCD1) is designed and synthesized to investigate and manipulate the supramolecular structure where geometrically isotropic [such as [60]fullerene (C{sub 60})] and anisotropic [such as porphyrin (Por)] units coexist. It is observed that PCD1 possesses an enantiomeric phase behavior. The melting temperature of the stable PCD1 thermotropic phase is 160 C with a latent heat ({Delta}H) of 18.5 kJ mol{sup -1}. The phase formation is majorly driven by the cooperative intermolecular Por-Por and C{sub 60}-C{sub 60} interactions. Structural analysis reveals that this stable phase possesses a supramolecular ''double-cable'' structure with one p-type Por core columnar channel and three helical n-type C{sub 60} peripheral channels. These ''double-cable'' columns further pack into a hexagonal lattice with a = b = 4.65 nm, c = 41.3 nm, {alpha} = {beta} = 90 , and {gamma} = 120 . The column repeat unit is determined to possess a 129{sub 44} helix. With both donor (D; Pro) and acceptor (A; C{sub 60}) units having their own connecting channels as well as the large D/A interface within the supramolecular ''double-cable'' structure, PCD1 has photogenerated carriers with longer lifetimes compared to the conventional electron acceptor [6,6]-phenyl-C{sub 61}-butyric acid methyl ester. A phase-separated columnar morphology is observed in a bulk-heterojunction (BHJ) material made by the physical blend of a low band-gap conjugated polymer, poly[2,6-(4,4-bis-(2-ethylhexyl)-4H-cyclopenta [2,1-b;3,4-b']-dithiophene)-alt-4,7-(2,1,3-benzothia-diazole)] (PCPDTBT), and PCD1. With a specific phase structure in the solid state and in the blend, PCD1 is shown to be a promising candidate as a new electron acceptor in high performance BHJ polymer solar cells. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  7. The Dynamics and Structures of Adsorbed Surfaces

    DEFF Research Database (Denmark)

    Nielsen, M; Ellenson, W. D.; McTague, J. P.

    1978-01-01

    . Elastic neutron diffraction measurements, determining the two-dimensional structural ordering of the adsorbed films, have been performed on layers of N2, Ar, H2, D2, O2, Kr, and He. Measurements on layers of larger molecules such as CD4 and ND3 have also been reported. Inelastic neutron scattering...... measurements, studying the dynamics of the adsorbed films are only possible in a few especially favourable cases such as 36Ar and D2 films, where the coherent phonon scattering cross-sections are very large. In other cases incoherent scattering from hydrogen can give information about e.g. the mobility...

  8. Structural dynamics of turbo-machines

    CERN Document Server

    Rangwala, AS

    2009-01-01

    The book presents a detailed and comprehensive treatment of structural vibration evaluation of turbo-machines. Starting with the fundamentals of the theory of vibration as related to various aspects of rotating machines, the dynamic analysis procedures of a broad spectrum of turbo-machines is covered. An in-depth procedure for analyzing the torsional and flexural oscillations of the components and of the rotor-bearing system is presented. The latest trends in design and analysis are presented, chief among them: Blade and coupled disk-blade mod

  9. Dynamical structure of pure Lovelock gravity

    Science.gov (United States)

    Dadhich, Naresh; Durka, Remigiusz; Merino, Nelson; Miskovic, Olivera

    2016-03-01

    We study the dynamical structure of pure Lovelock gravity in spacetime dimensions higher than four using the Hamiltonian formalism. The action consists of a cosmological constant and a single higher-order polynomial in the Riemann tensor. Similarly to the Einstein-Hilbert action, it possesses a unique constant curvature vacuum and charged black hole solutions. We analyze physical degrees of freedom and local symmetries in this theory. In contrast to the Einstein-Hilbert case, the number of degrees of freedom depends on the background and can vary from zero to the maximal value carried by the Lovelock theory.

  10. Band structure dynamics in indium wires

    Science.gov (United States)

    Chávez-Cervantes, M.; Krause, R.; Aeschlimann, S.; Gierz, I.

    2018-05-01

    One-dimensional indium wires grown on Si(111) substrates, which are metallic at high temperatures, become insulating below ˜100 K due to the formation of a charge density wave (CDW). The physics of this transition is not conventional and involves a multiband Peierls instability with strong interband coupling. This CDW ground state is readily destroyed with femtosecond laser pulses resulting in a light-induced insulator-to-metal phase transition. The current understanding of this transition remains incomplete, requiring measurements of the transient electronic structure to complement previous investigations of the lattice dynamics. Time- and angle-resolved photoemission spectroscopy with extreme ultraviolet radiation is applied to this end. We find that the transition from the insulating to the metallic band structure occurs within ˜660 fs, which is a fraction of the amplitude mode period. The long lifetime of the transient state (>100 ps) is attributed to trapping in a metastable state in accordance with previous work.

  11. Structure and dynamics of molten salts

    International Nuclear Information System (INIS)

    Rovere, M.; Tosi, M.P.

    1986-02-01

    Modern techniques of liquid state physics have been successfully used over the last decade to probe the microscopic structure and dynamics of a variety of multicomponent liquids in which relative ordering of the species is present near freezing. The alkali halides are prototypes for this specific type of short range order in relation to the nature of bonding, but the systems in question include also other monovalent and polyvalent metal-ion halides, alkali-based intermetallic compounds, and chalcogen-based alloys. A viewpoint is taken in this review which gives attention to relations between liquid and solid phase properties across melting for compound systems at stoichiometric composition. In addition, large deviations from stoichiometry can be realized in the liquid phase, to display trends of evolution of structure, bonding and electronic states with composition. (author)

  12. Molecular structures and intramolecular dynamics of pentahalides

    Science.gov (United States)

    Ischenko, A. A.

    2017-03-01

    This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface - barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.

  13. Structural Dynamics of Tropical Moist Forest Gaps

    Science.gov (United States)

    Hunter, Maria O.; Keller, Michael; Morton, Douglas; Cook, Bruce; Lefsky, Michael; Ducey, Mark; Saleska, Scott; de Oliveira, Raimundo Cosme; Schietti, Juliana

    2015-01-01

    Gap phase dynamics are the dominant mode of forest turnover in tropical forests. However, gap processes are infrequently studied at the landscape scale. Airborne lidar data offer detailed information on three-dimensional forest structure, providing a means to characterize fine-scale (1 m) processes in tropical forests over large areas. Lidar-based estimates of forest structure (top down) differ from traditional field measurements (bottom up), and necessitate clear-cut definitions unencumbered by the wisdom of a field observer. We offer a new definition of a forest gap that is driven by forest dynamics and consistent with precise ranging measurements from airborne lidar data and tall, multi-layered tropical forest structure. We used 1000 ha of multi-temporal lidar data (2008, 2012) at two sites, the Tapajos National Forest and Ducke Reserve, to study gap dynamics in the Brazilian Amazon. Here, we identified dynamic gaps as contiguous areas of significant growth, that correspond to areas > 10 m2, with height gap at Tapajos National Forest (4.8 %) as compared to Ducke Reserve (2.0 %). On average, gaps were smaller at Ducke Reserve and closed slightly more rapidly, with estimated height gains of 1.2 m y-1 versus 1.1 m y-1 at Tapajos. At the Tapajos site, height growth in gap centers was greater than the average height gain in gaps (1.3 m y-1 versus 1.1 m y-1). Rates of height growth between lidar acquisitions reflect the interplay between gap edge mortality, horizontal ingrowth and gap size at the two sites. We estimated that approximately 10 % of gap area closed via horizontal ingrowth at Ducke Reserve as opposed to 6 % at Tapajos National Forest. Height loss (interpreted as repeat damage and/or mortality) and horizontal ingrowth accounted for similar proportions of gap area at Ducke Reserve (13 % and 10 %, respectively). At Tapajos, height loss had a much stronger signal (23 % versus 6 %) within gaps. Both sites demonstrate limited gap contagiousness defined by an

  14. Chemical Structure and Dynamics annual report 1997

    International Nuclear Information System (INIS)

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

    1998-03-01

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

  15. Modeling Insurgent Network Structure and Dynamics

    Science.gov (United States)

    Gabbay, Michael; Thirkill-Mackelprang, Ashley

    2010-03-01

    We present a methodology for mapping insurgent network structure based on their public rhetoric. Indicators of cooperative links between insurgent groups at both the leadership and rank-and-file levels are used, such as joint policy statements or joint operations claims. In addition, a targeting policy measure is constructed on the basis of insurgent targeting claims. Network diagrams which integrate these measures of insurgent cooperation and ideology are generated for different periods of the Iraqi and Afghan insurgencies. The network diagrams exhibit meaningful changes which track the evolution of the strategic environment faced by insurgent groups. Correlations between targeting policy and network structure indicate that insurgent targeting claims are aimed at establishing a group identity among the spectrum of rank-and-file insurgency supporters. A dynamical systems model of insurgent alliance formation and factionalism is presented which evolves the relationship between insurgent group dyads as a function of their ideological differences and their current relationships. The ability of the model to qualitatively and quantitatively capture insurgent network dynamics observed in the data is discussed.

  16. Chemical Structure and Dynamics annual report 1997

    Energy Technology Data Exchange (ETDEWEB)

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

    1998-03-01

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

  17. Geometry of the toroidal N-helix: optimal-packing and zero-twist

    DEFF Research Database (Denmark)

    Olsen, Kasper; Bohr, Jakob

    2012-01-01

    Two important geometrical properties of N-helix structures are influenced by bending. One is maximizing the volume fraction, which is called optimal-packing, and the other is having a vanishing strain-twist coupling, which is called zero-twist. Zero-twist helices rotate neither in one nor...... helix. General N-helices are discussed, as well as zero-twist helices for N > 1. The derived geometrical restrictions are gradually modified by changing the aspect ratio of the torus....

  18. Nonlinear time-dependent simulation of helix traveling wave tubes

    International Nuclear Information System (INIS)

    Peng Wei-Feng; Yang Zhong-Hai; Hu Yu-Lu; Li Jian-Qing; Lu Qi-Ru; Li Bin

    2011-01-01

    A one-dimensional nonlinear time-dependent theory for helix traveling wave tubes is studied. A generalized electromagnetic field is applied to the expression of the radio frequency field. To simulate the variations of the high frequency structure, such as the pitch taper and the effect of harmonics, the spatial average over a wavelength is substituted by a time average over a wave period in the equation of the radio frequency field. Under this assumption, the space charge field of the electron beam can be treated by a space charge wave model along with the space charge coefficient. The effects of the radio frequency and the space charge fields on the electrons are presented by the equations of the electron energy and the electron phase. The time-dependent simulation is compared with the frequency-domain simulation for a helix TWT, which validates the availability of this theory. (interdisciplinary physics and related areas of science and technology)

  19. Dynamic Analysis of Partially Embedded Structures Considering Soil-Structure Interaction in Time Domain

    OpenAIRE

    Mahmoudpour, Sanaz; Attarnejad, Reza; Behnia, Cambyse

    2011-01-01

    Analysis and design of structures subjected to arbitrary dynamic loadings especially earthquakes have been studied during past decades. In practice, the effects of soil-structure interaction on the dynamic response of structures are usually neglected. In this study, the effect of soil-structure interaction on the dynamic response of structures has been examined. The substructure method using dynamic stiffness of soil is used to analyze soil-structure system. A coupled model based on finite el...

  20. Fluctuations in the DNA double helix

    Science.gov (United States)

    Peyrard, M.; López, S. C.; Angelov, D.

    2007-08-01

    DNA is not the static entity suggested by the famous double helix structure. It shows large fluctuational openings, in which the bases, which contain the genetic code, are temporarily open. Therefore it is an interesting system to study the effect of nonlinearity on the physical properties of a system. A simple model for DNA, at a mesoscopic scale, can be investigated by computer simulation, in the same spirit as the original work of Fermi, Pasta and Ulam. These calculations raise fundamental questions in statistical physics because they show a temporary breaking of equipartition of energy, regions with large amplitude fluctuations being able to coexist with regions where the fluctuations are very small, even when the model is studied in the canonical ensemble. This phenomenon can be related to nonlinear excitations in the model. The ability of the model to describe the actual properties of DNA is discussed by comparing theoretical and experimental results for the probability that base pairs open an a given temperature in specific DNA sequences. These studies give us indications on the proper description of the effect of the sequence in the mesoscopic model.

  1. Electrostatic bending response of a charged helix

    Science.gov (United States)

    Zampetaki, A. V.; Stockhofe, J.; Schmelcher, P.

    2018-04-01

    We explore the electrostatic bending response of a chain of charged particles confined on a finite helical filament. We analyze how the energy difference Δ E between the bent and the unbent helical chain scales with the length of the helical segment and the radius of curvature and identify features that are not captured by the standard notion of the bending rigidity, normally used as a measure of bending tendency in the linear response regime. Using Δ E to characterize the bending response of the helical chain we identify two regimes with qualitatively different bending behaviors for the ground state configuration: the regime of small and the regime of large radius-to-pitch ratio, respectively. Within the former regime, Δ E changes smoothly with the variation of the system parameters. Of particular interest are its oscillations with the number of charged particles encountered for commensurate fillings which yield length-dependent oscillations in the preferred bending direction of the helical chain. We show that the origin of these oscillations is the nonuniformity of the charge distribution caused by the long-range character of the Coulomb interactions and the finite length of the helix. In the second regime of large values of the radius-to-pitch ratio, sudden changes in the ground state structure of the charges occur as the system parameters vary, leading to complex and discontinuous variations in the ground state bending response Δ E .

  2. Nonparametric inference of network structure and dynamics

    Science.gov (United States)

    Peixoto, Tiago P.

    The network structure of complex systems determine their function and serve as evidence for the evolutionary mechanisms that lie behind them. Despite considerable effort in recent years, it remains an open challenge to formulate general descriptions of the large-scale structure of network systems, and how to reliably extract such information from data. Although many approaches have been proposed, few methods attempt to gauge the statistical significance of the uncovered structures, and hence the majority cannot reliably separate actual structure from stochastic fluctuations. Due to the sheer size and high-dimensionality of many networks, this represents a major limitation that prevents meaningful interpretations of the results obtained with such nonstatistical methods. In this talk, I will show how these issues can be tackled in a principled and efficient fashion by formulating appropriate generative models of network structure that can have their parameters inferred from data. By employing a Bayesian description of such models, the inference can be performed in a nonparametric fashion, that does not require any a priori knowledge or ad hoc assumptions about the data. I will show how this approach can be used to perform model comparison, and how hierarchical models yield the most appropriate trade-off between model complexity and quality of fit based on the statistical evidence present in the data. I will also show how this general approach can be elegantly extended to networks with edge attributes, that are embedded in latent spaces, and that change in time. The latter is obtained via a fully dynamic generative network model, based on arbitrary-order Markov chains, that can also be inferred in a nonparametric fashion. Throughout the talk I will illustrate the application of the methods with many empirical networks such as the internet at the autonomous systems level, the global airport network, the network of actors and films, social networks, citations among

  3. Structure, dynamics, and function of biomolecules

    International Nuclear Information System (INIS)

    Frauenfelder, H.; Berendzen, J.R.; Garcia, A.; Gupta, G.; Olah, G.A.; Terwilliger, T.C.; Trewhella, J.; Wood, C.C.; Woodruff, W.H.

    1998-01-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The authors enhanced Los Alamos' core competency in Bioscience and Biotechnology by building on present strengths in experimental techniques, theory, high-performance computing, modeling, and simulation applied to biomolecular structure, dynamics, and function. Specifically, the authors strengthened their capabilities in neutron/x-ray scattering, x-ray crystallography, NMR, laser, and optical spectroscopies. Initially they focused on supporting the Los alamos Neutron Science Center (LANSCE) in the design and implementation of new neutron scattering instrumentation, they developed new methods for analysis of scattering data, and they developed new projects to study the structures of biomolecular complexes. The authors have also worked to strengthen interactions between theory and experiment, and between the biological and physical sciences. They sponsored regular meetings of members from all interested LANL technical divisions, and supported two lecture series: ''Biology for Physicists'' and ''Issues in Modern Biology''. They also supported the formation of interdisciplinary/inter-divisional teams to develop projects in science-based bioremediation and an integrated structural biology resource. Finally, they successfully worked with a multidisciplinary team to put forward the Laboratory's Genome and Beyond tactical goal

  4. Plasma and current structures in dynamical pinches

    International Nuclear Information System (INIS)

    Butov, I.Ya.; Matveev, Yu.V.

    1981-01-01

    Dynamics of plasma layers and current structure in aZ-pinch device has been experimentally investigated. It is found that shaping of a main current envelope is ended with its explosion-like expansion, the pinch decaying after compression to separated current filaments. It is also shown that filling of a region outside the pinch with plasma and currents alternating in directions occurs owing to interaction of current loops (inductions) formed in a magnetic piston during its compression with reflected shock wave. Current circulating in the loops sometimes exceeds 1.5-2 times the current of discharge circuit. The phenomena noted appear during development of superheat instability and can be realized, for example, in theta-pinches, plasma focuses, tokamaks. The experiments were carried out at the Dynamic Zeta-pinch device at an energy reserse of up to 15 kJ (V 0 =24 kV) in a capacitor bank. Half-period of the discharge current is 9 μs; Isub(max)=3.5x10sup(5) A. Back current guide surrounding a china chamber of 28 cm diameter and 50 cm length is made in the form of a hollow cylinder. Initial chamber vacuum is 10 -6 torr [ru

  5. Wheat yield dynamics: a structural econometric analysis.

    Science.gov (United States)

    Sahin, Afsin; Akdi, Yilmaz; Arslan, Fahrettin

    2007-10-15

    In this study we initially have tried to explore the wheat situation in Turkey, which has a small-open economy and in the member countries of European Union (EU). We have observed that increasing the wheat yield is fundamental to obtain comparative advantage among countries by depressing domestic prices. Also the changing structure of supporting schemes in Turkey makes it necessary to increase its wheat yield level. For this purpose, we have used available data to determine the dynamics of wheat yield by Ordinary Least Square Regression methods. In order to find out whether there is a linear relationship among these series we have checked each series whether they are integrated at the same order or not. Consequently, we have pointed out that fertilizer usage and precipitation level are substantial inputs for producing high wheat yield. Furthermore, in respect for our model, fertilizer usage affects wheat yield more than precipitation level.

  6. Chemical structure and dynamics. Annual report 1994

    Energy Technology Data Exchange (ETDEWEB)

    Colson, S.D.

    1995-07-01

    The Chemical Structure and Dynamics program was organized as a major component of Pacific Northwest Laboratory`s Environmental and Molecular Sciences Laboratory (EMSL), a state-of-the-art collaborative facility for studies of chemical structure and dynamics. Our program responds to the need for a fundamental, molecular-level understanding of chemistry at the wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces, and (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage. This research effort was initiated in 1989 and will continue to evolve over the next few years into a program of rigorous studies of fundamental molecular processes in model systems, such as well-characterized surfaces, single-component solutions, clusters, and biological molecules; and studies of complex systems found in the environment (multispecies, multiphase solutions; solid/liquid, liquid/liquid, and gas/surface interfaces; colloidal dispersions; ultrafine aerosols; and functioning biological systems). The success of this program will result in the achievement of a quantitative understanding of chemical reactions at interfaces, and more generally in condensed media, that is comparable to that currently available for gas-phase reactions. This understanding will form the basis for the development of a priori theories for predictions of macroscopic chemical behavior in condensed and heterogeneous media, adding significantly to the value of field-scale environmental models, the prediction of short- and long-term nuclear waste storage stabilities, and other problems related to the primary missions of the DOE.

  7. MULTISCALE DYNAMICS OF SOLAR MAGNETIC STRUCTURES

    International Nuclear Information System (INIS)

    Uritsky, Vadim M.; Davila, Joseph M.

    2012-01-01

    Multiscale topological complexity of the solar magnetic field is among the primary factors controlling energy release in the corona, including associated processes in the photospheric and chromospheric boundaries. We present a new approach for analyzing multiscale behavior of the photospheric magnetic flux underlying these dynamics as depicted by a sequence of high-resolution solar magnetograms. The approach involves two basic processing steps: (1) identification of timing and location of magnetic flux origin and demise events (as defined by DeForest et al.) by tracking spatiotemporal evolution of unipolar and bipolar photospheric regions, and (2) analysis of collective behavior of the detected magnetic events using a generalized version of the Grassberger-Procaccia correlation integral algorithm. The scale-free nature of the developed algorithms makes it possible to characterize the dynamics of the photospheric network across a wide range of distances and relaxation times. Three types of photospheric conditions are considered to test the method: a quiet photosphere, a solar active region (NOAA 10365) in a quiescent non-flaring state, and the same active region during a period of M-class flares. The results obtained show (1) the presence of a topologically complex asymmetrically fragmented magnetic network in the quiet photosphere driven by meso- and supergranulation, (2) the formation of non-potential magnetic structures with complex polarity separation lines inside the active region, and (3) statistical signatures of canceling bipolar magnetic structures coinciding with flaring activity in the active region. Each of these effects can represent an unstable magnetic configuration acting as an energy source for coronal dissipation and heating.

  8. Annual Report 1998: Chemical Structure and Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    SD Colson; RS McDowell

    1999-05-10

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

  9. DNA binding specificity of the basic-helix-loop-helix protein MASH-1.

    Science.gov (United States)

    Meierhan, D; el-Ariss, C; Neuenschwander, M; Sieber, M; Stackhouse, J F; Allemann, R K

    1995-09-05

    Despite the high degree of sequence similarity in their basic-helix-loop-helix (BHLH) domains, MASH-1 and MyoD are involved in different biological processes. In order to define possible differences between the DNA binding specificities of these two proteins, we investigated the DNA binding properties of MASH-1 by circular dichroism spectroscopy and by electrophoretic mobility shift assays (EMSA). Upon binding to DNA, the BHLH domain of MASH-1 underwent a conformational change from a mainly unfolded to a largely alpha-helical form, and surprisingly, this change was independent of the specific DNA sequence. The same conformational transition could be induced by the addition of 20% 2,2,2-trifluoroethanol. The apparent dissociation constants (KD) of the complexes of full-length MASH-1 with various oligonucleotides were determined from half-saturation points in EMSAs. MASH-1 bound as a dimer to DNA sequences containing an E-box with high affinity KD = 1.4-4.1 x 10(-14) M2). However, the specificity of DNA binding was low. The dissociation constant for the complex between MASH-1 and the highest affinity E-box sequence (KD = 1.4 x 10(-14) M2) was only a factor of 10 smaller than for completely unrelated DNA sequences (KD = approximately 1 x 10(-13) M2). The DNA binding specificity of MASH-1 was not significantly increased by the formation of an heterodimer with the ubiquitous E12 protein. MASH-1 and MyoD displayed similar binding site preferences, suggesting that their different target gene specificities cannot be explained solely by differential DNA binding. An explanation for these findings is provided on the basis of the known crystal structure of the BHLH domain of MyoD.

  10. The swimming of a perfect deforming helix

    Science.gov (United States)

    Koens, Lyndon; Zhang, Hang; Mourran, Ahmed; Lauga, Eric

    2017-11-01

    Many bacteria rotate helical flagellar filaments in order to swim. When at rest or rotated counter-clockwise these flagella are left handed helices but they undergo polymorphic transformations to right-handed helices when the motor is reversed. These helical deformations themselves can generate motion, with for example Rhodobacter sphaeroides using the polymorphic transformation of the flagellum to generate rotation, or Spiroplasma propagating a change of helix handedness across its body's length to generate forward motion. Recent experiments reported on an artificial helical microswimmer generating motion without a propagating change in handedness. Made of a temperature sensitive gel, these swimmers moved by changing the dimensions of the helix in a non-reciprocal way. Inspired by these results and helix's ubiquitous presence in the bacterial world, we investigate how a deforming helix moves within a viscous fluid. Maintaining a single handedness along its entire length, we discuss how a perfect deforming helix can create a non-reciprocal swimming stroke, identify its principle directions of motion, and calculate the swimming kinematics asymptotically.

  11. A smallest 6 kda metalloprotease, mini-matrilysin, in living world: a revolutionary conserved zinc-dependent proteolytic domain- helix-loop-helix catalytic zinc binding domain (ZBD

    Directory of Open Access Journals (Sweden)

    Yu Wei-Hsuan

    2012-05-01

    Full Text Available Abstract Background The Aim of this study is to study the minimum zinc dependent metalloprotease catalytic folding motif, helix B Met loop-helix C, with proteolytic catalytic activities in metzincin super family. The metzincin super family share a catalytic domain consisting of a twisted five-stranded β sheet and three long α helices (A, B and C. The catalytic zinc is at the bottom of the cleft and is ligated by three His residues in the consensus sequence motif, HEXXHXXGXXH, which is located in helix B and part of the adjacent Met turn region. An interesting question is - what is the minimum portion of the enzyme that still possesses catalytic and inhibitor recognition?” Methods We have expressed a 60-residue truncated form of matrilysin which retains only the helix B-Met turn-helix C region and deletes helix A and the five-stranded β sheet which form the upper portion of the active cleft. This is only 1/4 of the full catalytic domain. The E. coli derived 6 kDa MMP-7 ZBD fragments were purified and refolded. The proteolytic activities were analyzed by Mca-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2 peptide assay and CM-transferrin zymography analysis. SC44463, BB94 and Phosphoramidon were computationally docked into the 3day structure of the human MMP7 ZBD and TAD and thermolysin using the docking program GOLD. Results This minimal 6 kDa matrilysin has been refolded and shown to have proteolytic activity in the Mca-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2 peptide assay. Triton X-100 and heparin are important factors in the refolding environment for this mini-enzyme matrilysin. This minienzyme has the proteolytic activity towards peptide substrate, but the hexamer and octamer of the mini MMP-7 complex demonstrates the CM-transferrin proteolytic activities in zymographic analysis. Peptide digestion is inhibited by SC44463, specific MMP7 inhibitors, but not phosphorimadon. Interestingly, the mini MMP-7 can be processed by autolysis and producing ~ 6

  12. Localization of binding sites of Ulex europaeus I, Helix pomatia and Griffonia simplicifolia I-B4 lectins and analysis of their backbone structures by several glycosidases and poly-N-acetyllactosamine-specific lectins in human breast carcinomas.

    Science.gov (United States)

    Ito, N; Imai, S; Haga, S; Nagaike, C; Morimura, Y; Hatake, K

    1996-09-01

    Several studies have shown the deletion of blood group A or B antigens and the accumulation of H antigens in human breast carcinomas. Other studies have independently demonstrated that the binding sites of lectins such as Helix pomatia agglutinin (HPA) and Griffonia simplicifolia agglutinin I-B4 (GSAI-B4) are highly expressed in these cells. In order to clarify the molecular mechanisms of malignant transformation and metastasis of carcinoma cells, it is important to understand the relationship between such phenotypically distinct events. For this purpose, we examined whether the binding sites of these lectins and Ulex europaeus agglutinin I (UEA-I) are expressed concomitantly in the same carcinoma cells and analyzed their backbone structures. The expression of the binding sites of these lectins was observed independently of the blood group (ABO) of the patients and was not affected by the histological type of the carcinomas. Observation of serial sections stained with these lectins revealed that the distribution of HPA binding sites was almost identical to that of GSAI-B4 in most cases. Furthermore, in some cases, UEA-I binding patterns were similar to those of HPA and GSAI-B4 but in other cases, mosaic staining patterns with these lectins were also observed, i.e., some cell clusters were stained with both HPA and GSAI-B4 but not with UEA-I and adjacent cell clusters were stained only with UEA-I. Digestion with endo-beta-galactosidase or N-glycosidase F markedly reduced the staining intensity of these lectins. Together with the reduction of staining by these lectins, reactivity with Griffonia simplicifolia agglutinin II appeared in carcinoma cells following endo-beta-galactosidase digestion. Among the lectins specific to poly-N-acetyllactosamine, Lycopersicon esculentum agglutinin (LEA) most vividly and consistently stained the cancer cells. Next to LEA, pokeweed mitogen agglutinin was also effective in staining these cells. Carcinoma cells reactive with these

  13. Indoor footstep localization from structural dynamics instrumentation

    Science.gov (United States)

    Poston, Jeffrey D.; Buehrer, R. Michael; Tarazaga, Pablo A.

    2017-05-01

    Measurements from accelerometers originally deployed to measure a building's structural dynamics can serve a new role: locating individuals moving within a building. Specifically, this paper proposes measurements of footstep-generated vibrations as a novel source of information for localization. The complexity of wave propagation in a building (e.g., dispersion and reflection) limits the utility of existing algorithms designed to locate, for example, the source of sound in a room or radio waves in free space. This paper develops enhancements for arrival time determination and time difference of arrival localization in order to address the complexities posed by wave propagation within a building's structure. Experiments with actual measurements from an instrumented public building demonstrate the potential of locating footsteps to sub-meter accuracy. Furthermore, this paper explains how to forecast performance in other buildings with different sensor configurations. This localization capability holds the potential to assist public safety agencies in building evacuation and incidence response, to facilitate occupancy-based optimization of heating or cooling and to inform facility security.

  14. An α-Helix-Mimicking 12,13-Helix: Designed α/β/γ-Foldamers as Selective Inhibitors of Protein-Protein Interactions.

    Science.gov (United States)

    Grison, Claire M; Miles, Jennifer A; Robin, Sylvie; Wilson, Andrew J; Aitken, David J

    2016-09-05

    A major current challenge in bioorganic chemistry is the identification of effective mimics of protein secondary structures that act as inhibitors of protein-protein interactions (PPIs). In this work, trans-2-aminocyclobutanecarboxylic acid (tACBC) was used as the key β-amino acid component in the design of α/β/γ-peptides to structurally mimic a native α-helix. Suitably functionalized α/β/γ-peptides assume an α-helix-mimicking 12,13-helix conformation in solution, exhibit enhanced proteolytic stability in comparison to the wild-type α-peptide parent sequence from which they are derived, and act as selective inhibitors of the p53/hDM2 interaction. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  15. Structure-preserving integrators in nonlinear structural dynamics and flexible multibody dynamics

    CERN Document Server

    2016-01-01

    This book focuses on structure-preserving numerical methods for flexible multibody dynamics, including nonlinear elastodynamics and geometrically exact models for beams and shells. It also deals with the newly emerging class of variational integrators as well as Lie-group integrators. It discusses two alternative approaches to the discretization in space of nonlinear beams and shells. Firstly, geometrically exact formulations, which are typically used in the finite element community and, secondly, the absolute nodal coordinate formulation, which is popular in the multibody dynamics community. Concerning the discretization in time, the energy-momentum method and its energy-decaying variants are discussed. It also addresses a number of issues that have arisen in the wake of the structure-preserving discretization in space. Among them are the parameterization of finite rotations, the incorporation of algebraic constraints and the computer implementation of the various numerical methods. The practical application...

  16. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

    Science.gov (United States)

    2018-01-01

    With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA–ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field. PMID:29297679

  17. Matrix of transmission in structural dynamics

    International Nuclear Information System (INIS)

    Mukherjee, S.

    1975-01-01

    Within the last few years numerous papers have been published on the subject of matrix method in elasto-mechanics. 'Matrix of Transmission' is one of the methods in this field which has gained considerable attention in recent years. The basic philosophy adopted in this method is based on the idea of breaking up a complicated system into component parts with simple elastic and dynamic properties which can be readily expressed in matrix form. These component matrices are considered as building blocks, which are fitted together according to a set of predetermined rules which then provide the static and dynamic properties of the entire system. A common type of system occuring in engineering practice consists of a number of elements linked together end to end in the form of a chain. The 'Transfer Matrix' is ideally suited for such a system, because only successive multiplication is necessary to connect these elements together. The number of degrees of freedom and intermediate conditions present no difficulty. Although the 'Transfer Matrix' method is suitable for the treatment of branched and coupled systems its application to systems which do not have predominant chain topology is not effective. Apart from the requirement that the system be linearely elastic, no other restrictions are made. In this paper, it is intended to give a general outline and theoretical formulation of 'Transfer Matrix' and then its application to actual problems in structural dynamics related to seismic analysis. The natural frequencies of a freely vibrating elastic system can be found by applying proper end conditions. The end conditions will yield the frequency determinate to zero. By using a suitable numerical method, the natural frequencies and mode shapes are determined by making a frequency sweep within the range of interest. Results of an analysis of a typical nuclear building by this method show very close agreement with the results obtained by using ASKA and SAP IV program. Therefore

  18. Study on Human-structure Dynamic Interaction in Civil Engineering

    Science.gov (United States)

    Gao, Feng; Cao, Li Lin; Li, Xing Hua

    2018-06-01

    The research of human-structure dynamic interaction are reviewed. Firstly, the influence of the crowd load on structural dynamic characteristics is introduced and the advantages and disadvantages of different crowd load models are analyzed. Then, discussing the influence of structural vibration on the human-induced load, especially the influence of different stiffness structures on the crowd load. Finally, questions about human-structure interaction that require further study are presented.

  19. Simulating CubeSat Structure Deployment Dynamics, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — There is high value in simulating the nonlinear dynamics of stowing, deploying, and performance of deployable space structures, especially given the profound...

  20. Structural dynamics in fast reactor accident analysis

    International Nuclear Information System (INIS)

    Fistedis, S.H.

    1975-01-01

    Analyses and codes are under development combining the hydrodynamics and solid mechanics (and more recently the bubble dynamics) phenomena to gage the stresses, strains, and deformations of important primary components, as well as the overall adequacy of primary and secondary containments. An arbitrary partition of the structural components treated evolves into (1) a core mechanics effort; and (2) a primary system and containment program. The primary system and containment program treats the structural response of components beyond the core, starting with the core barrel. Combined hydrodynamics-solid mechanics codes provide transient stresses and strains and final deformations for components such as the reactor vessel, reactor cover, cover holddown bolts, as well as the pulses for which the primary piping system is to be analyzed. Both, Lagrangian and Eulerian two-dimensional codes are under development, which provide greater accuracy and longer durations for the treatment of HCDA. The codes are being augmented with bubble migration capability pertaining to the latter stages of the HCDA, after slug impact. Recent developments involve the adaptation of the 2-D Eulerian primary system code to the 2-D elastic-plastic treatment of primary piping. Pulses are provided at the vessel-primary piping interfaces of the inlet and outlet nozzles, calculation includes the elbows and pressure drops along the components of the primary piping system. Recent improvements to the primary containment codes include introduction of bending strength in materials, Langrangian mesh regularization techniques, and treatment of energy absorbing materials for the slug impact. Another development involves the combination of a 2-D finite element code for the reactor cover with the hydrodynamic containment code

  1. Dynamical structure of hadron emission sources

    CERN Document Server

    Zhao Xi; Zhao Shu Song

    2000-01-01

    NA22 experimental data of the triplet seagull effects show that the Doppler effects of hadron emission sources exist exactly in hadron- hadron collisions. Every source possesses the same average energy (CMS) approximately. The collective seagull effects can be also explained by the (aQ)/sup nu /K/sub nu / (aQ) distributions (generalized functions). The dynamical structure of a hadron emission source is described by the (aQ)/sup nu /K/sub nu / (aQ) distributions. The anomalous dimensions of the pionic quantum fields are gamma /sub B/(g/sub R/)=-0.045+or-0.012, which control the singularities of the production amplitude in quantum field theory. The mathematical parameter epsilon =4-D (the dimension D of space time) in the Feynman integrals can be replaced by the anomalous gamma /sub B/(g/sub R/) of the quantum fields for the regularization. (-2 gamma /sub B/(g/sub R/) to or from epsilon /2=1/ln( Lambda /sup 2//m /sup 2/) Lambda to infinity ). (26 refs).

  2. Dynamical structure of hadron emission sources

    International Nuclear Information System (INIS)

    Zhao Xi; Huang Bangrong; Zhao Shusong

    2000-01-01

    NA22 experimental data of the triplet seagull effects show that the Doppler effects of the hadron emission sources exist exactly in the hadron-hadron collisions. Every source possesses the same average energy (CMS) approximately. The collective seagull effects can be also explained by the (aQ) ν K ν (aQ) distributions (Generalized functions). The dynamical structure of a hadron emission source is described by the (aQ) ν K ν (aQ) distributions. The anomalous dimensions of the pionic quantum fields are γ B (g R ) = - 0.045 +- 0.012, which control the singularities of the production amplitude in quantum field theory. The mathematical parameter ε = 4-D (the dimension D of space time) in the Feynman integrals can be replaced by the anomalous γ B (g R ) of the quantum fields for the regularization. (-2γ B (g R )↔ε/2 1/ln(Λ 2 /m 2 )Λ→∞)

  3. Dynamical structure of linearized GL(4) gravities

    International Nuclear Information System (INIS)

    Aragone, C.; Restuccia, A.

    1978-01-01

    The physical content of the three more natural models of GL(4) gravity is analyzed, for the case of weak fields. It is shown that the first model is the linearized version of Yang's one-tensor-field gravity and is a scalar-tensor theory, with its scalar part contained in a symmetric tensor. The second and the third linearized models, which can both be derived from the fourth-order action postulated by Yang, are two-tensor decoupled systems. In both cases one of the tensors is the symmetric weak metric gravity tensor field. the second tensor appearing in these two models, representing the GL(4)-gauge field, is either a linearized symmetric affinity (in the second model) or a linearized but nonsymmetric affinity (for the third model). It is shown that in these last two cases the affinity contains a helicity-3 propagating field. Owing to the presence of helicity-3 fields it is shown that it is better to regard Yang's action as an action for a two-tensor system instead of trying to recover from a pure gravity (one-tensor-field) action. Finally, it is shown what is the dynamical structure of the second and third linearized two-tensor models which can be derived from Yang's action. (author)

  4. Flexible joints in structural and multibody dynamics

    Directory of Open Access Journals (Sweden)

    O. A. Bauchau

    2013-02-01

    Full Text Available Flexible joints, sometimes called bushing elements or force elements, are found in all structural and multibody dynamics codes. In their simplest form, flexible joints simply consist of sets of three linear and three torsional springs placed between two nodes of the model. For infinitesimal deformations, the selection of the lumped spring constants is an easy task, which can be based on a numerical simulation of the joint or on experimental measurements. If the joint undergoes finite deformations, identification of its stiffness characteristics is not so simple, specially if the joint is itself a complex system. When finite deformations occur, the definition of deformation measures becomes a critical issue. This paper proposes a family of tensorial deformation measures suitable for elastic bodies of finite dimension. These families are generated by two parameters that can be used to modify the constitutive behavior of the joint, while maintaining the tensorial nature of the deformation measures. Numerical results demonstrate the objectivity of the deformations measures, a feature that is not shared by the deformations measures presently used in the literature. The impact of the choice of the two parameters on the constitutive behavior of the flexible joint is also investigated.

  5. Chirality-specific lift forces of helix under shear flows: Helix perpendicular to shear plane.

    Science.gov (United States)

    Zhang, Qi-Yi

    2017-02-01

    Chiral objects in shear flow experience a chirality-specific lift force. Shear flows past helices in a low Reynolds number regime were studied using slender-body theory. The chirality-specific lift forces in the vorticity direction experienced by helices are dominated by a set of helix geometry parameters: helix radius, pitch length, number of turns, and helix phase angle. Its analytical formula is given. The chirality-specific forces are the physical reasons for the chiral separation of helices in shear flow. Our results are well supported by the latest experimental observations. © 2016 Wiley Periodicals, Inc.

  6. Elevated temperature triggers human respiratory syncytial virus F protein six-helix bundle formation

    International Nuclear Information System (INIS)

    Yunus, Abdul S.; Jackson, Trent P.; Crisafi, Katherine; Burimski, Irina; Kilgore, Nicole R.; Zoumplis, Dorian; Allaway, Graham P.; Wild, Carl T.; Salzwedel, Karl

    2010-01-01

    Human respiratory syncytial virus (RSV) is a major cause of severe lower respiratory tract infection in infants, immunocompromised patients, and the elderly. The RSV fusion (F) protein mediates fusion of the viral envelope with the target cell membrane during virus entry and is a primary target for antiviral drug and vaccine development. The F protein contains two heptad repeat regions, HR1 and HR2. Peptides corresponding to these regions form a six-helix bundle structure that is thought to play a critical role in membrane fusion. However, characterization of six-helix bundle formation in native RSV F protein has been hindered by the fact that a trigger for F protein conformational change has yet to be identified. Here we demonstrate that RSV F protein on the surface of infected cells undergoes a conformational change following exposure to elevated temperature, resulting in the formation of the six-helix bundle structure. We first generated and characterized six-helix bundle-specific antibodies raised against recombinant peptides modeling the RSV F protein six-helix bundle structure. We then used these antibodies as probes to monitor RSV F protein six-helix bundle formation in response to a diverse array of potential triggers of conformational changes. We found that exposure of 'membrane-anchored' RSV F protein to elevated temperature (45-55 deg. C) was sufficient to trigger six-helix bundle formation. Antibody binding to the six-helix bundle conformation was detected by both flow cytometry and cell-surface immunoprecipitation of the RSV F protein. None of the other treatments, including interaction with a number of potential receptors, resulted in significant binding by six-helix bundle-specific antibodies. We conclude that native, untriggered RSV F protein exists in a metastable state that can be converted in vitro to the more stable, fusogenic six-helix bundle conformation by an increase in thermal energy. These findings help to better define the mechanism of

  7. Knottin cyclization: impact on structure and dynamics

    Directory of Open Access Journals (Sweden)

    Gracy Jérôme

    2008-12-01

    Full Text Available Abstract Background Present in various species, the knottins (also referred to as inhibitor cystine knots constitute a group of extremely stable miniproteins with a plethora of biological activities. Owing to their small size and their high stability, knottins are considered as excellent leads or scaffolds in drug design. Two knottin families contain macrocyclic compounds, namely the cyclotides and the squash inhibitors. The cyclotide family nearly exclusively contains head-to-tail cyclized members. On the other hand, the squash family predominantly contains linear members. Head-to-tail cyclization is intuitively expected to improve bioactivities by increasing stability and lowering flexibility as well as sensitivity to proteolytic attack. Results In this paper, we report data on solution structure, thermal stability, and flexibility as inferred from NMR experiments and molecular dynamics simulations of a linear squash inhibitor EETI-II, a circular squash inhibitor MCoTI-II, and a linear analog lin-MCoTI. Strikingly, the head-to-tail linker in cyclic MCoTI-II is by far the most flexible region of all three compounds. Moreover, we show that cyclic and linear squash inhibitors do not display large differences in structure or flexibility in standard conditions, raising the question as to why few squash inhibitors have evolved into cyclic compounds. The simulations revealed however that the cyclization increases resistance to high temperatures by limiting structure unfolding. Conclusion In this work, we show that, in contrast to what could have been intuitively expected, cyclization of squash inhibitors does not provide clear stability or flexibility modification. Overall, our results suggest that, for squash inhibitors in standard conditions, the circularization impact might come from incorporation of an additional loop sequence, that can contribute to the miniprotein specificity and affinity, rather than from an increase in conformational rigidity

  8. The C-Terminal RpoN Domain of sigma54 Forms an unpredictedHelix-Turn-Helix Motif Similar to domains of sigma70

    Energy Technology Data Exchange (ETDEWEB)

    Doucleff, Michaeleen; Malak, Lawrence T.; Pelton, Jeffrey G.; Wemmer, David E.

    2005-11-01

    The ''{delta}'' subunit of prokaryotic RNA-polymerase allows gene-specific transcription initiation. Two {sigma} families have been identified, {sigma}{sup 70} and {sigma}{sup 54}, which use distinct mechanisms to initiate transcription and share no detectable sequence homology. Although the {sigma}{sup 70}-type factors have been well characterized structurally by x-ray crystallography, no high-resolution structural information is available for the {sigma}{sup 54}-type factors. Here we present the NMR derived structure of the C-terminal domain of {sigma}{sup 54} from Aquifex aeolicus. This domain (Thr323 to Gly389), which contains the highly conserved RpoN box sequence, consists of a poorly structured N-terminal tail followed by a three-helix bundle, which is surprisingly similar to domains of the {sigma}{sup 70}-type proteins. Residues of the RpoN box, which have previously been shown to be critical for DNA binding, form the second helix of an unpredicted helix-turn-helix motif. This structure's homology with other DNA binding proteins, combined with previous biochemical data, suggest how the C-terminal domain of {sigma}{sup 54} binds to DNA.

  9. Gradient-based optimization in nonlinear structural dynamics

    DEFF Research Database (Denmark)

    Dou, Suguang

    The intrinsic nonlinearity of mechanical structures can give rise to rich nonlinear dynamics. Recently, nonlinear dynamics of micro-mechanical structures have contributed to developing new Micro-Electro-Mechanical Systems (MEMS), for example, atomic force microscope, passive frequency divider......, 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......, 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...

  10. Triple helix interactions for eco-innovation

    DEFF Research Database (Denmark)

    Hermann, Roberto Rivas; Riisgaard, Henrik; Remmen, Arne

    the role of science parks in promoting eco-innovation. This study uses qualitative data gathered in two units of analysis: Panama Canal Authority and City of Knowledge Science Park. The study examines how Triple Helix interactions have built the regional system of eco-innovation at the Panama Canal...

  11. Conformational Diffusion and Helix Formation Kinetics

    International Nuclear Information System (INIS)

    Hummer, Gerhard; Garcia, Angel E.; Garde, Shekhar

    2000-01-01

    The time, temperature, and sequence dependences of helix formation kinetics of fully atomistic peptide models in explicit solvent are described quantitatively by a diffusive search within the coil state with barrierless transitions into the helical state. Conformational diffusion leads to nonexponential kinetics and jump-width dependences in temperature jump experiments. (c) 2000 The American Physical Society

  12. The Discovery of the Double Helix

    CERN Multimedia

    CERN. Geneva

    2011-01-01

    Professor James D. Watson has kindly agreed to make a presentation on the 1953 finding of the Double Helix at the Cavendish Laboratory by Francis Crick and himself. Being one of the greatest scientific discoveries in human history, little else needs to be added.

  13. Solitons in an isolated helix chain

    DEFF Research Database (Denmark)

    Christiansen, Peter Leth; Zolotaryuk, Alexander; Savin, A.V.

    1997-01-01

    as a generalization of the well-known one-dimensional Fermi-Pasta-Ulam model to include transverse degrees of freedom of the chain molecules. In the particular case of the alpha-helix molecular chain, the intermolecular interactions involved into the model are the point-point bonds connecting the first-, second...

  14. Conformational Diffusion and Helix Formation Kinetics

    Energy Technology Data Exchange (ETDEWEB)

    Hummer, Gerhard [Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520 (United States); Garcia, Angel E. [Theoretical Biology and Biophysics Group T-10, MS K710, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Garde, Shekhar [Department of Chemical Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180 (United States)

    2000-09-18

    The time, temperature, and sequence dependences of helix formation kinetics of fully atomistic peptide models in explicit solvent are described quantitatively by a diffusive search within the coil state with barrierless transitions into the helical state. Conformational diffusion leads to nonexponential kinetics and jump-width dependences in temperature jump experiments. (c) 2000 The American Physical Society.

  15. Genome-wide identification of basic helix-loop-helix and NF-1 motifs underlying GR binding sites in male rat hippocampus

    DEFF Research Database (Denmark)

    Pooley, John R.; Flynn, Ben P.; Grøntved, Lars

    2017-01-01

    linked to structural and organizational roles, an absence of major tethering partners for GRs, and little or no evidence for binding at negative glucocorticoid response elements. A basic helix-loop-helix motif closely resembling a NeuroD1 or Olig2 binding site was found underlying a subset of GR binding......Glucocorticoids regulate hippocampal function in part by modulating gene expression through the glucocorticoid receptor (GR). GR binding is highly cell type specific, directed to accessible chromatin regions established during tissue differentiation. Distinct classes of GR binding sites...

  16. Modal analysis application for dynamic characterization of simple structures

    International Nuclear Information System (INIS)

    Pastorini, A.J.; Belinco, C.G.

    1987-01-01

    The knowledge of the dynamic characteristics of a structure helps to foresee the vibrating behaviour under operating conditions. The modal analysis techniques offer a method to perform the dynamic characterization of a studied structure from the vibration modes of such structure. A hammer provided with a loaded cell to excite a wide frequency band and accelerometer and, on the basis of a measurement of the transfer function at different points, various simple structures were given with a dynamic structures analysis (of the type of Fourier's rapidly transformation) and the results were compared with those obtained by other methods. Different fields where these techniques are applied, are also enumerated. (Author)

  17. An Investigation of dynamic characteristics of structures subjected to dynamic load from the viewpoint of design

    International Nuclear Information System (INIS)

    Lee, Hyun Ah; Kim, Yong Il; Park, Gyung Jin; Kang, Byung Soo; Kim, Joo Sung

    2006-01-01

    All the loads in the real world are dynamic loads and structural optimization under dynamic loads is very difficult. Thus the dynamic loads are often transformed to static loads by dynamic factors, which are believed equivalent to the dynamic loads. However, due to the difference of load characteristics, there can be considerable differences between the results from static and dynamic analyses. When the natural frequency of a structure is high, the dynamic analysis result is similar to that of static analysis due to the small inertia effect on the behavior of the structure. However, if the natural frequency of the structure is low, the inertia effect should not be ignored. then, the behavior of the dynamic system is different from that of the static system. The difference of the two cases can be explained from the relationship between the homogeneous and the particular solutions of the differential equation that governs the behavior of the structure. Through various examples, the difference between the dynamic analysis and the static analysis are shown. Also dynamic response optimization results are compared with the results with static loads transformed from dynamic loads by dynamic factors, which show the necessity of the design considering dynamic loads

  18. Structure and dynamics of cationic membrane peptides and proteins: Insights from solid-state NMR

    Science.gov (United States)

    Hong, Mei; Su, Yongchao

    2011-01-01

    Many membrane peptides and protein domains contain functionally important cationic Arg and Lys residues, whose insertion into the hydrophobic interior of the lipid bilayer encounters significant energy barriers. To understand how these cationic molecules overcome the free energy barrier to insert into the lipid membrane, we have used solid-state NMR spectroscopy to determine the membrane-bound topology of these peptides. A versatile array of solid-state NMR experiments now readily yields the conformation, dynamics, orientation, depth of insertion, and site-specific protein–lipid interactions of these molecules. We summarize key findings of several Arg-rich membrane peptides, including β-sheet antimicrobial peptides, unstructured cell-penetrating peptides, and the voltage-sensing helix of voltage-gated potassium channels. Our results indicate the central role of guanidinium-phosphate and guanidinium-water interactions in dictating the structural topology of these cationic molecules in the lipid membrane, which in turn account for the mechanisms of this functionally diverse class of membrane peptides. PMID:21344534

  19. Dynamics and structure of ignition process in plasma. Ignition dynamics and structure of laboratory plasmas

    International Nuclear Information System (INIS)

    Nagasaki, Kazunobu; Takamura, Shuichi; Razzak, Md. Abdur; Uesugi, Yoshihiko; Yoshimura, Yasuo; Cappa, Alvaro

    2008-01-01

    The dynamics and structure of plasma production are stated by the results of two experiments such as the radio frequency thermal plasmas produced by inductively coupled plasma technique at atmospheric pressure and the second harmonic ECH. The first experiment results explained transition from the electrostatic discharge mode of forming streamer to the induced discharge mode after forming the discharge channel that the streamer connected to in the azimuth direction. The other experiment explained the dynamics which the initial plasma produced at the ECH resonance point spread in the direction of radius. The divergence and transition related to the nonlinear process were observed independently existing the magnetic field or incident power. The experiment devices, conditions, results, and modeling are reported. (S.Y.)

  20. Bacterial morphogenesis and the enigmatic MreB helix.

    Science.gov (United States)

    Errington, Jeff

    2015-04-01

    Work over the past decade has highlighted the pivotal role of the actin-like MreB family of proteins in the determination and maintenance of rod cell shape in bacteria. Early images of MreB localization revealed long helical filaments, which were suggestive of a direct role in governing cell wall architecture. However, several more recent, higher-resolution studies have questioned the existence or importance of the helical structures. In this Opinion article, I navigate a path through these conflicting reports, revive the helix model and summarize the key questions that remain to be answered.

  1. Looking for a Framework for Analyzing Eco-innovation Dynamics

    DEFF Research Database (Denmark)

    Yang, Yan

    2011-01-01

    Looking for a Framework for Analyzing Eco-innovation Dynamics: A Triple Helix Model of Innovation Perspective.......Looking for a Framework for Analyzing Eco-innovation Dynamics: A Triple Helix Model of Innovation Perspective....

  2. Structure and dynamics of the magnetopause

    International Nuclear Information System (INIS)

    Wang, Z.

    1992-01-01

    This thesis addresses several topics concerning the structure and dynamics of the magnetopause. These topics include the role of the magnetopause in global convection, the Kelvin-Helmholtz (K-H) instability, which accounts for momentum transport at the magnetopause, the formation of flux ropes by the tearing and twisting modes and particle diffusion across the magnetopause resulting from the destruction of magnetic surfaces. The author establishs an analytic electric field model for an open magnetosphere and introduce a magnetopause to control the reconnection rate and momentum transport. A realistic magnetospheric configuration is realized by 'stretch transformation'. The role of magnetic nulls in the electric field is approached with a technique for direct calculation of electric fields along field lines. Results indicate that electric fields associated with A-type or B-type nulls are generally singular. Then the author considers kinetic effects on the K-H instability. Contrary to the logical assumption that Landau damping damps the instability, it can instead enhance the growth and increase the spatial extent of the instability because the heating of resonance particles enhances the pressure perturbation. A gravitational analogy is used to determine the effect of curvature on K-H instability and it is found that the critical Richardson number for stability increases from 1/4 for incompressible fluids to 1/2 for compressible fluids. The flux rope, which accounts for flux transfer events (FTE), can be formed by a tearing or twisting mode. The tearing mode is self excited by the free energy associated with the magnetic configuration, while the twisting mode must be externally driven. The shear flow generates the twisting mode and reduces the growth rate of the tearing mode. The flux ropes resulting from the twisting mode closely resemble FTE's which have a longer pitch length than that from tearing mode

  3. Unpredictable responses of garden snail (Helix aspersa) populations to climate change

    NARCIS (Netherlands)

    Bezemer, T.M.; Knight, K.J.

    2001-01-01

    We studied the impact of climate change on the population dynamics of the garden snail (Helix aspersa) in the Ecotron controlled environment facility. The experimental series ran for three plant generations, allowing the snails to reproduce. We investigated the isolated and combined effects of

  4. CFD analysis and flow model reduction for surfactant production in helix reactor

    NARCIS (Netherlands)

    Nikačević, N.M.; Thielen, L.; Twerda, A.; Hof, P.M.J. van den

    2014-01-01

    Flow pattern analysis in a spiral Helix reactor is conducted, for the application in the commercial surfactant production. Step change response curves (SCR) were obtained from numerical tracer experiments by three-dimensional computational fluid dynamics (CFD) simulations. Non-reactive flow is

  5. Visualizing Structure and Dynamics of Disaccharide Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Matthews, J. F.; Beckham, G. T.; Himmel, M. E.; Crowley, M. F.

    2012-01-01

    We examine the effect of several solvent models on the conformational properties and dynamics of disaccharides such as cellobiose and lactose. Significant variation in timescale for large scale conformational transformations are observed. Molecular dynamics simulation provides enough detail to enable insight through visualization of multidimensional data sets. We present a new way to visualize conformational space for disaccharides with Ramachandran plots.

  6. Structures in dynamics finite dimensional deterministic studies

    CERN Document Server

    Broer, HW; van Strien, SJ; Takens, F

    1991-01-01

    The study of non-linear dynamical systems nowadays is an intricate mixture of analysis, geometry, algebra and measure theory and this book takes all aspects into account. Presenting the contents of its authors' graduate courses in non-linear dynamical systems, this volume aims at researchers who wish to be acquainted with the more theoretical and fundamental subjects in non-linear dynamics and is designed to link the popular literature with research papers and monographs. All of the subjects covered in this book are extensively dealt with and presented in a pedagogic

  7. Ergodic Theory, Open Dynamics, and Coherent Structures

    CERN Document Server

    Bose, Christopher; Froyland, Gary

    2014-01-01

    This book is comprised of selected research articles developed from a workshop on Ergodic Theory, Probabilistic Methods and Applications, held in April 2012 at the Banff International Research Station. It contains contributions from world leading experts in ergodic theory, dynamical systems, numerical analysis, fluid dynamics, and networks. The volume will serve as a valuable reference for mathematicians, physicists, engineers, physical oceanographers, atmospheric scientists, biologists, and climate scientists, who currently use, or wish to learn how to use, probabilistic techniques to cope with dynamical models that display open, coherent, or non-equilibrium behavior.

  8. Structure of the GH1 domain of guanylate kinase-associated protein from Rattus norvegicus

    International Nuclear Information System (INIS)

    Tong, Junsen; Yang, Huiseon; Eom, Soo Hyun; Chun, ChangJu; Im, Young Jun

    2014-01-01

    Graphical abstract: - Highlights: • The crystal structure of GKAP homology domain 1 (GH1) was determined. • GKAP GH1 is a three-helix bundle connected by short flexible loops. • The predicted helix α4 associates weakly with the helix α3, suggesting dynamic nature of the GH1 domain. - Abstract: Guanylate-kinase-associated protein (GKAP) is a scaffolding protein that links NMDA receptor-PSD-95 to Shank–Homer complexes by protein–protein interactions at the synaptic junction. GKAP family proteins are characterized by the presence of a C-terminal conserved GKAP homology domain 1 (GH1) of unknown structure and function. In this study, crystal structure of the GH1 domain of GKAP from Rattus norvegicus was determined in fusion with an N-terminal maltose-binding protein at 2.0 Å resolution. The structure of GKAP GH1 displays a three-helix bundle connected by short flexible loops. The predicted helix α4 which was not visible in the crystal structure associates weakly with the helix α3 suggesting dynamic nature of the GH1 domain. The strict conservation of GH1 domain across GKAP family members and the lack of a catalytic active site required for enzyme activity imply that the GH1 domain might serve as a protein–protein interaction module for the synaptic protein clustering

  9. Structure of the GH1 domain of guanylate kinase-associated protein from Rattus norvegicus

    Energy Technology Data Exchange (ETDEWEB)

    Tong, Junsen; Yang, Huiseon [College of Pharmacy, Chonnam National University, Gwangju 500-757 (Korea, Republic of); Eom, Soo Hyun [School of Life Sciences, Steitz Center for Structural Biology, and Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 500-712 (Korea, Republic of); Chun, ChangJu, E-mail: cchun1130@jnu.ac.kr [College of Pharmacy, Chonnam National University, Gwangju 500-757 (Korea, Republic of); Im, Young Jun, E-mail: imyoungjun@jnu.ac.kr [College of Pharmacy, Chonnam National University, Gwangju 500-757 (Korea, Republic of)

    2014-09-12

    Graphical abstract: - Highlights: • The crystal structure of GKAP homology domain 1 (GH1) was determined. • GKAP GH1 is a three-helix bundle connected by short flexible loops. • The predicted helix α4 associates weakly with the helix α3, suggesting dynamic nature of the GH1 domain. - Abstract: Guanylate-kinase-associated protein (GKAP) is a scaffolding protein that links NMDA receptor-PSD-95 to Shank–Homer complexes by protein–protein interactions at the synaptic junction. GKAP family proteins are characterized by the presence of a C-terminal conserved GKAP homology domain 1 (GH1) of unknown structure and function. In this study, crystal structure of the GH1 domain of GKAP from Rattus norvegicus was determined in fusion with an N-terminal maltose-binding protein at 2.0 Å resolution. The structure of GKAP GH1 displays a three-helix bundle connected by short flexible loops. The predicted helix α4 which was not visible in the crystal structure associates weakly with the helix α3 suggesting dynamic nature of the GH1 domain. The strict conservation of GH1 domain across GKAP family members and the lack of a catalytic active site required for enzyme activity imply that the GH1 domain might serve as a protein–protein interaction module for the synaptic protein clustering.

  10. Model reduction tools for nonlinear structural dynamics

    NARCIS (Netherlands)

    Slaats, P.M.A.; Jongh, de J.; Sauren, A.A.H.J.

    1995-01-01

    Three mode types are proposed for reducing nonlinear dynamical system equations, resulting from finite element discretizations: tangent modes, modal derivatives, and newly added static modes. Tangent modes are obtained from an eigenvalue problem with a momentary tangent stiffness matrix. Their

  11. 4th International Conference on Structural Nonlinear Dynamics and Diagnosis

    CERN Document Server

    2018-01-01

    This book presents contributions on the most active lines of recent advanced research in the field of nonlinear mechanics and physics selected from the 4th International Conference on Structural Nonlinear Dynamics and Diagnosis. It includes fifteen chapters by outstanding scientists, covering various aspects of applications, including road tanker dynamics and stability, simulation of abrasive wear, energy harvesting, modeling and analysis of flexoelectric nanoactuator, periodic Fermi–Pasta–Ulam problems, nonlinear stability in Hamiltonian systems, nonlinear dynamics of rotating composites, nonlinear vibrations of a shallow arch, extreme pulse dynamics in mode-locked lasers, localized structures in a photonic crystal fiber resonator, nonlinear stochastic dynamics, linearization of nonlinear resonances, treatment of a linear delay differential equation, and fractional nonlinear damping. It appeals to a wide range of experts in the field of structural nonlinear dynamics and offers researchers and engineers a...

  12. Complex-Dynamic Cosmology and Emergent World Structure

    OpenAIRE

    Kirilyuk, Andrei P.

    2004-01-01

    Universe structure emerges in the unreduced, complex-dynamic interaction process with the simplest initial configuration (two attracting homogeneous fields, quant-ph/9902015). The unreduced interaction analysis gives intrinsically creative cosmology, describing the real, explicitly emerging world structure with dynamic randomness on each scale. Without imposing any postulates or entities, we obtain physically real space, time, elementary particles with their detailed structure and intrinsic p...

  13. Discretization model for nonlinear dynamic analysis of three dimensional structures

    International Nuclear Information System (INIS)

    Hayashi, Y.

    1982-12-01

    A discretization model for nonlinear dynamic analysis of three dimensional structures is presented. The discretization is achieved through a three dimensional spring-mass system and the dynamic response obtained by direct integration of the equations of motion using central diferences. First the viability of the model is verified through the analysis of homogeneous linear structures and then its performance in the analysis of structures subjected to impulsive or impact loads, taking into account both geometrical and physical nonlinearities is evaluated. (Author) [pt

  14. Tunable single photonic defect-mode in cholesteric liquid crystals with laser-induced local modifications of helix

    International Nuclear Information System (INIS)

    Yoshida, Hiroyuki; Lee, Chee Heng; Fujii, Akihiko; Ozaki, Masanori

    2006-01-01

    The authors demonstrate a tunable single photonic defect-mode in a single cholesteric liquid crystal material based on a structural defect introduced by local modification of the helix. An unpolymerized region of cholesteric liquid crystal acting as the defect was left between two polymerized regions via a two-photon excitation laser-lithography process. Upon polymerization, the cholesteric liquid crystal helix elongated and became thermally stable, and a single photonic defect mode was exhibited due to the contrast in the helix pitch at the defect. The defect mode showed tunability upon heating, and a 36 nm redshift was seen over a temperature range of 30 deg. C

  15. FPGA helix tracking algorithm for PANDA

    Energy Technology Data Exchange (ETDEWEB)

    Liang, Yutie; Galuska, Martin; Gessler, Thomas; Kuehn, Wolfgang; Lange, Jens Soeren; Muenchow, David; Spruck, Bjoern [II. Physikalisches Institut, Giessen University (Germany); Ye, Hua [Institute of High Energy Physics, Beijing (China); Collaboration: PANDA-Collaboration

    2015-07-01

    The PANDA detector is a general-purpose detector for physics with high luminosity cooled antiproton beams, planed to operate at the FAIR facility in Darmstadt, Germany. The central detector includes a silicon Micro Vertex Detector (MVD) and a Straw Tube Tracker (STT). Without any hardware trigger, large amounts of raw data are streaming into the data acquisition system. The data reduction task is performed in the online system by reconstruction algorithms programmed on FPGAs (Field Programmable Gate Arrays) as first level and on a farm of GPUs or PCs as a second level. One important part in the system is the online track reconstruction. In this presentation, an online tracking algorithm for helix tracking reconstruction in the solenoidal field is shown. The tracking algorithm is composed by two parts, a road finding module followed by an iterative helix parameter calculation module. A performance study using C++ and the status of the VHDL implementation are presented.

  16. Molecular dynamics analysis reveals structural insights into mechanism of nicotine N-demethylation catalyzed by tobacco cytochrome P450 mono-oxygenase.

    Directory of Open Access Journals (Sweden)

    Shan Wang

    Full Text Available CYP82E4, a cytochrome P450 monooxygenase, has nicotine N-demethylase (NND activity, which mediates the bioconversion of nicotine into nornicotine in senescing tobacco leaves. Nornicotine is a precursor of the carcinogen, tobacco-specific nitrosamine. CYP82E3 is an ortholog of CYP82E4 with 95% sequence identity, but it lacks NND activity. A recent site-directed mutagenesis study revealed that a single amino acid substitution, i.e., cysteine to tryptophan at the 330 position in the middle of protein, restores the NND activity of CYP82E3 entirely. However, the same amino acid change caused the loss of the NND activity of CYP82E4. To determine the mechanism of the functional turnover of the two molecules, four 3D structures, i.e., the two molecules and their corresponding cys-trp mutants were modeled. The resulting structures exhibited that the mutation site is far from the active site, which suggests that no direct interaction occurs between the two sites. Simulation studies in different biological scenarios revealed that the mutation introduces a conformation drift with the largest change at the F-G loop. The dynamics trajectories analysis using principal component analysis and covariance analysis suggests that the single amino acid change causes the opening and closing of the transfer channels of the substrates, products, and water by altering the motion of the F-G and B-C loops. The motion of helix I is also correlated with the motion of both the F-G loop and the B-C loop and; the single amino acid mutation resulted in the curvature of helix I. These results suggest that the single amino acid mutation outside the active site region may have indirectly mediated the flexibility of the F-G and B-C loops through helix I, causing a functional turnover of the P450 monooxygenase.

  17. Dynamical load factor of impact loaded shell structures

    International Nuclear Information System (INIS)

    Hammel, J.

    1977-01-01

    Dynamical loaded structures can be analysed by spectral representations, which usually lead to an enormous computational effort. If it is possible to find a fitting dynamical load factor, the dynamical problem can be reduced to a statical one. The computation of this statical problem is much simpler. The disadvantage is that the dynamical load factor usually leads to a very rough approximation. In this paper it will be shown, that by combination of these two methods, the approximation of the dynamical load factor can be improved and the consumption of computation time can be enormously reduced. (Auth.)

  18. Kevlar: Transitioning Helix for Research to Practice

    Science.gov (United States)

    2016-03-01

    x86 binaries, although it can be targeted to any platform that is targeted by IDA Pro. Currently, IDA Pro targets more than 40 processors and...effects its own transformations. Helix/Kevlar then automatically generates SPRI rules for any program variants by essentially performing a “ smart diff...execute permission on the pages of memory it uses, leaving only execute (but not write) permission on the code cache. Strata also watches for attempts

  19. Fundamental structures of dynamic social networks

    DEFF Research Database (Denmark)

    Sekara, Vedran; Stopczynski, Arkadiusz; Jørgensen, Sune Lehmann

    2016-01-01

    Social systems are in a constant state of flux, with dynamics spanning from minute-by-minute changes to patterns present on the timescale of years. Accurate models of social dynamics are important for understanding the spreading of influence or diseases, formation of friendships...... and their interactions in the network of real-world person-to-person proximity measured via Bluetooth, as well as their telecommunication networks, online social media contacts, geolocation, and demographic data. These high-resolution data allow us to observe social groups directly, rendering community detection......, and the productivity of teams. Although there has been much progress on understanding complex networks over the past decade, little is known about the regularities governing the microdynamics of social networks. Here, we explore the dynamic social network of a densely-connected population of ∼1,000 individuals...

  20. THE DYNAMICS OF THE MATRICS STRUCTURE

    Directory of Open Access Journals (Sweden)

    Dumitru CONSTANTINESCU

    2007-01-01

    Full Text Available The relationships organization-suppliers-customers have recently known major changes in the structure of services and have made the organization develop its managerial and professional competencies in order to do projects. The qualified organization is the most trust-worthy in the process of doing a project. The participation of an organization in doing projects depends on a multitude of factors. Out of these factors, the structural organization comes forth, as it represents the variable with the most important impact on a project’s quality, costs and lead time. From the organizational point of view, the matrix structure is frequently chosen for projects. The matrix structure generally coexists with the line structure. The two structures are contrastive. The line structure is based on the unity of command principle and is not open to cooperation and dialogue. The matrix structure encourages cooperation and communication, favours conflict, which is considered here a healthy and essential process. The matrix structure and the line structure claim their right to initiative. Conflict and the multidimensional integration of multiple hierarchies can be negotiated through the concept charisma – mediation, sustained by the matrix structure.

  1. Nonlinear structural mechanics theory, dynamical phenomena and modeling

    CERN Document Server

    Lacarbonara, Walter

    2013-01-01

    Nonlinear Structural Mechanics: Theory, Dynamical Phenomena and Modeling offers a concise, coherent presentation of the theoretical framework of nonlinear structural mechanics, computational methods, applications, parametric investigations of nonlinear phenomena and their mechanical interpretation towards design. The theoretical and computational tools that enable the formulation, solution, and interpretation of nonlinear structures are presented in a systematic fashion so as to gradually attain an increasing level of complexity of structural behaviors, under the prevailing assumptions on the geometry of deformation, the constitutive aspects and the loading scenarios. Readers will find a treatment of the foundations of nonlinear structural mechanics towards advanced reduced models, unified with modern computational tools in the framework of the prominent nonlinear structural dynamic phenomena while tackling both the mathematical and applied sciences. Nonlinear Structural Mechanics: Theory, Dynamical Phenomena...

  2. Exploring the membrane fusion mechanism through force-induced disassembly of HIV-1 six-helix bundle

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Kai [Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Zhang, Yong [Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Lou, Jizhong, E-mail: jlou@ibp.ac.cn [Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China)

    2016-05-13

    Enveloped virus, such as HIV-1, employs membrane fusion mechanism to invade into host cell. HIV-1 gp41 ectodomain uses six-helix bundle configuration to accomplish this process. Using molecular dynamic simulations, we confirmed the stability of this six-helix bundle by showing high occupancy of hydrogen bonds and hydrophobic interactions. Key residues and interactions important for the bundle integration were characterized by force-induced unfolding simulations of six-helix bundle, exhibiting the collapse order of these groups of interactions. Moreover, our results in some way concerted with a previous theory that the formation of coiled-coil choose a route which involved cooperative interactions between the N-terminal and C-terminal helix. -- Highlights: •Unfolding of HIV-1 gp41 six-helix bundle is studied by molecular dynamics simulations. •Specific interactions responsible for the stability of HIV-1 envelope post-fusion conformation were identified. •The gp41 six-helix bundle transition inducing membrane fusion might be a cooperative process of the three subunits.

  3. Dynamic Capital Structure: Dynamics, Determinants and Speed of Adjustment

    NARCIS (Netherlands)

    Tamirat, A.S.; Trujillo Barrera, A.A.; Pennings, J.M.E.

    2017-01-01

    The corporate finance literature has focused on explaining the determinants of firms target capital structure and speed of adjustment using the well-established theories such as pecking order, signaling and trade-off theories. However, less attention has been paid to understanding the financing

  4. Recent Progress in Heliogyro Solar Sail Structural Dynamics

    Science.gov (United States)

    Wilkie, William K.; Warren, Jerry E.; Horta, Lucas G.; Juang, Jer-Nan; Gibbs, Samuel C.; Dowell, E.; Guerrant, Daniel; Lawrence Dale

    2014-01-01

    Results from recent National Aeronautics and Space Administration (NASA) research on the structural dynamics and control characteristics of heliogyro solar sails are summarized. Specific areas under investigation include coupled nonlinear finite element analysis of heliogyro membrane blade with solar radiation pressure effects, system identification of spinning membrane structures, solarelastic stability analysis of heliogyro solar sails, including stability during blade deployment, and results from small-scale in vacuo dynamics experiments with spinning high-aspect ratio membranes. A low-cost, rideshare payload heliogyro technology demonstration mission concept, used as a mission context for these heliogyro structural dynamics and solarelasticity investigations, is also described.

  5. Friends and foes : The dynamics of dual social structures

    NARCIS (Netherlands)

    Sytch, M.; Tatarynowicz, A.

    2014-01-01

    This paper investigates the evolutionary dynamics of a dual social structure encompassing collaboration and conflict among corporate actors. We apply and advance structural balance theory to examine the formation of balanced and unbalanced dyadic and triadic structures, and to explore how these

  6. DSIbin : Identifying dynamic data structures in C/C++ binaries

    NARCIS (Netherlands)

    Rupprecht, Thomas; Chen, Xi; White, David H.; Boockmann, Jan H.; Luttgen, Gerald; Bos, Herbert

    2017-01-01

    Reverse engineering binary code is notoriously difficult and, especially, understanding a binary's dynamic data structures. Existing data structure analyzers are limited wrt. program comprehension: they do not detect complex structures such as skip lists, or lists running through nodes of different

  7. Dynamic fracture toughness testing of structural steels

    International Nuclear Information System (INIS)

    Debel, C.P.

    1978-01-01

    Two candidate test methods aimed at producing materials properties of interest in connection with crack arrest assessments are currently under evaluation. These methods and the significance of the results are described. The quasi-static as well as the dynamic fracture toughness of a plain C-Mn steel in the as-quenched and tempered condition have been examined at temperatures between -115 0 C and the ambient temperature. Wedge-loaded duplex DCB-specimens were used in dynamic tests. The crack extension velocity was measured using a surface deposited grid and a registration circuit based on TTL-electronics. The toughness transition-temperature at quasi-static loading rate is found to be low; but during dynamic crack-extension a substantial shift of the transition-region to higher temperatures is produced, and fast fracture was obtained even at ambient temperature. Even though the dynamic fracture toughness Ksub(ID) increases with temperature, it decreases with increasing crack-extension velocity at a given temperature and the rate of decrease with respect to crack-extension velocity seems to be independent of temperature. Ksub(ID) appears to be insensitive to heat treatments. Test results indicate insufficient load-train stiffness, and problems due to crack branching were encountered. (author)

  8. Nucleic acid helices: I. Structure of M1 RNA from E. coli as determined bypsoralen crosslinking. II. Thermodynamics of the helix-coil transition of DNA oligonucleotides in solutions containing 3.0 M tetramethylammonium chloride

    International Nuclear Information System (INIS)

    Lipson, S.E.

    1987-01-01

    This work includes two different investigations examining nucleic acid helices. The first study discusses secondary and tertiary interactions in the RNA moiety of ribonuclease P from Escherichia coli. The second study discusses the thermodynamics of the helix-coil transition of DNA oligonucleotides in solutions containing tetramethylammonium chloride. The RNA moiety of ribonuclease P from Escherichia coli (M1 RNA) has been photoreacted with 4'-hydroxymethyl-4,5'8-trimethylpsoralen and long wave UV light (320-380 nm) in a buffer in which the M1 RNA alone acts as a true catalyst of tRNA processing. Limited specific digestion followed by two dimensional gel electrophoresis yields fragments crosslinked by HMT. The positions of the crosslinks have been determined to within ±15 nucleotides by photoreversal of the isolated crosslinked fragments and enzymatic sequencing of the resulting RNA. Further assignments of the exact locations of the crosslinks have been made on the known photoreactivity of the psoralen with different bases

  9. Full scale dynamic testing of Kozloduy NPP unit 5 structures

    International Nuclear Information System (INIS)

    Da Rin, E.M.

    1999-01-01

    As described in this report, the Kozloduy NPP western site has been subjected to low level earthquake-like ground shaking - through appropriately devised underground explosions - and the resulting dynamic response of the NPP reactor Unit 5 important structures appropriately measured and digitally recorded. In-situ free-field response was measured concurrently more than 100 m aside the main structures of interest. The collected experimental data provide reference information on the actual dynamic characteristics of the Kozloduy NPPs main structures, as well as give some useful indications on the dynamic soil-structure interaction effects for the case of low level excitation. Performing the present full-scale dynamic structural testing activities took advantage of the experience gained by ISMES during similar tests, lately performed in Italy and abroad (in particular, at the Paks NPP in 1994). The IAEA promoted dynamic testing of the Kozloduy NPP Unit 5 by means of pertinently designed buried explosion-induced ground motions which has provided a large amount of data on the dynamic structural response of its major structures. In the present report, the conducted investigation is described and the acquired digital data presented. A series of preliminary analyses were undertaken for examining in detail the ground excitation levels that were produced by these weak earthquake simulation experiments, as well as for inferring some structural characteristics and behaviour information from the collected data. These analyses ascertained the high quality of the collected digital data. Presumably due to soil-structure dynamic interaction effects, reduced excitation levels were observed at the reactor building foundation raft level with respect to the concurrent free-field ground motions. measured at a 140 m distance from the reactor building centre. Further more detailed and systematic analyses are worthwhile to be performed for extracting more complete information about the

  10. Invariant molecular-dynamics approach to structural phase transitions

    International Nuclear Information System (INIS)

    Wentzcovitch, R.M.

    1991-01-01

    Two fictitious Lagrangians to be used in molecular-dynamics simulations with variable cell shape and suitable to study problems like structural phase transitions are introduced. Because they are invariant with respect to the choice of the simulation cell edges and eliminate symmetry breaking associated with the fictitious part of the dynamics, they improve the physical content of numerical simulations that up to now have been done by using Parrinello-Rahman dynamics

  11. Modulating Transmembrane α-Helix Interactions through pH-Sensitive Boundary Residues.

    Science.gov (United States)

    Ng, Derek P; Deber, Charles M

    2016-08-09

    Changes in pH can alter the structure and activity of proteins and may be used by the cell to control molecular function. This coupling can also be used in non-native applications through the design of pH-sensitive biomolecules. For example, the pH (low) insertion peptide (pHLIP) can spontaneously insert into a lipid bilayer when the pH decreases. We have previously shown that the α-helicity and helix-helix interactions of the TM2 α-helix of the proteolipid protein (PLP) are sensitive to the local hydrophobicity at its C-terminus. Given that there is an ionizable residue (Glu-88) at the C-terminus of this transmembrane (TM) segment, we hypothesized that changing the ionization state of this residue through pH may alter the local hydrophobicity of the peptide enough to affect both its secondary structure and helix-helix interactions. To examine this phenomenon, we synthesized peptide analogues of the PLP TM2 α-helix (wild-type sequence (66)AFQYVIYGTASFFFLYGALLLAEGF(90)). Using circular dichroism and Förster resonance energy transfer in the membrane-mimetic detergent sodium dodecyl sulfate, we found that a decrease in pH increases both peptide α-helicity and the extent of self-association. This pH-dependent effect is due specifically to the presence of Glu-88 at the C-terminus. Additional experiments in which Phe-90 was mutated to residues of varying hydrophobicities indicated that the strength of this effect is dependent on the local hydrophobicity near Glu-88. Our results have implications for the design of TM peptide switches and improve our understanding of how membrane protein structure and activity can be regulated through local molecular environmental changes.

  12. Quantifying and modeling soil structure dynamics

    Science.gov (United States)

    Characterization of soil structure has been a topic of scientific discussions ever since soil structure has been recognized as an important factor affecting soil physical, mechanical, chemical, and biological processes. Beyond semi-quantitative soil morphology classes, it is a challenge to describe ...

  13. From Dynamic Condition Response Structures to Büchi Automata

    DEFF Research Database (Denmark)

    Mukkamala, Raghava Rao; Hildebrandt, Thomas

    2010-01-01

    Recently we have presented distributed dynamic condition response structures (DCR structures) as a declarative process model conservatively generalizing labelled event structures to allow for finite specifications of repeated, possibly infinite behavior. The key ideas are to split the causality...... relation of event structures in two dual relations: the condition relation and the response relation, to split the conflict relation in two relations: the dynamic exclusion and dynamic inclusion, and finally to allow configurations to be multi sets of events. In the present abstract we recall the model...... and show how to characterise the execution of DCR structures and the acceptance condition for infinite runs by giving a map to Bu ̈chi-automata. This is the first step towards automatic verification of processes specified as DCR structures....

  14. Dynamical community structure of populations evolving on genotype networks

    International Nuclear Information System (INIS)

    Capitán, José A.; Aguirre, Jacobo; Manrubia, Susanna

    2015-01-01

    Neutral evolutionary dynamics of replicators occurs on large and heterogeneous networks of genotypes. These networks, formed by all genotypes that yield the same phenotype, have a complex architecture that conditions the molecular composition of populations and their movements on genome spaces. Here we consider as an example the case of populations evolving on RNA secondary structure neutral networks and study the community structure of the network revealed through dynamical properties of the population at equilibrium and during adaptive transients. We unveil a rich hierarchical community structure that, eventually, can be traced back to the non-trivial relationship between RNA secondary structure and sequence composition. We demonstrate that usual measures of modularity that only take into account the static, topological structure of networks, cannot identify the community structure disclosed by population dynamics

  15. Dynamic analysis of CHASNUPP steam generator structure during shipping

    International Nuclear Information System (INIS)

    Han Liangbi; Xu Jinkang; Zhou Meiwu; He Yinbiao

    1998-07-01

    The dynamic analysis of CHASNUPP steam generator during shipping is described, including the simplified mathematical model, acceleration power spectrum of ocean wave induced random vibration, the dynamic analysis of steam generator structure under random loading, the applied computer code and calculated results

  16. Crystal structure and pair potentials: A molecular-dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Parrinello, M.; Rahman, A.

    1980-10-06

    With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different crystal structures.

  17. Simulation of Protein Structure, Dynamics and Function in Organic Media

    National Research Council Canada - National Science Library

    Daggett, Valerie

    1998-01-01

    The overall goal of our ONR-sponsored research is to pursue realistic molecular modeling strudies pertinnent to the related properties of protein stability, dynamics, structure, function, and folding in aqueous solution...

  18. pH-jump induced α-helix folding of poly-L-glutamic acid

    International Nuclear Information System (INIS)

    Donten, Mateusz L.; Hamm, Peter

    2013-01-01

    Highlights: ► pH-jump as truly biomimetic tool to initiate non-equilibrium dynamics of biomolecules. ► Design criteria to widen the applicability of pH-jumps are developed. ► Folding of poly-L-Glu in dependence of starting pH, pH jump size and helix length. ► Length dependence provides strong evidence for a nucleation–propagation scenario. - Abstract: pH jumps are a truly biomimetic technique to initiate non-equilibrium dynamics of biomolecules. In this work, the pH jump induced α-helix folding of poly-L-glutamic acid is investigated upon proton release from o-nitrobenzaldehyde. The aim of this work is twofold: On the one hand, design criteria of pH jump experiments are discussed, on the other hand, the folding mechanism of poly-L-glutamic acid is clarified by probing the IR response of the amide I band. Its folding kinetics is studied in dependence of the starting pD, the size of the pD jump and the length of the helix. While no dependence on the first two parameters could be detected, the folding time varies from 0.6 μs to 1.8 μs for helix lengths of 20 residue to 440 residue, respectively. It converges to a long-length limit at about 50 residue, a result which is attributed to a nucleation–propagation mechanism

  19. Structure, dynamics and RNA binding of the multi-domain splicing factor TIA-1

    Science.gov (United States)

    Wang, Iren; Hennig, Janosch; Jagtap, Pravin Kumar Ankush; Sonntag, Miriam; Valcárcel, Juan; Sattler, Michael

    2014-01-01

    Alternative pre-messenger ribonucleic acid (pre-mRNA) splicing is an essential process in eukaryotic gene regulation. The T-cell intracellular antigen-1 (TIA-1) is an apoptosis-promoting factor that modulates alternative splicing of transcripts, including the pre-mRNA encoding the membrane receptor Fas. TIA-1 is a multi-domain ribonucleic acid (RNA) binding protein that recognizes poly-uridine tract RNA sequences to facilitate 5′ splice site recognition by the U1 small nuclear ribonucleoprotein (snRNP). Here, we characterize the RNA interaction and conformational dynamics of TIA-1 by nuclear magnetic resonance (NMR), isothermal titration calorimetry (ITC) and small angle X-ray scattering (SAXS). Our NMR-derived solution structure of TIA-1 RRM2–RRM3 (RRM2,3) reveals that RRM2 adopts a canonical RNA recognition motif (RRM) fold, while RRM3 is preceded by an non-canonical helix α0. NMR and SAXS data show that all three RRMs are largely independent structural modules in the absence of RNA, while RNA binding induces a compact arrangement. RRM2,3 binds to pyrimidine-rich FAS pre-mRNA or poly-uridine (U9) RNA with nanomolar affinities. RRM1 has little intrinsic RNA binding affinity and does not strongly contribute to RNA binding in the context of RRM1,2,3. Our data unravel the role of binding avidity and the contributions of the TIA-1 RRMs for recognition of pyrimidine-rich RNAs. PMID:24682828

  20. Past and future trends in structures and dynamics

    International Nuclear Information System (INIS)

    Bader, R.M.; Goesch, W.H.; Olsen, J.J.

    1981-01-01

    An historical review and a series of prognostications based on current developments are presented for the fields of structural design and structural dynamics analysis. It is shown that while weight and cost reduction and improved durability have been the primary forces in structural technology development in the past, emphasis has shifted to such things as productivity, quality assurance, low observables for military aircraft and increased fuel efficiency. Prominent among recent advances in future developments are damage tolerance durability, computer-aided design, active flutter suppression, adhesive bonding of primary structures, cast aluminum structures, titanium and graphite-epoxy primary aircraft structures, aeroelastic tailoring composites, metal matrix composites, and radar-absorbing structures

  1. Limitations and corrections in measuring dynamic characteristics of structural systems

    International Nuclear Information System (INIS)

    Walter, P.L.

    1978-10-01

    The work deals with limitations encountered in measuring the dynamic characteristics of structural systems. Structural loading and response are measured by transducers possessing multiple resonant frequencies in their transfer function. In transient environments, the resultant signals from these transducers are shown to be analytically unpredictable in amplitude level and frequency content. Data recorded during nuclear effects simulation testing on structures are analyzed. Results of analysis can be generalized to any structure which encounters dynamic loading. Methods to improve the recorded data are described which can be implemented on a frequency selective basis during the measurement process. These improvements minimize data distortion attributable to the transfer characteristics of the measuring transducers

  2. Assembly of Liposomes Controlled by Triple Helix Formation

    DEFF Research Database (Denmark)

    Vogel, Stefan; Jakobsen, Ulla

    2013-01-01

    Attachment of DNA to the surface of different solid nanoparticles (e.g. gold- and silica nanoparticles) is well established and a number of DNA-modified solid nanoparticle systems have been applied to thermal denaturation analysis of oligonucleotides. We report herein the non-covalent immobilizat...... analysis (NTA) and dynamic light scattering (DLS) show independently from ultraviolet spectroscopy experiments the formation of liposome aggregates.......-covalent immobilization of oligonucleotides on the surface of soft nanoparticles (e.g. liposomes) and the subsequent controlled assembly by DNA triple helix formation. The non-covalent approach avoids tedious surface chemistry and necessary purification procedures and can simplify and extend the available methodology...... sequences (G or C-rich) to explore the applicability of the method for different triple helical assembly modes. We demonstrate advantages and limitations of the approach and proof the reversible and reproducible formation of liposome aggregates during thermal denaturation cycles. Nanoparticle tracking...

  3. THE DYNAMICS OF THE MATRICS STRUCTURE

    OpenAIRE

    Dumitru CONSTANTINESCU

    2007-01-01

    The relationships organization-suppliers-customers have recently known major changes in the structure of services and have made the organization develop its managerial and professional competencies in order to do projects. The qualified organization is the most trust-worthy in the process of doing a project. The participation of an organization in doing projects depends on a multitude of factors. Out of these factors, the structural organization comes forth, as it represents the variable with...

  4. Origin and Diversification of Basic-Helix-Loop-Helix Proteins in Plants

    OpenAIRE

    Pires, Nuno; Dolan, Liam

    2009-01-01

    Basic helix-loop-helix (bHLH) proteins are a class of transcription factors found throughout eukaryotic organisms. Classification of the complete sets of bHLH proteins in the sequenced genomes of Arabidopsis thaliana and Oryza sativa (rice) has defined the diversity of these proteins among flowering plants. However, the evolutionary relationships of different plant bHLH groups and the diversity of bHLH proteins in more ancestral groups of plants are currently unknown. In this study, we use wh...

  5. Dynamical stability in fluid-structure interaction

    International Nuclear Information System (INIS)

    Planchard, J.; Thomas, B.

    1991-01-01

    The aim of the paper is to investigate the dynamical stability of a group of elastic tubes placed in a cross-flow which obeys to the Navier-Stokes equations. The stability of this coupled system is deduced from the study of a quadratic eigenvalue problem arising in the linearized equations. The instability occurs when the real part of one of the eigenvalues becomes positive; the steady state is then replaced by a time-periodic state which is stable (Hopf bifurcation phenomenon). Some numerical methods for solving the quadratic eigenvalue problem are described [fr

  6. Atomic probes of surface structure and dynamics

    International Nuclear Information System (INIS)

    Heller, E.J.; Jonsson, H.

    1992-01-01

    Progress for the period Sept. 15, 1992 to Sept. 14, 1993 is discussed. Semiclassical methods that will allow much faster and more accurate three-dimensional atom--surface scattering calculations, both elastic and inelastic, are being developed. The scattering of He atoms from buckyballs is being investigated as a test problem. Somewhat more detail is given on studies of He atom scattering from defective Pt surfaces. Molecular dynamics simulations of He + and Ar + ion sputtering of Pt surfaces are also being done. He atom scattering from Xe overlayers on metal surfaces and the thermalized dissociation of H 2 on Cu(110) are being studied. (R.W.R.) 64 refs

  7. Dynamics of structures '89. Vol. 3

    International Nuclear Information System (INIS)

    1989-01-01

    The proceedings, comprising 3 volumes published by the Plzen Centre of the Czechoslovak Society for Science and Technology (Vol. 1 and 2) and by Skoda Works in Plzen (Vol. 3), contain 107 papers, out of which 8 fall within the INIS Subject Scope; these deal with problems related to the earthquake resistance of nuclear power plants. Attention is paid to the evaluation of seismic characteristics of nuclear power plant equipment, to the equipment testing and to calculations of its dynamic characteristics under simulated seismic stress. (Z.M.)

  8. Dynamic isoperimetry and the geometry of Lagrangian coherent structures

    International Nuclear Information System (INIS)

    Froyland, Gary

    2015-01-01

    The study of transport and mixing processes in dynamical systems is particularly important for the analysis of mathematical models of physical systems. We propose a novel, direct geometric method to identify subsets of phase space that remain strongly coherent over a finite time duration. This new method is based on a dynamic extension of classical (static) isoperimetric problems; the latter are concerned with identifying submanifolds with the smallest boundary size relative to their volume.The present work introduces dynamic isoperimetric problems; the study of sets with small boundary size relative to volume as they are evolved by a general dynamical system. We formulate and prove dynamic versions of the fundamental (static) isoperimetric (in)equalities; a dynamic Federer–Fleming theorem and a dynamic Cheeger inequality. We introduce a new dynamic Laplace operator and describe a computational method to identify coherent sets based on eigenfunctions of the dynamic Laplacian.Our results include formal mathematical statements concerning geometric properties of finite-time coherent sets, whose boundaries can be regarded as Lagrangian coherent structures. The computational advantages of our new approach are a well-separated spectrum for the dynamic Laplacian, and flexibility in appropriate numerical approximation methods. Finally, we demonstrate that the dynamic Laplace operator can be realised as a zero-diffusion limit of a newly advanced probabilistic transfer operator method [9] for finding coherent sets, which is based on small diffusion. Thus, the present approach sits naturally alongside the probabilistic approach [9], and adds a formal geometric interpretation. (paper)

  9. Cardiolipin effects on membrane structure and dynamics.

    Science.gov (United States)

    Unsay, Joseph D; Cosentino, Katia; Subburaj, Yamunadevi; García-Sáez, Ana J

    2013-12-23

    Cardiolipin (CL) is a lipid with unique properties solely found in membranes generating electrochemical potential. It contains four acyl chains and tends to form nonlamellar structures, which are believed to play a key role in membrane structure and function. Indeed, CL alterations have been linked to disorders such as Barth syndrome and Parkinson's disease. However, the molecular effects of CL on membrane organization remain poorly understood. Here, we investigated the structure and physical properties of CL-containing membranes using confocal microscopy, fluorescence correlation spectroscopy, and atomic force microscopy. We found that the fluidity of the lipid bilayer increased and its mechanical stability decreased with CL concentration, indicating that CL decreases the packing of the membrane. Although the presence of up to 20% CL gave rise to flat, stable bilayers, the inclusion of 5% CL promoted the formation of flowerlike domains that grew with time. Surprisingly, we often observed two membrane-piercing events in atomic force spectroscopy experiments with CL-containing membranes. Similar behavior was observed with a lipid mixture mimicking the mitochondrial outer membrane composition. This suggests that CL promotes the formation of membrane areas with apposed double bilayers or nonlamellar structures, similar to those proposed for mitochondrial contact sites. All together, we show that CL induces membrane alterations that support the role of CL in facilitating bilayer structure remodeling, deformation, and permeabilization.

  10. Forced evolution of a regulatory RNA helix in the HIV-1 genome

    NARCIS (Netherlands)

    Berkhout, B.; Klaver, B.; Das, A. T.

    1997-01-01

    The 5'and 3'end of the HIV-1 RNA genome forms a repeat (R) element that encodes a double stem-loop structure (the TAR and polyA hairpins). Phylogenetic analysis of the polyA hairpin in different human and simian immunodeficiency viruses suggests that the thermodynamic stability of the helix is

  11. Chaos, dynamical structure and climate variability

    Energy Technology Data Exchange (ETDEWEB)

    Stewart, H.B. [Brookhaven National Lab., Upton, NY (United States). Dept. of Applied Science

    1995-09-01

    Deterministic chaos in dynamical systems offers a new paradigm for understanding irregular fluctuations. Techniques for identifying deterministic chaos from observed data, without recourse to mathematical models, are being developed. Powerful methods exist for reconstructing multidimensional phase space from an observed time series of a single scalar variable; these methods are invaluable when only a single scalar record of the dynamics is available. However, in some applications multiple concurrent time series may be available for consideration as phase space coordinates. Here the authors propose some basic analytical tools for such multichannel time series data, and illustrate them by applications to a simple synthetic model of chaos, to a low-order model of atmospheric circulation, and to two high-resolution paleoclimate proxy data series. The atmospheric circulation model, originally proposed by Lorenz, has 27 principal unknowns; they establish that the chaotic attractor can be embedded in a subspace of eight dimensions by exhibiting a specific subset of eight unknowns which pass multichannel tests for false nearest neighbors. They also show that one of the principal unknowns in the 27-variable model--the global mean sea surface temperature--is of no discernible usefulness in making short-term forecasts.

  12. Nonlinear and stochastic dynamics of coherent structures

    DEFF Research Database (Denmark)

    Rasmussen, Kim

    1997-01-01

    This Thesis deals with nonlinear and stochastic dynamics in systems which can be described by nonlinear Schrödinger models. Basically three different models are investigated. The first is the continuum nonlinear Schröndinger model in one and two dimensions generalized by a tunable degree of nonli......This Thesis deals with nonlinear and stochastic dynamics in systems which can be described by nonlinear Schrödinger models. Basically three different models are investigated. The first is the continuum nonlinear Schröndinger model in one and two dimensions generalized by a tunable degree...... introduces the nonlinear Schrödinger model in one and two dimensions, discussing the soliton solutions in one dimension and the collapse phenomenon in two dimensions. Also various analytical methods are described. Then a derivation of the nonlinear Schrödinger equation is given, based on a Davydov like...... system described by a tight-binding Hamiltonian and a harmonic lattice coupled b y a deformation-type potential. This derivation results in a two-dimensional nonline ar Schrödinger model, and considering the harmonic lattice to be in thermal contact with a heat bath w e show that the nonlinear...

  13. Structural and dynamical insights into the membrane-bound α-synuclein.

    Directory of Open Access Journals (Sweden)

    Neha Jain

    Full Text Available Membrane-induced disorder-to-helix transition of α-synuclein, a presynaptic protein, has been implicated in a number of important neuronal functions as well as in the etiology of Parkinson's disease. In order to obtain structural insights of membrane-bound α-synuclein at the residue-specific resolution, we took advantage of the fact that the protein is devoid of tryptophan and incorporated single tryptophan at various residue positions along the sequence. These tryptophans were used as site-specific markers to characterize the structural and dynamical aspects of α-synuclein on the negatively charged small unilamellar lipid vesicles. An array of site-specific fluorescence readouts, such as the spectral-shift, quenching efficiency and anisotropy, allowed us to discern various features of the conformational rearrangements occurring at different locations of α-synuclein on the lipid membrane. In order to define the spatial localization of various regions of the protein near the membrane surface, we utilized a unique and sensitive indicator, namely, red-edge excitation shift (REES, which originates when a fluorophore is located in a highly ordered micro-environment. The extent of REES observed at different residue positions allowed us to directly identify the residues that are localized at the membrane-water interface comprising a thin (∼ 15 Å layer of motionally restrained water molecules and enabled us to construct a dynamic hydration map of the protein. The combination of site-specific fluorescence readouts allowed us to unravel the intriguing molecular details of α-synuclein on the lipid membrane in a direct model-free fashion. Additionally, the combination of methodologies described here are capable of distinguishing subtle but important structural alterations of α-synuclein bound to different negatively charged lipids with varied head-group chemistry. We believe that the structural modulations of α-synuclein on the membrane could

  14. Hadron structure with light dynamical quarks

    International Nuclear Information System (INIS)

    Edwards, R.G.; Richards, D.G.; Fleming, G.T.; Haegler, P.; Negele, J.W.; Orginos, K.; Pochinsky, A.; Renner, D.B.; Schroers, W.

    2005-09-01

    Generalized parton distributions encompass a wealth of information concerning the three-dimensional quark and gluon structure of the nucleon, and thus provide an ideal focus for the study of hadron structure using lattice QCD. The special limits corresponding to form factors and parton distributions are well explored experimentally, providing clear tests of lattice calculations, and the lack of experimental data for more general cases provides opportunities for genuine predictions and for guiding experiment. We present results from hybrid calculations with improved staggered (Asqtad) sea quarks and domain wall valence quarks at pion masses down to 350 MeV. (orig.)

  15. Genome-wide identification and analysis of basic helix-loop-helix domains in dog, Canis lupus familiaris.

    Science.gov (United States)

    Wang, Xu-Hua; Wang, Yong; Liu, A-Ke; Liu, Xiao-Ting; Zhou, Yang; Yao, Qin; Chen, Ke-Ping

    2015-04-01

    The basic helix-loop-helix (bHLH) domain is a highly conserved amino acid motif that defines a group of DNA-binding transcription factors. bHLH proteins play essential regulatory roles in a variety of biological processes in animal, plant, and fungus. The domestic dog, Canis lupus familiaris, is a good model organism for genetic, physiological, and behavioral studies. In this study, we identified 115 putative bHLH genes in the dog genome. Based on a phylogenetic analysis, 51, 26, 14, 4, 12, and 4 dog bHLH genes were assigned to six separate groups (A-F); four bHLH genes were categorized as ''orphans''. Within-group evolutionary relationships inferred from the phylogenetic analysis were consistent with positional conservation, other conserved domains flanking the bHLH motif, and highly conserved intron/exon patterns in other vertebrates. Our analytical results confirmed the GenBank annotations of 89 dog bHLH proteins and provided information that could be used to update the annotations of the remaining 26 dog bHLH proteins. These data will provide good references for further studies on the structures and regulatory functions of bHLH proteins in the growth and development of dogs, which may help in understanding the mechanisms that underlie the physical and behavioral differences between dogs and wolves.

  16. A framework of DYNAMIC data structures for string processing

    DEFF Research Database (Denmark)

    Prezza, Nicola

    2017-01-01

    implemented using DYNAMIC with those of stateof-the-art tools performing the same task. Our experiments show that algorithms making use of dynamic compressed data structures can be up to three orders of magnitude more space-efficient (albeit slower) than classical ones performing the same tasks.......In this paper we present DYNAMIC, an open-source C++ library implementing dynamic compressed data structures for string manipulation. Our framework includes useful tools such as searchable partial sums, succinct/gap-encoded bitvectors, and entropy/run-length compressed strings and FM indexes. We...... prove close-to-optimal theoretical bounds for the resources used by our structures, and show that our theoretical predictions are empirically tightly verified in practice. To conclude, we turn our attention to applications. We compare the performance of five recently-published compression algorithms...

  17. Mid-frequency Band Dynamics of Large Space Structures

    Science.gov (United States)

    Coppolino, Robert N.; Adams, Douglas S.

    2004-01-01

    High and low intensity dynamic environments experienced by a spacecraft during launch and on-orbit operations, respectively, induce structural loads and motions, which are difficult to reliably predict. Structural dynamics in low- and mid-frequency bands are sensitive to component interface uncertainty and non-linearity as evidenced in laboratory testing and flight operations. Analytical tools for prediction of linear system response are not necessarily adequate for reliable prediction of mid-frequency band dynamics and analysis of measured laboratory and flight data. A new MATLAB toolbox, designed to address the key challenges of mid-frequency band dynamics, is introduced in this paper. Finite-element models of major subassemblies are defined following rational frequency-wavelength guidelines. For computational efficiency, these subassemblies are described as linear, component mode models. The complete structural system model is composed of component mode subassemblies and linear or non-linear joint descriptions. Computation and display of structural dynamic responses are accomplished employing well-established, stable numerical methods, modern signal processing procedures and descriptive graphical tools. Parametric sensitivity and Monte-Carlo based system identification tools are used to reconcile models with experimental data and investigate the effects of uncertainties. Models and dynamic responses are exported for employment in applications, such as detailed structural integrity and mechanical-optical-control performance analyses.

  18. Structural Identifiability of Dynamic Systems Biology Models.

    Science.gov (United States)

    Villaverde, Alejandro F; Barreiro, Antonio; Papachristodoulou, Antonis

    2016-10-01

    A powerful way of gaining insight into biological systems is by creating a nonlinear differential equation model, which usually contains many unknown parameters. Such a model is called structurally identifiable if it is possible to determine the values of its parameters from measurements of the model outputs. Structural identifiability is a prerequisite for parameter estimation, and should be assessed before exploiting a model. However, this analysis is seldom performed due to the high computational cost involved in the necessary symbolic calculations, which quickly becomes prohibitive as the problem size increases. In this paper we show how to analyse the structural identifiability of a very general class of nonlinear models by extending methods originally developed for studying observability. We present results about models whose identifiability had not been previously determined, report unidentifiabilities that had not been found before, and show how to modify those unidentifiable models to make them identifiable. This method helps prevent problems caused by lack of identifiability analysis, which can compromise the success of tasks such as experiment design, parameter estimation, and model-based optimization. The procedure is called STRIKE-GOLDD (STRuctural Identifiability taKen as Extended-Generalized Observability with Lie Derivatives and Decomposition), and it is implemented in a MATLAB toolbox which is available as open source software. The broad applicability of this approach facilitates the analysis of the increasingly complex models used in systems biology and other areas.

  19. Oxide Interfaces: emergent structure and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Clarke, Roy [Univ. of Michigan, Ann Arbor, MI (United States)

    2016-08-16

    This Final Report describes the scientific accomplishments that have been achieved with support from grant DE-FG02-06ER46273 during the period 6/1/2012– 5/31/2016. The overall goals of this program were focused on the behavior of epitaxial oxide heterostructures at atomic length scales (Ångstroms), and correspondingly short time-scales (fs -ns). The results contributed fundamentally to one of the currently most active frontiers in condensed matter physics research, namely to better understand the intricate relationship between charge, lattice, orbital and spin degrees of freedom that are exhibited by complex oxide heterostructures. The findings also contributed towards an important technological goal which was to achieve a better basic understanding of structural and electronic correlations so that the unusual properties of complex oxides can be exploited for energy-critical applications. Specific research directions included: probing the microscopic behavior of epitaxial interfaces and buried layers; novel materials structures that emerge from ionic and electronic reconfiguration at epitaxial interfaces; ultrahigh-resolution mapping of the atomic structure of heterointerfaces using synchrotron-based x-ray surface scattering, including direct methods of phase retrieval; using ultrafast lasers to study the effects of transient strain on coherent manipulation of multi-ferroic order parameters; and investigating structural ordering and relaxation processes in real-time.

  20. Structure and dynamics of magnetic nanoparticles

    DEFF Research Database (Denmark)

    Clausen, K.N.; Bødker, F.; Hansen, M.F.

    2000-01-01

    In this paper we present X-ray and neutron diffraction data illustrating aspects of crystal and magnetic structures of ferromagnetic alpha-Fe and antiferromagnetic NiO nanoparticles, as well as inelastic neutron scattering studies of the magnetic fluctuations in NiO and in canted antiferromagnetic...

  1. Emergence of structured communities through evolutionary dynamics.

    Science.gov (United States)

    Shtilerman, Elad; Kessler, David A; Shnerb, Nadav M

    2015-10-21

    Species-rich communities, in which many competing species coexist in a single trophic level, are quite frequent in nature, but pose a formidable theoretical challenge. In particular, it is known that complex competitive systems become unstable and unfeasible when the number of species is large. Recently, many studies have attributed the stability of natural communities to the structure of the interspecific interaction network, yet the nature of such structures and the underlying mechanisms responsible for them remain open questions. Here we introduce an evolutionary model, based on the generic Lotka-Volterra competitive framework, from which a stable, structured, diverse community emerges spontaneously. The modular structure of the competition matrix reflects the phylogeny of the community, in agreement with the hierarchial taxonomic classification. Closely related species tend to have stronger niche overlap and weaker fitness differences, as opposed to pairs of species from different modules. The competitive-relatedness hypothesis and the idea of emergent neutrality are discussed in the context of this evolutionary model. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Dynamic structure in self-sustained turbulence

    International Nuclear Information System (INIS)

    Itoh, K.; Itoh, S.; Yagi, M.; Fukuyama, A.

    1995-06-01

    Dynamical equation for the self-sustained and pressure-driven turbulence in toroidal plasmas is derived. The growth rate of the dressed-test mode, which belongs to the subcritical turbulence, is obtained as a function of the turbulent transport coefficient. In the limit of the low fluctuation level, the mode has the feature of the nonlinear instability and shows the explosive growth. The growth rate vanishes when the driven transport reaches to the stationarily-turbulent level. The stationary solution is thermodynamically stable. The characteristic time, by which the stationary and self-sustained turbulence is established, scales with the ion-sound transit time and is accelerated by the bad magnetic curvature. Influences of the pressure gradient as well as the radial electric field inhomogeneity are quantified. (author)

  3. Structure an dynamics in cavity quantum electrodynamics

    International Nuclear Information System (INIS)

    Kimble, H.J.

    1994-01-01

    Much of the theoretical background related to the radiative processes for atoms in the presence of boundaries comes from two often disjoint areas, namely cavity quantum electrodynamics and optical bistability with two-state atoms. While the former of these areas has been associated to a large degree with studies in a perturbative domain of altered associated to a large degree with studies in a perturbative domain of altered emission processes in the presence of boundaries other than those of free space, the latter is often viewed from the perspective of hysteresis cycles and device applications. With the exception of the laser, however, perhaps the most extensive investigations of quantum statistical processes in quantum optics are to be found in the literature on bistability with two-state atoms and on cavity QED. Unfortunately, the degree of overlap of these two areas has not always been fully appreciated. This circumstance is perhaps due in part to the fact that the investigation of dynamical processes in cavity QED has had as its cornerstone the Jaynes-Cummings problem, with extensions to include, for example, small amounts of dissipation. On the other hand, a principle aspect of the bistability literature has been the study of quantum fluctuations in open systems for which dissipation plays a central role, but for which the coherent quantum dynamics of the Haynes-Cummings model are to a large measure lost due to the usual assumption of large system size and weak coupling (as in the standard theory of the laser). 132 refs., 26 figs., 1 tab

  4. Dynamic loads during failure risk assessment of bridge crane structures

    Science.gov (United States)

    Gorynin, A. D.; Antsev, V. Yu; Shaforost, A. N.

    2018-03-01

    The paper presents the method of failure risk assessment associated with a bridge crane metal structure at the design stage. It also justifies the necessity of taking into account dynamic loads with regard to the operational cycle of a bridge crane during failure risk assessment of its metal structure.

  5. Molecular dynamics of the structure and thermodynamics of dusty ...

    African Journals Online (AJOL)

    The static structure and thermodynamic properties of two-dimensional dusty plasma are analyzed for some typical values of coupling and screening parameters using classical molecular dynamics. Radial distribution function and static structure factor are computed. The radial distribution functions display the typical ...

  6. Molecular dynamic analysis of the structure of dendrimers

    Energy Technology Data Exchange (ETDEWEB)

    Canetta, E.; Maino, G. E-mail: maino@bologna.enea.it

    2004-01-01

    We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques.

  7. Molecular dynamic analysis of the structure of dendrimers

    International Nuclear Information System (INIS)

    Canetta, E.; Maino, G.

    2004-01-01

    We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques

  8. Dynamic kirigami structures for integrated solar tracking

    Science.gov (United States)

    Lamoureux, Aaron; Lee, Kyusang; Shlian, Matthew; Forrest, Stephen R.; Shtein, Max

    2015-01-01

    Optical tracking is often combined with conventional flat panel solar cells to maximize electrical power generation over the course of a day. However, conventional trackers are complex and often require costly and cumbersome structural components to support system weight. Here we use kirigami (the art of paper cutting) to realize novel solar cells where tracking is integral to the structure at the substrate level. Specifically, an elegant cut pattern is made in thin-film gallium arsenide solar cells, which are then stretched to produce an array of tilted surface elements which can be controlled to within ±1°. We analyze the combined optical and mechanical properties of the tracking system, and demonstrate a mechanically robust system with optical tracking efficiencies matching conventional trackers. This design suggests a pathway towards enabling new applications for solar tracking, as well as inspiring a broader range of optoelectronic and mechanical devices. PMID:26348820

  9. Structure and dynamics of ringed galaxies

    International Nuclear Information System (INIS)

    Buta, R.J.

    1984-01-01

    In many spiral and SO galaxies, single or multiple ring structures are visible in the disk. These inner rings (r), outer rings (R), and nuclear rings (nr) were investigated by means of morphology, photometry, and spectroscopy in order to provide basic data on a long neglected phenomenon. The metric properties of each ring are investigated and found to correlate with the structure of the parent galaxy. When properly calibrated, inner rings in barred (SB) systems can be used as geometric extragalactic distance indicators to distances in excess of 100 Mpc. Other statistics are presented that confirm previous indications that the rings have preferred shapes, relative sizes, and orientations with respect to bars. A survey is made of the less homogeneous non-barred (SA) ringed systems, and the causes of the inhomogeneity are isolated. It is shown that rings can be identified in multiple-ring SA systems that are exactly analogous to those in barred spirals

  10. International Conference on Structural Nonlinear Dynamics and Diagnosis

    CERN Document Server

    CSNDD 2012; CSNDD 2014

    2015-01-01

    This book, which presents the peer-reviewed post-proceedings of CSNDD 2012 and CSNDD 2014, addresses the important role that relevant concepts and tools from nonlinear and complex dynamics could play in present and future engineering applications. It includes 22 chapters contributed by outstanding researchers and covering various aspects of applications, including: structural health monitoring, diagnosis and damage detection, experimental methodologies, active vibration control and smart structures, passive control of structures using nonlinear energy sinks, vibro-impact dynamic MEMS/NEMS/AFM, energy-harvesting materials and structures, and time-delayed feedback control, as well as aspects of deterministic versus stochastic dynamics and control of nonlinear phenomena in physics.  Researchers and engineers interested in the challenges posed and opportunities offered by nonlinearities in the development of passive and active control strategies, energy harvesting, novel design criteria, modeling and characteriz...

  11. Nucleic acid helices: I. Structure of M1 RNA from E. coli as determined bypsoralen crosslinking. II. Thermodynamics of the helix-coil transition of DNA oligonucleotides in solutions containing 3. 0 M tetramethylammonium chloride

    Energy Technology Data Exchange (ETDEWEB)

    Lipson, S.E.

    1987-01-01

    This work includes two different investigations examining nucleic acid helices. The first study discusses secondary and tertiary interactions in the RNA moiety of ribonuclease P from Escherichia coli. The second study discusses the thermodynamics of the helix-coil transition of DNA oligonucleotides in solutions containing tetramethylammonium chloride. The RNA moiety of ribonuclease P from Escherichia coli (M1 RNA) has been photoreacted with 4{prime}-hydroxymethyl-4,5{prime}8-trimethylpsoralen and long wave UV light (320-380 nm) in a buffer in which the M1 RNA alone acts as a true catalyst of tRNA processing. Limited specific digestion followed by two dimensional gel electrophoresis yields fragments crosslinked by HMT. The positions of the crosslinks have been determined to within {plus minus}15 nucleotides by photoreversal of the isolated crosslinked fragments and enzymatic sequencing of the resulting RNA. Further assignments of the exact locations of the crosslinks have been made on the known photoreactivity of the psoralen with different bases.

  12. Structural dynamics of the cell nucleus

    Science.gov (United States)

    Wiegert, Simon; Bading, Hilmar

    2011-01-01

    Neuronal morphology plays an essential role in signal processing in the brain. Individual neurons can undergo use-dependent changes in their shape and connectivity, which affects how intracellular processes are regulated and how signals are transferred from one cell to another in a neuronal network. Calcium is one of the most important intracellular second messengers regulating cellular morphologies and functions. In neurons, intracellular calcium levels are controlled by ion channels in the plasma membrane such as NMDA receptors (NMDARs), voltage-gated calcium channels (VGCCs) and certain α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) as well as by calcium exchange pathways between the cytosol and internal calcium stores including the endoplasmic reticulum and mitochondria. Synaptic activity and the subsequent opening of ligand and/or voltage-gated calcium channels can initiate cytosolic calcium transients which propagate towards the cell soma and enter the nucleus via its nuclear pore complexes (NPCs) embedded in the nuclear envelope. We recently described the discovery that in hippocampal neurons the morphology of the nucleus affects the calcium dynamics within the nucleus. Here we propose that nuclear infoldings determine whether a nucleus functions as an integrator or detector of oscillating calcium signals. We outline possible ties between nuclear mophology and transcriptional activity and discuss the importance of extending the approach to whole cell calcium signal modeling in order to understand synapse-to-nucleus communication in healthy and dysfunctional neurons. PMID:21738832

  13. Dynamic structure factor on liquid Pb

    International Nuclear Information System (INIS)

    Padureanu, I.; Rapeanu, S.; Rotarascu, G.; Craciun, C.

    1979-01-01

    Dinamic structure factor S(Q,hω) in liquid Pb has been measured at 350 deg C and 400 deg C using the inelastic scattering of the slow neutrons. The measurements were performed in the momentum transfer range 0.6 A -1 -1 . The intermediate scattering function F(Q,t) is also calculated from S(Q,hω). Multiple scattering calculation shows that it is very large especially at small scattering angles. The comparison of the experimental data with the theory is made in terms of two theoretical models. (author)

  14. Dynamical effects of QCD vacuum structure

    International Nuclear Information System (INIS)

    Ferreira, Erasmo

    1994-01-01

    The role of the QCD vacuum structure in the determination of the properties of states and processes occurring in the confinement regime of QCD is reviewed. The finite range of the vacuum correlations is discussed, and an analytical form is suggested for the correlation functions. The role of the vacuum quantum numbers in the phenomenology of high-energy scattering is reviewed. The vacuum correlation model of non-perturbative QCD is mentioned as a bridge between the fundamental theory and the description of the experiments. (author). 13 refs., 1 fig

  15. Dynamical structure of extreme ultraviolet macrospicules

    Science.gov (United States)

    Karovska, Margarita; Habbal, Shadia Rifai

    1994-01-01

    We describe the substructures forming the macrospicules and their temporal evolution, as revealed by the application of an image enhancement algorithm to extreme ultraviolet (EUV) observations of macrospicules. The enhanced images uncover, for the first time, the substructures forming the column-like structures within the macrospicules and the low-lying arches at their base. The spatial and temporal evolution of macrospicules clearly show continuous interaction between these substructures with occasional ejection of plasma following a ballistic trajectory. We comment on the importance of these results for planning near future space observations of macrospicules with better temporal and spatial resolution.

  16. Effect of support conditions on structural response under dynamic loading

    International Nuclear Information System (INIS)

    Akram, T.; Memon, S.A.

    2008-01-01

    In design practice, dynamic structural analysis is carried out with base of structure considered as fixed; this means that foundation is placed on rock like soil material. While conducting this type of analyses the role of foundation and soil behaviour is totally neglected. The actions in members and loads transferred at foundation level obtained in this manner do not depict the true structural behaviour. FEM (Finite Element Methods) analysis where both superstructure and foundation soil are coupled together is quite complicated and expensive for design environments. A simplified model is required to depict dynamic response of structures with foundations based on flexible soils. The primary purpose of this research is to compare the superstructure dynamic responses of structural systems with fixed base to that of simple soil model base. The selected simple soil model is to be suitable for use in a design environment to give more realistic results. For this purpose building models are idealized with various heights and structural systems in both 2D (Two Dimensional) and 3D (Three Dimensional) space. These models are then provided with visco-elastic supports representing three soil bearing capacities and the analysis results are compared to that of fixed supports models. The results indicate that fixed support system underestimates natural time period of the structures. Dynamic behavior and force response of visco-elastic support is different from fixed support model. Fixed support models result in over designed base columns and under designed beams. (author)

  17. PDB2CD visualises dynamics within protein structures.

    Science.gov (United States)

    Janes, Robert W

    2017-10-01

    Proteins tend to have defined conformations, a key factor in enabling their function. Atomic resolution structures of proteins are predominantly obtained by either solution nuclear magnetic resonance (NMR) or crystal structure methods. However, when considering a protein whose structure has been determined by both these approaches, on many occasions, the resultant conformations are subtly different, as illustrated by the examples in this study. The solution NMR approach invariably results in a cluster of structures whose conformations satisfy the distance boundaries imposed by the data collected; it might be argued that this is evidence of the dynamics of proteins when in solution. In crystal structures, the proteins are often in an energy minimum state which can result in an increase in the extent of regular secondary structure present relative to the solution state depicted by NMR, because the more dynamic ends of alpha helices and beta strands can become ordered at the lower temperatures. This study examines a novel way to display the differences in conformations within an NMR ensemble and between these and a crystal structure of a protein. Circular dichroism (CD) spectroscopy can be used to characterise protein structures in solution. Using the new bioinformatics tool, PDB2CD, which generates CD spectra from atomic resolution protein structures, the differences between, and possible dynamic range of, conformations adopted by a protein can be visualised.

  18. Elements of earthquake engineering and structural dynamics. 2. ed.

    International Nuclear Information System (INIS)

    Filiatrault, A.

    2002-01-01

    This book is written for practising engineers, senior undergraduate and junior structural-engineering students, and university educators. Its main goal is to provide basic knowledge to structural engineers who have no previous knowledge about earthquake engineering and structural dynamics. Earthquake engineering is a multidisciplinary science. This book is not limited to structural analysis and design. The basics of other relevant topics (such as geology, seismology, and geotechnical engineering) are also covered to ensure that structural engineers can interact efficiently with other specialists during a construction project in a seismic zone

  19. Plasma turbulence. Structure formation, selection rule, dynamic response and dynamics transport

    International Nuclear Information System (INIS)

    Ito, Sanae I.

    2010-01-01

    The five-year project of Grant-in-Aid for Specially Promoted Research entitled general research on the structure formation and selection rule in plasma turbulence had brought many outcomes. Based on these outcomes, the Grant-in-Aid for Scientific Research (S) program entitled general research on dynamic response and dynamic transport in plasma turbulence has started. In the present paper, the state-of-the-art of the research activities on the structure formation, selection rule and dynamics in plasma turbulence are reviewed with reference to outcomes of these projects. (author)

  20. Structure-based control of complex networks with nonlinear dynamics.

    Science.gov (United States)

    Zañudo, Jorge Gomez Tejeda; Yang, Gang; Albert, Réka

    2017-07-11

    What can we learn about controlling a system solely from its underlying network structure? Here we adapt a recently developed framework for control of networks governed by a broad class of nonlinear dynamics that includes the major dynamic models of biological, technological, and social processes. This feedback-based framework provides realizable node overrides that steer a system toward any of its natural long-term dynamic behaviors, regardless of the specific functional forms and system parameters. We use this framework on several real networks, identify the topological characteristics that underlie the predicted node overrides, and compare its predictions to those of structural controllability in control theory. Finally, we demonstrate this framework's applicability in dynamic models of gene regulatory networks and identify nodes whose override is necessary for control in the general case but not in specific model instances.

  1. DYNAMIC PARTICLE SYSTEMS FOR OBJECT STRUCTURE EXTRACTION

    Directory of Open Access Journals (Sweden)

    Olivier Lavialle

    2011-05-01

    Full Text Available A new deformable model based on the use of a particle system is introduced. By defining the local behavior of each particle, the system behaves as an active contour model showing a variable topology and regularization properties. The efficiency of the particle system is illustrated by two applications: the first one concerns the use of the system as a skeleton extractor based on the propagation of particles inside a treeshaped object. Using this method, it is possible to generate a cartography of structures such as veins or channels. In a second illustration, the system avoids the problem of initialization of a piecewise cubic Bspline network used to straighten curved text lines.

  2. Structure and dynamics of photosynthetic proteins studied by neutron scattering and molecular dynamic simulation

    International Nuclear Information System (INIS)

    Dellerue, Serge

    2000-01-01

    Understand the structure-dynamics-function relation in the case of proteins is essential. But few experimental techniques allow to have access to knowledge of fast internal movements of biological macromolecules. With the neutron scattering method, it has been possible to study the reorientation dynamics of side chains and of polypeptide skeleton for two proteins in terms of water or detergent and of temperature. With the use of the molecular dynamics method, essential for completing and interpreting the experimental data, it has been possible to assess the different contributions of the whole structure of proteins to the overall dynamics. It has been shown that the polypeptide skeleton presents an energy relaxation comparable to those of the side chains. Moreover, it has been explained that the protein dynamics can only be understood in terms of relaxation time distribution. (author) [fr

  3. Structure and dynamics of weakly bound complexes

    International Nuclear Information System (INIS)

    Skouteris, D.

    1998-01-01

    The present thesis deals with the spectroscopic and theoretical investigation of weakly bound complexes involving a methane molecule. Studies of these Van der Waals complexes can give valuable information on the relevant intermolecular dynamics and promote the understanding of the interactions between molecules (which can ultimately lead to chemical reactions). Especially interesting are complexes involving molecules of high symmetry (e.g. tetrahedral, such as methane) because of the unusual effects arising from it (selection rules, nuclear Spin statistical weights etc.). The infrared spectrum of the Van der Waals complex between a CH 4 and a N 2 O molecule has been recorded and most of it has been assigned in the region of the N - O stretch (approximately 2225.0 cm -1 ). Despite the fact that this is really a weakly bound complex, it is nevertheless rigid enough so that the standard model for asymmetric top spectra can be applied to it with the usual quantum numbers. From the value of the inertial defect, it turns out that the methane unit is locked in a rigid configuration within the complex rather than freely rotating. The intermolecular distance as well as the tilting angle of the N 2 O linear unit are determined from the rotational constants. The complex itself turns out to have a T - shaped configuration. The infrared spectrum of the Ar - CH 4 complex at the ν 4 (bending) band of methane is also assigned. This is different from the previous one in that the methane unit rotates almost freely Within the complex. As a result, the quantum numbers used to classify rovibrational energy levels include these of the free unit. The concept of 'overall symmetry' is made use of to rationalise selection rules in various sub-bands of the spectrum. Moreover, new terms in the potential anisotropy Hamiltonian are calculated through the use of the overall symmetry concept. These are termed 'mixed anisotropy' terms since they involve both rotational and vibrational degrees of

  4. PWL approximation of nonlinear dynamical systems, part I: structural stability

    International Nuclear Information System (INIS)

    Storace, M; De Feo, O

    2005-01-01

    This paper and its companion address the problem of the approximation/identification of nonlinear dynamical systems depending on parameters, with a view to their circuit implementation. The proposed method is based on a piecewise-linear approximation technique. In particular, this paper describes the approximation method and applies it to some particularly significant dynamical systems (topological normal forms). The structural stability of the PWL approximations of such systems is investigated through a bifurcation analysis (via continuation methods)

  5. The Return to Schooling in Structural Dynamic Models: A Survey

    OpenAIRE

    Christian Belzil

    2007-01-01

    Working paper du GATE 2006-09; This papers contains a survey of the recent literature devoted to the returns to schooling within a dynamic structural framework. I present a historical perspective on the evolution of the literature, from early static models set in a selectivity framework (Willis and Rosen, 1979) to the recent literature, stimulated by Keane and Wolpin (1997), and which uses stochastic dynamic programming techniques. After reviewing the literature thoroughly, I compare the stru...

  6. Unraveling the Role of the C-terminal Helix Turn Helix of the Coat-binding Domain of Bacteriophage P22 Scaffolding Protein*

    Science.gov (United States)

    Padilla-Meier, G. Pauline; Gilcrease, Eddie B.; Weigele, Peter R.; Cortines, Juliana R.; Siegel, Molly; Leavitt, Justin C.; Teschke, Carolyn M.; Casjens, Sherwood R.

    2012-01-01

    Many viruses encode scaffolding and coat proteins that co-assemble to form procapsids, which are transient precursor structures leading to progeny virions. In bacteriophage P22, the association of scaffolding and coat proteins is mediated mainly by ionic interactions. The coat protein-binding domain of scaffolding protein is a helix turn helix structure near the C terminus with a high number of charged surface residues. Residues Arg-293 and Lys-296 are particularly important for coat protein binding. The two helices contact each other through hydrophobic side chains. In this study, substitution of the residues of the interface between the helices, and the residues in the β-turn, by aspartic acid was used examine the importance of the conformation of the domain in coat binding. These replacements strongly affected the ability of the scaffolding protein to interact with coat protein. The severity of the defect in the association of scaffolding protein to coat protein was dependent on location, with substitutions at residues in the turn and helix 2 causing the most significant effects. Substituting aspartic acid for hydrophobic interface residues dramatically perturbs the stability of the structure, but similar substitutions in the turn had much less effect on the integrity of this domain, as determined by circular dichroism. We propose that the binding of scaffolding protein to coat protein is dependent on angle of the β-turn and the orientation of the charged surface on helix 2. Surprisingly, formation of the highly complex procapsid structure depends on a relatively simple interaction. PMID:22879595

  7. The assessment of structural dynamics problems in nuclear reactor safety

    International Nuclear Information System (INIS)

    Liebe, R.

    1978-10-01

    The paper discusses important physical features of structural dynamics problems in reactor safety. First a general characterization is given of the following problems: Containment deformation due to pool-dynamics during BWR-blowdown; behavior of the core internals due to PWR-blowdown loads; dynamic response of a nuclear power plant during an earthquake; fuel element deformation due to local pressure pulses in an LMFBR core. Several criterias are formulated to classify typical problems so that a better choise can be made both of appropriate mathematical/numerical as well as experimental techniques. The degree of physical coupling between structural dynamics and fluid dynamics is discussed in more detail since it requires particular attention when selecting problem-oriented methods of solution. Some examples are given to illustrate the application and to compare advantages and disadvantages of several numerical methods. Then description is given of experimental techniques in structural dynamics and typical problem areas are identified. Finally some results are presented concerning the fuel element deformation problem in LMFBRs and from the general considerations some important conclusions are summarized. (orig.) 891 RW 892 AP [de

  8. Dynamic characteristics analysis of deployable space structures considering joint clearance

    Science.gov (United States)

    Li, Tuanjie; Guo, Jian; Cao, Yuyan

    2011-04-01

    The clearance in joints influences the dynamic stability and the performance of deployable space structures (DSS). A virtual experimental modal analysis (VEMA) method is proposed to deal with the effects of joint clearance and link flexibility on the dynamic characteristics of the DSS in this paper. The focus is on the finite element modeling of the clearance joint, VEMA and the modal parameters identification of the DSS. The finite element models (FEM) of the clearance joint and the deployable structure are established in ANSYS. The transient dynamic analysis is conducted to provide the time history data of excitation and response for the VEMA. The fast Fourier transform (FFT) technique is used to transform the data from time domain to frequency domain. The frequency response function is calculated to identify the modal parameters of the deployable structure. Experimental verification is provided to indicate the VEMA method is both a cost and time efficient approach to obtain the dynamic characteristics of the DSS. Finally, we analyze the effects of clearance size and gravity on the dynamic characteristics of the DSS. The analysis results indicate that the joint clearance and gravity strongly influence the dynamic characteristics of the DSS.

  9. Dynamics of a bistable Miura-origami structure

    Science.gov (United States)

    Fang, Hongbin; Li, Suyi; Ji, Huimin; Wang, K. W.

    2017-05-01

    Origami-inspired structures and materials have shown extraordinary properties and performances originating from the intricate geometries of folding. However, current state of the art studies have mostly focused on static and quasistatic characteristics. This research performs a comprehensive experimental and analytical study on the dynamics of origami folding through investigating a stacked Miura-Ori (SMO) structure with intrinsic bistability. We fabricate and experimentally investigated a bistable SMO prototype with rigid facets and flexible crease lines. Under harmonic base excitation, the SMO exhibits both intrawell and interwell oscillations. Spectrum analyses reveal that the dominant nonlinearities of SMO are quadratic and cubic, which generate rich dynamics including subharmonic and chaotic oscillations. The identified nonlinearities indicate that a third-order polynomial can be employed to approximate the measured force-displacement relationship. Such an approximation is validated via numerical study by qualitatively reproducing the phenomena observed in the experiments. The dynamic characteristics of the bistable SMO resemble those of a Helmholtz-Duffing oscillator (HDO); this suggests the possibility of applying the established tools and insights of HDO to predict origami dynamics. We also show that the bistability of SMO can be programmed within a large design space via tailoring the crease stiffness and initial stress-free configurations. The results of this research offer a wealth of fundamental insights into the dynamics of origami folding, and provide a solid foundation for developing foldable and deployable structures and materials with embedded dynamic functionalities.

  10. Dynamics of a bistable Miura-origami structure.

    Science.gov (United States)

    Fang, Hongbin; Li, Suyi; Ji, Huimin; Wang, K W

    2017-05-01

    Origami-inspired structures and materials have shown extraordinary properties and performances originating from the intricate geometries of folding. However, current state of the art studies have mostly focused on static and quasistatic characteristics. This research performs a comprehensive experimental and analytical study on the dynamics of origami folding through investigating a stacked Miura-Ori (SMO) structure with intrinsic bistability. We fabricate and experimentally investigated a bistable SMO prototype with rigid facets and flexible crease lines. Under harmonic base excitation, the SMO exhibits both intrawell and interwell oscillations. Spectrum analyses reveal that the dominant nonlinearities of SMO are quadratic and cubic, which generate rich dynamics including subharmonic and chaotic oscillations. The identified nonlinearities indicate that a third-order polynomial can be employed to approximate the measured force-displacement relationship. Such an approximation is validated via numerical study by qualitatively reproducing the phenomena observed in the experiments. The dynamic characteristics of the bistable SMO resemble those of a Helmholtz-Duffing oscillator (HDO); this suggests the possibility of applying the established tools and insights of HDO to predict origami dynamics. We also show that the bistability of SMO can be programmed within a large design space via tailoring the crease stiffness and initial stress-free configurations. The results of this research offer a wealth of fundamental insights into the dynamics of origami folding, and provide a solid foundation for developing foldable and deployable structures and materials with embedded dynamic functionalities.

  11. Algorithm of Dynamic Model Structural Identification of the Multivariable Plant

    Directory of Open Access Journals (Sweden)

    Л.М. Блохін

    2004-02-01

    Full Text Available  The new algorithm of dynamic model structural identification of the multivariable stabilized plant with observable and unobservable disturbances in the regular operating  modes is offered in this paper. With the help of the offered algorithm it is possible to define the “perturbed” models of dynamics not only of the plant, but also the dynamics characteristics of observable and unobservable casual disturbances taking into account the absence of correlation between themselves and control inputs with the unobservable perturbations.

  12. Structure Learning in Stochastic Non-linear Dynamical Systems

    Science.gov (United States)

    Morris, R. D.; Smelyanskiy, V. N.; Luchinsky, D. G.

    2005-12-01

    A great many systems can be modeled in the non-linear dynamical systems framework, as x˙ = f(x) + ξ(t), where f(x) is the potential function for the system, and ξ(t) is the driving noise. Modeling the potential using a set of basis functions, we derive the posterior for the basis coefficients. A more challenging problem is to determine the set of basis functions that are required to model a particular system. We show that using the Bayesian Information Criteria (BIC) to rank models, and the beam search technique, that we can accurately determine the structure of simple non-linear dynamical system models, and the structure of the coupling between non-linear dynamical systems where the individual systems are known. This last case has important ecological applications, for example in predator-prey systems, where the very structure of the coupling between predator-prey pairs can have great ecological significance.

  13. Matrix of transmission in structural dynamics

    International Nuclear Information System (INIS)

    Mukherjee, S.

    1975-01-01

    The problem of close-coupled systems and cantilever type buildings can be treated efficiently by means of the very general and versatile method of transmission matrix. The expression 'matrix of transmission' is used to point out the fact that the method to be described differs fundamentally from another method related to matrix calculus, and also successfully used in vibration problem. In this method, forces and displacements are introduced as the 'unknowns' of the problem. The 'matrix of transmission' relates these quantities at one point of the structure to those at the neighbouring point. The natural frequencies of a freely vibrating elastic system can be found by applying proper end conditions. The end conditions will yield the frequency determinate to zero. By using suitable numerical method, the natural frequencies and mode shapes are determined, by making a frequency sweep within the range of interest. Results of analysis of a typical nuclear building by this method show very close agreement with the results obtained by using ASKA and SAP IV Program

  14. Organoactinide chemistry: synthesis, structure, and solution dynamics

    International Nuclear Information System (INIS)

    Brennan, J.G.

    1985-12-01

    This thesis considers three aspects of organoactinide chemistry. In chapter one, a bidentate phosphine ligand was used to kinetically stabilize complexes of the type Cp 2 MX 2 . Ligand redistribution processes are present throughout the synthetic work, as has often been observed in uranium cyclopentadienyl chemistry. The effects of covalent M-L bonding on the solution and solid state properties of U(III) coordination complexes are considered. In particular, the nature of the more subtle interaction between the metal and the neutral ligand are examined. Using relative basicity data obtained in solution, and solid state structural data (and supplemented by gas phase photoelectron measurements), it is demonstrated that the more electron rich U(III) centers engage in significant U → L π-donation. Trivalent uranium is shown to be capable of acting either as a one- or two-electron reducing agent toward a wide variety of unsaturated organic and inorganic molecules, generating molecular classes unobtainable via traditional synthetic approaches, as well as offering an alternative synthetic approach to molecules accessible via metathesis reactions. Ligand redistribution processes are again observed, but given the information concerning ligand lability, this reactivity pattern is applied to the synthesis of pure materials inaccessible from redox chemistry. 214 refs., 33 figs., 10 tabs

  15. In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

    Science.gov (United States)

    Yoo, Jejoong; Aksimentiev, Aleksei

    2013-12-10

    The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.

  16. Full scale dynamic testing of Paks nuclear power plant structures

    International Nuclear Information System (INIS)

    Da Rin, E.M.

    1995-01-01

    This report refers to the full-scale dynamic structural testing activities that have been performed in December 1994 at the Paks (H) Nuclear Power Plant, within the framework of: the IAEA Coordinated research Programme 'Benchmark Study for the Seismic Analysis and Testing of WWER-type Nuclear Power Plants, and the nuclear research activities of ENEL-WR/YDN, the Italian National Electricity Board in Rome. The specific objective of the conducted investigation was to obtain valid data on the dynamic behaviour of the plant's major constructions, under normal operating conditions, for enabling an assessment of their actual seismic safety to be made. As described in more detail hereafter, the Paks NPP site has been subjected to low level earthquake like ground shaking, through appropriately devised underground explosions, and the dynamic response of the plant's 1 st reactor unit important structures was appropriately measured and digitally recorded. In-situ free field response was measured concurrently and, moreover, site-specific geophysical and seismological data were simultaneously acquired too. The above-said experimental data is to provide basic information on the geophysical and seismological characteristics of the Paks NPP site, together with useful reference information on the true dynamic characteristics of its main structures and give some indications on the actual dynamic soil-structure interaction effects for the case of low level excitation

  17. De novo design, synthesis and characterisation of MP3, a new catalytic four-helix bundle hemeprotein.

    Science.gov (United States)

    Faiella, Marina; Maglio, Ornella; Nastri, Flavia; Lombardi, Angela; Lista, Liliana; Hagen, Wilfred R; Pavone, Vincenzo

    2012-12-07

    A new artificial metalloenzyme, MP3 (MiniPeroxidase 3), designed by combining the excellent structural properties of four-helix bundle protein scaffolds with the activity of natural peroxidases, was synthesised and characterised. This new hemeprotein model was developed by covalently linking the deuteroporphyrin to two peptide chains of different compositions to obtain an asymmetric helix-loop-helix/heme/helix-loop-helix sandwich arrangement, characterised by 1) a His residue on one chain that acts as an axial ligand to the iron ion; 2) a vacant distal site that is able to accommodate exogenous ligands or substrates; and 3) an Arg residue in the distal site that should assist in hydrogen peroxide activation to give an HRP-like catalytic process. MP3 was synthesised and characterised as its iron complex. CD measurements revealed the high helix-forming propensity of the peptide, confirming the appropriateness of the model procedure; UV/Vis, MCD and EPR experiments gave insights into the coordination geometry and the spin state of the metal. Kinetic experiments showed that Fe(III)-MP3 possesses peroxidase-like activity comparable to R38A-hHRP, highlighting the possibility of mimicking the functional features of natural enzymes. The synergistic application of de novo design methods, synthetic procedures, and spectroscopic characterisation, described herein, demonstrates a method by which to implement and optimise catalytic activity for an enzyme mimetic. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Two stage approach to dynamic soil structure interaction

    International Nuclear Information System (INIS)

    Nelson, I.

    1981-01-01

    A two stage approach is used to reduce the effective size of soil island required to solve dynamic soil structure interaction problems. The ficticious boundaries of the conventional soil island are chosen sufficiently far from the structure so that the presence of the structure causes only a slight perturbation on the soil response near the boundaries. While the resulting finite element model of the soil structure system can be solved, it requires a formidable computational effort. Currently, a two stage approach is used to reduce this effort. The combined soil structure system has many frequencies and wavelengths. For a stiff structure, the lowest frequencies are those associated with the motion of the structure as a rigid body. In the soil, these modes have the longest wavelengths and attenuate most slowly. The higher frequency deformational modes of the structure have shorter wavelengths and their effect attenuates more rapidly with distance from the structure. The difference in soil response between a computation with a refined structural model, and one with a crude model, tends towards zero a very short distance from the structure. In the current work, the 'crude model' is a rigid structure with the same geometry and inertial properties as the refined model. Preliminary calculations indicated that a rigid structure would be a good low frequency approximation to the actual structure, provided the structure was much stiffer than the native soil. (orig./RW)

  19. Integrating Solid-State NMR and Computational Modeling to Investigate the Structure and Dynamics of Membrane-Associated Ghrelin

    Science.gov (United States)

    Els-Heindl, Sylvia; Chollet, Constance; Scheidt, Holger A.; Beck-Sickinger, Annette G.; Meiler, Jens; Huster, Daniel

    2015-01-01

    The peptide hormone ghrelin activates the growth hormone secretagogue receptor 1a, also known as the ghrelin receptor. This 28-residue peptide is acylated at Ser3 and is the only peptide hormone in the human body that is lipid-modified by an octanoyl group. Little is known about the structure and dynamics of membrane-associated ghrelin. We carried out solid-state NMR studies of ghrelin in lipid vesicles, followed by computational modeling of the peptide using Rosetta. Isotropic chemical shift data of isotopically labeled ghrelin provide information about the peptide’s secondary structure. Spin diffusion experiments indicate that ghrelin binds to membranes via its lipidated Ser3. Further, Phe4, as well as electrostatics involving the peptide’s positively charged residues and lipid polar headgroups, contribute to the binding energy. Other than the lipid anchor, ghrelin is highly flexible and mobile at the membrane surface. This observation is supported by our predicted model ensemble, which is in good agreement with experimentally determined chemical shifts. In the final ensemble of models, residues 8–17 form an α-helix, while residues 21–23 and 26–27 often adopt a polyproline II helical conformation. These helices appear to assist the peptide in forming an amphipathic conformation so that it can bind to the membrane. PMID:25803439

  20. Integrating solid-state NMR and computational modeling to investigate the structure and dynamics of membrane-associated ghrelin.

    Directory of Open Access Journals (Sweden)

    Gerrit Vortmeier

    Full Text Available The peptide hormone ghrelin activates the growth hormone secretagogue receptor 1a, also known as the ghrelin receptor. This 28-residue peptide is acylated at Ser3 and is the only peptide hormone in the human body that is lipid-modified by an octanoyl group. Little is known about the structure and dynamics of membrane-associated ghrelin. We carried out solid-state NMR studies of ghrelin in lipid vesicles, followed by computational modeling of the peptide using Rosetta. Isotropic chemical shift data of isotopically labeled ghrelin provide information about the peptide's secondary structure. Spin diffusion experiments indicate that ghrelin binds to membranes via its lipidated Ser3. Further, Phe4, as well as electrostatics involving the peptide's positively charged residues and lipid polar headgroups, contribute to the binding energy. Other than the lipid anchor, ghrelin is highly flexible and mobile at the membrane surface. This observation is supported by our predicted model ensemble, which is in good agreement with experimentally determined chemical shifts. In the final ensemble of models, residues 8-17 form an α-helix, while residues 21-23 and 26-27 often adopt a polyproline II helical conformation. These helices appear to assist the peptide in forming an amphipathic conformation so that it can bind to the membrane.

  1. Structural dynamics and vibration 1995. PD-Volume 70

    International Nuclear Information System (INIS)

    Ovunc, B.A.; Esat, I.I.; Sabir, A.B.; Karadag, V.

    1995-01-01

    The themes of this symposium focused on: dynamic responses to temperature cycles and wind excitation; the influence of the hydraulic feedback on stability; structural reliability; vibratory stress relief; fault detection by signal processing; dynamic contact in mechanisms; vibration of thick flexible mechanisms; higher order mechanisms in flexible mechanisms; natural circular frequencies by finite element method; elastic buckling, stability, and vibration of linear and nonlinear structures; buckling of stiffened plates and rings; mixed variable optimization; vibration optimization; and optimization in a constrained space. Separate abstracts were prepared for 20 papers in this book

  2. Structural, dynamical, and electronic properties of amorphous silicon: An ab initio molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Car, R.; Parrinello, M.

    1988-01-18

    An amorphous silicon structure is obtained with a computer simulation based on a new molecular-dynamics technique in which the interatomic potential is derived from a parameter-free quantum mechanical method. Our results for the atomic structure, the phonon spectrum, and the electronic properties are in excellent agreement with experiment. In addition we study details of the microscopic dynamics which are not directly accessible to experiment. We find in particular that structural defects are associated with weak bonds. These may give rise to low-frequency vibrational modes.

  3. Dynamic soil-structure interactions on embedded buildings

    International Nuclear Information System (INIS)

    Kobarg, J.; Werkle, H.; Henseleit, O.

    1983-01-01

    The dynamic soil-structure interaction on the horizontal seismic excitation is investigated on two typical embedded auxiliary buildings of a nuclear power plant. The structure and the soil are modelled by various analytical and numerical methods. Under the condition of the linear viscoelastic theory, i.e. soil characteristic constant in time and independent of strain, the interaction influences between a homogenous soil layer and a structure are analysied for the following parameters: 4) mathematical soil modells; 4) mathematical structure modells; 4) shear wave velocities; 3) embedment conditions; 4) earthquake time histories. (orig.) [de

  4. Government and Governance of Regional Triple Helix Interactions

    Science.gov (United States)

    Danson, Mike; Todeva, Emanuela

    2016-01-01

    This conceptual paper contributes to the discussion of the role of regional government and regional Triple Helix constellations driving economic development and growth within regional boundaries. The impact of regionalism and subsidiarity on regional Triple Helix constellations, and the questions of governmentality, governance and institutional…

  5. Regional Dimensions of the Triple Helix Model: Setting the Context

    Science.gov (United States)

    Todeva, Emanuela; Danson, Mike

    2016-01-01

    This paper introduces the rationale for the special issue and its contributions, which bridge the literature on regional development and the Triple Helix model. The concept of the Triple Helix at the sub-national, and specifically regional, level is established and examined, with special regard to regional economic development founded on…

  6. "Special Issue": Regional Dimensions of the Triple Helix Model

    Science.gov (United States)

    Todeva, Emanuela; Danson, Mike

    2016-01-01

    This paper introduces the rationale for the special issue and its contributions, which bridge the literature on regional development and the Triple Helix model. The concept of the Triple Helix at the sub-national, and specifically regional, level is established and examined, with special regard to regional economic development founded on…

  7. Fabrication experiments for large helix heat exchangers

    International Nuclear Information System (INIS)

    Burgsmueller, P.

    1978-01-01

    The helical tube has gained increasing attention as a heat transfer element for various kinds of heat exchangers over the last decade. Regardless of reactor type and heat transport medium, nuclear steam generators of the helix type are now in operation, installlation, fabrication or in the project phase. As a rule, projects are based on the extrapolation of existing technologies. In the particlular case of steam generators for HTGR power stations, however, existing experience is with steam generators of up to about 2 m diameter whereas several projects involve units more than twice as large. For this reason it was felt that a fabrication experiment was necessary in order to verify the feasibility of modern steam generator designs. A test rig was erected in the SULZER steam generator shops at Mantes, France, and skilled personnel and conventional production tools were employed in conducting experiments relating to the coiling, handling and threading of large helices. (Auth.)

  8. FPGA helix tracking algorithm for PANDA

    Energy Technology Data Exchange (ETDEWEB)

    Liang, Yutie; Galuska, Martin; Gessler, Thomas; Kuehn, Wolfgang; Lange, Jens Soeren; Muenchow, David [II. Physikalisches Institut, University of Giessen (Germany); Ye, Hua [Institute of High Energy Physics, CAS (China); Collaboration: PANDA-Collaboration

    2016-07-01

    The PANDA detector is a general-purpose detector for physics with high luminosity cooled antiproton beams, planed to operate at the FAIR facility in Darmstadt, Germany. The central detector includes a silicon Micro Vertex Detector (MVD) and a Straw Tube Tracker (STT). Without any hardware trigger, large amounts of raw data are streaming into the data acquisition system. The data reduction task is performed in the online system by reconstruction algorithms programmed on FPGAs (Field Programmable Gate Arrays) as first level and on a farm of GPUs or PCs as a second level. One important part in the system is the online track reconstruction. In this presentation, an online tracking algorithm for helix tracking reconstruction in the solenoidal field is shown. The VHDL-based algorithm is tested with different types of events, at different event rate. Furthermore, a study of T0 extraction from the tracking algorithm is performed. A concept of simultaneous tracking and T0 determination is presented.

  9. FPGA helix tracking algorithm for PANDA

    Energy Technology Data Exchange (ETDEWEB)

    Liang, Yutie; Galuska, Martin; Gessler, Thomas; Hu, Jifeng; Kuehn, Wolfgang; Lange, Jens Soeren; Muenchow, David; Spruck, Bjoern [II. Physikalisches, Giessen University (Germany); Ye, Hua [II. Physikalisches, Giessen University (Germany); Institute of High Energy Physics, Beijing (China); Collaboration: PANDA-Collaboration

    2014-07-01

    The PANDA detector is a general-purpose detector for physics with high luminosity cooled antiproton beams, planed to operate at the FAIR facility in Darmstadt, Germany. The central detector includes a silicon Micro Vertex Detector (MVD) and a Straw Tube Tracker (STT). Without any hardware trigger, large amounts of raw data are streaming into the data acquisition system. The data reduction task is performed in the online system by reconstruction algorithms programmed in VHDL (Very High Speed Integrated Circuit Hardware Description Language) on FPGAs (Field Programmable Gate Arrays) as first level and on a farm of GPUs or PCs as a second level. One important part in the system is the online track reconstruction. In this presentation, an online tracking finding algorithm for helix track reconstruction in the solenoidal field is shown. A performance study using C++ and the status of the VHDL implementation are presented.

  10. Gas Price Formation, Structure and Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Davoust, R.

    2008-07-01

    Our study, focused on gas prices in importing economies, describes wholesale prices and retail prices, their evolution for the last one or two decades, the economic mechanisms of price formation. While an international market for oil has developed thanks to moderate storage and transportation charges, these costs are much higher in the case of natural gas, which involves that this energy is still traded inside continental markets. There are three regional gas markets around the world: North America (the United States, importing mainly from Canada and Mexico), Europe (importing mainly from Russia, Algeria and Norway) and Asia (Japan, Korea, Taiwan, China and India, importing mainly from Indonesia, Malaysia and Australia). A market for gas has also developed in South America, but it will not be covered by our paper. In Europe and the US, due to large domestic resources and strong grids, natural gas is purchased mostly through pipelines. In Northeast Asia, there is a lack of such infrastructures, so imported gas takes mainly the form of Liquefied Natural Gas (LNG), shipped on maritime tankers. Currently, the LNG market is divided into two zones: the Atlantic Basin (Europe and US) and the Pacific Basin (Asia and the Western Coast of America). For the past few years, the Middle East and Africa have tended to be crucial suppliers for both LNG zones. Gas price formation varies deeply between regional markets, depending on several structural factors (regulation, contracting practises, existence of a spot market, liquidity, share of imports). Empirically, the degree of market opening (which corresponds to the seniority in the liberalization process) seems to be the primary determinant of pricing patterns. North America has the most liberalized and well-performing natural gas industry in the world. Gas pricing is highly competitive and is based on supply/demand balances. Spot and futures markets are developed. The British gas sector is also deregulated and thus follows a

  11. Gas Price Formation, Structure and Dynamics

    International Nuclear Information System (INIS)

    Davoust, R.

    2008-01-01

    Our study, focused on gas prices in importing economies, describes wholesale prices and retail prices, their evolution for the last one or two decades, the economic mechanisms of price formation. While an international market for oil has developed thanks to moderate storage and transportation charges, these costs are much higher in the case of natural gas, which involves that this energy is still traded inside continental markets. There are three regional gas markets around the world: North America (the United States, importing mainly from Canada and Mexico), Europe (importing mainly from Russia, Algeria and Norway) and Asia (Japan, Korea, Taiwan, China and India, importing mainly from Indonesia, Malaysia and Australia). A market for gas has also developed in South America, but it will not be covered by our paper. In Europe and the US, due to large domestic resources and strong grids, natural gas is purchased mostly through pipelines. In Northeast Asia, there is a lack of such infrastructures, so imported gas takes mainly the form of Liquefied Natural Gas (LNG), shipped on maritime tankers. Currently, the LNG market is divided into two zones: the Atlantic Basin (Europe and US) and the Pacific Basin (Asia and the Western Coast of America). For the past few years, the Middle East and Africa have tended to be crucial suppliers for both LNG zones. Gas price formation varies deeply between regional markets, depending on several structural factors (regulation, contracting practises, existence of a spot market, liquidity, share of imports). Empirically, the degree of market opening (which corresponds to the seniority in the liberalization process) seems to be the primary determinant of pricing patterns. North America has the most liberalized and well-performing natural gas industry in the world. Gas pricing is highly competitive and is based on supply/demand balances. Spot and futures markets are developed. The British gas sector is also deregulated and thus follows a

  12. The structure and dynamics of boron nitride nanoscrolls

    International Nuclear Information System (INIS)

    Perim, Eric; Galvao, Douglas S

    2009-01-01

    Carbon nanoscrolls (CNSs) are structures formed by rolling up graphene layers into a scroll-like shape. CNNs have been experimentally produced by different groups. Boron nitride nanoscrolls (BNNSs) are similar structures using boron nitride instead of graphene layers. In this paper we report molecular mechanics and molecular dynamics results for the structural and dynamical aspects of BNNS formation. Similarly to CNS, BNNS formation is dominated by two major energy contributions, the increase in the elastic energy and the energetic gain due to van der Waals interactions of the overlapping surface of the rolled layers. The armchair scrolls are the most stable configuration while zigzag scrolls are metastable structures which can be thermally converted to armchairs. Chiral scrolls are unstable and tend to evolve into zigzag or armchair configurations depending on their initial geometries. The possible experimental routes to produce BNNSs are also addressed.

  13. Stochastic Erosion of Fractal Structure in Nonlinear Dynamical Systems

    Science.gov (United States)

    Agarwal, S.; Wettlaufer, J. S.

    2014-12-01

    We analyze the effects of stochastic noise on the Lorenz-63 model in the chaotic regime to demonstrate a set of general issues arising in the interpretation of data from nonlinear dynamical systems typical in geophysics. The model is forced using both additive and multiplicative, white and colored noise and it is shown that, through a suitable choice of the noise intensity, both additive and multiplicative noise can produce similar dynamics. We use a recently developed measure, histogram distance, to show the similarity between the dynamics produced by additive and multiplicative forcing. This phenomenon, in a nonlinear fractal structure with chaotic dynamics can be explained by understanding how noise affects the Unstable Periodic Orbits (UPOs) of the system. For delta-correlated noise, the UPOs erode the fractal structure. In the presence of memory in the noise forcing, the time scale of the noise starts to interact with the period of some UPO and, depending on the noise intensity, stochastic resonance may be observed. This also explains the mixing in dissipative dynamical systems in presence of white noise; as the fractal structure is smoothed, the decay of correlations is enhanced, and hence the rate of mixing increases with noise intensity.

  14. Structure and dynamics of aqueous solution of uranyl ions

    International Nuclear Information System (INIS)

    Chopra, Manish; Choudhury, Niharendu

    2014-01-01

    The present work describes a molecular dynamics simulation study of structure and dynamics of aqueous solution of uranyl ions in water. Structural properties of the system in terms of radial distribution functions and dynamical characteristics as obtained through velocity autocorrelation function and mean square displacements have been analyzed. The results for radial distribution functions show the oxygen of water to form the first solvation shell at 2.4 Å around the uranium atom, whereas the hydrogen atoms of water are distributed around the uranium atom with the major peak at around 3.0 Å. Analyses of transport behaviors of ions and water through MSD indicates that the diffusion of the uranyl ion is much less as compared to that of the water molecules. It is also observed that the dynamical behavior of water molecules gets modified due to the presence of uranyl ion. The effect of increase in concentration of uranyl ions on the structure and dynamics of water molecules is also studied

  15. Interfacial ionic 'liquids': connecting static and dynamic structures.

    Science.gov (United States)

    Uysal, Ahmet; Zhou, Hua; Feng, Guang; Lee, Sang Soo; Li, Song; Cummings, Peter T; Fulvio, Pasquale F; Dai, Sheng; McDonough, John K; Gogotsi, Yury; Fenter, Paul

    2015-01-28

    It is well known that room temperature ionic liquids (RTILs) often adopt a charge-separated layered structure, i.e. with alternating cation- and anion-rich layers, at electrified interfaces. However, the dynamic response of the layered structure to temporal variations in applied potential is not well understood. We used in situ, real-time x-ray reflectivity to study the potential-dependent electric double layer (EDL) structure of an imidazolium-based RTIL on charged epitaxial graphene during potential cycling as a function of temperature. The results suggest that the graphene-RTIL interfacial structure is bistable in which the EDL structure at any intermediate potential can be described by the combination of two extreme-potential structures whose proportions vary depending on the polarity and magnitude of the applied potential. This picture is supported by the EDL structures obtained by fully atomistic molecular dynamics simulations at various static potentials. The potential-driven transition between the two structures is characterized by an increasing width but with an approximately fixed hysteresis magnitude as a function of temperature. The results are consistent with the coexistence of distinct anion- and cation-adsorbed structures separated by an energy barrier (∼0.15 eV).

  16. 32nd IMAC Conference and Exposition on Structural Dynamics

    CERN Document Server

    Mayes, Randy; Rixen, Daniel; Catbas, Fikret; Atamturktur, H; Moaveni, Babak; Papadimitriou, Costas; Schoenherr, Tyler; Foss, Gary; Niezrecki, Christopher; Allemang, Randall; Kerschen, Gaetan

    2014-01-01

    This critical collection examines a range of topics in modal analysis, from experimental techniques to acoustics to biodynamics,  as presented in early findings and case studies from the Proceedings of the 32nd IMAC, A Conference and Exposition on Structural Dynamics, 2014. The collection includes papers in the following general technical research areas: Experimental Techniques, Processing Modal Data, Rotating Machinery, Acoustics, Adaptive Structures, Biodynamics, Damping

  17. Proton structure functions in the dipole picture of BFKL dynamics

    International Nuclear Information System (INIS)

    Navelet, H.; Peschanski, R.; Wallon, S.; Royon, Ch.

    1996-06-01

    The proton structure functions are derived in the QCD dipole picture. Assuming k T and renormalization-group factorization, deep-inelastic proton scattering is related to deep-inelastic onium scattering. A three parameter fit of the 1994 H1 data in the low-x, moderate Q 2 range has been obtained. The dipole picture of BFKL dynamics is shown to provide a relevant model for quantitatively describing the proton structure functions at HERA. (author)

  18. Capital Structure, Environmental Dynamism, Innovation Strategy, and Strategic Risk Management

    DEFF Research Database (Denmark)

    Juul Andersen, Torben

    2005-01-01

    Previous research found that capital structure affects performance when it is adapted to the level of environmental dynamism and pursuit of an innovation strategy. The current study reproduces some of these relationships in a more recent dataset but also identifies significant nuances across...... industrial environments. Analyses of a large cross sectional sample and various industry sub-samples suggest that other factors have influenced capital structure effects in recent years including flexibilities in multinational organization and effective strategic risk management capabilities....

  19. Helix-length compensation studies reveal the adaptability of the VS ribozyme architecture

    OpenAIRE

    Lacroix-Labonté, Julie; Girard, Nicolas; Lemieux, Sébastien; Legault, Pascale

    2011-01-01

    Compensatory mutations in RNA are generally regarded as those that maintain base pairing, and their identification forms the basis of phylogenetic predictions of RNA secondary structure. However, other types of compensatory mutations can provide higher-order structural and evolutionary information. Here, we present a helix-length compensation study for investigating structure–function relationships in RNA. The approach is demonstrated for stem-loop I and stem-loop V of the Neurospora VS riboz...

  20. Development of structural health monitoring techniques using dynamics testing

    Energy Technology Data Exchange (ETDEWEB)

    James, G.H. III [Sandia National Labs., Albuquerque, NM (United States). Experimental Structural Dynamics Dept.

    1996-03-01

    Today`s society depends upon many structures (such as aircraft, bridges, wind turbines, offshore platforms, buildings, and nuclear weapons) which are nearing the end of their design lifetime. Since these structures cannot be economically replaced, techniques for structural health monitoring must be developed and implemented. Modal and structural dynamics measurements hold promise for the global non-destructive inspection of a variety of structures since surface measurements of a vibrating structure can provide information about the health of the internal members without costly (or impossible) dismantling of the structure. In order to develop structural health monitoring for application to operational structures, developments in four areas have been undertaken within this project: operational evaluation, diagnostic measurements, information condensation, and damage identification. The developments in each of these four aspects of structural health monitoring have been exercised on a broad range of experimental data. This experimental data has been extracted from structures from several application areas which include aging aircraft, wind energy, aging bridges, offshore structures, structural supports, and mechanical parts. As a result of these advances, Sandia National Laboratories is in a position to perform further advanced development, operational implementation, and technical consulting for a broad class of the nation`s aging infrastructure problems.

  1. Functional clustering in hippocampal cultures: relating network structure and dynamics

    International Nuclear Information System (INIS)

    Feldt, S; Dzakpasu, R; Olariu, E; Żochowski, M; Wang, J X; Shtrahman, E

    2010-01-01

    In this work we investigate the relationship between gross anatomic structural network properties, neuronal dynamics and the resultant functional structure in dissociated rat hippocampal cultures. Specifically, we studied cultures as they developed under two conditions: the first supporting glial cell growth (high glial group), and the second one inhibiting it (low glial group). We then compared structural network properties and the spatio-temporal activity patterns of the neurons. Differences in dynamics between the two groups could be linked to the impact of the glial network on the neuronal network as the cultures developed. We also implemented a recently developed algorithm called the functional clustering algorithm (FCA) to obtain the resulting functional network structure. We show that this new algorithm is useful for capturing changes in functional network structure as the networks evolve over time. The FCA detects changes in functional structure that are consistent with expected dynamical differences due to the impact of the glial network. Cultures in the high glial group show an increase in global synchronization as the cultures age, while those in the low glial group remain locally synchronized. We additionally use the FCA to quantify the amount of synchronization present in the cultures and show that the total level of synchronization in the high glial group is stronger than in the low glial group. These results indicate an interdependence between the glial and neuronal networks present in dissociated cultures

  2. Dynamic analysis on market structure of China's coal industry

    International Nuclear Information System (INIS)

    Yang, Qing; Zhang, Lei; Wang, Xin

    2017-01-01

    According to industrial organization theory, market structure is a crucial factor to market performance. Based on the VAR model and the data from 1994 to 2014, we revealed the dynamic response route of the market structure to these factors and the change process of contribution rate of these factors to the market structure. It shows that market structure is inertial adjustment; technology advance and industry policy have continuous effects on improvement of market concentration ratio; market size and production scale have sustained negative effects on market concentration ratio; fixed capital has barrier effect, which is mainly the entry barrier effect at the beginning, and then the exit barrier effect continues to play a leading role. Therefore, the government has no need to introduce special policies to encourage merger or expansion on the capacity as enterprises would do it spontaneously; it is necessary to make market access system stricter, to improve exit compensation mechanism and to promote technological innovation; all these policies need dynamic adjustment based on the stages of economic cycle. - Highlights: • The adjustment mechanism of China's coal market structure is revealed. • Technology and industry policy are significant factors to optimize the market structure. • The government need not introduce special policy to encourage merger. • The market access system should be stricter. • Policies strength should be dynamically adjusted based on the economic cycle.

  3. Structural relaxation dynamics and annealing effects of sodium silicate glass.

    Science.gov (United States)

    Naji, Mohamed; Piazza, Francesco; Guimbretière, Guillaume; Canizarès, Aurélien; Vaills, Yann

    2013-05-09

    Here we report high-precision measurements of structural relaxation dynamics in the glass transition range at the intermediate and short length scale for a strong sodium silicate glass during long annealing times. We evidence for the first time the heterogeneous dynamics at the intermediate range order by probing the acoustic longitudinal frequency in the GHz region by Brillouin light scattering spectroscopy. Or, from in-situ Raman measurements, we show that relaxation is indeed homogeneous at the interatomic length scale. Our results show that the dynamics at the intermediate range order contains two distinct relaxation time scales, a fast and a slow component, differing by about a 10-fold factor below Tg and approaching to one another past the glass transition. The slow relaxation time agrees with the shear relaxation time, proving that Si-O bond breaking constitutes the primary control of structural relaxation at the intermediate range order.

  4. Parameter and Structure Inference for Nonlinear Dynamical Systems

    Science.gov (United States)

    Morris, Robin D.; Smelyanskiy, Vadim N.; Millonas, Mark

    2006-01-01

    A great many systems can be modeled in the non-linear dynamical systems framework, as x = f(x) + xi(t), where f() is the potential function for the system, and xi is the excitation noise. Modeling the potential using a set of basis functions, we derive the posterior for the basis coefficients. A more challenging problem is to determine the set of basis functions that are required to model a particular system. We show that using the Bayesian Information Criteria (BIC) to rank models, and the beam search technique, that we can accurately determine the structure of simple non-linear dynamical system models, and the structure of the coupling between non-linear dynamical systems where the individual systems are known. This last case has important ecological applications.

  5. Strong contributions from vertical triads to helix-partner preferences in parallel coiled coils.

    Science.gov (United States)

    Steinkruger, Jay D; Bartlett, Gail J; Woolfson, Derek N; Gellman, Samuel H

    2012-09-26

    Pairing preferences in heterodimeric coiled coils are determined by complementarities among side chains that pack against one another at the helix-helix interface. However, relationships between dimer stability and interfacial residue identity are not fully understood. In the context of the "knobs-into-holes" (KIH) packing pattern, one can identify two classes of interactions between side chains from different helices: "lateral", in which a line connecting the adjacent side chains is perpendicular to the helix axes, and "vertical", in which the connecting line is parallel to the helix axes. We have previously analyzed vertical interactions in antiparallel coiled coils and found that one type of triad constellation (a'-a-a') exerts a strong effect on pairing preferences, while the other type of triad (d'-d-d') has relatively little impact on pairing tendencies. Here, we ask whether vertical interactions (d'-a-d') influence pairing in parallel coiled-coil dimers. Our results indicate that vertical interactions can exert a substantial impact on pairing specificity, and that the influence of the d'-a-d' triad depends on the lateral a' contact within the local KIH motif. Structure-informed bioinformatic analyses of protein sequences reveal trends consistent with the thermodynamic data derived from our experimental model system in suggesting that heterotriads involving Leu and Ile are preferred over homotriads involving Leu and Ile.

  6. Disruption of the LOV-Jalpha helix interaction activates phototropin kinase activity.

    Science.gov (United States)

    Harper, Shannon M; Christie, John M; Gardner, Kevin H

    2004-12-28

    Light plays a crucial role in activating phototropins, a class of plant photoreceptors that are sensitive to blue and UV-A wavelengths. Previous studies indicated that phototropin uses a bound flavin mononucleotide (FMN) within its light-oxygen-voltage (LOV) domain to generate a protein-flavin covalent bond under illumination. In the C-terminal LOV2 domain of Avena sativa phototropin 1, formation of this bond triggers a conformational change that results in unfolding of a helix external to this domain called Jalpha [Harper, S. M., et al. (2003) Science 301, 1541-1545]. Though the structural effects of illumination were characterized, it was unknown how these changes are coupled to kinase activation. To examine this, we made a series of point mutations along the Jalpha helix to disrupt its interaction with the LOV domain in a manner analogous to light activation. Using NMR spectroscopy and limited proteolysis, we demonstrate that several of these mutations displace the Jalpha helix from the LOV domain independently of illumination. When placed into the full-length phototropin protein, these point mutations display constitutive kinase activation, without illumination of the sample. These results indicate that unfolding of the Jalpha helix is the critical event in regulation of kinase signaling for the phototropin proteins.

  7. Probing α-3(10) transitions in a voltage-sensing S4 helix.

    Science.gov (United States)

    Kubota, Tomoya; Lacroix, Jérôme J; Bezanilla, Francisco; Correa, Ana M

    2014-09-02

    The S4 helix of voltage sensor domains (VSDs) transfers its gating charges across the membrane electrical field in response to changes of the membrane potential. Recent studies suggest that this process may occur via the helical conversion of the entire S4 between α and 310 conformations. Here, using LRET and FRET, we tested this hypothesis by measuring dynamic changes in the transmembrane length of S4 from engineered VSDs expressed in Xenopus oocytes. Our results suggest that the native S4 from the Ciona intestinalis voltage-sensitive phosphatase (Ci-VSP) does not exhibit extended and long-lived 310 conformations and remains mostly α-helical. Although the S4 of NavAb displays a fully extended 310 conformation in x-ray structures, its transplantation in the Ci-VSP VSD scaffold yielded similar results as the native Ci-VSP S4. Taken together, our study does not support the presence of long-lived extended α-to-310 helical conversions of the S4 in Ci-VSP associated with voltage activation. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  8. Tah1 helix-swap dimerization prevents mixed Hsp90 co-chaperone complexes

    International Nuclear Information System (INIS)

    Morgan, Rhodri M. L.; Pal, Mohinder; Roe, S. Mark; Pearl, Laurence H.; Prodromou, Chrisostomos

    2015-01-01

    A helix swap involving the fifth helix between two adjacently bound Tah1 molecules restores the normal binding environment of the conserved MEEVD peptide of Hsp90. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes with Hsp90 and Tah1. Specific co-chaperone adaptors facilitate the recruitment of client proteins to the Hsp90 system. Tah1 binds the C-terminal conserved MEEVD motif of Hsp90, thus linking an eclectic set of client proteins to the R2TP complex for their assembly and regulation by Hsp90. Rather than the normal complement of seven α-helices seen in other tetratricopeptide repeat (TPR) domains, Tah1 unusually consists of the first five only. Consequently, the methionine of the MEEVD peptide remains exposed to solvent when bound by Tah1. In solution Tah1 appears to be predominantly monomeric, and recent structures have failed to explain how Tah1 appears to prevent the formation of mixed TPR domain-containing complexes such as Cpr6–(Hsp90) 2 –Tah1. To understand this further, the crystal structure of Tah1 in complex with the MEEVD peptide of Hsp90 was determined, which shows a helix swap involving the fifth α-helix between two adjacently bound Tah1 molecules. Dimerization of Tah1 restores the normal binding environment of the bound Hsp90 methionine residue by reconstituting a TPR binding site similar to that in seven-helix-containing TPR domain proteins. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes

  9. Tah1 helix-swap dimerization prevents mixed Hsp90 co-chaperone complexes

    Energy Technology Data Exchange (ETDEWEB)

    Morgan, Rhodri M. L.; Pal, Mohinder; Roe, S. Mark; Pearl, Laurence H., E-mail: laurence.pearl@sussex.ac.uk; Prodromou, Chrisostomos, E-mail: laurence.pearl@sussex.ac.uk [University of Sussex, Falmer, Brighton BN1 9RQ (United Kingdom)

    2015-05-01

    A helix swap involving the fifth helix between two adjacently bound Tah1 molecules restores the normal binding environment of the conserved MEEVD peptide of Hsp90. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes with Hsp90 and Tah1. Specific co-chaperone adaptors facilitate the recruitment of client proteins to the Hsp90 system. Tah1 binds the C-terminal conserved MEEVD motif of Hsp90, thus linking an eclectic set of client proteins to the R2TP complex for their assembly and regulation by Hsp90. Rather than the normal complement of seven α-helices seen in other tetratricopeptide repeat (TPR) domains, Tah1 unusually consists of the first five only. Consequently, the methionine of the MEEVD peptide remains exposed to solvent when bound by Tah1. In solution Tah1 appears to be predominantly monomeric, and recent structures have failed to explain how Tah1 appears to prevent the formation of mixed TPR domain-containing complexes such as Cpr6–(Hsp90){sub 2}–Tah1. To understand this further, the crystal structure of Tah1 in complex with the MEEVD peptide of Hsp90 was determined, which shows a helix swap involving the fifth α-helix between two adjacently bound Tah1 molecules. Dimerization of Tah1 restores the normal binding environment of the bound Hsp90 methionine residue by reconstituting a TPR binding site similar to that in seven-helix-containing TPR domain proteins. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes.

  10. The Fine Structure of Equity-Index Option Dynamics

    DEFF Research Database (Denmark)

    Andersen, Torben G.; Bondarenko, Oleg; Todorov, Viktor

    We analyze the high-frequency dynamics of S&P 500 equity-index option prices by constructing an assortment of implied volatility measures. This allows us to infer the underlying fine structure behind the innovations in the latent state variables driving the movements of the volatility surface...

  11. Zooplankton community structure and dynamics during the transition ...

    African Journals Online (AJOL)

    This study investigates the zooplankton community structure and dynamics of Kufena Rock Pool during the transition from dry season (March to April) to rainy season (May to June) in Zaria, Nigeria. Physicochemical parameters such as temperature, hydrogen ion concentration, electrical conductivity and total dissolved ...

  12. Progression of 3D Protein Structure and Dynamics Measurements

    Science.gov (United States)

    Sato-Tomita, Ayana; Sekiguchi, Hiroshi; Sasaki, Yuji C.

    2018-06-01

    New measurement methodologies have begun to be proposed with the recent progress in the life sciences. Here, we introduce two new methodologies, X-ray fluorescence holography for protein structural analysis and diffracted X-ray tracking (DXT), to observe the dynamic behaviors of individual single molecules.

  13. Structure of hydrogenated amorphous silicon from ab initio molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Buda, F. (Department of Physics, The Ohio State University, 174 West 18th Avenue, Columbus, Ohio (USA)); Chiarotti, G.L. (International School for Advanced Studies, Strada Costiera 11, I-34014 Trieste (Italy) Laboratorio Tecnologie Avanzate Superfici e Catalisi del Consorzio Interuniversitario Nazionale di Fisica della Materia, Padriciano 99, I-34012 Trieste (Italy)); Car, R. (International School for Advanced Studies, Strada Costiera 11, I-34014 Trieste (Italy) Institut Romard de Recherche Numerique en Physique des Materiaux, CH-1015 Lausanne, Switzerland Department of Condensed Matter Physics, University of Geneva, CH-1211 Geneva (Switzerland)); Parrinello, M. (IBM Research Division, Zurich Research Laboratory, CH-8803 Rueschlikon (Switzerland))

    1991-09-15

    We have generated a model of hydrogenated amorphous silicon by first-principles molecular dynamics. Our results are in good agreement with the available experimental data and provide new insight into the microscopic structure of this material. The calculation lends support to models in which monohydride complexes are prevalent, and indicates a strong tendency of hydrogen to form small clusters.

  14. Gauge-invariant cosmic structures---A dynamic systems approach

    International Nuclear Information System (INIS)

    Woszczyna, A.

    1992-01-01

    Gravitational instability is expressed in terms of the dynamic systems theory. The gauge-invariant Ellis-Bruni equation and Bardeen's equation are discussed in detail. It is shown that in an open universe filled with matter of constant sound velocity the Jeans criterion does not adequately define the length scale of the gravitational structure

  15. A new dynamic null model for phylogenetic community structure

    NARCIS (Netherlands)

    Pigot, Alex L; Etienne, Rampal S

    Phylogenies are increasingly applied to identify the mechanisms structuring ecological communities but progress has been hindered by a reliance on statistical null models that ignore the historical process of community assembly. Here, we address this, and develop a dynamic null model of assembly by

  16. Isomorph invariance of the structure and dynamics of classical crystals

    DEFF Research Database (Denmark)

    Albrechtsen, Dan; Olsen, Andreas Elmerdahl; Pedersen, Ulf Rørbæk

    2014-01-01

    This paper shows by computer simulations that some crystalline systems have curves in their thermodynamic phase diagrams, so-called isomorphs, along which structure and dynamics in reduced units are invariant to a good approximation. The crystals are studied in a classical-mechanical framework...

  17. Nuclear visions enhanced: chromatin structure, organization and dynamics

    OpenAIRE

    Meshorer, Eran; Herrmann, Harald; Raška, Ivan

    2011-01-01

    The EMBO Workshop on ‘Chromatin Structure, Organization and Dynamics' took place in April 2011 in Prague, Czech Republic. Participants presented data on the generation of models of the genome, working to correlate changes in the organization of chromatin with the functional state of the genome.

  18. From dynamics to structure and function of model biomolecular systems

    NARCIS (Netherlands)

    Fontaine-Vive-Curtaz, F.

    2007-01-01

    The purpose of this thesis was to extend recent works on structure and dynamics of hydrogen bonded crystals to model biomolecular systems and biological processes. The tools that we have used are neutron scattering (NS) and density functional theory (DFT) and force field (FF) based simulation

  19. Fluorescence relaxation spectroscopy : light on dynamical structures of flavoproteins

    NARCIS (Netherlands)

    Burten - Bastiaens, P.I.H.

    1992-01-01

    Refinements in technique and data analysis have opened new avenues for a detailed interpretation of protein fluorescence. What is more, by combining new insights in protein structure and dynamics with improved knowledge of photophysics of biological chromophores, the coupling between

  20. Dynamics and control of twisting bi-stable structures

    Science.gov (United States)

    Arrieta, Andres F.; van Gemmeren, Valentin; Anderson, Aaron J.; Weaver, Paul M.

    2018-02-01

    Compliance-based morphing structures have the potential to offer large shape adaptation, high stiffness and low weight, while reducing complexity, friction, and scalability problems of mechanism based systems. A promising class of structure that enables these characteristics are multi-stable structures given their ability to exhibit large deflections and rotations without the expensive need for continuous actuation, with the latter only required intermittently. Furthermore, multi-stable structures exhibit inherently fast response due to the snap-through instability governing changes between stable states, enabling rapid configuration switching between the discrete number of programmed shapes of the structure. In this paper, the design and utilisation of the inherent nonlinear dynamics of bi-stable twisting I-beam structures for actuation with low strain piezoelectric materials is presented. The I-beam structure consists of three compliant components assembled into a monolithic single element, free of moving parts, and showing large deflections between two stable states. Finite element analysis is utilised to uncover the distribution of strain across the width of the flange, guiding the choice of positioning for piezoelectric actuators. In addition, the actuation authority is maximised by calculating the generalised coupling coefficient for different positions of the piezoelectric actuators. The results obtained are employed to tailor and test I-beam designs exhibiting desired large deflection between stable states, while still enabling the activation of snap-through with the low strain piezoelectric actuators. To this end, the dynamic response of the I-beams to piezoelectric excitation is investigated, revealing that resonant excitations are insufficient to dynamically trigger snap-through. A novel bang-bang control strategy, which exploits the nonlinear dynamics of the structure successfully triggers both single and constant snap-through between the stable states

  1. Dynamical Heterogeneity in Granular Fluids and Structural Glasses

    Science.gov (United States)

    Avila, Karina E.

    Our current understanding of the dynamics of supercooled liquids and other similar slowly evolving (glassy) systems is rather limited. One aspect that is particularly poorly understood is the origin and behavior of the strong non trivial fluctuations that appear in the relaxation process toward equilibrium. Glassy systems and granular systems both present regions of particles moving cooperatively and at different rates from other regions. This phenomenon is known as spatially heterogeneous dynamics. A detailed explanation of this phenomenon may lead to a better understanding of the slow relaxation process, and perhaps it could even help to explain the presence of the glass transition. This dissertation concentrates on studying dynamical heterogeneity by analyzing simulation data for models of granular materials and structural glasses. For dissipative granular fluids, the growing behavior of dynamical heterogeneities is studied for different densities and different degrees of inelasticity in the particle collisions. The correlated regions are found to grow rapidly as the system approaches dynamical arrest. Their geometry is conserved even when probing at different cutoff length in the correlation function or when the energy dissipation in the system is increased. For structural glasses, I test a theoretical framework that models dynamical heterogeneity as originated in the presence of Goldstone modes, which emerge from a broken continuous time reparametrization symmetry. This analysis is based on quantifying the size and the spatial correlations of fluctuations in the time variable and of other kinds of fluctuations. The results obtained here agree with the predictions of the hypothesis. In particular, the fluctuations associated to the time reparametrization invariance become stronger for low temperatures, long timescales, and large coarse graining lengths. Overall, this research points to dynamical heterogeneity to be described for granular systems similarly than

  2. Uncertainty Quantification in Experimental Structural Dynamics Identification of Composite Material Structures

    DEFF Research Database (Denmark)

    Luczak, Marcin; Peeters, Bart; Kahsin, Maciej

    2014-01-01

    for uncertainty evaluation in experimentally estimated models. Investigated structures are plates, fuselage panels and helicopter main rotor blades as they represent different complexity levels ranging from coupon, through sub-component up to fully assembled structures made of composite materials. To evaluate......Aerospace and wind energy structures are extensively using components made of composite materials. Since these structures are subjected to dynamic environments with time-varying loading conditions, it is important to model their dynamic behavior and validate these models by means of vibration...

  3. Neighborhood structure effects on the Dynamic response of soil-structure interaction by harmonic analysis

    Directory of Open Access Journals (Sweden)

    Pan Dan-guang

    2015-01-01

    Full Text Available For realizing the variation of structural dynamic characteristics due to neighbor structure in buildings group, the surface structure is idealized as an equivalent single degree of freedom system with rigid base whose site consists of a single homogeneous layer. Based on the model, a equivalent method on the equivalent seismic excitation is proposed. Then, the differences of seismic response and equivalent seismic input between soil - structure interaction (SSI system and structure -soil-structure interaction (SSSI system are investigated by harmonic analysis. The numerical results show that dynamic responses would be underestimated in SSSI system when the forcing frequencies are close to the Natural frequency if the effects of neighborhood structure were ignored. Neighborhood structure would make the translational displacement increase and rocking vibration decrease. When establishing an effective seismic input, it is necessary to consider the impact of inertia interaction.

  4. Interactions between an alpha-helix and a beta-sheet. Energetics of alpha/beta packing in proteins.

    Science.gov (United States)

    Chou, K C; Némethy, G; Rumsey, S; Tuttle, R W; Scheraga, H A

    1985-12-05

    Conformational energy computations have been carried out to determine the favorable ways of packing a right-handed alpha-helix on a right-twisted antiparallel or parallel beta-sheet. Co-ordinate transformations have been developed to relate the position and orientation of the alpha-helix to the beta-sheet. The packing was investigated for a CH3CO-(L-Ala)16-NHCH3 alpha-helix interacting with five-stranded beta-sheets composed of CH3CO-(L-Val)6-NHCH3 chains. All internal and external variables for both the alpha-helix and the beta-sheet were allowed to change during energy minimization. Four distinct classes of low-energy packing arrangements were found for the alpha-helix interacting with both the parallel and the anti-parallel beta-sheet. The classes differ in the orientation of the axis of the alpha-helix relative to the direction of the strands of the right-twisted beta-sheet. In the class with the most favorable arrangement, the alpha-helix is oriented along the strands of the beta-sheet, as a result of attractive non-bonded side-chain-side-chain interactions along the entire length of the alpha-helix. A class with nearly perpendicular orientation of the helix axis to the strands is also of low energy, because it allows similarly extensive attractive interactions. In the other two classes, the helix is oriented diagonally relative to the strands of the beta-sheet. In one of them, it interacts with the convex surface near the middle of the saddle-shaped twisted beta-sheet. In the other, it is oriented along the concave diagonal of the beta-sheet and, therefore, it interacts only with the corner regions of the sheet, so that this packing is energetically less favorable. The packing arrangements involving an antiparallel and a parallel beta-sheet are generally similar, although the antiparallel beta-sheet has been found to be more flexible. The major features of 163 observed alpha/beta packing arrangements in 37 proteins are accounted for in terms of the computed

  5. Lipid-mediated interactions tune the association of glycophorin A helix and its disruptive mutants in membranes

    NARCIS (Netherlands)

    Sengupta, Durba; Marrink, Siewert J.

    2010-01-01

    The specific and non-specific driving forces of helix association within membranes are still poorly understood. Here, we use coarse-grain molecular dynamics simulations to study the association behavior of glycophorin A and two disruptive mutants, T87F and a triple mutant of the GxxxG motif

  6. Metastable structures and size effects in small group dynamics.

    Science.gov (United States)

    Lauro Grotto, Rosapia; Guazzini, Andrea; Bagnoli, Franco

    2014-01-01

    In his seminal works on group dynamics Bion defined a specific therapeutic setting allowing psychoanalytic observations on group phenomena. In describing the setting he proposed that the group was where his voice arrived. This physical limit was later made operative by assuming that the natural dimension of a therapeutic group is around 12 people. Bion introduced a theory of the group aspects of the mind in which proto-mental individual states spontaneously evolve into shared psychological states that are characterized by a series of features: (1) they emerge as a consequence of the natural tendency of (both conscious and unconscious) emotions to combine into structured group patterns; (2) they have a certain degree of stability in time; (3) they tend to alternate so that the dissolution of one is rapidly followed by the emergence of another; (4) they can be described in qualitative terms according to the nature of the emotional mix that dominates the state, in structural terms by a kind of typical "leadership" pattern, and in "cognitive" terms by a set of implicit expectations that are helpful in explaining the group behavior (i.e., the group behaves "as if" it was assuming that). Here we adopt a formal approach derived from Socio-physics in order to explore some of the structural and dynamic properties of this small group dynamics. We will described data from an analytic DS model simulating small group interactions of agents endowed with a very simplified emotional and cognitive dynamic in order to assess the following main points: (1) are metastable collective states allowed to emerge in the model and if so, under which conditions in the parameter space? (2) can these states be differentiated in structural terms? (3) to what extent are the emergent dynamic features of the systems dependent of the system size? We will finally discuss possible future applications of the quantitative descriptions of the interaction structure in the small group clinical setting.

  7. Metastable structures and size effects in small group dynamics

    Directory of Open Access Journals (Sweden)

    Rosapia eLauro Grotto

    2014-07-01

    Full Text Available In his seminal works on group dynamics Bion defined a specific therapeutic setting allowing psychoanalytic observations on group phenomena. In describing the setting he proposed that the group was where his voice arrived. This physical limit was later made operative by assuming that the natural dimension of a therapeutic group is around 12 people. Bion introduced a theory of the group aspects of the mind in which proto-mental individual states spontaneously evolve into shared psychological states that are characterized by a series of features: 1 they emerge as a consequence of the natural tendency of (both conscious and unconscious emotions to combine into structured group patterns; 2 they have a certain degree of stability in time; 3 they tend to alternate so that the dissolution of one is rapidly followed by the emergence of another; 4 they can be described in qualitative terms according to the nature of the emotional mix that dominates the state, in structural terms by a kind of typical 'leadership’ pattern, and in 'cognitive’ terms by a set of implicit expectations that are helpful in explaining the group behavior (i.e. the group behaves 'as if’ it was assuming that…. Here we adopt a formal approach derived from Socio-physics in order to explore some of the structural and dynamic properties of this small group dynamics. We will described data from an analytic DS model simulating small group interactions of agents endowed with a very simplified emotional and cognitive dynamic in order to assess the following main points: 1 are metastable collective states allowed to emerge in the model and if so, under which conditions in the parameter space? 3 can these states be differentiated in structural terms? 3 to what extent are the emergent dynamic features of the systems dependent of the system size? We will finally discuss possible future applications of the quantitative descriptions of the interaction structure in the small group clinical

  8. The Effect of a Helix-Coil Transition on the Extension Elasticity

    Science.gov (United States)

    Buhot, Arnaud; Halperin, Avi

    2000-03-01

    The secondary structure of a polymer affects its deformation behavior in accordance with the Le Chatelier principle. An important example of such secondary structure is the alpha helix encountered in polypeptides. Similar structure was recently proposed for PEO in aqueous media. Our discussion concerns the coupling of the cooperative helix-coil transition and the extension elasticity. In particular, we analyze the extension of a long single chain by use of optical tweezers or AFM. We consider chains that exist in the coil-state when unperturbed. The transition nevertheless occurs because the extension favors the low entropy helical state. As a result, the corresponding force law exhibits a plateau. The analysis of this situation involves two ingredients: (I) the stretching free energy penalty for a rod-coil mutiblock copolymer (II) the entropy associated with the possible placements of the rod and coil blocks.

  9. Structure and dynamics of thylakoids in land plants

    DEFF Research Database (Denmark)

    Pribil, Mathias; Labs, Mathias; Leister, Dario

    2014-01-01

    Thylakoids of land plants have a bipartite structure, consisting of cylindrical grana stacks, made of membranous discs piled one on top of the other, and stroma lamellae which are helically wound around the cylinders. Protein complexes predominantly located in the stroma lamellae and grana end....... Depending on light conditions, thylakoid membranes undergo dynamic structural changes that involve alterations in granum diameter and height, vertical unstacking of grana, and swelling of the thylakoid lumen. This plasticity is realized predominantly by reorganization of the supramolecular structure...

  10. Dynamic vortex dust structures in a nuclear-track plasma

    International Nuclear Information System (INIS)

    Rykov, V A; Khudyakov, A V; Filinov, V S; Vladimirov, V I; Deputatova, L V; Krutov, D V; Fortov, V E

    2003-01-01

    Results are presented from Monte Carlo calculations of the electric charge on dust grains in a plasma produced during the slowing down of radioactive decay products of californium nuclei in neon. The dust grain charging is explained as being due to the drift of electrons and ions in an external electric field. It is shown that the charges of the grains depend on their coordinates and strongly fluctuate with time. The time-averaged grain charges agree with the experimental data obtained on ordered liquid-like dust structures in a nuclear-track plasma. The time-averaged dust grain charges are used to carry out computer modelling of the formation of dynamic vortex structures observed in experiments. Evidence is obtained for the fact that the electrostatic forces experienced by the dust grains are potential in character. The paper is supplemented by a video clip showing the typical dynamics of the simulated vortex dust structure

  11. Applications of Asymptotic Sampling on High Dimensional Structural Dynamic Problems

    DEFF Research Database (Denmark)

    Sichani, Mahdi Teimouri; Nielsen, Søren R.K.; Bucher, Christian

    2011-01-01

    The paper represents application of the asymptotic sampling on various structural models subjected to random excitations. A detailed study on the effect of different distributions of the so-called support points is performed. This study shows that the distribution of the support points has consid...... dimensional reliability problems in structural dynamics.......The paper represents application of the asymptotic sampling on various structural models subjected to random excitations. A detailed study on the effect of different distributions of the so-called support points is performed. This study shows that the distribution of the support points has...... is minimized. Next, the method is applied on different cases of linear and nonlinear systems with a large number of random variables representing the dynamic excitation. The results show that asymptotic sampling is capable of providing good approximations of low failure probability events for very high...

  12. Modeling structural change in spatial system dynamics: A Daisyworld example.

    Science.gov (United States)

    Neuwirth, C; Peck, A; Simonović, S P

    2015-03-01

    System dynamics (SD) is an effective approach for helping reveal the temporal behavior of complex systems. Although there have been recent developments in expanding SD to include systems' spatial dependencies, most applications have been restricted to the simulation of diffusion processes; this is especially true for models on structural change (e.g. LULC modeling). To address this shortcoming, a Python program is proposed to tightly couple SD software to a Geographic Information System (GIS). The approach provides the required capacities for handling bidirectional and synchronized interactions of operations between SD and GIS. In order to illustrate the concept and the techniques proposed for simulating structural changes, a fictitious environment called Daisyworld has been recreated in a spatial system dynamics (SSD) environment. The comparison of spatial and non-spatial simulations emphasizes the importance of considering spatio-temporal feedbacks. Finally, practical applications of structural change models in agriculture and disaster management are proposed.

  13. Dynamic Analysis of Partially Embedded Structures Considering Soil-Structure Interaction in Time Domain

    Directory of Open Access Journals (Sweden)

    Sanaz Mahmoudpour

    2011-01-01

    Full Text Available Analysis and design of structures subjected to arbitrary dynamic loadings especially earthquakes have been studied during past decades. In practice, the effects of soil-structure interaction on the dynamic response of structures are usually neglected. In this study, the effect of soil-structure interaction on the dynamic response of structures has been examined. The substructure method using dynamic stiffness of soil is used to analyze soil-structure system. A coupled model based on finite element method and scaled boundary finite element method is applied. Finite element method is used to analyze the structure, and scaled boundary finite element method is applied in the analysis of unbounded soil region. Due to analytical solution in the radial direction, the radiation condition is satisfied exactly. The material behavior of soil and structure is assumed to be linear. The soil region is considered as a homogeneous half-space. The analysis is performed in time domain. A computer program is prepared to analyze the soil-structure system. Comparing the results with those in literature shows the exactness and competency of the proposed method.

  14. Uncertainty propagation through dynamic models of assemblies of mechanical structures

    International Nuclear Information System (INIS)

    Daouk, Sami

    2016-01-01

    When studying the behaviour of mechanical systems, mathematical models and structural parameters are usually considered deterministic. Return on experience shows however that these elements are uncertain in most cases, due to natural variability or lack of knowledge. Therefore, quantifying the quality and reliability of the numerical model of an industrial assembly remains a major question in low-frequency dynamics. The purpose of this thesis is to improve the vibratory design of bolted assemblies through setting up a dynamic connector model that takes account of different types and sources of uncertainty on stiffness parameters, in a simple, efficient and exploitable in industrial context. This work has been carried out in the framework of the SICODYN project, led by EDF R and D, that aims to characterise and quantify, numerically and experimentally, the uncertainties in the dynamic behaviour of bolted industrial assemblies. Comparative studies of several numerical methods of uncertainty propagation demonstrate the advantage of using the Lack-Of-Knowledge theory. An experimental characterisation of uncertainties in bolted structures is performed on a dynamic test rig and on an industrial assembly. The propagation of many small and large uncertainties through different dynamic models of mechanical assemblies leads to the assessment of the efficiency of the Lack-Of-Knowledge theory and its applicability in an industrial environment. (author)

  15. Dynamic changes in the secondary structure of ECE-1 and XCE account for their different substrate specificities

    Directory of Open Access Journals (Sweden)

    Ul-Haq Zaheer

    2012-11-01

    Full Text Available Abstract Background X-converting enzyme (XCE involved in nervous control of respiration, is a member of the M13 family of zinc peptidases, for which no natural substrate has been identified yet. In contrast, it’s well characterized homologue endothelin-converting enzyme-1 (ECE-1 showed broad substrate specificity and acts as endopeptidase as well as dipeptidase. To explore the structural differences between XCE and ECE-1, homology model of XCE was built using the complex structure of ECE-1 with phosphoramidon (pdb-id: 3DWB as template. Phosphoramidon was docked into the binding site of XCE whereas phosphate oxygen of the inhibitor was used as water molecule to design the apo forms of both enzymes. Molecular dynamics simulation of both enzymes was performed to analyze the dynamic nature of their active site residues in the absence and presence of the inhibitor. Results Homology model of XCE explained the role of non-conserved residues of its S2’ subsite. Molecular dynamics (MD simulations identified the flexible transitions of F149/I150, N566/N571, W714/W719, and R145/R723 residues of ECE-1/XCE for the strong binding of the inhibitor. Secondary structure calculations using DSSP method reveals the folding of R145/R723 residue of ECE-1/XCE into β-sheet structure while unfolding of the S2’ subsite residues in aECE-1 and sustained compact folding of that of aXCE. The results evaluated are in good agreement with available experimental data, thus providing detailed molecular models which can explain the structural and specificities differences between both zinc peptidases. Conclusions Secondary structure changes of both enzymes during the simulation time revealed the importance of β-sheet structure of R145/R723 for its binding with the terminal carboxylate group of the inhibitor. Unfolding of the α-helix comprising the S2’ subsite residues in aECE-1 correlate well with its endopeptidase activity while their compact folding in aXCE may

  16. Solution structure and dynamics of melanoma inhibitory activity protein

    International Nuclear Information System (INIS)

    Lougheed, Julie C.; Domaille, Peter J.; Handel, Tracy M.

    2002-01-01

    Melanoma inhibitory activity (MIA) is a small secreted protein that is implicated in cartilage cell maintenance and melanoma metastasis. It is representative of a recently discovered family of proteins that contain a Src Homologous 3 (SH3) subdomain. While SH3 domains are normally found in intracellular proteins and mediate protein-protein interactions via recognition of polyproline helices, MIA is single-domain extracellular protein, and it probably binds to a different class of ligands.Here we report the assignments, solution structure, and dynamics of human MIA determined by heteronuclear NMR methods. The structures were calculated in a semi-automated manner without manual assignment of NOE crosspeaks, and have a backbone rmsd of 0.38 A over the ordered regions of the protein. The structure consists of an SH3-like subdomain with N- and C-terminal extensions of approximately 20 amino acids each that together form a novel fold. The rmsd between the solution structure and our recently reported crystal structure is 0.86 A over the ordered regions of the backbone, and the main differences are localized to the most dynamic regions of the protein. The similarity between the NMR and crystal structures supports the use of automated NOE assignments and ambiguous restraints to accelerate the calculation of NMR structures

  17. Structure, entanglements and dynamics of polymer nanocomposites containing spherical nanoparticles

    International Nuclear Information System (INIS)

    Karatrantos, A; Clarke, N; Composto, R J; Winey, K I

    2014-01-01

    We investigate the effect of nanoparticles on polymer structure, nanoparticle dynamics and topological constraints (entanglements) in polymer melts for nanoparticle loading above percolation threshold as high as 40.9% using stochastic molecular dynamics (MD) simulations. An increase in the number of entanglements (decrease of N e with 40.9% volume fraction of nanoparticles dispersed in the polymer matrix) in the nanocomposites is observed as evidenced by larger contour lengths of the primitive paths. Attraction between polymers and nanoparticles affects the entanglements in the nanocomposites and alters the primitive path. The diffusivity of small sized nanoparticles deviates significantly from the Stokes- Einstein relation

  18. Coalescence of silver unidimensional structures by molecular dynamics simulation

    International Nuclear Information System (INIS)

    Perez A, M.; Gutierrez W, C.E.; Mondragon, G.; Arenas, J.

    2007-01-01

    The study of nanoparticles coalescence and silver nano rods phenomena by means of molecular dynamics simulation under the thermodynamic laws is reported. In this work we focus ourselves to see the conditions under which the one can be given one dimension growth of silver nano rods for the coalescence phenomenon among two nano rods or one nano rod and one particle; what allows us to study those structural, dynamic and morphological properties of the silver nano rods to different thermodynamic conditions. The simulations are carried out using the Sutton-Chen potentials of interaction of many bodies that allow to obtain appropriate results with the real physical systems. (Author)

  19. An age-structured population balance model for microbial dynamics

    Directory of Open Access Journals (Sweden)

    Duarte M.V.E.

    2003-01-01

    Full Text Available This work presents an age-structured population balance model (ASPBM for a bioprocess in a continuous stirred-tank fermentor. It relates the macroscopic properties and dynamic behavior of biomass to the operational parameters and microscopic properties of cells. Population dynamics is governed by two time- and age-dependent density functions for living and dead cells, accounting for the influence of substrate and dissolved oxygen concentrations on cell division, aging and death processes. The ASPBM described biomass and substrate oscillations in aerobic continuous cultures as experimentally observed. It is noteworthy that a small data set consisting of nonsegregated measurements was sufficient to adjust a complex segregated mathematical model.

  20. Estimating spatio-temporal dynamics of size-structured populations

    DEFF Research Database (Denmark)

    Kristensen, Kasper; Thygesen, Uffe Høgsbro; Andersen, Ken Haste

    2014-01-01

    with simple stock dynamics, to estimate simultaneously how size distributions and spatial distributions develop in time. We demonstrate the method for a cod population sampled by trawl surveys. Particular attention is paid to correlation between size classes within each trawl haul due to clustering...... of individuals with similar size. The model estimates growth, mortality and reproduction, after which any aspect of size-structure, spatio-temporal population dynamics, as well as the sampling process can be probed. This is illustrated by two applications: 1) tracking the spatial movements of a single cohort...

  1. Effect of Hedera helix on lung histopathology in chronic asthma.

    Science.gov (United States)

    Hocaoglu, Arzu Babayigit; Karaman, Ozkan; Erge, Duygu Olmez; Erbil, Guven; Yilmaz, Osman; Kivcak, Bijen; Bagriyanik, H Alper; Uzuner, Nevin

    2012-12-01

    Hedera helix is widely used to treat bronchial asthma for many years. However, effects of this herb on lung histopathology is still far from clear. We aimed to determine the effect of oral administration of Hedera helix on lung histopathology in a murine model of chronic asthma.BALB/c mice were divided into four groups; I (Placebo), II (Hedera helix), III (Dexamethasone) and IV (Control). All mice except controls were sensitized and challenged with ovalbumin. Then, mice in group I received saline, group II 100 mg/kg Hedera helix and group III 1 mg/kg dexamethasone via orogastic gavage once daily for one week. Airway histopathology was evaluated by using light and electron microscopy in all groups.Goblet cell numbers and thicknesses of basement membrane were found significantly lower in group II, but there was no statistically significant difference in terms of number of mast cells, thicknesses of epithelium and subepithelial smooth muscle layers between group I and II. When Hedera helix and dexamethasone groups were compared with each other, thickness of epithelium, subepithelial muscle layers, number of mast cells and goblet cells of group III were significantly ameliorated when compared with the group II. Although Hedera helix administration reduced only goblet cell counts and the thicknesses of basement membrane in the asthmatic airways, dexamethasone ameliorated all histopathologic parameters except thickness of basement membrane better than Hedera helix.

  2. Probing the Structure and Dynamics of Proteins by Combining Molecular Dynamics Simulations and Experimental NMR Data.

    Science.gov (United States)

    Allison, Jane R; Hertig, Samuel; Missimer, John H; Smith, Lorna J; Steinmetz, Michel O; Dolenc, Jožica

    2012-10-09

    NMR experiments provide detailed structural information about biological macromolecules in solution. However, the amount of information obtained is usually much less than the number of degrees of freedom of the macromolecule. Moreover, the relationships between experimental observables and structural information, such as interatomic distances or dihedral angle values, may be multiple-valued and may rely on empirical parameters and approximations. The extraction of structural information from experimental data is further complicated by the time- and ensemble-averaged nature of NMR observables. Combining NMR data with molecular dynamics simulations can elucidate and alleviate some of these problems, as well as allow inconsistencies in the NMR data to be identified. Here, we use a number of examples from our work to highlight the power of molecular dynamics simulations in providing a structural interpretation of solution NMR data.

  3. The structure and dynamics of patterns of Benard convection cells

    International Nuclear Information System (INIS)

    Rivier, N.; Imperial Coll. of Science and Technology, London; Lausanne Univ.

    1990-08-01

    Benard-Marangoni convection, in containers with large aspect ratio, exhibits space-filling cellular structures, highly deformable, but crystallized. They contain dislocations and grain boundaries generated and moved by elementary topological transformations, and are subjected to a weak shear stress due to the earth's rotation. The cellular structure and its fluctuations are analyzed from a crystallographic viewpoint, by using two complementary approaches. One is a global analysis of cellular structures in cylindrical symmetry. Their structural stability and defect pattern are obtained as topological mode-locking of a continuous structural parameter. The other, a local, molecular dynamics of the cells, gives a realistic parametrization of the forces and the transformations by generalizing the Voronoi cell construction in one extra dimension. 23 refs., 8 figs

  4. Structure and dynamics of a silica melt in neutral confinement

    Science.gov (United States)

    Geske, Julian; Drossel, Barbara; Vogel, Michael

    2017-04-01

    We analyze the effects of spatial confinement on viscous silica using molecular dynamics simulations. For this purpose, we prepare a silica melt in a cylindrical pore, which is produced by pinning appropriate fractions of silicon and oxygen atoms in a bulk system after an equilibration period. In this way, the structure of the confined silica melt remains unaffected, while the confinement has a strong impact on the dynamics. We find that the structural relaxation of viscous silica is slowed down according to a double exponential law when approaching the pore wall. Moreover, we observe that static density correlations exist in the vicinity of the pore wall. Based on these effects, we determine dynamical and structural length scales of the silica melt. Both length scales show a similar increase upon cooling, with values on the order of the next-neighbor distances in the studied temperature range. Interestingly, we find no evidence that the growth of the length scales is affected by a fragile-to-strong transition of the silica melt. This observation casts serious doubts on the relevance of these length scales for the structural relaxation, at least for the studied glass former.

  5. Dynamic testing of MFTF containment-vessel structural system

    International Nuclear Information System (INIS)

    Weaver, H.J.; McCallen, D.B.; Eli, M.W.

    1982-01-01

    Dynamic (modal) testing was performed on the Magnetic Fusion Test Facility (MFTF) containment vessel. The seismic design of this vessel was heavily dependent upon the value of structural damping used in the analysis. Typically for welded steel vessels, a value of 2 to 3% of critical is used. However, due to the large mass of the vessel and magnet supported inside, we felt that the interaction between the structure and its foundation would be enhanced. This would result in a larger value of damping because vibrational energy in the structure would be transferred through the foundation into the surrounding soil. The dynamic test performed on this structure (with the magnet in place) confirmed this later theory and resulted in damping values of approximately 4 to 5% for the whole body modes. This report presents a brief description of dynamic testing emphasizing the specific test procedure used on the MFTF-A system. It also presents an interpretation of the damping mechanisms observed (material and geometric) based upon the spatial characteristics of the modal parameters

  6. Structural fluctuation governed dynamic diradical character in pentacene.

    Science.gov (United States)

    Yang, Hongfang; Chen, Mengzhen; Song, Xinyu; Bu, Yuxiang

    2015-06-07

    We unravel intriguing dynamical diradical behavior governed by structural fluctuation in pentacene using ab initio molecular dynamics simulation. In contrast to static equilibrium configuration of pentacene with a closed-shell ground state without diradical character, due to structural fluctuation, some of its dynamical snapshot configurations exhibit an open-shell broken-symmetry singlet ground state with diradical character, and such diradical character presents irregular pulsing behavior in time evolution. Not all structural changes can lead to diradical character, only those involving the shortening of cross-linking C-C bonds and variations of the C-C bonds in polyacetylene chains are the main contributors. This scenario about diradicalization is distinctly different from that in long acenes. The essence is that structural distortion cooperatively raises the HOMO and lowers the LUMO, efficiently reducing the HOMO-LUMO and singlet-triplet energy gaps, which facilitate the formation of a broken-symmetry open-shell singlet state. The irregular pulsing behavior originates from the mixing of normal vibrations in pentacene. This fascinating behavior suggests the potential application of pentacene as a suitable building block in the design of new electronic devices due to its magnetism-controllability through energy induction. This work provides new insight into inherent electronic property fluctuation in acenes.

  7. A rare polyglycine type II-like helix motif in naturally occurring proteins.

    Science.gov (United States)

    Warkentin, Eberhard; Weidenweber, Sina; Schühle, Karola; Demmer, Ulrike; Heider, Johann; Ermler, Ulrich

    2017-11-01

    Common structural elements in proteins such as α-helices or β-sheets are characterized by uniformly repeating, energetically favorable main chain conformations which additionally exhibit a completely saturated hydrogen-bonding network of the main chain NH and CO groups. Although polyproline or polyglycine type II helices (PP II or PG II ) are frequently found in proteins, they are not considered as equivalent secondary structure elements because they do not form a similar self-contained hydrogen-bonding network of the main chain atoms. In this context our finding of an unusual motif of glycine-rich PG II -like helices in the structure of the acetophenone carboxylase core complex is of relevance. These PG II -like helices form hexagonal bundles which appear to fulfill the criterion of a (largely) saturated hydrogen-bonding network of the main-chain groups and therefore may be regarded in this sense as a new secondary structure element. It consists of a central PG II -like helix surrounded by six nearly parallel PG II -like helices in a hexagonal array, plus an additional PG II -like helix extending the array outwards. Very related structural elements have previously been found in synthetic polyglycine fibers. In both cases, all main chain NH and CO groups of the central PG II -helix are saturated by either intra- or intermolecular hydrogen-bonds, resulting in a self-contained hydrogen-bonding network. Similar, but incomplete PG II -helix patterns were also previously identified in a GTP-binding protein and an antifreeze protein. © 2017 Wiley Periodicals, Inc.

  8. Dynamic Analysis of Wind Turbines Including Soil-Structure Interaction

    DEFF Research Database (Denmark)

    Harte, M.; Basu, B.; Nielsen, Søren R.K.

    2012-01-01

    This paper investigates the along-wind forced vibration response of an onshore wind turbine. The study includes the dynamic interaction effects between the foundation and the underlying soil, as softer soils can influence the dynamic response of wind turbines. A Multi-Degree-of-Freedom (MDOF......) horizontal axes onshore wind turbine model is developed for dynamic analysis using an Euler–Lagrangian approach. The model is comprised of a rotor blade system, a nacelle and a flexible tower connected to a foundation system using a substructuring approach. The rotor blade system consists of three rotating...... for displacement of the turbine system are obtained and the modal frequencies of the combined turbine-foundation system are estimated. Simulations are presented for the MDOF turbine structure subjected to wind loading for different soil stiffness conditions. Steady state and turbulent wind loading, developed using...

  9. IUTAM Symposium on Hamiltonian Dynamics, Vortex Structures, Turbulence

    CERN Document Server

    Borisov, Alexey V; Mamaev, Ivan S; Sokolovskiy, Mikhail A; IUTAM BOOKSERIES : Volume 6

    2008-01-01

    This work brings together previously unpublished notes contributed by participants of the IUTAM Symposium on Hamiltonian Dynamics, Vortex Structures, Turbulence (Moscow, 25-30 August 2006). The study of vortex motion is of great interest to fluid and gas dynamics: since all real flows are vortical in nature, applications of the vortex theory are extremely diverse, many of them (e.g. aircraft dynamics, atmospheric and ocean phenomena) being especially important. The last few decades have shown that serious possibilities for progress in the research of real turbulent vortex motions are essentially related to the combined use of mathematical methods, computer simulation and laboratory experiments. These approaches have led to a series of interesting results which allow us to study these processes from new perspectives. Based on this principle, the papers collected in this proceedings volume present new results on theoretical and applied aspects of the processes of formation and evolution of various flows, wave a...

  10. Population and evolutionary dynamics in spatially structured seasonally varying environments.

    Science.gov (United States)

    Reid, Jane M; Travis, Justin M J; Daunt, Francis; Burthe, Sarah J; Wanless, Sarah; Dytham, Calvin

    2018-03-25

    Increasingly imperative objectives in ecology are to understand and forecast population dynamic and evolutionary responses to seasonal environmental variation and change. Such population and evolutionary dynamics result from immediate and lagged responses of all key life-history traits, and resulting demographic rates that affect population growth rate, to seasonal environmental conditions and population density. However, existing population dynamic and eco-evolutionary theory and models have not yet fully encompassed within-individual and among-individual variation, covariation, structure and heterogeneity, and ongoing evolution, in a critical life-history trait that allows individuals to respond to seasonal environmental conditions: seasonal migration. Meanwhile, empirical studies aided by new animal-tracking technologies are increasingly demonstrating substantial within-population variation in the occurrence and form of migration versus year-round residence, generating diverse forms of 'partial migration' spanning diverse species, habitats and spatial scales. Such partially migratory systems form a continuum between the extreme scenarios of full migration and full year-round residence, and are commonplace in nature. Here, we first review basic scenarios of partial migration and associated models designed to identify conditions that facilitate the maintenance of migratory polymorphism. We highlight that such models have been fundamental to the development of partial migration theory, but are spatially and demographically simplistic compared to the rich bodies of population dynamic theory and models that consider spatially structured populations with dispersal but no migration, or consider populations experiencing strong seasonality and full obligate migration. Second, to provide an overarching conceptual framework for spatio-temporal population dynamics, we define a 'partially migratory meta-population' system as a spatially structured set of locations that can

  11. Phason thermal transport of three-helix state in insulating chiral magnets

    Science.gov (United States)

    Tatara, Gen

    2018-06-01

    Thermal dynamics of the three-helix state in a chiral magnet is studied based on a phason representation. Although phason representation is convenient for intuitive description, it is not straightforwardly compatible with microscopic linear response calculation of transport phenomena, because it is a (semi)macroscopic picture obtained by a coarse graining. By separating the slow phason mode and fast magnon mode, we show that phason thermal dynamics is driven by thermal magnon flow via the spin-transfer effect. The magnon and phason velocities are calculated by use of thermal vector potential formalism.

  12. Transient electromagnetic and dynamic structural analyses of a blanket structure with coupling effects

    Energy Technology Data Exchange (ETDEWEB)

    Koganezawa, K. [Mitsubishi Atomic Power Industries, Inc., Yokohama (Japan); Kushiyama, M. [Mitsubishi Atomic Power Industries, Inc., Yokohama (Japan); Niikura, S. [Mitsubishi Atomic Power Industries, Inc., Yokohama (Japan); Kudough, F. [Mitsubishi Atomic Power Industries, Inc., Yokohama (Japan); Onozuka, M. [Mitsubishi Heavy Industries Ltd., Yokohama (Japan); Koizumi, K. [Japan Atomic Energy Research Inst., Ibaraki (Japan)

    1995-12-31

    Transient electromagnetic and dynamic structural analyses of a blanket structure in the fusion experimental reactor (FER) under a plasma disruption event and a vertical displacement event (VDE) have been performed to investigate the dynamic structural characteristics and the feasibility of the structure. Coupling effects between eddy currents and dynamic deflections have also been taken into account in these analyses. In this study, the inboard blanket was employed because of our computer memory limitation. A 1/192 segment model of a full torus was analyzed using the analytical code, EDDYCUFF. In the plasma disruption event, the maximum magnetic pressure caused by eddy currents and poloidal fields was 1.2MPa. The maximum stress intensity by this magnetic pressure was 114MPa. In the VDE, the maximum magnetic pressure was 2.4MPa and the maximum stress intensity was 253MPa. This stress was somewhat beyond the allowable stress limit. Therefore, the blanket structure and support design should be reviewed to reduce the stress to a suitable value. In summary, the dynamic structural characteristics and design issues of the blanket structure have been identified. (orig.).

  13. Excited State Structural Dynamics of Carotenoids and Charge Transfer Systems

    International Nuclear Information System (INIS)

    Van Tassle, Aaron Justin

    2006-01-01

    This dissertation describes the development and implementation of a visible/near infrared pump/mid-infrared probe apparatus. Chapter 1 describes the background and motivation of investigating optically induced structural dynamics, paying specific attention to solvation and the excitation selection rules of highly symmetric molecules such as carotenoids. Chapter 2 describes the development and construction of the experimental apparatus used throughout the remainder of this dissertation. Chapter 3 will discuss the investigation of DCM, a laser dye with a fluorescence signal resulting from a charge transfer state. By studying the dynamics of DCM and of its methyl deuterated isotopomer (an otherwise identical molecule), we are able to investigate the origins of the charge transfer state and provide evidence that it is of the controversial twisted intramolecular (TICT) type. Chapter 4 introduces the use of two-photon excitation to the S1 state, combined with one-photon excitation to the S2 state of the carotenoid beta-apo-8'-carotenal. These 2 investigations show evidence for the formation of solitons, previously unobserved in molecular systems and found only in conducting polymers Chapter 5 presents an investigation of the excited state dynamics of peridinin, the carotenoid responsible for the light harvesting of dinoflagellates. This investigation allows for a more detailed understanding of the importance of structural dynamics of carotenoids in light harvesting

  14. Polarizability effects on the structure and dynamics of ionic liquids

    Energy Technology Data Exchange (ETDEWEB)

    Cavalcante, Ary de Oliveira, E-mail: arycavalcante@ufam.edu.br [Institute of Chemistry, University of Campinas – UNICAMP, Cx. P. 6154, Campinas, SP 13084-862 (Brazil); Departamento de Química, Universidade Federal do Amazonas, Av. Rodrigo Octávio, 6200, Coroado, Manaus, AM (Brazil); Ribeiro, Mauro C. C. [Laboratório de Espectroscopia Molecular, Instituto de Química, Universidade de São Paulo, São Paulo, SP C.P. 26077, 05513 970 São Paulo, SP (Brazil); Skaf, Munir S. [Institute of Chemistry, University of Campinas – UNICAMP, Cx. P. 6154, Campinas, SP 13084-862 (Brazil)

    2014-04-14

    Polarization effects on the structure and dynamics of ionic liquids are investigated using molecular dynamics simulations. Four different ionic liquids were simulated, formed by the anions Cl{sup −} and PF{sub 6}{sup −}, treated as single fixed charge sites, and the 1-n-alkyl-3-methylimidazolium cations (1-ethyl and 1-butyl-), which are polarizable. The partial charge fluctuation of the cations is provided by the electronegativity equalization model (EEM) and a complete parameter set for the cations electronegativity (χ) and hardness (J) is presented. Results obtained from a non-polarizable model for the cations are also reported for comparison. Relative to the fixed charged model, the equilibrium structure of the first solvation shell around the imidazolium cations shows that inclusion of EEM polarization forces brings cations closer to each other and that anions are preferentially distributed above and below the plane of the imidazolium ring. The polarizable model yields faster translational and reorientational dynamics than the fixed charges model in the rotational-diffusion regime. In this sense, the polarizable model dynamics is in better agreement with the experimental data.

  15. Differentiable dynamical systems an introduction to structural stability and hyperbolicity

    CERN Document Server

    Wen, Lan

    2016-01-01

    This is a graduate text in differentiable dynamical systems. It focuses on structural stability and hyperbolicity, a topic that is central to the field. Starting with the basic concepts of dynamical systems, analyzing the historic systems of the Smale horseshoe, Anosov toral automorphisms, and the solenoid attractor, the book develops the hyperbolic theory first for hyperbolic fixed points and then for general hyperbolic sets. The problems of stable manifolds, structural stability, and shadowing property are investigated, which lead to a highlight of the book, the \\Omega-stability theorem of Smale. While the content is rather standard, a key objective of the book is to present a thorough treatment for some tough material that has remained an obstacle to teaching and learning the subject matter. The treatment is straightforward and hence could be particularly suitable for self-study. Selected solutions are available electronically for instructors only. Please send email to textbooks@ams.org for more informatio...

  16. Ultrafast Dynamic Pressure Sensors Based on Graphene Hybrid Structure.

    Science.gov (United States)

    Liu, Shanbiao; Wu, Xing; Zhang, Dongdong; Guo, Congwei; Wang, Peng; Hu, Weida; Li, Xinming; Zhou, Xiaofeng; Xu, Hejun; Luo, Chen; Zhang, Jian; Chu, Junhao

    2017-07-19

    Mechanical flexible electronic skin has been focused on sensing various physical parameters, such as pressure and temperature. The studies of material design and array-accessible devices are the building blocks of strain sensors for subtle pressure sensing. Here, we report a new and facile preparation of a graphene hybrid structure with an ultrafast dynamic pressure response. Graphene oxide nanosheets are used as a surfactant to prevent graphene restacking in aqueous solution. This graphene hybrid structure exhibits a frequency-independent pressure resistive sensing property. Exceeding natural skin, such pressure sensors, can provide transient responses from static up to 10 000 Hz dynamic frequencies. Integrated by the controlling system, the array-accessible sensors can manipulate a robot arm and self-rectify the temperature of a heating blanket. This may pave a path toward the future application of graphene-based wearable electronics.

  17. Musical structure analysis using similarity matrix and dynamic programming

    Science.gov (United States)

    Shiu, Yu; Jeong, Hong; Kuo, C.-C. Jay

    2005-10-01

    Automatic music segmentation and structure analysis from audio waveforms based on a three-level hierarchy is examined in this research, where the three-level hierarchy includes notes, measures and parts. The pitch class profile (PCP) feature is first extracted at the note level. Then, a similarity matrix is constructed at the measure level, where a dynamic time warping (DTW) technique is used to enhance the similarity computation by taking the temporal distortion of similar audio segments into account. By processing the similarity matrix, we can obtain a coarse-grain music segmentation result. Finally, dynamic programming is applied to the coarse-grain segments so that a song can be decomposed into several major parts such as intro, verse, chorus, bridge and outro. The performance of the proposed music structure analysis system is demonstrated for pop and rock music.

  18. Annual Report 2000. Chemical Structure and Dynamics; FINAL

    International Nuclear Information System (INIS)

    Colson, Steve D; McDowell, Rod S

    2001-01-01

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

  19. Integrative Analysis of Metabolic Models – from Structure to Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Hartmann, Anja, E-mail: hartmann@ipk-gatersleben.de [Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben (Germany); Schreiber, Falk [Monash University, Melbourne, VIC (Australia); Martin-Luther-University Halle-Wittenberg, Halle (Germany)

    2015-01-26

    The characterization of biological systems with respect to their behavior and functionality based on versatile biochemical interactions is a major challenge. To understand these complex mechanisms at systems level modeling approaches are investigated. Different modeling formalisms allow metabolic models to be analyzed depending on the question to be solved, the biochemical knowledge and the availability of experimental data. Here, we describe a method for an integrative analysis of the structure and dynamics represented by qualitative and quantitative metabolic models. Using various formalisms, the metabolic model is analyzed from different perspectives. Determined structural and dynamic properties are visualized in the context of the metabolic model. Interaction techniques allow the exploration and visual analysis thereby leading to a broader understanding of the behavior and functionality of the underlying biological system. The System Biology Metabolic Model Framework (SBM{sup 2} – Framework) implements the developed method and, as an example, is applied for the integrative analysis of the crop plant potato.

  20. A general modeling framework for describing spatially structured population dynamics

    Science.gov (United States)

    Sample, Christine; Fryxell, John; Bieri, Joanna; Federico, Paula; Earl, Julia; Wiederholt, Ruscena; Mattsson, Brady; Flockhart, Tyler; Nicol, Sam; Diffendorfer, James E.; Thogmartin, Wayne E.; Erickson, Richard A.; Norris, D. Ryan

    2017-01-01

    Variation in movement across time and space fundamentally shapes the abundance and distribution of populations. Although a variety of approaches model structured population dynamics, they are limited to specific types of spatially structured populations and lack a unifying framework. Here, we propose a unified network-based framework sufficiently novel in its flexibility to capture a wide variety of spatiotemporal processes including metapopulations and a range of migratory patterns. It can accommodate different kinds of age structures, forms of population growth, dispersal, nomadism and migration, and alternative life-history strategies. Our objective was to link three general elements common to all spatially structured populations (space, time and movement) under a single mathematical framework. To do this, we adopt a network modeling approach. The spatial structure of a population is represented by a weighted and directed network. Each node and each edge has a set of attributes which vary through time. The dynamics of our network-based population is modeled with discrete time steps. Using both theoretical and real-world examples, we show how common elements recur across species with disparate movement strategies and how they can be combined under a unified mathematical framework. We illustrate how metapopulations, various migratory patterns, and nomadism can be represented with this modeling approach. We also apply our network-based framework to four organisms spanning a wide range of life histories, movement patterns, and carrying capacities. General computer code to implement our framework is provided, which can be applied to almost any spatially structured population. This framework contributes to our theoretical understanding of population dynamics and has practical management applications, including understanding the impact of perturbations on population size, distribution, and movement patterns. By working within a common framework, there is less chance

  1. Adaptive control of structural balance for complex dynamical networks based on dynamic coupling of nodes

    Science.gov (United States)

    Gao, Zilin; Wang, Yinhe; Zhang, Lili

    2018-02-01

    In the existing research results of the complex dynamical networks controlled, the controllers are mainly used to guarantee the synchronization or stabilization of the nodes’ state, and the terms coupled with connection relationships may affect the behaviors of nodes, this obviously ignores the dynamic common behavior of the connection relationships between the nodes. In fact, from the point of view of large-scale system, a complex dynamical network can be regarded to be composed of two time-varying dynamic subsystems, which can be called the nodes subsystem and the connection relationships subsystem, respectively. Similar to the synchronization or stabilization of the nodes subsystem, some characteristic phenomena can be also emerged in the connection relationships subsystem. For example, the structural balance in the social networks and the synaptic facilitation in the biological neural networks. This paper focuses on the structural balance in dynamic complex networks. Generally speaking, the state of the connection relationships subsystem is difficult to be measured accurately in practical applications, and thus it is not easy to implant the controller directly into the connection relationships subsystem. It is noted that the nodes subsystem and the relationships subsystem are mutually coupled, which implies that the state of the connection relationships subsystem can be affected by the controllable state of nodes subsystem. Inspired by this observation, by using the structural balance theory of triad, the controller with the parameter adaptive law is proposed for the nodes subsystem in this paper, which may ensure the connection relationship matrix to approximate a given structural balance matrix in the sense of the uniformly ultimately bounded (UUB). That is, the structural balance may be obtained by employing the controlling state of the nodes subsystem. Finally, the simulations are used to show the validity of the method in this paper.

  2. Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach.

    Science.gov (United States)

    Zhang, Kaiming; Keane, Sarah C; Su, Zhaoming; Irobalieva, Rossitza N; Chen, Muyuan; Van, Verna; Sciandra, Carly A; Marchant, Jan; Heng, Xiao; Schmid, Michael F; Case, David A; Ludtke, Steven J; Summers, Michael F; Chiu, Wah

    2018-03-06

    Cryoelectron microscopy (cryo-EM) and nuclear magnetic resonance (NMR) spectroscopy are routinely used to determine structures of macromolecules with molecular weights over 65 and under 25 kDa, respectively. We combined these techniques to study a 30 kDa HIV-1 dimer initiation site RNA ([DIS] 2 ; 47 nt/strand). A 9 Å cryo-EM map clearly shows major groove features of the double helix and a right-handed superhelical twist. Simulated cryo-EM maps generated from time-averaged molecular dynamics trajectories (10 ns) exhibited levels of detail similar to those in the experimental maps, suggesting internal structural flexibility limits the cryo-EM resolution. Simultaneous inclusion of the cryo-EM map and 2 H-edited NMR-derived distance restraints during structure refinement generates a structure consistent with both datasets and supporting a flipped-out base within a conserved purine-rich bulge. Our findings demonstrate the power of combining global and local structural information from these techniques for structure determination of modest-sized RNAs. Copyright © 2018 Elsevier Ltd. All rights reserved.

  3. Spectroscopic Tools for Quantitative Studies of DNA Structure and Dynamics

    DEFF Research Database (Denmark)

    Preus, Søren

    The main objective of this thesis is to develop quantitative fluorescence-based, spectroscopic tools for probing the 3D structure and dynamics of DNA and RNA. The thesis is founded on six peer-reviewed papers covering mainly the development, characterization and use of fluorescent nucleobase...... analogues. In addition, four software packages is presented for the simulation and quantitative analysis of time-resolved and steady-state UV-Vis absorption and fluorescence experiments....

  4. Yaw control for active damping of structural dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Ekelund, T. [Chalmers Univ. of Technology, Goeteborg (Sweden). Control Engineering Lab.

    1996-12-01

    Yaw torque control for reduction of structural dynamic loads in a two-bladed wind turbine is investigated. The models are obtained using rigid-body mechanics. Linear quadratic control theory is utilized for design and analysis. The analysis of two simple examples, where the teeter angle and the tower lateral bending motion are regarded, shows that a time-varying controller has some advantages compared with a time-invariant controller. 6 refs, 9 figs

  5. Sierra Structural Dynamics User's Notes

    Energy Technology Data Exchange (ETDEWEB)

    Reese, Garth M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-10-19

    Sierra/SD provides a massively parallel implementation of structural dynamics finite element analysis, required for high fidelity, validated models used in modal, vibration, static and shock analysis of weapons systems. This document provides a users guide to the input for Sierra/SD. Details of input specifications for the different solution types, output options, element types and parameters are included. The appendices contain detailed examples, and instructions for running the software on parallel platforms.

  6. Feedback Linearized Aircraft Control Using Dynamic Cell Structure

    Science.gov (United States)

    Jorgensen, C. C.

    1998-01-01

    A Dynamic Cell Structure (DCS ) Neural Network was developed which learns a topology representing network (TRN) of F-15 aircraft aerodynamic stability and control derivatives. The network is combined with a feedback linearized tracking controller to produce a robust control architecture capable of handling multiple accident and off-nominal flight scenarios. This paper describes network and its performance for accident scenarios including differential stabilator lock, soft sensor failure, control, stability derivative variation, and turbulence.

  7. Control of Spin Wave Dynamics in Spatially Twisted Magnetic Structures

    Science.gov (United States)

    2017-06-27

    control the spin wave dynamics of magnetic structures twisted spatially, we prepared the exchange-coupled films with the hard magnetic L10-FePt and...information writing of magnetic storage and spintronic applications. Introduction and Objective: Recent rapid progress in the research field of nano...scaled bilayer elements is also an important aim of this project. Approach/Method: The exchange-coupled films with the hard magnetic L10-FePt and

  8. Doublet vs. FODO structure: beam dynamics and layout

    CERN Document Server

    Eshraqi, M; CERN. Geneva. BE Department

    2010-01-01

    A FoDo (singlet) structure is designed for the CERN Superconducting Proton LINAC. This architecture is compared to the baseline (doublet) architecture of SPL on the basis of its beam dynamics performance and the required investment. The sensitivity of both layouts to quadrupole gradient errors and misalignment is checked and a correction scheme for beam steering is proposed. Finally a single quad beam dilution scheme is studied and designed for the pilot beam dump.

  9. Dynamic Capital Structure with Callable Debt and Debt Renegotiations

    DEFF Research Database (Denmark)

    Christensen, Peter Ove; Flor, Christian Riis; Lando, David

    2014-01-01

    We consider a dynamic trade-off model of a firm’s capital structure with debt renegotiation. Debt holders only accept restructuring offers from equity holders backed by threats which are in the equity holders’ own interest to execute. Our model shows that in a complete information model in which...... taxes and bankruptcy costs are the only frictions, violations of the absolute priority rule (APR) are typically optimal. The size of the bankruptcy costs and the equity holders’ bargaining power affect the size of APR violations, but they have only a minor impact on the choice of capital structure....

  10. Map updates in a dynamic Voronoi data structure

    DEFF Research Database (Denmark)

    Mioc, Darka; Antón Castro, Francesc/François; Gold, C. M.

    2006-01-01

    In this paper we are using local and sequential map updates in the Voronoi data structure, which allows us to automatically record each event and performed map updates within the system. These map updates are executed through map construction commands that are composed of atomic actions (geometric...... algorithms for addition, deletion, and motion of spatial objects) on the dynamic Voronoi data structure. The formalization of map commands led to the development of a spatial language comprising a set of atomic operations or constructs on spatial primitives (points and lines), powerful enough to define...

  11. Dynamic soil-structure interaction of monopod and polypod foundations

    DEFF Research Database (Denmark)

    Andersen, Lars Vabbersgaard

    2016-01-01

    within the time domain, frequency-independent lumped-parameter models are developed. The paper proposes a decision criterion for determination of which components must be included within a lumped-parameter model in order to account for the structure–soil–structure interaction in an adequate and efficient......The paper concerns the importance of through–soil coupling for structures having foundations with more footings. First, a model for dynamic analysis of polypod footings is established in the frequency domain, employing Green’s function for wave propagation in a layered half-space. To allow analysis...

  12. Dynamic calculation of structures in seismic zones. 2. ed.

    International Nuclear Information System (INIS)

    Capra, Alain; Davidovici, Victor

    1982-01-01

    The aims of this book are both didactic and practical. It is therefore addressed to both experienced engineers and students. Some general information about earthquakes and their occurrence is first given. The problem of a simple oscillator is presented. In this way, the reader is provided with an insight into undestanding the dynamic phenomena taking place and is introduced to the concept of response spectra and to an intuitive comprehension of the behavior of structures during earthquakes. The next chapter is devoted to the cases most frequently encountered with multiple oscillator structures. Theoretical studies are based on the usual modal decomposition method. The various practical methods of calculation employed are then examined, emphasis being given to the various different stages involved and to which of them is the best suited for a particular type of structure. Advise is given on how to select the model whose behavior best describes the real structure, both manual and computer methods of calculation being envisaged [fr

  13. Dynamic Changes in Sarcoplasmic Reticulum Structure in Ventricular Myocytes

    Directory of Open Access Journals (Sweden)

    Amanda L. Vega

    2011-01-01

    sarcoplasmic reticulum (SR and the sarcolemma where Ca2+ release is activated. Here, we tested the hypothesis that the SR is a structurally inert organelle in ventricular myocytes. Our data suggest that rather than being static, the SR undergoes frequent dynamic structural changes. SR boutons expressing functional ryanodine receptors moved throughout the cell, approaching or moving away from the sarcolemma of ventricular myocytes. These changes in SR structure occurred in the absence of changes in [Ca2+] during EC coupling. Microtubules and the molecular motors dynein and kinesin 1(Kif5b were important regulators of SR motility. These findings support a model in which the SR is a motile organelle capable of molecular motor protein-driven structural changes.

  14. Dynamic testing of nuclear power plant structures: an evaluation

    International Nuclear Information System (INIS)

    Weaver, H.J.

    1980-02-01

    Lawrence Livermore Laboratory (LLL) evaluated the applications of system identification techniques to the dynamic testing of nuclear power plant structures and subsystems. These experimental techniques involve exciting a structure and measuring, digitizing, and processing the time-history motions that result. The data can be compared to parameters calculated using finite element or other models of the test systems to validate the model and to verify the seismic analysis. This report summarizes work in three main areas: (1) analytical qualification of a set of computer programs developed at LLL to extract model parameters from the time histories; (2) examination of the feasibility of safely exciting nuclear power plant structures and accurately recording the resulting time-history motions; (3) study of how the model parameters that are extracted from the data be used best to evaluate structural integrity and analyze nuclear power plants

  15. Age structure and cooperation in coevolutionary games on dynamic network

    Science.gov (United States)

    Qin, Zilong; Hu, Zhenhua; Zhou, Xiaoping; Yi, Jingzhang

    2015-04-01

    Our proposed model imitates the growth of a population and describes the age structure and the level of cooperation in games on dynamic network with continuous changes of structure and topology. The removal of nodes and links caused by age-dependent attack, together with the nodes addition standing for the newborns of population, badly ruins Matthew effect in this coevolutionary process. Though the network is generated by growth and preferential attachment, it degenerates into random network and it is no longer heterogeneous. When the removal of nodes and links is equal to the addition of nodes and links, the size of dynamic network is maintained in steady-state, so is the low level of cooperation. Severe structure variation, homogeneous topology and continuous invasion of new defection jointly make dynamic network unsuitable for the survival of cooperator even when the probability with which the newborn players initially adopt the strategy cooperation is high, while things change slightly when the connections of newborn players are restricted. Fortunately, moderate interactions in a generation trigger an optimal recovering process to encourage cooperation. The model developed in this paper outlines an explanation of the cohesion changes in the development process of an organization. Some suggestions for cooperative behavior improvement are given in the end.

  16. Impact of constrained rewiring on network structure and node dynamics

    Science.gov (United States)

    Rattana, P.; Berthouze, L.; Kiss, I. Z.

    2014-11-01

    In this paper, we study an adaptive spatial network. We consider a susceptible-infected-susceptible (SIS) epidemic on the network, with a link or contact rewiring process constrained by spatial proximity. In particular, we assume that susceptible nodes break links with infected nodes independently of distance and reconnect at random to susceptible nodes available within a given radius. By systematically manipulating this radius we investigate the impact of rewiring on the structure of the network and characteristics of the epidemic. We adopt a step-by-step approach whereby we first study the impact of rewiring on the network structure in the absence of an epidemic, then with nodes assigned a disease status but without disease dynamics, and finally running network and epidemic dynamics simultaneously. In the case of no labeling and no epidemic dynamics, we provide both analytic and semianalytic formulas for the value of clustering achieved in the network. Our results also show that the rewiring radius and the network's initial structure have a pronounced effect on the endemic equilibrium, with increasingly large rewiring radiuses yielding smaller disease prevalence.

  17. Stress, strain, and structural dynamics an interactive handbook of formulas, solutions, and Matlab toolboxes

    CERN Document Server

    Yang, Bingen

    2005-01-01

    Stress, Strain, and Structural Dynamics is a comprehensive and definitive reference to statics and dynamics of solids and structures, including mechanics of materials, structural mechanics, elasticity, rigid-body dynamics, vibrations, structural dynamics, and structural controls. This text integrates the development of fundamental theories, formulas and mathematical models with user-friendly interactive computer programs, written in the powerful and popular MATLAB. This unique merger of technical referencing and interactive computing allows instant solution of a variety of engineering problems

  18. Dynamical simulation of structural multiplicity in grain boundaries

    International Nuclear Information System (INIS)

    Majid, I.; Bristowe, P.D.

    1987-06-01

    Work on a computer simulation study of a low-energy high-angle boundary structure which is not periodic have been recently reported. This result is of interest since grain boundary structures are usually assumed to have a periodicity corresponding to the appropriate coincidence site lattice (CSL) and many experimental observations of the structure of grain boundaries performed using conventional and high-resolution electron microscopy, electron diffraction and x-ray diffraction appear to support this work. However, this work, using empirical interatomic pair potentials and the relaxation method of molecular statics, have simulated a Σ = 5 36.87 0 (001) twist boundary and found a low energy structure having a larger repeat cell than the CSL and is composed of two different types of structural unit that are randomly distributed in the boundary plane. This result, which has been termed the multiplicity of grain boundary structures, has also been found in the simulation of tilt boundaries. The multiplicity phenomenon is of special interest in twist boundaries since it is used as a structural model to explain the x-ray scattering from a Σ = 5 boundary in gold. These scattering patterns had previously remained unexplained using stable structures that had simple CSL periodicity. Also, the effect of having a multiple number of low energy structural units coexisting in the grain boundary is of more general interest since it implies that the boundary structures may be quasi-periodic and, in some circumstances, may even result in a roughening of the boundary plane. This paper extends this work by showing, using molecular dynamics, that a multiplicity of structural units can actually nucleate spontaneously in a high-angle grain boundary at finite temperatures

  19. Regulation of TCF ETS-domain transcription factors by helix-loop-helix motifs.

    Science.gov (United States)

    Stinson, Julie; Inoue, Toshiaki; Yates, Paula; Clancy, Anne; Norton, John D; Sharrocks, Andrew D

    2003-08-15

    DNA binding by the ternary complex factor (TCF) subfamily of ETS-domain transcription factors is tightly regulated by intramolecular and intermolecular interactions. The helix-loop-helix (HLH)-containing Id proteins are trans-acting negative regulators of DNA binding by the TCFs. In the TCF, SAP-2/Net/ERP, intramolecular inhibition of DNA binding is promoted by the cis-acting NID region that also contains an HLH-like motif. The NID also acts as a transcriptional repression domain. Here, we have studied the role of HLH motifs in regulating DNA binding and transcription by the TCF protein SAP-1 and how Cdk-mediated phosphorylation affects the inhibitory activity of the Id proteins towards the TCFs. We demonstrate that the NID region of SAP-1 is an autoinhibitory motif that acts to inhibit DNA binding and also functions as a transcription repression domain. This region can be functionally replaced by fusion of Id proteins to SAP-1, whereby the Id moiety then acts to repress DNA binding in cis. Phosphorylation of the Ids by cyclin-Cdk complexes results in reduction in protein-protein interactions between the Ids and TCFs and relief of their DNA-binding inhibitory activity. In revealing distinct mechanisms through which HLH motifs modulate the activity of TCFs, our results therefore provide further insight into the role of HLH motifs in regulating TCF function and how the inhibitory properties of the trans-acting Id HLH proteins are themselves regulated by phosphorylation.

  20. Genome-wide identification and analysis of the chicken basic helix-loop-helix factors.

    Science.gov (United States)

    Liu, Wu-Yi; Zhao, Chun-Jiang

    2010-01-01

    Members of the basic helix-loop-helix (bHLH) family of transcription factors play important roles in a wide range of developmental processes. In this study, we conducted a genome-wide survey using the chicken (Gallus gallus) genomic database, and identified 104 bHLH sequences belonging to 42 gene families in an effort to characterize the chicken bHLH transcription factor family. Phylogenetic analyses revealed that chicken has 50, 21, 15, 4, 8, and 3 bHLH members in groups A, B, C, D, E, and F, respectively, while three members belonging to none of these groups were classified as ''orphans". A comparison between chicken and human bHLH repertoires suggested that both organisms have a number of lineage-specific bHLH members in the proteomes. Chromosome distribution patterns and phylogenetic analyses strongly suggest that the bHLH members should have arisen through gene duplication at an early date. Gene Ontology (GO) enrichment statistics showed 51 top GO annotations of biological processes counted in the frequency. The present study deepens our understanding of the chicken bHLH transcription factor family and provides much useful information for further studies using chicken as a model system.

  1. Genome-Wide Identification and Analysis of the Chicken Basic Helix-Loop-Helix Factors

    Directory of Open Access Journals (Sweden)

    Wu-yi Liu

    2010-01-01

    Full Text Available Members of the basic helix-loop-helix (bHLH family of transcription factors play important roles in a wide range of developmental processes. In this study, we conducted a genome-wide survey using the chicken (Gallus gallus genomic database, and identified 104 bHLH sequences belonging to 42 gene families in an effort to characterize the chicken bHLH transcription factor family. Phylogenetic analyses revealed that chicken has 50, 21, 15, 4, 8, and 3 bHLH members in groups A, B, C, D, E, and F, respectively, while three members belonging to none of these groups were classified as ‘‘orphans’’. A comparison between chicken and human bHLH repertoires suggested that both organisms have a number of lineage-specific bHLH members in the proteomes. Chromosome distribution patterns and phylogenetic analyses strongly suggest that the bHLH members should have arisen through gene duplication at an early date. Gene Ontology (GO enrichment statistics showed 51 top GO annotations of biological processes counted in the frequency. The present study deepens our understanding of the chicken bHLH transcription factor family and provides much useful information for further studies using chicken as a model system.

  2. Accuracy Enhanced Stability and Structure Preserving Model Reduction Technique for Dynamical Systems with Second Order Structure

    DEFF Research Database (Denmark)

    Tahavori, Maryamsadat; Shaker, Hamid Reza

    A method for model reduction of dynamical systems with the second order structure is proposed in this paper. The proposed technique preserves the second order structure of the system, and also preserves the stability of the original systems. The method uses the controllability and observability...... gramians within the time interval to build the appropriate Petrov-Galerkin projection for dynamical systems within the time interval of interest. The bound on approximation error is also derived. The numerical results are compared with the counterparts from other techniques. The results confirm...

  3. Structural dynamic and resistance to nuclear air blast

    International Nuclear Information System (INIS)

    Qureshi, S.M.

    2003-01-01

    A need exists to design protective shelters attached to specialized facilities against nuclear airbursts, explosive shocks and impacting projectiles. Designing such structures against nuclear and missile impact is a challenging task that needs to be looked into for design methodology formulation and practicability. Structures can be designed for overpressure pulsed generated by a nuclear explosion as well as the scabbing and perforation/punching of an impacting projectile. This paper discuses and formulates the methods of dynamic analysis and design required to undertake such a task. Structural resistance to peak overpressure pulse for a 20 KT weapons and smaller tactical nuclear weapons of 1 KT (16 psi, overpressure) size as a direct air blast overpressure has been considered in design of walls, beams and slabs of a special structure under review. The design of shear reinforcement as lacing is also carried out. Adopting the philosophy of strengthening and hardening can minimize the effect of air blast overpressure and projectile impact. The objective is to avoid a major structural failure. The structure then needs to be checked against ballistic penetration by a range of weapons or be required to resist explosive penetration from the charge detonated in contact with the structure. There is also a dire need to formulate protective guidelines for all existing and future critical facilities. (author)

  4. A Molecular Dynamics Study of the Structural and Dynamical Properties of Putative Arsenic Substituted Lipid Bilayers

    Directory of Open Access Journals (Sweden)

    Ratna Juwita

    2013-04-01

    Full Text Available Cell membranes are composed mainly of phospholipids which are in turn, composed of five major chemical elements: carbon, hydrogen, nitrogen, oxygen, and phosphorus. Recent studies have suggested the possibility of sustaining life if the phosphorus is substituted by arsenic. Although this issue is still controversial, it is of interest to investigate the properties of arsenated-lipid bilayers to evaluate this possibility. In this study, we simulated arsenated-lipid, 1-palmitoyl-2-oleoyl-sn-glycero-3-arsenocholine (POAC, lipid bilayers using all-atom molecular dynamics to understand basic structural and dynamical properties, in particular, the differences from analogous 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, (POPC lipid bilayers. Our simulations showed that POAC lipid bilayers have distinct structural and dynamical properties from those of native POPC lipid bilayers. Relative to POPC lipid bilayers, POAC lipid bilayers have a more compact structure with smaller lateral areas and greater order. The compact structure of POAC lipid bilayers is due to the fact that more inter-lipid salt bridges are formed with arsenate-choline compared to the phosphate-choline of POPC lipid bilayers. These inter-lipid salt bridges bind POAC lipids together and also slow down the head group rotation and lateral diffusion of POAC lipids. Thus, it would be anticipated that POAC and POPC lipid bilayers would have different biological implications.

  5. Structure and Dynamics of Urea/Water Mixtures Investigated by Vibrational Spectroscopy and Molecular Dynamics Simulation

    Science.gov (United States)

    Carr, J. K.; Buchanan, L. E.; Schmidt, J. R.; Zanni, M. T.; Skinner, J. L.

    2013-01-01

    Urea/water is an archetypical “biological” mixture, and is especially well known for its relevance to protein thermodynamics, as urea acts as a protein denaturant at high concentration. This behavior has given rise to an extended debate concerning urea’s influence on water structure. Based on a variety of methods and of definitions of water structure, urea has been variously described as a structure-breaker, a structure-maker, or as remarkably neutral towards water. Because of its sensitivity to microscopic structure and dynamics, vibrational spectroscopy can help resolve these debates. We report experimental and theoretical spectroscopic results for the OD stretch of HOD/H2O/urea mixtures (linear IR, 2DIR, and pump-probe anisotropy decay) and for the CO stretch of urea-D4/D2O mixtures (linear IR only). Theoretical results are obtained using existing approaches for water, and a modification of a frequency map developed for acetamide. All absorption spectra are remarkably insensitive to urea concentration, consistent with the idea that urea only very weakly perturbs water structure. Both this work and experiments by Rezus and Bakker, however, show that water’s rotational dynamics are slowed down by urea. Analysis of the simulations casts doubt on the suggestion that urea immobilizes particular doubly hydrogen bonded water molecules. PMID:23841646

  6. Basic Tilted Helix Bundle – A new protein fold in human FKBP25/FKBP3 and HectD1

    Energy Technology Data Exchange (ETDEWEB)

    Helander, Sara; Montecchio, Meri [Department of Physics, Chemistry and Biology, Division of Chemistry, Linköping University, SE-58183 Linköping (Sweden); Lemak, Alexander [Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7 (Canada); Northeast Structural Genomics Consortium, Toronto, Ontario (Canada); Farès, Christophe [Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7 (Canada); Almlöf, Jonas [Department of Physics, Chemistry and Biology, Division of Chemistry, Linköping University, SE-58183 Linköping (Sweden); Li, Yanjun [Structural Genomics Consortium, University of Toronto, 101 College St, Toronto, Ontario M5G 1L7 (Canada); Yee, Adelinda [Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7 (Canada); Northeast Structural Genomics Consortium, Toronto, Ontario (Canada); Arrowsmith, Cheryl H. [Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7 (Canada); Northeast Structural Genomics Consortium, Toronto, Ontario (Canada); Structural Genomics Consortium, University of Toronto, 101 College St, Toronto, Ontario M5G 1L7 (Canada); Dhe-Paganon, Sirano [Structural Genomics Consortium, University of Toronto, 101 College St, Toronto, Ontario M5G 1L7 (Canada); Sunnerhagen, Maria, E-mail: maria.sunnerhagen@liu.se [Department of Physics, Chemistry and Biology, Division of Chemistry, Linköping University, SE-58183 Linköping (Sweden)

    2014-04-25

    Highlights: • We describe the structure of a novel fold in FKBP25 and HectD. • The new fold is named the Basic Tilted Helix Bundle (BTHB) domain. • A conserved basic surface patch is presented, suggesting a functional role. - Abstract: In this paper, we describe the structure of a N-terminal domain motif in nuclear-localized FKBP25{sub 1–73}, a member of the FKBP family, together with the structure of a sequence-related subdomain of the E3 ubiquitin ligase HectD1 that we show belongs to the same fold. This motif adopts a compact 5-helix bundle which we name the Basic Tilted Helix Bundle (BTHB) domain. A positively charged surface patch, structurally centered around the tilted helix H4, is present in both FKBP25 and HectD1 and is conserved in both proteins, suggesting a conserved functional role. We provide detailed comparative analysis of the structures of the two proteins and their sequence similarities, and analysis of the interaction of the proposed FKBP25 binding protein YY1. We suggest that the basic motif in BTHB is involved in the observed DNA binding of FKBP25, and that the function of this domain can be affected by regulatory YY1 binding and/or interactions with adjacent domains.

  7. Basic Tilted Helix Bundle – A new protein fold in human FKBP25/FKBP3 and HectD1

    International Nuclear Information System (INIS)

    Helander, Sara; Montecchio, Meri; Lemak, Alexander; Farès, Christophe; Almlöf, Jonas; Li, Yanjun; Yee, Adelinda; Arrowsmith, Cheryl H.; Dhe-Paganon, Sirano; Sunnerhagen, Maria

    2014-01-01

    Highlights: • We describe the structure of a novel fold in FKBP25 and HectD. • The new fold is named the Basic Tilted Helix Bundle (BTHB) domain. • A conserved basic surface patch is presented, suggesting a functional role. - Abstract: In this paper, we describe the structure of a N-terminal domain motif in nuclear-localized FKBP25 1–73 , a member of the FKBP family, together with the structure of a sequence-related subdomain of the E3 ubiquitin ligase HectD1 that we show belongs to the same fold. This motif adopts a compact 5-helix bundle which we name the Basic Tilted Helix Bundle (BTHB) domain. A positively charged surface patch, structurally centered around the tilted helix H4, is present in both FKBP25 and HectD1 and is conserved in both proteins, suggesting a conserved functional role. We provide detailed comparative analysis of the structures of the two proteins and their sequence similarities, and analysis of the interaction of the proposed FKBP25 binding protein YY1. We suggest that the basic motif in BTHB is involved in the observed DNA binding of FKBP25, and that the function of this domain can be affected by regulatory YY1 binding and/or interactions with adjacent domains

  8. Gibberellin-regulated gene in the basal region of rice leaf sheath encodes basic helix-loop-helix transcription factor.

    Science.gov (United States)

    Komatsu, Setsuko; Takasaki, Hironori

    2009-07-01

    Genes regulated by gibberellin (GA) during leaf sheath elongation in rice seedlings were identified using the transcriptome approach. mRNA from the basal regions of leaf sheaths treated with GA3 was analyzed by high-coverage gene expression profiling. 33,004 peaks were detected, and 30 transcripts showed significant changes in the presence of GA3. Among these, basic helix-loop-helix transcription factor (AK073385) was significantly upregulated. Quantitative PCR analysis confirmed that expression of AK073385 was controlled by GA3 in a time- and dose-dependent manner. Basic helix-loop-helix transcription factor (AK073385) is therefore involved in the regulation of gene expression by GA3.

  9. Structure and dynamics of interfacial water. Role of hydratation water in the globular proteins dynamics

    International Nuclear Information System (INIS)

    Zanotti, J.M.

    1997-01-01

    This memoir includes five chapters. In the first chapter, are given the elements of the neutrons scattering theory that is used in this study. the second chapter is devoted to a general presentation of the interaction between biological macro molecule and water. The third part is dedicated to the study of the structure and the dynamics of interfacial water in the neighbouring of model systems, the vycor and the amorphous carbon. The results presented in this part are compared with these one relative to water dynamics at the C-phycocyanin surface. This study makes the object of the fourth chapter. Then, in the fifth and last chapter are discussed the results relative to the role of hydratation on the parv-albumin dynamics for which have been combined the neutron quasi elastic incoherent scattering and the nuclear magnetic resonance of the carbon 13 solid in natural abundance

  10. Testing the Lag Structure of Assets’ Realized Volatility Dynamics

    Directory of Open Access Journals (Sweden)

    Francesco Audrino

    2017-12-01

    Full Text Available A (conservative test is applied to investigate the optimal lag structure for modelingrealized volatility dynamics. The testing procedure relies on the recent theoretical results that showthe ability of the adaptive least absolute shrinkage and selection operator (adaptive lasso to combinee cient parameter estimation, variable selection, and valid inference for time series processes. In anapplication to several constituents of the S&P 500 index it is shown that (i the optimal significantlag structure is time-varying and subject to drastic regime shifts that seem to happen across assetssimultaneously; (ii in many cases the relevant information for prediction is included in the first 22lags, corroborating previous results concerning the accuracy and the diffculty of outperforming outof-sample the heterogeneous autoregressive (HAR model; and (iii some common features of theoptimal lag structure can be identified across assets belonging to the same market segment or showinga similar beta with respect to the market index.

  11. Optical Fibres Contactless Sensor for Dynamic Testing of Lightweight Structures

    Directory of Open Access Journals (Sweden)

    L. Bregant

    2008-01-01

    Full Text Available With dynamic testing, engineers describe activities focused on the identification of some properties of vibrating structures. This step requires for the measurements of excitations and responses signals, applying appropriate sensors directly on the test article. These instruments modify the system's mass and stiffness distributions and eventually the eigen-properties of the structure. These errors become unacceptable especially when testing lightweight structures. This paper shows the results of some tests performed on a small compressor with the purpose of identifying the blades’ natural frequencies and modes. It compares the acquisitions performed with standard accelerometers and two different contact-less systems using as exciters either a micro-hammer or a micro inertial shaker. The paper shows how the contact-less sensors provide good quality data and consistent results in the mode identification phase.

  12. Fouling Kinetics and Associated Dynamics of Structural Modifications

    DEFF Research Database (Denmark)

    Jacob, Jerome; Prádanos, Pedro; Calvo, J. I.

    1998-01-01

    It is shown that the fouling behaviour of microfiltration membranes does not agree within all the time ranges of any of the commonly used membrane blocking models (i.e. complete, standard, intermediate or cake blocking). The resulting experimental kinetics of flux decline do not fit to only one...... of these models, but according to a successive or simultaneous coexistence of two or more of them. This is studied by analysing the structural modifications associated with the fouling kinetics. To achieve this goal, here we analyse the dynamical changes on the structure of four microporous membranes made...... by Sartorius (ST02 and ST045, neutral) and Spectrum (SP02 and SP045, positively charged) when fouled by permeating a protein aqueous solution (bovine serum albumin (BSA) at 1 g l(-1)) under 10 kPa in a dead-end device. The structure after different fouling times is obtained by using an extended bubble point...

  13. Mapping the structural and dynamical features of kinesin motor domains.

    Directory of Open Access Journals (Sweden)

    Guido Scarabelli

    Full Text Available Kinesin motor proteins drive intracellular transport by coupling ATP hydrolysis to conformational changes that mediate directed movement along microtubules. Characterizing these distinct conformations and their interconversion mechanism is essential to determining an atomic-level model of kinesin action. Here we report a comprehensive principal component analysis of 114 experimental structures along with the results of conventional and accelerated molecular dynamics simulations that together map the structural dynamics of the kinesin motor domain. All experimental structures were found to reside in one of three distinct conformational clusters (ATP-like, ADP-like and Eg5 inhibitor-bound. These groups differ in the orientation of key functional elements, most notably the microtubule binding α4-α5, loop8 subdomain and α2b-β4-β6-β7 motor domain tip. Group membership was found not to correlate with the nature of the bound nucleotide in a given structure. However, groupings were coincident with distinct neck-linker orientations. Accelerated molecular dynamics simulations of ATP, ADP and nucleotide free Eg5 indicate that all three nucleotide states could sample the major crystallographically observed conformations. Differences in the dynamic coupling of distal sites were also evident. In multiple ATP bound simulations, the neck-linker, loop8 and the α4-α5 subdomain display correlated motions that are absent in ADP bound simulations. Further dissection of these couplings provides evidence for a network of dynamic communication between the active site, microtubule-binding interface and neck-linker via loop7 and loop13. Additional simulations indicate that the mutations G325A and G326A in loop13 reduce the flexibility of these regions and disrupt their couplings. Our combined results indicate that the reported ATP and ADP-like conformations of kinesin are intrinsically accessible regardless of nucleotide state and support a model where neck

  14. Dynamico-FE: A Structure-Preserving Hydrostatic Dynamical Core

    Science.gov (United States)

    Eldred, Christopher; Dubos, Thomas; Kritsikis, Evaggelos

    2017-04-01

    It is well known that the inviscid, adiabatic equations of atmospheric motion constitute a non-canonical Hamiltonian system, and therefore posses many important conserved quantities such as as mass, potential vorticity and total energy. In addition, there are also key mimetic properties (such as curl grad = 0) of the underlying continuous vector calculus. Ideally, a dynamical core should have similar properties. A general approach to deriving such structure-preserving numerical schemes has been developed under the frameworks of Hamiltonian methods and mimetic discretizations, and over the past decade, there has been a great deal of work on the development of atmospheric dynamical cores using these techniques. An important example is Dynamico, which conserves mass, potential vorticity and total energy; and possesses additional mimetic properties such as a curl-free pressure gradient. Unfortunately, the underlying finite-difference discretization scheme used in Dynamico has been shown to be inconsistent on general grids. To resolve these accuracy issues, a scheme based on mimetic Galerkin discretizations has been developed that achieves higher-order accuracy while retaining the structure-preserving properties of the existing discretization. This presentation will discuss the new dynamical core, termed Dynamico-FE, and show results from a standard set of test cases on both the plane and the sphere.

  15. Polyacrylic acids–bovine serum albumin complexation: Structure and dynamics

    International Nuclear Information System (INIS)

    Othman, Mohamed; Aschi, Adel; Gharbi, Abdelhafidh

    2016-01-01

    The study of the mixture of BSA with polyacrylic acids at different masses versus pH allowed highlighting the existence of two regimes of weak and strong complexation. These complexes were studied in diluted regime concentration, by turbidimetry, dynamic light scattering (DLS), zeta-potential measurements and nuclear magnetic resonance (NMR). We have followed the pH effect on the structure and properties of the complex. This allowed refining the interpretation of the phase diagram and understanding the observed phenomena. The NMR measurements allowed probing the dynamics of the constituents versus the pH. The computational method was used to precisely determine the electrostatic potential of BSA and how the polyelectrolyte binds to it at different pH. - Highlights: • Influence of physico-chemical parameters on the electrostatic interactions in the complex system (polyelectrolyte/protein). • Stabilization and encapsulation of biological macromolecules solution by mean of polyelectrolyte. • Properties and structure of mixture obtained by screening the charges of globular protein and at different masses of polyacrylic acids. • Dynamic of the constituents formed by complexes particles. • Evaluation of the electrostatic properties of bovine serum albumin versus pH through solution of the Poisson-Boltzmann equation.

  16. Dynamical soil-structure interactions: influence of soil behaviour nonlinearities

    International Nuclear Information System (INIS)

    Gandomzadeh, Ali

    2011-01-01

    The interaction of the soil with the structure has been largely explored the assumption of material and geometrical linearity of the soil. Nevertheless, for moderate or strong seismic events, the maximum shear strain can easily reach the elastic limit of the soil behavior. Considering soil-structure interaction, the nonlinear effects may change the soil stiffness at the base of the structure and therefore energy dissipation into the soil. Consequently, ignoring the nonlinear characteristics of the dynamic soil-structure interaction (DSSI) this phenomenon could lead to erroneous predictions of structural response. The goal of this work is to implement a fully nonlinear constitutive model for soils into a numerical code in order to investigate the effect of soil nonlinearity on dynamic soil structure interaction. Moreover, different issues are taken into account such as the effect of confining stress on the shear modulus of the soil, initial static condition, contact elements in the soil-structure interface, etc. During this work, a simple absorbing layer method based on a Rayleigh/Caughey damping formulation, which is often already available in existing Finite Element softwares, is also presented. The stability conditions of the wave propagation problems are studied and it is shown that the linear and nonlinear behavior are very different when dealing with numerical dispersion. It is shown that the 10 points per wavelength rule, recommended in the literature for the elastic media is not sufficient for the nonlinear case. The implemented model is first numerically verified by comparing the results with other known numerical codes. Afterward, a parametric study is carried out for different types of structures and various soil profiles to characterize nonlinear effects. Different features of the DSSI are compared to the linear case: modification of the amplitude and frequency content of the waves propagated into the soil, fundamental frequency, energy dissipation in

  17. Helix 11 Dynamics is Critical for Constitutive Androstane Receptor Activity

    OpenAIRE

    Wright, Edward; Busby, Scott A.; Wisecarver, Sarah; Vincent, Jeremy; Griffin, Patrick R.; Fernandez, Elias J.

    2011-01-01

    The constitutive androstane receptor (CAR) transactivation can occur in the absence of exogenous ligand and this activity is enhanced by agonists TCPOBOP and meclizine. We use biophysical and cell-based assays to show that increased activity of CAR(TCPOBOP) relative to CAR(meclizine) corresponds to a higher affinity of CAR(TCPOBOP) for the steroid receptor coactivator-1. Additionally, steady-state fluorescence spectra suggest conformational differences between CAR(TCPOBOP):RXR and CAR(meclizi...

  18. An amphipathic alpha-helix controls multiple roles of brome mosaic virus protein 1a in RNA replication complex assembly and function.

    Directory of Open Access Journals (Sweden)

    Ling Liu

    2009-03-01

    Full Text Available Brome mosaic virus (BMV protein 1a has multiple key roles in viral RNA replication. 1a localizes to perinuclear endoplasmic reticulum (ER membranes as a peripheral membrane protein, induces ER membrane invaginations in which RNA replication complexes form, and recruits and stabilizes BMV 2a polymerase (2a(Pol and RNA replication templates at these sites to establish active replication complexes. During replication, 1a provides RNA capping, NTPase and possibly RNA helicase functions. Here we identify in BMV 1a an amphipathic alpha-helix, helix A, and use NMR analysis to define its structure and propensity to insert in hydrophobic membrane-mimicking micelles. We show that helix A is essential for efficient 1a-ER membrane association and normal perinuclear ER localization, and that deletion or mutation of helix A abolishes RNA replication. Strikingly, mutations in helix A give rise to two dramatically opposite 1a function phenotypes, implying that helix A acts as a molecular switch regulating the intricate balance between separable 1a functions. One class of helix A deletions and amino acid substitutions markedly inhibits 1a-membrane association and abolishes ER membrane invagination, viral RNA template recruitment, and replication, but doubles the 1a-mediated increase in 2a(Pol accumulation. The second class of helix A mutations not only maintains efficient 1a-membrane association but also amplifies the number of 1a-induced membrane invaginations 5- to 8-fold and enhances viral RNA template recruitment, while failing to stimulate 2a(Pol accumulation. The results provide new insights into the pathways of RNA replication complex assembly and show that helix A is critical for assembly and function of the viral RNA replication complex, including its central role in targeting replication components and controlling modes of 1a action.

  19. Performance of Process Damping in Machining Titanium Alloys at Low Cutting Speed with Different Helix Tools

    International Nuclear Information System (INIS)

    Shaharun, M A; Yusoff, A R; Reza, M S; Jalal, K A

    2012-01-01

    Titanium is a strong, lustrous, corrosion-resistant and transition metal with a silver color to produce strong lightweight alloys for industrial process, automotive, medical instruments and other applications. However, it is very difficult to machine the titanium due to its poor machinability. When machining titanium alloys with the conventional tools, the wear rate of the tool is rapidly accelerate and it is generally difficult to achieve at high cutting speed. In order to get better understanding of machining titanium alloy, the interaction between machining structural system and the cutting process which result in machining instability will be studied. Process damping is a useful phenomenon that can be exploited to improve the limited productivity of low speed machining. In this study, experiments are performed to evaluate the performance of process damping of milling under different tool helix geometries. The results showed that the helix of 42° angle is significantly increase process damping performance in machining titanium alloy.

  20. Application of Incremental Dynamic Analysis (IDA Method for Studying the Dynamic Behavior of Structures During Earthquakes

    Directory of Open Access Journals (Sweden)

    M. Javanpour

    2017-02-01

    Full Text Available Prediction of existing buildings’ vulnerability by future earthquakes is one of the most essential topics in structural engineering. Modeling steel structures is a giant step in determining the damage caused by the earthquake, as such structures are increasingly being used in constructions. Hence, two same-order steel structures with two types of structural systems were selected (coaxial moment frames and moment frame. In most cases, a specific structure needs to satisfy several functional levels. For this purpose, a method is required to determine the input request to the structures under possible earthquakes. Therefore, the Incremental Dynamic Analysis (IDA was preferred to the Push-Over non-linear static method for the analysis and design of the considered steel structures, due its accuracy and effect of higher modes at the same time intervals. OpenSees software was used to perform accurate nonlinear analysis of the steel structure. Two parameters (spectral acceleration and maximum ground acceleration were introduced to the modeled frames to compare the numerical correlations of seismic vulnerability obtained by two statistical methods based on the "log-normal distribution" and "logistics distribution", and finally, the parameters of displacement and drift were assessed after analysis.

  1. Ruby-Helix: an implementation of helical image processing based on object-oriented scripting language.

    Science.gov (United States)

    Metlagel, Zoltan; Kikkawa, Yayoi S; Kikkawa, Masahide

    2007-01-01

    Helical image analysis in combination with electron microscopy has been used to study three-dimensional structures of various biological filaments or tubes, such as microtubules, actin filaments, and bacterial flagella. A number of packages have been developed to carry out helical image analysis. Some biological specimens, however, have a symmetry break (seam) in their three-dimensional structure, even though their subunits are mostly arranged in a helical manner. We refer to these objects as "asymmetric helices". All the existing packages are designed for helically symmetric specimens, and do not allow analysis of asymmetric helical objects, such as microtubules with seams. Here, we describe Ruby-Helix, a new set of programs for the analysis of "helical" objects with or without a seam. Ruby-Helix is built on top of the Ruby programming language and is the first implementation of asymmetric helical reconstruction for practical image analysis. It also allows easier and semi-automated analysis, performing iterative unbending and accurate determination of the repeat length. As a result, Ruby-Helix enables us to analyze motor-microtubule complexes with higher throughput to higher resolution.

  2. Turbulent structure and dynamics of swirled, strongly pulsed jet diffusion flames

    KAUST Repository

    Liao, Ying-Hao; Hermanson, James C.

    2013-01-01

    The structure and dynamics of swirled, strongly pulsed, turbulent jet diffusion flames were examined experimentally in a co-flow swirl combustor. The dynamics of the large-scale flame structures, including variations in flame dimensions, the degree

  3. Structure from Dynamics: Vibrational Dynamics of Interfacial Water as a Probe of Aqueous Heterogeneity

    Science.gov (United States)

    2018-01-01

    The structural heterogeneity of water at various interfaces can be revealed by time-resolved sum-frequency generation spectroscopy. The vibrational dynamics of the O–H stretch vibration of interfacial water can reflect structural variations. Specifically, the vibrational lifetime is typically found to increase with increasing frequency of the O–H stretch vibration, which can report on the hydrogen-bonding heterogeneity of water. We compare and contrast vibrational dynamics of water in contact with various surfaces, including vapor, biomolecules, and solid interfaces. The results reveal that variations in the vibrational lifetime with vibrational frequency are very typical, and can frequently be accounted for by the bulk-like heterogeneous response of interfacial water. Specific interfaces exist, however, for which the behavior is less straightforward. These insights into the heterogeneity of interfacial water thus obtained contribute to a better understanding of complex phenomena taking place at aqueous interfaces, such as photocatalytic reactions and protein folding. PMID:29490138

  4. Dynamical spin structure factors of α-RuCl3

    Science.gov (United States)

    Suzuki, Takafumi; Suga, Sei-ichiro

    2018-03-01

    Honeycomb-lattice magnet α-RuCl3 is considered to be a potential candidate of realizing Kitaev spin liquid, although this material undergoes a phase transition to the zigzag magnetically ordered state at T N ∼ 7 K. Quite recently, inelastic neutron-scattering experiments using single crystal α-RuCl3 have unveiled characteristic dynamical properties. We calculate dynamical spin structure factors of three ab-initio models for α-RuCl3 with an exact numerical diagonalization method. We also calculate temperature dependences of the specific heat by employing thermal pure quantum states. We compare our numerical results with the experiments and discuss characteristics obtained by using three ab-initio models.

  5. Stage-Structured Population Dynamics of AEDES AEGYPTI

    Science.gov (United States)

    Yusoff, Nuraini; Budin, Harun; Ismail, Salemah

    Aedes aegypti is the main vector in the transmission of dengue fever, a vector-borne disease affecting world population living in tropical and sub-tropical countries. Better understanding of the dynamics of its population growth will help in the efforts of controlling the spread of this disease. In looking at the population dynamics of Aedes aegypti, this paper explored the stage-structured modeling of the population growth of the mosquito using the matrix population model. The life cycle of the mosquito was divided into five stages: eggs, larvae, pupae, adult1 and adult2. Developmental rates were obtained for the average Malaysian temperature and these were used in constructing the transition matrix for the matrix model. The model, which was based only on temperature, projected that the population of Aedes aegypti will blow up with time, which is not realistic. For further work, other factors need to be taken into account to obtain a more realistic result.

  6. Structural Influence on Excited State Dynamics in Simple Amines

    DEFF Research Database (Denmark)

    Klein, Liv Bærenholdt

    experiments with calculations, provides new insight into the nature of the internal conversion processes that mediate the dynamical evolution between Rydberg states, and how structural variations in simple amine system have a large impact on the non-adiabatic processes. The experimental method of choice...... is femtosecond time-resolved photoelectron velocity map imaging (VMI), which is a newtechnique in the Copenhagen lab. The design, building and implementation of the VMI spectrometer has been a very substantial part of the thesis work. This techniques oers enhanced information content in the form of ecient...... and sensitive collection of photoelectron spectra. In particular, the angleresolved data available from the VMI approach provides highly detailed mechanistic insight about the relaxation pathways. One striking novel nding is that for tertiary amines, the critical factor driving the non-adiabatic dynamics...

  7. Neutrons probing the structure and dynamics of liquids

    International Nuclear Information System (INIS)

    Leclercq-Hugeux, F.; Coulet, M.V.; Gaspard, J.P.; Pouget, St.; Zanotti, J.M.

    2007-01-01

    This article illustrates the benefits of neutron techniques to the understanding of the liquid state. As opposed to the nearly complete order of crystals or the nearly complete disorder of gas, the disorder of a liquid is partial and results from dynamical events acting on a broad range of space and time scales. Consequently, no single, simple parameter can encompass the concept of order or disorder in the liquid state. The wide variety of neutron techniques (diffraction, quasi-elastic and inelastic scattering) is a key asset to solve the issue. Selected studies ranging over typical interactions and conditions relevant to liquids (metallic, covalent, molecular, liquids near a phase transition and confined fluids) are presented. In each case, both structural and dynamical aspects, along with the connections to complementary techniques (computer simulation, X-ray absorption and/or scattering) are highlighted. (authors)

  8. Poisson structure of dynamical systems with three degrees of freedom

    Science.gov (United States)

    Gümral, Hasan; Nutku, Yavuz

    1993-12-01

    It is shown that the Poisson structure of dynamical systems with three degrees of freedom can be defined in terms of an integrable one-form in three dimensions. Advantage is taken of this fact and the theory of foliations is used in discussing the geometrical structure underlying complete and partial integrability. Techniques for finding Poisson structures are presented and applied to various examples such as the Halphen system which has been studied as the two-monopole problem by Atiyah and Hitchin. It is shown that the Halphen system can be formulated in terms of a flat SL(2,R)-valued connection and belongs to a nontrivial Godbillon-Vey class. On the other hand, for the Euler top and a special case of three-species Lotka-Volterra equations which are contained in the Halphen system as limiting cases, this structure degenerates into the form of globally integrable bi-Hamiltonian structures. The globally integrable bi-Hamiltonian case is a linear and the SL(2,R) structure is a quadratic unfolding of an integrable one-form in 3+1 dimensions. It is shown that the existence of a vector field compatible with the flow is a powerful tool in the investigation of Poisson structure and some new techniques for incorporating arbitrary constants into the Poisson one-form are presented herein. This leads to some extensions, analogous to q extensions, of Poisson structure. The Kermack-McKendrick model and some of its generalizations describing the spread of epidemics, as well as the integrable cases of the Lorenz, Lotka-Volterra, May-Leonard, and Maxwell-Bloch systems admit globally integrable bi-Hamiltonian structure.

  9. Portrait of a discovery. Watson, Crick, and the double helix.

    Science.gov (United States)

    de Chadarevian, Soraya

    2003-03-01

    This essay examines an iconic image of twentieth-century science: Antony Barrington Brown's photograph of James Watson, Francis Crick, and the double-helical model of DNA. The detailed reconstruction of the production, reception, and uses of the photograph reveals the central role of the image in making the discovery it portrays. Taken in May 1953, two full months after the scientists built the model, to accompany a report on the structure in Time magazine, the photograph (like the report) was never published. It came into circulation only fifteen years later, as an illustration in Watson's best-selling book The Double Helix. While the image served as a historical document and advertisement for the book, only the book provided the description that made the image as well as the people and the model it represented famous. The history of the image provides insights into the retrospective construction of the discovery, which has since been celebrated as the origin of a new science of life.

  10. Electronic structure and molecular dynamics of Na2Li

    Science.gov (United States)

    Malcolm, Nathaniel O. J.; McDouall, Joseph J. W.

    Following the first report (Mile, B., Sillman, P. D., Yacob, A. R. and Howard, J. A., 1996, J. chem. Soc. Dalton Trans , 653) of the EPR spectrum of the mixed alkali-metal trimer Na2Li a detailed study has been made of the electronic structure and structural dynamics of this species. Two isomeric forms have been found: one of the type, Na-Li-Na, of C , symmetry and another, Li-Na-Na, of C symmetry. Also, there are two linear saddle points which correspond to 'inversion' transition structures, and a saddle point of C symmetry which connects the two minima. A molecular dynamics investigation of these species shows that, at the temperature of the reported experiments (170 K), the C minimum is not 'static', but undergoes quite rapid inversion. At higher temperatures the C minimum converts to the C form, but by a mechanism very different from that suggested by minimum energy path considerations. 2 2v s s 2v 2v s

  11. The Response of Simple Polymer Structures Under Dynamic Loading

    Science.gov (United States)

    Proud, William; Ellison, Kay; Yapp, Su; Cole, Cloe; Galimberti, Stefano; Institute of Shock Physics Team

    2017-06-01

    The dynamic response of polymeric materials has been widely studied with the effects of degree of crystallinity, strain rate, temperature and sample size being commonly reported. This study uses a simple PMMA structure, a right cylindrical sample, with structural features such as holes. The features are added an varied in a systematic fashion. Samples were dynamically loaded using a Split Hopkinson Pressure Bar up to failure. The resulting stress-strain curves are presented showing the change in sample response. The strain to failure is shown to increase initially with the presence of holes, while failure stress is relatively unaffected. The fracture patterns seen in the failed samples change, with tensile cracks, Hertzian cones, shear effects being dominant for different holes sizes and geometries. The sample were prepared by laser cutting and checked for residual stress before experiment. The data is used to validate predictive model predictions where material, structure and damage are included.. The Institute of Shock Physics acknowledges the support of Imperial College London and the Atomic Weapons Establishment.

  12. A Comparative Study on Optimal Structural Dynamics Using Wavelet Functions

    Directory of Open Access Journals (Sweden)

    Seyed Hossein Mahdavi

    2015-01-01

    Full Text Available Wavelet solution techniques have become the focus of interest among researchers in different disciplines of science and technology. In this paper, implementation of two different wavelet basis functions has been comparatively considered for dynamic analysis of structures. For this aim, computational technique is developed by using free scale of simple Haar wavelet, initially. Later, complex and continuous Chebyshev wavelet basis functions are presented to improve the time history analysis of structures. Free-scaled Chebyshev coefficient matrix and operation of integration are derived to directly approximate displacements of the corresponding system. In addition, stability of responses has been investigated for the proposed algorithm of discrete Haar wavelet compared against continuous Chebyshev wavelet. To demonstrate the validity of the wavelet-based algorithms, aforesaid schemes have been extended to the linear and nonlinear structural dynamics. The effectiveness of free-scaled Chebyshev wavelet has been compared with simple Haar wavelet and two common integration methods. It is deduced that either indirect method proposed for discrete Haar wavelet or direct approach for continuous Chebyshev wavelet is unconditionally stable. Finally, it is concluded that numerical solution is highly benefited by the least computation time involved and high accuracy of response, particularly using low scale of complex Chebyshev wavelet.

  13. Evolutionary game dynamics in a growing structured population

    Energy Technology Data Exchange (ETDEWEB)

    Poncela, Julia; Gomez-Gardenes, Jesus; Moreno, Yamir [Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, E-50009 Zaragoza (Spain); Traulsen, Arne [Emmy-Noether Group for Evolutionary Dynamics, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24306 Ploen (Germany)], E-mail: traulsen@evolbio.mpg.de

    2009-08-15

    We discuss a model for evolutionary game dynamics in a growing, network-structured population. In our model, new players can either make connections to random preexisting players or preferentially attach to those that have been successful in the past. The latter depends on the dynamics of strategies in the game, which we implement following the so-called Fermi rule such that the limits of weak and strong strategy selection can be explored. Our framework allows to address general evolutionary games. With only two parameters describing the preferential attachment and the intensity of selection, we describe a wide range of network structures and evolutionary scenarios. Our results show that even for moderate payoff preferential attachment, over represented hubs arise. Interestingly, we find that while the networks are growing, high levels of cooperation are attained, but the same network structure does not promote cooperation as a static network. Therefore, the mechanism of payoff preferential attachment is different to those usually invoked to explain the promotion of cooperation in static, already-grown networks.

  14. Evolutionary game dynamics in a growing structured population

    International Nuclear Information System (INIS)

    Poncela, Julia; Gomez-Gardenes, Jesus; Moreno, Yamir; Traulsen, Arne

    2009-01-01

    We discuss a model for evolutionary game dynamics in a growing, network-structured population. In our model, new players can either make connections to random preexisting players or preferentially attach to those that have been successful in the past. The latter depends on the dynamics of strategies in the game, which we implement following the so-called Fermi rule such that the limits of weak and strong strategy selection can be explored. Our framework allows to address general evolutionary games. With only two parameters describing the preferential attachment and the intensity of selection, we describe a wide range of network structures and evolutionary scenarios. Our results show that even for moderate payoff preferential attachment, over represented hubs arise. Interestingly, we find that while the networks are growing, high levels of cooperation are attained, but the same network structure does not promote cooperation as a static network. Therefore, the mechanism of payoff preferential attachment is different to those usually invoked to explain the promotion of cooperation in static, already-grown networks.

  15. Efficient placement of structural dynamics sensors on the space station

    Science.gov (United States)

    Lepanto, Janet A.; Shepard, G. Dudley

    1987-01-01

    System identification of the space station dynamic model will require flight data from a finite number of judiciously placed sensors on it. The placement of structural dynamics sensors on the space station is a particularly challenging problem because the station will not be deployed in a single mission. Given that the build-up sequence and the final configuration for the space station are currently undetermined, a procedure for sensor placement was developed using the assembly flights 1 to 7 of the rephased dual keel space station as an example. The procedure presented approaches the problem of placing the sensors from an engineering, as opposed to a mathematical, point of view. In addition to locating a finite number of sensors, the procedure addresses the issues of unobserved structural modes, dominant structural modes, and the trade-offs involved in sensor placement for space station. This procedure for sensor placement will be applied to revised, and potentially more detailed, finite element models of the space station configuration and assembly sequence.

  16. Modeling structured population dynamics using data from unmarked individuals

    Science.gov (United States)

    Grant, Evan H. Campbell; Zipkin, Elise; Thorson, James T.; See, Kevin; Lynch, Heather J.; Kanno, Yoichiro; Chandler, Richard; Letcher, Benjamin H.; Royle, J. Andrew

    2014-01-01

    The study of population dynamics requires unbiased, precise estimates of abundance and vital rates that account for the demographic structure inherent in all wildlife and plant populations. Traditionally, these estimates have only been available through approaches that rely on intensive mark–recapture data. We extended recently developed N-mixture models to demonstrate how demographic parameters and abundance can be estimated for structured populations using only stage-structured count data. Our modeling framework can be used to make reliable inferences on abundance as well as recruitment, immigration, stage-specific survival, and detection rates during sampling. We present a range of simulations to illustrate the data requirements, including the number of years and locations necessary for accurate and precise parameter estimates. We apply our modeling framework to a population of northern dusky salamanders (Desmognathus fuscus) in the mid-Atlantic region (USA) and find that the population is unexpectedly declining. Our approach represents a valuable advance in the estimation of population dynamics using multistate data from unmarked individuals and should additionally be useful in the development of integrated models that combine data from intensive (e.g., mark–recapture) and extensive (e.g., counts) data sources.

  17. Improving the Dynamic Characteristics of Body-in-White Structure Using Structural Optimization

    Directory of Open Access Journals (Sweden)

    Aizzat S. Yahaya Rashid

    2014-01-01

    Full Text Available The dynamic behavior of a body-in-white (BIW structure has significant influence on the noise, vibration, and harshness (NVH and crashworthiness of a car. Therefore, by improving the dynamic characteristics of BIW, problems and failures associated with resonance and fatigue can be prevented. The design objectives attempt to improve the existing torsion and bending modes by using structural optimization subjected to dynamic load without compromising other factors such as mass and stiffness of the structure. The natural frequency of the design was modified by identifying and reinforcing the structure at critical locations. These crucial points are first identified by topology optimization using mass and natural frequencies as the design variables. The individual components obtained from the analysis go through a size optimization step to find their target thickness of the structure. The thickness of affected regions of the components will be modified according to the analysis. The results of both optimization steps suggest several design modifications to achieve the target vibration specifications without compromising the stiffness of the structure. A method of combining both optimization approaches is proposed to improve the design modification process.

  18. Structure and Dynamics of Polymer/Polymer grafted nanoparticle composite

    Science.gov (United States)

    Archer, Lynden

    Addition of nanoparticles to polymers is a well-practiced methodology for augmenting various properties of the polymer host, including mechanical strength, thermal stability, barrier properties, dimensional stability and wear resistance. Many of these property changes are known to arise from nanoparticle-induced modification of polymer structure and chain dynamics, which are strong functions of the dispersion state of the nanoparticles' and on their relative size (D) to polymer chain dimensions (e.g. Random coil radius Rg or entanglement mesh size a) . This talk will discuss polymer nanocomposites (PNCs) comprised of Polyethylene Glycol (PEG) tethered silica nanoparticles (SiO2-PEG) dispersed in polymers as model systems for investigating phase stability and dynamics of PNCs. On the basis of small-angle X-ray Scattering, it will be shown that favorable enthalpic interactions between particle-tethered chains and a polymer host provides an important mechanism for creating PNCs in which particle aggregation is avoided. The talk will report on polymer and particle scale dynamics in these materials and will show that grafted nanoparticles well dispersed in a polymer host strongly influence the host polymer relaxation dynamics on all timescales and the polymers in turn produce dramatic changes in the nature (from diffusive to hyperdiffusive) and speed of nano particle decorrelation dynamics at the polymer entanglement threshold. A local viscosity model capable of explaining these observations is discussed and the results compared with scaling theories for NP motions in polymers This material is based on work supported by the National Science Foundation Award Nos. DMR-1609125 and CBET-1512297.

  19. Changes in the reproductive system of the snail Helix aspersa caused by mucus from the love dart

    NARCIS (Netherlands)

    Koene, J M; Chase, R.

    The function of the love dart in certain species of terrestrial snails is unknown. In Helix aspersa, the dart is a sharp calcareous structure that is used to pierce the partner's skin during courtship. When expelled, the dart is covered with a thick mucus. The hypothesis tested here is that the

  20. Peptide-oligonucleotide conjugates as nanoscale building blocks for assembly of an artificial three-helix protein mimic

    DEFF Research Database (Denmark)

    Lou, Chenguang; Martos-Maldonado, Manuel C.; Madsen, Charlotte Stahl

    2016-01-01

    Peptide-based structures can be designed to yield artificial proteins with specific folding patterns and functions. Template-based assembly of peptide units is one design option, but the use of two orthogonal self-assembly principles, oligonucleotide triple helix and a coiled coil protein domain ...

  1. Kinetic and structural fragility—a correlation between structures and dynamics in metallic liquids and glasses

    International Nuclear Information System (INIS)

    Kelton, K F

    2017-01-01

    The liquid phase remains poorly understood. In many cases, the densities of liquids and their crystallized solid phases are similar, but since they are amorphous they lack the spatial order of the solid. Their dynamical properties change remarkably over a very small temperature range. At high temperatures, near their melting temperature, liquids flow easily under shear. However, only a few hundred degrees lower flow effectively ceases, as the liquid transforms into a solid-like glass. This temperature-dependent dynamical behavior is frequently characterized by the concept of kinetic fragility (or, generally, simply fragility). Fragility is believed to be an important quantity in glass formation, making it of significant practical interest. The microscopic origin of fragility remains unclear, however, making it also of fundamental interest. It is widely (although not uniformly) believed that the dynamical behavior is linked to the atomic structure of the liquid, yet experimental studies show that although the viscosity changes by orders of magnitude with temperature, the structural change is barely perceptible. In this article the concept of fragility is discussed, building to a discussion of recent results in metallic glass-forming liquids that demonstrate the presumed connection between structural and dynamical changes. In particular, it becomes possible to define a structural fragility parameter that can be linked with the kinetic fragility. (topical review)

  2. The effect of S-substitution at the O6-guanine site on the structure and dynamics of a DNA oligomer containing a G:T mismatch.

    Directory of Open Access Journals (Sweden)

    Elaine Ann Moore

    Full Text Available The effect of S-substitution on the O6 guanine site of a 13-mer DNA duplex containing a G:T mismatch is studied using molecular dynamics. The structure, dynamic evolution and hydration of the S-substituted duplex are compared with those of a normal duplex, a duplex with S-substitution on guanine, but no mismatch and a duplex with just a G:T mismatch. The S-substituted mismatch leads to cell death rather than repair. One suggestion is that the G:T mismatch recognition protein recognises the S-substituted mismatch (GS:T as G:T. This leads to a cycle of futile repair ending in DNA breakage and cell death. We find that some structural features of the helix are similar for the duplex with the G:T mismatch and that with the S-substituted mismatch, but differ from the normal duplex, notably the helical twist. These differences arise from the change in the hydrogen-bonding pattern of the base pair. However a marked feature of the S-substituted G:T mismatch duplex is a very large opening. This showed considerable variability. It is suggested that this enlarged opening would lend support to an alternative model of cell death in which the mismatch protein attaches to thioguanine and activates downstream damage-response pathways. Attack on the sulphur by reactive oxygen species, also leading to cell death, would also be aided by the large, variable opening.

  3. Performance of dynamic safety barriers-Structuring, modelling and visualization

    OpenAIRE

    Wikdahl, Olga

    2014-01-01

    The main objective of this master thesis is to discuss performance of dynamic safety barriers. A comprehensive literature review is performed in order to get understanding what dynamic safety barrier is. Three different concepts of dynamic safety barriers based on various meanings of dynamic were derived from the literature review: - dynamic safety barriers related to motion or physical force - dynamic safety barriers as updated barriers from dynamic risk analysis - dynamic safety ...

  4. Phase Structure and Dynamics of QCD–A Functional Perspective

    International Nuclear Information System (INIS)

    Strodthoff, Nils

    2017-01-01

    The understanding of the phase structure and the fundamental properties of QCD matter from its microscopic description requires appropriate first-principle approaches. Here I review the progress towards a quantitative first-principle continuum approach within the framework of the Functional Renormalization group established by the fQCD collaboration. I focus on recent quantitative results for quenched QCD and Yang-Mills in the vacuum before addressing the calculation of dynamical quantities such as spectral functions and transport coefficients in this framework. (paper)

  5. Dynamic analysis of clustered building structures using substructures methods

    International Nuclear Information System (INIS)

    Leimbach, K.R.; Krutzik, N.J.

    1989-01-01

    The dynamic substructure approach to the building cluster on a common base mat starts with the generation of Ritz-vectors for each building on a rigid foundation. The base mat plus the foundation soil is subjected to kinematic constraint modes, for example constant, linear, quadratic or cubic constraints. These constraint modes are also imposed on the buildings. By enforcing kinematic compatibility of the complete structural system on the basis of the constraint modes a reduced Ritz model of the complete cluster is obtained. This reduced model can now be analyzed by modal time history or response spectrum methods

  6. Structure and Dynamics of Interfaces: Drops and Films

    Science.gov (United States)

    Mann, J. Adin, Jr.; Mann, Elizabeth K.; Meyer, William V.; Neumann, A. Wilhelm; Tavana, Hossein

    2015-01-01

    We aim to acquire measurements of the structure and dynamics of certain liquid-fluid interfaces using an ensemble of techniques in collaboration: (1) Total internal reflection (TIR) Surface light scattering spectroscopy (SLSS), (2) Brewster angle microscopy (BAM), and (3) Drop-shape analysis. SLSS and BAM can be done on a shared interfacial footprint. Results using a 50-50 mixture of pentane-isohexane, which extends the range of NASA's Confined Vapor Bubble (CVB) experiment, yield surface tension results that differ from the expected Langmuir Fit. These results were confirmed using both the SLSS and drop-shape analysis approaches.

  7. Dependence of ICF reaction dynamics on target structure

    International Nuclear Information System (INIS)

    Kumar, Kamal; Dutt, Sunil; GulI, Muntazir; Ahmad, Tauseef; Rizvi, I.A.; Ali, Sabir; Agarwal, Avinash; Kumar, R.; Chaubey, A.K.

    2016-01-01

    The projectile structure is also found responsible for the ICF reaction processes. It is found that projectile having bigger alpha cluster is more unstable towards break up. In this context, a comparative study of 12 C and 16 O ion-beams induced reactions with different targets has been done. The deduced ICF contributions for different systems have been plotted against the target charge of different targets. It is observed that target properties may also be responsible for the interplay between CF and ICF reaction dynamics

  8. Dynamical quadrupole structure factor of frustrated ferromagnetic chain

    Science.gov (United States)

    Onishi, Hiroaki

    2018-05-01

    We investigate the dynamical quadrupole structure factor of a spin-1/2 J1-J2 Heisenberg chain with competing ferromagnetic J1 and antiferromagnetic J2 in a magnetic field by exploiting density-matrix renormalization group techniques. In a field-induced spin nematic regime, we observe gapless excitations at q = π according to quasi-long-range antiferro-quadrupole correlations. The gapless excitation mode has a quadratic form at the saturation, while it changes into a linear dispersion as the magnetization decreases.

  9. Dynamic structurization in solutions of hydrodynamically active polymers

    International Nuclear Information System (INIS)

    Pogrebnyak, V.G.; Tverdokhleb, S.V.; Naumchuk, N.V.

    1993-01-01

    The processes of ordering and self-regulation in nonlinear systems have attracted great attention because understanding the principles of self-regulation and its thermodynamics can become a clue to many physical phenomena. In this work, it is experimentally established that, under the condition of elongational flows, dynamic structurization and periodic processes may originate in the solutions of flexible, hydrodynamically-active polymers due to self-regulation in these systems. The hydrodynamic elongational field was created using the flow of a Newtonian liquid (water, acetone, dioxane) converging to a small opening. The hydrodynamically-active polymers were polyethylene oxide or hydrolyzed polyacrylamide

  10. Structural and dynamical characterization of the Miz-1 zinc fingers 5-8 by solution-state NMR

    Energy Technology Data Exchange (ETDEWEB)

    Bernard, David; Bedard, Mikaeel; Bilodeau, Josee; Lavigne, Pierre, E-mail: pierre.lavigne@usherbrooke.ca [Universite de Sherbrooke, Departement de Biochimie, Faculte de Medecine et des Sciences de la Sante, Institut de Pharmacologie de Sherbrooke (Canada)

    2013-10-15

    Myc-interacting zinc finger protein-1 (Miz-1) is a BTB/POZ transcription factor that activates the transcription of cytostatic genes, such as p15{sup INK4B} or p21{sup CIP1}. The C-terminus of Miz-1 contains 13 consensus C{sub 2}H{sub 2} zinc finger domains (ZF). ZFs 1-4 have been shown to interact with SMAD3/4, while the remaining ZFs are expected to bind the promoters of target genes. We have noted unusual features in ZF 5 and the linker between ZFs 5 and 6. Indeed, a glutamate is found instead of the conserved basic residue two positions before the second zinc-coordinating histidine on the ZF 5 helix, and the linker sequence is DTDKE in place of the classical TGEKP sequence. In a canonical {beta}{beta}{alpha} fold, such unusual primary structure elements should cause severe electrostatic repulsions. In this context, we have characterized the structure and the dynamics of a Miz-1 construct comprising ZFs 5-8 (Miz 5-8) by solution-state NMR. Whilst ZFs 5, 7 and 8 were shown to adopt the classical {beta}{beta}{alpha} fold for C{sub 2}H{sub 2} ZFs, the number of long-range NOEs was insufficient to define a classical fold for ZF 6. We show by using {sup 15}N-relaxation dispersion experiments that this lack of NOEs is due to the presence of extensive motions on the {mu}s-ms timescale. Since this negatively charged region would have to be located near the phosphodiester backbone in a DNA complex, we propose that in addition to promoting conformational searches, it could serve as a hinge region to keep ZFs 1-4 away from DNA.

  11. Structure and Dynamics of the Liver Receptor Homolog 1–PGC1 α Complex

    Energy Technology Data Exchange (ETDEWEB)

    Mays, Suzanne G.; Okafor, C. Denise; Tuntland, Micheal L.; Whitby, Richard J.; Dharmarajan, Venkatasubramanian; Stec, Józef; Griffin, Patrick R.; Ortlund, Eric A.

    2017-03-31

    Peroxisome proliferator-activated gamma coactivator 1-α (PGC1α) regulates energy metabolism by directly interacting with transcription factors to modulate gene expression. Among the PGC1α binding partners is liver receptor homolog 1 (LRH-1; NR5A2), an orphan nuclear hormone receptor that controls lipid and glucose homeostasis. Although PGC1α is known to bind and activate LRH-1, mechanisms through which PGC1α changes LRH-1 conformation to drive transcription are unknown. Here, we used biochemical and structural methods to interrogate the LRH-1–PGC1α complex. Purified, full-length LRH-1, as well as isolated ligand binding domain, bound to PGC1α with higher affinity than to the coactivator, nuclear receptor coactivator-2 (Tif2), in coregulator peptide recruitment assays. We present the first crystal structure of the LRH-1–PGC1α complex, which depicts several hydrophobic contacts and a strong charge clamp at the interface between these partners. In molecular dynamics simulations, PGC1α induced correlated atomic motion throughout the entire LRH-1 activation function surface, which was dependent on charge-clamp formation. In contrast, Tif2 induced weaker signaling at the activation function surface than PGC1α but promoted allosteric signaling from the helix 6/β-sheet region of LRH-1 to the activation function surface. These studies are the first to probe mechanisms underlying the LRH-1–PGC1α interaction and may illuminate strategies for selective therapeutic targeting of PGC1α-dependent LRH-1 signaling pathways.

  12. 1D helix, 2D brick-wall and herringbone, and 3D interpenetration d10 metal-organic framework structures assembled from pyridine-2,6-dicarboxylic acid N-oxide.

    Science.gov (United States)

    Wen, Li-Li; Dang, Dong-Bin; Duan, Chun-Ying; Li, Yi-Zhi; Tian, Zheng-Fang; Meng, Qing-Jin

    2005-10-03

    Five novel interesting d(10) metal coordination polymers, [Zn(PDCO)(H2O)2]n (PDCO = pyridine-2,6-dicarboxylic acid N-oxide) (1), [Zn2(PDCO)2(4,4'-bpy)2(H2O)2.3H2O]n (bpy = bipyridine) (2), [Zn(PDCO)(bix)]n (bix = 1,4-bis(imidazol-1-ylmethyl)benzene) (3), [Zn(PDCO)(bbi).0.5H2O]n (bbi = 1,1'-(1,4-butanediyl)bis(imidazole)) (4), and [Cd(PDCO)(bix)(1.5).1.5H2O]n (5), have been synthesized under hydrothermal conditions and structurally characterized. Polymer 1 possesses a one-dimensional (1D) helical chainlike structure with 4(1) helices running along the c-axis with a pitch of 10.090 Angstroms. Polymer 2 has an infinite chiral two-dimensional (2D) brick-wall-like layer structure in the ac plane built from achiral components, while both 3 and 4 exhibit an infinite 2D herringbone architecture, respectively extended in the ac and ab plane. Polymer 5 features a most remarkable and unique three-dimensional (3D) porous framework with 2-fold interpenetration related by symmetry, which contains channels in the b and c directions, both distributed in a rectangular grid fashion. Compounds 1-5, with systematic variation in dimensionality from 1D to 2D to 3D, are the first examples of d(10) metal coordination polymers into which pyridinedicarboxylic acid N-oxide has been introduced. In addition, polymers 1, 4, and 5 display strong blue fluorescent emissions in the solid state. Polymer 3 exhibits a strong SHG response, estimated to be approximately 0.9 times that of urea.

  13. Dynamical measurements of the interior structure of exoplanets

    International Nuclear Information System (INIS)

    Becker, Juliette C.; Batygin, Konstantin

    2013-01-01

    Giant gaseous planets often reside on orbits in sufficient proximity to their host stars for the planetary quadrupole gravitational field to become non-negligible. In presence of an additional planetary companion, a precise characterization of the system's orbital state can yield meaningful constraints on the transiting planet's interior structure. However, such methods can require a very specific type of system. This paper explores the dynamic range of applicability of these methods and shows that interior structure calculations are possible for a wide array of orbital architectures. The HAT-P-13 system is used as a case study, and the implications of perturbations arising from a third distant companion on the feasibility of an interior calculation are discussed. We find that the method discussed here is likely to be useful in studying other planetary systems, allowing the possibility of an expanded survey of the interiors of exoplanets.

  14. Proton structure functions in the dipole picture of BFKL dynamics

    International Nuclear Information System (INIS)

    Navelet, H.; Wallon, S.

    1996-06-01

    The F 2 , F G , R=F L /F T proton structure functions are derived in the QCD dipole picture. Assuming k T and renormalization-group factorization, we relate deep-inelastic proton scattering to deep-inelastic onium scattering. We get a three-parameter fit of the 1994 H1 data in the low-x, moderate Q 2 range. The ratios F G /F 2 and R are predicted without further adjustment. The dipole picture of BFKL dynamics is shown to provide a relevant model for quantitatively describing the proton structure functions at HERA. The predictions for F 2 and F G are compatible with next-to-leading DGLAP analysis, while R is expected to be significantly lower at very small x. (orig.)

  15. Structural and dynamic properties of solid state ionics

    International Nuclear Information System (INIS)

    Sakuma, T.

    1995-01-01

    The structural and dynamic properties of solid state ionics are reviewed. The low temperature phase transition of the copper halide-chalcogen compounds by specific heat measurements, electrical conductivity measurements and x-ray diffraction measurements are explained. The structures of solid state ionics investigated by the usual x-ray diffraction method and the anomalous x-ray scattering (AXS) measurement are discussed. The expression of the diffuse scattering intensity including the correlations among the thermal displacements of atoms has been given and applied to α-AgI type solid state ionics and lithium sulphate. The presence of low-energy excitations in crystalline copper ion conductors and the superionic conducting glass is investigated by neutron inelastic scattering measurements. The relation between the excitation energy and the mass of the cations is discussed. (author). 141 refs., 21 figs., 7 tabs

  16. Parallel processors and nonlinear structural dynamics algorithms and software

    Science.gov (United States)

    Belytschko, Ted

    1989-01-01

    A nonlinear structural dynamics finite element program was developed to run on a shared memory multiprocessor with pipeline processors. The program, WHAMS, was used as a framework for this work. The program employs explicit time integration and has the capability to handle both the nonlinear material behavior and large displacement response of 3-D structures. The elasto-plastic material model uses an isotropic strain hardening law which is input as a piecewise linear function. Geometric nonlinearities are handled by a corotational formulation in which a coordinate system is embedded at the integration point of each element. Currently, the program has an element library consisting of a beam element based on Euler-Bernoulli theory and trianglar and quadrilateral plate element based on Mindlin theory.

  17. Global structure of exact scalar hairy dynamical black holes

    Energy Technology Data Exchange (ETDEWEB)

    Fan, Zhong-Ying [Center for High Energy Physics, Peking University,No. 5 Yiheyuan Rd, Beijing, 100871 P.R. (China); Chen, Bin [Center for High Energy Physics, Peking University,No. 5 Yiheyuan Rd, Beijing, 100871 P.R. (China); Department of Physics and State Key Laboratory of Nuclear Physics and Technology,Peking University, No. 5 Yiheyuan Rd, Beijing, 100871 P.R. (China); Collaborative Innovation Center of Quantum Matter,No. 5 Yiheyuan Rd, Beijing, 100871 P.R. (China); Lü, H. [Center for Advanced Quantum Studies, Department of Physics, Beijing Normal University,Beijing, 100875 P.R. (China)

    2016-05-30

    We study the global structure of some exact scalar hairy dynamical black holes which were constructed in Einstein gravity either minimally or non-minimally coupled to a scalar field. We find that both the apparent horizon and the local event horizon (measured in luminosity coordinate) monotonically increase with the advanced time as well as the Vaidya mass. At late advanced times, the apparent horizon approaches the event horizon and gradually becomes future outer. Correspondingly, the space-time arrives at stationary black hole states with the relaxation time inversely proportional to the 1/(n−1) power of the final black hole mass, where n is the space-time dimension. These results strongly support the solutions describing the formation of black holes with scalar hair. We also obtain new charged dynamical solutions in the non-minimal theory by introducing an Maxwell field which is non-minimally coupled to the scalar. The presence of the electric charge strongly modifies the dynamical evolution of the space-time.

  18. Electrostatic cloaking of surface structure for dynamic wetting

    Science.gov (United States)

    Shiomi, Junichiro; Nita, Satoshi; Do-Quang, Minh; Wang, Jiayu; Chen, Yu-Chung; Suzuki, Yuji; Amberg, Gustav

    2017-11-01

    Dynamic wetting problems are fundamental to the understanding of the interaction between liquids and solids. Even in a superficially simple experimental situation, such as a droplet spreading over a dry surface, the result may depend not only on the liquid properties but also strongly on the substrate-surface properties; even for macroscopically smooth surfaces, the microscopic geometrical roughness can be important. In addition, as surfaces may often be naturally charged, or electric fields are used to manipulate fluids, electric effects are crucial components that influence wetting phenomena. Here we investigate the interplay between electric forces and surface structures in dynamic wetting. While surface microstructures can significantly hinder the spreading, we find that the electrostatics can ``cloak'' the microstructures, i.e. deactivate the hindering. We identify the physics in terms of reduction in contact-line friction, which makes the dynamic wetting inertial force dominant and insensitive to the substrate properties. This work was financially supported in part by, the Japan Society for the Promotion of Science, Swedish Governmental Agency for Innovation Systems, and the Japan Science and Technology Agency.

  19. Automatic anatomical structures location based on dynamic shape measurement

    Science.gov (United States)

    Witkowski, Marcin; Rapp, Walter; Sitnik, Robert; Kujawinska, Malgorzata; Vander Sloten, Jos; Haex, Bart; Bogaert, Nico; Heitmann, Kjell

    2005-09-01

    New image processing methods and active photonics apparatus have made possible the development of relatively inexpensive optical systems for complex shape and object measurements. We present dynamic 360° scanning method for analysis of human lower body biomechanics, with an emphasis on the analysis of the knee joint. The anatomical structure (of high medical interest) that is possible to scan and analyze, is patella. Tracking of patella position and orientation under dynamic conditions may lead to detect pathological patella movements and help in knee joint disease diagnosis. The processed data is obtained from a dynamic laser triangulation surface measurement system, able to capture slow to normal movements with a scan frequency between 15 and 30 Hz. These frequency rates are enough to capture controlled movements used e.g. for medical examination purposes. The purpose of the work presented is to develop surface analysis methods that may be used as support of diagnosis of motoric abilities of lower limbs. The paper presents algorithms used to process acquired lower limbs surface data in order to find the position and orientation of patella. The algorithms implemented include input data preparation, curvature description methods, knee region discrimination and patella assumed position/orientation calculation. Additionally, a method of 4D (3D + time) medical data visualization is proposed. Also some exemplary results are presented.

  20. Dynamic multiprotein assemblies shape the spatial structure of cell signaling.

    Science.gov (United States)

    Nussinov, Ruth; Jang, Hyunbum

    2014-01-01

    Cell signaling underlies critical cellular decisions. Coordination, efficiency as well as fail-safe mechanisms are key elements. How the cell ensures that these hallmarks are at play are important questions. Cell signaling is often viewed as taking place through discrete and cross-talking pathways; oftentimes these are modularized to emphasize distinct functions. While simple, convenient and clear, such models largely neglect the spatial structure of cell signaling; they also convey inter-modular (or inter-protein) spatial separation that may not exist. Here our thesis is that cell signaling is shaped by a network of multiprotein assemblies. While pre-organized, the assemblies and network are loose and dynamic. They contain transiently-associated multiprotein complexes which are often mediated by scaffolding proteins. They are also typically anchored in the membrane, and their continuum may span the cell. IQGAP1 scaffolding protein which binds proteins including Raf, calmodulin, Mek, Erk, actin, and tens more, with actin shaping B-cell (and likely other) membrane-anchored nanoclusters and allosterically polymerizing in dynamic cytoskeleton formation, and Raf anchoring in the membrane along with Ras, provides a striking example. The multivalent network of dynamic proteins and lipids, with specific interactions forming and breaking, can be viewed as endowing gel-like properties. Collectively, this reasons that efficient, productive and reliable cell signaling takes place primarily through transient, preorganized and cooperative protein-protein interactions spanning the cell rather than stochastic, diffusion-controlled processes. Copyright © 2014 Elsevier Ltd. All rights reserved.