The effects of bolted joints on dynamic response of structures
Zaman, I.; Khalid, A.; Manshoor, B.; Araby, S.; Ghazali, M. I.
2013-12-01
Joint is an universal fastening technology for structural members; in particular bolted joints are extensively used in mechanical structures due to their simple maintenance and low cost. However, the components of bolted joints are imperative because failure could be catastrophic and endanger lives. Hence, in this study, the effects of bolted joints on vibrating structures are investigated by determining the structural dynamic properties, such as mode shapes, damping ratios and natural frequencies, and these are compared with the monolithic structures (welding). Two approaches of experimental rigs are developed: a beam and a frame where both are subjected to dynamic loading. The analysis reveals the importance of bolted joints in increasing the damping properties and minimizing the vibration magnitude of structures, this indicates the significant influence of bolted joints on the dynamic behaviour of assembled structures. The outcome of this study provides a good model for predicting the experimental variable response in different types of structural joints.
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.
Effects of Dragonfly Wing Structure on the Dynamic Performances
Institute of Scientific and Technical Information of China (English)
Huaihui Ren; Xishu Wang; Xudong Li; Yinglong Chen
2013-01-01
The configurations of dragonfly wings,including the corrugations of the chordwise cross-section,the microstructure of the longitudinal veins and membrane,were comprehensively investigated using the Environmental Scanning Electron Microscopy (ESEM).Based on the experimental results reported previously,the multi-scale and multi-dimensional models with different structural features of dragonfly wing were created,and the biological dynamic behaviors of wing models were discussed through the Finite Element Method (FEM).The results demonstrate that the effects of different structural features on dynamic behaviors of dragonfly wing such as natural frequency/modal,bending/torsional deformation,reaction force/torque are very significant.The corrugations of dragonfly wing along the chordwise can observably improve the flapping frequency because of the greater structural stiffness of wings.In updated model,the novel sandwich microstructure of the longitudinal veins remarkably improves the torsional deformation of dragonfly wing while it has a little effect on the flapping frequency and bending deformation.These integrated structural features can adjust the deformation of wing oneself,therefore the flow field around the wings can be controlled adaptively.The fact is that the flights of dragonfly wing with sandwich microstructure of longitudinal veins are more efficient and intelligent.
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.
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.
Metastable structures and size effects in small group dynamics.
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.
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
Andersen, Christian Walther; Sibani, Paolo
2016-05-01
Based on the stochastic dynamics of interacting agents which reproduce, mutate, and die, the tangled nature model (TNM) describes key emergent features of biological and cultural ecosystems' evolution. While trait inheritance is not included in many applications, i.e., the interactions of an agent and those of its mutated offspring are taken to be uncorrelated, in the family of TNMs introduced in this work correlations of varying strength are parametrized by a positive integer K . We first show that the interactions generated by our rule are nearly independent of K . Consequently, the structural and dynamical effects of trait inheritance can be studied independently of effects related to the form of the interactions. We then show that changing K strengthens the core structure of the ecology, leads to population abundance distributions better approximated by log-normal probability densities, and increases the probability that a species extant at time tw also survives at t >tw . Finally, survival probabilities of species are shown to decay as powers of the ratio t /tw , a so-called pure aging behavior usually seen in glassy systems of physical origin. We find a quantitative dynamical effect of trait inheritance, namely, that increasing the value of K numerically decreases the decay exponent of the species survival probability.
Nonlinear dynamics of structures
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.
Institute of Scientific and Technical Information of China (English)
Xu Long; Fei Ge; Lei Wang; Youshi Hong
2009-01-01
This paper investigates the effects of structure parameters on dynamic responses of submerged floating tunnel (SFT) under hydrodynamic loads. The structure parameters includes buoyancy-weight ratio (BWR), stiffness coefficients of the cable systems, tunnel net buoyancy and tunnel length. First, the importance of structural damp in relation to the dynamic responses of SFT is demonstrated and the mechanism of structural damp effect is discussed. Thereafter, the fundamental structure parameters are investi-gated through the analysis of SFT dynamic responses under hydrodynamic loads. The results indicate that the BWR of SFT is a key structure parameter. When BWR is 1.2, there is a remarkable trend change in the vertical dynamic response of SFT under hydrodynamic loads. The results also indicate that the ratio of the tunnel net buoyancy to the cable stiffness coefficient is not a characteristic factor affecting the dynamic responses of SFT under hydrodynamic loads.
Electromagnetic effects on dynamics of high-beta filamentary structures
Energy Technology Data Exchange (ETDEWEB)
Lee, Wonjae; Krasheninnikov, Sergei I., E-mail: skrash@mae.ucsd.edu [University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093 (United States); Umansky, Maxim V. [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550 (United States); Angus, J. R. [Naval Research Laboratory, 4555 Overlook Avenue, Washington, DC 20375 (United States)
2015-01-15
The impacts of the electromagnetic effects on blob dynamics are considered. Electromagnetic BOUT++ simulations on seeded high-beta blobs demonstrate that inhomogeneity of magnetic curvature or plasma pressure along the filament leads to bending of the blob filaments and the magnetic field lines due to increased propagation time of plasma current (Alfvén time). The bending motion can enhance heat exchange between the plasma facing materials and the inner scrape-off layer (SOL) region. The effects of sheath boundary conditions on the part of the blob away from the boundary are also diminished by the increased Alfvén time. Using linear analysis and BOUT++ simulations, it is found that electromagnetic effects in high temperature and high density plasmas reduce the growth rate of resistive drift wave instability when resistivity drops below a certain value. The blobs temperature decreases in the course of its motion through the SOL and so the blob can switch from the electromagnetic to the electrostatic regime where resistive drift waves become important again.
Effects on dynamic characters of antenna structures in satellite induced by disordered parameters
Institute of Scientific and Technical Information of China (English)
Liu Xiangqiu; Wang Cong; Wang Weiyuan; Zou Zhenzhu
2009-01-01
A simplified dynamic model of a dish antenna in satellite is established in this article. The model can be easily used to analyze the dynamic behaviour of the antenna structure. In terms of the simplified model, effects on dynamic characters due to the disorder of parameters are investigated in details. The frequencies calculated by the simplified model accord with those computed by ANSYS. Based on the mode shapes of disordered and perfect structure, the influence law and varying trend of dynamic characters of antenna structures in satellites produced by stiffness and mass of antenna ribs, stiffness of antenna membranes and angles between adjacent ribs, are obtained. The analyses in the paper indicate that the effects by disordered parameters can not be ignored in the dynamic analysis of such structures.
The effect of pure state structure on nonequilibrium dynamics
Energy Technology Data Exchange (ETDEWEB)
Newman, C M; Stein, D L [Courant Institute of Mathematical Sciences, New York University, New York, NY 10012 (United States)], E-mail: newman@cims.nyu.edu, E-mail: daniel.stein@nyu.edu
2008-06-18
Motivated by short-range Ising spin glasses, we review some rigorous results and their consequences for the relation between the number/nature of equilibrium pure states and nonequilibrium dynamics. Two of the consequences for spin glass dynamics following an instantaneous deep quench to a temperature with broken spin flip symmetry are: (1) almost all initial configurations lie on the boundary between the basins of attraction of multiple pure states; (2) unless there are uncountably many pure states with almost all pairs having zero overlap, there can be no equilibration to a pure state as time t {yields} {infinity}. We discuss the relevance of these results to the difficulty of equilibration of spin glasses. We also review some results concerning the 'nature versus nurture' problem of whether the large-t behavior of both ferromagnets and spin glasses following a deep quench is determined more by the initial configuration (nature) or by the dynamics realization (nurture)
Metastable structures and size effects in small group dynamics
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 s...
Metastable structures and size effects in small group dynamics
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 st...
Fundamentals of structural dynamics
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
The effect of dynamical quark mass on the calculation of a strange quark star's structure
Institute of Scientific and Technical Information of China (English)
Gholam Hossein Bordbar; Babak Ziaei
2012-01-01
We discuss the dynamical behavior of strange quark matter components,in particular the effects of density dependent quark mass on the equation of state of strange quark matter.The dynamical masses of quarks are computed within the Nambu-Jona-Lasinio model,then we perform strange quark matter calculations employing the MIT bag model with these dynamical masses.For the sake of comparing dynamical mass interaction with QCD quark-quark interaction,we consider the one-gluon-exchange term as the effective interaction between quarks for the MIT bag model.Our dynamical approach illustrates an improvement in the obtained equation of state values.We also investigate the structure of the strange quark star using TolmanOppenheimer-Volkoff equations for all applied models.Our results show that dynamical mass interaction leads to lower values for gravitational mass.
Topology of Branched Polymers: Effect on Structure and Dynamic Properties
Ramachandran, Ramnath; Beaucage, Gregory; Kulkarni, Amit S.; Galiatsatos, Vassilios; McFaddin, Douglas C.
2008-03-01
We investigated linear and branched polyethylene (PE) using small-angle neutron scattering (SANS). The experiments were conducted on dilute solutions of PE in deuterated p-xylene. A variety of structural information^ such as fractal dimension (df), connectivity dimension (c), minimum path dimension (dmin), long chain branch fraction (φbr), radius of gyration (Rg) and persistence length (lp) were obtained. Such information presents a qualitative and quantitative assessment of branching in polymers. Theoretical models such as `binary contacts per pervaded volume' model^* were employed to correlate the structural information of the polymer to its entanglement molecular weight (Me). Me was used to predict physical properties of the polymer such as plateau modulus (GN^0 ) and zero-shear viscosity (η0). ^Beaucage G. Physical Review E 70,031401 (2004) ^*Colby et al. Macromolecules 25, p.996 (1992)
A structural dynamic factor model for the effects of monetary policy estimated by the EM algorithm
DEFF Research Database (Denmark)
Bork, Lasse
This paper applies the maximum likelihood based EM algorithm to a large-dimensional factor analysis of US monetary policy. Specifically, economy-wide effects of shocks to the US federal funds rate are estimated in a structural dynamic factor model in which 100+ US macroeconomic and financial time...... series are driven by the joint dynamics of the federal funds rate and a few correlated dynamic factors. This paper contains a number of methodological contributions to the existing literature on data-rich monetary policy analysis. Firstly, the identification scheme allows for correlated factor dynamics...... as opposed to the orthogonal factors resulting from the popular principal component approach to structural factor models. Correlated factors are economically more sensible and important for a richer monetary policy transmission mechanism. Secondly, I consider both static factor loadings as well as dynamic...
A structural dynamic factor model for the effects of monetary policy estimated by the EM algorithm
DEFF Research Database (Denmark)
Bork, Lasse
This paper applies the maximum likelihood based EM algorithm to a large-dimensional factor analysis of US monetary policy. Specifically, economy-wide effects of shocks to the US federal funds rate are estimated in a structural dynamic factor model in which 100+ US macroeconomic and financial time...... series are driven by the joint dynamics of the federal funds rate and a few correlated dynamic factors. This paper contains a number of methodological contributions to the existing literature on data-rich monetary policy analysis. Firstly, the identification scheme allows for correlated factor dynamics...... as opposed to the orthogonal factors resulting from the popular principal component approach to structural factor models. Correlated factors are economically more sensible and important for a richer monetary policy transmission mechanism. Secondly, I consider both static factor loadings as well as dynamic...
An effective pair potential for liquid semiconductor, Se: Structure and related dynamical properties
Indian Academy of Sciences (India)
P P Nath; S Sarkar; R N Joarder
2005-07-01
The effective pair potential of liquid semiconductor Se is extracted from its experimental structure factor data using an accurate liquid state theory and this shows important basic features. A model potential incorporating the basic features of the structure factor extracted potential is suggested. This model potential is then used to describe through low-order perturbation theory, the structure and related dynamical properties like self-diffusion coefficient and shear viscosity of this complex liquid over a wide range of temperatures.
Directory of Open Access Journals (Sweden)
Mothanna Y. Abd
2012-01-01
Full Text Available A beam-type absorber has been known as one of the dynamic vibration absorbers used to suppress excessive vibration of an engineering structure. This paper studies an absorbing beam which is attached through a visco-elastic layer on a primary beam structure. Solutions of the dynamic response are presented at the midspan of the primary and absorbing beams in simply supported edges subjected to a stationary harmonic load. The effect of structural parameters, namely, rigidity ratio, mass ratio, and damping of the layer and the structure as well as the layer stiffness on the response is investigated to reduce the vibration amplitude at the fundamental frequency of the original single primary beam. It is found that this can considerably reduce the amplitude at the corresponding troublesome frequency, but compromised situation should be noted by controlling the structural parameters. The model is also validated with measured data with reasonable agreement.
DEFF Research Database (Denmark)
Domenici, Paolo; Ferrari, R Silvana; Steffensen, John F
2002-01-01
The effect of progressive hypoxia on the structure and dynamics of herring (Clupea harengus) schools in laboratory conditions was investigated. The length, width and depth of schools of about 20 individuals were measured from video recordings to test the hypothesis that during hypoxia fish school...
2013-08-01
effective material properties using a multiscale analysis technique. 3 Multiscale Analysis of Composite Structures The schematic diagram in Fig. 3...Strain Rate on Mechanical Properties and Failure Mechanism of Structural Al-Mg Alloys,” Mater. Sci. Eng., A, 492, pp. 283–292. 2 Mukai, T., Ishikawa ...A, 492, pp. 283–292. 2 Mukai, T., Ishikawa , K., and Higashi, K., 1995, “Influence of Strain Rate on the Mechanical Properties in Fine-Grained
Structural Dynamics Laboratory (SDL)
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...
Barwey, D.; Gaonkar, Gopal H.
1994-04-01
The effects of blade and root-flexure elasticity and dynamic stall on the stability of hingeless rotor blades are investigated. The dynamic stall description is based on the ONERA models of lift, drag, and pitching moment. The structural analysis is based on three blade models that range from a rigid flap-lag model to two elastic flap-lag-torsion models, which differ in representing root-flexure elasticity. The predictions are correlated with the measured lag damping of an experimental isolated three-blade rotor; the correlation covers rotor operations from near-zero-thrust conditions in hover to highly stalled, high-thrust conditions in foward flight. That correlation shows sensitivity of lag-damping predictions to structural refinements in blade and root-flexure modeling. Moreover, this sensitivity increases with increasing control pitch angle and advance ratio. For high-advance-ratio and high-thrust conditions, inclusion of dynamic stall generally improves the correlation.
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
Sulfation effect on levan polysaccharide chains structure with molecular dynamics simulations
Coskunkan, Binnaz; Turgut, Deniz; Rende, Deniz; Malta, Seyda; Baysal, Nihat; Ozisik, Rahmi; Toksoy-Oner, Ebru
Diversity in conformations and structural heterogeneity make polysaccharides the most challenging biopolymer type for experimental and theoretical characterization studies. Levan is a biopolymer chain that consists of fructose rings with β(2-6) linkages. It is a glycan that has great potential as a functional biopolymer in foods, feeds, cosmetics, pharmaceutical and chemical industries. Sulfated polysaccharides are group of macromolecules with sulfated groups in their hydroxyl parts with a range of important biological properties. Sulfate groups and their positions have a major effect on anticoagulant activity. It is reported that sulfate modified levan has anticoagulant activity such as heparin. In the current study, the effect of sulfation on the structure and dynamics of unmodified and sulfate modified levan are investigated via fully atomistic Molecular Dynamics simulations in aqueous media and varying salt concentrations at 310 K. This material is based upon work supported by the National Science Foundation under Grant No. CMMI-1538730.
The effect of glycosylation on the transferrin structure: A molecular dynamic simulation analysis.
Ghanbari, Z; Housaindokht, M R; Bozorgmehr, M R; Izadyar, M
2016-09-07
Transferrins have been defined by the highly cooperative binding of iron and a carbonate anion to form a Fe-CO3-Tf ternary complex. As such, the layout of the binding site residues affects transferrin function significantly; In contrast to N-lobe, C-lobe binding site of the transferrin structure has been less characterized and little research which surveyed the interaction of carbonate with transferrin in the C-lobe binding site has been found. In the present work, molecular dynamic simulation was employed to gain access into the molecular level understanding of carbonate binding site and their interactions in each lobe. Residues responsible for carbonate binding of transferrin structure were pointed out. In addition, native human transferrin is a glycoprotein that two N-linked complex glycan chains located in the C-lobe. Usually, in the molecular dynamic simulation for simplifying, glycan is removed from the protein structure. Here, we explore the effect of glycosylation on the transferrin structure. Glycosylation appears to have an effect on the layout of the binding site residue and transferrin structure. On the other hand, sometimes the entire transferrin formed by separated lobes that it allows the results to be interpreted in a straightforward manner rather than more parameters required for full length protein. But, it should be noted that there are differences between the separated lobe and full length transferrin, hence, a comparative analysis by the molecular dynamic simulation was performed to investigate such structural variations. Results revealed that separation in C-lobe caused a significant structural variation in comparison to N-lobe. Consequently, the separated lobes and the full length one are different, showing the importance of the interlobe communication and the impact of the lobes on each other in the transferrin structure. Copyright © 2016 Elsevier Ltd. All rights reserved.
Lima, Mauricio; Navarrete, Luis; González-Andujar, José Luis
2012-01-01
Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years) on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors). Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements. PMID:22272362
Lima, Mauricio; Navarrete, Luis; González-Andujar, José Luis
2012-01-01
Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years) on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors). Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements.
Directory of Open Access Journals (Sweden)
Mauricio Lima
Full Text Available Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors. Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements.
DEFF Research Database (Denmark)
Damgaard, M.; Zania, Varvara; Andersen, L.V.
2014-01-01
, a computationally efficient modelling approach of including the dynamic soil–structure interaction into aeroelastic codes is presented with focus on monopile foundations. Semi-analytical frequency-domain solutions are applied to evaluate the dynamic impedance functions of the soil–pile system at a number......Offshore wind turbines are highly dynamically loaded structures, their response being dominated by the interrelation effects between the turbine and the support structure. Since the dynamic response of wind turbine structures occurs in a frequency range close to the excitation frequencies related...... to environmental and parametric harmonic loads, the effects of the support structure and the subsoil on the natural vibration characteristics of the turbine have to be taken into account during the dynamic simulation of the structural response in order to ensure reliable and cost-effective designs. In this paper...
Kobayashi, Fumiharu
2015-01-01
We extend the method of antisymmetrized molecular dynamics to investigate dineutron correlation. We apply this method to $^{10}$Be as an example and investigate the motion of two neutrons around a largely deformed $^8$Be core by analyzing the two-neutron overlap function around the core. We show that the core structure plays an important role in dineutron formation and expansion from the core and that the present framework is effective for the studies of dineutron correlation.
Structure and dynamics of a dizinc metalloprotein: effect of charge transfer and polarization.
Li, Yong L; Mei, Ye; Zhang, Da W; Xie, Dai Q; Zhang, John Z H
2011-08-25
Structures and dynamics of a recently designed dizinc metalloprotein (DFsc) (J. Mol. Biol. 2003, 334, 1101) are studied by molecular dynamics simulation using a dynamically adapted polarized force field derived from fragment quantum calculation for protein in solvent. To properly describe the effect of charge transfer and polarization in the present approach, quantum chemistry calculation of the zinc-binding group is periodically performed (on-the-fly) to update the atomic charges of the zinc-binding group during the MD simulation. Comparison of the present result with those obtained from simulations under standard AMBER force field reveals that charge transfer and polarization are critical to maintaining the correct asymmetric metal coordination in the DFsc. Detailed analysis of the result also shows that dynamic fluctuation of the zinc-binding group facilitates solvent interaction with the zinc ions. In particular, the dynamic fluctuation of the zinc-zinc distance is shown to be an important feature of the catalytic function of the di-ion zinc-binding group. Our study demonstrates that the dynamically adapted polarization approach is computationally practical and can be used to study other metalloprotein systems.
Directory of Open Access Journals (Sweden)
M Rajasekaran
Full Text Available BACKGROUND: Arylamine N-acetyltransferase 2 (NAT2 is an important catalytic enzyme that metabolizes the carcinogenic arylamines, hydrazine drugs and chemicals. This enzyme is highly polymorphic in different human populations. Several polymorphisms of NAT2, including the single amino acid substitutions R64Q, I114T, D122N, L137F, Q145P, R197Q, and G286E, are classified as slow acetylators, whereas the wild-type NAT2 is classified as a fast acetylator. The slow acetylators are often associated with drug toxicity and efficacy as well as cancer susceptibility. The biological functions of these 7 mutations have previously been characterized, but the structural basis behind the reduced catalytic activity and reduced protein level is not clear. METHODOLOGY/PRINCIPAL FINDINGS: We performed multiple molecular dynamics simulations of these mutants as well as NAT2 to investigate the structural and dynamical effects throughout the protein structure, specifically the catalytic triad, cofactor binding site, and the substrate binding pocket. None of these mutations induced unfolding; instead, their effects were confined to the inter-domain, domain 3 and 17-residue insert region, where the flexibility was significantly reduced relative to the wild-type. Structural effects of these mutations propagate through space and cause a change in catalytic triad conformation, cofactor binding site, substrate binding pocket size/shape and electrostatic potential. CONCLUSIONS/SIGNIFICANCE: Our results showed that the dynamical properties of all the mutant structures, especially in inter-domain, domain 3 and 17-residue insert region were affected in the same manner. Similarly, the electrostatic potential of all the mutants were altered and also the functionally important regions such as catalytic triad, cofactor binding site, and substrate binding pocket adopted different orientation and/or conformation relative to the wild-type that may affect the functions of the mutants
Lifting shell structures in the dynamically assisted Schwinger effect in periodic fields
Otto, Andreas; Blaschke, David; Kampfer, Burkhard; Smolyansky, Stanislav Alexandrovich
2015-01-01
The dynamically assisted pair creation (Schwinger effect) is considered for the superposition of two periodic electric fields acting a finite time interval. We find a strong enhancement by orders of magnitude caused by a weak field with a frequency being a multitude of the strong-field frequency. The strong low-frequency field leads to shell structures which are lifted by the weaker high-frequency field. The resonance type amplification refers to a new, monotonously increasing mode, often hidden in some strong oscillatory transient background which disappears during the smoothly switching off the background fields, thus leaving a pronounced residual shell structure in phase space.
Lifting shell structures in the dynamically assisted Schwinger effect in periodic fields
Directory of Open Access Journals (Sweden)
A. Otto
2015-01-01
Full Text Available The dynamically assisted pair creation (Schwinger effect is considered for the superposition of two periodic electric fields acting in a finite time interval. We find a strong enhancement by orders of magnitude caused by a weak field with a frequency being a multitude of the strong-field frequency. The strong low-frequency field leads to shell structures which are lifted by the weaker high-frequency field. The resonance type amplification refers to a new, monotonously increasing mode, often hidden in some strong oscillatory transient background, which disappears during the smoothly switching off the background fields, thus leaving a pronounced residual shell structure in phase space.
Lifting shell structures in the dynamically assisted Schwinger effect in periodic fields
Energy Technology Data Exchange (ETDEWEB)
Otto, A., E-mail: a.otto@hzdr.de [Institute of Radiation Physics, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden (Germany); Institut für Theoretische Physik, Technische Universität Dresden, Zellescher Weg 17, 01062 Dresden (Germany); Seipt, D. [Helmholtz-Institut Jena, Fröbelstieg 3, 07743 Jena (Germany); Blaschke, D. [Group of Elementary Particle Theory, Institute for Theoretical Physics, University of Wroclaw, pl. M. Borna 9, 50-204 Wroclaw (Poland); Kämpfer, B. [Institute of Radiation Physics, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden (Germany); Institut für Theoretische Physik, Technische Universität Dresden, Zellescher Weg 17, 01062 Dresden (Germany); Smolyansky, S.A. [Department of Physics, Saratov State University, 410071 Saratov (Russian Federation)
2015-01-05
The dynamically assisted pair creation (Schwinger effect) is considered for the superposition of two periodic electric fields acting in a finite time interval. We find a strong enhancement by orders of magnitude caused by a weak field with a frequency being a multitude of the strong-field frequency. The strong low-frequency field leads to shell structures which are lifted by the weaker high-frequency field. The resonance type amplification refers to a new, monotonously increasing mode, often hidden in some strong oscillatory transient background, which disappears during the smoothly switching off the background fields, thus leaving a pronounced residual shell structure in phase space.
Garashchuk, Sophya; Jakowski, Jacek; Wang, Lei; Sumpter, Bobby G
2013-12-10
A massively parallel, direct quantum molecular dynamics method is described. The method combines a quantum trajectory (QT) representation of the nuclear wave function discretized into an ensemble of trajectories with an electronic structure (ES) description of electrons, namely using the density functional tight binding (DFTB) theory. Quantum nuclear effects are included into the dynamics of the nuclei via quantum corrections to the classical forces. To reduce computational cost and increase numerical accuracy, the quantum corrections to dynamics resulting from localization of the nuclear wave function are computed approximately and included into selected degrees of freedom representing light particles where the quantum effects are expected to be the most pronounced. A massively parallel implementation, based on the message passing interface allows for efficient simulations of ensembles of thousands of trajectories at once. The QTES-DFTB dynamics approach is employed to study the role of quantum nuclear effects on the interaction of hydrogen with a model graphene sheet, revealing that neglect of nuclear effects can lead to an overestimation of adsorption.
From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors.
Directory of Open Access Journals (Sweden)
Ana Zafra Ruano
2016-05-01
Full Text Available Src Homology 3 domains are ubiquitous small interaction modules known to act as docking sites and regulatory elements in a wide range of proteins. Prior experimental NMR work on the SH3 domain of Src showed that ligand binding induces long-range dynamic changes consistent with an induced fit mechanism. The identification of the residues that participate in this mechanism produces a chart that allows for the exploration of the regulatory role of such domains in the activity of the encompassing protein. Here we show that a computational approach focusing on the changes in side chain dynamics through ligand binding identifies equivalent long-range effects in the Src SH3 domain. Mutation of a subset of the predicted residues elicits long-range effects on the binding energetics, emphasizing the relevance of these positions in the definition of intramolecular cooperative networks of signal transduction in this domain. We find further support for this mechanism through the analysis of seven other publically available SH3 domain structures of which the sequences represent diverse SH3 classes. By comparing the eight predictions, we find that, in addition to a dynamic pathway that is relatively conserved throughout all SH3 domains, there are dynamic aspects specific to each domain and homologous subgroups. Our work shows for the first time from a structural perspective, which transduction mechanisms are common between a subset of closely related and distal SH3 domains, while at the same time highlighting the differences in signal transduction that make each family member unique. These results resolve the missing link between structural predictions of dynamic changes and the domain sectors recently identified for SH3 domains through sequence analysis.
From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors.
Zafra Ruano, Ana; Cilia, Elisa; Couceiro, José R; Ruiz Sanz, Javier; Schymkowitz, Joost; Rousseau, Frederic; Luque, Irene; Lenaerts, Tom
2016-05-01
Src Homology 3 domains are ubiquitous small interaction modules known to act as docking sites and regulatory elements in a wide range of proteins. Prior experimental NMR work on the SH3 domain of Src showed that ligand binding induces long-range dynamic changes consistent with an induced fit mechanism. The identification of the residues that participate in this mechanism produces a chart that allows for the exploration of the regulatory role of such domains in the activity of the encompassing protein. Here we show that a computational approach focusing on the changes in side chain dynamics through ligand binding identifies equivalent long-range effects in the Src SH3 domain. Mutation of a subset of the predicted residues elicits long-range effects on the binding energetics, emphasizing the relevance of these positions in the definition of intramolecular cooperative networks of signal transduction in this domain. We find further support for this mechanism through the analysis of seven other publically available SH3 domain structures of which the sequences represent diverse SH3 classes. By comparing the eight predictions, we find that, in addition to a dynamic pathway that is relatively conserved throughout all SH3 domains, there are dynamic aspects specific to each domain and homologous subgroups. Our work shows for the first time from a structural perspective, which transduction mechanisms are common between a subset of closely related and distal SH3 domains, while at the same time highlighting the differences in signal transduction that make each family member unique. These results resolve the missing link between structural predictions of dynamic changes and the domain sectors recently identified for SH3 domains through sequence analysis.
The effect of prediction error correlation on optimal sensor placement in structural dynamics
Papadimitriou, Costas; Lombaert, Geert
2012-04-01
The problem of estimating the optimal sensor locations for parameter estimation in structural dynamics is re-visited. The effect of spatially correlated prediction errors on the optimal sensor placement is investigated. The information entropy is used as a performance measure of the sensor configuration. The optimal sensor location is formulated as an optimization problem involving discrete-valued variables, which is solved using computationally efficient sequential sensor placement algorithms. Asymptotic estimates for the information entropy are used to develop useful properties that provide insight into the dependence of the information entropy on the number and location of sensors. A theoretical analysis shows that the spatial correlation length of the prediction errors controls the minimum distance between the sensors and should be taken into account when designing optimal sensor locations with potential sensor distances up to the order of the characteristic length of the dynamic problem considered. Implementation issues for modal identification and structural-related model parameter estimation are addressed. Theoretical and computational developments are illustrated by designing the optimal sensor configurations for a continuous beam model, a discrete chain-like stiffness-mass model and a finite element model of a footbridge in Wetteren (Belgium). Results point out the crucial effect the spatial correlation of the prediction errors have on the design of optimal sensor locations for structural dynamics applications, revealing simultaneously potential inadequacies of spatially uncorrelated prediction errors models.
Effect of group walking traffic on dynamic properties of pedestrian structures
Shahabpoor, E.; Pavic, A.; Racic, V.; Zivanovic, S.
2017-01-01
The increasing number of reported vibration serviceability problems in newly built pedestrian structures, such as footbridges and floors, under walking load has attracted considerable attention in the civil engineering community over the past two decades. The key design challenges are: the inter- and intra-subject variability of walking people, the unknown mechanisms of their interaction with the vibrating walking surfaces and the synchronisation between individuals in a group. Ignoring all or some of these factors makes the current design methods an inconsistent approximation of reality. This often leads to considerable over- or under-estimation of the structural response, yielding an unreliable assessment of vibration performance. Changes to the dynamic properties of an empty structure due to the presence of stationary people have been studied extensively over the past two decades. The understanding of the similar effect of walking people on laterally swaying bridges has improved tremendously in the past decade, due to considerable research prompted by the Millennium Bridge problem. However, there is currently a gap in knowledge about how moving pedestrians affect the dynamic properties of vertically vibrating structures. The key reason for this gap is the scarcity of credible experimental data pertinent to moving pedestrians on vertically vibrating structures, especially for multi-pedestrian traffic. This paper addresses this problem by studying the dynamic properties of the combined human-structure system, i.e. occupied structure damping ratio, natural frequency and modal mass. This was achieved using a comprehensive set of frequency response function records, measured on a full-scale test structure, which was occupied by various numbers of moving pedestrians under different walking scenarios. Contrary to expectations, it was found that the natural frequency of the joint moving human-structure system was higher than that of the empty structure, while it was
Dynamic soil-pile-interaction effects on eigenfrequency and damping of slender structures
DEFF Research Database (Denmark)
Zania, Varvara
2014-01-01
of the dynamic soil-pile-interaction on the natural vibration characteristics of the flexibly supported structure. For this purpose a two-step iterative procedure has been developed based on two analytical solutions. The frequency dependent dynamic stiffness and damping coefficients are taken into consideration...... after a rigorous solution of horizontal soil – pile vibration, while the modified SSI eigenperiod and damping are calculated accounting for the cross coupling stiffness and damping terms of the soil – pile system. Disregarding the off diagonal terms is considered inappropriate since it results to non......-conservative overestimation of the eigenfrequency and underestimation of damping especially for small slenderness ratios and high flexibility factor of the soil – pile system (short, rigid piles). The observed trends become even more prominent as the height of the slender structure increases. The effect of the monopile...
DEFF Research Database (Denmark)
Thomsen, Jon Juel; Blekhman, Iliya I.
2007-01-01
, and to call these dynamic materials or spatiotemporal composites. Also, according to theoretical predictions, structural nonlinearity enhances the possibilities of achieving specific effective properties. For example, with an elastic rod having cubical elastic nonlinearities, it seems possible to control......, and exemplified. Then simple approximate analytical expressions are derived for the effective wave speed and natural frequencies for one-dimensional wave propagation in a nonlinear elastic rod, where the spatiotemporal modulation is imposed as a high-frequency standing wave, supposed to be given. Finally the more...
Energy Technology Data Exchange (ETDEWEB)
Naito, Yukio [Kajima Corp., Kajima Technical Research Institute, Tokyo (Japan); Yano, Tatsuo [Kajima Corp., Nuclear Power Department, Tokyo (Japan); Iguchi, Michio [Science Univ. of Tokyo, Faculty of Science and Technology, Noda, Chiba (Japan); Kitada, Yoshio [Nuclear Power Engineering Corp., Tokyo (Japan)
2003-02-01
High-rigidity and heavy buildings such as reactor buildings usually have large soil-structure interaction effect in its dynamic response. In such cases, spectrum ratio of the top of the building to the bottom for horizontal motion gives different result from the dynamic characteristics of the building under fixed-base condition because the effect of the rocking motion of the base is not eliminated. This paper presented a new method for such problems; applied it to a ground blast vibration, microtremors and forced vibration test results; and transfer functions of the building for fixed-base condition were obtained. The proposed method can be applied when the exciter is set at the upper part of the buildings. (author)
Espinoza-Fonseca, L. Michel; Colson, Brett A.; Thomas, David D.
2014-01-01
We have performed 50 independent molecular dynamics (MD) simulations to determine the effect of pseudophosphorylation mutants on the structural dynamics of smooth muscle myosin (SMM) regulatory light chain (RLC). We previously showed that the N-terminal phosphorylation domain of RLC simultaneously populates two structural states in equilibrium, closed and open, and that phosphorylation at S19 induces a modest shift toward the open state, which is sufficient to activate smooth muscle. However, it remains unknown why pseudophosphorylation mutants poorly mimic phosphorylation-induced activation of SMM. We performed MD simulations of unphosphorylated, phosphorylated, and three pseudophosphorylatedRLC mutants: S19E, T18D/S19D and T18E/S19E. We found that the S19E mutation does not shift the equilibrium toward the open state, indicating that simple charge replacement at position S19 does not mimic the activating effect of phosphorylation, providing a structural explanation for previously published functional data. In contrast, mutants T18D/S19D and T18E/S19E shift the equilibrium toward the open structure and partially activate in vitro motility, further supporting the model that an increase in the mol fraction of the open state is coupled to SMM motility. Structural analyses of the doubly-charged pseudophosphorylation mutants suggest that alterations in an interdomain salt bridge between residues R4 and D100 results in impaired signal transmission from RLC to the catalytic domain of SMM, which explains the low ATPase activity of these mutants. Our results demonstrate that phosphorylation produces a unique structural balance in the RLC. These observations have important implications for our understanding of the structural aspects of activation and force potentiation in smooth and striated muscle. PMID:25091814
The Town Effect: Dynamic Interaction between a Group of Structures and Waves in the Ground
Uenishi, Koji
2010-11-01
In a conventional approach, the mechanical behaviour of a structure subjected to seismic or blast waves is treated separately from its surroundings, and in many cases, the dynamic coupling effect between multiple structures and the waves propagating in the ground is disregarded. However, if many structures are built densely in a developed urban area, this dynamic interaction may not become negligible. The first purpose of this contribution is to briefly show the effect of multiple interactions between waves and surface buildings in a town. The analysis is based on a recently developed, fully coupled, rigorous mathematical study, and for simplicity, each building in the town is represented by a rigid foundation, a mass at the top and an elastic spring that connects the foundation and mass. The buildings stand at regular spatial intervals on a linear elastic half-space and are subjected to two-dimensional anti-plane vibrations. It is found that the buildings in this model significantly interact with each other through the elastic ground, and the resonant (eigen) frequencies of the collective system (buildings or town) become lower than that of a single building with the same rigid foundation. This phenomenon may be called the “town effect” or “city effect.” Then, second, it is shown that the actual, unique structural damage pattern caused by the 1976 Friuli, Italy, earthquake may better be explained by this “town effect,” rather than by investigating the seismic performance of each damaged building individually. The results suggest that it may also be possible to evaluate the physical characteristics of incident seismic/blast waves “inversely” from the damage patterns induced to structures by the waves.
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...
Brownian dynamics simulation of the effect of histone modification on nucleosome structure
Li, Wei; Dou, Shuo-Xing; Xie, Ping; Wang, Peng-Ye
2007-05-01
Using Brownian dynamics we simulate the effect of histone modification, such as phosphorylation, acetylation, and methylation, on nucleosome structure by varying the interaction force between DNA and the histone octamer. The simulation shows that the structural stability of nucleosome is very sensitive to the interaction force, and the DNA unwrapping from the modified histone octamer usually occurs turn by turn. Furthermore, the effects of temperature and DNA break as well as the competition between modified and normal histone octamers are investigated, with the simulation results being in agreement with the experimental observation that phosphorylated nucleosomes near DNA breaks are more easily depleted. Though the simulation study may only give a coarse grained view of the DNA unwrapping process for the modified histone octamer, it may provide insight into the mechanism of DNA repair.
Ordoñez, Alexandra; Doropoulos, Christopher; Diaz-Pulido, Guillermo
2014-06-01
Calcification and growth of crustose coralline algae (CCA) are affected by elevated seawater pCO2 and associated changes in carbonate chemistry. However, the effects of ocean acidification (OA) on population and community-level responses of CCA have barely been investigated. We explored changes in community structure and population dynamics (size structure and reproduction) of CCA in response to OA. Recruited from an experimental flow-through system, CCA settled onto the walls of plastic aquaria and developed under exposure to one of three pCO2 treatments (control [present day, 389±6 ppm CO2], medium [753±11 ppm], and high [1267±19 ppm]). Elevated pCO2 reduced total CCA abundance and affected community structure, in particular the density of the dominant species Pneophyllum sp. and Porolithon onkodes. Meanwhile, the relative abundance of P. onkodes declined from 24% under control CO2 to 8.3% in high CO2 (65% change), while the relative abundance of Pneophyllum sp. remained constant. Population size structure of P. onkodes differed significantly across treatments, with fewer larger individuals under high CO2. In contrast, the population size structure and number of reproductive structures (conceptacles) per crust of Pneophyllum sp. was similar across treatments. The difference in the magnitude of the response of species abundance and population size structure between species may have the potential to induce species composition changes in the future. These results demonstrate that the impacts of OA on key coral reef builders go beyond declines in calcification and growth, and suggest important changes to aspects of population dynamics and community ecology.
Fathi, Narges; Moradi, Ali-Reza; Habibi, Mehdi; Vashaee, Daryoosh; Tayebi, Lobat
2013-01-01
Myelin figures (MFs) are cylindrical multilamellar lipid tubes that can be found in various healthy and diseased living cells. Their formation and dynamics involve some of the most mysterious configurations that lipid molecules can adopt under certain conditions. They have been studied with different microscopy methods. Due to the frequent coiling of their structure, the usual methods of microscopy fail to give precise quantitative information about their dynamics. In this paper, we introduced Digital Holographic Microscopy (DHM) as a useful method to calculate the precise dynamical volume, thickness, surface and length of the myelin figures. As an example of DHM imaging of myelin figures, their structure and growth rate in the presence and absence of temperature gradient have been studied in this work. We showed that the thickness of a myelin figure can be changed during the first few seconds. However, after approximately ten seconds, the thickness stabilizes and does not alter significantly. We further studied the effect of the thermal gradient on the length growth. The calculation of the length growth from the measurement of the myelin figure volume shows that the length (L) grows in time (t) as L∝tat the early stage of the myelin protrusion in both the presence and the absence of the thermal gradient. However, thermal gradient facilitates the growth and increases its rate. PMID:23760951
DEFF Research Database (Denmark)
Damgaard, M.; Zania, Varvara; Andersen, L.V.;
2014-01-01
, a computationally efficient modelling approach of including the dynamic soil–structure interaction into aeroelastic codes is presented with focus on monopile foundations. Semi-analytical frequency-domain solutions are applied to evaluate the dynamic impedance functions of the soil–pile system at a number...... normal operating mode. The aeroelastic response is evaluated for three different foundation conditions, i.e. apparent fixity length, the consistent lumped-parameter model and fixed support at the seabed. The effect of soil–structure interaction is shown to be critical for the design, estimated in terms......Offshore wind turbines are highly dynamically loaded structures, their response being dominated by the interrelation effects between the turbine and the support structure. Since the dynamic response of wind turbine structures occurs in a frequency range close to the excitation frequencies related...
DEFF Research Database (Denmark)
Tsakalidis, Konstantinos
We study dynamic data structures for diﬀerent variants of orthogonal range reporting query problems. In particular, we consider (1) the planar orthogonal 3-sided range reporting problem: given a set of points in the plane, report the points that lie within a given 3-sided rectangle with one....... Dynamic problems like the above arise in various applications of network optimization, VLSI layout design, computer graphics and distributed computing. For the ﬁrst problem, we present dynamic data structures for internal and external memory that support planar orthogonal 3-sided range reporting queries......, and insertions and deletions of points eﬃciently over an average case sequence of update operations. The external memory data structures ﬁnd applications in constraint and temporal databases. In particular, we assume that the coordinates of the points are drawn from diﬀerent probabilistic distributions...
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
Housner, J. M.; Anderson, M.; Belvin, W.; Horner, G.
1985-01-01
Dynamic analysis of large space antenna systems must treat the deployment as well as vibration and control of the deployed antenna. Candidate computer programs for deployment dynamics, and issues and needs for future program developments are reviewed. Some results for mast and hoop deployment are also presented. Modeling of complex antenna geometry with conventional finite element methods and with repetitive exact elements is considered. Analytical comparisons with experimental results for a 15 meter hoop/column antenna revealed the importance of accurate structural properties including nonlinear joints. Slackening of cables in this antenna is also a consideration. The technology of designing actively damped structures through analytical optimization is discussed and results are presented.
Effects of seed magnetic fields on magnetohydrodynamic implosion structure and dynamics
Mostert, W.
2014-12-01
The effects of various seed magnetic fields on the dynamics of cylindrical and spherical implosions in ideal magnetohydrodynamics are investigated. Here, we present a fundamental investigation of this problem utilizing cylindrical and spherical Riemann problems under three seed field configurations to initialize the implosions. The resulting flows are simulated numerically, revealing rich flow structures, including multiple families of magnetohydrodynamic shocks and rarefactions that interact non-linearly. We fully characterize these flow structures, examine their axi- and spherisymmetry-breaking behaviour, and provide data on asymmetry evolution for different field strengths and driving pressures for each seed field configuration. We find that out of the configurations investigated, a seed field for which the implosion centre is a saddle point in at least one plane exhibits the least degree of asymmetry during implosion.
[Effect of dynamic high-pressure micro-fluidization on the structure of maize amylose].
Tu, Zong-Cai; Yin, Yue-Bin; Zhang, Qiu; Wang, Hui
2013-05-01
The effect of dynamic high-pressure micro-fluidization (DHPM) at 80, 120, 160, and 200 MPa on the structure of maize amylose was investigated using scanning electron microscopy (SEM), atomic force microscope (AFM), Xray diffraction, and FT-IR spectroscopy. SEM analysis showed that the surface appearances of maize amylose were altered and the starch granules were partially congregated together after DHPM treatment. AFM images showed that the treated starch molecules are cross-linked to each other and arranged in a close mesh structure. Xray diffraction spectra and IR spectra indicated that relative crystallinity declined gradually with the pressure increasing. The results provide a theoretical basis for starch modification of DHPM.
Electromagnetic-field effects on structure and dynamics of amyloidogenic peptides
Todorova, Nevena; Bentvelzen, Alan; English, Niall J.; Yarovsky, Irene
2016-02-01
Electromagnetic fields (EMFs) are ever-present, and so is the need to better understand their influence on human health and biological matter in general. The interaction between a molecular system and external EMF can alter the structure, and dynamical behaviour, and, hence, biological function of proteins with uncertain health consequences. This urges a detailed investigation of EMF-induced effects on basic protein biophysics. Here, we used all-atom non-equilibrium molecular dynamics simulations to understand and quantify the response mechanisms of the amyloidogenic apoC-II(60-70) peptides to non-ionising radiation by modelling their behaviour under external electromagnetic and electric fields of different strengths. Our simulations show high strength fields (>0.04 V/nm) cause structural changes in apoC-II(60-70) due to the peptide dipole alignment along the applied field direction, which disrupts the inherent β-hairpin conformation known to be the intermediate state for fibril formation. The intermediate field-strength range (0.04-0.004 V/nm) causes a significant acceleration in peptide dynamics, which leads to the increased population of structures with fibril-inhibiting characteristics, such as the separated N- and C-termini and colocation of the aromatic residues at the same peptide face. In contrast, lower field strengths (electromagnetic fields could be considered for designing alternative treatments of amyloid diseases, while the very high and low field strengths could be employed for engineering well-ordered fibrillar aggregates for non-medicinal applications.
Song, Yang; Bian, Yongrong; Wang, Fang; Xu, Min; Ni, Ni; Yang, Xinglun; Gu, Chenggang; Jiang, Xin
2017-08-16
Amending soil with biochar is an effective soil remediation strategy for organic contaminants. This study investigated the dynamic effects of wheat straw biochar on the bacterial community structure during remediation by high-throughput sequencing. The wheat straw biochar amended into the soil significantly reduced the bioavailability and toxicity of polycyclic aromatic hydrocarbons (PAHs). Biochar amendment helped to maintain the bacterial diversity in the PAH-contaminated soil. The relationship between the immobilization of PAHs and the soil bacterial diversity fit a quadratic model. Before week 12 of the incubation, the incubation time was the main factor contributing to the changes in the soil bacterial community structure. However, biochar greatly affected the bacterial community structure after 12 weeks of amendment, and the effects were dependent upon the biochar type. Amendment with biochar mainly facilitated the growth of rare bacterial genera (relative abundance of 0.01-1%) in the studied soil. Therefore, the application of wheat straw biochar into PAH-contaminated soil can reduce the environmental risks of PAHs and benefit the soil microbial ecology.
Kassler, Kristin; Horn, Anselm H C; Sticht, Heinrich
2010-05-01
Converging lines of evidence suggest that soluble A beta-amyloid oligomers play a pivotal role in the pathogenesis of Alzheimer's disease, and present direct effectors of synaptic and cognitive dysfunction. Three pathological E22-A beta-amyloid point mutants (E22G, E22K, E22Q) and the deletion mutant E22 Delta exhibit an enhanced tendency to form prefibrillar aggregates. The present study assessed the effect of these four mutations using molecular dynamics simulations and subsequent structural and energetic analyses. Our data shows that E22 plays a unique role in wild type A beta, since it has a destabilising effect on the oligomer structure due to electrostatic repulsion between adjacent E22 side chains. Mutations in which E22 is replaced by an uncharged residue result in higher oligomer stability. This effect is also observed to a lesser extent for the E22K mutation and is consistent with its lower pathogenicity compared to other mutants. Interestingly, deletion of E22 does not destroy the amyloid fold but is compensated by local changes in the backbone geometry that allow the preservation of a structurally important salt bridge. The finding that all mutant oligomers investigated exhibit higher internal stability than the wild type offers an explanation for the experimentally observed enhanced oligomer formation and stability.
Effect of Space Vehicle Structure Vibration on Control Moment Gyroscope Dynamics
Dobrinskaya, Tatiana
2008-01-01
Control Moment Gyroscopes (CMGs) are used for non-propulsive attitude control of satellites and space stations, including the International Space Station (ISS). CMGs could be essential for future long duration space missions due to the fact that they help to save propellant. CMGs were successfully tested on the ground for many years, and have been successfully used on satellites. However, operations have shown that the CMG service life on the ISS is significantly shorter than predicted. Since the dynamic environment of the ISS differs greatly from the nominal environment of satellites, it was important to analyze how operations specific to the station (dockings and undockings, huge solar array motion, crew exercising, robotic operations, etc) can affect the CMG performance. This task became even more important since the first CMG failure onboard the ISS. The CMG failure resulted in the limitation of the attitude control capabilities, more propellant consumption, and additional operational issues. Therefore, the goal of this work was to find out how the vibrations of a space vehicle structure, caused by a variety of onboard operations, can affect the CMG dynamics and performance. The equations of CMG motion were derived and analyzed for the case when the gyro foundation can vibrate in any direction. The analysis was performed for unbalanced CMG gimbals to match the CMG configuration on ISS. The analysis showed that vehicle structure vibrations can amplify and significantly change the CMG motion if the gyro gimbals are unbalanced in flight. The resonance frequencies were found. It was shown that the resonance effect depends on the magnitude of gimbal imbalance, on the direction of a structure vibration, and on gimbal bearing friction. Computer modeling results of CMG dynamics affected by the external vibration are presented. The results can explain some of the CMG vibration telemetry observed on ISS. This work shows that balancing the CMG gimbals decreases the effect
Effect of Space Vehicle Structure Vibration on Control Moment Gyroscope Dynamics
Dobrinskaya, Tatiana
2008-01-01
Control Moment Gyroscopes (CMGs) are used for non-propulsive attitude control of satellites and space stations, including the International Space Station (ISS). CMGs could be essential for future long duration space missions due to the fact that they help to save propellant. CMGs were successfully tested on the ground for many years, and have been successfully used on satellites. However, operations have shown that the CMG service life on the ISS is significantly shorter than predicted. Since the dynamic environment of the ISS differs greatly from the nominal environment of satellites, it was important to analyze how operations specific to the station (dockings and undockings, huge solar array motion, crew exercising, robotic operations, etc) can affect the CMG performance. This task became even more important since the first CMG failure onboard the ISS. The CMG failure resulted in the limitation of the attitude control capabilities, more propellant consumption, and additional operational issues. Therefore, the goal of this work was to find out how the vibrations of a space vehicle structure, caused by a variety of onboard operations, can affect the CMG dynamics and performance. The equations of CMG motion were derived and analyzed for the case when the gyro foundation can vibrate in any direction. The analysis was performed for unbalanced CMG gimbals to match the CMG configuration on ISS. The analysis showed that vehicle structure vibrations can amplify and significantly change the CMG motion if the gyro gimbals are unbalanced in flight. The resonance frequencies were found. It was shown that the resonance effect depends on the magnitude of gimbal imbalance, on the direction of a structure vibration, and on gimbal bearing friction. Computer modeling results of CMG dynamics affected by the external vibration are presented. The results can explain some of the CMG vibration telemetry observed on ISS. This work shows that balancing the CMG gimbals decreases the effect
Directory of Open Access Journals (Sweden)
Wei Peng
2017-01-01
Full Text Available In this study, we proposed a game-theory based framework to model the dynamic pricing process in the cloud manufacturing (CMfg system. We considered a service provider (SP, a broker agent (BA, and a dynamic service demander (SD population that is composed of price takers and bargainers in this study. The pricing processes under linear demand and constant elasticity demand were modeled, respectively. The combined effects of SD population structure, negotiation, and demand forms on the SP’s and the BA’s equilibrium prices and expected revenues were examined. We found that the SP’s optimal wholesale price, the BA’s optimal reservation price, and posted price all increase with the proportion of price takers under linear demand but decrease with it under constant elasticity demand. We also found that the BA’s optimal reservation price increases with bargainers’ power no matter under what kind of demand. Through analyzing the participants’ revenues, we showed that a dynamic SD population with a high ratio of price takers would benefit the SP and the BA.
DEFF Research Database (Denmark)
Tsakalidis, Konstantinos
We study dynamic data structures for diﬀerent variants of orthogonal range reporting query problems. In particular, we consider (1) the planar orthogonal 3-sided range reporting problem: given a set of points in the plane, report the points that lie within a given 3-sided rectangle with one....... Dynamic problems like the above arise in various applications of network optimization, VLSI layout design, computer graphics and distributed computing. For the ﬁrst problem, we present dynamic data structures for internal and external memory that support planar orthogonal 3-sided range reporting queries...... unbounded side, (2) the planar orthogonal range maxima reporting problem: given a set of points in the plane, report the points that lie within a given orthogonal range and are not dominated by any other point in the range, and (3) the problem of designing fully persistent B-trees for external memory...
Effect of velocity ratio on coherent-structure dynamics in turbulent free shear layers
Suryanarayanan, Saikishan; Narasimha, Roddam
2014-11-01
The relevance of the vortex-gas model to the large scale dynamics of temporally evolving turbulent free shear layers has been established by extensive simulations (Phys. Rev. E 89, 013009 (2014)). The effects of velocity ratio (r =U2 /U1) on shear layer dynamics are revealed by spatially evolving vortex-gas shear-layer simulations using a computational model based on Basu et al. (Appl. Math. Modelling 19, (1995)), but with a crucial improvement that ensures conservation of global circulation. The simulations show that the initial conditions and downstream boundaries can significantly affect the flow over substantial part of the domain, but the equilibrium spread rate is a universal function of r, and is within the experimental scatter. The spread in the r = 0 limit is higher than Galilean-transformed temporal value. The present 2D simulations at r = 0 show continuous growth of structures, while merger-dominated evolution is observed for r = 0 . 23 (and higher). These two mechanisms were observed across the same two values of r in the experiments of D'Ovidio & Coats (J. Fluid Mech. 737, 2013), but the continuous growth was instead attributed to mixing-transition and 3D. The 2D mechanisms responsible for the observed continuous growth of structures are analyzed in detail. Supported in part by RN/Intel/4288 and RN/DRDO/4124.
DEFF Research Database (Denmark)
Kejlberg-Rasmussen, Casper
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...... 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...
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...
Structure and dynamical effects of the thermal tide in the Venus atmosphere
Takagi, Masahiro; Sugimoto, Norihiko; Ando, Hiroki; Matsuda, Yoshihisa
2016-10-01
We investigate structure and dynamical effects of the thermal tide in the Venus atmosphere by using a general circulation model (GCM). The thermal tide is important for the Venus atmospheric dynamics (Fels and Lindzen, 1974; Plumb, 1975; Newman and Leovy, 1992; Takagi and Matsuda, 2007). However, its three-dimensional structure has not been fully investigated so far. It is expected that detailed wind distributions of the thermal tide will be obtained by the Venus Climate Orbiter Akatsuki in the near future. It is necessary to investigate its structure so that the observational results can be interpreted in terms of dynamics. The GCM used in the present study is AFES for Venus (Sugimoto et al., 2014a, b). The resolution is set to T64L120. The model atmosphere extends from the ground to ~120 km. The infrared radiative transfer process is simplified by the Newtonian cooling approximation. See Sugimoto et al. (2014a, b) for more model details. The initial state is an idealized superrotating flow in solid body rotation. The GCM is integrated for 5 Earth years. The result shows that the semidiurnal and diurnal tides are predominant in low and high latitudes poleward of 60 degrees, respectively. The diurnal tide is trapped at 55-75 km levels; the phase is almost unchanged in the vertical direction. This result indicates that the subsolar-antisolar (SS-AS) circulation is predominant at these levels. The strong upward wind is located at early afternoon and near the morning and evening terminators. The vertical velocity of the SS-AS circulation is 0.04 m/s, which is ~10 times as fast as that of the mean meridional circulation (MMC). Titov et al. (2012) pointed out that dark regions are observed in the evening region, suggesting that the dark material is transported from below. These results suggest that the SS-AS circulation is quite important to the material transport at the cloud levels in the Venus atmosphere. The preliminary analysis also shows that the MMC at 50-90 km
Structural dynamic modification using additive damping
Indian Academy of Sciences (India)
B C Nakra
2000-06-01
In order to control dynamic response in structures and machines, modofications using additive viscoelastic damping materials are highlighted. The techniques described for analysis include analytical methods for structural elements, FEM and perturbation methods for reanalysis or structural dynamic modifications for complex structures. Optimisation techniques are used for damping effectiveness include multi-parameter optimisatoin techniques and a technique using dynamic sensitivity analysis and structural dynamic modification. These have been applied for optimum dynamic design of structures incorporating viscoelastic damping. Some current trends for vibraton control are also discussed.
Dynamical Structure of Baryons
Aleksejevs, A
2013-01-01
Compton scattering offers a unique opportunity to study the dynamical structure of hadrons over a wide kinematic range, with polarizabilities characterizing the hadron active internal degrees of freedom. We present calculations and detailed analysis of electric and magnetic and the spin-dependent dynamical polarizabilities for the lowest in mass SU(3) octet of baryons. These extensive calculations are made possible by the recent implementation of semi-automatized calculations in chiral perturbation theory which allows evaluating polarizabilities from Compton scattering up to next-to-the-leading order. The dependencies for the range of photon energies covering the majority of the meson photoproduction channels are analyzed.
Hiebeler, David E; Morin, Benjamin R
2007-05-01
Previous models of locally dispersing populations have shown that in the presence of spatially structured fixed habitat heterogeneity, increasing local spatial autocorrelation in habitat generally has a beneficial effect on such populations, increasing equilibrium population density. It has also been shown that with large-scale disturbance events which simultaneously affect contiguous blocks of sites, increasing spatial autocorrelation in the disturbances has a harmful effect, decreasing equilibrium population density. Here, spatial population models are developed which include both of these spatially structured exogenous influences, to determine how they interact with each other and with the endogenously generated spatial structure produced by the population dynamics. The models show that when habitat is fragmented and disturbance occurs at large spatial scales, the population cannot persist no matter how large its birth rate, an effect not seen in previous simpler models of this type. The behavior of the model is also explored when the local autocorrelation of habitat heterogeneity and disturbance events are equal, i.e. the two effects occur at the same spatial scale. When this scale parameter is very small, habitat fragmentation prevents the population from persisting because sites attempting to reproduce will drop most of their offspring on unsuitable sites; when the parameter is very large, large-scale disturbance events drive the population to extinction. Population levels reach their maximum at intermediate values of the scale parameter, and the critical values in the model show that the population will persist most easily at these intermediate scales of spatial influences. The models are investigated via spatially explicit stochastic simulations, traditional (infinite-dispersal) and improved (local-dispersal) mean-field approximations, and pair approximations.
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...... 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...... represents an attempt to construct a local stiffness for the unbounded soil domain....
Edge effects in game-theoretic dynamics of spatially structured tumours.
Kaznatcheev, Artem; Scott, Jacob G; Basanta, David
2015-07-06
Cancer dynamics are an evolutionary game between cellular phenotypes. A typical assumption in this modelling paradigm is that the probability of a given phenotypic strategy interacting with another depends exclusively on the abundance of those strategies without regard for local neighbourhood structure. We address this limitation by using the Ohtsuki-Nowak transform to introduce spatial structure to the go versus grow game. We show that spatial structure can promote the invasive (go) strategy. By considering the change in neighbourhood size at a static boundary--such as a blood vessel, organ capsule or basement membrane--we show an edge effect that allows a tumour without invasive phenotypes in the bulk to have a polyclonal boundary with invasive cells. We present an example of this promotion of invasive (epithelial-mesenchymal transition-positive) cells in a metastatic colony of prostate adenocarcinoma in bone marrow. Our results caution that pathologic analyses that do not distinguish between cells in the bulk and cells at a static edge of a tumour can underestimate the number of invasive cells. Although we concentrate on applications in mathematical oncology, we expect our approach to extend to other evolutionary game models where interaction neighbourhoods change at fixed system boundaries.
Turton, David A; Sonnleitner, Thomas; Ortner, Alex; Walther, Markus; Hefter, Glenn; Seddon, Kenneth R; Stana, Simona; Plechkova, Natalia V; Buchner, Richard; Wynne, Klaas
2012-01-01
The structure and dynamics of ionic liquids (ILs) are unusual due to the strong interactions between the ions and counter ions. These microscopic properties determine the bulk transport properties critical to applications of ILs such as advanced fuel cells. The terahertz dynamics and slower relaxations of simple alkylammonium nitrate protic ionic liquids (PILs) are here studied using femtosecond optical Kerr-effect spectroscopy, dielectric relaxation spectroscopy, and terahertz time-domain spectroscopy. The observed dynamics give insight into more general liquid behaviour while comparison with glass-forming liquids reveals an underlying power-law decay and relaxation rates suggest supramolecular structure and nanoscale segregation.
Dynamic Weighted Data Structures.
1982-06-01
and Bonnie Hampton, who taught me much more than how to play the cello . Finally, for hours of artistic satisfaction, I thank Johannes Brahms, Ludwig...van "j Beethoven, Igor Stravinsky, Glan-Carlo Menotti, and Johann Sebastian Bach . Dynamic Weighted Data Structures Samuel W. Bent This thesis discusses...34I find It a matter of some difficulty to arrange these cards In a manner suited to my needs.’ I glanced at the cards and noticed each was labelled
Structural dynamic modification
Indian Academy of Sciences (India)
A Sestieri
2000-06-01
Vibration and acoustic requirements are becoming increasingly important in the design of mechanical structures, but they are not usually of primary concern in the design process. So the need to vary the structural behaviour to solve noise and vibration problems often occurs at the prototype stage, giving rise to the so-called structural modification problem. In this paper, the direct problem of determing the new response of a system, after some modifications are introduced into the sestem, is analysed using two different databases: the modal database and the frequency response function database. The limitaions of the modal database are discussed. Structural modifications that can be accounted for are lumped masses, springs, dampers and dynamic absorbers.
Effect of alcohol on the structure of cytochrome C: FCS and molecular dynamics simulations
Amin, Md. Asif; Halder, Ritaban; Ghosh, Catherine; Jana, Biman; Bhattacharyya, Kankan
2016-12-01
Effect of ethanol on the size and structure of a protein cytochrome C (Cyt C) is investigated using fluorescence correlation spectroscopy (FCS) and molecular dynamics (MD) simulations. For FCS studies, Cyt C is covalently labeled with a fluorescent probe, alexa 488. FCS studies indicate that on addition of ethanol, the size of the protein varies non-monotonically. The size of Cyt C increases (i.e., the protein unfolds) on addition of alcohol (ethanol) up to a mole fraction of 0.2 (44.75% v/v) and decreases at higher alcohol concentration. In order to provide a molecular origin of this structural transition, we explore the conformational free energy landscape of Cyt C as a function of radius of gyration (Rg) at different compositions of water-ethanol binary mixture using MD simulations. Cyt C exhibits a minimum at Rg ˜ 13 Å in bulk water (0% alcohol). Upon increasing ethanol concentration, a second minimum appears in the free energy surface with gradually larger Rg up to χEtOH ˜ 0.2 (44.75% v/v). This suggests gradual unfolding of the protein. At a higher concentration of alcohol (χEtOH > 0.2), the minimum at large Rg vanishes, indicating compaction. Analysis of the contact map and the solvent organization around protein indicates a preferential solvation of the hydrophobic residues by ethanol up to χEtOH = 0.2 (44.75% v/v) and this causes the gradual unfolding of the protein. At high concentration (χEtOH = 0.3 (58% v/v)), due to structural organization in bulk water-ethanol binary mixture, the extent of preferential solvation by ethanol decreases. This causes a structural transition of Cyt C towards a more compact state.
Marchetti, Barbara; Karsili, Tolga N. V.; Cipriani, Maicol; Hansen, Christopher S.; Ashfold, Michael N. R.
2017-07-01
The near ultraviolet spectroscopy and photodissociation dynamics of two families of asymmetrically substituted thiophenols (2- and 3-YPhSH, with Y = F and Me) have been investigated experimentally (by H (Rydberg) atom photofragment translational spectroscopy) and by ab initio electronic structure calculations. Photoexcitation in all cases populates the 11ππ* and/or 11πσ* excited states and results in S-H bond fission. Analyses of the experimentally obtained total kinetic energy release (TKER) spectra yield the respective parent S-H bond strengths, estimates of ΔE(A ˜ -X ˜ ), the energy splitting between the ground (X ˜ ) and first excited (A ˜ ) states of the resulting 2-(3-)YPhS radicals, and reveal a clear propensity for excitation of the C-S in-plane bending vibration in the radical products. The companion theory highlights roles for both geometric (e.g., steric effects and intramolecular H-bonding) and electronic (i.e., π (resonance) and σ (inductive)) effects in determining the respective parent minimum energy geometries, and the observed substituent and position-dependent trends in S-H bond strength and ΔE(A ˜ -X ˜ ). 2-FPhSH shows some clear spectroscopic and photophysical differences. Intramolecular H-bonding ensures that most 2-FPhSH molecules exist as the syn rotamer, for which the electronic structure calculations return a substantial barrier to tunnelling from the photoexcited 11ππ* state to the 11πσ* continuum. The 11ππ* ← S0 excitation spectrum of syn-2-FPhSH thus exhibits resolved vibronic structure, enabling photolysis studies with a greater parent state selectivity. Structure apparent in the TKER spectrum of the H + 2-FPhS products formed when exciting at the 11ππ* ← S0 origin is interpreted by assuming unintended photoexcitation of an overlapping resonance associated with syn-2-FPhSH(v33 = 1) molecules. The present data offer tantalising hints that such out-of-plane motion influences non-adiabatic coupling in the vicinity
Structural dynamic modifications via models
Indian Academy of Sciences (India)
T K Kundra
2000-06-01
Structural dynamic modification techniques attempt to reduce dynamic design time and can be implemented beginning with spatial models of structures, dynamic test data or updated models. The models assumed in this discussion are mathematical models, namely mass, stiffness, and damping matrices of the equations of motion of a structure. These models are identified/extracted from dynamic test data viz. frequency response functions (FRFs). Alternatively these models could have been obtained by adjusting or updating the finite element model of the structure in the light of the test data. The methods of structural modification for getting desired dynamic characteristics by using modifiers namely mass, beams and tuned absorbers are discussed.
Indian Academy of Sciences (India)
APRAMITA CHAND; SNEHASIS CHOWDHURI
2016-06-01
Effects of dimethyl-sulfoxide (DMSO) on the hydrogen bonding structure and dynamics in aqueousN-methylacetamide (NMA) solution are investigated by classical molecular dynamics simulations. Themodifications of structure and interaction between water and NMA in presence of DMSO molecules are calculatedby various site-site radial distribution functions and average interaction energies between these speciesin the solution. It is observed that the aqueous peptide hydrogen bond interaction is relatively stronger withincreasing concentration of DMSO, whereas methyl-methyl interaction between NMA and DMSO decreasessignificantly. The DMSO molecule prefers to interact with amide-hydrogen of NMA even at lower DMSO concentration.The lifetimes and structural-relaxation times of NMA-water, water-water and DMSO-water hydrogenbonds are found to increase with increasing DMSO concentration in the solution. The slower translationaland rotational dynamics of NMA is observed in concentrated DMSO solution due to formation of strongerinter-species hydrogen bonds in the solution.
Effect of node attributes on the temporal dynamics of network structure
Momeni, Naghmeh; Fotouhi, Babak
2017-03-01
Many natural and social networks evolve in time and their structures are dynamic. In most networks, nodes are heterogeneous, and their roles in the evolution of structure differ. This paper focuses on the role of individual attributes on the temporal dynamics of network structure. We focus on a basic model for growing networks that incorporates node attributes (which we call "quality"), and we focus on the problem of forecasting the structural properties of the network in arbitrary times for an arbitrary initial network. That is, we address the following question: If we are given a certain initial network with given arbitrary structure and known node attributes, then how does the structure change in time as new nodes with given distribution of attributes join the network? We solve the model analytically and obtain the quality-degree joint distribution and degree correlations. We characterize the role of individual attributes in the position of individual nodes in the hierarchy of connections. We confirm the theoretical findings with Monte Carlo simulations.
Hou, X. N.; Liu, Y. H.; Huang, F.; Jiang, S. Z.; Chen, Z. Y.; Zhang, R. Y.
2016-09-01
Effects of radial electric field on the structures and dynamics of dust dipoles are studied by molecular dynamics simulations. The dipoles' configuration and mean distance to the system center are used to illustrate the structures of the whole system. It is shown that the dipole particles can arrange themselves into ring-like structures in the absence of external electric field, which can gradually transform to vortex, and then to radial arrangement with the increase of the strength of electric field. The trajectories, mean square displacement, and the mean speed in radial and tangential directions of dipoles are investigated to depict the effects of the radial electric filed on the collective motion of dust dipolar particles, which are closely associated with the growth of dust particle, especially for the formation of rod-like and some other complex fractal dust particles.
Structural Dynamics of Maneuvering Aircraft.
1987-09-01
AD-RI92 376 STRUCTURAL DYNAMICS OF MANEUVERING RIRCRAFT(U) CONRAD I TECHNOLOGIES INC KING OF PRUSSIA PR M M REDDI SEP 97 CTI-8601 NRDC-88014-69...REPORT NO. NADC-8014-60 STRUCTURAL DYNAMICS OF MANEUVERING AIRCRAFT M. Mahadeva Reddi .4 Conrad Technologies, Inc. 650 S. Henderson Rd. D T IQ King of...NO A0 CCESSION NO. R02303001 107601 11. TITLE (Include Security Classfication) (u) STRUCTURAL DYNAMICS OF MANEUVERING AIRCRAFT 12. PERSONAL AUTHORS) M
Effect of asphaltene structure on association and aggregation using molecular dynamics.
Sedghi, Mohammad; Goual, Lamia; Welch, William; Kubelka, Jan
2013-05-01
The aggregation of asphaltenes has been established for decades by numerous experimental techniques; however, very few studies have been performed on the association free energy and asphaltene aggregation in solvents. The lack of reliable and coherent data on the free energy of association and aggregation size of asphaltene has imposed severe limitations on the thermodynamic modeling of asphaltene phase behavior. Current thermodynamic models either consider asphaltenes as non-associating components or use fitting parameters to characterize the association. In this work, the relations between Gibbs free energy of asphaltene association and asphaltene molecular structure are studied using molecular dynamics (MD). The free energy of association is computed from the potential of mean force profile along the separation distance between the centers of mass of two asphaltene molecules using the umbrella sampling technique in the GROMACS simulation package. The average aggregation number for asphaltene nanoaggregates and clusters is also calculated through MD simulations of 36 asphaltene molecules in toluene and heptane in order to estimate the effects of association free energy and steric repulsion on the aggregation behavior of asphaltenes. Our simulation results confirm that the interactions between aromatic cores of asphaltene molecules are the major driving force for association as the energy of association increases substantially with the number of aromatic rings. Moreover, heteroatoms attached to the aromatic cores have much more influence on the association free energy than to ones attached to the aliphatic chains. The length and number of aliphatic chains do not seem to have a noticeable effect on asphaltene dimerization; however, they have a profound effect on asphaltene aggregation size since steric repulsion can prevent asphaltenes from forming T-shape configurations and therefore decrease the aggregation size of asphaltenes significantly. Our MD simulation
Neutron Scattering Studies of Collective Effects in the Dynamic and Static Structure of Dense Fluids
Youden, James P. A.
The dynamic structure factors S(Q,omega ) for dense nitrogen (1.3 rho_ {c} and 0.9 rho_ {c}, where rho_{c } is the critical density) and krypton (1.8 rho_{c}) were measured in the low Q region of 0.5-1.5 nm ^{-1}. While the continuum theory of linearized hydrodynamics is valid up to the lower limit of this Q-range, deviations are observed for larger Q. For the two states of nitrogen, the experimental spectra are successfully described by the modification of the hydrodynamic theory to include the viscosity relaxation time tau_{nu}. Furthermore, the values of tau_{nu} derived from the experimental S(Q,omega ) spectra are in agreement with the estimates provided within the equal relaxation time approximation. The use of the relaxation time tau_{ nu} can also be used to explain the S( Q,omega) spetra for ^ {36}Ar gas (0.63 rho_ {c} and 0.25 rho_ {c}) as measured by Bafile et al. (1990), and which have been previously examined in terms of the three generalized Lorentzians of the extended hydrodynamic model (Bafile et al., 1990). The differences between these two approaches to a generalized hydrodynamic model are briefly discussed. For the krypton S(Q,omega), the deviations from the continuum theory at the larger Q values are more pronounced, especially as manifested through the dominance of the central mode in the experimental spectra. This behaviour has yet to be explained; and indeed a detailed analysis of the krypton data is limited by the relatively poor quality of the data, which suffers from the large neutron absorption in the natural isotopic compositition. In the static structure, the effects of the many -body interactions in dense gaseous krypton (0.9 -2.1 rho_{c}) and xenon (2.2-2.6 rho_ {c}) were investigated in the range 4 Egelstaff, 1988a). While the observed variation, as determined through the position of the main diffraction maxima, is similar to that given by the inclusion of the Axilrod-Teller (1943) triple-dipole interaction, further small deviations
Energy Technology Data Exchange (ETDEWEB)
Persano Adorno, D.; Capizzo, M.C.; Zarcone, M. [Dipartimento di Fisica e Tecnologie Relative, Viale delle Scienze, Ed. 18, 90128, Palermo (Italy)
2006-08-15
We present results obtained using a three-dimensional multivalleys Monte Carlo (MC) model to simulate the nonlinear carrier dynamics under the influence of an intense sub-terahertz electric field in a doped bulk semiconductor. By self-consistently coupling a one-dimensional Poisson solver to the ensemble MC code we simulate also the nonlinear carrier dynamics in n{sup +}nn{sup +} structures operating under large-amplitude periodic signals and investigate the voltage-current characteristic hysteresis cycle and the high-order harmonic efficiency. For both cases we discuss the dependence of the nonlinearities and of the harmonic generation efficiency on the frequency and the intensity of the alternating signal. (copyright 2006 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)
Energy Technology Data Exchange (ETDEWEB)
Harrach, Michael F., E-mail: harrach@fkp.tu-darmstadt.de; Klameth, Felix; Drossel, Barbara; Vogel, Michael, E-mail: michael.vogel@physik.tu-darmstadt.de [Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt (Germany)
2015-01-21
We perform molecular dynamics simulations to observe the structure and dynamics of SPC/E water in amorphous silica pores and amorphous ice pores with radii slightly larger than 10 Å. In addition to atomically rough pores, we construct completely smooth pores such that the potential felt at a given distance from the pore wall is an averaged atomic potential. As compared to rough walls, smooth walls induce stronger distortions of water structure for both silica and ice confinements. On the other hand, unlike the smooth pores, the rough pores strongly slow down water dynamics at the pore wall. The slowdown vanishes when reducing the atomic charges in the wall, i.e., when varying the hydroaffinity, while keeping the surface topology, indicating that it is not a geometric effect. Rather, it is due to the fact that the wall atoms provide a static energy landscape along the surface, e.g., fixed anchor-points for hydrogen bonds, to which the water molecules need to adapt, blocking channels for structural rearrangement. In the smooth pores, water dynamics can be faster than in the bulk liquid not only at the pore wall but also in the pore center. Changes in the tetrahedral order rather than in the local density are identified as the main cause for this change of the dynamical behavior in the center of smooth pores.
Films, layers, and droplets: The effect of near-wall fluid structure on spreading dynamics
Yin, Hanyu; Sibley, David N.; Thiele, Uwe; Archer, Andrew J.
2017-02-01
We present a study of the spreading of liquid droplets on a solid substrate at very small scales. We focus on the regime where effective wetting energy (binding potential) and surface tension effects significantly influence steady and spreading droplets. In particular, we focus on strong packing and layering effects in the liquid near the substrate due to underlying density oscillations in the fluid caused by attractive substrate-liquid interactions. We show that such phenomena can be described by a thin-film (or long-wave or lubrication) model including an oscillatory Derjaguin (or disjoining or conjoining) pressure and explore the effects it has on steady droplet shapes and the spreading dynamics of droplets on both an adsorption (or precursor) layer and completely dry substrates. At the molecular scale, commonly used two-term binding potentials with a single preferred minimum controlling the adsorption layer height are inadequate to capture the rich behavior caused by the near-wall layered molecular packing. The adsorption layer is often submonolayer in thickness, i.e., the dynamics along the layer consists of single-particle hopping, leading to a diffusive dynamics, rather than the collective hydrodynamic motion implicit in standard thin-film models. We therefore modify the model in such a way that for thicker films the standard hydrodynamic theory is realized, but for very thin layers a diffusion equation is recovered.
Separdar, L.; Davatolhagh, S.
2016-12-01
Molecular dynamics simulations at constant (N , V , T) are used to study the mutual effects of gold nanoparticles on the structure and dynamics of Kob-Andersen binary Lennard-Jones (BLJ) liquid within the framework of mode coupling theory of dynamic glass transition in the reciprocal space. The results show the 'softening' effect of the gold nanoparticles on the liquid dynamics in terms of (i) reducing the mode coupling crossover temperature Tc with respect to that of the bulk BLJ (i.e. BLJ without nanoparticles), (ii) decreasing the time interval of β-relaxation, and (iii) decreasing the exponent γ characterizing the power-law behavior of the α-relaxation time. This softening effect is explained in terms of the van der Waals attraction between the gold atoms comprising the nanoparticle and the BLJ host atoms, such that adsorption of host atoms onto the nanoparticle surface creates more space or free-volume for the other atoms to diffuse. By the same token interactions of purely excluded-volume-type are expected to result in the opposite effect. It is also noted that, much unlike BLJ host particles, the dynamics of gold nanoparticles is much less dependent on the wave-vector and that it exhibits a nearly exponential behavior in the α-relaxation regime.
Efficiency of fiber reinforced concrete application in structures subjected to dynamic effects
Directory of Open Access Journals (Sweden)
Morozov Valeriy Ivanovich
2014-03-01
Full Text Available Fiber reinforced concretes possess high strength under dynamic loadings, which include impact loads, thanks to their high structural viscosity. This is the reason for using them in difficult operating conditions, where increasing the performance characteristics and the structure durability is of prime importance, and the issues of the cost become less significant. Applying methods of disperse reinforcement is most challenging in case of subtle high-porous materials on mineral binders, for example foamed concrete. At the same time, the experiments conducted in Russia and abroad show, that also in other cases the concrete strength resistance several times increases as a result of disperse reinforcement. This doesn't depend on average density of the concrete and type of fiber used. In the article the fibre reinforced concrete impact resistance is analysed. Recommendations are given in regard to fibre concrete application in manufacture of monolithic floor units for industrial buildings and precast piles.
Dynamic analysis and design of offshore structures
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...
Zafar Mujawar; Prakarsh Sangave
2015-01-01
Steel-concrete composite construction has gained wide acceptance all over the world as an alternative for pure steel and pure concrete construction. However this approach is a new concept for construction industry. R.C.C are no longer economical because of their increased dead load, hazardous formwork. The present study deals with comparison of reinforced concrete, steel and composite structures under the effect of static and dynamic loads. The results of this work show that compo...
Films, layers and droplets: The effect of near-wall fluid structure on spreading dynamics
Yin, Hanyu; Thiele, Uwe; Archer, Andrew J
2016-01-01
We present a study of the spreading of liquid droplets on a solid substrate at very small scales. We focus on the regime where effective wetting energy (binding potential) and surface tension effects significantly influence steady and spreading droplets. In particular, we focus on strong packing and layering effects in the liquid near the substrate due to underlying density oscillations in the fluid caused by attractive substrate-liquid interactions. We show that such phenomena can be described by a thin-film (or long-wave or lubrication) model including an oscillatory Derjaguin (or disjoining/conjoining) pressure, and explore the effects it has on steady droplet shapes and the spreading dynamics of droplets on both, an adsorption (or precursor) layer and completely dry substrates. At the molecular scale, commonly used two-term binding potentials with a single preferred minimum controlling the adsorption layer height are inadequate to capture the rich behaviour caused by the near-wall layered molecular packin...
Jung, Kwanghee; Takane, Yoshio; Hwang, Heungsun; Woodward, Todd S.
2012-01-01
We propose a new method of structural equation modeling (SEM) for longitudinal and time series data, named Dynamic GSCA (Generalized Structured Component Analysis). The proposed method extends the original GSCA by incorporating a multivariate autoregressive model to account for the dynamic nature of data taken over time. Dynamic GSCA also…
The effect of network structure on innovation initiation process: an evolutionary dynamics approach
Jafari, Afshin; Zolfagharzadeh, Mohammad Mahdi; Mohammadi, Mehdi
2016-01-01
In this paper we have proposed a basic agent-based model based on evolutionary dynamics for investigating innovation initiation process. In our model we suppose each agent will represent a firm which is interacting with other firms through a given network structure. We consider a two-hit process for presenting a potentially successful innovation in this model and therefore at each time step each firm can be in on of three different stages which are respectively, Ordinary, Innovative, and Successful. We design different experiments in order to investigate how different interaction networks may affect the process of presenting a successful innovation to the market. In this experiments, we use five different network structures, i.e. Erd\\H{o}s and R\\'enyi, Ring Lattice, Small World, Scale-Free and Distance-Based networks. According to the results of the simulations, for less frequent innovations like radical innovation, local structures are showing a better performance comparing to Scale-Free and Erd\\H{o}s and R\\...
Directory of Open Access Journals (Sweden)
Yotam Luz
Full Text Available Spike-Timing Dependent Plasticity (STDP is characterized by a wide range of temporal kernels. However, much of the theoretical work has focused on a specific kernel - the "temporally asymmetric Hebbian" learning rules. Previous studies linked excitatory STDP to positive feedback that can account for the emergence of response selectivity. Inhibitory plasticity was associated with negative feedback that can balance the excitatory and inhibitory inputs. Here we study the possible computational role of the temporal structure of the STDP. We represent the STDP as a superposition of two processes: potentiation and depression. This allows us to model a wide range of experimentally observed STDP kernels, from Hebbian to anti-Hebbian, by varying a single parameter. We investigate STDP dynamics of a single excitatory or inhibitory synapse in purely feed-forward architecture. We derive a mean-field-Fokker-Planck dynamics for the synaptic weight and analyze the effect of STDP structure on the fixed points of the mean field dynamics. We find a phase transition along the Hebbian to anti-Hebbian parameter from a phase that is characterized by a unimodal distribution of the synaptic weight, in which the STDP dynamics is governed by negative feedback, to a phase with positive feedback characterized by a bimodal distribution. The critical point of this transition depends on general properties of the STDP dynamics and not on the fine details. Namely, the dynamics is affected by the pre-post correlations only via a single number that quantifies its overlap with the STDP kernel. We find that by manipulating the STDP temporal kernel, negative feedback can be induced in excitatory synapses and positive feedback in inhibitory. Moreover, there is an exact symmetry between inhibitory and excitatory plasticity, i.e., for every STDP rule of inhibitory synapse there exists an STDP rule for excitatory synapse, such that their dynamics is identical.
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.
Directory of Open Access Journals (Sweden)
Tufoi Marius
2014-07-01
Full Text Available This paper series presents an analysis regarding the dynamics of sandwich composite beams, embedded at one end, in order to highlight the effect of geometrical and material discontinuities upon the natural frequencies. In first part (Part I, analysis was performed with EulerBernoulli analytical method for determining the vibration modes and in second part (Part II, analysis was performed with numerical simulation in SolidWorks software for a five-layer composite. In the last section of the paper, an example is shown regarding how to interpret the obtained results.
Horner, Ian J; Kraut, Nadine D; Hurst, Jerod J; Rook, Alyssa M; Collado, Crystal M; Atilla-Gokcumen, G Ekin; Maziarz, E Peter; Liu, X Michael; Merchea, Mohinder M; Bright, Frank V
2015-08-20
Multipurpose solutions (MPS) are a single solution that functions to simultaneously rinse, disinfect, clean, and store soft contact lenses. Several commercial MPS products contain polyhexamethylene biguanide (PHMB) and/or polyquaternium-1 (PQ-1) as antimicrobial agents. In this paper we have created an in vitro small unilamellar vesicle (SUV) model of the corneal epithelial surface, and we have assessed the interactions of PHMB and PQ-1 with several model biomembranes by using fluorescence spectroscopy, dynamic light scattering (DLS), and liquid chromatography-mass spectrometry (LC-MS). Steady-state and time-resolved fluorescence were used to assess the membrane acyl chain and polar headgroup region local microenvironment as a function of added PHMB or PQ-1. DLS was used to detect and quantify SUV aggregation induced by PHMB and PQ-1. LC-MS was used to determine the liposomal composition from any precipitated materials in comparison to the as-prepared SUVs. The results are consistent with PHMB adsorbing onto and PQ-1 intercalating into the biomembrane structure. The differences between the two interaction mechanisms have substantial impacts on the biomembrane dynamics and stability.
Effects of Structured Ionomer Interfaces on Water Diffusion: Molecular Dynamics Simulation Insight
Aryal, Dipak; Perahia, Dvora; Grest, Gary
The dynamics of solvent molecules across structured ionomers interfaces is crucial to innovative technologies with selective controlled transport. These polymers consist of ionizable blocks facilitating transport tethered to mechanical stability enhancing ones, where their incompatibility drives compounded interfaces. Here water penetration through the interface of an A-B-C-B-A co-polymer is probed by atomistic molecular dynamics simulations where C is a randomly sulfonated polystyrene with sulfonation fractions f = 0 to 0.55, B is poly (ethylene-r-propylene) and A is poly (t-butyl styrene). For f>0, a two-step process with slow diffusion at the early stages is observed where water molecules transverse the hydrophobic rich surface before reaching the hydrophilic regime. Water molecules then diffuse along the percolating network of the ionic center block. Increasing the temperature and sulfonation fraction enhances both the rate of diffusion and the overall water uptake. This work is partially supported by DOE: DE-SC007908.
Nikolaev, V P
2000-07-01
To gain insight into the special nature of gas bubbles that may form in astronauts, aviators and divers, we developed a mathematical model which describes the following: 1) the dynamics of extravascular bubbles formed in intercellular cavities of a hypothetical tissue undergoing decompression; and 2) the dynamics of nitrogen tension in a thin layer of intercellular fluid and in a thick layer of cells surrounding the bubbles. This model is based on the assumption that, due to limited cellular membrane permeability for gas, a value of effective nitrogen diffusivity in the massive layer of cells in the radial direction is essentially lower compared to conventionally accepted values of nitrogen diffusivity in water and body tissues. Due to rather high nitrogen diffusivity in intercellular fluid, a bubble formed just at completion of fast one-stage reduction of ambient pressure almost instantly grows to the size determined by the initial volume of the intercellular cavity, surface tension of the fluid, the initial nitrogen tension in the tissue, and the level of final pressure. The rate of further bubble growth and maximum bubble size depend on comparatively low effective nitrogen diffusivity in the cell layer, the tissue perfusion rate, the initial nitrogen tension in the tissue, and the final ambient pressure. The tissue deformation pressure performs its conservative action on bubble dynamics only in a limited volume of tissue (at a high density of formed bubbles). Our model is completely consistent with the available data concerning the random latency times to the onset of decompression sickness (DCS) symptoms associated with hypobaric decompressions simulating extravehicular activity. We believe that this model could be used as a theoretical basis for development of more adequate methods for the DCS risk prediction.
Directory of Open Access Journals (Sweden)
Zafar Mujawar
2015-01-01
Full Text Available Steel-concrete composite construction has gained wide acceptance all over the world as an alternative for pure steel and pure concrete construction. However this approach is a new concept for construction industry. R.C.C are no longer economical because of their increased dead load, hazardous formwork. The present study deals with comparison of reinforced concrete, steel and composite structures under the effect of static and dynamic loads. The results of this work show that composite structures are best suited for high rise buildings compared to that of steel and reinforced concrete structures. Response spectrum method is used for comparison of three structures with the help of ETABS software.
Optical Kerr effect of liquid water: a new insight into the vibrational and structural dynamics
Taschin, A; Eramo, R; Righini, R; Torre, R
2013-01-01
The liquid and supercooled states of water show a series of anomalies whose nature is lively debated. A key role is attributed to the formation of structural aggregations induced by critical phenomena occurring deep in the supercooled region, not experimentally accessible for bulk water. This explain why, despite the numerous experimental investigations, the nature of water anomalies and the hidden critical processes remain elusive. Here we present a time-resolved optical Kerr effect investigation of the vibrational and relaxation processes in supercooled bulk water. The experiment measures the water intermolecular vibrations and the structural relaxation process in an extended temperature range, and with unpreceded data quality. A mode-coupling analysis of the experimental data allows the characterization of the intermolecular vibrational modes and of their interplay with the structural relaxation process.
Density, structure, and dynamics of water: the effect of van der Waals interactions.
Wang, Jue; Román-Pérez, G; Soler, Jose M; Artacho, Emilio; Fernández-Serra, M-V
2011-01-14
It is known that ab initio molecular dynamics (AIMD) simulations of liquid water at ambient conditions, based on the generalized gradient approximation (GGA) to density functional theory (DFT), with commonly used functionals fail to produce structural and diffusive properties in reasonable agreement with experiment. This is true for canonical, constant temperature simulations where the density of the liquid is fixed to the experimental density. The equilibrium density, at ambient conditions, of DFT water has recently been shown by Schmidt et al. [J. Phys. Chem. B, 113, 11959 (2009)] to be underestimated by different GGA functionals for exchange and correlation, and corrected by the addition of interatomic pair potentials to describe van der Waals (vdW) interactions. In this contribution we present a DFT-AIMD study of liquid water using several GGA functionals as well as the van der Waals density functional (vdW-DF) of Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)]. As expected, we find that the density of water is grossly underestimated by GGA functionals. When a vdW-DF is used, the density improves drastically and the experimental diffusivity is reproduced without the need of thermal corrections. We analyze the origin of the density differences between all the functionals. We show that the vdW-DF increases the population of non-H-bonded interstitial sites, at distances between the first and second coordination shells. However, it excessively weakens the H-bond network, collapsing the second coordination shell. This structural problem is partially associated to the choice of GGA exchange in the vdW-DF. We show that a different choice for the exchange functional is enough to achieve an overall improvement both in structure and diffusivity.
Structural dynamics in rotating systems
Kiraly, Louis J.
1993-01-01
Major issues and recent advances in the structural dynamics of rotating systems are summarized. The objectives and benefits of such systems are briefly discussed. Directions for future research are suggested.
Hysteresis in structural dynamics
Energy Technology Data Exchange (ETDEWEB)
Ivanyi, A., E-mail: aivanyi@morpheus.pte.hu [Pollack Mihaly Faculty of Engineering, University of Pecs, Boszorkany u. 2, H-7624 Pecs (Hungary); Ivanyi, P., E-mail: peteri@morpheus.pte.hu [Pollack Mihaly Faculty of Engineering, University of Pecs, Boszorkany u. 2, H-7624 Pecs (Hungary); Ivanyi, M.M., E-mail: ivanyi@uvaterv.hu [Pollack Mihaly Faculty of Engineering, University of Pecs, Boszorkany u. 2, H-7624 Pecs (Hungary); UVATERV Ltd, Budapest, 1117, Dombovari ut 17, Budapest (Hungary); Ivanyi, M., E-mail: drivanyi@pmmk.pte.hu [Pollack Mihaly Faculty of Engineering, University of Pecs, Boszorkany u. 2, H-7624 Pecs (Hungary)
2012-05-01
In this paper the Preisach hysteresis model is applied to determine the dynamic behavior of a steel column with mass on the top and loaded by an impulse force. The column is considered as a rigid element, while the fixed end of the column is modeled with a rotational spring of hysterestic characteristic. In the solution of the non-linear dynamical equation of motion the fix-point technique is inserted to the time marching iteration. In the investigation the non-linearity of the rotation spring is modeled with the Preisach hysteresis model. The variation of amplitude and the action time interval of force are changing. The results are plotted in figures.
Liu, Hongjun; Maginn, Edward
2013-09-01
Molecular dynamics simulations were performed to examine the role cation and anion structure have on the performance of ionic liquid (IL) electrolytes for lithium conduction over the temperature range of 320-450 K. Two model ionic liquids were studied: 1-butyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide ([bmim][Tf2N]) and 1-butyl-4-methylpyridinium pyrrolide ([bmpyr][pyl]) doped with Li[Tf2N] and Li[pyl], respectively. The results have demonstrated that the Li+ doped IL containing the planar [bmpyr] cation paired with the planar [pyl] anion significantly outperformed the [bmim][Tf2N] IL. The different coordination of Li+ with the [Tf2N]- or [pyl]- anions produces a remarkable change in IL structure with a concomitant effect on the transport of all ions. For the doped [bmim][Tf2N], each Li+ is coordinated by four oxygen atoms from [Tf2N]- anions. Formation of a rigid structure between Li+ and [Tf2N]- induces a decrease in the mobility of all ions. In contrast, for the doped [bmpyr][pyl], each Li+ is coordinated by two nitrogen atoms from [pyl]- anions. The original alternating structure cation|anion|cation in the neat [bmpyr][pyl] is replaced by another alternating structure cation|anion|Li+|anion|cation in the doped [bmpyr][pyl]. Increases of Li+ mole fraction in doped [bmpyr][pyl] affects the dynamics to a much lesser extent compared with [bmim][Tf2N] and leads to reduced diffusivities of cations and anions, but little change in the dynamics of Li+. More importantly, the calculations predict that the Li+ ion conductivity of doped [bmpyr][pyl] is comparable to that observed in organic liquid electrolytes and is about an order of magnitude higher than that of doped [bmim][Tf2N]. Such Li+ conductivity improvement suggests that this and related ILs may be promising candidates for use as electrolytes in lithium ion batteries and capacitors.
Bossa, Cecilia; Amadei, Andrea; Daidone, Isabella; Anselmi, Massimiliano; Vallone, Beatrice; Brunori, Maurizio; Di Nola, Alfredo
2005-01-01
The results of extended (80-ns) molecular dynamics simulations of wild-type and YQR triple mutant of sperm whale deoxy myoglobin in water are reported and compared with the results of the simulation of the intermediate(s) obtained by photodissociation of CO in the wild-type protein. The opening/closure of pathways between preexistent cavities is different in the three systems. For the photodissociated state, we previously reported a clear-cut correlation between the opening probability and th...
Anisimov, V. N.; Arutiunian, R. V.; Bol'Shov, L. A.; Derkach, O. N.; Kanevskii, M. F.
1989-03-01
The effect of the transverse structure of pulsed CO2 laser emission on the dynamics of laser-induced detonation waves propagating from a metal surface and on plasma transparency recovery is investigated theoretically and experimentally. Particular attention is given to breakdown initiation near the surface. It is suggested that the inclusion of refraction in the plasma into a self-consistent numerical mode is essential for the adequate quantitative description of experimental data on the interaction of laser emission with low-threshold optical breakdown plasmas.
The effect of structurally complex corals and herbivory on the dynamics of Halimeda
Castro-Sanguino, Carolina; Lovelock, Catherine; Mumby, Peter J.
2016-06-01
The calcareous green alga Halimeda is a key contributor to carbonate sediment production on coral reefs. As herbivores have a direct negative effect on the abundance of Halimeda, protection from herbivory is critical for Halimeda growth. Branching corals such as Acropora are likely to provide refugia for Halimeda from grazers, yet studies are scarce. Here, we investigated the vulnerability of two Halimeda species to herbivory using fish exclusion cages and assessed the contribution of coral structural complexity to seasonal changes in Halimeda biomass and morphometrics. While up to 50 % Halimeda abundance was depleted outside cages due to herbivory and the exclusion of large herbivores resulted in an increase in net growth up to threefold, Halimeda recruitment was positively affected by herbivory, more than two times greater outside cages. However, these responses differed between species and seasons; only one species was affected in winter but not summer. Coral structural complexity facilitated an increase of total algal biomass particularly in summer. At the individual level, thalli growing inside the Acropora canopy were always significantly larger (thallus biomass, volume and height) than those growing in exposed areas. We estimated that the carbonate production of Halimeda was nearly three times greater inside refuges provided by Acropora. Because Halimeda species differ in growth rates and susceptibility to grazing, we predict that the ongoing degradation of the habitat complexity provided by branching corals will alter Halimeda community structure and its contribution to local sediment budgets.
Bossa, Cecilia; Amadei, Andrea; Daidone, Isabella; Anselmi, Massimiliano; Vallone, Beatrice; Brunori, Maurizio; Di Nola, Alfredo
2005-01-01
The results of extended (80-ns) molecular dynamics simulations of wild-type and YQR triple mutant of sperm whale deoxy myoglobin in water are reported and compared with the results of the simulation of the intermediate(s) obtained by photodissociation of CO in the wild-type protein. The opening/closure of pathways between preexistent cavities is different in the three systems. For the photodissociated state, we previously reported a clear-cut correlation between the opening probability and the presence of the photolyzed CO in the proximity of the passage; here we show that in wild-type deoxy myoglobin, opening is almost random. In wild-type deoxy myoglobin, the passage between the distal pocket and the solvent is strictly correlated to the presence/absence of a water molecule that simultaneously interacts with the distal histidine side chain and the heme iron; conversely, in the photodissociated myoglobin, the connection with the bulk solvent is always open when CO is in the vicinity of the A pyrrole ring. In YQR deoxy myoglobin, the mutated Gln(E7)64 is stably H-bonded with the mutated Tyr(B10)29. The essential dynamics analysis unveils a different behavior for the three systems. The motion amplitude is progressively restricted in going from wild-type to YQR deoxy myoglobin and to wild-type myoglobin photoproduct. In all cases, the principal motions involve mainly the same regions, but their directions are different. Analysis of the dynamics of the preexisting cavities indicates large fluctuations and frequent connections with the solvent, in agreement with the earlier hypothesis that some of the ligand may escape from the protein through these pathways. PMID:15849248
Antonius, Gabriel; Poncé, Samuel; Lantagne-Hurtubise, Étienne; Auclair, Gabriel; Côté, Michel; Gonze, Xavier
2015-03-01
The electron-phonon coupling in solids renormalizes the band structure, reducing the band gap by several tenths of an eV in light-atoms semiconductors. Using the Allen-Heine-Cardona theory (AHC), we compute the zero-point renormalization (ZPR) as well as the quasiparticle lifetimes of the full band structure in diamond, BN, LiF and MgO. We show how dynamical effects can be included in the AHC theory, and still allow for the use of a Sternheimer equation to avoid the summation over unoccupied bands. The convergence properties of the electron-phonon coupling self-energy with respect to the Brillouin zone sampling prove to be strongly affected by dynamical effects. We complement our study with a frozen-phonon approach, which reproduces the static AHC theory, but also allows to probe the phonon wavefunctions at finite displacements and include anharmonic effects in the self-energy. We show that these high-order components tend to reduce the strongest electron-phonon coupling elements, which affects significantly the band gap ZPR.
Lymphotactin structural dynamics
Volkman, Brian F.; Liu, Tina Y.; Peterson, Francis C.
2009-01-01
Lymphotactin/XCL1, the defining member of the C class of chemokines, undergoes a conformational change that involves the complete restructuring of all stabilizing interactions. Other chemokines are restricted to a single conformation by a pair of conserved disulfide crosslinks, one of which is absent in lymphotactin. This structural interconversion is entirely reversible, and the two-state equilibrium is sensitive to changes in temperature and ionic strength. One species adopts the conserved ...
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.
Hamiltonian mean field model: Effect of network structure on synchronization dynamics.
Virkar, Yogesh S; Restrepo, Juan G; Meiss, James D
2015-11-01
The Hamiltonian mean field model of coupled inertial Hamiltonian rotors is a prototype for conservative dynamics in systems with long-range interactions. We consider the case where the interactions between the rotors are governed by a network described by a weighted adjacency matrix. By studying the linear stability of the incoherent state, we find that the transition to synchrony begins when the coupling constant K is inversely proportional to the largest eigenvalue of the adjacency matrix. We derive a closed system of equations for a set of local order parameters to study the effect of network heterogeneity on the synchronization of the rotors. When K is just beyond the transition to synchronization, we find that the degree of synchronization is highly dependent on the network's heterogeneity, but that for large K the degree of synchronization is robust to changes in the degree distribution. Our results are illustrated with numerical simulations on Erdös-Renyi networks and networks with power-law degree distributions.
Regand, A; Goff, H D
2002-11-01
Ice crystal growth and microstructure of sugarsolutions prepared with stabilizers (carboxymethyl cellulose [CMC], xanthan gum, locust bean gum [LBG], and gelatin) with or without milk solids-nonfat (MSNF) after freezing in a scraped surface heat exchanger and temperature cycling (5 cycles from -6 degrees C to -20 degrees C) were studied. Ice crystal growth was calculated from brightfield microscopic images acquired from samples before and after cycling. Freeze-substitution and low-temperature embedding (LR-Gold resin) were sample preparation techniques utilized for structure analyses by light microscopy and transmission electron microscopy. Differential staining for carbohydrates and proteins allowed the identification of stabilizer gel-like structures in LBG, gelatin, and gelatin/MSNF solutions. In the absence of milk proteins, xanthan and LBG were the most effective at retarding recrystallization, while in their presence, only xanthan had an effect. Cryo-gelation of the LBG was observed but is not the only mechanism of stabilizer action. Thermodynamic incompatibility between biopolymers was observed to promote localized high concentrations of milk proteins located at the ice crystal interface, probably exerting a water-holding action that significantly enhanced the stabilizer effect. Qualitatively, solution heterogeneity (phase separation) was directly proportional to ice crystal growth inhibition. It is suggested that water-holding by stabilizer and proteins, and in some cases steric hindrance induced by a stabilizer gel-like network, caused a reduction in the kinetics of the ice recrystallization phenomena and promoted mechanisms of melt-regrow instead of melt-diffuse-grow recrystallization, thus resulting in the preservation of the ice crystal size and in a small span of the ice crystal size distribution.
Zhang, Ning; Song, Yuechun; Ruan, Xuehua; Yan, Xiaoming; Liu, Zhao; Shen, Zhuanglin; Wu, Xuemei; He, Gaohong
2016-09-21
The relationship between the proton conductive channel and the hydrated proton structure is of significant importance for understanding the deformed hydrogen bonding network of the confined protons which matches the nanochannel. In general, the structure of hydrated protons in the nanochannel of the proton exchange membrane is affected by several factors. To investigate the independent effect of each factor, it is necessary to eliminate the interference of other factors. In this paper, a one-dimensional carbon nanotube decorated with fluorine was built to investigate the independent effects of nanoscale confinement and fluorination on the structural properties of hydrated protons in the nanochannel using classical molecular dynamics simulation. In order to characterize the structure of hydrated protons confined in the channel, the hydrogen bonding interaction between water and the hydrated protons has been studied according to suitable hydrogen bond criteria. The hydrogen bond criteria were proposed based on the radial distribution function, angle distribution and pair-potential energy distribution. It was found that fluorination leads to an ordered hydrogen bonding structure of the hydrated protons near the channel surface, and confinement weakens the formation of the bifurcated hydrogen bonds in the radial direction. Besides, fluorination lowers the free energy barrier of hydronium along the nanochannel, but slightly increases the barrier for water. This leads to disintegration of the sequential hydrogen bond network in the fluorinated CNTs with small size. In the fluorinated CNTs with large diameter, the lower degree of confinement produces a spiral-like sequential hydrogen bond network with few bifurcated hydrogen bonds in the central region. This structure might promote unidirectional proton transfer along the channel without random movement. This study provides the cooperative effect of confinement dimension and fluorination on the structure and hydrogen
Structural Mechanics and Dynamics Branch
Stefko, George
2003-01-01
The 2002 annual report of the Structural Mechanics and Dynamics Branch reflects the majority of the work performed by the branch staff during the 2002 calendar year. Its purpose is to give a brief review of the branch s technical accomplishments. The Structural Mechanics and Dynamics Branch develops innovative computational tools, benchmark experimental data, and solutions to long-term barrier problems in the areas of propulsion aeroelasticity, active and passive damping, engine vibration control, rotor dynamics, magnetic suspension, structural mechanics, probabilistics, smart structures, engine system dynamics, and engine containment. Furthermore, the branch is developing a compact, nonpolluting, bearingless electric machine with electric power supplied by fuel cells for future "more electric" aircraft. An ultra-high-power-density machine that can generate projected power densities of 50 hp/lb or more, in comparison to conventional electric machines, which generate usually 0.2 hp/lb, is under development for application to electric drives for propulsive fans or propellers. In the future, propulsion and power systems will need to be lighter, to operate at higher temperatures, and to be more reliable in order to achieve higher performance and economic viability. The Structural Mechanics and Dynamics Branch is working to achieve these complex, challenging goals.
Yahashiri, Atsushi; Rubach, Jon K; Plapp, Bryce V
2014-02-11
A role for protein dynamics in enzymatic catalysis of hydrogen transfer has received substantial scientific support, but the connections between protein structure and catalysis remain to be established. Valine residues 203 and 207 are at the binding site for the nicotinamide ring of the coenzyme in liver alcohol dehydrogenase and have been suggested to facilitate catalysis with "protein-promoting vibrations" (PPV). We find that the V207A substitution has small effects on steady-state kinetic constants and the rate of hydrogen transfer; the introduced cavity is empty and is tolerated with minimal effects on structure (determined at 1.2 Å for the complex with NAD(+) and 2,3,4,5,6-pentafluorobenzyl alcohol). Thus, no evidence is found to support a role for Val-207 in the dynamics of catalysis. The protein structures and ligand geometries (including donor-acceptor distances) in the V203A enzyme complexed with NAD(+) and 2,3,4,5,6-pentafluorobenzyl alcohol or 2,2,2-trifluoroethanol (determined at 1.1 Å) are very similar to those for the wild-type enzyme, except that the introduced cavity accommodates a new water molecule that contacts the nicotinamide ring. The structures of the V203A enzyme complexes suggest, in contrast to previous studies, that the diminished tunneling and decreased rate of hydride transfer (16-fold, relative to that of the wild-type enzyme) are not due to differences in ground-state ligand geometries. The V203A substitution may alter the PPV and the reorganization energy for hydrogen transfer, but the protein scaffold and equilibrium thermal motions within the Michaelis complex may be more significant for enzyme catalysis.
Dynamics of structural priming
Malhotra, Gaurav
2009-01-01
This thesis is about how our syntactic choice changes with linguistic experience. Studies on syntactic priming show that our decisions are influenced by sentences that we have recently heard or recently spoken. They also show that not all sentences have an equal amount of influence; that repetition of verbs increases priming (the lexical-boost effect) and that some verbs are more susceptible to priming than others. This thesis explores how and why syntactic decisions change with time and what...
Bowerman, Samuel
2015-01-01
Eukaryotes tune the transcriptional activity of their genome by altering the nucleosome core particle through multiple chemical processes. In particular, replacement of the canonical H2A histone with the variants macroH2A and H2A.Z has been shown to affect DNA accessibility and nucleosome stability; however, the processes by which this occurs remain poorly understood. Here, we elucidate the molecular mechanisms of these variants with an extensive molecular dynamics study of the canonical nucleosome along with three variant-containing structures: H2A.Z, macroH2A, and an H2A mutant with macroH2A-like L1 loops. Simulation results show that variant L1 loops play a pivotal role in stabilizing DNA binding to the octamer through direct interactions, core structural rearrangements, and altered allosteric networks in the nucleosome. All variants influence dynamics; however, macroH2A-like systems have the largest effect on energetics. In addition, we provide a comprehensive analysis of allosteric networks in the nucleo...
Structural Dynamic Behavior of Wind Turbines
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).
Coherent Structure Dynamics and Turbulent Effects of Horizontal Axis Marine Energy Devices
Gajardo, D. I.; Escauriaza, C. R.; Ingram, D.
2016-12-01
Harnessing the energy available in the oceans constitutes one of the most promising alternatives for generating clean electricity. There are vast amounts of energy present both in waves and tidal currents so it is anticipated that marine energy will have a major role in non-conventional renewable energy generation in the near to mid future. Nevertheless, before marine hydrokinetic (MHK) devices can be installed in large numbers a better understanding of the physical, social and environmental implications of their operation is needed. This includes understanding the: hydrodynamic processes, interaction with bathymetry, and the local flow characteristics. This study is focused on the effects horizontal axis MHK devices have on flow turbulence and coherent structures. This is especially relevant considering that sites with favourable conditions for MHK devices are tidal channels where a delicate balance exists between the strong tidal currents and the ecosystems. Understanding how MHK devices influence flow conditions, turbulence and energy flux is essential for predicting and assessing the environmental implications of deploying MHK technologies. We couple a Blade Element Momentum Actuator Disk (BEM-AD) model to a Detached Eddy Simulation (DES) flow solver in order to study flow conditions for different configurations of horizontal axis MHK turbines. In this study, we contribute to the understanding of the hydrodynamic behaviour of MHK technologies, and give insights into the effects devices will have on their environment, with emphasis in ambient turbulence and flow characteristics, while keeping in mind that these effects can alter electricity quality and device performance. Work supported by CONICYT grant 80160084, Fondecyt grant 1130940, Chile's Marine Energy Research & Innovation Center (MERIC) CORFO project 14CEI2-28228, and the collaboration between the Pontificia Universidad Católica de Chile and the University of Edinburgh, UK, partially supported by the RC
Relating structure and dynamics in organisation models
Jonkers, C.M.; Treur, J.
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,
Sijtsema, J. J.; Oldehinkel, A. J.; Veenstra, René; Verhulst, F. C.; Ormel, J.
2014-01-01
Both structural (i.e., SES, familial psychopathology, family composition) and dynamic (i.e., parental warmth and rejection) family characteristics have been associated with aggressive and depressive problem development. However, it is unclear to what extent (changes in) dynamic family characteristic
Lesch, Volker; Montes-Campos, Hadrián; Méndez-Morales, Trinidad; Gallego, Luis Javier; Heuer, Andreas; Schröder, Christian; Varela, Luis M
2016-11-28
We report a molecular dynamics study on the effect of electronic polarization on the structure and single-particle dynamics of mixtures of the aprotic ionic liquid 1-ethyl-3-methylimidazolium bis-(trifluoromethylsulfonyl)-imide ([EMIM][TFSI]) doped with a lithium salt with the same anion at 298 K and 1 bar. In particular, we analyze the effect of electron density fluctuations on radial distribution functions, velocity autocorrelation functions, cage correlation functions, mean-squared displacements, and vibrational densities of states, comparing the predictions of the quantum-chemistry-based Atomistic Polarizable Potential for Liquids, Electrolytes, & Polymers (APPLE&P) with those of its nonpolarizable version and those of the standard non-polarizable Optimized Potentials for Liquid Simulations-All Atom (OPLS-AA). We found that the structure of the mixture is scarcely modified by the fluctuations in electron charge of their constituents, but their transport properties are indeed quite drastically changed, with larger mobilities being predicted for the different species in the bulk mixtures with the polarizable force field. Specifically, the mean-squared displacements are larger for the polarizable potentials at identical time intervals and the intermediate subdiffusive plateaus are greatly reduced, so the transition to the diffusive regime takes place much earlier than in the non-polarizable media. Moreover, the correlations of the added cations inside their cages are weakened out earlier and their vibrational densities of states are slightly red-shifted, reflecting the weakening effect of the electronic polarization on the Coulomb coupling in these dense ionic media. The comparison of OPLS-AA with non-polarizable APPLE&P indicates that adding polarization to OPLS-AA is not sufficient to achieve results close to experiments.
Lesch, Volker; Montes-Campos, Hadrián; Méndez-Morales, Trinidad; Gallego, Luis Javier; Heuer, Andreas; Schröder, Christian; Varela, Luis M.
2016-11-01
We report a molecular dynamics study on the effect of electronic polarization on the structure and single-particle dynamics of mixtures of the aprotic ionic liquid 1-ethyl-3-methylimidazolium bis-(trifluoromethylsulfonyl)-imide ([EMIM][TFSI]) doped with a lithium salt with the same anion at 298 K and 1 bar. In particular, we analyze the effect of electron density fluctuations on radial distribution functions, velocity autocorrelation functions, cage correlation functions, mean-squared displacements, and vibrational densities of states, comparing the predictions of the quantum-chemistry-based Atomistic Polarizable Potential for Liquids, Electrolytes, & Polymers (APPLE&P) with those of its nonpolarizable version and those of the standard non-polarizable Optimized Potentials for Liquid Simulations-All Atom (OPLS-AA). We found that the structure of the mixture is scarcely modified by the fluctuations in electron charge of their constituents, but their transport properties are indeed quite drastically changed, with larger mobilities being predicted for the different species in the bulk mixtures with the polarizable force field. Specifically, the mean-squared displacements are larger for the polarizable potentials at identical time intervals and the intermediate subdiffusive plateaus are greatly reduced, so the transition to the diffusive regime takes place much earlier than in the non-polarizable media. Moreover, the correlations of the added cations inside their cages are weakened out earlier and their vibrational densities of states are slightly red-shifted, reflecting the weakening effect of the electronic polarization on the Coulomb coupling in these dense ionic media. The comparison of OPLS-AA with non-polarizable APPLE&P indicates that adding polarization to OPLS-AA is not sufficient to achieve results close to experiments.
Algebraic Structure of Dynamical Systems
2017-05-22
Scholar project report; no. 461 (2017) ALGEBRAIC STRUCTURE OF DYNAMICAL SYSTEMS by MIDN 1/C James P. Talisse United States Naval Academy Annapolis, MD...based on the structure of algebraic objects associated with it. In this project we study two algebraic objects, centralizers and topological full groups...group completely defines the system up to time reversal. We apply numerical estimates to draw conclusions about the algebraic properties of this group
Energy Technology Data Exchange (ETDEWEB)
Marlowe, Ashley E.; Singh, Abhishek; Yingling, Yaroslava G., E-mail: yara_yingling@ncsu.edu
2012-12-01
Understanding sequence dependent mechanical and structural properties of collagen fibrils is important for the development of artificial biomaterials for medical and nanotechnological applications. Moreover, point mutations are behind many collagen associated diseases, including Osteogenesis Imperfecta (OI). We conducted a combination of classical and steered atomistic molecular dynamics simulations to examine the effect of point mutations on structure and mechanical properties of short collagen fibrils which include mutations of glycine to alanine, aspartic acid, cysteine, and serine or mutations of hydroxyproline to arginine, asparagine, glutamine, and lysine. We found that all mutations disrupt structure and reduce strength of the collagen fibrils, which may affect the hierarchical packing of the fibrils. The glycine mutations were more detrimental to mechanical strength of the fibrils (WT > Ala > Ser > Cys > Asp) than that of hydroxyproline (WT > Arg > Gln > Asn > Lys). The clinical outcome for glycine mutations agrees well with the trend in reduction of fibril's tensile strength predicted by our simulations. Overall, our results suggest that the reduction in mechanical properties of collagen fibrils may be used to predict the clinical outcome of mutations. Highlights: Black-Right-Pointing-Pointer All mutations disrupt structure and bonding pattern and reduce strength of the collagen fibrils. Black-Right-Pointing-Pointer Gly based mutations are worst to mechanical integrity of fibrils than that of Hyp. Black-Right-Pointing-Pointer Lys and Arg mutations most dramatically destabilize collagen fibril properties. Black-Right-Pointing-Pointer Clinical outcome of mutations may be related to the reduced mechanical properties of fibrils.
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.
Midfrequency band dynamics of large space structures
Coppolino, Robert N.; Adams, Douglas S.; Levine, Marie B.
2004-09-01
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.
From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors
Ana Zafra Ruano; Elisa Cilia; Couceiro, José R.; Javier Ruiz Sanz; Joost Schymkowitz; Frederic Rousseau; Irene Luque; Tom Lenaerts
2016-01-01
Src Homology 3 domains are ubiquitous small interaction modules known to act as docking sites and regulatory elements in a wide range of proteins. Prior experimental NMR work on the SH3 domain of Src showed that ligand binding induces long-range dynamic changes consistent with an induced fit mechanism. The identification of the residues that participate in this mechanism produces a chart that allows for the exploration of the regulatory role of such domains in the activity of the encompassing...
Directory of Open Access Journals (Sweden)
Zhenyun Tang
2017-01-01
Full Text Available Because of the limitations of testing facilities and techniques, the seismic performance of soil-structure interaction (SSI system can only be tested in a quite small scale model in laboratory. Especially for long-span bridge, a smaller tested model is required when SSI phenomenon is considered in the physical test. The scale effect resulting from the small scale model is always coupled with the dynamic performance, so that the seismic performance of bridge considering SSI effect cannot be uncovered accurately by the traditional testing method. This paper presented the implementation of real-time dynamic substructuring (RTDS, involving the combined use of shake table array and computational engines for the seismic simulation of SSI. In RTDS system, the bridge with soil-foundation system is divided into physical and numerical substructures, in which the bridge is seen as physical substructures and the remaining part is seen as numerical substructures. The interface response between the physical and numerical substructures is imposed by shake table and resulting reaction force is fed back to the computational engine. The unique aspect of the method is to simulate the SSI systems subjected to multisupport excitation in terms of a larger physical model. The substructuring strategy and the control performance associated with the real-time substructuring testing for SSI were performed. And the influence of SSI on a long-span bridge was tested by this novel testing method.
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...... repeated, possibly infinite behavior, 2) finitely specify fine-grained acceptance conditions for (possibly infinite) runs based on the notion of responses and 3) distribute events via roles. We give a graphical notation inspired by related work by van der Aalst et al and formalize the execution semantics...
Structural Dynamics of the Ribosome
Korostelev, Andrei; Ermolenko, Dmitri N.; Noller, Harry F.
2008-01-01
Protein synthesis is inherently a dynamic process, requiring both small- and large-scale movements of tRNA and mRNA. It has long been suspected that these movements might be coupled to conformational changes in the ribosome, and in its RNA moieties in particular. Recently, the nature of ribosome structural dynamics has begun to emerge from a combination of approaches, most notably cryo-EM, X-ray crystallography and FRET. Ribosome movement occurs both on a grand scale, as in the intersubunit r...
Strength of concrete structures under dynamic loading
Energy Technology Data Exchange (ETDEWEB)
Kumpyak, O. G., E-mail: ogkumpyak@yandex.ru; Galyautdinov, Z. R., E-mail: gazr@yandex.ru; Kokorin, D. N., E-mail: kokorindenn@yandex.ru [Tomsk State University of Architecture and Building, 2, Solyanaya Sq., 634003, Tomsk (Russian Federation)
2016-01-15
The use of elastic supports is one the efficient methods of decreasing the dynamic loading. The paper describes the influence of elastic supports on the stress-strain state of steel concrete structures exposed to one-time dynamic loading resulting in failure. Oblique bending beams on elastic supports and their elastic, elastoplastic, and elastoplastic consolidation behavior are considered in this paper. For numerical calculations the developed computer program is used based on the finite element method. Research findings prove high efficiency of elastic supports under dynamic loading conditions. The most effective behavior of elastic supports is demonstrated at the elastoplastic stage. A good agreement is observed between the theoretical and experimental results.
Effects of GPI-anchored TNAP on the dynamic structure of model membranes
Garcia, A. F.; Simão, A. M. S.; Bolean, M; Hoylaerts, M. F.; Millán, J. L.; Ciancaglini, P; Costa-Filho, A. J.
2017-01-01
Tissue-nonspecific alkaline phosphatase (TNAP) plays a crucial role during skeletal mineralization, and TNAP deficiency leads to the soft bone disease hypophosphatasia. TNAP is anchored to the external surface of the plasma membranes by means of a GPI (glycosylphosphatidylinositol) anchor. Membrane-anchored and solubilized TNAP displays different kinetic properties against physiological substrates, indicating that membrane anchoring influences the enzyme function. Here, we used Electron Spin Resonance (ESR) measurements along with spin labeled phospholipids to probe the possible dynamic changes prompted by the interaction of GPI-anchored TNAP with model membranes. The goal was to systematically analyze the ESR data in terms of line shape changes and of alterations in parameters such as rotational diffusion rates and order parameters obtained from non-linear least-squares simulations of the ESR spectra of probes incorporated into DPPC liposomes and proteoliposomes. Overall, the presence of TNAP increased the dynamics and decreased the ordering in the three distinct regions probed by the spin labeled lipids DOPTC (headgroup), and 5- and 16-PCSL (acyl chains). The largest change was observed for 16-PCSL, thus suggesting that GPI-anchored TNAP can give rise to long reaching modifications that could influence membrane processes halfway through the bilayer. PMID:26389140
Directory of Open Access Journals (Sweden)
Zheng-Shou Chen
2012-03-01
Full Text Available This article presents a numerical investigation concerning the effect of two kinds of axially progressing internal flows (namely, upward and downward on fluid–structure interaction (FSI dynamics about a marine riser model which is subject to external shear current. The CAE technology behind the current research is a proposed FSI solution, which combines structural analysis software with CFD technology together. Efficiency validation for the CFD software was carried out first. It has been proved that the result from numerical simulations agrees well with the observation from relating model test cases in which the fluidity of internal flow is ignorable. After verifying the numerical code accuracy, simulations are conducted to study the vibration response that attributes to the internal progressive flow. It is found that the existence of internal flow does play an important role in determining the vibration mode (/dominant frequency and the magnitude of instantaneous vibration amplitude. Since asymmetric curvature along the riser span emerges in the case of external shear current, the centrifugal and Coriolis accelerations owing to up- and downward internal progressive flows play different roles in determining the fluid–structure interaction response. The discrepancy between them becomes distinct, when the velocity ratio of internal flow against external shear current is relatively high.
Smolin, Nikolai; Winter, Roland
2008-01-24
It is now generally agreed that the hydration water and solvational properties play a crucial role in determining the dynamics and hence the functionality of proteins. We present molecular dynamics computer simulation studies on staphylococcal nuclease (SNase) at various temperatures and pressures as well as in different cosolvent solutions containing various concentrations of urea and glycerol. The aim is to provide a molecular level understanding of how different types of cosolvents (chaotropic and kosmotropic) as well as temperature and high hydrostatic pressure modify the structure and dynamics of the hydration water. Taken together, these three intrinsic thermodynamic variables, temperature, pressure, and chemical potential (or activity) of the solvent, are able to influence the stability and function of the protein by protein-solvent dynamic coupling in different ways. A detailed analysis of the structural and dynamical properties of the water and cosolvents at the protein surface (density profile, coordination numbers, hydrogen-bond distribution, average H-bond lifetimes (water-protein and water-water), and average residence time of water in the hydration shell) was carried out, and differences in the structural and dynamical properties of the hydration water in the presence of the different cosolvents and at temperatures between 300 and 400 K and pressures up to 5000 bar are discussed. Furthermore, the results obtained help understand various thermodynamic properties measured for the protein.
Primary structural dynamics in graphite
Energy Technology Data Exchange (ETDEWEB)
Schaefer, Sascha; Liang Wenxi; Zewail, Ahmed H, E-mail: zewail@caltech.edu [Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125 (United States)
2011-06-15
The structural dynamics of graphite and graphene are unique, because of the selective coupling between electron and lattice motions and hence the limit on electric and electro-optic properties. Here, we report on the femtosecond probing of graphite films (1-3 nm) using ultrafast electron crystallography in the transmission mode. Two time scales are observed for the dynamics: a 700 fs initial decrease in diffraction intensity due to lattice phonons in optically dark regions of the Brillouin zone, followed by a 12 ps decrease due to phonon thermalization near the {Gamma} and K regions. These results indicate the non-equilibrium distortion of the unit cells at early time and the subsequent role of long-wavelength atomic motions in the thermalization process. Theory and experiment are now in agreement regarding the nature of nuclear motions, but the results suggest that potential change plays a role in the lateral dynamics of the lattice.
Structurally Dynamic Spin Market Networks
Horváth, Denis; Kuscsik, Zoltán
The agent-based model of stock price dynamics on a directed evolving complex network is suggested and studied by direct simulation. The stationary regime is maintained as a result of the balance between the extremal dynamics, adaptivity of strategic variables and reconnection rules. The inherent structure of node agent "brain" is modeled by a recursive neural network with local and global inputs and feedback connections. For specific parametric combination the complex network displays small-world phenomenon combined with scale-free behavior. The identification of a local leader (network hub, agent whose strategies are frequently adapted by its neighbors) is carried out by repeated random walk process through network. The simulations show empirically relevant dynamics of price returns and volatility clustering. The additional emerging aspects of stylized market statistics are Zipfian distributions of fitness.
Friedmann, P. P.
1984-01-01
An aeroelastic model suitable for the study of aeroelastic and structural dynamic effects in multirotor vehicles simulating a hybrid heavy lift vehicle was developed and applied to the study of a number of diverse problems. The analytical model developed proved capable of modeling a number of aeroelastic problems, namely: (1) isolated blade aeroelastic stability in hover and forward flight, (2) coupled rotor/fuselage aeromechanical problem in air or ground resonance, (3) tandem rotor coupled rotor/fuselage problems, and (4) the aeromechanical stability of a multirotor vehicle model representing a hybrid heavy lift airship (HHLA). The model was used to simulate the ground resonance boundaries of a three bladed hingeless rotor model, including the effect of aerodynamic loads, and the theoretical predictions compared well with experimental results. Subsequently the model was used to study the aeromechanical stability of a vehicle representing a hybrid heavy lift airship, and potential instabilities which could occur for this type of vehicle were identified. The coupling between various blade, supporting structure and rigid body modes was identified.
Numerical Study of Effects of Fluid-Structure Interaction on Dynamic Responses of Composite Plates
2009-09-01
Structure Strain and Kine tic Energy Comparison for Elastic Modulus Variations with Concentrated Force and Clamped Boundary .........................31...side wet) slightly greater for the rectangular shape. 24 The strain and kine tic energy response between the two shap es of plates are shown in...having the same surface area for i mpact and equal mass. A cylindrical shaped impacto r has a circular shape area of i mpact and a rectangular
Directory of Open Access Journals (Sweden)
Mehrnoosh Khajehzadeh
2016-01-01
Conclusion: It can be concluded that the native conformation of the enzyme was stabilized in the sorbitol and glycerol and tend to exclude from the PZase surface, forcing the enzyme to keep it in the compactly folded conformation. The glycerol molecules stabilized PZase by decreasing the loops flexibility and then compacting the enzyme structure. It appears that more stability of PZase in glycerol solution correlates with its amphiphilic orientation, which decreases the unfavorable interactions of hydrophobic regions.
Effects of Structural Damage on Dynamic Behavior at Sandwich Composite Beams – Part II- FEM Analysis
Directory of Open Access Journals (Sweden)
Marius Tufoi
2014-07-01
Full Text Available This paper presents results obtained by modal analysis on composite beam like structures in healthy and damaged state. The aim is to obtain damage “signatures” for all possible damage scenarios and to use these data to assess transversal cracks based on vibration techniques, by involving natural frequency shifts. The analysis was performed in SolidWorks software for a five-layer composite, 20 vibration modes being obtained by numerical simulation.
Dynamic molecular graphs: "hopping" structures.
Cortés-Guzmán, Fernando; Rocha-Rinza, Tomas; Guevara-Vela, José Manuel; Cuevas, Gabriel; Gómez, Rosa María
2014-05-05
This work aims to contribute to the discussion about the suitability of bond paths and bond-critical points as indicators of chemical bonding defined within the theoretical framework of the quantum theory of atoms in molecules. For this purpose, we consider the temporal evolution of the molecular structure of [Fe{C(CH2 )3 }(CO)3 ] throughout Born-Oppenheimer molecular dynamics (BOMD), which illustrates the changing behaviour of the molecular graph (MG) of an electronic system. Several MGs with significant lifespans are observed across the BOMD simulations. The bond paths between the trimethylenemethane and the metallic core are uninterruptedly formed and broken. This situation is reminiscent of a "hopping" ligand over the iron atom. The molecular graph wherein the bonding between trimethylenemethane and the iron atom takes place only by means of the tertiary carbon atom has the longest lifespan of all the considered structures, which is consistent with the MG found by X-ray diffraction experiments and quantum chemical calculations. In contrast, the η(4) complex predicted by molecular-orbital theory has an extremely brief lifetime. The lifespan of different molecular structures is related to bond descriptors on the basis of the topology of the electron density such as the ellipticities at the FeCH2 bond-critical points and electron delocalisation indices. This work also proposes the concept of a dynamic molecular graph composed of the different structures found throughout the BOMD trajectories in analogy to a resonance hybrid of Lewis structures. It is our hope that the notion of dynamic molecular graphs will prove useful in the discussion of electronic systems, in particular for those in which analysis on the basis of static structures leads to controversial conclusions. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Dynamic Range Majority Data Structures
Elmasry, Amr; HE, MENG; Munro, J. Ian; Nicholson, Patrick K.
2011-01-01
Given a set $P$ of coloured points on the real line, we study the problem of answering range $\\alpha$-majority (or "heavy hitter") queries on $P$. More specifically, for a query range $Q$, we want to return each colour that is assigned to more than an $\\alpha$-fraction of the points contained in $Q$. We present a new data structure for answering range $\\alpha$-majority queries on a dynamic set of points, where $\\alpha \\in (0,1)$. Our data structure uses O(n) space, supports queries in $O((\\lg...
Hu, Lin; Wirth, Brian D.; Maroudas, Dimitrios
2017-08-01
We report results on the lattice thermal conductivities of tungsten single crystals containing nanoscale-sized pores or voids and helium (He) nanobubbles as a function of void/bubble size and gas pressure in the He bubbles based on molecular-dynamics simulations. For reference, we calculated lattice thermal conductivities of perfect tungsten single crystals along different crystallographic directions at room temperature and found them to be about 10% of the overall thermal conductivity of tungsten with a weak dependence on the heat flux direction. The presence of nanoscale voids in the crystal causes a significant reduction in its lattice thermal conductivity, which decreases with increasing void size. Filling the voids with He to form He nanobubbles and increasing the bubble pressure leads to further significant reduction of the tungsten lattice thermal conductivity, down to ˜20% of that of the perfect crystal. The anisotropy in heat conduction remains weak for tungsten single crystals containing nanoscale-sized voids and He nanobubbles throughout the pressure range examined. Analysis of the pressure and atomic displacement fields in the crystalline region that surrounds the He nanobubbles reveals that the significant reduction of tungsten lattice thermal conductivity in this region is due to phonon scattering from the nanobubbles, as well as lattice deformation around the nanobubbles and formation of lattice imperfections at higher bubble pressure.
Effects of growth curve plasticity on size-structured population dynamics
DEFF Research Database (Denmark)
Zhang, Lai; Lin, Zhigui; Pedersen, Michael
2011-01-01
primarily exerts destabilizing effects on the system but considerably promotes species coexistence, in comparison with the size-independent mechanism. We conclude that the size-dependent mechanism is, to a large extent, a dispensable component of model ingredients when ontogeny is explicitly taken...
Dynamic Range Majority Data Structures
He, Meng; Nicholson, Patrick K
2011-01-01
Given a set $P$ of coloured points on the real line, we study the problem of answering range $\\alpha$-majority (or "heavy hitter") queries on $P$. More specifically, for a query range $Q$, we want to return each colour that is assigned to more than an $\\alpha$-fraction of the points contained in $Q$. We present a new data structure for answering range $\\alpha$-majority queries on a dynamic set of points, where $\\alpha \\in (0,1)$. Our data structure uses O(n) space, supports queries in $O((\\lg n) / \\alpha)$ time, and updates in $O((\\lg n) / \\alpha)$ amortized time. If the coordinates of the points are integers, then the query time can be improved to $O(\\lg n / (\\alpha \\lg \\lg n) + (\\lg(1/\\alpha))/\\alpha))$. For constant values of $\\alpha$, this improved query time matches an existing lower bound, for any data structure with polylogarithmic update time. We also generalize our data structure to handle sets of points in d-dimensions, for $d \\ge 2$, as well as dynamic arrays, in which each entry is a colour.
Twelve lectures on structural dynamics
Preumont, André
2013-01-01
This text addresses the modeling of vibrating systems with the perspective of finding the model of minimum complexity which accounts for the physics of the phenomena at play. The first half of the book (Ch.1-6) deals with the dynamics of discrete and continuous mechanical systems; the classical approach emphasizes the use of Lagrange's equations. The second half of the book (Ch.7-12) deals with more advanced topics, rarely encountered in the existing literature: seismic excitation, random vibration (including fatigue), rotor dynamics, vibration isolation and dynamic vibration absorbers; the final chapter is an introduction to active control of vibrations. The first part of this text may be used as a one semester course for 3rd year students in Mechanical, Aerospace or Civil Engineering. The second part of the text is intended for graduate classes. A set of problems is provided at the end of every chapter. The author has a 35 years experience in various aspects of Structural dynamics, both in industry (nuclea...
RESEARCH ON NONLINEAR PROBLEMS IN STRUCTURAL DYNAMICS.
Research on nonlinear problems structural dynamics is briefly summarized. Panel flutter was investigated to make a critical comparison between theory...panel flutter in aerospace vehicles, plausible simplifying assumptions are examined in the light of experimental results. Structural dynamics research
Substrate structure and dynamics effect on sorption properties: Theory and experiment
Connolly, Matthew James
Adsorbent materials such as activated carbon and metal organic frameworks (MOFs) have received significant attention for their potential for storage of hydrogen and natural gas. Typically the adsorbent is assumed to consist of rigid slit- or cylindrical-shaped pores. Recent experimental adsorption measurements, however, suggest significant mechanical response breathing of the adsorbent in the presence of an adsorbate. In this thesis, I develop theoretical and computational models which predict high adsorbate densities in narrow carbon pores which give rise to a strong pressure on pore walls. I then present predictions of the mechanical response of the solid to this pressure, and the effect of this response on adsorption isotherms. Neutron scattering measurements of this mechanical response as well as the diffusion of the adsorbate in the breathing Graphene Oxide Framework (GOF) material is presented. In addition, calculations are presented which support a route toward enhancing the binding energy in carbonaceous adsorbates through boron doping via decaborane adsorption and subsequent decomposition.
Effect of joint damping and joint nonlinearity on the dynamics of space structures
Bowden, Mary; Dugundji, John
1988-01-01
Analyses of the effect of linear joint characteristics on the vibrations of a free-free, three-joint beam model show that increasing joint damping increases resonant frequencies and increases modal damping but only to the point where the joint gets 'locked up' by damping. This behavior is different from that predicted by modeling joint damping as proportional damping. Nonlinear analyses of the three-joint model with cubic springs at the joints show all the classical single DOF nonlinear response behavior at each resonance of the multiple DOF system: nondoubling of response for a doubling of forcing amplitude, multiple solutions, jump behavior, and resonant frequency shifts. These properties can be concisely quantified by characteristic backbone curves, which show the locus of resonant peaks for increasing forcing amplitude.
Multiscale structure in eco-evolutionary dynamics
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.
Akaygun, Sevil
2016-01-01
Visualizing the chemical structure and dynamics of particles has been challenging for many students; therefore, various visualizations and tools have been used in chemistry education. For science educators, it has been important to understand how students visualize and represent particular phenomena--i.e., their mental models-- to design more…
Directory of Open Access Journals (Sweden)
J.G. Santos da Silva
2016-11-01
Full Text Available This work aims the development of an analysis methodology to investigate the dynamic behaviour of steelconcrete composite footbridges. The composite footbridge dynamic response is analysed based on two different strategies. Firstly, the traditional simulation of human walking, without consideration of the pedestrianfootbridge dynamic interaction effect is considered. On the other hand, the effect of the dynamics of the pedestrians while crossing footbridges in crowd situations is analysed and the pedestrian-footbridge dynamic interaction, based on the use of biodynamic models is investigated using a second strategy. The investigated structural system corresponds to an existing pedestrian footbridge built on Ayrton Senna Av. in the city of Rio de Janeiro/RJ, Brazil, with a central span of 68.6m. The footbridge dynamic response was obtained and compared to the limiting values proposed by several authors and design standards. The results indicate that the biodynamic loading models lead to peak accelerations values lower than those produced by the traditional methods. These results provided evidence that the pedestrian-structure dynamic interaction effect should be considered when composite footbridges are subjected to flow of pedestrians.
Yanuka-Golub, Keren; Reshef, Leah; Rishpon, Judith; Gophna, Uri
2016-07-01
For microbial fuel cells (MFCs) to become a cost-effective wastewater treatment technology, they must produce a stable electro-active microbial community quickly and operate under realistic wastewater nutrient conditions. The composition of the anodic-biofilm and planktonic-cells communities was followed temporally for MFCs operated under typical laboratory phosphate concentrations (134mgL(-1)P) versus wastewater phosphate concentrations (16mgL(-1)P). A stable peak voltage was attained two-fold faster in MFCs operating under lower phosphate concentration. All anodic-biofilms were composed of well-known exoelectrogenic bacterial families; however, MFCs showing faster startup and a stable voltage had a Desulfuromonadaceae-dominated-biofilm, while biofilms co-dominated by Desulfuromonadaceae and Geobacteraceae characterized slower or less stable MFCs. Interestingly,planktonic-cell concentrations of these bacteria followed a similar trend as the anodic-biofilm and could therefore serve as a biomarker for its formation. These results demonstrate that wastewater-phosphate concentrations do not compromise MFCs efficiency, and considerably speed up startup times.
Structure and dynamics of solutions
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
Dynamic Response of Embedded Structures.
1991-07-15
1 (202) 767-6963 AFOSR/Nh 00 FORM 1473, 83 APR EDITION OF I JAN 73 IS OBSOLETE. Uwc A ____________ SECURITY CLASSIFICATION OF THIS PAGE...4. Baker W. E., Westine P. S., Dodge F. T., "Similarity Methods in Engineering Dynamics", Hayden Book Company, Inc., New Jerset, 1978. 5. Bazant , Z...P., "Size Effect in Blunt Fracture: Concrete, Rock, Metal", ASCE, Journal of Engineering Mechanics, Vol. 110, No. 4, April 1984. 6. Bazant , Z. P
Dynamic range majority data structures
DEFF Research Database (Denmark)
Elmasry, Amr Ahmed Abd Elmoneim; He, Meng; Munro, J. Ian
2011-01-01
Given a set P of n coloured points on the real line, we study the problem of answering range α-majority (or "heavy hitter") queries on P. More specifically, for a query range Q, we want to return each colour that is assigned to more than an α-fraction of the points contained in Q. We present a new...... data structure for answering range α-majority queries on a dynamic set of points, where α ε (0,1). Our data structure uses O(n) space, supports queries in O((lg n)/α) time, and updates in O((lg n)/α) amortized time. If the coordinates of the points are integers, then the query time can be improved to O...
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.
Structural Dynamics of Electronic Systems
Suhir, E.
2013-03-01
The published work on analytical ("mathematical") and computer-aided, primarily finite-element-analysis (FEA) based, predictive modeling of the dynamic response of electronic systems to shocks and vibrations is reviewed. While understanding the physics of and the ability to predict the response of an electronic structure to dynamic loading has been always of significant importance in military, avionic, aeronautic, automotive and maritime electronics, during the last decade this problem has become especially important also in commercial, and, particularly, in portable electronics in connection with accelerated testing of various surface mount technology (SMT) systems on the board level. The emphasis of the review is on the nonlinear shock-excited vibrations of flexible printed circuit boards (PCBs) experiencing shock loading applied to their support contours during drop tests. At the end of the review we provide, as a suitable and useful illustration, the exact solution to a highly nonlinear problem of the dynamic response of a "flexible-and-heavy" PCB to an impact load applied to its support contour during drop testing.
Directory of Open Access Journals (Sweden)
DuBois Debra C
2010-10-01
Full Text Available Abstract Background Comprehensively understanding corticosteroid pharmacogenomic effects is an essential step towards an insight into the underlying molecular mechanisms for both beneficial and detrimental clinical effects. Nevertheless, even in a single tissue different methods of corticosteroid administration can induce different patterns of expression and regulatory control structures. Therefore, rich in vivo datasets of pharmacological time-series with two dosing regimens sampled from rat liver are examined for temporal patterns of changes in gene expression and their regulatory commonalities. Results The study addresses two issues, including (1 identifying significant transcriptional modules coupled with dynamic expression patterns and (2 predicting relevant common transcriptional controls to better understand the underlying mechanisms of corticosteroid adverse effects. Following the orientation of meta-analysis, an extended computational approach that explores the concept of agreement matrix from consensus clustering has been proposed with the aims of identifying gene clusters that share common expression patterns across multiple dosing regimens as well as handling challenges in the analysis of microarray data from heterogeneous sources, e.g. different platforms and time-grids in this study. Six significant transcriptional modules coupled with typical patterns of expression have been identified. Functional analysis reveals that virtually all enriched functions (gene ontologies, pathways in these modules are shown to be related to metabolic processes, implying the importance of these modules in adverse effects under the administration of corticosteroids. Relevant putative transcriptional regulators (e.g. RXRF, FKHD, SP1F are also predicted to provide another source of information towards better understanding the complexities of expression patterns and the underlying regulatory mechanisms of those modules. Conclusions We have proposed a
Directory of Open Access Journals (Sweden)
Frank H Schumann
2015-04-01
Full Text Available Understanding of the effects of the backbone cyclization on the structure and dynamics of a protein is essential for using protein topology engineering to alter protein stability and function. Here we have determined, for the first time, the structure and dynamics of the linear and various circular constructs of the N-SH3 domain from protein c-Crk. These constructs differ in the length and amino acid composition of the cyclization region. The backbone cyclization was carried out using intein-mediated intramolecular chemical ligation between the juxtaposed N- and the C-termini. The structure and backbone dynamics studies were performed using solution NMR. Our data suggest that the backbone cyclization has little effect on the overall three-dimensional structure of the SH3 domain: besides the termini, only minor structural changes were found in the proximity of the cyclization region. In contrast to the structure, backbone dynamics are significantly affected by the cyclization. On the subnanosecond time scale, the backbone of all circular constructs on average appears more rigid than that of the linear SH3 domain; this effect is observed over the entire backbone and is not limited to the cyclization site. The backbone mobility of the circular constructs becomes less restricted with increasing length of the circularization loop. In addition, significant conformational exchange motions (on the sub-millisecond time scale were found in the N-Src loop and in the adjacent β-strands in all circular constructs studied in this work. These effects of backbone cyclization on protein dynamics have potential implications for the stability of the protein fold and for ligand binding.
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.
Li, H.; Gisler, T.
2009-11-01
Single-molecule experiments on polymeric DNA show that the molecule can be overstretched at nearly constant force by about 70% beyond its relaxed contour length. In this publication we use steered molecular dynamics (MD) simulation to study the effect of structural defects on force-extension curves and structures at high elongation in a 30 base pair duplex pulled by its torsionally unconstrained 5' -5' ends. The defect-free duplex shows a plateau in the force-extension curve at 120pN in which large segments with inclined and paired bases (“S-DNA”) near both ends of the duplex coexist with a central B-type segment separated from the former by small denaturation bubbles. In the presence of a base mismatch or a nick, force-extension curves are very similar to the ones of the defect-free duplex. For the duplex with a base mismatch, S-type segments with highly inclined base pairs are not observed; rather, the overstretched duplex consists of B-type segments separated by denaturation bubbles. The nicked duplex evolves, via a two-step transition, into a two-domain structure characterized by a large S-type segment coexisting with several short S-type segments which are separated by short denaturation bubbles. Our results suggest that in the presence of nicks the force-extension curve of highly elongated duplex DNA might reflect locally highly inhomogeneous stretching. Supplementary material in the form of a PDF file available from the Journal web page at 10.1140/epje/i2009-10524-5 and is accessible for authorised users.
Shan, Xiu-Juan; Zhuang, Zhi-Meng; Jin, Xian-Shi; Dai, Fang-Qun
2011-12-01
Based on the bottom trawl survey data in May 2007 and May and June 2008, this paper analyzed the effects of the abundance dynamics of macro-jellyfish on the species composition, distribution, and abundance of fishery resource in the Yangtze River estuary and its adjacent waters. From May 2007 to June 2008, the average catch per haul and the top catch per haul of macro-jellyfish increased, up to 222.2 kg x h(-1) and 1800 kg x h(-1) in June 2008, respectively. The macro-jellyfish were mainly distributed in the areas around 50 m isobath, and not beyond 100 m isobath where was the joint front of the coastal waters of East China Sea, Yangtze River runoff, and Taiwan Warm Current. The main distribution area of macro-jellyfish in June migrated northward, as compared with that in May, and the highest catches of macro-jellyfish in May 2007 and May 2008 were found in the same sampling station (122.5 degrees E, 28.5 degrees N). In the sampling stations with higher abundance of macro-jellyfish, the fishery abundance was low, and the fishery species also changed greatly, mainly composed by small-sized species (Trachurus japonicus, Harpadon nehereus, and Acropoma japonicum) and pelagic species (Psenopsis anomala, Octopus variabilis) and Trichiurus japonicus, and P. anomala accounted for 23.7% of the total catch in June 2008. Larimichthys polyactis also occupied higher proportion of the total catch in sampling stations with higher macro-jellyfish abundance, but the demersal species Lophius litulon was not found, and a few crustaceans were collected. This study showed that macro-jellyfish had definite negative effects on the fishery community structure and abundance in the Yangtze River estuary fishery ecosystem, and further, changed the energy flow patterns of the ecosystem through cascading trophic interactions. Therefore, macro-jellyfish was strongly suggested to be an independent ecological group when the corresponding fishery management measures were considered.
Relating structure and dynamics in organisation models
Jonkers, C.M.; Treur, J.
2008-01-01
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 t
Knock, S.A.; McIntosh, A.R.; Sporns, O.; Kotter, R.; Hagmann, P.; Jirsa, V.K.
2009-01-01
Functionally relevant large scale brain dynamics operates within the framework imposed by anatomical connectivity and time delays due to finite transmission speeds. To gain insight on the reliability and comparability of large scale brain network simulations, we investigate the effects of variations
Resolution of structural heterogeneity in dynamic crystallography.
Ren, Zhong; Chan, Peter W Y; Moffat, Keith; Pai, Emil F; Royer, William E; Šrajer, Vukica; Yang, Xiaojing
2013-06-01
Dynamic behavior of proteins is critical to their function. X-ray crystallography, a powerful yet mostly static technique, faces inherent challenges in acquiring dynamic information despite decades of effort. Dynamic `structural changes' are often indirectly inferred from `structural differences' by comparing related static structures. In contrast, the direct observation of dynamic structural changes requires the initiation of a biochemical reaction or process in a crystal. Both the direct and the indirect approaches share a common challenge in analysis: how to interpret the structural heterogeneity intrinsic to all dynamic processes. This paper presents a real-space approach to this challenge, in which a suite of analytical methods and tools to identify and refine the mixed structural species present in multiple crystallographic data sets have been developed. These methods have been applied to representative scenarios in dynamic crystallography, and reveal structural information that is otherwise difficult to interpret or inaccessible using conventional methods.
Gupta, S.; Fischer, J. K. H.; Lunkenheimer, P.; Loidl, A.; Novak, E.; Jalarvo, N.; Ohl, M.
2016-10-01
We present the relaxation dynamics of glass-forming glycerol mixed with 1.1 nm sized polyhedral oligomeric silsesquioxane (POSS) molecules using dielectric spectroscopy (DS) and two different neutron scattering (NS) techniques. Both, the reorientational dynamics as measured by DS and the density fluctuations detected by NS reveal a broadening of the α relaxation when POSS molecules are added. Moreover, we find a significant slowing down of the α-relaxation time. These effects are in accord with the heterogeneity scenario considered for the dynamics of glasses and supercooled liquids. The addition of POSS also affects the excess wing in glycerol arising from a secondary relaxation process, which seems to exhibit a dramatic increase in relative strength compared to the α relaxation.
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.
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.
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.
Sharma, Anirban; Ghorai, Pradip Kr.
2016-03-01
Composition dependent structural and dynamical properties of aqueous hydrophobic 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) ionic liquid (IL) have been investigated by using all-atom molecular dynamics simulation. We observe that addition of water does not increase significant number of dissociated ions in the solution over the pure state. As a consequence, self-diffusion coefficient of the cation and anion is comparable to each other at all water concentration similar to that is observed for the pure state. Voronoi polyhedra analysis exhibits strong dependence on the local environment of IL concentration. Void and neck distributions in Voronoi tessellation are approximately Gaussian for pure IL but upon subsequent addition of water, we observe deviation from the Gaussian behaviour with an asymmetric broadening with long tail of exponential decay at large void radius, particularly at higher water concentrations. The increase in void space and neck size at higher water concentration facilitates ionic motion, thus, decreasing dynamical heterogeneity and IL reorientation time and increases self-diffusion coefficient significantly.
Pan, Lurong; Aller, Stephen G.
2015-01-01
P-glycoprotein (Pgp) is an ATP-binding cassette (ABC) transporter that alternates between inward- and outward-facing conformations to capture and force substrates out of cells like a peristaltic pump. The high degree of similarity in outward-facing structures across evolution of ABC transporters allowed construction of a high-confidence outward-facing Pgp atomic model based on crystal structures of outward-facing Sav1866 and inward-facing Pgp. The model adhered to previous experimentally determined secondary- and tertiary- configurations during all-atom molecular dynamics simulations in the presence or absence of MgATP. Three long lasting (>100 ns) meta-stable states were apparent in the presence of MgATP revealing new insights into alternating access. The two ATP-binding pockets are highly asymmetric resulting in differential control of overall structural dynamics and allosteric regulation of the drug-binding pocket. Equilibrated Pgp has a considerably different electrostatic profile compared to Sav1866 that implicates significant kinetic and thermodynamic differences in transport mechanisms. PMID:25600711
Heckman, James J; Humphries, John Eric; Veramendi, Gregory
2016-02-01
This paper develops robust models for estimating and interpreting treatment effects arising from both ordered and unordered multistage decision problems. Identification is secured through instrumental variables and/or conditional independence (matching) assumptions. We decompose treatment effects into direct effects and continuation values associated with moving to the next stage of a decision problem. Using our framework, we decompose the IV estimator, showing that IV generally does not estimate economically interpretable or policy relevant parameters in prototypical dynamic discrete choice models, unless policy variables are instruments. Continuation values are an empirically important component of estimated total treatment effects of education. We use our analysis to estimate the components of what LATE estimates in a dynamic discrete choice model.
Colson, Brett A; Thompson, Andrew R; Espinoza-Fonseca, L Michel; Thomas, David D
2016-03-22
We have used the site-directed spectroscopies of time-resolved fluorescence resonance energy transfer (TR-FRET) and double electron-electron resonance (DEER), combined with complementary molecular dynamics (MD) simulations, to resolve the structure and dynamics of cardiac myosin-binding protein C (cMyBP-C), focusing on the N-terminal region. The results have implications for the role of this protein in myocardial contraction, with particular relevance to β-adrenergic signaling, heart failure, and hypertrophic cardiomyopathy. N-terminal cMyBP-C domains C0-C2 (C0C2) contain binding regions for potential interactions with both thick and thin filaments. Phosphorylation by PKA in the MyBP-C motif regulates these binding interactions. Our spectroscopic assays detect distances between pairs of site-directed probes on cMyBP-C. We engineered intramolecular pairs of labeling sites within cMyBP-C to measure, with high resolution, the distance and disorder in the protein's flexible regions using TR-FRET and DEER. Phosphorylation reduced the level of molecular disorder and the distribution of C0C2 intramolecular distances became more compact, with probes flanking either the motif between C1 and C2 or the Pro/Ala-rich linker (PAL) between C0 and C1. Further insight was obtained from microsecond MD simulations, which revealed a large structural change in the disordered motif region in which phosphorylation unmasks the surface of a series of residues on a stable α-helix within the motif with high potential as a protein-protein interaction site. These experimental and computational findings elucidate structural transitions in the flexible and dynamic portions of cMyBP-C, providing previously unidentified molecular insight into the modulatory role of this protein in cardiac muscle contractility.
Feature extraction for structural dynamics model validation
Energy Technology Data Exchange (ETDEWEB)
Hemez, Francois [Los Alamos National Laboratory; Farrar, Charles [Los Alamos National Laboratory; Park, Gyuhae [Los Alamos National Laboratory; Nishio, Mayuko [UNIV OF TOKYO; Worden, Keith [UNIV OF SHEFFIELD; Takeda, Nobuo [UNIV OF TOKYO
2010-11-08
This study focuses on defining and comparing response features that can be used for structural dynamics model validation studies. Features extracted from dynamic responses obtained analytically or experimentally, such as basic signal statistics, frequency spectra, and estimated time-series models, can be used to compare characteristics of structural system dynamics. By comparing those response features extracted from experimental data and numerical outputs, validation and uncertainty quantification of numerical model containing uncertain parameters can be realized. In this study, the applicability of some response features to model validation is first discussed using measured data from a simple test-bed structure and the associated numerical simulations of these experiments. issues that must be considered were sensitivity, dimensionality, type of response, and presence or absence of measurement noise in the response. Furthermore, we illustrate a comparison method of multivariate feature vectors for statistical model validation. Results show that the outlier detection technique using the Mahalanobis distance metric can be used as an effective and quantifiable technique for selecting appropriate model parameters. However, in this process, one must not only consider the sensitivity of the features being used, but also correlation of the parameters being compared.
Tahira, Rabia; Ge, Guoqin; Ikram, Manzoor
2016-12-01
We investigate the time evolution of a general two-qubit pure entangled state in different structured environments. A general expression is obtained to evaluate the entanglement dynamics of two-qubit systems for two different dissipative environments in the non-Markovian regime. In one case it is single Lorentzian and is detuned from the system while in the other case two Lorentzians form a photonic band gap and is resonant with the system. In the first case, we show that entanglement can be generated from the initial separable state in the non-Markovian regime. Compared to our earlier work under Markov approximation (Tahira et al 2008 J. Phys. B: At. Mol. Opt. Phys. 41 205501), we show that disentanglement rates as well as sudden death times are modified in structured environments. Therefore, we can retain the entanglement for a longer time by controlling the system-environment coupling parameters.
Hernandez, Susana
2011-07-01
Understanding the factors that shapes the microbial community assembly in activated sludge wastewater treatment processes provide a conceptual foundation for improving process performance. The aim of this study was to compare two major theories (deterministic theory and neutral theory) regarding the assembly of microorganisms in activated sludge: Six lab-scale activated sludge sequencing batch reactors were inoculated with activated sludge collected from three different sources (domestic, industrial, and sugar industry WWTP). Additionally, two reactors were seeded with equal proportion of sludge from the three WWTPs. Duplicate reactors were used for each sludge source (i.e. domestic, industrial, sugar and mix). Reactors were operated in parallel for 11 weeks under identical conditions. Bacterial diversity and community structure in the eight SBRs were assessed by 16S rRNA gene pyrosequencing. The 16S rRNA gene sequences were analyzed using taxonomic and clustering analysis and by measuring diversity indices (Shannon-weaver and Chao1 indices). Cluster analysis revealed that the microbial community structure was dynamic and that replicate reactors evolved differently. Also the microbial community structure in the SBRs seeded with a different sludge did not converge after 11 weeks of operation under identical conditions. These results suggest that history and distribution of taxa in the source inoculum were stronger regulating factors in shaping bacterial community structure than environmental factors. This supports the neutral theory which states that the assembly of the local microbial community from the metacommunity is random and is regulated by the size and diversity of the metacommunity. Furthermore, sludge performance, measured by COD and ammonia removal, confirmed that broad-scale functions (e.g. COD removal) are not influenced by dynamics in the microbial composition, while specific functions (e.g. nitrification) are more susceptible to these changes.
Energy Technology Data Exchange (ETDEWEB)
Bahramian, Alireza, E-mail: abahramian57@gmail.com
2014-08-30
Graphical abstract: - Highlights: • We study the surface structure of PANI nanostructured films based on the roughness parameters obtained by AFM analysis and Molecular dynamics approach. • In the T{sub g} ≤ T < T{sub m} range, film shows an increase in surface roughness. • In the T < T{sub g} range, film exhibits a smooth surface. • A scheme for height correction relying on optical profilometer was employed for compensation of errors in determination of surface roughness. • The expected power law behavior was confirmed experimentally and computationally. - Abstract: The influence of drying temperature, T on the surface structure of polyaniline (PANI) nanostructured films dried at temperatures less than the glass transition temperature, T{sub g} and between T{sub g} and melting temperature, T{sub m} was investigated by atomic force microscopy (AFM) and ZeScope optical profilometry. The expected power law behavior associated with surface roughness over small length scales was confirmed at different drying temperatures. To correlate the value of the film thickness determined based on AFM with that obtained from ZeScope measurements, a model of height correcting factor is introduced. The variation in saturated roughness of the PANI film was determined to follow a power law model in the range of T < T{sub g}, with a saturated roughness exponent of 4.48 ± 0.4. The structure of the PANI film has been investigated based on molecular dynamics simulation. The applicability of power law model was confirmed by simulations, based on which the saturated roughness exponent was determined to be 4.90 ± 0.5.
Dynamic Failure of Composite and Sandwich Structures
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...
Dynamic structure of dense krypton gas
Egelstaff, P. A.; Salacuse, J. J.; Schommers, W.; Ram, J.
1984-07-01
We have made molecular-dynamics computer simulations of dense krypton gas (10.6×1027 atoms/m3 and 296 K) using reasonably realistic pair potentials. Comparisons are made with the recent experimental data[P. A. Egelstaff et al., Phys. Rev. A 27, 1106 (1983)] for the dynamic structure factor S(q,ω) over the range 0.4effects are found in the region q~2.7 Å-1. Some suggestions for future work are made.
Transforming Static Data Structures to Dynamic Structures.
1979-09-03
2C*(N))) f?, (Ps(N)) n (N). The last two Inequalities both follow from the fact that PS grows at least linearly. QED. Maurer and Ottmann [1979...Maurer, H. A. and T. Ottmann C1979]. "Dynamic solutions of decomposable searching problems," Report 33, Institut fur Informationsverabeltung
Energy Technology Data Exchange (ETDEWEB)
Jin, Jiaqi; Miller, Jan D.; Dang, Liem X.; Wick, Collin D.
2015-12-10
In the first part of this paper, an experimental contact angle study of the fresh and Cu2+ activated sphalerite-ZnS surface as well as the covellite-CuS (001) surface is reported describing the increased hydrophobic character of the surface during Cu2+ activation. In addition to these experimental results, the fresh sphalerite-ZnS (110), copper-zinc sulfide-CuZnS2 (110), villamaninite- CuS2 (100), and covellite-CuS (001) surfaces were examined using Molecular Dynamics Simulation (MDS). Our MDS results on the behavior of interfacial water at the fresh sphalerite-ZnS (110), copper-zinc sulfide-CuZnS2 (110), villamaninite-CuS2 (100), and covellite-CuS (001) surfaces include simulated contact angles, water number density distribution, water dipole orientation, water residence time, and hydrogen-bonding considerations. The copper content at the Cu2+ activated sphalerite surface seems to account for the increased hydrophobicity as revealed by both experimental and MD simulated contact angle measurements. The relatively greater hydrophobic character developed at the Cu2+ activated sphalerite surface and at the copper-zinc sulfide surface has been described by MDS, based on the structure of interfacial water and its dynamic properties. L.X.D. acknowledges funding from the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences.
Hayasi, Ryoei; Masuda, Yoshiharu; Hashimoto, Shozo; Kuriyama, Shinhou
2008-06-01
Experimental studies have been conducted using the dynamic photoelastic technique combined with a strain gauge to investigate geometric effects on stress wave propagation in axially impacted epoxy resins of plate-like structure. Dynamic photoelasticity provides a means of visualizing the stress wave field inside a solid. A device that triggers the generation of stress waves by direct projectile impact is used to conduct high-speed photoelasticity and strain gauge measurements. This triggering is achieved by an electrical connection between projectile and sample. The geometric effects of the width-to-wavelength ratio on the propagation speed and attenuation coefficient of stress waves were analyzed for isotropic rectangular rods of different width-to-thickness ratios, the thickness being the same in each case. The experimental results for stress wave speed as a function of width-to-wavelength ratio are in reasonable agreement with theoretical predictions based on a modified Love's equation involving the geometric effects due to lateral inertia.
Predicting protein dynamics from structural ensembles
Copperman, J
2015-01-01
The biological properties of proteins are uniquely determined by their structure and dynamics. A protein in solution populates a structural ensemble of metastable configurations around the global fold. From overall rotation to local fluctuations, the dynamics of proteins can cover several orders of magnitude in time scales. We propose a simulation-free coarse-grained approach which utilizes knowledge of the important metastable folded states of the protein to predict the protein dynamics. This approach is based upon the Langevin Equation for Protein Dynamics (LE4PD), a Langevin formalism in the coordinates of the protein backbone. The linear modes of this Langevin formalism organize the fluctuations of the protein, so that more extended dynamical cooperativity relates to increasing energy barriers to mode diffusion. The accuracy of the LE4PD is verified by analyzing the predicted dynamics across a set of seven different proteins for which both relaxation data and NMR solution structures are available. Using e...
Salacuse, J. J.; Denton, A. R.; Egelstaff, P. A.; Tau, M.; Reatto, L.
1996-03-01
The method described in the preceding paper [J. J. Salacuse, A. R. Denton, and P. A. Egelstaff, preceding paper, Phys. Rev. E 53, 2382 (1996)] for computing the static structure factor S(Q) of a bulk fluid is used to analyze molecular dynamics computer simulation data for a model krypton fluid whose atoms interact via a truncated Aziz pair potential. Simulations have been carried out for two system sizes of N=706 and 2048 particles and two thermodynamic states, described by a common reduced temperature T*=1.51 and reduced densities ρ*=0.25 and 0.4. Results presented include the N-particle radial distribution function gN(r) and the bulk static structure factor S(Q). In addition we calculate the direct correlation function c(r) from the full S(Q). In comparison with corresponding predictions of the modified hypernetted chain theory, the results are generally in excellent agreement at all r and Q, to within random statistical errors in the simulation data.
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.
Structural Dynamics Model of a Cartesian Robot
1985-10-01
34 D FILE COPY AD-A198 053 *.CC Technical Report 1009 Structural Dynamics Model of a Cartesian Robot "DTIC SELEC T E 0 Alfonso Garcia Reynoso MIT...COVERED Structural Dynamics Model of a Cartesian Robot technical report G. PERFORMING ORG. REPORT NUM9ER 7. AUTHO0R(@) S. CONTRACT On GRANT NUMSER...8217 %S S Structural Dynamics Model of a Cartesian Robot by Alfonso Garcia Reynoso BSME Instituto Tecnol6gico de Veracruz (1967) MSME Instituto Tecnol6gico
Structurally dynamic spin market networks
Horváth, D
2007-01-01
The agent-based model of price dynamics on a directed evolving complex network is suggested and studied by direct simulation. The resulting stationary regime is maintained as a result of the balance between the extremal dynamics, adaptivity of strategic variables and reconnection rules. For some properly selected parametric combination the network displays small-world phenomenon with high mean clustering coefficient and power-law node degree distribution. The mechanism of repeated random walk through network combined with a fitness recognition is proposed and tested to generate modular multi-leader market. The simulations suggest that dynamics of fitness is the slowest process that manifests itself in the volatility clustering of the log-price returns.
Chattoraj, Shyamtanu; Mandal, Amit Kumar; Bhattacharyya, Kankan
2014-03-01
Effect of ethanol-water mixture on the hydrodynamic radius (rH) and conformational dynamics of lysozyme has been studied by circular dichroism, emission spectra, and fluorescence correlation spectroscopy. For this purpose, the protein lysozyme is covalently labeled near the active site with a fluorescent probe, alexa 488. The ethanol molecules are sequestered near the hydrophobic tryptophan residues as indicated by the blue shift of the emission maximum of tryptophan. It is observed that both size (rH) and time constant of conformational relaxation (τR) of lysozyme oscillate with increase in ethanol concentration. The rH of the protein fluctuates from 19 Å in the native state, to a minimum of 13 Å, and a maximum of 29 Å. It is proposed that the oscillating behavior arises from competition between mutual interaction among protein, ethanol, and water. The fluorescence intensity fluctuates because of quenching of the fluorescence of the probe (alexa) by the free amino group of certain residues (e.g., tryptophan). Rate of inter-conversion (folding dynamics) between the open (fluorescent) and closed (non-fluorescent) form has been determined and is found to exhibit similar oscillation with variation in ethanol content.
Calabrese, Justin; Vázquez, Federico; López, Cristóbal; San Miguel, Maxi; Grimm, Volker
2010-01-01
The mechanisms regulating savanna tree populations are still not well understood. Recent empirical work suggests that both tree-tree competition and fire are key factors in semi-arid to mesic savannas. However, the potential for competition to structure savannas, particularly in interaction with fire, has received little theoretical attention. We develop a minimalistic and analytically tractable stochastic cellular automaton to study the individual and combined effects of competition and fire...
Institute of Scientific and Technical Information of China (English)
无
2006-01-01
In this paper, a Si-doped single-walled carbon nanotube (SWCNT) (7,7) and several perfect armchair SWCNTs are investigated using the classical molecular dynamics simulations method. The inter-atomic short-range interaction is represented by empirical Tersoff bond order potential. The computational results show that the axial Young's modulus of the perfect SWCNTs are in the range of 1.099 ± 0.005 TPa, which is in good agreement with the existing experimental results. From our simulation, the Si-doping decreases the Young's modulus of SWCNT, and with the increased strain levels, the effect of Si-doped layer in enhancing the local stress level increases. The Young's modulus of armchair SWCNTs are weakly affected by tube radius.
Visualizing structural dynamics of thylakoid membranes
Iwai, Masakazu; Yokono, Makio; Nakano, Akihiko
2014-01-01
To optimize photosynthesis, light-harvesting antenna proteins regulate light energy dissipation and redistribution in chloroplast thylakoid membranes, which involve dynamic protein reorganization of photosystems I and II. However, direct evidence for such protein reorganization has not been visualized in live cells. Here we demonstrate structural dynamics of thylakoid membranes by live cell imaging in combination with deconvolution. We observed chlorophyll fluorescence in the antibiotics-induced macrochloroplast in the moss Physcomitrella patens. The three-dimensional reconstruction uncovered the fine thylakoid membrane structure in live cells. The time-lapse imaging shows that the entire thylakoid membrane network is structurally stable, but the individual thylakoid membrane structure is flexible in vivo. Our observation indicates that grana serve as a framework to maintain structural integrity of the entire thylakoid membrane network. Both the structural stability and flexibility of thylakoid membranes would be essential for dynamic protein reorganization under fluctuating light environments. PMID:24442007
Unascertained Factor Method of Dynamic Characteristic Analysis for Antenna Structures
Institute of Scientific and Technical Information of China (English)
ZHU Zeng-qing; LIANG Zhen-tao; CHEN Jian-jun
2008-01-01
The dynamic characteristic analysis model of antenna structures is built, in which the structural physical parameters and geometrical dimensions are all considered as unascertained variables, And a structure dynamic characteristic analysis method based on the unascertained factor method is given. The computational expression of structural characteristic is developed by the mathematics expression of unascertained factor and the principles of unascertained rational numbers arithmetic. An example is given, in which the possible values and confidence degrees of the unascertained structure characteristics are obtained. The calculated results show that the method is feasible and effective.
Dynamic energy absorption characteristics of hollow microlattice structures
Energy Technology Data Exchange (ETDEWEB)
Liu, YL; Schaedler, TA; Chen, X
2014-10-01
Hollow microlattice structures are promising candidates for advanced energy absorption and their characteristics under dynamic crushing are explored. The energy absorption can be significantly enhanced by inertial stabilization, shock wave effect and strain rate hardening effect. In this paper we combine theoretical analysis and comprehensive finite element method simulation to decouple the three effects, and then obtain a simple model to predict the overall dynamic effects of hollow microlattice structures. Inertial stabilization originates from the suppression of sudden crushing of the microlattice and its contribution scales with the crushing speed, v. Shock wave effect comes from the discontinuity across the plastic shock wave front during dynamic loading and its contribution scales with e. The strain rate effect increases the effective yield strength upon dynamic deformation and increases the energy absorption density. A mechanism map is established that illustrates the dominance of these three dynamic effects at a range of crushing speeds. Compared with quasi-static loading, the energy absorption capacity a dynamic loading of 250 m/s can be enhanced by an order of magnitude. The study may shed useful insight on designing and optimizing the energy absorption performance of hollow microlattice structures under various dynamic loads. (C) 2014 Elsevier Ltd. All rights reserved.
Energy Technology Data Exchange (ETDEWEB)
Jin, Jiaqi; Miller, Jan D.; Dang, Liem X.; Wick, Collin D.
2015-06-01
In the first part of this paper, a Scanning Electron Microscopy and contact angle study of a pyrite surface (100) is reported describing the relationship between surface oxidation and the hydrophilic surface state. In addition to these experimental results, the following simulated surface states were examined using Molecular Dynamics Simulation (MDS): fresh unoxidized (100) surface; polysulfide at the (100) surface; elemental sulfur at the (100) surface. Crystal structures for the polysulfide and elemental sulfur at the (100) surface were simulated using Density Functional Theory (DFT) quantum chemical calculations. The well known oxidation mechanism which involves formation of a metal deficient layer was also described with DFT. Our MDS results of the behavior of interfacial water at the fresh and oxidized pyrite (100) surfaces without/with the presence of ferric hydroxide include simulated contact angles, number density distribution for water, water dipole orientation, water residence time, and hydrogen-bonding considerations. The significance of the formation of ferric hydroxide islands in accounting for the corresponding hydrophilic surface state is revealed not only from experimental contact angle measurements but also from simulated contact angle measurements using MDS. The hydrophilic surface state developed at oxidized pyrite surfaces has been described by MDS, on which basis the surface state is explained based on interfacial water structure. The Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences (BES), of the DOE funded work performed by Liem X. Dang. Battelle operates the Pacific Northwest National Laboratory for DOE. The calculations were carried out using computer resources provided by BES.
Structure and dynamics of interphase chromosomes.
Directory of Open Access Journals (Sweden)
Angelo Rosa
Full Text Available During interphase chromosomes decondense, but fluorescent in situ hybridization experiments reveal the existence of distinct territories occupied by individual chromosomes inside the nuclei of most eukaryotic cells. We use computer simulations to show that the existence and stability of territories is a kinetic effect that can be explained without invoking an underlying nuclear scaffold or protein-mediated interactions between DNA sequences. In particular, we show that the experimentally observed territory shapes and spatial distances between marked chromosome sites for human, Drosophila, and budding yeast chromosomes can be reproduced by a parameter-free minimal model of decondensing chromosomes. Our results suggest that the observed interphase structure and dynamics are due to generic polymer effects: confined Brownian motion conserving the local topological state of long chain molecules and segregation of mutually unentangled chains due to topological constraints.
Simultaneous determination of protein structure and dynamics
DEFF Research Database (Denmark)
Lindorff-Larsen, Kresten; Best, Robert B.; DePristo, M. A.
2005-01-01
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 at ...
Recent Progress in Heliogyro Solar Sail Structural Dynamics
Wilkie, W.; Warren, J.; Horta, L.; Juang, J.; Gibbs, S.; Dowell, E.; Guerrant, D.; Lawrence, D.
2014-06-01
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.
Recent Progress in Heliogyro Solar Sail Structural Dynamics
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.
The Sun's interior structure and dynamics, and the solar cycle
Broomhall, A -M; Howe, R; Norton, A A; Thompson, M J
2014-01-01
The Sun's internal structure and dynamics can be studied with helioseismology, which uses the Sun's natural acoustic oscillations to build up a profile of the solar interior. We discuss how solar acoustic oscillations are affected by the Sun's magnetic field. Careful observations of these effects can be inverted to determine the variations in the structure and dynamics of the Sun's interior as the solar cycle progresses. Observed variations in the structure and dynamics can then be used to inform models of the solar dynamo, which are crucial to our understanding of how the Sun's magnetic field is generated and maintained.
Understanding Microbial Communities: Function, Structure and Dynamics
2015-02-11
microbial communities: Function, structure and dynamics’, at the Isaac Newton Institute, University of Cambridge, United Kingdom, from August to...dynamics’, at the Isaac Newton Institute, University of Cambridge, United Kingdom, from August to December 2014. The programme involved over 150...Communities: Function, Structure and Dynamics’, at the Isaac Newton Institute, Cambridge University, UK, from 19th August 2014 – 19th December 2014
31st IMAC Conference on Structural Dynamics
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.
Dynamic Analysis of Structures Using Neural Networks
Directory of Open Access Journals (Sweden)
N. Ahmadi
2008-01-01
Full Text Available In the recent years, neural networks are considered as the best candidate for fast approximation with arbitrary accuracy in the time consuming problems. Dynamic analysis of structures against earthquake has the time consuming process. We employed two kinds of neural networks: Generalized Regression neural network (GR and Back-Propagation Wavenet neural network (BPW, for approximating of dynamic time history response of frame structures. GR is a traditional radial basis function neural network while BPW categorized as a wavelet neural network. In BPW, sigmoid activation functions of hidden layer neurons are substituted with wavelets and weights training are achieved using Scaled Conjugate Gradient (SCG algorithm. Comparison the results of BPW with those of GR in the dynamic analysis of eight story steel frame indicates that accuracy of the properly trained BPW was better than that of GR and therefore, BPW can be efficiently used for approximate dynamic analysis of structures.
Li, Jianbo; Lin, Gao; Liu, Jun; Li, Zhiyuan
2017-01-01
Consideration of the dynamic effects of the site and structural parameter uncertainty is required by the standards for nuclear power plants (NPPs) in most countries. The anti-seismic standards provide two basic methods to analyze parameter uncertainty. Directly manually dealing with the calculated floor response spectra (FRS) values of deterministic approaches is the first method. The second method is to perform probability statistical analysis of the FRS results on the basis of the Monte Carlo method. The two methods can only reflect the overall effects of the uncertain parameters, and the results cannot be screened for a certain parameter's influence and contribution. In this study, based on the dynamic analyses of the floor response spectra of NPPs, a comprehensive index of the assessed impact for various uncertain parameters is presented and recommended, including the correlation coefficient, the regression slope coefficient and Tornado swing. To compensate for the lack of guidance in the NPP seismic standards, the proposed method can effectively be used to evaluate the contributions of various parameters from the aspects of sensitivity, acuity and statistical swing correlations. Finally, examples are provided to verify the set of indicators from systematic and intuitive perspectives, such as the uncertainty of the impact of the structure parameters and the contribution to the FRS of NPPs. The index is sensitive to different types of parameters, which provides a new technique for evaluating the anti-seismic parameters required for NPPs.
Damping mechanisms and models in structural dynamics
DEFF Research Database (Denmark)
Krenk, Steen
2002-01-01
Several aspects of damping models for dynamic analysis of structures are investigated. First the causality condition for structural response is used to identify rules for the use of complex-valued frequency dependent material models, illustrated by the shortcomings of the elastic hysteretic model...
Lagrangian coherent structures and inertial particle dynamics
Sudharsan, M; Riley, James J
2015-01-01
In this work we investigate the dynamics of inertial particles using finite-time Lyapunov exponents (FTLE). In particular, we characterize the attractor and repeller structures underlying preferential concentration of inertial particles in terms of FTLE fields of the underlying carrier fluid. Inertial particles that are heavier than the ambient fluid (aerosols) attract onto ridges of the negative-time fluid FTLE. This negative-time FTLE ridge becomes a repeller for particles that are lighter than the carrier fluid (bubbles). We also examine the inertial FTLE (iFTLE) determined by the trajectories of inertial particles evolved using the Maxey-Riley equations with non-zero Stokes number and density ratio. Finally, we explore the low-pass filtering effect of Stokes number. These ideas are demonstrated on two-dimensional numerical simulations of the unsteady double gyre flow.
Dynamical 3-Space Gravitational Waves: Reverberation Effect
Cahill, Reginald T
2012-01-01
Gravity theory missed a key dynamical process that became apparent only when expressed in terms of a velocity field, instead of the Newtonian gravitational acceleration field. This dynamical process involves an additional self-interaction of the dynamical 3-space, and experimental data reveals that its strength is set by the fine structure constant, implying a fundamental link between gravity and quantum theory. The dynamical 3-space has been directly detected in numerous light-speed anisotropy experiments. Quantum matter has been shown to exhibit an acceleration caused by the time-dependence and inhomogeneity of the 3-space flow, giving the first derivation of gravity from a deeper theory, as a quantum wave refraction effect. EM radiation is also refracted in a similar manner. The anisotropy experiments have all shown 3-space wave/turbulence effects, with the latest revealing the fractal structure of 3-space. Here we report the prediction of a new effect, namely a reverberation effect, when the gravitational...
Dynamical effects in electron spectroscopy
Energy Technology Data Exchange (ETDEWEB)
Zhou, Jianqiang Sky, E-mail: jianqiang.zhou@polytechnique.edu; Reshetnyak, Igor; Giorgetti, Christine; Sottile, Francesco; Reining, Lucia [Laboratoire des Solides Irradiés, École Polytechnique, CNRS, CEA-DSM-IRAMIS, Université Paris-Saclay, F-91128 Palaiseau (France); Kas, J. J.; Rehr, J. J. [Department of Physics, University of Washington, Seattle, Washington 98195-1560 (United States); Sponza, Lorenzo [Department of Physics, King’s College London, London WC2R 2LS (United Kingdom); Guzzo, Matteo [Institut für Physik und IRIS Adlershof, Humboldt-Universität zu Berlin, D-12489 Berlin (Germany); Gatti, Matteo [Laboratoire des Solides Irradiés, École Polytechnique, CNRS, CEA-DSM-IRAMIS, Université Paris-Saclay, F-91128 Palaiseau (France); Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, BP 48, F-91192 Gif-sur-Yvette (France)
2015-11-14
One of the big challenges of theoretical condensed-matter physics is the description, understanding, and prediction of the effects of the Coulomb interaction on materials properties. In electronic spectra, the Coulomb interaction causes a renormalization of energies and change of spectral weight. Most importantly, it can lead to new structures, often called satellites. These can be linked to the coupling of excitations, also termed dynamical effects. State-of-the-art methods in the framework of many-body perturbation theory, in particular, the widely used GW approximation, often fail to describe satellite spectra. Instead, approaches based on a picture of electron-boson coupling such as the cumulant expansion are promising for the description of plasmon satellites. In this work, we give a unified derivation of the GW approximation and the cumulant expansion for the one-body Green’s function. Using the example of bulk sodium, we compare the resulting spectral functions both in the valence and in the core region, and we discuss the dispersion of quasi-particles and satellites. We show that self-consistency is crucial to obtain meaningful results, in particular, at large binding energies. Very good agreement with experiment is obtained when the intrinsic spectral function is corrected for extrinsic and interference effects. Finally, we sketch how one can approach the problem in the case of the two-body Green’s function, and we discuss the cancellation of various dynamical effects that occur in that case.
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.
Structural dynamics of liganded myoglobin.
Frauenfelder, H; Petsko, G A
1980-01-01
X-ray crystallography can reveal the magnitudes and principal directions of the mean-square displacements of every atom in a protein. This structural information is complementary to the temporal information obtainable by spectroscopic techniques such as nuclear magnetic resonance. Determination of the temperature dependence of the mean-square displacements makes it possible to separate large conformational motions from simple thermal vibrations. The contribution of crystal lattice disorder to...
On Dynamics of Spinning Structures
Gupta, K. K.; Ibrahim, A.
2012-01-01
This paper provides details of developments pertaining to vibration analysis of gyroscopic systems, that involves a finite element structural discretization followed by the solution of the resulting matrix eigenvalue problem by a progressive, accelerated simultaneous iteration technique. Thus Coriolis, centrifugal and geometrical stiffness matrices are derived for shell and line elements, followed by the eigensolution details as well as solution of representative problems that demonstrates the efficacy of the currently developed numerical procedures and tools.
Dorelli, John C; Collinson, Glyn; Tóth, Gábor
2015-01-01
We present high resolution Hall MHD simulations of Ganymede's magnetosphere demonstrating that Hall electric fields in ion-scale magnetic reconnection layers have significant global effects not captured in resistive MHD simulations. Consistent with local kinetic simulations of magnetic reconnection, our global simulations show the development of intense field-aligned currents along the magnetic separatrices. These currents extend all the way down to the moon's surface, where they may contribute to Ganymede's aurora. Within the magnetopause and magnetotail current sheets, Hall currents in the reconnection plane accelerate ions to the local Alfv\\'en speed in the out-of-plane direction, producing a global system of ion drift belts that circulates Jovian magnetospheric plasma throughout Ganymede's magnetosphere. We discuss some observable consequences of these Hall-induced currents and ion drifts: the appearance of a sub-Jovian "double magnetopause" structure, an Alfv\\'enic ion jet extending across the upstream m...
Dorelli, J. C.; Glocer, Alex; Collinson, Glyn; Toth, Gabor
2015-01-01
We present high-resolution Hall MHD simulations of Ganymede's magnetosphere demonstrating that Hall electric fields in ion-scale magnetic reconnection layers have significant global effects not captured in resistive MHD simulations. Consistent with local kinetic simulations of magnetic reconnection, our global simulations show the development of intense field-aligned currents along the magnetic separatrices. These currents extend all the way down to the moon's surface, where they may contribute to Ganymede's aurora. Within the magnetopause and magnetotail current sheets, Hall J x B forces accelerate ions to the local Alfven speed in the out-of-plane direction, producing a global system of ion drift belts that circulates Jovian magnetospheric plasma throughout Ganymede's magnetosphere. We discuss some observable consequences of these Hall-induced currents and ion drifts: the appearance of a sub-Jovian 'double magnetopause' structure, an Alfvenic ion jet extending across the upstream magnetopause, and an asymmetric pattern of magnetopause Kelvin-Helmholtz waves.
Dynamic Study of Bicycle Frame Structure
Sani, M. S. M.; Nazri, N. A.; Zahari, S. N.; Abdullah, N. A. Z.; Priyandoko, G.
2016-11-01
Bicycle frames have to bear variety of loads and it is needed to ensure the frame can withstand dynamic loads to move. This paper focusing on dynamic study for bicycle frame structure with a purpose to avoid the problem regarding loads on the structure and to ensure the structure is safe when multiple loads are applied on it. The main objectives of dynamic study are to find the modal properties using two method; finite element analysis (FEA) and experimental modal analysis (EMA). The correlation between two studies will be obtained using percentage error. Firstly, 3D model of mountain bike frame structure has been draw using computer-aided design (CAD) software and normal mode analysis using MSC Nastran Patran was executed for numerical method meanwhile modal testing using impact hammer was performed for experimental counterpart. From the correlation result, it show that percentage error between FEA and EMA were below 10% due to noise, imperfect experiment setup during perform EMA and imperfect modeling of mountain bike frame structure in CAD software. Small percentage error differences makes both of the method can be applied to obtain the dynamic characteristic of structure. It is essential to determine whether the structure is safe or not. In conclusion, model updating method is required to reduce more percentage error between two results.
Structural Equation Modeling of Travel Choice Dynamics
Golob, Thomas F.
1988-01-01
This research has two objectives. The first objective is to explore the use of the modeling tool called "latent structural equations" (structural equations with latent variables) in the general field of travel behavior analysis and the more specific field of dynamic analysis of travel behavior. The second objective is to apply a latent structural equation model in order to determine the causal relationships between income, car ownership, and mobility. Many transportation researchers ...
Directory of Open Access Journals (Sweden)
Giordano Mancini
Full Text Available BACKGROUND: Human topoisomerase I catalyzes the relaxation of DNA supercoils in fundamental cell processes like transcription, replication and chromosomal segregation. It is the only target of the camptothecin family of anticancer drugs. Among these, topotecan has been used to treat lung and ovarian carcinoma for several years. Camptothecins reversibly binds to the covalent intermediate DNA-enzyme, stabilizing the cleavable complex and reducing the religation rate. The stalled complex then collides with the progression of the replication fork, producing lethal double strand DNA breaks and eventually cell death. METHODOLOGY/PRINCIPAL FINDINGS: Long lasting molecular dynamics simulations of the DNA-topoisomerase I binary complex and of the DNA-topoisomerase-topotecan ternary complex have been performed and compared. The conformational space sampled by the binary complex is reduced by the presence of the drug, as observed by principal component and cluster analyses. This conformational restraint is mainly due to the reduced flexibility of residues 633-643 (the region connecting the linker to the core domain that causes an overall mobility loss in the ternary complex linker domain. During the simulation, DNA/drug stacking interactions are fully maintained, and hydrogen bonds are maintained with the enzyme. Topotecan keeps the catalytic residue Lys532 far from the DNA, making it unable to participate to the religation reaction. Arg364 is observed to interact with both the B and E rings of topotecan with two stable direct hydrogen bonds. An interesting constrain exerted by the protein on the geometrical arrangement of topotecan is also observed. CONCLUSIONS/SIGNIFICANCE: Atomistic-scale understanding of topotecan interactions with the DNA-enzyme complex is fundamental to the explaining of its poisonous effect and of the drug resistance observed in several single residue topoisomerase mutants. We observed significant alterations due to topotecan in
[Oligoglycine surface structures: molecular dynamics simulation].
Gus'kova, O A; Khalatur, P G; Khokhlov, A R; Chinarev, A A; Tsygankova, S V; Bovin, N V
2010-01-01
The full-atomic molecular dynamics (MD) simulation of adsorption mode for diantennary oligoglycines [H-Gly4-NH(CH2)5]2 onto graphite and mica surface is described. The resulting structure of adsorption layers is analyzed. The peptide second structure motives have been studied by both STRIDE (structural identification) and DSSP (dictionary of secondary structure of proteins) methods. The obtained results confirm the possibility of polyglycine II (PGII) structure formation in diantennary oligoglycine (DAOG) monolayers deposited onto graphite surface, which was earlier estimated based on atomic-force microscopy measurements.
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.
Dynamics of localized structures in vector waves
Hernández-García, E; Colet, P; San Miguel, M; Hernandez-Garcia, Emilio; Hoyuelos, Miguel; Colet, Pere; Miguel, Maxi San
1999-01-01
Dynamical properties of topological defects in a twodimensional complex vector field are considered. These objects naturally arise in the study of polarized transverse light waves. Dynamics is modeled by a Vector Complex Ginzburg-Landau Equation with parameter values appropriate for linearly polarized laser emission. Creation and annihilation processes, and selforganization of defects in lattice structures, are described. We find "glassy" configurations dominated by vectorial defects and a melting process associated to topological-charge unbinding.
Spin Dynamics in Confined Magnetic Structures III
Hillebrands, Burkard
2006-01-01
This third volume of Spin Dynamics in Confined Magnetic Structures addresses central aspects of spin-dynamic phenomena, including recent new developments, on a tutorial level. Researchers will find a comprehensive compilation of the current work in the field. Introductory chapters help newcomers to understand the basic concepts. The more advanced chapters give the current state of the art of spin dynamic issues ranging from the femtosecond to the microsecond regime. This volume concentrates on new experimental techniques such as ferromagnetic-resonance-force microscopy and two-photon photoemission, as well as on aspects of precessional switching, spin-wave excitation, vortex dynamics, spin relaxation, domain-wall dynamics in nanowires and their applications to magnetic logic devices. An important chapter is devoted to the presently very hot subject of the spin-transfer torque, combining the physics of electronic transport and micromagnetics. The comprehensive presentation of these developments makes this volu...
Chiantia, Salvatore; London, Erwin
2012-12-05
A long-standing question about membrane structure and function is the degree to which the physical properties of the inner and outer leaflets of a bilayer are coupled to one another. Using our recently developed methods to prepare asymmetric vesicles, coupling was investigated for vesicles containing phosphatidylcholine (PC) in the inner leaflet and sphingomyelin (SM) in the outer leaflet. The coupling of both lateral diffusion and membrane order was monitored as a function of PC and SM acyl chain structure. The presence in the outer leaflet of brain SM, which decreased outer-leaflet lateral diffusion, had little effect upon lateral diffusion in inner leaflets composed of dioleoyl PC (i.e., diffusion was only weakly coupled in the two leaflets) but did greatly reduce lateral diffusion in inner leaflets composed of PC with one saturated and one oleoyl acyl chain (i.e., diffusion was strongly coupled in these cases). In addition, reduced outer-leaflet diffusion upon introduction of outer-leaflet milk SM or a synthetic C24:0 SM, both of which have long interdigitating acyl chains, also greatly reduce diffusion of inner leaflets composed of dioleoyl PC, indicative of strong coupling. Strikingly, several assays showed that the ordering of the outer leaflet induced by the presence of SM was not reflected in increased lipid order in the inner leaflet, i.e., there was no detectable coupling between inner and outer leaflet membrane order. We propose a model for how lateral diffusion can be coupled in opposite leaflets and discuss how this might impact membrane function.
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.
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).
Multiscale Dynamics of Solar Magnetic Structures
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.
Nonlinear Dynamics of Structures with Material Degradation
Soltani, P.; Wagg, D. J.; Pinna, C.; Whear, R.; Briody, C.
2016-09-01
Structures usually experience deterioration during their working life. Oxidation, corrosion, UV exposure, and thermo-mechanical fatigue are some of the most well-known mechanisms that cause degradation. The phenomenon gradually changes structural properties and dynamic behaviour over their lifetime, and can be more problematic and challenging in the presence of nonlinearity. In this paper, we study how the dynamic behaviour of a nonlinear system changes as the thermal environment causes certain parameters to vary. To this end, a nonlinear lumped mass modal model is considered and defined under harmonic external force. Temperature dependent material functions, formulated from empirical test data, are added into the model. Using these functions, bifurcation parameters are defined and the corresponding nonlinear responses are observed by numerical continuation. A comparison between the results gives a preliminary insight into how temperature induced properties affects the dynamic response and highlights changes in stability conditions of the structure.
A Dynamic Model for Energy Structure Analysis
Institute of Scientific and Technical Information of China (English)
无
2006-01-01
Energy structure is a complicated system concerning economic development, natural resources, technological innovation, ecological balance, social progress and many other elements. It is not easy to explain clearly the developmental mechanism of an energy system and the mutual relations between the energy system and its related environments by the traditional methods. It is necessary to develop a suitable dynamic model, which can reflect the dynamic characteristics and the mutual relations of the energy system and its related environments. In this paper, the historical development of China's energy structure was analyzed. A new quantitative analysis model was developed based on system dynamics principles through analysis of energy resources, and the production and consumption of energy in China and comparison with the world. Finally, this model was used to predict China's future energy structures under different conditions.
Simultaneous determination of protein structure and dynamics
DEFF Research Database (Denmark)
Lindorff-Larsen, Kresten; Best, Robert B.; DePristo, M. A.
2005-01-01
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...... 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...... 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...
Unifying dynamical and structural stability of equilibria
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.
Craig, Douglas B; Haslam, Allison M; Silverstein, Harlyn J; Chikamatsu, Miki; Shadabi, Elnaz; Nichols, Ellert R
2010-08-01
Single enzyme molecule assays were performed using capillary electrophoresis-based protocols on beta-galactosidase from Lactobacillus delbrueckii, Lactobacillus reuteri, Lactobacillus helveticus and Bacillus circulans. The enzyme was found to show static heterogeneity with respect to catalytic rate and the variance in rate increased with protein size. This is consistent with the proposal that random errors in translation may be an important underlying component of enzyme heterogeneity. Additionally these enzymes were found to show static heterogeneity with respect to electrophoretic mobility. Comparison of wild-type and rpsL E. coli beta-galactosidase expressed in the presence and absence of streptomycin suggested that increases in error do not result in detectable increases in the dynamic heterogeneity of activity with increasing temperature. Finally, a method was developed to measure the dynamic heterogeneity in electrophoretic mobility.
Structural dynamics of electronic and photonic systems
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
Koopmans, L V E; Treu, T; Czoske, O; Auger, M; Barnabe, M; Vegetti, S; Gavazzi, R; Moustakas, L; Burles, S
2009-01-01
Based on 58 SLACS strong-lens early-type galaxies to with direct total-mass and stellar-velocity dispersion measurements, we find that inside one effective radius massive elliptical galaxies with M_eff>=3x10^10 M_sun are kinematically almost indistinguishable from an isothermal ellipsoid with an average logaritmic density slope of _LD=dlog(\\rho_tot)/dlog(r)=2.085^{+0.025}_{-0.018} (rand.) (68 percent CL; isotropic orbits with \\beta_r=0), +-0.1 (syst.) and \\sigma_{\\gamma'}_SR=1.959+-0.077. Agreement between the two values is reached for =0.45+-0.25, consistent with mild radial anisotropy. This agreement supports the robustness of our results, despite the increase in mass-to-light ratio with total galaxy mass: M_eff ~ L_{V,eff}^(1.363+-0.056). We conclude that massive early-type galaxies are structurally close-to homologous with close-to isothermal total density profiles (<=10 percent scatter) and have at most some mild radial anisotropy. Our results provide tight observational limits on galaxy formation and...
Structure-based control of complex networks with nonlinear dynamics
Zañudo, Jorge G T; Albert, Réka
2016-01-01
Given the network of interactions underlying a complex system, what can we learn about controlling such a system solely from its structure? Over a century of research in control theory has given us tools to answer this question, which were widely applied in science and engineering. Yet the current tools do not always consider the inherently nonlinear dynamics of real systems and the naturally occurring system states in their definition of "control", a term whose interpretation varies across disciplines. Here we use a new mathematical framework for structure-based control of networks governed by a broad class of nonlinear dynamics that includes the major dynamic models of biological, technological, and social processes. This framework provides realizable node overrides that steer a system towards any of its natural long term dynamic behaviors and which are guaranteed to be effective regardless of the dynamic details and parameters of the underlying system. We use this framework on several real networks, compar...
Effect of Na2CO3 as Foaming Agent on Dynamics and Structure of Foam Glass Melts
DEFF Research Database (Denmark)
Petersen, Rasmus Rosenlund; König, Jakob; Smedskjær, Morten Mattrup;
2014-01-01
We investigate the kinetics and dynamics of the reaction between Na2CO3 and the cathode ray tube panel glass powder at 923-1173 K. The reaction causes foaming of the glass melt. After the reaction, the Tg decreases with increasing Na2CO3 content and reaches a minimum value of Tg. However, this Tg...
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.
DYNAMIC OPTIMIZATION FOR UNCERTAIN STRUCTURES USING INTERVAL METHOD
Institute of Scientific and Technical Information of China (English)
ChertSub-A-; WuJie; LiuChun
2003-01-01
An interval optimization method for the dynamic response of structures with interval parameters is presented. The matrices of structures with interval parameters are given. Combining the interval extension with the perturbation, the method for interval dynamic response analysis is derived. The interval optimization problem is transformed into a corresponding deterministic one. Because the mean values and the uncertainties of the interval parameters can be elected design variables, more information of the optimization results can be obtained by the present method than that obtained by the deterministic one. The present method is implemented for a truss structure. The numerical results show that the method is effective.
Punitha, V; Raman, S Sundar; Parthasarathi, R; Subramanian, V; Rao, J Raghava; Nair, Balachandran Unni; Ramasami, T
2009-07-02
Studies on the structure and stability of peptides and proteins during l-->d configurational change are certainly important for the designing of peptides with new biological activity and protein engineering. The l-->d amino acid (d AA) changes have been observed in aged proteins such as collagen. Hence, in this study, an attempt has been made to explore the effect of the replacement of l amino acid (l AA) in the model collagen-like peptides with d AA and the origin of structural stability (destability) has been traced using the molecular dynamics (MD) method employing the AMBER force field. Our results reveal that the substitution of d AA produces a large local disruption to the triple-helical structure. Formation of a kink (bulge) at the site of substitution is observed from the detailed analysis of MD trajectory. However, this local perturbation of kinked helix changes the direction of the helices and affects the relative orientation of the respective AA residues for helix-helix interaction, enough to affect the overall stability of the model collagen-like peptide. The destabilization energy per d Ala substitution is 7.87 kcal/mol, which is similar to the value for the Gly-->Ala mutation in collagen. Since the Gly-->Ala mutation is involved in genetic disorders such as osteogenesis imperfecta (OI), the l-->d configurational change may produce a similar effect on collagen.
Dynamic behaviors of pretensioned cable AERORail structure
Institute of Scientific and Technical Information of China (English)
李方元; 吴培峰
2015-01-01
The AERORail, a new aerial transport platform, was chosen as the object of this work. Following a review of the literature on static behaviors, model tests on the basic dynamic mechanical characteristics were conducted. A series of 90 tests were completed with different factors, including tension force, vehicle load and vehicle speed. With regard to the proper tension and vehicle load, at a certain speed range, the tension increments of the rail’s cable were proved relatively small. It can be assumed that the change of tension is small and can be reasonably ignored when the tension of an entire span is under a dynamic load. When the tension reaches a certain range, the calculation of the cable track structure using classical cable theory is acceptable. The tests prove that the average maximum dynamic amplification factor of the deflection is small, generally no more than 1.2. However, when the vehicle speed reaches a certain value, the amplified factor will reach 2.0. If the moving loads increase, the dynamic amplification factor of dynamic deflection will also increase. The tension will change the rigidity of the structure and the vibration frequency; furthermore, the resonance speed will change at a certain tension. The vibration is noticeable when vehicles pass through at the resonance speed, and this negative impact on driving comfort requires the right velocity to avoid the resonance. The results demonstrate that more design details are required for the AERORail structure.
Pallas, Benoît; Mialet-Serra, Isabelle; Rouan, Lauriane; Clément-Vidal, Anne; Caliman, Jean-Pierre; Dingkuhn, Michael
2013-04-01
Source/sink ratios are known to be one of the main determinants of oil palm growth and development. A long-term experiment (9 years) was conducted in Indonesia on mature oil palms subjected to continuous bunch ablation and partial defoliation treatments to artificially modify source/sink ratios. During the experiment, all harvested bunches were dissected and phenological measurements were carried out to analyse the effect of source/sink ratios on yield components explaining variations in bunch number, the number of fruits per bunch and oil dry weight per fruit. An integrative variable (supply/demand ratio) describing the ratio between the assimilate supply from sources and the growing organ demand for carbohydrate was computed for each plant on a daily basis from observations of the number of developing organs and their sink strength, and of climate variables. Defoliation and bunch ablation affected the bunch number and the fruit number per bunch. Variations in bunch number per month were mainly due to variations in the fraction of aborted inflorescence and in the ratio between female and male inflorescences. Under fluctuating trophic conditions, variations in fruit number per bunch resulted both from changes in fruit-set and in the number of branches (rachillae) per inflorescence. For defoliated plants, the decrease in the number of developing reproductive sinks appeared to be sufficient to maintain fruit weight and oil concentration at the control level, without any major decrease in the concentration of non-structural carbohydrate reserves. Computation of the supply/demand ratio revealed that each yield component had a specific phase of sensitivity to supply/demand ratios during inflorescence development. Establishing quantitative relationships between supply/demand ratios, competition and yield components is the first step towards a functional model for oil palm.
Structural Dynamics of Tropical Moist Forest Gaps
Hunter, Maria O.; Michael Keller; Douglas Morton; Bruce Cook; Michael Lefsky; Mark Ducey; Scott Saleska; Raimundo Cosme de Oliveira; Juliana Schietti
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...
Protein Secondary Structure Prediction Using Dynamic Programming
Institute of Scientific and Technical Information of China (English)
Jing ZHAO; Pei-Ming SONG; Qing FANG; Jian-Hua LUO
2005-01-01
In the present paper, we describe how a directed graph was constructed and then searched for the optimum path using a dynamic programming approach, based on the secondary structure propensity of the protein short sequence derived from a training data set. The protein secondary structure was thus predicted in this way. The average three-state accuracy of the algorithm used was 76.70%.
Identifying Community Structures in Dynamic Networks
Alvari, Hamidreza; Sukthankar, Gita; Lakkaraju, Kiran
2016-01-01
Most real-world social networks are inherently dynamic, composed of communities that are constantly changing in membership. To track these evolving communities, we need dynamic community detection techniques. This article evaluates the performance of a set of game theoretic approaches for identifying communities in dynamic networks. Our method, D-GT (Dynamic Game Theoretic community detection), models each network node as a rational agent who periodically plays a community membership game with its neighbors. During game play, nodes seek to maximize their local utility by joining or leaving the communities of network neighbors. The community structure emerges after the game reaches a Nash equilibrium. Compared to the benchmark community detection methods, D-GT more accurately predicts the number of communities and finds community assignments with a higher normalized mutual information, while retaining a good modularity.
Dynamic Analysis of Composite Structural System for Looms Industry
Directory of Open Access Journals (Sweden)
Jigar K. Sevalia
2014-02-01
Full Text Available All the structures subjected to any kind of loads or displacement tends to behave dynamically. Thus the structures are always under continuous loading. The industrial buildings have to support the machineries in motion which are under high degree of vibrations. And so the design of base and the foundations of such structures under vibrations are very important and need to be stable. Problems of dynamics of bases and foundations are to be studied carefully, so as to understand the response characteristics of the power loom industry structure. This is very important from the economic point of view as well as to secure the stability and safety of the structure; dynamic analysis was carried out for Ground + One storey industry load bearing structure using STAAD.Pro software. In this paper, an attempt has been made to study the dynamic analysis of the structure under vibrations caused by reciprocating type machines. This paper makes attempt to study the effects of various structural parameters like Beam Size, Column Size and Storey Height and Wall Thickness variation on Frequency and Displacement of the industrial building which in future will serve as guidelines to the structural engineers and the industry people.
Ultrafast structural dynamics of perovskite superlattices
Energy Technology Data Exchange (ETDEWEB)
Woerner, M.; Korff Schmising, C. von; Zhavoronkov, N.; Elsaesser, T. [Max-Born-Institut fuer Nichtlineare Optik und Kurzzeitspektroskopie, Berlin (Germany); Bargheer, M. [Universitaet Potsdam, Institut fuer Physik und Astronomie, Potsdam (Germany); Vrejoiu, I.; Hesse, D.; Alexe, M. [Max-Planck-Institut fuer Mikrostrukturphysik, Halle (Germany)
2009-07-15
Femtosecond X-ray diffraction provides direct insight into the ultrafast reversible lattice dynamics of materials with a perovskite structure. Superlattice (SL) structures consisting of a sequence of nanometer-thick layer pairs allow for optically inducing a tailored stress profile that drives the lattice motions and for limiting the influence of strain propagation on the observed dynamics. We demonstrate this concept in a series of diffraction experiments with femtosecond time resolution, giving detailed information on the ultrafast lattice dynamics of ferroelectric and ferromagnetic superlattices. Anharmonically coupled lattice motions in a SrRuO{sub 3}/PbZr{sub 0.2}Ti{sub 0.8}O{sub 3} (SRO/PZT) SL lead to a switch-off of the electric polarizations on a time scale of the order of 1 ps. Ultrafast magnetostriction of photoexcited SRO layers is demonstrated in a SRO/SrTiO{sub 3} (STO) SL. (orig.)
Phenomenology, Structure, and Dynamic of Psychedelic States.
Preller, Katrin H; Vollenweider, Franz X
2016-12-27
Classic serotonergic hallucinogens or psychedelics produce an altered states of consciousness (ASC) that is characterized by profound alterations in sensory perception, mood, thought including the perception of reality, and the sense of self. Over the past years, there has been considerable progress in the search for invariant and common features of psychedelic states. In the first part of this review, we outline contemporary approaches to characterize the structure of ASCs by means of three primary etiology-independent dimensions including oceanic boundlessness, anxious ego-dissolution, and visionary restructuralization as well as by 11 lower-order factors, all of which can be reliably measured by the altered state of consciousness questionnaire (APZ-OAV). The second part sheds light on the dynamic nature of psychedelic experiences. Frequently, psychedelic subjects progress through different stages over time and levels of changes along a perception-hallucination continuum of increasing arousal and ego-dissolution. We then review in detail the acute effects of psychedelics on sensory perception, emotion, cognition, creativity, and time perception along with possible neural mechanisms underlying them. The next part of this review outlines the influence of non-pharmacological factors (predictors) on the acute psychedelic experience, such as demographics, genetics, personality, mood, and setting, and also discusses some long-term effects succeeding the acute experience. The last part presents some recent concepts and models attempting to understand different facets of psychedelic states of consciousness from a neuroscientific perspective.
Structure and dynamics of the solar chromosphere
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
Structure and dynamics of the solar chromosphere
Krijger, Johannes Mattheus
2003-01-01
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
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....
Proteins with Novel Structure, Function and Dynamics
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.
Nonlinear dynamic analysis of quasi-symmetric anisotropic structures
Noor, Ahmed K.; Peters, Jeanne M.
1987-01-01
An efficient computational method for the nonlinear dynamic analysis of quasi-symmetric anisotropic structures is proposed. The application of mixed models simplifies the analytical development and improves the accuracy of the response predictions, and operator splitting allows the reduction of the analysis model of the quasi-symmetric structure to that of the corresponding symmetric structure. The preconditoned conjugate gradient provides a stable and effective technique for generating the unsymmetric response of the structure as the sum of a symmetrized response plus correction modes. The effectiveness of the strategy is demonstrated with the example of a laminated anisotropic shallow shell of quadrilateral planform subjected to uniform normal loading.
Chernyshev, V. A.; Petrov, V. P.; Nikiforov, A. E.; Zakir'yanov, D. O.
2015-06-01
The effect of hydrostatic compression on the lattice structure and dynamics of elpasolites Cs2NaYbF6 and Cs2NaYF6 (sp. gr. 225) has been investigated ab initio. The frequencies and types of fundamental oscillations are determined, and elastic constants are calculated. The computation is performed within the molecular orbitals-linear combinations of atomic orbitals (MO LCAO) approach using the density functional theory (DFT) method with hybrid functionals B3LYP and PBE0 in the CRYSTAL09 program. The rare-earth ion was described by representing the inner (in particular, 4 f) orbitals in the form of a pseudopotential. The outer 5 s and 5 p orbitals, which determine chemical bonding, were described using valence basis sets.
Dynamic object management for distributed data structures
Totty, Brian K.; Reed, Daniel A.
1992-01-01
In distributed-memory multiprocessors, remote memory accesses incur larger delays than local accesses. Hence, insightful allocation and access of distributed data can yield substantial performance gains. The authors argue for the use of dynamic data management policies encapsulated within individual distributed data structures. Distributed data structures offer performance, flexibility, abstraction, and system independence. This approach is supported by data from a trace-driven simulation study of parallel scientific benchmarks. Experimental data on memory locality, message count, message volume, and communication delay suggest that data-structure-specific data management is superior to a single, system-imposed policy.
Exploiting Dynamically Propositional Logic Structures in SAT
Chen, Jingchao
2011-01-01
The 32-bit hwb (hwb-n32 for short) problem is from equivalence checking that arises in combining two circuits computing the hidden weighted bit function. Since 2002, it remains still unsolvable in every SAT competition. This paper focuses on solving problems such as hwb-n32. Generally speaking, modern solvers can detect only XOR, AND, OR and ITE gates. Other non-clausal formulas (propositional logic structures) cannot be detected. To solve the hwb-n32 problem, we extract dynamically some special propositional logic structures, and then use a variant of DPLL-based solvers to solve the subproblem simplified by the extracted structure information. Using the dynamic extraction technique, we solved efficiently the hwb-n32 problem, even some of which were solved within 3000 seconds.
Correlation Measure Equivalence in Dynamic Causal Structures
Gyongyosi, Laszlo
2016-01-01
We prove an equivalence transformation between the correlation measure functions of the causally-unbiased quantum gravity space and the causally-biased standard space. The theory of quantum gravity fuses the dynamic (nonfixed) causal structure of general relativity and the quantum uncertainty of quantum mechanics. In a quantum gravity space, the events are causally nonseparable and all time bias vanishes, which makes it no possible to use the standard causally-biased entropy and the correlation measure functions. Since a corrected causally-unbiased entropy function leads to an undefined, obscure mathematical structure, in our approach the correction is made in the data representation of the causally-unbiased space. We prove that the standard causally-biased entropy function with a data correction can be used to identify correlations in dynamic causal structures. As a corollary, all mathematical properties of the causally-biased correlation measure functions are preserved in the causally-unbiased space. The eq...
Emotional effects of dynamic textures
Toet, A.; Henselmans, M.; Lucassen, M.P.; Gevers, T.
2011-01-01
This study explores the effects of various spatiotemporal dynamic texture characteristics on human emotions. The emotional experience of auditory (eg, music) and haptic repetitive patterns has been studied extensively. In contrast, the emotional experience of visual dynamic textures is still largely
Emotional Effects of Dynamic Textures
Directory of Open Access Journals (Sweden)
Alexander Toet
2011-12-01
Full Text Available This study explores the effects of various spatiotemporal dynamic texture characteristics on human emotions. The emotional experience of auditory (eg, music and haptic repetitive patterns has been studied extensively. In contrast, the emotional experience of visual dynamic textures is still largely unknown, despite their natural ubiquity and increasing use in digital media. Participants watched a set of dynamic textures, representing either water or various different media, and self-reported their emotional experience. Motion complexity was found to have mildly relaxing and nondominant effects. In contrast, motion change complexity was found to be arousing and dominant. The speed of dynamics had arousing, dominant, and unpleasant effects. The amplitude of dynamics was also regarded as unpleasant. The regularity of the dynamics over the textures' area was found to be uninteresting, nondominant, mildly relaxing, and mildly pleasant. The spatial scale of the dynamics had an unpleasant, arousing, and dominant effect, which was larger for textures with diverse content than for water textures. For water textures, the effects of spatial contrast were arousing, dominant, interesting, and mildly unpleasant. None of these effects were observed for textures of diverse content. The current findings are relevant for the design and synthesis of affective multimedia content and for affective scene indexing and retrieval.
NEW TYPE OF VIBRATION STRUCTURE OF VERTICAL DYNAMIC BALANCING MACHINE
Institute of Scientific and Technical Information of China (English)
Li Dinggen; Cao Jiguang; Chen Chuanyao; Wang Junwen
2004-01-01
A new type of vibration structure of vertical dynamic balancing machine is designed, which is based on the analysis for swing frame of a traditional vertical dynamic balancing machine. The static unbalance and couple unbalance can be separated effectively by using the new machine with the new swing frame. By building the dynamics model, the advantages of the new structure are discussed in detail. The modal and harmonic response are analyzed by using the ANSYS7.0. By comparing the finite element modal analysis with the experimental modal analysis, the natural frequencies and vibration modes are found out. There are many spring boards in the new swing frame. Their stiffness is different and assort with each other. Furthermore, there are three sensors on the measurement points. Therefore, the new dynamic balancing machine can measure the static unbalance and couple unbalance directly, and the influence between them is faint. The new structure has the function of belt-strain compensation to improve the measurement precision. The practical result indicates that the new vertical dynamic balancing machine is suitable for inertial measurement of flying objects, and can overcome the shortcomings of traditional double-plane vertical dynamic balancing machines. The vertical dynamic balancing machine with the new vibration structure can be widely used in the future applications. The modeling and analysis of the new vibration structure provide theoretic instruction and practical experience for designing new type of vertical dynamic balancing machines. Based on the design principles such as stiffness-matching, frequency-adjacence and strain-compensation and so on, various new type of vibration structures can be designed.
The fundamental structures of dynamic social networks
Sekara, Vedran; Lehmann, Sune
2015-01-01
Networks provide a powerful mathematical framework for analyzing the structure and dynamics of complex systems (1-3). The study of group behavior has deep roots in the social science literature (4,5) and community detection is a central part of modern network science. Network communities have been found to be highly overlapping and organized in a hierarchical structure (6-9). Recent technological advances have provided a toolset for measuring the detailed social dynamics at scale (10,11). In spite of great progress, a quantitative description of the complex temporal behavior of social groups-with dynamics spanning from minute-by-minute changes to patterns expressed on the timescale of years-is still absent. Here we uncover a class of fundamental structures embedded within highly dynamic social networks. On the shortest time-scale, we find that social gatherings are fluid, with members coming and going, but organized via a stable core of individuals. We show that cores represent social contexts (9), with recur...
Dynamic effects of diabatization in distillation columns
DEFF Research Database (Denmark)
Bisgaard, Thomas; Huusom, Jakob Kjøbsted; Abildskov, Jens
2013-01-01
The dynamic effects of diabatization in distillation columns are investigated in simulation emphasizing the heat-integrated distillation column (HIDiC). A generic, dynamic, first-principle model has been formulated, which is flexible enough to describe various diabatic distillation configurations....... Dynamic Relative Gain Array and Singular Value Analysis have been applied in a comparative study of a conventional distillation column and a HIDiC. The study showed increased input-output coupling due to diabatization. Feasible SISO control structures for the HIDiC were also found and control...
Soliton structure dynamics in inhomogeneous media
Guerrero, L E; González, J A
1998-01-01
We show that soliton interaction with finite-width inhomogeneities can activate a great number of soliton internal modes. We obtain the exact stationary soliton solution in the presence of inhomogeneities and solve exactly the stability problem. We present a Karhunen-Loeve analysis of the soliton structure dynamics as a time-dependent force pumps energy into the traslational mode of the kink. We show the importance of the internal modes of the soliton as they can generate shape chaos for the soliton as well as cases in which the first shape mode leads the dynamics.
Laghaei, Rozita; Mousseau, Normand; Wei, Guanghong
2010-05-27
The human Islet amyloid polypeptide (hIAPP or amylin) is a 37-residue peptide hormone that is normally cosecreted with insulin by the pancreatic beta-cells. In patients with type 2 diabetes, hIAPP deposits as amyloid fibrils in the extracellular spaces of the pancreatic islets. Recent experimental studies show that the intramolecular disulfide bond between Cys2 and Cys7 plays a central role in the process of fibril formation. However, the effect of the disulfide bond on the intrinsic structural properties of monomeric hIAPP is yet to be determined. In this study, we characterize the atomic structure and the thermodynamics of full-length hIAPP in the presence and absence of a disulfide bond using extensive combined Hamiltonian and temperature replica exchange molecular dynamics simulations (HT-REMD) with a coarse grained protein force field. Our simulations show that HT-REMD is more efficient in sampling than temperature REMD. On the basis of a total simulation time of 28 mus, we find that, although native hIAPP (in the presence of a disulfide bond) essentially adopts a disordered conformation in solution, consistent with the signal measured by ultraviolet-circular dichroism (UV-CD) spectroscopy, it also transiently samples alpha-helical structure for residues 5-16. In comparison with the N-terminal region, the C-terminal region is highly disordered and populates a much lesser content of isolated beta-strand conformation for residues 22-26 and 30-35. Moreover, the absence of the disulfide bond greatly decreases the extent of helix formed throughout residues 5-9 in favor of random coil and beta-sheet structure. Implications of the stabilization of N-terminal helical structure by disulfide bond on the initialization of hIAPP amyloid formation are discussed.
Ly, Hong Khoa; Sezer, Murat; Wisitruangsakul, Nattawadee; Feng, Jiu-Ju; Kranich, Anja; Millo, Diego; Weidinger, Inez M; Zebger, Ingo; Murgida, Daniel H; Hildebrandt, Peter
2011-05-01
Most of the biochemical and biophysical processes of proteins take place at membranes, and are thus under the influence of strong local electric fields, which are likely to affect the structure as well as the reaction mechanism and dynamics. To analyse such electric field effects, biomimetic interfaces may be employed that consist of membrane models deposited on nanostructured metal electrodes. For such devices, surface-enhanced resonance Raman and IR absorption spectroscopy are powerful techniques to disentangle the complex interfacial processes of proteins in terms of rotational diffusion, electron transfer, and protein and cofactor structural changes. The present article reviews the results obtained for the haem protein cytochrome c, which is widely used as a model protein for studying the various reaction steps of interfacial redox processes in general. In addition, it is shown that electric field effects may be functional for the natural redox processes of cytochrome c in the respiratory chain, as well as for the switch from the redox to the peroxidase function, one of the key events preceding apoptosis. © 2011 The Authors Journal compilation © 2011 FEBS.
Dynamics and control of diseases in networks with community structure.
Directory of Open Access Journals (Sweden)
Marcel Salathé
2010-04-01
Full Text Available The dynamics of infectious diseases spread via direct person-to-person transmission (such as influenza, smallpox, HIV/AIDS, etc. depends on the underlying host contact network. Human contact networks exhibit strong community structure. Understanding how such community structure affects epidemics may provide insights for preventing the spread of disease between communities by changing the structure of the contact network through pharmaceutical or non-pharmaceutical interventions. We use empirical and simulated networks to investigate the spread of disease in networks with community structure. We find that community structure has a major impact on disease dynamics, and we show that in networks with strong community structure, immunization interventions targeted at individuals bridging communities are more effective than those simply targeting highly connected individuals. Because the structure of relevant contact networks is generally not known, and vaccine supply is often limited, there is great need for efficient vaccination algorithms that do not require full knowledge of the network. We developed an algorithm that acts only on locally available network information and is able to quickly identify targets for successful immunization intervention. The algorithm generally outperforms existing algorithms when vaccine supply is limited, particularly in networks with strong community structure. Understanding the spread of infectious diseases and designing optimal control strategies is a major goal of public health. Social networks show marked patterns of community structure, and our results, based on empirical and simulated data, demonstrate that community structure strongly affects disease dynamics. These results have implications for the design of control strategies.
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...... rotational speed (3P effects). The effect of dynamic soil-structure interaction on the rotation of the foundation has also been investigated.......) 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...
Indian Academy of Sciences (India)
R J Sengwa; Sonu Sankhila
2006-08-01
Dielectric relaxation study of the binary mixtures of poly(vinyl pyrrolidone) (PVP) (Mw = 24000, 40000 and 360000 g mol-1) with ethyl alcohol (EA) and poly(ethylene glycol)s (PEGs) (Mw = 200 and 400 g mol-1) in dilute solutions of dioxane were carried out at 10.1 GHz and 35°} C. The relaxation time of PVP–EA mixtures was interpreted by the consideration of a wait-and-switch model in the local structure of self-associated ethyl alcohol molecules and also the PVP chain length as a geometric constraint for the reorientational motion of ethyl alcohol molecules. The formation of complexes and effect of PVP chain length on the molecular dynamics, chain flexibility and stretching of PEG molecules in PVP–PEG mixtures were explored from the comparative values of dielectric relaxation time. Further, relaxation time values in dioxane and benzene solvent confirm the viscosity independent molecular dynamics in PVP–EA mixtures but the values vary significantly with the non-polar solvent environment.
Structure and dynamics of confined alcohol-water mixtures
Bampoulis, Pantelis; Witteveen, J.P.; Kooij, Ernst S.; Lohse, Detlef; Poelsema, Bene; Zandvliet, Henricus J.W.
2016-01-01
The effect of confinement between mica and graphene on the structure and dynamics of alcohol–water mixtures has been studied in situ and in real time at the molecular level by atomic force microscopy (AFM) at room temperature. AFM images reveal that the adsorbed molecules are segregated into faceted
Time Collocation Method for Structural Dynamic Problems
Institute of Scientific and Technical Information of China (English)
TANG Chen; LUO Tao; YAN Haiqing; GU Xiaohui
2005-01-01
In order to achieve highly accurate and efficient numerical calculations of structural dynamics, time collocation method is presented. For a given time interval, the numerical solution of the method is approximated by a polynomial. The polynomial coefficients are evaluated by solving algebraic equation. Once the polynomial coefficients are evaluated, the numerical solutions at any time in the interval can be easily calculated. New formulae are derived for the polynomial coefficients,which are more practical and succinct than those previously given. Two structural dynamic equations are calculated by the proposed method. The numerical solutions are compared with the traditional fourth-order Runge-Kutta method. The results show that the method proposed is highly accurate and computationally efficient. In addition, an important advantage of the method is the simplicity in software programming.
Gul, Sheraz; Cooper, Jason Kyle; Glans, Per-Anders; Guo, Jinghua; Yachandra, Vittal K; Yano, Junko; Zhang, Jin Zhong
2013-10-22
The dopant local structure and optical properties of Cu-doped ZnSe (ZnSe:Cu) and Cu and Al co-doped ZnSe (ZnSe:Cu,Al) nanocrystals (NCs) were studied with an emphasis on understanding the impact of introducing Al as a co-dopant. Quantum-confined NCs with zinc blende crystal structure and particle size of 6 ± 0.6 Å were synthesized using a wet chemical route. The local structure of the Cu dopant, studied by extended X-ray absorption fine structure, indicated that Cu in ZnSe:Cu NCs occupies a site that is neither substitutional nor interstitial and is adjacent to a Se vacancy. Additionally, we estimated that approximately 25 ± 8% of Cu was located on the surface of the NC. Al(3+) co-doping aids in Cu doping by accounting for the charge imbalance originated by Cu(+) doping and consequently reduces surface Cu doping. The Cu ions remain distorted from the center of the tetrahedron to one of the triangular faces. The lifetime of the dopant-related photoluminescence was found to increase from 550 ± 60 to 700 ± 60 ns after Al co-doping. DFT calculations were used to obtain the density of states of a model system to help explain the optical properties and dynamics processes observed. This study demonstrates that co-doping using different cations with complementary oxidation states is an effective method to enhance optical properties of doped semiconductor NCs of interest for various photonics applications.
Dynamic active earth pressure on retaining structures
Indian Academy of Sciences (India)
Deepankar Choudhury; Santiram Chatterjee
2006-12-01
Earth-retaining structures constitute an important topic of research in civil engineering, more so under earthquake conditions. For the analysis and design of retaining walls in earthquake-prone zones, accurate estimation of dynamic earth pressures is very important. Conventional methods either use pseudo-static approaches of analysis even for dynamic cases or a simple single-degree of freedom model for the retaining wall–soil system. In this paper, a simpliﬁed two-degree of freedom mass–spring–dashpot (2-DOF) dynamic model has been proposed to estimate the active earth pressure at the back of the retaining walls for translation modes of wall movement under seismic conditions. The horizontal zone of inﬂuence on dynamic earth force on the wall is estimated. Results in terms of displacement, velocity and acceleration-time history are presented for some typical cases, which show the ﬁnal movement of the wall in terms of wall height, which is required for the design. The non-dimensional design chart proposed in the present study can be used to compute the total dynamic earth force on the wall under different input ground motion and backﬁll conditions. Finally, the results obtained have been compared with those of the available Scott model and the merits of the present results have been discussed.
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....
Dynamical Structure of Nuclear Excitation in Continuum
Institute of Scientific and Technical Information of China (English)
ZHANG Chun-Lei; ZHANG Huan-Qiao; ZHANG Xi-Zhen
2005-01-01
@@ Dynamical structures of collective excitation in continuum are studied by calculating the isoscalar and isovector strength as well as transition density of nuclei near the drip-line such as 28O and 34Ca. It is found that for some excited states in continuum the proton and neutron transition density calculated from isoscalar and isovector excitation at some given energies may be different, which will affect the calculation of the polarization for nuclei with N ≠ Z.
Nonlinear Dynamics and Control of Flexible Structures
1991-03-01
Freedom," Ph.D. Thesis, Department of Theoretical and Applied Mechanics, Cornell University, in preparation. 5I I URI Reorts Islam , Saiful and Mircea...Theoretical and Applied Mechanics I S. Islam Civil and Environmental Engineering I 2! I 3 URI Accomplishments 3 -Nonlinear Dynamics and Chaos in Flexible...Structures with Symmetry," 31 (1991) 265-285. Islam , S. and M. Grigoriu, "Nonlinear Random Vibration of Pin-Jointed Trusses with Imperfections," in
Flexible joints in structural and multibody dynamics
O. A. Bauchau; Han, S.
2013-01-01
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 deformat...
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.
Modal interactions in dynamical and structural systems
Energy Technology Data Exchange (ETDEWEB)
Nayfeh, A.H.; Balachandran, B. (Virginia Polytechnic Institute and State Univ., Blacksburg (USA))
1989-11-01
The authors review theoretical and experimental studies of the influence of modal interactions on the nonlinear response of harmonically excited structural and dynamical systems. In particular, they discuss the response of pendulums, ships, rings, shells, arches, beam structures, surface waves, and the similarities in the qualitative behavior of these systems. The systems are characterized by quadratic nonlinearities which may lead to two-to-one and combination autoparametric resonances. These resonances give rise to a coupling between the modes involved in the resonance leading to nonlinear periodic, quasi-periodic, and chaotic motions.
Some Modern Problems in Structural Engineering Dynamics
Directory of Open Access Journals (Sweden)
I. Elishakoff
2010-01-01
Full Text Available This review paper deals with two problems in structural engineering dynamics; one is deterministic, the other is of stochastic nature. One problem is linear, the other is nonlinear. Authors have a biased preferential view on these problems because of their active involvement in the discussed research topics. Still, these two problems reflect, at least in a small manner, some developments in this vast and fascinating field. The first part deals with deterministic linear vibrations of double-walled carbon nanotubes either in classical or refined setting; the second part is devoted to the nonlinear random vibrations of structures.
Dynamic ice loads on conical structures
Institute of Scientific and Technical Information of China (English)
无
2011-01-01
Two series of model tests were performed to observe the dynamic ice loads on conical structures.The variable testing parameters include the water line diameter of the model cone and ice parameters.During small water line diameter tests,two-time breaking is found to be the typical failure of ice on steep conical structure,and also be controlled by other factors,such as ice speed and the cone angle.During big water line diameter tests,the ice sheet failed nonsimultaneously around the cone.Several independe...
Wu, Yang; Hu, Na; Yue, Lili; Wei, Lihong; Guan, Wei
2015-02-01
An extended electronegativity equalization method/molecular mechanics (EEM/MM) model for ionic liquids is used to investigate the structures and properties of 1-alkyl-3-methylimidazolium glycine ionic liquids [Cnmim][Gly] (n = 1-4) with alkyl substituents of different lengths. The EEM/MM model describes the electrostatic interactions of atoms and their changes in different ambient environments. This property is the most outstanding characteristic of the model. EEM parameters (i.e., valence electronegativities and valence hardness parameters) are calibrated using linear regression and least-squares methods, which can accurately predict the gas-phase properties of [Cnmim]+, [Gly]-, and [Cnmim][Gly] ion pairs. We utilize the EEM/MM force field to systematically investigate the effects of polarizability on the accuracy of [Cnmim][Gly] properties predicted through the molecular dynamic simulations. EEM/MM explicitly describes the atom-based polarizability of [Cnmim][Gly]; thus, the densities, enthalpies of vaporization, self-diffusion coefficients, and conductivities of the [Cnmim][Gly] are consistent with the experimental values. The calculated radial distribution functions provide a mechanistic understanding of the effects of polarizability on ionic aggregations in amino acid ionic liquids. The effects of alkyl chain length on the diffusion coefficient and conductivity are also discussed.
Structural dynamic analysis of composite beams
Suresh, J. K.; Venkatesan, C.; Ramamurti, V.
1990-12-01
In the treatment of the structural dynamic problem of composite materials, two alternate types of formulations, based on the elastic modulus and compliance quantities, exist in the literature. The definitions of the various rigidities are observed to differ in these two approaches. Following these two types of formulation, the structural dynamic characteristics of a composite beam are analyzed. The results of the analysis are compared with those available in the literature. Based on the comparison, the influence of the warping function in defining the coupling terms in the modulus approach and also on the natural frequencies of the beam has been identified. It is found from the analysis that, in certain cases, the difference between the results of the two approaches is appreciable. These differences may be attributed to the constraints imposed on the deformation and flexibility of the beam by the choice of the description of the warping behaviour. Finally, the influence of material properties on the structural dynamic characteristics of the beam is studied for different composites for various angles of orthotropy.
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.
Duggleby, A; Paul, M R
2006-01-01
The results of a comparative analysis between turbulent pipe flow and drag reduced turbulent pipe flow by spanwise wall oscillation based upon a Karhunen-Loeve expansion are presented. The turbulent flow is generated by a direct numerical simulation at a Reynolds number Re_\\tau = 150. The spanwise wall oscillation is imposed as a velocity boundary condition with an amplitude of A^+ = 20 and a period of T^+ = 50. The flow is driven by a constant pressure gradient, resulting in a 27% mean velocity increase with wall oscillation. The peaks of the Reynolds stress and root-mean-squared velocities shift away from the wall and the Karhunen-Loeve dimension of the turbulent attractor is reduced from 2453 to 102. The coherent vorticity structures are pushed away from the wall into higher speed flow, causing an increase of their advection speed of 34% as determined by a normal speed locus. The mechanism of drag reduction by spanwise wall oscillation is discussed.
Controlling Proton Delivery through Catalyst Structural Dynamics
Energy Technology Data Exchange (ETDEWEB)
Cardenas, Allan Jay P. [Center for Molecular Electrocatalysis, Pacific Northwest National Laboratory, P.O. Box 999, K2-57 Richland WA 99352 USA; 221 Science Center, State University of New York at Fredonia, Fredonia NY 14063 USA; Ginovska, Bojana [Center for Molecular Electrocatalysis, Pacific Northwest National Laboratory, P.O. Box 999, K2-57 Richland WA 99352 USA; Kumar, Neeraj [Center for Molecular Electrocatalysis, Pacific Northwest National Laboratory, P.O. Box 999, K2-57 Richland WA 99352 USA; Hou, Jianbo [Center for Molecular Electrocatalysis, Pacific Northwest National Laboratory, P.O. Box 999, K2-57 Richland WA 99352 USA; Raugei, Simone [Center for Molecular Electrocatalysis, Pacific Northwest National Laboratory, P.O. Box 999, K2-57 Richland WA 99352 USA; Helm, Monte L. [Center for Molecular Electrocatalysis, Pacific Northwest National Laboratory, P.O. Box 999, K2-57 Richland WA 99352 USA; Appel, Aaron M. [Center for Molecular Electrocatalysis, Pacific Northwest National Laboratory, P.O. Box 999, K2-57 Richland WA 99352 USA; Bullock, R. Morris [Center for Molecular Electrocatalysis, Pacific Northwest National Laboratory, P.O. Box 999, K2-57 Richland WA 99352 USA; O' Hagan, Molly [Center for Molecular Electrocatalysis, Pacific Northwest National Laboratory, P.O. Box 999, K2-57 Richland WA 99352 USA
2016-09-27
The fastest synthetic molecular catalysts for production and oxidation of H2 emulate components of the active site of natural hydrogenases. The role of controlled structural dynamics is recognized as a critical component in the catalytic performance of many enzymes, including hydrogenases, but is largely neglected in the design of synthetic molecular cata-lysts. In this work, the impact of controlling structural dynamics on the rate of production of H2 was studied for a series of [Ni(PPh2NC6H4-R2)2]2+ catalysts including R = n-hexyl, n-decyl, n-tetradecyl, n-octadecyl, phenyl, or cyclohexyl. A strong correlation was observed between the ligand structural dynamics and the rates of electrocatalytic hydrogen production in acetonitrile, acetonitrile-water, and protic ionic liquid-water mixtures. Specifically, the turnover frequencies correlate inversely with the rates of ring inversion of the amine-containing ligand, as this dynamic process dictates the positioning of the proton relay in the second coordination sphere and therefore governs protonation at either catalytically productive or non-productive sites. This study demonstrates that the dynamic processes involved in proton delivery can be controlled through modifications of the outer coordination sphere of the catalyst, similar to the role of the protein architecture in many enzymes. The present work provides new mechanistic insight into the large rate enhancements observed in aqueous protic ionic liquid media for the [Ni(PPh2NR2)]2+ family of catalysts. The incorporation of controlled structural dynamics as a design parameter to modulate proton delivery in molecular catalysts has enabled H2 production rates that are up to three orders of magnitude faster than the [Ni(PPh2NPh2)]2+complex. The observed turnover frequencies are up to 106 s-1 in acetonitrile-water, and over 107 s-1 in protic ionic liquid-water mixtures, with a minimal increase in overpotential. This material is based upon work supported as part of
Molecular dynamics modeling of structural battery components
Verners, O.; Van Duin, A.C.T.; Wagemaker, M.; Simone, A.
2015-01-01
A crosslinked polymer based solid electrolyte prototype material –poly(propylene glycol) diacrylate– is studied using the reactive molecular dynamics force field ReaxFF. The focus of the study is the evaluation of the effects of equilibration and added plasticizer (ethylene carbonate) or anion compo
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;}
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.
Energy Technology Data Exchange (ETDEWEB)
Stebbins, J.F.; Ellsworth, S.E. [Stanford Univ., Stanford, CA (United States)
1996-09-01
The fictive temperature dependence of the relative abundances of three- and four-coordinated boron was investigated in several sodium borate and borosilicate glasses using high-resolution {sup 11}B nuclear magnetic resonance (NMR). In the compositions with low sodium/boron ratios, no effect was observed, but in the borosilicates, the fraction of the tetrahedral species decreased significantly as the fictive temperature increased because of the higher content of nonbridging oxygens. In situ, high-temperature magic-angle spinning NMR demonstrated the exchange of the two species at a rate comparable to the shear relaxation rate, indicating a close link between B-O bond breaking and viscous flow.
30th IMAC, A Conference on Structural Dynamics
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.
Structural optimization for nonlinear dynamic response
DEFF Research Database (Denmark)
Dou, Suguang; Strachan, B. Scott; Shaw, Steven W.
2015-01-01
condition, thereby providing a means for tailoring its nonlinear response. The method is applied to the fundamental nonlinear resonance of a clamped–clamped beam and to the coupled mode response of a frame structure, and the results show that one can modify essential normal form coefficients by an order...... 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...... 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...
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.
The structural dynamics of social class.
Kraus, Michael W; Park, Jun Won
2017-08-01
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.
Dynamical 3-Space Gravitational Waves: Reverberation Effects
Directory of Open Access Journals (Sweden)
Cahill R. T.
2013-04-01
Full Text Available Gravity theory missed a key dynamical process that became ap parent only when ex- pressed in terms of a velocity field, instead of the Newtonian gravitational acceleration field. This dynamical process involves an additional self-i nteraction of the dynam- ical 3-space, and experimental data reveals that its streng th is set by the fine struc- ture constant, implying a fundamental link between gravity and quantum theory. The dynamical 3-space has been directly detected in numerous li ght-speed anisotropy ex- periments. Quantum matter has been shown to exhibit an accel eration caused by the time-dependence and inhomogeneity of the 3-space flow, givi ng the first derivation of gravity from a deeper theory, as a quantum wave refraction effect. EM radiation is also refracted in a similar manner. The anisotropy experiments have all shown 3-space wave / turbulence effects, with the latest revealing the fractal structure of 3-s pace. Here we report the prediction of a new effect, namely a reverberation effect, when the gravi- tational waves propagate in the 3-space inflow of a large mass . This effect arises from the non-linear dynamics of 3-space. These reverberations c ould offer an explanation for the Shnoll effect, in which cosmological factors influence stochastic pro cesses, such as radioactive decay rates.
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....
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....
In situ characterization of structural dynamics in swelling hydrogels.
Guzman-Sepulveda, J R; Deng, J; Fang, J Y; Dogariu, A
2016-07-06
Characterizing the structural morphology and the local viscoelastic properties of soft complex systems raises significant challenges. Here we introduce a dynamic light scattering method capable of in situ, continuous monitoring of structural changes in evolving systems such as swelling gels. We show that the inherently non-stationary dynamics of embedded probes can be followed using partially coherent radiation, which effectively isolates only single scattering contributions even during the dramatic changes in the scattering regime. Using a simple and robust experimental setup, we demonstrate the ability to continuously monitor the structural dynamics of chitosan hydrogels formed by the Ag(+) ion-triggered gelation during their long-term swelling process. We demonstrate that both the local viscoelastic properties of the suspending medium and an effective cage size experienced by diffusing probe particles loaded into the hydrogel can be recovered and used to describe the structural dynamics of hydrogels with different levels of cross-linking. This characterization capability is critical for defining and controlling the hydrogel performance in different biomedical applications.
Fundamental structures of dynamic social networks.
Sekara, Vedran; Stopczynski, Arkadiusz; Lehmann, Sune
2016-09-06
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 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 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 unnecessary. Starting from 5-min time slices, we uncover dynamic social structures expressed on multiple timescales. On the hourly timescale, we find that gatherings are fluid, with members coming and going, but organized via a stable core of individuals. Each core represents a social context. Cores exhibit a pattern of recurring meetings across weeks and months, each with varying degrees of regularity. Taken together, these findings provide a powerful simplification of the social network, where cores represent fundamental structures expressed with strong temporal and spatial regularity. Using this framework, we explore the complex interplay between social and geospatial behavior, documenting how the formation of cores is preceded by coordination behavior in the communication networks and demonstrating that social behavior can be predicted with high precision.
The Hierarchical Structure and Dynamics of Voids
Aragon-Calvo, M A
2012-01-01
Contrary to the common view voids have very complex internal structure and dynamics. Here we show how the hierarchy of structures in the density field inside voids is reflected by a similar hierarchy of structures in the velocity field. Voids defined by dense filaments and clusters can de described as simple expanding domains with coherent flows everywhere except at their boundaries. At scales smaller that the void radius the velocity field breaks into expanding sub-domains corresponding to sub- voids. These sub-domains break into even smaller sub-sub domains at smaller scales resulting in a nesting hierarchy of locally expanding domains. The ratio between the magnitude of the velocity field responsible for the expansion of the void and the velocity field defining the sub voids is approximately one order of magnitude. The small-scale components of the velocity field play a minor role in the shaping of the voids but they define the local dynamics directly affecting the processes of galaxy formation and evoluti...
Structural Dynamics of Tropical Moist Forest Gaps
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 <10 m. Applying the dynamic definition at both sites, we found over twice as much area in 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
Structural Dynamics of Tropical Moist Forest Gaps.
Directory of Open Access Journals (Sweden)
Maria O Hunter
Full Text Available 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 <10 m. Applying the dynamic definition at both sites, we found over twice as much area in 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
Structural Dynamics of Tropical Moist Forest Gaps.
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 <10 m. Applying the dynamic definition at both sites, we found over twice as much area in 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
Order effects in dynamic semantics.
Graben, Peter Beim
2014-01-01
In their target article, Wang and Busemeyer (2013) discuss question order effects in terms of incompatible projectors on a Hilbert space. In a similar vein, Blutner recently presented an orthoalgebraic query language essentially relying on dynamic update semantics. Here, I shall comment on some interesting analogies between the different variants of dynamic semantics and generalized quantum theory to illustrate other kinds of order effects in human cognition, such as belief revision, the resolution of anaphors, and default reasoning that result from the crucial non-commutativity of mental operations upon the belief state of a cognitive agent.
Structural dynamics of turbo-machines
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
The chemical bond structure and dynamics
Zewail, Ahmed
1992-01-01
This inspired book by some of the most influential scientists of our time--including six Nobel laureates--chronicles our emerging understanding of the chemical bond through the last nine decades and into the future. From Pauling's early structural work using x-ray and electron diffraction to Zewail's femtosecond lasers that probe molecular dynamics in real time; from Crick's molecular biology to Rich's molecular recognition, this book explores a rich tradition of scientific heritage and accomplishment. The perspectives given by Pauling, Perutz, Rich, Crick, Porter, Polanyi, Herschbach, Zewail,
Inverse Eigenvalue Problem in Structural Dynamics Design
Institute of Scientific and Technical Information of China (English)
Huiqing Xie; Hua Dai
2006-01-01
A kind of inverse eigenvalue problem in structural dynamics design is considered. The problem is formulated as an optimization problem. The properties of this problem are analyzed, and the existence of the optimum solution is proved. The directional derivative of the objective function is obtained and a necessary condition for a point to be a local minimum point is given. Then a numerical algorithm for solving the problem is presented and a plane-truss problem is discussed to show the applications of the theories and the algorithm.
Baksht, E. Kh.; Blinova, O. M.; Erofeev, M. V.; Karelin, V. I.; Ripenko, V. S.; Tarasenko, V. F.; Trenkin, A. A.; Shibitov, Yu. M.; Shulepov, M. A.
2016-09-01
The dynamics of the spatial structure of the plasma of pulsed discharges in air and nitrogen in a nonuniform electric field and their erosion effect on the plane anode surface were studied experimentally. It is established that, at a nanosecond front of the voltage pulse, a diffuse discharge forms in the point cathode-plane anode gap due to the ionization wave propagating from the cathode. As the gap length decreases, the diffuse discharge transforms into a spark. A bright spot on the anode appears during the diffuse discharge, while the spark channel forms in the later discharge stage. The microstructure of autographs of anode spots and spark channels in discharges with durations of several nanoseconds is revealed. The autographs consist of up to 100 and more microcraters 5-100 μm in diameter. It is shown that, due to the short duration of the voltage pulse, a diffuse discharge can be implemented, several pulses of which do not produce appreciable erosion on the plane anode or the soot coating deposited on it.
Molten uranium dioxide structure and dynamics.
Skinner, L B; Benmore, C J; Weber, J K R; Williamson, M A; Tamalonis, A; Hebden, A; Wiencek, T; Alderman, O L G; Guthrie, M; Leibowitz, L; Parise, J B
2014-11-21
Uranium dioxide (UO2) is the major nuclear fuel component of fission power reactors. A key concern during severe accidents is the melting and leakage of radioactive UO2 as it corrodes through its zirconium cladding and steel containment. Yet, the very high temperatures (>3140 kelvin) and chemical reactivity of molten UO2 have prevented structural studies. In this work, we combine laser heating, sample levitation, and synchrotron x-rays to obtain pair distribution function measurements of hot solid and molten UO2. The hot solid shows a substantial increase in oxygen disorder around the lambda transition (2670 K) but negligible U-O coordination change. On melting, the average U-O coordination drops from 8 to 6.7 ± 0.5. Molecular dynamics models refined to this structure predict higher U-U mobility than 8-coordinated melts.
Cheng, Yuanhua; Lindert, Steffen; Kekenes-Huskey, Peter; Rao, Vijay S.; Solaro, R. John; Rosevear, Paul R.; Amaro, Rommie; McCulloch, Andrew D.; McCammon, J. Andrew; Regnier, Michael
2014-01-01
During β-adrenergic stimulation, cardiac troponin I (cTnI) is phosphorylated by protein kinase A (PKA) at sites S23/S24, located at the N-terminus of cTnI. This phosphorylation has been shown to decrease KCa and pCa50, and weaken the cTnC-cTnI (C-I) interaction. We recently reported that phosphorylation results in an increase in the rate of early, slow phase of relaxation (kREL,slow) and a decrease in its duration (tREL,slow), which speeds up the overall relaxation. However, as the N-terminus of cTnI (residues 1–40) has not been resolved in the whole cardiac troponin (cTn) structure, little is known about the molecular-level behavior within the whole cTn complex upon phosphorylation of the S23/S24 residues of cTnI that results in these changes in function. In this study, we built up the cTn complex structure (including residues cTnC 1–161, cTnI 1–172, and cTnT 236–285) with the N-terminus of cTnI. We performed molecular-dynamics (MD) simulations to elucidate the structural basis of PKA phosphorylation-induced changes in cTn structure and Ca2+ binding. We found that introducing two phosphomimic mutations into sites S23/S24 had no significant effect on the coordinating residues of Ca2+ binding site II. However, the overall fluctuation of cTn was increased and the C-I interaction was altered relative to the wild-type model. The most significant changes involved interactions with the N-terminus of cTnI. Interestingly, the phosphomimic mutations led to the formation of intrasubunit interactions between the N-terminus and the inhibitory peptide of cTnI. This may result in altered interactions with cTnC and could explain the increased rate and decreased duration of slow-phase relaxation seen in myofibrils. PMID:25296321
Chaos in effective classical and quantum dynamics
Casetti, L; Modugno, M; Casetti, Lapo; Gatto, Raoul; Modugno, Michele
1998-01-01
We investigate the dynamics of classical and quantum N-component phi^4 oscillators in presence of an external field. In the large N limit the effective dynamics is described by two-degree-of-freedom classical Hamiltonian systems. In the classical model we observe chaotic orbits for any value of the external field, while in the quantum case chaos is strongly suppressed. A simple explanation of this behaviour is found in the change in the structure of the orbits induced by quantum corrections. Consistently with Heisenberg's principle, quantum fluctuations are forced away from zero, removing in the effective quantum dynamics a hyperbolic fixed point that is a major source of chaos in the classical model.
Molecular structures and intramolecular dynamics of pentahalides
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.
Dynamical Franz-Keldysh Effect
DEFF Research Database (Denmark)
Jauho, Antti-Pekka; Johnsen, Kristinn
1996-01-01
We introduce and analyze the properties of dynamical Franz-Keldysh effect, i.e., the change of density of states, or absorption spectra, of semiconductors under the influence of time-dependent electric fields. In the case of a harmonic time dependence, we predict the occurrence of significant fine...
Effect research of labyrinth seal structure and dynamics parameters%迷宫密封结构与动力学参数影响因素
Institute of Scientific and Technical Information of China (English)
马文生; 陈照波; 焦映厚; 丁竹生; R.G.Kirk
2012-01-01
Numerical method is used for solving rotor-seal nonlinear dynamics equation,so that the dynamics effects of whirl speed,pre-whirl,labyrinth seal gap,pressure are investigated,and the leakage effects of seal gap,pressure,labyrinth seal structure are researched.The numerical method is verified to be correct by experiments.The results show that reducing pre-whirl and increasing seal gap can reduce the cross-stiffness coefficients,and improve stability purposes.There is a critical value of tooth width 1.04 mm,the leakage seal increases with the increasing of tooth width when it is more than the critical value,and the leakage seal decreases with the increasing of tooth width when it is less than the critical value.At the same whirl speed,the leakage increases with the increase of labyrinth seal and pressure,and decreases with the decrease of cavity depth.%针对迷宫密封-转子系统的特点,建立密封-转子系统动力学模型,分析转速、入口预旋比、密封间隙、压差等重要密封参数对密封动力学特性系数的影响.对三维模型的流体动力学（CFD）进行分析,总结出密封结构和压差对泄漏量的变化规律,并通过与实验的对比分析验证了本方法的正确性.研究结果表明：减小密封入口预旋速度,适当增大密封间隙,可以减小引起不稳定的交叉刚度系数,提高稳定性.齿宽存在一个临界值（1.04 mm）,高于这个临界值时,随着齿宽变大泄漏量变大;低于这个临界值时,随着齿宽变大泄漏量变小.在相同转速下,随着密封间隙的增大泄漏量增大,压差增大泄漏量增大,腔深增大泄漏量减小.
Dynamic behavior of reinforced concrete frame structure during construction
Institute of Scientific and Technical Information of China (English)
TIAN Ming-ge; YI Wei-jian
2008-01-01
The effects of concrete's time-variant elastic modulus, casting structural components, assembling temporary shoring framework system, and shock by operating construction equipment on dynamic behavior of the reinforced concrete frame structure during construction were investigated. The dynamic tests of an eight-storey reinforced concrete frame structure during full-scaled stages of the sixth storey construction cycle were carried out by ambient vibration. Natural frequencies, corresponding mode shapes and damping ratio were determined by power spectrum processing the tested signal data in frequency domain. The changes of frequencies, mode shapes and damping ratios at different construction stages were given. The results show that natural frequencies and modal damping ratios reach the maximum at stage of casting fresh concrete, especially for higher modes. Modal damping ratios at each construction stage are less than 5% of those during usage.
Structural optimization for nonlinear dynamic response.
Dou, Suguang; Strachan, B Scott; Shaw, Steven W; Jensen, Jakob S
2015-09-28
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 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 condition, thereby providing a means for tailoring its nonlinear response. The method is applied to the fundamental nonlinear resonance of a clamped-clamped beam and to the coupled mode response of a frame structure, and the results show that one can modify essential normal form coefficients by an order of magnitude by relatively simple changes in the shape of these elements. We expect the proposed approach, and its extensions, to be useful for the design of systems used for fundamental studies of nonlinear behaviour as well as for the development of commercial devices that exploit nonlinear behaviour.
Dynamical effects in fusion with exotic nuclei
Vo-Phuoc, K; Simpson, E C
2016-01-01
[Background] Reactions with stable beams have demonstrated a strong interplay between nuclear structure and fusion. Exotic beam facilities open new perspectives to understand the impact of neutron skin, large isospin, and weak binding energies on fusion. Microscopic theories of fusion are required to guide future experiments. [Purpose] To investigate new effects of exotic structures and dynamics in near-barrier fusion with exotic nuclei. [Method] Microscopic approaches based on the Hartree-Fock (HF) mean-field theory are used for studying fusion barriers in $^{40-54}$Ca+$^{116}$Sn reactions for even isotopes. Bare potential barriers are obtained assuming frozen HF ground-state densities. Dynamical effects on the barrier are accounted for in time-dependent Hartree-Fock (TDHF) calculations of the collisions. Vibrational couplings are studied in the coupled-channel framework and near-barrier nucleon transfer is investigated with TDHF calculations. [Results] The development of a neutron skin in exotic calcium iso...
Structural and dynamical properties of complex networks
Ghoshal, Gourab
Recent years have witnessed a substantial amount of interest within the physics community in the properties of networks. Techniques from statistical physics coupled with the widespread availability of computing resources have facilitated studies ranging from large scale empirical analysis of the worldwide web, social networks, biological systems, to the development of theoretical models and tools to explore the various properties of these systems. Following these developments, in this dissertation, we present and solve for a diverse set of new problems, investigating the structural and dynamical properties of both model and real world networks. We start by defining a new metric to measure the stability of network structure to disruptions, and then using a combination of theory and simulation study its properties in detail on artificially generated networks; we then compare our results to a selection of networks from the real world and find good agreement in most cases. In the following chapter, we propose a mathematical model that mimics the structure of popular file-sharing websites such as Flickr and CiteULike and demonstrate that many of its properties can solved exactly in the limit of large network size. The remaining part of the dissertation primarily focuses on the dynamical properties of networks. We first formulate a model of a network that evolves under the addition and deletion of vertices and edges, and solve for the equilibrium degree distribution for a variety of cases of interest. We then consider networks whose structure can be manipulated by adjusting the rules by which vertices enter and leave the network. We focus in particular on degree distributions and show that, with some mild constraints, it is possible by a suitable choice of rules to arrange for the network to have any degree distribution we desire. In addition we define a simple local algorithm by which appropriate rules can be implemented in practice. Finally, we conclude our
Effects of Curvature on Dynamics
Dutta, Gautam
2010-01-01
In this article we discuss the effect of curvature on dynamics when a physical system moves adiabatically in a curved space. These effects give a way to measure the curvature of the space intrinsically without referring to higher dimensional space. Two interesting examples, the Foucault Pendulum and the perihelion shift of planetary orbits, are presented in a simple geometric way. A paper model is presented to see the perihelion shift.
Structure and dynamics in network-forming materials
Wilson, Mark
2016-12-01
The study of the structure and dynamics of network-forming materials is reviewed. Experimental techniques used to extract key structural information are briefly considered. Strategies for building simulation models, based on both targeting key (experimentally-accessible) materials and on systematically controlling key model parameters, are discussed. As an example of the first class of materials, a key target system, SiO2, is used to highlight how the changing structure with applied pressure can be effectively modelled (in three dimensions) and used to link to both experimental results and simple structural models. As an example of the second class the topology of networks of tetrahedra in the MX2 stoichiometry are controlled using a single model parameter linked to the M-X-M bond angles. The evolution of ordering on multiple length-scales is observed as are the links between the static structure and key dynamical properties. The isomorphous relationship between the structures of amorphous Si and SiO2 is discussed as are the similarities and differences in the phase diagrams, the latter linked to potential polyamorphic and ‘anomalous’ (e.g. density maxima) behaviour. Links to both two-dimensional structures for C, Si and Ge and near-two-dimensional bilayers of SiO2 are discussed. Emerging low-dimensional structures in low temperature molten carbonates are also uncovered.
Takayanagi, Toshiyuki; Shiga, Motoyuki
2002-08-01
The structures and vibrational frequencies of Cl 2-helium clusters have been studied using the path integral molecular dynamics method combined with the discrete-variable-representation approach. It is found that the Cl 2-helium clusters form clear shell structures comprised of rings around the Cl 2 bond. The vibrational frequencies calculated show a monotonically increasing red shift with an increase in cluster size. It can be concluded that the first solvation shell and its density around T-shaped configurations play the most important role in the observed frequency shifts.
Finite Element Vibration and Dynamic Response Analysis of Engineering Structures
Directory of Open Access Journals (Sweden)
Jaroslav Mackerle
2000-01-01
Full Text Available This bibliography lists references to papers, conference proceedings, and theses/dissertations dealing with finite element vibration and dynamic response analysis of engineering structures that were published from 1994 to 1998. It contains 539 citations. The following types of structures are included: basic structural systems; ground structures; ocean and coastal structures; mobile structures; and containment structures.
Experiment and Formulations for the Dynamic Characteristics of Jointed Structures
Directory of Open Access Journals (Sweden)
Rongqiang Liu
2013-01-01
Full Text Available Clearance joints significantly affect the dynamic properties of deployable structures (DSs. This paper presents a spring-mass model with clearance for the study of the axial stiffness of a jointed structure. The nonlinear stiffness can be predicted by calculating the model's natural frequency which is the reciprocal of the motion period of the model. The results of the theoretical model show that the dynamic stiffness of the clearance joint increases with increases in the displacement amplitude; this finding is consistent with the experimental results. With the inclusion of sliding factors, contact friction, and impact, the established model of energy dissipation is useful for estimating the effects of joint damping on DSs. The energy dissipation model reveals the effects of joint features and excitation conditions on the dissipation of the jointed structure, that is, the excitation frequency and amplitude. Dynamic experiments were performed on jointed structures to characterize the dissipation variations. An exponentially fitting equation was developed based on the energy dissipation model and was verified through the experimental data. This formulation is more efficient than numerical integration for the calculation of the energy dissipation.
Ali, Mubarak; Lin, I.-Nan
2017-01-01
In addition to self-governing properties, tiny-sized particles of metallic colloids are the building blocks of large-sized particles; thus, their study has been the subject of a large number of publications. In the present work, it has been discussed that geometry structure of tiny particle made through atom-to-atom amalgamation depends on attained dynamics of gold atoms along with protruded orientations. The localized process conditions direct two-dimensional structure of a tiny particle at atomically flat air-solution interface while heating locally dynamically approached atoms, thus, negate the role of van der Waals interactions. At electronphoton-solution interface, impinging electrons stretch or deform atoms of tiny particles depending on the mechanism of impingement. In addition, to strike regular grid of electrons ejected on split of atoms not executing excitations and de-excitations of their electrons, atoms of tiny particles also deform or stretch while occupying various sites depending on the process of synergy. Under suitable impinging electron streams, those tiny particles in monolayer two-dimensional structure electron states of their atoms are diffused in the direction of transferred energy, thus, coincide to the next adjacent atoms in each one-dimensional array dealing the same sort of behavior. Instantaneously, photons of adequate energy propagate on the surfaces of such electronic structures and modify those into smooth elements, thus, disregard the phenomenon of localized surface plasmons. This study highlights the fundamental process of formation of tiny particles where the role of localized dynamics of atoms and their electronic structure along with interaction to light are discussed. Such a tool of processing materials, in nonequilibrium pulse-based process, opens a number of possibilities to develop engineered materials with specific chemical, optical, and electronic properties.
Nonparametric inference of network structure and dynamics
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
Structural Dynamics of the Cereblon Ligand Binding Domain
Hartmann, Marcus D.; Boichenko, Iuliia; Coles, Murray; Lupas, Andrei N.; Hernandez Alvarez, Birte
2015-01-01
Cereblon, a primary target of thalidomide and its derivatives, has been characterized structurally from both bacteria and animals. Especially well studied is the thalidomide binding domain, CULT, which shows an invariable structure across different organisms and in complex with different ligands. Here, based on a series of crystal structures of a bacterial representative, we reveal the conformational flexibility and structural dynamics of this domain. In particular, we follow the unfolding of large fractions of the domain upon release of thalidomide in the crystalline state. Our results imply that a third of the domain, including the thalidomide binding pocket, only folds upon ligand binding. We further characterize the structural effect of the C-terminal truncation resulting from the mental-retardation linked R419X nonsense mutation in vitro and offer a mechanistic hypothesis for its irresponsiveness to thalidomide. At 1.2Å resolution, our data provide a view of thalidomide binding at atomic resolution. PMID:26024445
Structural dynamics of the cereblon ligand binding domain.
Directory of Open Access Journals (Sweden)
Marcus D Hartmann
Full Text Available Cereblon, a primary target of thalidomide and its derivatives, has been characterized structurally from both bacteria and animals. Especially well studied is the thalidomide binding domain, CULT, which shows an invariable structure across different organisms and in complex with different ligands. Here, based on a series of crystal structures of a bacterial representative, we reveal the conformational flexibility and structural dynamics of this domain. In particular, we follow the unfolding of large fractions of the domain upon release of thalidomide in the crystalline state. Our results imply that a third of the domain, including the thalidomide binding pocket, only folds upon ligand binding. We further characterize the structural effect of the C-terminal truncation resulting from the mental-retardation linked R419X nonsense mutation in vitro and offer a mechanistic hypothesis for its irresponsiveness to thalidomide. At 1.2Å resolution, our data provide a view of thalidomide binding at atomic resolution.
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 r...
Structure and Dynamics of Water at Carbon-Based Interfaces
Directory of Open Access Journals (Sweden)
Jordi Martí
2017-03-01
Full Text Available Water structure and dynamics are affected by the presence of a nearby interface. Here, first we review recent results by molecular dynamics simulations about the effect of different carbon-based materials, including armchair carbon nanotubes and a variety of graphene sheets—flat and with corrugation—on water structure and dynamics. We discuss the calculations of binding energies, hydrogen bond distributions, water’s diffusion coefficients and their relation with surface’s geometries at different thermodynamical conditions. Next, we present new results of the crystallization and dynamics of water in a rigid graphene sieve. In particular, we show that the diffusion of water confined between parallel walls depends on the plate distance in a non-monotonic way and is related to the water structuring, crystallization, re-melting and evaporation for decreasing inter-plate distance. Our results could be relevant in those applications where water is in contact with nanostructured carbon materials at ambient or cryogenic temperatures, as in man-made superhydrophobic materials or filtration membranes, or in techniques that take advantage of hydrated graphene interfaces, as in aqueous electron cryomicroscopy for the analysis of proteins adsorbed on graphene.
Energy Technology Data Exchange (ETDEWEB)
Liu, Hui; Song, Yongduan; Xue, Fangzheng; Li, Xiumin, E-mail: xmli@cqu.edu.cn [Key Laboratory of Dependable Service Computing in Cyber Physical Society of Ministry of Education, Chongqing University, Chongqing 400044 (China); College of Automation, Chongqing University, Chongqing 400044 (China)
2015-11-15
In this paper, the generation of multi-clustered structure of self-organized neural network with different neuronal firing patterns, i.e., bursting or spiking, has been investigated. The initially all-to-all-connected spiking neural network or bursting neural network can be self-organized into clustered structure through the symmetric spike-timing-dependent plasticity learning for both bursting and spiking neurons. However, the time consumption of this clustering procedure of the burst-based self-organized neural network (BSON) is much shorter than the spike-based self-organized neural network (SSON). Our results show that the BSON network has more obvious small-world properties, i.e., higher clustering coefficient and smaller shortest path length than the SSON network. Also, the results of larger structure entropy and activity entropy of the BSON network demonstrate that this network has higher topological complexity and dynamical diversity, which benefits for enhancing information transmission of neural circuits. Hence, we conclude that the burst firing can significantly enhance the efficiency of clustering procedure and the emergent clustered structure renders the whole network more synchronous and therefore more sensitive to weak input. This result is further confirmed from its improved performance on stochastic resonance. Therefore, we believe that the multi-clustered neural network which self-organized from the bursting dynamics has high efficiency in information processing.
Liu, Hui; Song, Yongduan; Xue, Fangzheng; Li, Xiumin
2015-11-01
In this paper, the generation of multi-clustered structure of self-organized neural network with different neuronal firing patterns, i.e., bursting or spiking, has been investigated. The initially all-to-all-connected spiking neural network or bursting neural network can be self-organized into clustered structure through the symmetric spike-timing-dependent plasticity learning for both bursting and spiking neurons. However, the time consumption of this clustering procedure of the burst-based self-organized neural network (BSON) is much shorter than the spike-based self-organized neural network (SSON). Our results show that the BSON network has more obvious small-world properties, i.e., higher clustering coefficient and smaller shortest path length than the SSON network. Also, the results of larger structure entropy and activity entropy of the BSON network demonstrate that this network has higher topological complexity and dynamical diversity, which benefits for enhancing information transmission of neural circuits. Hence, we conclude that the burst firing can significantly enhance the efficiency of clustering procedure and the emergent clustered structure renders the whole network more synchronous and therefore more sensitive to weak input. This result is further confirmed from its improved performance on stochastic resonance. Therefore, we believe that the multi-clustered neural network which self-organized from the bursting dynamics has high efficiency in information processing.
Dynamic structural correlation via nonlinear programming techniques
Ting, T.; Ojalvo, I. U.
1988-01-01
A solution to the correlation between structural dynamic test results and finite element analyses of the same components is presented in this paper. Basically, the method can be categorized as a Levenberg-Marquardt type Gauss-Newton method which requires only the differences between FE modal analyses and test results and their first derivatives with respect to preassigned design variables. With proper variable normalization and equation scaling, the method has been made numerically better-conditioned and the inclusion of the Levenberg-Marquardt technique overcomes any remaining difficulty encountered in inverting singular or near-singular matrices. An important feature is that each iteration requires only one function evaluation along with the associated design sensitivity analysis and so the procedure is computationally efficient.
Wheat yield dynamics: a structural econometric analysis.
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.
Dynamic structure of active nematic shells
Zhang, Rui; Zhou, Ye; Rahimi, Mohammad; de Pablo, Juan J.
2016-11-01
When a thin film of active, nematic microtubules and kinesin motor clusters is confined on the surface of a vesicle, four +1/2 topological defects oscillate in a periodic manner between tetrahedral and planar arrangements. Here a theoretical description of nematics, coupled to the relevant hydrodynamic equations, is presented here to explain the dynamics of active nematic shells. In extensile microtubule systems, the defects repel each other due to elasticity, and their collective motion leads to closed trajectories along the edges of a cube. That motion is accompanied by oscillations of their velocities, and the emergence and annihilation of vortices. When the activity increases, the system enters a chaotic regime. In contrast, for contractile systems, which are representative of some bacterial suspensions, a hitherto unknown static structure is predicted, where pairs of defects attract each other and flows arise spontaneously.
Molecular dynamics study of ice structural evolution
Institute of Scientific and Technical Information of China (English)
Wang Yan; Dong Shun-Le
2008-01-01
Molecular dynamics simulation is employed to study the structural evolution of low density amorphous ice during its compression from one atmosphere to 2.5 GPa. Calculated results show that high density amorphous ice is formed at an intermediate pressure of～1.0GPa; the O-O-O bond angle ranges from 83° to 113°, and the O-H...O bond is bent from 112° to 160°. Very high density amorphous ice is obtained by quenching to 80K and decompressing the ice to ambient pressure from 160 K/1.3 GPa or 160 K/1.7 GPa; and the next-nearest O-O length is found to be 0.310 nm, just 0.035 nm beyond the nearest O-O distance of 0.275 nm.
Bharmoria, Pankaj; Gehlot, Praveen Singh; Gupta, Hariom; Kumar, Arvind
2014-11-06
Dual, aqueous solubility behavior of Na2SO4 as a function of temperatures is still a natural enigma lying unresolved in the literature. The solubility of Na2SO4 increases up to 32.38 °C and decreases slightly thereafter at higher temperatures. We have thrown light on this phenomenon by analyzing the Na2SO4-water clusters (growth and stability) detected from temperature-dependent dynamic light scattering experiments, solution compressibility changes derived from the density and speed of sound measurements, and water structural changes/Na2SO4 (ion pair)-water interactions observed from the FT-IR and 2D DOSY (1)H NMR spectroscopic investigations. It has been observed that Na2SO4-water clusters grow with an increase in Na2SO4 concentration (until the solubility transition temperature) and then start decreasing afterward. An unusual decrease in cluster size and solution compressibility has been observed with the rise in temperature for the Na2SO4 saturated solutions below the solubility transition temperature, whereas an inverse pattern is followed thereafter. DOSY experiments have indicated different types of water cluster species in saturated solutions at different temperatures with varying self-diffusion coefficients. The effect of NaCl (5-15 wt %) on the solubility behavior of Na2SO4 at different temperatures has also been examined. The studies are important from both fundamental and industrial application points of view, for example, toward the clean separation of NaCl and Na2SO4 from the effluent streams of textile and tannery industries.
Dynamic structure of joint-action stimulus-response activity.
Malone, MaryLauren; Castillo, Ramon D; Kloos, Heidi; Holden, John G; Richardson, Michael J
2014-01-01
The mere presence of a co-actor can influence an individual's response behavior. For instance, a social Simon effect has been observed when two individuals perform a Go/No-Go response to one of two stimuli in the presence of each other, but not when they perform the same task alone. Such effects are argued to provide evidence that individuals co-represent the task goals and the to-be-performed actions of a co-actor. Motivated by the complex-systems approach, the present study was designed to investigate an alternative hypothesis--that such joint-action effects are due to a dynamical (time-evolving) interpersonal coupling that operates to perturb the behavior of socially situated actors. To investigate this possibility, participants performed a standard Go/No-Go Simon task in joint and individual conditions. The dynamic structure of recorded reaction times was examined using fractal statistics and instantaneous cross-correlation. Consistent with our hypothesis that participants responding in a shared space would become behaviorally coupled, the analyses revealed that reaction times in the joint condition displayed decreased fractal structure (indicative of interpersonal perturbation processes modulating ongoing participant behavior) compared to the individual condition, and were more correlated across a range of time-scales compared to the reaction times of pseudo-pair controls. Collectively, the findings imply that dynamic processes might underlie social stimulus-response compatibility effects and shape joint cognitive processes in general.
Dynamic structure of joint-action stimulus-response activity.
Directory of Open Access Journals (Sweden)
MaryLauren Malone
Full Text Available The mere presence of a co-actor can influence an individual's response behavior. For instance, a social Simon effect has been observed when two individuals perform a Go/No-Go response to one of two stimuli in the presence of each other, but not when they perform the same task alone. Such effects are argued to provide evidence that individuals co-represent the task goals and the to-be-performed actions of a co-actor. Motivated by the complex-systems approach, the present study was designed to investigate an alternative hypothesis--that such joint-action effects are due to a dynamical (time-evolving interpersonal coupling that operates to perturb the behavior of socially situated actors. To investigate this possibility, participants performed a standard Go/No-Go Simon task in joint and individual conditions. The dynamic structure of recorded reaction times was examined using fractal statistics and instantaneous cross-correlation. Consistent with our hypothesis that participants responding in a shared space would become behaviorally coupled, the analyses revealed that reaction times in the joint condition displayed decreased fractal structure (indicative of interpersonal perturbation processes modulating ongoing participant behavior compared to the individual condition, and were more correlated across a range of time-scales compared to the reaction times of pseudo-pair controls. Collectively, the findings imply that dynamic processes might underlie social stimulus-response compatibility effects and shape joint cognitive processes in general.
Dynamics of Subauroral Polarization Stream (SAPS) Structures
Sazykin, S. Y.; Coster, A. J.; Huba, J.; Ridley, A. J.; Erickson, P. J.; Foster, J. C.; Baker, J. B. H.; Wolf, R.
2015-12-01
The Subauroral Polarization Stream (SAPS) flow structures are narrow ionospheric channels of fast (in excess of 100 m/s) westward drift just outside the equatorward edge of the diffuse aurora in the dusk-to-midnight local time sector. Other terms for this phenomenon include subauroral Ion Drift (SAID) events and Polarization Jets. SAPS structures represent a striking departure from the commonly-used two-cell convection pattern. They are thought to arise from the displacement of the downward region-2 Birkeland currents on the dusk side equatorward of the low-latitude boundary of the auroral oval during times of changing high-latitude convection. In this paper, we will use several event simulations with the SAMI3-RCM numerical model (a self-consistent ionosphere-inner magnetosphere model) and RCM-GITM (a self-consistent model of the ionosphere-thermosphere-inner magnetosphere) to analyze the relative roles of changes in the IMF Bz component, ionospheric electron density depletions, and thermospheric modifications in controlling the dynamics of SAPS. Simulation results will be compared to multi-instrument ionospheric observations.
Electronic structure and dynamics of nitrosyl porphyrins.
Scheidt, W Robert; Barabanschikov, Alexander; Pavlik, Jeffrey W; Silvernail, Nathan J; Sage, J Timothy
2010-07-19
Nitric oxide (NO) is a signaling molecule employed to regulate essential physiological processes. Thus, there is great interest in understanding the interaction of NO with heme, which is found at the active site of many proteins that recognize NO, as well as those involved in its creation and elimination. We summarize what we have learned from investigations of the structure, vibrational properties, and conformational dynamics of NO complexes with ferrous porphyrins, as well as computational investigations in support of these experimental studies. Multitemperature crystallographic data reveal variations in the orientational disorder of the nitrosyl ligand. In some cases, equilibria among NO orientations can be analyzed using the van't Hoff relationship and the free energy and enthalpy of the solid-state transitions evaluated experimentally. Density functional theory (DFT) calculations predict that intrinsic barriers to torsional rotation are smaller than thermal energies at physiological temperatures, and the coincidence of observed NO orientations with minima in molecular mechanics potentials indicates that nonbonded interactions with other chemical groups control the conformational freedom of the bound NO. In favorable cases, reduced disorder at low temperatures exposes subtle structural features including off-axis tilting of the Fe-NO bond and anisotropy of the equatorial Fe-N bonds. We also present the results of nuclear resonance vibrational spectroscopy measurements on oriented single crystals of [Fe(TPP)(NO)] and [Fe(TPP)(1-MeIm)(NO)]. These describe the anisotropic vibrational motion of iron in five- and six-coordinate heme-NO complexes and reveal vibrations of all Fe-ligand bonds as well as low-frequency molecular distortions associated with the doming of the heme upon ligand binding. A quantitative comparison with predicted frequencies, amplitudes, and directions facilitates identification of the vibrational modes but also suggests that commonly used DFT
Dynamical effects in fusion with exotic nuclei
Vo-Phuoc, K.; Simenel, C.; Simpson, E. C.
2016-08-01
Background: Reactions with stable beams have demonstrated strong interplay between nuclear structure and fusion. Exotic beam facilities open new perspectives to understand the impact of neutron skin, large isospin, and weak binding energies on fusion. Microscopic theories of fusion are required to guide future experiments. Purpose: To investigate new effects of exotic structures and dynamics in near-barrier fusion with exotic nuclei. Method: Microscopic approaches based on the Hartree-Fock (HF) mean-field theory are used for studying fusion barriers in -54Ca40+116Sn reactions for even isotopes. Bare potential barriers are obtained assuming frozen HF ground-state densities. Dynamical effects on the barrier are accounted for in time-dependent Hartree-Fock (TDHF) calculations of the collisions. Vibrational couplings are studied in the coupled-channel framework and near-barrier nucleon transfer is investigated with TDHF calculations. Results: The development of a neutron skin in exotic calcium isotopes strongly lowers the bare potential barrier. However, this static effect is not apparent when dynamical effects are included. On the contrary, a fusion hindrance is observed in TDHF calculations with the most neutron-rich calcium isotopes which cannot be explained by vibrational couplings. Transfer reactions are also important in these systems due to charge equilibration processes. Conclusions: Despite its impact on the bare potential, the neutron skin is not seen as playing an important role in the fusion dynamics. However, the charge transfer with exotic projectiles could lead to an increase of the Coulomb repulsion between the fragments, suppressing fusion. The effects of transfer and dissipative mechanisms on fusion with exotic nuclei deserve further studies.
Energy Technology Data Exchange (ETDEWEB)
Stuart, J.G.; Wright, A.D.; Butterfield, C.P.
1996-10-01
Mitigating the effects of damaging wind turbine loads and responses extends the lifetime of the turbine and, consequently, reduces the associated Cost of Energy (COE). Active control of aerodynamic devices is one option for achieving wind turbine load mitigation. Generally speaking, control system design and analysis requires a reasonable dynamic model of {open_quotes}plant,{close_quotes} (i.e., the system being controlled). This paper extends the wind turbine aileron control research, previously conducted at the National Wind Technology Center (NWTC), by presenting a more detailed development of the wind turbine dynamic model. In prior research, active aileron control designs were implemented in an existing wind turbine structural dynamics code, FAST (Fatigue, Aerodynamics, Structures, and Turbulence). In this paper, the FAST code is used, in conjunction with system identification, to generate a wind turbine dynamic model for use in active aileron control system design. The FAST code is described and an overview of the system identification technique is presented. An aileron control case study is used to demonstrate this modeling technique. The results of the case study are then used to propose ideas for generalizing this technique for creating dynamic models for other wind turbine control applications.
Recombination Dynamics in Quantum Well Semiconductor Structures
Fouquet, Julie Elizabeth
Time-resolved and time-integrated photoluminescence as a function of excitation energy density have been observed in order to study recombination dynamics in GaAs/Al(,x)Ga(,1 -x)As quantum well structures. The study of room temperature photoluminescence from the molecular beam epitaxy (MBE) -grown multiple quantum well structure and photoluminescence peak energy as a function of tem- perature shows that room temperature recombination at excitation densities above the low 10('16) cm('-3) level is due to free carriers, not excitons. This is the first study of time-resolved photoluminescence of impurities in quantum wells; data taken at different emission wave- lengths at low temperatures shows that the impurity-related states at photon energies lower than the free exciton peaks luminesce much more slowly than the free exciton states. Results from a similar structure grown by metal -organic chemical vapor deposition (MOCVD) are explained by saturation of traps. An unusual increase in decay rate observed tens of nanoseconds after excitation is probably due to carriers falling out of the trap states. Since this is the first study of time-resolved photoluminescence of MOCVD-grown quantum well structures, this unusual behavior may be realted to the MOCVD growth process. Further investigations indi- cate that the traps are not active at low temperatures; they become active at approximately 150 K. The traps are probably associated with the (hetero)interfaces rather than the bulk Al(,x)Ga(,1-x)As material. The 34 K photoluminescence spectrum of this sample revealed a peak shifted down by approximately 36 meV from the main peak. Time-resolved and time-integrated photoluminescence results here show that this peak is not a stimulated phonon emission sideband, but rather is an due to an acceptor impurity, probably carbon. Photo- luminescence for excitation above and below the barrier bandgap shows that carriers are efficiently collected in the wells in both single and multiple
Structure-preserving integrators in nonlinear structural dynamics and flexible multibody dynamics
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...
Le Roux, Sébastien; Bouzid, Assil; Kim, Kye Yeop; Han, Seungwu; Zeidler, Anita; Salmon, Philip S.; Massobrio, Carlo
2016-08-01
The structure of glassy GeSe9 was investigated by combining neutron diffraction with density-functional-theory-based first-principles molecular dynamics. In the simulations, three different models of N = 260 atoms were prepared by sampling three independent temporal trajectories, and the glass structures were found to be substantially different from those obtained for models in which smaller numbers of atoms or more rapid quench rates were employed. In particular, the overall network structure is based on Sen chains that are cross-linked by Ge(Se4)1/2 tetrahedra, where the latter are predominantly corner as opposed to edge sharing. The occurrence of a substantial proportion of Ge-Se-Se connections does not support a model in which the material is phase separated into Se-rich and GeSe2-rich domains. The appearance of a first-sharp diffraction peak in the Bhatia-Thornton concentration-concentration partial structure factor does, however, indicate a non-uniform distribution of the Ge-centered structural motifs on an intermediate length scale.
A Formal Framework for P Systems with Dynamic Structure
Freund, Rudolf; Pérez Hurtado de Mendoza, Ignacio; Riscos Núñez, Agustín; Verlan, Sergey
2012-01-01
This article introduces a formalism/framework able to describe different variants of P systems having a dynamic structure. This framework can be useful for the definition of new variants of P systems with dynamic structure, for the comparison of existing definitions as well as for their extension. We give a precise definition of the formalism and show how existing variants of P systems with dynamic structure can be translated to it.
Structural Dynamics of Education Reforms and Quality of Primary Education in Uganda
Nyenje, Aida
2016-01-01
This paper examines Uganda's recent undertaking to reform her Primary School education System with a focus on the effect of structural dynamics of education reforms and the quality of primary education. Structural dynamics in the context of this study is in reference to the organizational composition of the education system at the government,…
Dynamical Structure of the Fields in the Light Cone Coordinates
Kargar, Kianoosh
2016-01-01
It is well-known that additional constraints emerge in light cone coordinates. We enumerate the number of physical modes in light cone coordinates and compare it with conventional coordinates. We show that the number of Schrodinger modes is divided by two in light cone coordinates. We study the effect of this reduction in the number ladder operators acting on physical states of a system. We analyse the scaler, spinor and vector field theories carefully to see the effect of changes in the dynamical structure of these theories from the view point of the reduction of Schrodinger modes in light-cone coordinates.
Universal structural estimator and dynamics approximator for complex networks
Chen, Yu-Zhong
2016-01-01
Revealing the structure and dynamics of complex networked systems from observed data is of fundamental importance to science, engineering, and society. Is it possible to develop a universal, completely data driven framework to decipher the network structure and different types of dynamical processes on complex networks, regardless of their details? We develop a Markov network based model, sparse dynamical Boltzmann machine (SDBM), as a universal network structural estimator and dynamics approximator. The SDBM attains its topology according to that of the original system and is capable of simulating the original dynamical process. We develop a fully automated method based on compressive sensing and machine learning to find the SDBM. We demonstrate, for a large variety of representative dynamical processes on model and real world complex networks, that the equivalent SDBM can recover the network structure of the original system and predicts its dynamical behavior with high precision.
Impact of constrained rewiring on network structure and node dynamics.
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.
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.
Structured Counseling for Auditory Dynamic Range Expansion.
Gold, Susan L; Formby, Craig
2017-02-01
A structured counseling protocol is described that, when combined with low-level broadband sound therapy from bilateral sound generators, offers audiologists a new tool for facilitating the expansion of the auditory dynamic range (DR) for loudness. The protocol and its content are specifically designed to address and treat problems that impact hearing-impaired persons who, due to their reduced DRs, may be limited in the use and benefit of amplified sound from hearing aids. The reduced DRs may result from elevated audiometric thresholds and/or reduced sound tolerance as documented by lower-than-normal loudness discomfort levels (LDLs). Accordingly, the counseling protocol is appropriate for challenging and difficult-to-fit persons with sensorineural hearing losses who experience loudness recruitment or hyperacusis. Positive treatment outcomes for individuals with the former and latter conditions are highlighted in this issue by incremental shifts (improvements) in LDL and/or categorical loudness judgments, associated reduced complaints of sound intolerance, and functional improvements in daily communication, speech understanding, and quality of life leading to improved hearing aid benefit, satisfaction, and aided sound quality, posttreatment.
Optimizing Dynamical Network Structure for Pinning Control
Orouskhani, Yasin; Jalili, Mahdi; Yu, Xinghuo
2016-04-01
Controlling dynamics of a network from any initial state to a final desired state has many applications in different disciplines from engineering to biology and social sciences. In this work, we optimize the network structure for pinning control. The problem is formulated as four optimization tasks: i) optimizing the locations of driver nodes, ii) optimizing the feedback gains, iii) optimizing simultaneously the locations of driver nodes and feedback gains, and iv) optimizing the connection weights. A newly developed population-based optimization technique (cat swarm optimization) is used as the optimization method. In order to verify the methods, we use both real-world networks, and model scale-free and small-world networks. Extensive simulation results show that the optimal placement of driver nodes significantly outperforms heuristic methods including placing drivers based on various centrality measures (degree, betweenness, closeness and clustering coefficient). The pinning controllability is further improved by optimizing the feedback gains. We also show that one can significantly improve the controllability by optimizing the connection weights.
The stability and dynamic behaviour of fluid-loaded structures
CSIR Research Space (South Africa)
Suliman, Ridhwaan
2015-07-01
Full Text Available ECCOMAS Young Investigators Conference 6th GACM Colloquium, July 20–23, 2015, Aachen, Germany The stability and dynamic behaviour of fluid-loaded structures R. Suliman, N. Peake Abstract. The deformation of slender elastic structures due...
STRUCTURE AND DYNAMICS OF ALKALI BORATE GLASSES - A MOLECULAR-DYNAMICS STUDY
VERHOEF, AH; DENHARTOG, HW
1995-01-01
Structural and dynamical properties of lithium, cesium and mixed alkali (i.e., lithium and cesium) borate glasses have been studied by the molecular dynamics method. The calculations yield glass structures consisting of planar BO3 triangles and BO4 tetrahedrons with no sixfold ring structures at all
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
Crystal structures and dynamical properties of dense CO2.
Yong, Xue; Liu, Hanyu; Wu, Min; Yao, Yansun; Tse, John S; Dias, Ranga; Yoo, Choong-Shik
2016-10-04
Structural polymorphism in dense carbon dioxide (CO2) has attracted significant attention in high-pressure physics and chemistry for the past two decades. Here, we have performed high-pressure experiments and first-principles theoretical calculations to investigate the stability, structure, and dynamical properties of dense CO2 We found evidence that CO2-V with the 4-coordinated extended structure can be quenched to ambient pressure below 200 K-the melting temperature of CO2-I. CO2-V is a fully coordinated structure formed from a molecular solid at high pressure and recovered at ambient pressure. Apart from confirming the metastability of CO2-V (I-42d) at ambient pressure at low temperature, results of ab initio molecular dynamics and metadynamics (MD) simulations provided insights into the transformation processes and structural relationship from the molecular to the extended phases. In addition, the simulation also predicted a phase V'(Pna21) in the stability region of CO2-V with a diffraction pattern similar to that previously assigned to the CO2-V (P212121) structure. Both CO2-V and -V' are predicted to be recoverable and hard with a Vicker hardness of ∼20 GPa. Significantly, MD simulations found that the CO2 in phase IV exhibits large-amplitude bending motions at finite temperatures and high pressures. This finding helps to explain the discrepancy between earlier predicted static structures and experiments. MD simulations clearly indicate temperature effects are critical to understanding the high-pressure behaviors of dense CO2 structures-highlighting the significance of chemical kinetics associated with the transformations.
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.
A generalized gamma(s)-family of self-starting algorithms for computational structural dynamics
Namburu, Raju R.; Tamma, Kumar K.
1992-01-01
A generalized gamma(s)-family of self-starting single-step formulations are presented in order to provide simplified yet effective dynamic attributes to include features towards eliminating the need to involve accelerations in the computational process for structural dynamic problems. By appropriately selecting the parameters pertaining to gamma(s)(s = 1, 2, 3), both explicit and implicit formulations are obtained. The stability and accuracy characteristics of the gamma(s)-family of representations are presented to validate the robustness of the formulations for structural dynamic problems. Numerous illustrative examples are described and the results are in excellent agreement and validate the applicability of these formulations for structural dynamic computations.
A neighbor pixel communication filtering structure for Dynamic Vision Sensors
Xu, Yuan; Liu, Shiqi; Lu, Hehui; Zhang, Zilong
2017-02-01
For Dynamic Vision Sensors (DVS), thermal noise and junction leakage current induced Background Activity (BA) is the major cause of the deterioration of images quality. Inspired by the smoothing filtering principle of horizontal cells in vertebrate retina, A DVS pixel with Neighbor Pixel Communication (NPC) filtering structure is proposed to solve this issue. The NPC structure is designed to judge the validity of pixel's activity through the communication between its 4 adjacent pixels. The pixel's outputs will be suppressed if its activities are determined not real. The proposed pixel's area is 23.76×24.71μm2 and only 3ns output latency is introduced. In order to validate the effectiveness of the structure, a 5×5 pixel array has been implemented in SMIC 0.13μm CIS process. 3 test cases of array's behavioral model show that the NPC-DVS have an ability of filtering the BA.
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.
Study of the structure and dynamics of complex biological networks
Samal, Areejit
2008-12-01
In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large scale metabolic networks inside three organisms, Escherichia coli, Saccharomyces cerevisiae and Staphylococcus aureus. We also study the dynamics of the large scale genetic network controlling E. coli metabolism. We have tried to explain the observed system level dynamical properties of these networks in terms of their underlying structure. Our studies of the system level dynamics of these large scale biological networks provide a different perspective on their functioning compared to that obtained from purely structural studies. Our study also leads to some new insights on features such as robustness, fragility and modularity of these large scale biological networks. We also shed light on how different networks inside the cell such as metabolic networks and genetic networks are interrelated to each other.
Dou, Q; Sha, M L; Fu, H Y; Wu, G Z
2011-05-01
The structures and diffusion behaviors of a series of ionic liquids [C(n)mim][PF(6)] (n = 1, 4, 8 and 12) on a graphite surface have been investigated by means of molecular dynamics simulation. It was found that three or four ordering layers of ionic liquids were formed near the graphite surface, and this layering structure was stable over the temperature range investigated. At the liquid/vacuum interface, the ionic liquid with a butyl chain had a monolayer ordering surface, while [C(8)mim][PF(6)] and [C(12)mim][PF(6)] exhibited a bilayer ordering with a polar domain sandwiched between two orientational nonpolar domains. More impressively, the simulated results showed that for the ionic liquids with alkyl chains longer than C(4), the adjacent alkyl chains in the whole film tended to be parallel to each other, with the imidazolium rings packed closely together. This indicated that the ionic liquids have a better regulated short-range structure than was previously expected. It was also found that both in the bottom layer and in the bulk region, the diffusion of the alkyl chains was much faster than that of the polar groups. However, as the alkyl chain length increased, the charge delocalization in the cation and the enhanced van der Waals interaction between the nonpolar groups contributed by reducing this difference in the diffusivity of major groups.
Wang, N
2014-05-16
The growth and structure of ultrathin amorphous carbon films was investigated by molecular dynamics simulations. The second-generation reactive-empirical-bond-order potential was used to model atomic interactions. Films with different structures were simulated by varying the deposition energy of carbon atoms in the range of 1-120 eV. Intrinsic film characteristics (e.g. density and internal stress) were determined after the system reached equilibrium. Short- and intermediate-range carbon atom ordering is examined in the context of atomic hybridization and ring connectivity simulation results. It is shown that relatively high deposition energy (i.e., 80 eV) yields a multilayer film structure consisting of an intermixing layer, bulk film and surface layer, consistent with the classical subplantation model. The highest film density (3.3 g cm-3), sp3 fraction (∼43%), and intermediate-range carbon atom ordering correspond to a deposition energy of ∼80 eV, which is in good agreement with experimental findings. © 2014 IOP Publishing Ltd.
Directory of Open Access Journals (Sweden)
Anastassia N. Rissanou
2015-02-01
Full Text Available Detailed atomistic (united atoms molecular dynamics simulations of several graphene based polymer (polyethylene, PE nanocomposite systems have been performed. Systems with graphene sheets of different sizes have been simulated at the same graphene concentration (~3%. In addition, a periodic graphene layer (“infinite sheet” has been studied. Results concerning structural and dynamical properties of PE chains are presented for the various systems and compared to data from a corresponding bulk system. The final properties of the material are the result of a complex effect of the graphene’s sheet size, mobility and fluctuations. A detailed investigation of density, structure and dynamics of the hybrid systems has been conducted. Particular emphasis has been given in spatial heterogeneities due to the PE/graphene interfaces, which were studied through a detailed analysis based on radial distances form the graphene’s center-of-mass. Chain segmental dynamics is found to be slower, compared to the bulk one, at the PE/graphene interface by a factor of 5 to 10. Furthermore, an analysis on the graphene sheets characteristics is presented in terms of conformational properties (i.e., wrinkling and mobility.
DYNAMIC DESIGN OF INTERNAL COMBUSTION ENGINE BLOCK STRUCTURE
Institute of Scientific and Technical Information of China (English)
1998-01-01
Several main steps of internal combustion engine block structure dynamic design,such as model set-up,structure dynamic response analysis,optimizing design and vibration and noise control,are discussed for the type of EQ6100 gasoline engine block.
Structural dynamics branch research and accomplishments for fiscal year 1987
1988-01-01
This publication contains a collection of fiscal year 1987 research highlights from the Structural Dynamics Branch at NASA Lewis Research Center. Highlights from the branch's four major work areas, Aeroelasticity, Vibration Control, Dynamic Systems, and Computational Structural Methods, are included in the report as well as a complete listing of the FY87 branch publications.
Structural dynamics branch research and accomplishments to FY 1992
Lawrence, Charles
1992-12-01
This publication contains a collection of fiscal year 1992 research highlights from the Structural Dynamics Branch at NASA LeRC. Highlights from the branch's major work areas--Aeroelasticity, Vibration Control, Dynamic Systems, and Computational Structural Methods are included in the report as well as a listing of the fiscal year 1992 branch publications.
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, fr...
Dynamic Approach of Capital Structure of European Shipping Companies
Directory of Open Access Journals (Sweden)
Stavros H. Arvanitis
2012-12-01
Full Text Available The issue of capital structure of companies is one of the most debated problems of financialmanagement. According to economic theory, capital structure determines the stock market valueof firms and therefore their viability, while one of the most negative result of the crash of 2008 andthe persisting crisis (excess supply in markets of labor and money is their ongoing steep declineof lending by credit institutions and other sources. In this paper, considering the importanceof the issue and motivated by the conflicting results of previous empirical studies, we attemptthe analysis of capital structure of the European Maritime Enterprises (oceanic shipping.We focus on shipping companies, because of the large volume of funding that demands theirmain operation, due to the intensity of the assets held. The objectives of this research are firstlythe identification of factors that affect the capital structure of European oceanic shipping andsecondly to search for the existence of an ideal - target capital structure ratio. The determinantsof capital structure are examined through static (fixed effect method and FGLS and dynamic(GMM Methods econometric models, using data from the financial statements of 32 listedEuropean shipping companies for the period 2005-2010. The results suggest the prevalence ofpecking order theory in our case, while a positive relationship arises between tangible assets andtax benefits (arising from sources other than borrowing against leverage. Moreover, we observea negative relationship between size or profitability and debt. Our findings contribute to a deeperunderstanding of the decisions taken by European shipping on their capital structure.
Skadsem, Julie A.
1997-01-01
Examines the effects of conductor verbalization, dynamic markings, conductor gesture, and choir dynamic level on individual singers' dynamic responses. Indicates that verbal instructions from the conductor elicited significantly stronger dynamic performance responses than did the other instructional conditions. Suggests that additional research…
Dynamics and structure of the Alpine Fold Belt
Kahle, H. G.
1985-01-01
The structure and present-day dynamics of the Alps interms of geodesy and gravimetry are discusssed. A strong correlation of precise leveling and isostatic gravity along the central Alpine chain, especially in Canton Graubunden, East Switzerland are shown. It is assumed that the uplift is partly controlled by isostatic rebound effects. Field observations indicate that these phenomena are still active in the Alps. The study of the uplift processes by applying a number of geodetic and gravimetric measuring techniques, such as the determination of nonperiodic secular variations of gravity, of the deflections of the vertical and tilt changes monitored by hydrostatic leveling is proposed.
The dynamics and control of large flexible space structures
Bainum, P. M.; Krishna, R.; Kumar, V. K.; Reddy, A. S. S. R.
1981-01-01
The dynamics and attitude and shape control of very large, inherently flexible spacecraft systems were investigated. Increasingly more complex examples were examined, beginning with a uniform free-free beam, next a free-free uniform plate/platform and finally by considering a thin shallow spherical shell structure in orbit. The effects devices were modeled. For given sets of assumed actuator locations, the controllability of these systems was first established. Control laws for each of the actuators were developed based on decoupling techniques (including distributed modal control) pole placement algorithms and a application of the linear regulator problem for optical control theory.
Structure and dynamics of a constitutively active neurotensin receptor
Energy Technology Data Exchange (ETDEWEB)
Krumm, Brian E. [National Inst. of Health (NIH), Rockville, MD (United States). National Inst. of Neurological Disorders and Stroke, Dept. of Health and Human Services; Lee, Sangbae [Beckman Research Inst. of the City of Hope, Duarte, CA (United States). Dept. of Molecular Immunology; Bhattacharya, Supriyo [Beckman Research Inst. of the City of Hope, Duarte, CA (United States). Dept. of Molecular Immunology; Botos, Istvan [National Inst. of Health (NIH), Bethesda, MD (United States). National Inst. of Diabetes and; White, Courtney F. [National Inst. of Health (NIH), Rockville, MD (United States). National Inst. of Neurological Disorders and Stroke, Dept. of Health and Human Services; Du, Haijuan [National Inst. of Health (NIH), Rockville, MD (United States). National Inst. of Neurological Disorders and Stroke, Dept. of Health and Human Services; Vaidehi, Nagarajan [Beckman Research Inst. of the City of Hope, Duarte, CA (United States). Dept. of Molecular Immunology; Grisshammer, Reinhard [National Inst. of Health (NIH), Rockville, MD (United States). National Inst. of Neurological Disorders and Stroke, Dept. of Health and Human Services
2016-12-07
Many G protein-coupled receptors show constitutive activity, resulting in the production of a second messenger in the absence of an agonist; and naturally occurring constitutively active mutations in receptors have been implicated in diseases. To gain insight into mechanistic aspects of constitutive activity, we report here the 3.3 Å crystal structure of a constitutively active, agonist-bound neurotensin receptor (NTSR1) and molecular dynamics simulations of agonist-occupied and ligand-free receptor. Comparison with the structure of a NTSR1 variant that has little constitutive activity reveals uncoupling of the ligand-binding domain from conserved connector residues, that effect conformational changes during GPCR activation. Furthermore, molecular dynamics simulations show strong contacts between connector residue side chains and increased flexibility at the intracellular receptor face as features that coincide with robust signalling in cells. The loss of correlation between the binding pocket and conserved connector residues, combined with altered receptor dynamics, possibly explains the reduced neurotensin efficacy in the constitutively active NTSR1 and a facilitated initial engagement with G protein in the absence of agonist.
Directory of Open Access Journals (Sweden)
Reza Sharifanfar
2016-10-01
Full Text Available Background and Objectives: Pomegranate juice (PJ contains large particles that stick to evaporator walls causing off flavors in the concentrate due to burning. Microfiltration is used to clarify PJ. Fouling is a limiting phenomenon that can prevent the industrialization of membrane clarification. Changes in the geometry of the membrane module such as using baffles are useful to decrease this problem. Computational fluid dynamics (CFD is a powerful numerical tool used in modeling membrane processing. Materials and Methods: The effect of baffle geometry on the efficiency of membrane clarification of pomegranate juice in a flat-sheet module was simulated using computational fluid dynamics (CFD. The geometry of the membrane unit was plotted and meshed with Gambit software, and was solved using FLUENT software. A two-dimensional double-precision method at steady state was selected to simulate the membrane process. The convective terms were discretized with a standard first-order upwind scheme in computational solution. The RNG k- model was used due to its high accuracy in eddy flows with a low Reynolds number. The effects on the process performance of the number of baffles, their angle and the distance between the baffles and the membrane surface were evaluated. Results: The results showed that the configuration with the feed-channel height of 2 cm, the baffle angle of 90o and the distance between the membrane surface and baffles of 2 mm had maximum permeate flux. Conclusions: Reducing the distance between the baffles and the membrane surface increased the permeate flux due to create an eddy flow near the membrane surface in the flat-sheet module and reduced the total and cake-layer resistances. Keywords: Baffle, Computational fluid dynamics, Juice, Membrane, Pomegranate
Computational Fluid Dynamics Simulation of Multiphase Flow in Structured Packings
Directory of Open Access Journals (Sweden)
Saeed Shojaee
2012-01-01
Full Text Available A volume of fluid multiphase flow model was used to investigate the effective area and the created liquid film in the structured packings. The computational results revealed that the gas and liquid flow rates play significant roles in the effective interfacial area of the packing. In particular, the effective area increases as the flow rates of both phases increase. Numerical results were compared with the Brunazzi and SRP models, and a good agreement between them was found. Attention was given to the process of liquid film formation in both two-dimensional (2D and three-dimensional (3D models. The current study revealed that computational fluid dynamics (CFD can be used as an effective tool to provide information on the details of gas and liquid flows in complex packing geometries.
Structural dynamics for new launch vehicles
Neighbors, Joyce; Ryan, Robert S.
1992-01-01
An overview is presented of current studies that will permit more robust designs and reduce the safety hazards of maximum dynamic pressure during launches. Key considerations in the assessment of future operable launch capabilities are the dynamics problems that arise during the initial minutes of transition from the static configuration on the launch pad to the attainment of orbital velocity. Attention is given to a typical attempt to achieve robustness that involves creating a design in which the first bending mode will have a high enough frequency to allow decoupling between the autopilot design and the flexible body dynamics.
Ergodic Theory, Open Dynamics, and Coherent Structures
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.
Modeling structural dynamic behavior of SSME components
Kiefling, Larry A.; Saxon, J. B.; Prickett, T. L.
1991-01-01
FEM studies are presented of the nozzle and the low-pressure fuel-pump inducer designs for the Space Shuttle Main Engine (SSME) to analyze the effects of structural vibrations. FEM preprocessing software based on a CAD system is employed to develop a model of the component's sophisticated geometry. The nozzle geometry is also defined by means of the preprocessing technique and subsequently analyzed with respect to time-transient loading. The analysis is conducted with a Cray supercomputer using the SPAR/EAL FEM program. The investigation of the nozzle demonstrates the advantageous use of symmetry in the determination of nozzle response to SSME start-up transients. Plots of time vs strain are developed for gages on the nozzle wall and steerhorn tubing. The results of the inducer modeling are found to be adequate for investigating the component's principle modes, and the nozzle results indicate the suitability of the FEM techniques for optimizing the design of engine components.
Scalably Revealing the Dynamics of Soft Community Structure in Complex Networks
Institute of Scientific and Technical Information of China (English)
LI Huijia; LI Huiying
2016-01-01
Revealing the dynamics of community structure is of great concern for scientists from many fields.Specifically,how to quantify the dynamic details of soft community structure is a very interesting topic.In this paper,the authors propose a novel framework to study the scalable dynamic behavior of the soft community structure.First,the authors model the Potts dynamics to detect community structure using a "soft" Markov process.Then the soft stability of in a multiscale view is proposed to naturally uncover the local uniform behavior of spin values across multiple hierarchical levels.Finally,a new partition index is developed to detect fuzzy communities based on the stability and the dynamical information.Experiments on the both synthetically generated and real-world networks verify that the framework can be used to uncover hierarchical community structures effectively and efficiently.
Energy Technology Data Exchange (ETDEWEB)
Agniswamy, Johnson; Louis, John M.; Roche, Julien; Harrison, Robert W.; Weber, Irene T. (GSU); (NIH); (Iowa State)
2016-12-16
We report structural analysis of HIV protease variant PRS17 which was rationally selected by machine learning to represent wide classes of highly drug-resistant variants. Crystal structures were solved of PRS17 in the inhibitor-free form and in complex with antiviral inhibitor, darunavir. Despite its 17 mutations, PRS17 has only one mutation (V82S) in the inhibitor/substrate binding cavity, yet exhibits high resistance to all clinical inhibitors. PRS17 has none of the major mutations (I47V, I50V, I54ML, L76V and I84V) associated with darunavir resistance, but has 10,000-fold weaker binding affinity relative to the wild type PR. Comparable binding affinity of 8000-fold weaker than PR is seen for drug resistant mutant PR20, which bears 3 mutations associated with major resistance to darunavir (I47V, I54L and I84V). Inhibitor-free PRS17 shows an open flap conformation with a curled tip correlating with G48V flap mutation. NMR studies on inactive PRS17 D25N unambiguously confirm that the flaps adopt mainly an open conformation in solution very similar to that in the inhibitor-free crystal structure. In PRS17, the hinge loop cluster of mutations, E35D, M36I and S37D, contributes to the altered flap dynamics by a mechanism similar to that of PR20. An additional K20R mutation anchors an altered conformation of the hinge loop. Flap mutations M46L and G48V in PRS17/DRV complex alter the Phe53 conformation by steric hindrance between the side chains. Unlike the L10F mutation in PR20, L10I in PRS17 does not break the inter-subunit ion pair or diminish the dimer stability, consistent with a very low dimer dissociation constant comparable to that of wild type PR. Distal mutations A71V, L90M and I93L propagate alterations to the catalytic site of PRS17. PRS17 exhibits a molecular mechanism whereby mutations act synergistically to alter the flap dynamics resulting in significantly weaker binding yet maintaining active site contacts with darunavir.
Filipović, Vilim; Coquet, Yves; Pot, Valérie; Houot, Sabine; Benoit, Pierre
2014-11-15
Transport processes in soils are strongly affected by heterogeneity of soil hydraulic properties. Tillage practices and compost amendments can modify soil structure and create heterogeneity at the local scale within agricultural fields. The long-term field experiment QualiAgro (INRA-Veolia partnership 1998-2013) explores the impact of heterogeneity in soil structure created by tillage practices and compost application on transport processes. A modeling study was performed to evaluate how the presence of heterogeneity due to soil tillage and compost application affects water flow and pesticide dynamics in soil during a long-term period. The study was done on a plot receiving a co-compost of green wastes and sewage sludge (SGW) applied once every 2 years since 1998. The plot was cultivated with a biannual rotation of winter wheat-maize (except 1 year of barley) and a four-furrow moldboard plow was used for tillage. In each plot, wick lysimeter outflow and TDR probe data were collected at different depths from 2004, while tensiometer measurements were also conducted during 2007/2008. Isoproturon concentration was measured in lysimeter outflow since 2004. Detailed profile description was used to locate different soil structures in the profile, which was then implemented in the HYDRUS-2D model. Four zones were identified in the plowed layer: compacted clods with no visible macropores (Δ), non-compacted soil with visible macroporosity (Γ), interfurrows created by moldboard plowing containing crop residues and applied compost (IF), and the plow pan (PP) created by plowing repeatedly to the same depth. Isoproturon retention and degradation parameters were estimated from laboratory batch sorption and incubation experiments, respectively, for each structure independently. Water retention parameters were estimated from pressure plate laboratory measurements and hydraulic conductivity parameters were obtained from field tension infiltrometer experiments. Soil hydraulic
CISM course on exploiting nonlinear behaviour in structural dynamics
Virgin, Lawrence; Exploiting Nonlinear Behavior in Structural Dynamics
2012-01-01
The articles in this volume give an overview and introduction to nonlinear phenomena in structural dynamics. Topics treated are approximate methods for analyzing nonlinear systems (where the level of nonlinearity is assumed to be relatively small), vibration isolation, the mitigation of undesirable torsional vibration in rotating systems utilizing specifically nonlinear features in the dynamics, the vibration of nonlinear structures in which the motion is sufficiently large amplitude and structural systems with control.
Laser fields in dynamically ionized plasma structures for coherent acceleration
Luu-Thanh, Ph.; Pukhov, A.; Kostyukov, I.
2015-01-01
With the emergence of the CAN (Coherent Amplification Network) laser technology, a new scheme for direct particle acceleration in periodic plasma structures has been proposed. By using our full electromagnetic relativistic particle-in-cell (PIC) simulation code equipped with ionisation module, we simulate the laser fields dynamics in the periodic structures of different materials. We study how the dynamic ionization influences the field structure.
Directory of Open Access Journals (Sweden)
A. Salehian
2012-01-01
Full Text Available Motivated by deployable satellite technology, this article presents a homogenization model of an inflatable, rigidized lattice structure with distributed macro-fiber composite (MFC actuation. The model is based upon a general expression for the strain and kinetic energy of a fundamental repeated element of the structure. These expressions are reduced in order and expressed in terms of the strain and displacement components of an equivalent one-dimensional vibration model. The resulting model is used to analyze changes in the structural natural frequencies introduced by the local effects of the added macro-fiber composite actuators for several configurations. A finite element solution is used as a comparison for the homogenization model, and the two are shown to be in good agreement, although the latter requires significantly less computational effort.
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.
Enzymes: An integrated view of structure, dynamics and function
Directory of Open Access Journals (Sweden)
Agarwal Pratul K
2006-01-01
Full Text Available Abstract Microbes utilize enzymes to perform a variety of functions. Enzymes are biocatalysts working as highly efficient machines at the molecular level. In the past, enzymes have been viewed as static entities and their function has been explained on the basis of direct structural interactions between the enzyme and the substrate. A variety of experimental and computational techniques, however, continue to reveal that proteins are dynamically active machines, with various parts exhibiting internal motions at a wide range of time-scales. Increasing evidence also indicates that these internal protein motions play a role in promoting protein function such as enzyme catalysis. Moreover, the thermodynamical fluctuations of the solvent, surrounding the protein, have an impact on internal protein motions and, therefore, on enzyme function. In this review, we describe recent biochemical and theoretical investigations of internal protein dynamics linked to enzyme catalysis. In the enzyme cyclophilin A, investigations have lead to the discovery of a network of protein vibrations promoting catalysis. Cyclophilin A catalyzes peptidyl-prolyl cis/trans isomerization in a variety of peptide and protein substrates. Recent studies of cyclophilin A are discussed in detail and other enzymes (dihydrofolate reductase and liver alcohol dehydrogenase where similar discoveries have been reported are also briefly discussed. The detailed characterization of the discovered networks indicates that protein dynamics plays a role in rate-enhancement achieved by enzymes. An integrated view of enzyme structure, dynamics and function have wide implications in understanding allosteric and co-operative effects, as well as protein engineering of more efficient enzymes and novel drug design.
Dynamic Analysis of Structural Columns Subjected to Impulsive Loading
Institute of Scientific and Technical Information of China (English)
GONG Shunfeng; LU Yong; GAO Feng; JIN Weiliang
2006-01-01
For a building structure subjected to impulsive loading,particularly shock and impact loading,the response of the critical columns is crucial to the behaviour of the entire system during and after the blast loading phase.Therefore,an appropriate evaluation of the column response and damage under short-duration impulsive loading is important in a comprehensive assessment of the performance of a building system.This paper reports a dynamic analysis approach for the response of RC columns subjected to impulsive loading.Considering that the dynamic response of a column in a frame structure can also be affected by the floor movement which relates to the global vibration of the frame system,a generic column-mass model is used,in which a concentrated mass is attached to the column top to simulate the effect of a global vibration.To take into account the high shear effect under impulsive load,the model is formulated using Timoshenko beam theory,and three main nonlinear mechanisms are considered.Two typical scenarios,one under a direct air blast loading,and another under a blast-induced ground excitation,are analyzed and the primary response features are highlighted.
Yang, Zhitong
Due to its unique combination of tensile strength and elasticity, the dragline silk of the orb-weaving spider Nephila clavipes has attracted much attention. Most importantly, it has a high energy to break that is unparalleled in other fibers. Though the basis for the strength of the silk fiber has been uncovered, the molecular reason of the fiber's large shrinkage in water is unknown. This has been a major hurdle in the practical applications of the fiber, and to any man-made copy of this material. Small-angle X-ray scattering (SAXS) is used to probe of the long-range structures in the semicrystalline silk. Scattering patterns of wet and dry samples indicate that the crystalline regions stack along the fiber axis to form lamellar structures. These structures are sparsely dispersed in a softer matrix with a long spacing of 8.4 nm. This spacing increases reversibly by 4% when fibers are stretched by 10%, and shrinks to 5.8 nm when fibers shrink 45% in length on wetting. Solid-state nuclear magnetic resonance (NMR) experiments are performed to reveal the microscopic details of the dynamics in the silk. Cross-polarization magic-angle spinning 13C NMR demonstrates that a substantial fraction of the glycine, glutamine, tyrosine, serine, and leucine residues experience dramatic increases in the rate of large-amplitude reorientation at the protein backbone when fibers are wet. Variable temperature deuterium NMR measurements were carried out on silk samples that incorporate leucine deuterated at the methyl group. Results show that only a subset of these leucine residues is strongly affected by water. Quantitative analysis and chemical considerations suggest that the highly conserved YGGLGS(N)QGAGR blocks, only found in the dragline silk protein, play a major role in the supercontraction process. Protein sequences are proposed to produce artificial spider silk with similar mechanical properties, but without the undesired phenomenon of supercontraction. The spinning and
The Dynamic Similitude Design Method of Thin Walled Structures and Experimental Validation
Directory of Open Access Journals (Sweden)
Zhong Luo
2016-01-01
Full Text Available For the applicability of dynamic similitude models of thin walled structures, such as engine blades, turbine discs, and cylindrical shells, the dynamic similitude design of typical thin walled structures is investigated. The governing equation of typical thin walled structures is firstly unified, which guides to establishing dynamic scaling laws of typical thin walled structures. Based on the governing equation, geometrically complete scaling law of the typical thin walled structure is derived. In order to determine accurate distorted scaling laws of typical thin walled structures, three principles are proposed and theoretically proved by combining the sensitivity analysis and governing equation. Taking the thin walled annular plate as an example, geometrically complete and distorted scaling laws can be obtained based on the principles of determining dynamic scaling laws. Furthermore, the previous five orders’ accurate distorted scaling laws of thin walled annular plates are presented and numerically validated. Finally, the effectiveness of the similitude design method is validated by experimental annular plates.
Collins, Scott L; Ladwig, Laura M; Petrie, Matthew D; Jones, Sydney K; Mulhouse, John M; Thibault, James R; Pockman, William T
2017-03-01
Global environmental change is altering temperature, precipitation patterns, resource availability, and disturbance regimes. Theory predicts that ecological presses will interact with pulse events to alter ecosystem structure and function. In 2006, we established a long-term, multifactor global change experiment to determine the interactive effects of nighttime warming, increased atmospheric nitrogen (N) deposition, and increased winter precipitation on plant community structure and aboveground net primary production (ANPP) in a northern Chihuahuan Desert grassland. In 2009, a lightning-caused wildfire burned through the experiment. Here, we report on the interactive effects of these global change drivers on pre- and postfire grassland community structure and ANPP. Our nighttime warming treatment increased winter nighttime air temperatures by an average of 1.1 °C and summer nighttime air temperature by 1.5 °C. Soil N availability was 2.5 times higher in fertilized compared with control plots. Average soil volumetric water content (VWC) in winter was slightly but significantly higher (13.0% vs. 11.0%) in plots receiving added winter rain relative to controls, and VWC was slightly higher in warmed (14.5%) compared with control (13.5%) plots during the growing season even though surface soil temperatures were significantly higher in warmed plots. Despite these significant treatment effects, ANPP and plant community structure were highly resistant to these global change drivers prior to the fire. Burning reduced the cover of the dominant grasses by more than 75%. Following the fire, forb species richness and biomass increased significantly, particularly in warmed, fertilized plots that received additional winter precipitation. Thus, although unburned grassland showed little initial response to multiple ecological presses, our results demonstrate how a single pulse disturbance can interact with chronic alterations in resource availability to increase ecosystem
Balancer effects in opinion dynamics
Cheon, Taksu
2016-01-01
We introduce a novel type of contrarian agent, the balancer, to Galam model of opinion dynamics, in order to account for the skepticism over one-sidedness and for the sense of fairness. We find that the inclusion of balancers along with floaters and inflexibles brings about a critical point on parametric plane of the dynamical system, which results in the new kind of stable final states of the opinion dynamics, that seem to capture several intriguing features found often in mature democracies.
Virtual sensing of structural vibrations using dynamic substructuring
Kullaa, Jyrki
2016-10-01
Virtual sensing techniques use information available from a limited set of physical sensors together with the finite element model to calculate an estimate of the quantity of interest. In structural dynamics applications, analytical mode shapes from the finite element model are typically used as a basis to estimate the response at unmeasured locations by an expansion algorithm. An alternative is to model only the interesting part of the structure using substructuring techniques, in which the natural modes are replaced by component modes consisting of a selected number of fixed interface modes plus the interface constraint modes. They are mutually independent and compose a valid subspace for estimating the unmeasured response. If the number of interface degrees of freedom is large, interface reduction is applied. The main advantage of the proposed approach is that the modelling effort can be substantially decreased, because only part of the structure is modelled and the modelling uncertainties, non-linearities, or changes in the omitted structure can be ignored. The method is validated by numerical simulations of three different structures under unknown excitation. Different types and locations of virtual sensors are studied. Also, the effects of noise and model errors are investigated. The most accurate estimation is obtained if the virtual sensor is located away from the interface and close to a physical sensor.
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.
On the dynamics of floating structures
Lannes, David
2016-01-01
This paper addresses the floating body problem which consists in studying the interaction of surface water waves with a floating body. We propose a new formulation of the water waves problem that can easily be generalized in order to take into account the presence of a floating body. The resulting equations have a compressible-incompressible structure in which the interior pressure exerted by the fluid on the floating body is a Lagrange multiplier that can be determined through the resolution of a $d$-dimensional elliptic equation, where $d$ is the horizontal dimension. In the case where the object is freely floating, we decompose the hydrodynamic force and torque exerted by the fluid on the solid in order to exhibit an added mass effect; in the one dimensional case $d=1$, the computations can be carried out explicitly. We also show that this approach in which the interior pressure appears as a Lagrange multiplier can be implemented on reduced asymptotic models such as the nonlinear shallow water equations an...
Organoactinide chemistry: synthesis, structure, and solution dynamics
Energy Technology Data Exchange (ETDEWEB)
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/sub 2/MX/sub 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 ..pi..-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.
Sensitive dependence of network dynamics on network structure
Nishikawa, Takashi; Motter, Adilson E
2016-01-01
The relation between network structure and dynamics is determinant for the behavior of complex systems in numerous domains. An important longstanding problem concerns the properties of the networks that optimize the dynamics with respect to a given performance measure. Here we show that such optimization can lead to sensitive dependence of the dynamics on the structure of the network. Specifically, we demonstrate that the stability of the dynamical state, as determined by the maximum Lyapunov exponent, can exhibit a cusp-like dependence on the number of nodes and links as well as on the size of perturbations applied to the network structure. As mechanisms underlying this sensitivity, we identify discontinuous transitions occurring in the complement of optimal networks and the prevalence of eigenvector degeneracy in these networks. These findings establish a unified characterization of networks optimized for dynamical stability in diffusively coupled systems, which we illustrate using Turing instability in act...
Segmenting Dynamic Human Action via Statistical Structure
Baldwin, Dare; Andersson, Annika; Saffran, Jenny; Meyer, Meredith
2008-01-01
Human social, cognitive, and linguistic functioning depends on skills for rapidly processing action. Identifying distinct acts within the dynamic motion flow is one basic component of action processing; for example, skill at segmenting action is foundational to action categorization, verb learning, and comprehension of novel action sequences. Yet…
Electronic-structural dynamics in graphene
Directory of Open Access Journals (Sweden)
Isabella Gierz
2016-09-01
meV, a transient enhancement of the electron-phonon coupling constant is observed, providing interesting perspective for experiments that report light-enhanced superconductivity in doped fullerites in which a similar lattice mode was excited. All the studies reviewed here have important implications for applications of graphene in optoelectronic devices and for the dynamical engineering of electronic properties with light.
Dynamic network structure of interhemispheric coordination.
Doron, Karl W; Bassett, Danielle S; Gazzaniga, Michael S
2012-11-13
Fifty years ago Gazzaniga and coworkers published a seminal article that discussed the separate roles of the cerebral hemispheres in humans. Today, the study of interhemispheric communication is facilitated by a battery of novel data analysis techniques drawn from across disciplinary boundaries, including dynamic systems theory and network theory. These techniques enable the characterization of dynamic changes in the brain's functional connectivity, thereby providing an unprecedented means of decoding interhemispheric communication. Here, we illustrate the use of these techniques to examine interhemispheric coordination in healthy human participants performing a split visual field experiment in which they process lexical stimuli. We find that interhemispheric coordination is greater when lexical information is introduced to the right hemisphere and must subsequently be transferred to the left hemisphere for language processing than when it is directly introduced to the language-dominant (left) hemisphere. Further, we find that putative functional modules defined by coherent interhemispheric coordination come online in a transient manner, highlighting the underlying dynamic nature of brain communication. Our work illustrates that recently developed dynamic, network-based analysis techniques can provide novel and previously unapproachable insights into the role of interhemispheric coordination in cognition.
Structures and Dynamics of Social Networks: Selection, Influence, and Self-Organization
Go, Myong-Hyun
2010-01-01
This dissertation studies the social structures and dynamics of human networks: how peers at the micro level and physical environments at the macro level interact with the individual preferences and attributes and shape social dynamics. It is composed of three parts. The first essay, "Friendship Choices and Group Effects in Adolescent…
Chen, Tsu-Wei; Nguyen, Thi My Nguyet; Kahlen, Katrin; Stützel, Hartmut
2014-12-01
There is increasing interest in evaluating the environmental effects on crop architectural traits and yield improvement. However, crop models describing the dynamic changes in canopy structure with environmental conditions and the complex interactions between canopy structure, light interception, and dry mass production are only gradually emerging. Using tomato (Solanum lycopersicum L.) as a model crop, a dynamic functional-structural plant model (FSPM) was constructed, parameterized, and evaluated to analyse the effects of temperature on architectural traits, which strongly influence canopy light interception and shoot dry mass. The FSPM predicted the organ growth, organ size, and shoot dry mass over time with high accuracy (>85%). Analyses of this FSPM showed that, in comparison with the reference canopy, shoot dry mass may be affected by leaf angle by as much as 20%, leaf curvature by up to 7%, the leaf length:width ratio by up to 5%, internode length by up to 9%, and curvature ratios and leaf arrangement by up to 6%. Tomato canopies at low temperature had higher canopy density and were more clumped due to higher leaf area and shorter internodes. Interestingly, dry mass production and light interception of the clumped canopy were more sensitive to changes in architectural traits. The complex interactions between architectural traits, canopy light interception, dry mass production, and environmental conditions can be studied by the dynamic FSPM, which may serve as a tool for designing a canopy structure which is 'ideal' in a given environment. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.
Institute of Scientific and Technical Information of China (English)
Wang, Mian; Yang, Jipeng; Wang, Jianyi; Wang, Xiaojuan
2012-01-01
The conformation change picture of human islet amyloid polypeptide （hlAPP） is outlined using molecular dynamics simulation, and the structural influences of L16Q, S20G, and L16Q-S20G mutations on the conformation of hlAPP are analyzed. Particularly, the conformational changes of the amyloidogenic-related regions of residues 15-- 17 and 20--29 are emphasized. Our studies find that, for WT hlAPP, residues 15--17 always maintain a stable a-helix structure, residues 20--25 structurally fluctuate between turn and 5-helix, and residues 26--29 mainly adopt coil and bend structures. The hydrogen bonds between the polar groups of hlAPP, long-rang van der Waals forces between the residues, and hydrophobic interactions between the residues of hlAPP are important driving forces to maintain the secondary structure of hlAPP. The replacement of leucine 16 by glutamine stabilizes the helix structure of residues 15--17 and 20--23 of hlAPP monomer, and the structure of residues 24--29 fluctuates be- tween helix and turn. The relatively stable helix structures of residues 15--17 and 20--29 are supposed to be beneficial for L16Q hlAPP to resist the aggregation as observed in the experiment. The substitution of serine20 by glycinc drives residues 15--17 and 20--29 of hlAPP to transform from helix structure to β-strands or coil structures with higher extension and flexibility, which may promote the aggregation of hlAPP as the experiments reported. These results are significant to understand the aggregation mechanism of hlAPP monomer into the dimer, trimer, oligomers and fibrils associated with the type 2 diabetes at the atomic level.
Analysis of Nonlinear Structural Dynamics and Resonance in Trees
Directory of Open Access Journals (Sweden)
H. Doumiri Ganji
2012-01-01
Full Text Available Wind and gravity both impact trees in storms, but wind loads greatly exceed gravity loads in most situations. Complex behavior of trees in windstorms is gradually turning into a controversial concern among ecological engineers. To better understand the effects of nonlinear behavior of trees, the dynamic forces on tree structures during periods of high winds have been examined as a mass-spring system. In fact, the simulated dynamic forces created by strong winds are studied in order to determine the responses of the trees to such dynamic loads. Many of such nonlinear differential equations are complicated to solve. Therefore, this paper focuses on an accurate and simple solution, Differential Transformation Method (DTM, to solve the derived equation. In this regard, the concept of differential transformation is briefly introduced. The approximate solution to this equation is calculated in the form of a series with easily computable terms. Then, the method has been employed to achieve an acceptable solution to the presented nonlinear differential equation. To verify the accuracy of the proposed method, the obtained results from DTM are compared with those from the numerical solution. The results reveal that this method gives successive approximations of high accuracy solution.
Cavalli, Andrea; Camilloni, Carlo; Vendruscolo, Michele
2013-03-07
In order to characterise the dynamics of proteins, a well-established method is to incorporate experimental parameters as replica-averaged structural restraints into molecular dynamics simulations. Here, we justify this approach in the case of interproton distance information provided by nuclear Overhauser effects by showing that it generates ensembles of conformations according to the maximum entropy principle. These results indicate that the use of replica-averaged structural restraints in molecular dynamics simulations, given a force field and a set of experimental data, can provide an accurate approximation of the unknown Boltzmann distribution of a system.
Framing Effects: Dynamics and Task Domains
Wang
1996-11-01
The author examines the mechanisms and dynamics of framing effects in risky choices across three distinct task domains (i.e., life-death, public property, and personal money). The choice outcomes of the problems presented in each of the three task domains had a binary structure of a sure thing vs a gamble of equal expected value; the outcomes differed in their framing conditions and the expected values, raging from 6000, 600, 60, to 6, numerically. It was hypothesized that subjects would become more risk seeking, if the sure outcome was below their aspiration level (the minimum requirement). As predicted, more subjects preferred the gamble when facing the life-death choice problems than facing the counterpart problems presented in the other two task domains. Subjects' risk preference varied categorically along the group size dimension in the life-death domain but changed more linearly over the expected value dimension in the monetary domain. Framing effects were observed in 7 of 13 pairs of problems, showing a positive frame-risk aversion and negative frame-risk seeking relationship. In addition, two types of framing effects were theoretically defined and empirically identified. A bidirectional framing effect involves a reversal in risk preference, and occurs when a decision maker's risk preference is ambiguous or weak. Four bidirectional effects were observed; in each case a majority of subjects preferred the sure outcome under a positive frame but the gamble under a negative frame. In contrast, a unidirectional framing effect refers to a preference shift due to the framing of choice outcomes: A majority of subjects preferred one choice outcome (either the sure thing or the gamble) under both framing conditions, with positive frame augmented the preference for the sure thing and negative frame augmented the preference for the gamble. These findings revealed some dynamic regularities of framing effects and posed implications for developing predictive and testable
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
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......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...... considerable effect on the final estimations of the method, in particular on the coefficient of variation of the estimated failure probability. Based on these observations, a simple optimization algorithm is proposed which distributes the support points so that the coefficient of variation of the method...
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
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......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...... considerable effect on the final estimations of the method, in particular on the coefficient of variation of the estimated failure probability. Based on these observations, a simple optimization algorithm is proposed which distributes the support points so that the coefficient of variation of the method...
Site-directed spectroscopic probes of actomyosin structural dynamics.
Thomas, David D; Kast, David; Korman, Vicci L
2009-01-01
Spectroscopy of myosin and actin has entered a golden age. High-resolution crystal structures of isolated actin and myosin have been used to construct detailed models for the dynamic actomyosin interactions that move muscle. Improved protein mutagenesis and expression technologies have facilitated site-directed labeling with fluorescent and spin probes. Spectroscopic instrumentation has achieved impressive advances in sensitivity and resolution. Here we highlight the contributions of site-directed spectroscopic probes to understanding the structural dynamics of myosin II and its actin complexes in solution and muscle fibers. We emphasize studies that probe directly the movements of structural elements within the myosin catalytic and light-chain domains, and changes in the dynamics of both actin and myosin due to their alternating strong and weak interactions in the ATPase cycle. A moving picture emerges in which single biochemical states produce multiple structural states, and transitions between states of order and dynamic disorder power the actomyosin engine.
Structures and ultrafast dynamics of interfacial water assemblies on smooth hydrophobic surfaces
Yang, Ding-Shyue; He, Xing
2017-09-01
Using time-averaged and ultrafast electron diffraction, structures and ultrafast dynamics of interfacial water assemblies on smooth hydrophobic surfaces are reported. The lack of hydrophilic interaction and topographical template effect from the support surface leads to the formation of small, mostly randomly-oriented, ice crystallites with the cubic structure. Dynamically, following the substrate photoexcitation, interfacial water assemblies undergo four stages of changes-ultrafast melting, nonequilibrium isotropic phase transformation, annealing, and restructuring-which are closely correlated with the substrate dynamics. The connectivity and cooperative nature of the hydrogen-bonded network is considered crucial for water assemblies to withstand large structural motions without sublimation on ultrashort times.
Institute of Scientific and Technical Information of China (English)
姚志远; 汪凤泉
2004-01-01
An online method of identification of dynamic characteristics only using measured ambient response of structural dynamic system is widely focused on. The Ibrahim and ARMA (AutoRegressive Moving Average ) methods are basic identification methods. A model on dynamic system suffered by random ambient excitation was researched into, and a subspace decomposition method being different from traditional harmonic retrieval method was introduced. Robustness and effectiveness of this approach on identification of vibration characteristics are demonstrated on numerical experiment.
THE DESIGN AND ANALYSIS OF VIBRATION STRUCTURE OF VERTICAL DYNAMIC BALANCING MACHINE
Institute of Scientific and Technical Information of China (English)
LiDinggen; CaoJiguang; WangJtmwen; ChenChuanyao
2004-01-01
A new type of vibration structure (i.e. supporting system, called swing frame customarily) of vertical dynamic balancing machine has been designed, which is based on an analysis for the swing frame of a traditional double-plane vertical dynamic balancing machine. The static unbalance and couple unbalance can be effectively separated by using the new dynamic balancing machine with the new swing frame. By building the dynamics model, the advantages of the new structure are discussed in detail. The modal and harmonic response are analyzed by using the ANSYS7.0. By comparing the finite element modal analysis with the experimental modal analysis, the natural frequencies and vibration modes are found. There are many spring boards in the new swing frame. Their stiffnesses are different and assorted with each other. Furthermore, there are three sensors on the measuring points. Therefore, the new dynamic balancing machine can measure static unbalance and coupling unbalance directly, and the interaction between them is faint. The result shows that the new vertical dynamic balancing machine is suitable for inertial measurement of flying objects, and can overcome the shortcomings of traditional double-plane vertical dynamic balancing machines, which the effect of plane-separation is inferior. The vertical dynamic balancing machine with the new vibration structure can find wide application in the future. The modelling and analysis of the new vibration structure will provide theoretical basis and practical experience for designing new-type vertical dynamic balancing machines.
Structural Dynamics Within and Between Organizations.
Fombrun, Charles J.
1986-01-01
The concept of structure is recast as an instantaneous correspondence between an infrastructure, a sociostructure, and a superstructure--manifestations of collective life juxtaposed through technological solutions, political exchanges, and social interpretations involving organizations. Ultimately, structuring is a dialectical unfolding of…
Nonlinear dynamic behaviors of a floating structure in focused waves
Cao, Fei-feng; Zhao, Xi-zeng
2015-12-01
Floating structures are commonly seen in coastal and offshore engineering. They are often subjected to extreme waves and, therefore, their nonlinear dynamic behaviors are of great concern. In this paper, an in-house CFD code is developed to investigate the accurate prediction of nonlinear dynamic behaviors of a two-dimensional (2-D) box-shaped floating structure in focused waves. Computations are performed by an enhanced Constrained Interpolation Profile (CIP)-based Cartesian grid model, in which a more accurate VOF (Volume of Fluid) method, the THINC/SW scheme (THINC: tangent of hyperbola for interface capturing; SW: Slope Weighting), is used for interface capturing. A focusing wave theory is used for the focused wave generation. The wave component of constant steepness is chosen. Comparisons between predictions and physical measurements show good agreement including body motions and free surface profiles. Although the overall agreement is good, some discrepancies are observed for impact pressure on the superstructure due to water on deck. The effect of grid resolution on the results is checked. With a fine grid, no obvious improvement is seen in the global body motions and impact pressures due to water on deck. It is concluded that highly nonlinear phenomena, such as distorted free surface, large-amplitude body motions, and violent impact flow, have been predicted successfully.
Evolutionary principles underlying structure and response dynamics of cellular networks.
Steinacher, Arno; Soyer, Orkun S
2012-01-01
The network view in systems biology, in conjunction with the continuing development of experimental technologies, is providing us with the key structural and dynamical features of both cell-wide and pathway-level regulatory, signaling and metabolic systems. These include for example modularity and presence of hub proteins at the structural level and ultrasensitivity and feedback control at the level of dynamics. The uncovering of such features, and the seeming commonality of some of them, makes many systems biologists believe that these could represent design principles that underpin cellular systems across organisms. Here, we argue that such claims on any observed feature requires an understanding of how it has emerged in evolution and how it can shape subsequent evolution. We review recent and past studies that aim to achieve such evolutionary understanding for observed features of cellular networks. We argue that this evolutionary framework could lead to deciphering evolutionary origin and relevance of proposed design principles, thereby allowing to predict their presence or absence in an organism based on its environment and biochemistry and their effect on its future evolution.
Dynamical Structure of a Traditional Amazonian Social Network
Directory of Open Access Journals (Sweden)
Paul L. Hooper
2013-11-01
Full Text Available Reciprocity is a vital feature of social networks, but relatively little is known about its temporal structure or the mechanisms underlying its persistence in real world behavior. In pursuit of these two questions, we study the stationary and dynamical signals of reciprocity in a network of manioc beer (Spanish: chicha; Tsimane’: shocdye’ drinking events in a Tsimane’ village in lowland Bolivia. At the stationary level, our analysis reveals that social exchange within the community is heterogeneously patterned according to kinship and spatial proximity. A positive relationship between the frequencies at which two families host each other, controlling for kinship and proximity, provides evidence for stationary reciprocity. Our analysis of the dynamical structure of this network presents a novel method for the study of conditional, or non-stationary, reciprocity effects. We find evidence that short-timescale reciprocity (within three days is present among non- and distant-kin pairs; conversely, we find that levels of cooperation among close kin can be accounted for on the stationary hypothesis alone.
Dynamic characteristics of large repetitive framelike structures
Nayfeh, A. H.; Hartle, M. S.
1984-01-01
Using a building block approach and starting with a single element, expressions for the energy of various two-dimensional frametype gridwork configurations are derived. These are then used to develop energy equivalent continua for the gridworks. Equations of motion and associated boundary conditions are obtained for the continua. Some dynamic characteristics of these continua are investigated and compared with corresponding results obtained from finite element codes and also with some available theoretical predictions.
Jellyfish modulate bacterial dynamic and community structure.
Tinta, Tinkara; Kogovšek, Tjaša; Malej, Alenka; Turk, Valentina
2012-01-01
Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into possible changes in
Jellyfish modulate bacterial dynamic and community structure.
Directory of Open Access Journals (Sweden)
Tinkara Tinta
Full Text Available Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into
A molecular dynamics study of structure and dynamics in high-density liquids
Variyar, Jayasankar E.; Noro, Massimo; Kivelson, Daniel
By means of molecular dynamics simulations we have investigated increasing configurational ordering and decreasing particle mobility with increasing density ρ of a three-dimensional equilibrated liquid composed of soft discs. The equal-time correlation function h(n)3 (0) which includes two-, three- and four-body correlations is introduced as a measure of structural order; this function is related to the dipole-induced-dipole equal-time correlation function and its sensitivity to structural order in the liquid is associated with the cancellation effect, i.e. the cancellation of the positive contributions of the two- and four- body correlations by the negative contribution of the three-body correlations. The analogous time-dependent correlation function h(4)3 (t) is also studied. The possible implications of these results to the study of supercooled liquids and glasses is discussed.
Yoshida, Satoru; Takinoue, Masahiro; Iwase, Eiji; Onoe, Hiroaki
2016-08-01
This paper describes a system through which the self-assembly of anisotropic hydrogel microparticles is achieved, which also enables dynamic transformation of the assembled structures. Using a centrifuge-based microfluidic device, anisotropic hydrogel microparticles encapsulating superparamagnetic materials on one side are fabricated, which respond to a magnetic field. We successfully achieve dynamic assembly using these hydrogel microparticles and realize three different self-assembled structures (single and double pearl chain structures, and close-packed structures), which can be transformed to other structures dynamically via tuning of the precessional magnetic field. We believe that the developed system has potential application as an effective platform for a dynamic cell manipulation and cultivation system, in biomimetic autonomous microrobot organization, and that it can facilitate further understanding of the self-organization and complex systems observed in nature.
Protein dynamics derived from clusters of crystal structures.
van Aalten, D M; Conn, D A; de Groot, B L; Berendsen, H J; Findlay, J B; Amadei, A
1997-01-01
A method is presented to mathematically extract concerted structural transitions in proteins from collections of crystal structures. The "essential dynamics" procedure is used to filter out small-amplitude fluctuations from such a set of structures; the remaining large conformational changes describe motions such as those important for the uptake/release of substrate/ligand and in catalytic reactions. The method is applied to sets of x-ray structures for a number of proteins, and the results ...
2010-08-18
annual progress in this effort in four research areas: (1) structural health monitoring, (2) experimental structural dynamics , (3) spectral modeling of wave propagation, and (4) wavelet analysis for damage detection.
Principal axes of M-DOF structures Part Ⅱ: Dynamic loading
Institute of Scientific and Technical Information of China (English)
无
2003-01-01
This paper is the second in a two-part series that discusses the principal axes of M-DOF structures subjected to static and dynamic loads. The primary purpose of this series is to understand the magnitude of the dynamic response of structures to enable better design of structures and response modification devices/systems. Under idealized design conditions, the structural responses are obtained by using single direction input ground motions in the direction of the intended response modification devices/systems, and by assuming that the responses of the structure is decoupleable in three mutually perpendicular directions. This standard practice has been applied to both new and retrofitted structures using various seismic protective systems. Very limited information is available on the effects of neglecting the impact of directional couplings (cross effects of which torsion is a component) of the dynamic response of structures. In order to quantify such effects, it is necessary to examine the principal axes of structures under both static and dynamic loading. In this two-part series, the first paper is concerned with static loading, which provides definitions and fundamental formulations, with the conclusion that cross effects of a statically loaded M-DOF structure resulting from the lack of principal axes are of insignificant magnitude. However, under dynamic or earthquake loading, a relatively small amount of energy transferred across perpendicular directions is accumulated, which may result in significant enlargement of the structural response. This paper deals with a formulation to define the principal axes of M-DOF structures under dynamic loading and develops quantitative measures to identify cross effects resulting from the non-existence of principal axes.
Dynamics of generalized Gaussian polymeric structures in random layered flows
Katyal, Divya; Kant, Rama
2015-04-01
We develop a formalism for the dynamics of a flexible branched polymer with arbitrary topology in the presence of random flows. This is achieved by employing the generalized Gaussian structure (GGS) approach and the Matheron-de Marsily model for the random layered flow. The expression for the average square displacement (ASD) of the center of mass of the GGS is obtained in such flow. The averaging is done over both the thermal noise and the external random flow. Although the formalism is valid for branched polymers with various complex topologies, we mainly focus here on the dynamics of the flexible star and dendrimer. We analyze the effect of the topology (the number and length of branches for stars and the number of generations for dendrimers) on the dynamics under the influence of external flow, which is characterized by their root-mean-square velocity, persistence flow length, and flow exponent α . Our analysis shows two anomalous power-law regimes, viz., subdiffusive (intermediate-time polymer stretching and flow-induced diffusion) and superdiffusive (long-time flow-induced diffusion). The influence of the topology of the GGS is unraveled in the intermediate-time regime, while the long-time regime is only weakly dependent on the topology of the polymer. With the decrease in the value of α , the magnitude of the ASD decreases, while the temporal exponent of the ASD increases in both the time regimes. Also there is an increase in both the magnitude of the ASD and the crossover time (from the subdiffusive to the superdiffusive regime) with an increase in the total mass of the polymeric structure.
Effects of Telecoupling on Global Vegetation Dynamics
Viña, A.; Liu, J.
2016-12-01
With the ever increasing trend in telecoupling processes, such as international trade, all countries around the world are becoming more interdependent. However, the effects of this growing interdependence on vegetation (e.g., shifts in the geographic extent and distribution) remain unknown even though vegetation dynamics are crucially important for food production, carbon sequestration, provision of other ecosystem services, and biodiversity conservation. In this study we evaluate the effects of international trade on the spatio-temporal trajectories of vegetation at national and global scales, using vegetation index imagery collected over more than three decades by the Advanced Very High Resolution Radiometer (AVHRR) satellite sensor series together with concurrent national and international data on international trade (and its associated movement of people, goods, services and information). The spatio-temporal trajectories of vegetation are obtained using the scale of fluctuation technique, which is based on the decomposition of the AVHRR image time series to obtain information on its spatial dependence structure over time. Similar to the correlation length, the scale of fluctuation corresponds to the range over which fluctuations in the vegetation index are spatially correlated. Results indicate that global vegetation has changed drastically over the last three decades. These changes are not uniform across space, with hotspots in active trading countries. This study not only has direct implications for understanding global vegetation dynamics, but also sheds important insights on the complexity of human-nature interactions across telecoupled systems.
The structural and dynamical variables of pentane isomers
Patel, Tarika K.; Vaghela, M. V.; Gajjar, P. N.
2016-05-01
We derived structural and dynamical properties of pentane isomers: normal pentane, iso-pentane and neo pentane for liquid and gaseous state. We use molecular dynamics simulation to calculate the dynamical properties of pentane isomers for number of particles 729 using the intermolecular potential and force due to Lenard Jones potential. The computations also include mean square displacement and self diffusion co-efficient using Einstein relation. In structural properties, structure factor and phonon frequency are obtaining from P Y Method and Hubbard and Beeby Approach respectively. The Intermolecular potential and self diffusion co-efficient depend on the branching in the structure. The pair correlation function and phonon dispersion curves revels the complex structure of neo-pentane with respect to iso-pentane and n-pentane.
Directory of Open Access Journals (Sweden)
Christine Schauer
Full Text Available Although blattid cockroaches and termites share a common ancestor, their diets are distinctly different. While termites consume a highly specialized diet of lignocellulose, cockroaches are omnivorous and opportunistic feeders. The role of the termite gut microbiota has been studied intensively, but little is known about the cockroach gut microbiota and its function in digestion and nutrition, particularly the adaptation to different diets. Our analyses of the bacterial gut microbiota of the blattid cockroach Shelfordella lateralis combining terminal restriction fragment length polymorphism of their 16S rRNA genes with physiological parameters (microbial metabolites, hydrogen and methane emission indicated substantial variation between individuals but failed to identify any diet-related response. Subsequent deep-sequencing of the 16S rRNA genes of the colonic gut microbiota of S. lateralis fed either a high- or a low-fiber diet confirmed the absence of bacterial taxa that responded to diet. Instead, we found a small number of abundant phylotypes that were consistently present in all samples and made up half of the community in both diet groups. They varied strongly in abundance between individual samples at the genus but not at the family level. The remaining phylotypes were inconsistently present among replicate batches. Our findings suggest that S. lateralis harbors a highly dynamic core gut microbiota that is maintained even after fundamental dietary shifts, and that any dietary effects on the gut community are likely to be masked by strong individual variations.
Parasitic Effects on Memristor Dynamics
Itoh, Makoto; Chua, Leon O.
2016-06-01
In this paper, we show that parasitic elements have a significant effect on the dynamics of memristor circuits. We first show that certain 2-terminal elements such as memristors, memcapacitors, and meminductors can be used as nonvolatile memories, if the principle of conservation of state variables hold by open-circuiting, or short-circuiting, their terminals. We also show that a passive memristor with a strictly-increasing constitutive relation will eventually lose its stored flux when we switch off the power if there is a parasitic capacitance across the memristor. Similarly, a memcapacitor (resp., meminductor) with a positive memcapacitance (resp., meminductance) will eventually lose their stored physical states when we switch off the power, if it is connected to a parasitic resistance. We then show that the discontinuous jump that circuit engineers assumed to occur at impasse points of memristor circuits contradicts the principles of conservation of charge and flux at the time of the discontinuous jump. A parasitic element can be used to break an impasse point, resulting in the emergence of a continuous oscillation in the circuit. We also define a distance, a diameter, and a dimension, for each circuit element in order to measure the complexity order of the parasitic elements. They can be used to find higher-order parasitic elements which can break impasse points. Furthermore, we derived a memristor-based Chua’s circuit from a three-element circuit containing a memristor by connecting two parasitic memcapacitances to break the impasse points. We finally show that a higher-order parasitic element can be used for breaking the impasse points on two-dimensional and three-dimensional constrained spaces.
Opinion dynamics on a group structured adaptive network
Gargiulo, F
2009-01-01
Many models have been proposed to analyze the evolution of opinion structure due to the interaction of individuals in their social environment. Such models analyze the spreading of ideas both in completely interacting backgrounds and on social networks, where each person has a finite set of interlocutors.Moreover also the investigation on the topological structure of social networks has been object of several analysis, both from the theoretical and the empirical point of view. In this framework a particularly important area of study regards the community structure inside social networks.In this paper we analyze the reciprocal feedback between the opinions of the individuals and the structure of the interpersonal relationships at the level of community structures. For this purpose we define a group based random network and we study how this structure co-evolve with opinion dynamics processes. We observe that the adaptive network structure affects the opinion dynamics process helping the consensus formation. Th...
Cluster structure and dynamics in gels and glasses
Pastore, Raffaele; Fierro, Anallisa; Ciamarra, Massimo Pica; Coniglio, Antonio
2016-01-01
The dynamical arrest of gels is the consequence of a well defined structural phase transition, leading to the formation of a spanning cluster of bonded particles. The dynamical glass transition, instead, is not accompanied by any clear structural signature. Nevertheless, both transitions are characterized by the emergence of dynamical heterogeneities. Reviewing recent results from numerical simulations, we discuss the behavior of dynamical heterogeneities in different systems and show that a clear connection with the structure exists in the case of gels. The emerging picture may be also relevant for the more elusive case of glasses. We show, as an example, that the relaxation process of a simple glass-forming model can be related to a reverse percolation transition and discuss further perspective in this direction.
Phase Space Structures of k-threshold Sequential Dynamical Systems
Rani, Raffaele
2011-01-01
Sequential dynamical systems (SDS) are used to model a wide range of processes occurring on graphs or networks. The dynamics of such discrete dynamical systems is completely encoded by their phase space, a directed graph whose vertices and edges represent all possible system configurations and transitions between configurations respectively. Direct calculation of the phase space is in most cases a computationally demanding task. However, for some classes of SDS one can extract information on the connected component structure of phase space from the constituent elements of the SDS, such as its base graph and vertex functions. We present a number of novel results about the connected component structure of the phase space for k-threshold dynamical system with binary state spaces. We establish relations between the structure of the components, the threshold value, and the update sequence. Also fixed-point reachability from garden of eden configurations is investigated and upper bounds for the length of paths in t...
The semi-dynamical reflection equation: solutions and structure matrices
Energy Technology Data Exchange (ETDEWEB)
Avan, J; Zambon, C [Laboratoire de Physique Theorique et Modelisation, Universite de Cergy-Pontoise (CNRS UMR 8089), Saint-Martin 2 avenue Adolphe Chauvin, 95302 Cergy-Pontoise Cedex (France)], E-mail: avan@u-cergy.fr, E-mail: cristina.zambon@u-cergy.fr
2008-05-16
Explicit solutions of the non-constant semi-dynamical reflection equation are constructed, together with suitable parametrizations of their structure matrices. Considering the semi-dynamical reflection equation with rational non-constant Arutyunov-Chekhov-Frolov structure matrices, and a specific meromorphic ansatz, it is found that only two sets of the previously found constant solutions are extendible to the non-constant case. In order to simplify future constructions of spin-chain Hamiltonians, a parametrization procedure is applied explicitly to all elements of the semi-dynamical reflection equation available. Interesting expressions for 'twists' and R-matrices entering the parametrization procedure are found. In particular, some expressions for the R-matrices seem to appear here for the first time. In addition, a new set of consistent structure matrices for the semi-dynamical reflection equation is obtained.
Mochida, Tomoyuki; Funasako, Yusuke; Inagaki, Takashi; Li, Meng-Jiao; Asahara, Kotaro; Kuwahara, Daisuke
2013-05-10
Crystal structures and thermal properties of cobaltocenium salts with bis(perfluoroalkylsulfonyl)amide (C(n)F2(n+1)SO2)2N anions [n = 0 (1), 1 (1 a), 2 (1 b), 3 (1 c), and 4 (1 d)] and the 1,1,2,2,3,3-hexafluoropropane-1,3-disulfonylamide anion (2) were investigated. In these solids, the cations are surrounded by four anions around their C5 axis, and stacking of these local structures forms two kinds of assembled structures. In the salts with even n (1, 1 b, and 1 d), the cation and anion are arranged alternately to form mixed-stack columns in the crystal. In contrast, in the salts with odd n (1 a and 1 c), the cations and anions independently form segregated-stack columns. An odd-even effect was also observed in the sum of the phase-change entropies from crystal to melt. All of the salts exhibited phase transitions in the solid state. The phase transitions to the lowest-temperature phase in 1, 1 a, and 2 are accompanied by order-disorder of the anions and symmetry lowering of the space group, which results in the formation of an ion pair. Solid-state (13)C NMR measurements on 1 a and 1 b revealed enhanced molecular motions of the cation in the higher-temperature phases. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Theoretical Studies on Docking Dynamics and Electronic Structure in Metalloprotein Complexes
Sugiyama, Ayumu; Nishikawa, Keigo; Yamamoto, Tetsunori; Purqon, Acep; Nishikawa, Kiyoshi; Nagao, Hidemi
2007-12-01
An investigating of docking structure and dynamics between metalloprotein is interested from the viewpoint of searching the function of protein. We investigate the cytochrome c551 and azurin complexes by three computational methods, quantum mechanical calculation, docking searching algorism and molecular dynamics simulation. At first we present the docking structure of the cytochrome c551-azurin complexes expected by ZDOCK searching algorism. Quantum chemical calculation is tools to estimate the charge distrubution around the active site for each protein and force field parameters. From these parameters, we reproduce the protein docking dynamics by molecular dynamics simulation. We analyze some physical properties of complex system such as binding free energy, dynamical cross correlation map, and so on. We discuss the docking stability and dynamical effect of the cytochrome c551-azurin complexes.
Robust dynamical effects in traffic and chaotic maps on trees
Indian Academy of Sciences (India)
Bosiljka Tadić; Zoran Levnajić
2008-06-01
In the dynamic processes on networks collective effects emerge due to the couplings between nodes, where the network structure may play an important role. Interaction along many network links in the nonlinear dynamics may lead to a kind of chaotic collective behavior. Here we study two types of well-defined diffusive dynamics on scale-free trees: traffic of packets as navigated random walks, and chaotic standard maps coupled along the network links. We show that in both cases robust collective dynamic effects appear, which can be measured statistically and related to non-ergodicity of the dynamics on the network. Specifically, we find universal features in the fluctuations of time series and appropriately defined return-time statistics.
Introducing Students to Structural Dynamics and Earthquake Engineering
Anthoine, Armelle; Marazzi, Francesco; Tirelli, Daniel
2010-01-01
The European Laboratory for Structural Assessment (ELSA) is one of the world's main laboratories for seismic studies. Besides its research activities, it also aims to bring applied science closer to the public. This article describes teaching activities based on a demonstration shaking table which is used to introduce the structural dynamics of…
Structure and Dynamics of the VAULT COMPLEX
A. van Zon (Arend)
2004-01-01
textabstractVaults are the largest ribonucleoprotein particles found in eukaryotic cells. The maincomponent of these 13 MDa structures is the Mr 100,000 major vault protein (MVP).In mammalian cells, about 96 copies of this protein are necessary to form one vaultparticle. Two additional proteins are
Emergence of structured communities through evolutionary dynamics.
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.
Dynamical structure of magnetized dissipative accretion flow around black holes
Sarkar, Biplob
2016-01-01
We study the global structure of optically thin, advection dominated, magnetized accretion flow around black holes. We consider the magnetic field to be turbulent in nature and dominated by the toroidal component. With this, we obtain the complete set of accretion solutions for dissipative flows where bremsstrahlung process is regarded as the dominant cooling mechanism. We show that rotating magnetized accretion flow experiences virtual barrier around black hole due to centrifugal repulsion that can trigger the discontinuous transition of the flow variables in the form of shock waves. We examine the properties of the shock waves and find that the dynamics of the post-shock corona (PSC) is controlled by the flow parameters, namely viscosity, cooling rate and strength of the magnetic field, respectively. We separate the effective region of the parameter space for standing shock and observe that shock can form for wide range of flow parameters. We obtain the critical viscosity parameter that allows global accret...
Dynamic SU(2) structure from seven-branes
Energy Technology Data Exchange (ETDEWEB)
Heidenreich, Ben; McAllister, Liam; /Cornell U., Phys. Dept.; Torroba, Gonzalo; /SLAC /Stanford U., Phys. Dept.
2010-12-16
We obtain a family of supersymmetric solutions of type IIB supergravity with dynamic SU(2) structure, which describe the local geometry near a stack of four D7-branes and one O7-plane wrapping a rigid four-cycle. The deformation to a generalized complex geometry is interpreted as a consequence of nonperturbative effects in the seven-brane gauge theory. We formulate the problem for seven-branes wrapping the base of an appropriate del Pezzo cone, and in the near-stack limit in which the four-cycle is flat, we obtain an exact solution in closed form. Our solutions serve to characterize the local geometry of nonperturbatively-stabilized flux compactifications.
Fallah, Zohreh; Jamali, Yousef; Rafii-Tabar, Hashem
2016-01-01
Dopamine as a neurotransmitter plays a critical role in the functioning of the central nervous system. The structure of D3 receptor as a member of class A G-protein coupled receptors (GPCRs) has been reported. We used MD simulation to investigate the effect of an oscillating electric field, with frequencies in the range 0.6–800 GHz applied along the z-direction, on the dopamine-D3R complex. The simulations showed that at some frequencies, the application of an external oscillating electric field along the z-direction has a considerable effect on the dopamine-D3R. However, there is no enough evidence for prediction of changes in specific frequency, implying that there is no order in changes. Computing the correlation coefficient parameter showed that increasing the field frequency can weaken the interaction between dopamine and D3R and may decrease the Arg128{3.50}-Glu324{6.30} distance. Because of high stability of α helices along the z-direction, applying an oscillating electric field in this direction with an amplitude 10-time higher did not have a considerable effect. However, applying the oscillating field at the frequency of 0.6 GHz along other directions, such as X-Y and Y-Z planes, could change the energy between the dopamine and the D3R, and the number of internal hydrogen bonds of the protein. This can be due to the effect of the direction of the electric field vis-à-vis the ligands orientation and the interaction of the oscillating electric field with the dipole moment of the protein. PMID:27832207
λ-PDF AND GEGENBAUER POLYNOMIAL APPROXIMATION FOR DYNAMIC RESPONSE PROBLEMS OF RANDOM STRUCTURES
Institute of Scientific and Technical Information of China (English)
FANG Tong; LENG Xiaolei; MA Xiaoping; MENG Guang
2004-01-01
A bounded, mono-peak, and symmetrically distributed probability density function,called λ-PDF, together with the Gegenbauer polynomial approximation, is used in dynamic response problems of random structures. The λ-PDF can reasonably model a variety of random parameters in engineering random structures. The Gegenbauer polynomial approximation can be viewed as a new extension of the weighted residual method into the random space. Both of them can be easily used by scientists and engineers, and applied to a variety of response problems of random structures. The numerical example shows the effectiveness of the proposed method to study dynamic phenomena in random structures.
Crystal structural and diffusion property in titanium carbides: A molecular dynamics study
Lv, Yanan; Gao, Weimin
2016-09-01
Titanium carbides were studied via molecular dynamics simulation to characterize TiCx structures with respect to the carbon diffusion properties in this study. The effect of carbon concentration on atomic structures of titanium carbides was investigated through discussing the structure variation and the radial distribution functions of carbon atoms in titanium carbides. The carbon diffusion in titanium carbides was also analyzed, focusing on the dependence on carbon concentration and carbide structure. Carbon diffusivity with different carbon concentrations was determined by molecular dynamics (MD) calculations and compared with the available experimental data. The simulation results showed an atomic exchange mechanism for carbon diffusion in titanium carbide.
International Conference on Structural Nonlinear Dynamics and Diagnosis
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...
Assessing Numerical Error in Structural Dynamics Using Energy Balance
Directory of Open Access Journals (Sweden)
Rabindranath Andujar
2013-01-01
Full Text Available This work applies the variational principles of Lagrange and Hamilton to the assessment of numerical methods of linear structural analysis. Different numerical methods are used to simulate the behaviour of three structural configurations and benchmarked in their computation of the Lagrangian action integral over time. According to the principle of energy conservation, the difference at each time step between the kinetic and the strain energies must equal the work done by the external forces. By computing this difference, the degree of accuracy of each combination of numerical methods can be assessed. Moreover, it is often difficult to perceive numerical instabilities due to the inherent complexities of the modelled structures. By means of the proposed procedure, these complexities can be globally controlled and visualized in a straightforward way. The paper presents the variational principles to be considered for the collection and computation of the energy-related parameters (kinetic, strain, dissipative, and external work. It then introduces a systematic framework within which the numerical methods can be compared in a qualitative as well as in a quantitative manner. Finally, a series of numerical experiments is conducted using three simple 2D models subjected to the effect of four different dynamic loadings.
Lerbret, A; Affouard, F; Hedoux, A; Guinet, Y; Descamps, M
2007-01-01
The influence of three well-known disaccharides, namely trehalose, maltose and sucrose, on some structural and dynamical properties of lysozyme has been investigated by means of molecular dynamics computer simulations in the 37-60 wt % concentration range. The effects of sugars on the protein conformation are found relatively weak, in agreement with the preferential hydration of lysozyme. Conversely, sugars seem to increase significantly the relaxation times of the protein. These effects are shown to be correlated to the fractional solvent accessibilities of lysozyme residues and further support the slaving of protein dynamics. Moreover, a significant increase in the relaxation times of lysozyme, sugars and water molecules is observed within the studied concentration range and may result from the percolation of the hydrogen-bond network of sugar molecules. This percolation appears to be of primary importance to explain the influence of sugars on the dynamical properties of lysozyme and water.
The Hyades distance, structure, dynamics, and age
Perryman, M A C; Lebreton, Y; Gómez, A; Turon, C; De Strobel, G C; Mermilliod, J C; Robichon, N; Kovalevsky, J; Crifo, F
1997-01-01
We use absolute trigonometric parallaxes from the Hipparcos Catalogue to determine individual distances to members of the Hyades cluster, from which the 3-dimensional structure of the cluster can be derived. Inertially-referenced proper motions are used to rediscuss distance determinations based on convergent-point analyses. A combination of parallaxes and proper motions from Hipparcos, and radial velocities from ground-based observations, are used to determine the position and velocity components of candidate members with respect to the cluster centre, providing new information on cluster membership: 13 new candidate members within 20 pc of the cluster centre have been identified. Farther from the cluster centre there is a gradual merging between certain cluster members and field stars, both spatially and kinematically. Within the cluster, the kinematical structure is fully consistent with parallel space motion of the component stars with an internal velocity dispersion of about 0.3 km/s. The spatial structu...
Cosmic Voids: structure, dynamics and galaxies
van de Weygaert, Rien
2009-01-01
In this review we discuss several aspects of Cosmic Voids. Voids are a major component of the large scale distribution of matter and galaxies in the Universe. They are of instrumental importance for understanding the emergence of the Cosmic Web. Their relatively simple shape and structure makes them into useful tools for extracting the value of a variety cosmic parameters, possibly including even that of the influence of dark energy. Perhaps most promising and challenging is the issue of the galaxies found within their realm. Not only does the pristine environment of voids provide a promising testing ground for assessing the role of environment on the formation and evolution of galaxies, the dearth of dwarf galaxies may even represent a serious challenge to the standard view of cosmic structure formation.
Spatial Dynamic Structures and Mobility in Computation
Aman, Bogdan
2011-01-01
Membrane computing is a well-established and successful research field which belongs to the more general area of molecular computing. Membrane computing aims at defining parallel and non-deterministic computing models, called membrane systems or P Systems, which abstract from the functioning and structure of the cell. A membrane system consists of a spatial structure, a hierarchy of membranes which do not intersect, with a distinguishable membrane called skin surrounding all of them. A membrane without any other membranes inside is elementary, while a non-elementary membrane is a composite membrane. The membranes define demarcations between regions; for each membrane there is a unique associated region. Since we have a one-to-one correspondence, we sometimes use membrane instead of region, and vice-versa. The space outside the skin membrane is called the environment. In this thesis we define and investigate variants of systems of mobile membranes as models for molecular computing and as modelling paradigms fo...
Dynamic kirigami structures for integrated solar tracking.
Lamoureux, Aaron; Lee, Kyusang; Shlian, Matthew; Forrest, Stephen R; Shtein, Max
2015-09-08
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.
Information diversity in structure and dynamics of simulated neuronal networks.
Mäki-Marttunen, Tuomo; Aćimović, Jugoslava; Nykter, Matti; Kesseli, Juha; Ruohonen, Keijo; Yli-Harja, Olli; Linne, Marja-Leena
2011-01-01
Neuronal networks exhibit a wide diversity of structures, which contributes to the diversity of the dynamics therein. The presented work applies an information theoretic framework to simultaneously analyze structure and dynamics in neuronal networks. Information diversity within the structure and dynamics of a neuronal network is studied using the normalized compression distance. To describe the structure, a scheme for generating distance-dependent networks with identical in-degree distribution but variable strength of dependence on distance is presented. The resulting network structure classes possess differing path length and clustering coefficient distributions. In parallel, comparable realistic neuronal networks are generated with NETMORPH simulator and similar analysis is done on them. To describe the dynamics, network spike trains are simulated using different network structures and their bursting behaviors are analyzed. For the simulation of the network activity the Izhikevich model of spiking neurons is used together with the Tsodyks model of dynamical synapses. We show that the structure of the simulated neuronal networks affects the spontaneous bursting activity when measured with bursting frequency and a set of intraburst measures: the more locally connected networks produce more and longer bursts than the more random networks. The information diversity of the structure of a network is greatest in the most locally connected networks, smallest in random networks, and somewhere in between in the networks between order and disorder. As for the dynamics, the most locally connected networks and some of the in-between networks produce the most complex intraburst spike trains. The same result also holds for sparser of the two considered network densities in the case of full spike trains.
Dynamics-based Nondestructive Structural Monitoring Techniques
2012-06-21
in the practice of non- destructive evaluation ( NDE ) and structural health monitoring (SHM). Guided wave techniques have several advantages over...conventional bulk wave ultrasonic NDE /SHM techniques. Some of these advantages are outlined in Table I. However, in addition to the advantages of...PVDF transducers for SHM applications with controlled guided wave modes and frequencies [7]. Wilcox used EMATs with circular coils in a guided wave
Dynamics-based Nondestructive Structural Monitoring Teclrniques
2012-05-21
destructive evaluation ( NDE ) and structural health monitoring (SHM). Guided wave techniques have several advantages over conventional bulk wave...ultrasonic NDE /SHM techniques. Some of these advantages are outlined in Table I. However, in addition to the advantages of guided waves comes an...PVDF transducers for SHM applications with controlled guided wave modes and frequencies [7]. Wilcox used EMATs with circular coils in a guided wave
Byrne, Aaron
2015-12-24
Ab initio, density functional theory (DFT)-based molecular dynamics (MD) has been carried out to investigate the effect of explicit solvation on the dynamical and structural properties of a [bmim][NTf2] room-temperature ionic liquid (RTIL), solvating a N719 sensitizing dye adsorbed onto an anatase titania (101) surface. The effect of explicit dispersion on the properties of this dye-sensitized solar cell (DSC) interface has also been studied. Upon inclusion of dispersion interactions in simulations of the solvated system, the average separation between the cations and anions decreases by 0.6 Å; the mean distance between the cations and the surface decreases by about 0.5 Å; and the layering of the RTIL is significantly altered in the first layer surrounding the dye, with the cation being on average 1.5 Å further from the center of the dye. Inclusion of dispersion effects when a solvent is not explicitly included (to dampen longer-range interactions) can result in unphysical "kinking" of the adsorbed dye\\'s configuration. The inclusion of solvent shifts the HOMO and LUMO levels of the titania surface by +3 eV. At this interface, the interplay between the effects of dispersion and solvation combines in ways that are often subtle, such as enhancement or inhibition of specific vibrational modes. © 2015 American Chemical Society.
Dynamic Response of Concrete and Concrete Structures.
1986-05-30
Strain Rate Effects on Fracture (ed. S. Mindess and S. P. Shah), Symposium ’- S, Boston, Dec. 1985, Materials Research Society Symp. Proceedings, ". Vol...Reinforced Concrete Subjected to Impact Loading," in Cement-Based Composites: Strain-Rate Effects on Fracture (ed. S. Mindess and S.P. Shah) Materials
Hyperbolic Structures and the Stickiness Effect
Institute of Scientific and Technical Information of China (English)
周济林; 周礼勇; 孙义燧
2002-01-01
The stickiness effect of invariant tori in the phase space is widely studied, and extended to the slow-down of orbital diffusion due to some other invariant sets, such as Cantori, island-chains and hyperbolic periodic orbits.We report on two models in which hyperbolic periodic orbits show the stickiness effect. We discuss the generalized stickiness effects caused by different invariant sets. We believe that the main cause of the generalized stickiness effects is the hyperbolic structures in the phase space of the dynamical systems.
Structural Optimization of Machine Gun Based on Dynamic Stability Concept
Institute of Scientific and Technical Information of China (English)
LI Yong-jian; WANG Rui-lin; ZHANG Ben-jun
2008-01-01
Improving the firing accuracy is a final goal of structural optimization of machine guns. The main factors which affect the dispersion accuracy of machine gun are analyzed. Based on the concept of dynamic stability, a structural optimization model is built up, and the sensitivity of dispersion accuracy to design variables is analyzed. The optimization results of a type of machine gun show that the method is valid, feasible, and can be used as a guide to the structural optimization of other automatic weapons.
On the use of Stockwell transform in structural dynamic analysis
Indian Academy of Sciences (India)
H Serdar Kuyuk
2015-02-01
Time-frequency analysis of earthquake records using Fourier transform is a fundamental, reliable and useful tool in earthquake engineering and engineering seismology. It will be however no longer functional if the frequency variation is analysed in time domain. Short time Fourier transform is utilized for the same purpose but this has also its own limitations and restrictions. In this research, Stockwell transform (S-transform), is evaluated in investigating frequency content of signal in time domain. First, the effectiveness of S-transform was tested by a non-stationary synthetic signal series with a sum of various instantaneous time varying frequency functions. Then, transform was employed to three different earthquake waveforms of Iwate-Miyagi Nairiku earthquake (Mw 6.9, 2008); recorded in near, moderate and far sites. Finally, an application was demonstrated for determining dynamic response of three-story frame structure by using El Centro earthquake compiled with harmonic motion. Unlike widely used continuous wavelet transform, which provides temporal and spectral information simultaneously, S-transform is very straightforward and easy to manipulate for interpretations. All cases considered in this research showed that Stransform can be implemented for further research activities related with frequencydependent strong motion analysis by practitioners and engineers. S-transform can distinguish abrupt frequency changes in structures effectively and accurately.
Z-ring Structure and Constriction Dynamics in E. coli
Directory of Open Access Journals (Sweden)
Pramod Kumar
2017-09-01
Full Text Available The Z-ring plays a central role in bacterial division. It consists of FtsZ filaments, but the way these reorganize in the ring-like structure during septation remains largely unknown. Here, we measure the effective constriction dynamics of the ring. Using an oscillating optical trap, we can switch individual rod-shaped E. coli cells between horizontal and vertical orientations. In the vertical orientation, the fluorescent Z-ring image appears as a symmetric circular structure that renders itself to quantitative analysis. In the horizontal orientation, we use phase-contrast imaging to determine the extent of the cell constriction and obtain the effective time of division. We find evidence that the Z-ring constricts at a faster rate than the cell envelope such that its radial width (inwards from the cytoplasmic membrane grows during septation. In this respect, our results differ from those recently obtained using photoactivated localization microscopy (PALM where the radial width of the Z-ring was found to be approximately constant as the ring constricts. A possible reason for the different behavior of the constricting Z-rings could be the significant difference in the corresponding cell growth rates.
Nonlocalized cluster dynamics and nuclear molecular structure
Zhou, Bo; Horiuchi, Hisashi; Ren, Zhongzhou; Röpke, Gerd; Schuck, Peter; Tohsaki, Akihiro; Xu, Chang; Yamada, Taiichi
2013-01-01
A container picture is proposed for understanding cluster dynamics where the clusters make nonlocalized motion occupying the lowest orbit of the cluster mean-field potential characterized by the size parameter $``B"$ in the THSR (Tohsaki-Horiuchi-Schuck-R\\"{o}pke) wave function. The nonlocalized cluster aspects of the inversion-doublet bands in $^{20}$Ne which have been considered as a typical manifestation of localized clustering are discussed. So far unexplained puzzling features of the THSR wave function, namely that after angular-momentum projection for two cluster systems the prolate THSR wave function is almost 100$\\%$ equivalent to an oblate THSR wave function is clarified. It is shown that the true intrinsic two-cluster THSR configuration is nonetheless prolate. The proposal of the container picture is based on the fact that typical cluster systems, 2$\\alpha$, 3$\\alpha$, and $\\alpha$+$^{16}$O, are all well described by a single THSR wave function. It will be shown for the case of linear-chain states w...
Linking extinction-colonization dynamics to genetic structure in a salamander metapopulation.
Cosentino, Bradley J; Phillips, Christopher A; Schooley, Robert L; Lowe, Winsor H; Douglas, Marlis R
2012-04-22
Theory predicts that founder effects have a primary role in determining metapopulation genetic structure. However, ecological factors that affect extinction-colonization dynamics may also create spatial variation in the strength of genetic drift and migration. We tested the hypothesis that ecological factors underlying extinction-colonization dynamics influenced the genetic structure of a tiger salamander (Ambystoma tigrinum) metapopulation. We used empirical data on metapopulation dynamics to make a priori predictions about the effects of population age and ecological factors on genetic diversity and divergence among 41 populations. Metapopulation dynamics of A. tigrinum depended on wetland area, connectivity and presence of predatory fish. We found that newly colonized populations were more genetically differentiated than established populations, suggesting that founder effects influenced genetic structure. However, ecological drivers of metapopulation dynamics were more important than age in predicting genetic structure. Consistent with demographic predictions from metapopulation theory, genetic diversity and divergence depended on wetland area and connectivity. Divergence was greatest in small, isolated wetlands where genetic diversity was low. Our results show that ecological factors underlying metapopulation dynamics can be key determinants of spatial genetic structure, and that habitat area and isolation may mediate the contributions of drift and migration to divergence and evolution in local populations.
DYNAMIC EFFECTIVE SHEAR STRENGTH OF SATURATED SAND
Institute of Scientific and Technical Information of China (English)
邵生俊; 谢定义
2002-01-01
The dynamic effective shear strength of saturated sand under cyclic loading is discussed in this paper. The discussion includes the transient time dependency behaviors based on the analysis of the results obtained in conventional cyclic triaxial tests and cyclic torsional shear triaxial tests. It has been found that the dynamic effective shear strength is composed of effective frictional resistance and viscous resistance, which are characterized by the strain rate dependent feature of strength magnitude, the coupling of consolidation stress with cyclic stress and the dependency of time needed to make the soil strength suffciently mobilized, and can also be expressed by the extended Mohr-Coulomb's law. The two strength parameters of the dynamic effective internal frictional angle φd and the dynamic viscosity coefficient η are determined. The former is unvaried for different number of cyclic loading, dynamic stress form and consolidation stress ratio. And the later is unvaried for the different dynamic shear strain rate γt developed during the sand liquefaction, but increases with the increase of initial density of sand. The generalization of dynamic effective stress strength criterion in the 3-dimensional effective stress space is studied in detail for the purpose of its practical use.
Dynamics in Sequence Space for RNA Secondary Structure Design.
Matthies, Marco C; Bienert, Stefan; Torda, Andrew E
2012-10-01
We have implemented a method for the design of RNA sequences that should fold to arbitrary secondary structures. A popular energy model allows one to take the derivative with respect to composition, which can then be interpreted as a force and used for Newtonian dynamics in sequence space. Combined with a negative design term, one can rapidly sample sequences which are compatible with a desired secondary structure via simulated annealing. Results for 360 structures were compared with those from another nucleic acid design program using measures such as the probability of the target structure and an ensemble-weighted distance to the target structure.
Structure and Dynamics of the Interstellar Medium
Tenorio-Tagle, Guillermo; Moles, Mariano; Melnick, Jorge
Here for the first time is a book that treats practically all aspects of modern research in interstellar matter astrophysics. 20 review articles and 40 carefully selected and refereed papers give a thorough overview of the field and convey the flavor of enthusiastic colloquium discussions to the reader. The book includes sections on: - Molecular clouds, star formation and HII regions - Mechanical energy sources - Discs, outflows, jets and HH objects - The Orion Nebula - The extragalactic interstellar medium - Interstellar matter at high galactic latitudes - The structure of the interstellar medium
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 antiferromagneti...... alpha-Fe2O3. In the inelastic case we make use of the fact that we can study both the superparamagnetic relaxation and collective magnetic excitations of the whole particle moment at the antiferromagnetic Bragg positions. (C) 2000 Elsevier Science B.V. All rights reserved....
Schwinger's Dynamical Casimir Effect Bulk Energy Contribution
Carlson, C E; Pérez-Mercader, J; Visser, M; Carlson, C E; Carlson, Carl E.; Molina-Paris, Carmen; Perez-Mercader, Juan; Visser, Matt
1997-01-01
Schwinger's Dynamical Casimir Effect is one of several candidate explanations for sonoluminescence. Recently, several papers have claimed that Schwinger's estimate of the Casimir energy involved is grossly inaccurate. In this letter, we show that these calculations omit the crucial volume term. When the missing term is correctly included one finds full agreement with Schwinger's result for the Dynamical Casimir Effect. We have nothing new to say about sonoluminescence itself except to affirm that the Casimir effect is energetically adequate as a candidate explanation. Schwinger's Dynamical Casimir Effect is one of several candidate explanations for sonoluminescence. Recently, several papers have claimed that Schwinger's estimate of the Casimir energy involved is grossly inaccurate. In this letter, we show that these calculations omit the crucial volume term. When the missing term is correctly included one finds full agreement with Schwinger's result for the Dynamical Casimir Effect. We have nothing new to say...
Structure and Dynamics of Dinucleosomes Assessed by Atomic Force Microscopy
Directory of Open Access Journals (Sweden)
Nina A. Filenko
2012-01-01
Full Text Available Dynamics of nucleosomes and their interactions are important for understanding the mechanism of chromatin assembly. Internucleosomal interaction is required for the formation of higher-order chromatin structures. Although H1 histone is critically involved in the process of chromatin assembly, direct internucleosomal interactions contribute to this process as well. To characterize the interactions of nucleosomes within the nucleosome array, we designed a dinucleosome and performed direct AFM imaging. The analysis of the AFM data showed dinucleosomes are very dynamic systems, enabling the nucleosomes to move in a broad range along the DNA template. Di-nucleosomes in close proximity were observed, but their population was low. The use of the zwitterionic detergent, CHAPS, increased the dynamic range of the di-nucleosome, facilitating the formation of tight di-nucleosomes. The role of CHAPS and similar natural products in chromatin structure and dynamics is also discussed.
Dynamic Effects of Diabatization in Distillation Columns
DEFF Research Database (Denmark)
Bisgaard, Thomas; Huusom, Jakob Kjøbsted; Abildskov, Jens
2012-01-01
The dynamic eects of diabatization in distillation columns are investigated in simulation with primary focus on the heat-integrated distillation column (HIDiC). A generic, dynamic, rst-principle model has been formulated, which is exible to describe various diabatic distillation congurations....... Dynamic Relative Gain Array and Singular Value Analysis have been applied in a comparative study of a conventional distillation column and a HIDiC. The study showed increased input-output coupling due to diabatization. Feasible SISO control structures for the HIDiC were also found. Control...
Intrinsically disordered proteins: structural and functional dynamics
Directory of Open Access Journals (Sweden)
Wallin S
2017-02-01
Full Text Available Stefan Wallin Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John’s, NL, Canada Abstract: The classical view holds that proteins fold into essentially unique three-dimensional structures before becoming biologically active. However, studies over the last several years have provided broad and convincing evidence that some proteins do not adopt a single structure and yet are fully functional. These intrinsically disordered proteins (IDPs have been found to be highly prevalent in many genomes, including human, and play key roles in central cellular processes, such as regulation of transcription and translation, cell cycle, and cell signaling. Moreover, IDPs are overrepresented among proteins implicated in disease, including various cancers and neurodegenerative disorders. Intense efforts, by using both experimental and computational approaches, are consequently under way to uncover the molecular mechanisms that underpin the roles of IDPs in biology and disease. This review provides an introduction to the general biophysical properties of IDPs and discusses some of the recent emerging areas in IDP research, including the roles of IDPs in allosteric regulation, regulatory unfolding, and formation of intracellular membrane-less organelles. In addition, recent attempts at therapeutic targeting of IDPs by small molecules, noting in particular that IDPs represent a potentially important source of new drug targets in light of their central role in protein–protein interaction networks, are also reviewed. Keywords: natively unfolded proteins, unstructured proteins, protein folding, protein–protein interaction, cell regulation, signaling, drug development, inhibitors
Ab initio theory for ultrafast magnetization dynamics with a dynamic band structure
Mueller, B. Y.; Haag, M.; Fähnle, M.
2016-09-01
Laser-induced modifications of magnetic materials on very small spatial dimensions and ultrashort timescales are a promising field for novel storage and spintronic devices. Therefore, the contribution of electron-electron spin-flip scattering to the ultrafast demagnetization of ferromagnets after an ultrashort laser excitation is investigated. In this work, the dynamical change of the band structure resulting from the change of the magnetization in time is taken into account on an ab initio level. We find a large influence of the dynamical band structure on the magnetization dynamics and we illustrate the thermalization and relaxation process after laser irradiation. Treating the dynamical band structure yields a demagnetization comparable to the experimental one.
Wdowik, U. D.; Piekarz, P.; Legut, D.; Jagło, G.
2016-08-01
Uranium monocarbide, a potential fuel material for the generation IV reactors, is investigated within density functional theory. Its electronic, magnetic, elastic, and phonon properties are analyzed and discussed in terms of spin-orbit interaction and localized versus itinerant behavior of the 5 f electrons. The localization of the 5 f states is tuned by varying the local Coulomb repulsion interaction parameter. We demonstrate that the theoretical electronic structure, elastic constants, phonon dispersions, and their densities of states can reproduce accurately the results of x-ray photoemission and bremsstrahlung isochromat measurements as well as inelastic neutron scattering experiments only when the 5 f states experience the spin-orbit interaction and simultaneously remain partially localized. The partial localization of the 5 f electrons could be represented by a moderate value of the on-site Coulomb interaction parameter of about 2 eV. The results of the present studies indicate that both strong electron correlations and spin-orbit effects are crucial for realistic theoretical description of the ground-state properties of uranium carbide.
Structure and conformational dynamics of scaffolded DNA origami nanoparticles.
Pan, Keyao; Bricker, William P; Ratanalert, Sakul; Bathe, Mark
2017-06-20
Synthetic DNA is a highly programmable nanoscale material that can be designed to self-assemble into 3D structures that are fully determined by underlying Watson-Crick base pairing. The double crossover (DX) design motif has demonstrated versatility in synthesizing arbitrary DNA nanoparticles on the 5-100 nm scale for diverse applications in biotechnology. Prior computational investigations of these assemblies include all-atom and coarse-grained modeling, but modeling their conformational dynamics remains challenging due to their long relaxation times and associated computational cost. We apply all-atom molecular dynamics and coarse-grained finite element modeling to DX-based nanoparticles to elucidate their fine-scale and global conformational structure and dynamics. We use our coarse-grained model with a set of secondary structural motifs to predict the equilibrium solution structures of 45 DX-based DNA origami nanoparticles including a tetrahedron, octahedron, icosahedron, cuboctahedron and reinforced cube. Coarse-grained models are compared with 3D cryo-electron microscopy density maps for these five DNA nanoparticles and with all-atom molecular dynamics simulations for the tetrahedron and octahedron. Our results elucidate non-intuitive atomic-level structural details of DX-based DNA nanoparticles, and offer a general framework for efficient computational prediction of global and local structural and mechanical properties of DX-based assemblies that are inaccessible to all-atom based models alone. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
Ab initio lattice dynamics of complex structures
DEFF Research Database (Denmark)
Voss, Johannes
2008-01-01
systems in particular. A more detailed analysis of the phonon spectrum has been performed for the compound Mg(BH4)2, where several crystal symmetries have been proposed theoretically and experimentally. By means of an analysis of the instabilities of these structures, a new, stable phase has been......In this thesis, density functional theory is applied in a study of thermodynamic properties of so-called complex metal hydrides, which are promising materials for hydrogen storage applications. Since the unit cells of these crystals can be relatively large with many symmetrically inequivalent...... determined. Aiming at finding scaling relationships between alloy stabilities and computationally inexpensive properties, the stabilities of cation-alloyed metal aluminum hexahydrides have been studied. The analysis shows that charge density symmetries are correlated to the stability. In addition...
Fundamental structures of dynamic social networks
DEFF Research Database (Denmark)
Sekara, Vedran; Stopczynski, Arkadiusz; Jørgensen, Sune Lehmann
2016-01-01
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...... a pattern of recurring meetings across weeks and months, each with varying degrees of regularity. Taken together, these findings provide a powerful simplification of the social network, where cores represent fundamental structures expressed with strong temporal and spatial regularity. Using this framework......, we explore the complex interplay between social and geospatial behavior, documenting how the formation of cores is preceded by coordination behavior in the communication networks and demonstrating that social behavior can be predicted with high precision....
In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.
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.
Multiscale simulation of microbe structure and dynamics.
Joshi, Harshad; Singharoy, Abhishek; Sereda, Yuriy V; Cheluvaraja, Srinath C; Ortoleva, Peter J
2011-10-01
A multiscale mathematical and computational approach is developed that captures the hierarchical organization of a microbe. It is found that a natural perspective for understanding a microbe is in terms of a hierarchy of variables at various levels of resolution. This hierarchy starts with the N -atom description and terminates with order parameters characterizing a whole microbe. This conceptual framework is used to guide the analysis of the Liouville equation for the probability density of the positions and momenta of the N atoms constituting the microbe and its environment. Using multiscale mathematical techniques, we derive equations for the co-evolution of the order parameters and the probability density of the N-atom state. This approach yields a rigorous way to transfer information between variables on different space-time scales. It elucidates the interplay between equilibrium and far-from-equilibrium processes underlying microbial behavior. It also provides framework for using coarse-grained nanocharacterization data to guide microbial simulation. It enables a methodical search for free-energy minimizing structures, many of which are typically supported by the set of macromolecules and membranes constituting a given microbe. This suite of capabilities provides a natural framework for arriving at a fundamental understanding of microbial behavior, the analysis of nanocharacterization data, and the computer-aided design of nanostructures for biotechnical and medical purposes. Selected features of the methodology are demonstrated using our multiscale bionanosystem simulator DeductiveMultiscaleSimulator. Systems used to demonstrate the approach are structural transitions in the cowpea chlorotic mosaic virus, RNA of satellite tobacco mosaic virus, virus-like particles related to human papillomavirus, and iron-binding protein lactoferrin.
Structure and dynamics of core-periphery networks
Csermely, Peter; Wu, Ling-Yun; Uzzi, Brian
2013-01-01
Recent studies uncovered important core/periphery network structures characterizing complex sets of cooperative and competitive interactions between network nodes, be they proteins, cells, species or humans. Better characterization of the structure, dynamics and function of core/periphery networks is a key step of our understanding cellular functions, species adaptation, social and market changes. Here we summarize the current knowledge of the structure and dynamics of "traditional" core/periphery networks, rich-clubs, nested, bow-tie and onion networks. Comparing core/periphery structures with network modules, we discriminate between global and local cores. The core/periphery network organization lies in the middle of several extreme properties, such as random/condensed structures, clique/star configurations, network symmetry/asymmetry, network assortativity/disassortativity, as well as network hierarchy/anti-hierarchy. These properties of high complexity together with the large degeneracy of core pathways e...
Dynamics of a bistable Miura-origami structure
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.
Stabilization of structure-preserving power networks with market dynamics
Stegink, Tjerk W; van der Schaft, Arjan J
2016-01-01
This paper studies the problem of maximizing the social welfare while stabilizing both the physical power network as well as the market dynamics. For the physical power grid a third-order structure-preserving model is considered involving both frequency and voltage dynamics. By applying the primal-dual gradient method to the social welfare problem, a distributed dynamic pricing algorithm in port-Hamiltonian form is obtained. After interconnection with the physical system a closed-loop port-Hamiltonian system of differential-algebraic equations is obtained, whose properties are exploited to prove local asymptotic stability of the optimal points.
Accelerating Dynamic Cardiac MR Imaging Using Structured Sparse Representation
Directory of Open Access Journals (Sweden)
Nian Cai
2013-01-01
Full Text Available Compressed sensing (CS has produced promising results on dynamic cardiac MR imaging by exploiting the sparsity in image series. In this paper, we propose a new method to improve the CS reconstruction for dynamic cardiac MRI based on the theory of structured sparse representation. The proposed method user the PCA subdictionaries for adaptive sparse representation and suppresses the sparse coding noise to obtain good reconstructions. An accelerated iterative shrinkage algorithm is used to solve the optimization problem and achieve a fast convergence rate. Experimental results demonstrate that the proposed method improves the reconstruction quality of dynamic cardiac cine MRI over the state-of-the-art CS method.
Cluster structure and dynamics in gels and glasses
Pastore, R.; de Candia, A.; Fierro, A.; Pica Ciamarra, M.; Coniglio, A.
2016-07-01
The dynamical arrest of gels is the consequence of a well defined structural phase transition, leading to the formation of a spanning cluster of bonded particles. The glass transition, instead, is not accompanied by any clear structural signature. Nevertheless, both transitions are characterized by the emergence of dynamical heterogeneities. Reviewing recent results from numerical simulations, we discuss the behavior of dynamical heterogeneities in different systems and show that a clear connection with the structure exists in the case of gels. The emerging picture may also be relevant for the more elusive case of glasses. We show, as an example, that the relaxation process of a simple glass-forming model can be related to a reverse percolation transition and discuss further perspective in this direction.
Fluid Dynamic - Structural Interactions of Labyrinth Seals.
1986-08-01
Linear rotor speeds comparable with the axial gap flow velocity, i.e., of the order of 100 m/sec. (d) Provision for controllable inlet flow swirl with...34Experimental Determination of Gap Flow -Conditioned Forces at Turbine Stages and Their Effect on the Running Stability of Simple Rotors". NASA TM
An Aspect of Dynamic Human-structure Interaction
DEFF Research Database (Denmark)
Pedersen, Lars
2008-01-01
. Focus is on how modal characteristics of the structure, i.e. its frequency and damping, are influenced by the presence of stationary humans. Vertical vibrations are considered, and particular focus is given the influence of human posture on modal characteristics of the supporting structure. Insight......It is known that humans and structures interact. Humans can cause structures to vibrate, and excessive vibrations may occur if the motion frequency of humans coincides with a resonant frequency of the structural system. It is also known that stationary humans (such as humans sitting or standing...... on the structure) influence the dynamic behaviour and modal characteristics of the structure carrying them, whether being a grandstand, an office floor or similar. However, the interaction between the stationary humans and the structure is generally not well understood, and the paper addresses this interaction...
Fluid dynamic effects on staphylococci bacteria biofilms
Sherman, Erica; Bayles, Kenneth; Endres, Jennifer; Wei, Timothy
2016-11-01
Staphylococcus aureus bacteria are able to form biofilms and distinctive tower structures that facilitate their ability to tolerate treatment and to spread within the human body. The formation of towers, which break off, get carried downstream and serve to initiate biofilms in other parts of the body are of particular interest here. It is known that flow conditions play a role in the development, dispersion and propagation of biofilms in general. The influence of flow on tower formation, however, is not at all understood. This work is focused on the effect of applied shear on tower development. The hypothesis being examined is that tower structures form within a specific range of shear stresses and that there is an as yet ill defined fluid dynamic phenomenon that occurs hours before a tower forms. In this study, a range of shear stresses is examined that brackets 0.6 dynes/cm2, the nominal shear stress where towers seem most likely to form. This talk will include µPTV measurements and cell density data indicating variations in flow and biofilm evolution as a function of the applied shear. Causal relations between flow and biofilm development will be discussed.
Modeling dynamic effects of promotion on interpurchase times
D. Fok (Dennis); R. Paap (Richard); Ph.H.B.F. Franses (Philip Hans)
2002-01-01
textabstractIn this paper we put forward a duration model to analyze the dynamic effects of marketing-mix variables on interpurchase times. We extend the accelerated failure-time model with an autoregressive structure. An important feature of our model is that it allows for different long-run and
Modeling dynamic effects of promotion on interpurchase times
D. Fok (Dennis); R. Paap (Richard); Ph.H.B.F. Franses (Philip Hans)
2002-01-01
textabstractIn this paper we put forward a duration model to analyze the dynamic effects of marketing-mix variables on interpurchase times. We extend the accelerated failure-time model with an autoregressive structure. An important feature of our model is that it allows for different long-run and
A Contribution to Documenting and Validating Dynamic Interaction Effects
DEFF Research Database (Denmark)
Pedersen, Lars
2007-01-01
On structures carrying humans (e.g. floors, grandstands in stadia etc.) there may be two different types of crowds present: Active and passive crowds of people. The active crowd, comprising people in motion, may generate dynamic loads causing the structure to vibrate. The passive (stationary) crowd....... Controlled laboratory tests, employing a vibrating test floor carrying stationary crowds of people, are designed and carried out to investigate the dynamic interaction. The paper describes the tests and the modal identification procedures employed for the assessment of model validity. Besides from aspects...... and a floor in vertical motion. The mechanism of crowd-structure interaction is not well understood and the primary aim of the paper is to present results of experimental investigations documenting effects of crowd-structure interaction and to exploring the validity of a crowd-structure interaction model...
On Natural Genetic Engineering: Structural Dynamism in Random Boolean Networks
Bull, Larry
2012-01-01
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include changes in node connectivity based upon the current cell state, e.g., via transposable elements. The underlying behaviour of the resulting dynamical networks is investigated before their evolvability is explored using a version of the NK model of fitness landscapes. Structural dynamism is found to be selected for in non-stationary environments and subsequently shown capable of providing a mechanism for evolutionary innovation when such reorganizations are inherited.
Sensitivity analysis of asphalt-pavement structure dynamic responses under heavy load
Directory of Open Access Journals (Sweden)
ZHANG Lijuan
2015-04-01
Full Text Available With the 3-Dimensional finite-element dynamic model,the influence of axis-load,axis-speed,and pavement structure parameters on dynamic performance of pavement structure is studied.The results show that with the increase in load,the dynamic response of pavement is nearly proportional to axis-load and increases noticeably;Axis-speed influences the dynamic response to some extent.With the increase of axis-speed,dynamic response of pavement structure increases firstly.With axis-speed further increasing,dynamic response of pavement structure then decreases gradually.For fatigue failure,the influence of heavy-load with common moving speed is much greater than that of static load.Among the pavement structure parameters,thickness of surface-layer has a significant effect on shear stress and the compression stress at road surface.Subgrade modulus has a significant effect on road surface deflection,tensile stress at the bottom of subbase,and compression-strain at the top of subgrade.
A Structural Dynamics Approach to the Simulation of Spacecraft Control/Structure Interaction
Young, J. W.
1985-01-01
A relatively simple approach to the analysis of linear spacecraft control/structure interaction problems is presented. The approach uses a commercially available structural system dynamic analysis package for both controller and plant dynamics, thus obviating the need to transfer data between separate programs. The unilateral coupling between components in the control system block diagram is simulated using sparse matrix stiffness and damping elements available in the structural dynamic code. The approach is illustrated with a series of simple tutorial examples of a rigid spacecraft core with flexible appendages.
Dynamic test and finite element model updating of bridge structures based on ambient vibration
Institute of Scientific and Technical Information of China (English)
2008-01-01
The dynamic characteristics of bridge structures are the basis of structural dynamic response and seismic analysis,and are also an important target of health condition monitoring.In this paper,a three-dimensional finite-element model is first established for a highway bridge over a railroad on No.312 National Highway.Based on design drawings,the dynamic characteristics of the bridge are studied using finite element analysis and ambient vibration measurements.Thus,a set of data is selected based on sensitivity analysis and optimization theory;the finite element model of the bridge is updated.The numerical and experimental results show that the updated method is more simple and effective,the updated finite element model can reflect the dynamic characteristics of the bridge better,and it can be used to predict the dynamic response under complex external forces.It is also helpful for further damage identification and health condition monitoring.
Dynamical mean field theory-based electronic structure calculations for correlated materials.
Biermann, Silke
2014-01-01
We give an introduction to dynamical mean field approaches to correlated materials. Starting from the concept of electronic correlation, we explain why a theoretical description of correlations in spectroscopic properties needs to go beyond the single-particle picture of band theory.We discuss the main ideas of dynamical mean field theory and its use within realistic electronic structure calculations, illustrated by examples of transition metals, transition metal oxides, and rare-earth compounds. Finally, we summarise recent progress on the calculation of effective Hubbard interactions and the description of dynamical screening effects in solids.
Structure and dynamics of stock market in times of crisis
Zhao, Longfeng; Li, Wei; Cai, Xu
2016-02-01
Daily correlations among 322 S&P 500 constituent stocks are investigated by means of correlation-based (CB) network. By using the heterogeneous time scales, we identify global expansion and local clustering market behaviors during crises, which are mainly caused by community splits and inter-sector edge number decreases. The CB networks display distinctive community and sector structures. Graph edit distance is applied to capturing the dynamics of CB networks in which drastic structure reconfigurations can be observed during crisis periods. Edge statistics reveal the power-law nature of edges' duration time distribution. Despite the networks' strong structural changes during crises, we still find some long-duration edges that serve as the backbone of the stock market. Finally the dynamical change of network structure has shown its capability in predicting the implied volatility index (VIX).
A compact data structure for representing a dynamic multiset
DEFF Research Database (Denmark)
Katajainen, Jyrki; Rao, S. Srinivasa
2010-01-01
We develop a data structure for maintaining a dynamic multiset that uses O(nlglgn/lgn) bits and O(1) words, in addition to the space required by the n elements stored, supports searches in O(lgn) worst-case time and updates in O(lgn) amortized time. Compared to earlier data structures, we improve...... the space requirements from O(n) bits to O(nlglgn/lgn) bits, but the running time of updates is amortized, not worst-case. © 2010 Elsevier B.V. All rights reserved.......We develop a data structure for maintaining a dynamic multiset that uses O(nlglgn/lgn) bits and O(1) words, in addition to the space required by the n elements stored, supports searches in O(lgn) worst-case time and updates in O(lgn) amortized time. Compared to earlier data structures, we improve...
Synchronization in dynamical networks with unconstrained structure switching
del Genio, Charo I; Criado, Regino; Boccaletti, Stefano
2015-01-01
We provide a rigorous solution to the problem of constructing a structural evolution for a network of coupled identical dynamical units that switches between specified topologies without constraints on their structure. The evolution of the structure is determined indirectly, from a carefully built transformation of the eigenvector matrices of the coupling Laplacians, which are guaranteed to change smoothly in time. In turn, this allows to extend the Master Stability Function formalism, which can be used to assess the stability of a synchronized state. This approach is independent from the particular topologies that the network visits, and is not restricted to commuting structures. Also, it does not depend on the time scale of the evolution, which can be faster than, comparable to, or even secular with respect to the the dynamics of the units.
Connectivity, dynamics, and structure in a tetrahedral network liquid.
Roldán-Vargas, Sándalo; Rovigatti, Lorenzo; Sciortino, Francesco
2017-01-04
We report a detailed computational study by Brownian dynamics simulations of the structure and dynamics of a liquid of patchy particles which forms an amorphous tetrahedral network upon decreasing the temperature. The highly directional particle interactions allow us to investigate the system connectivity by discriminating the total set of particles into different populations according to a penta-modal distribution of bonds per particle. With this methodology we show how the particle bonding process is not randomly independent but it manifests clear bond correlations at low temperatures. We further explore the dynamics of the system in real space and establish a clear relation between particle mobility and particle connectivity. In particular, we provide evidence of anomalous diffusion at low temperatures and reveal how the dynamics is affected by the short-time hopping motion of the weakly bounded particles. Finally we widely investigate the dynamics and structure of the system in Fourier space and identify two quantitatively similar length scales, one dynamic and the other static, which increase upon cooling the system and reach distances of the order of few particle diameters. We summarize our findings in a qualitative picture where the low temperature regime of the viscoelastic liquid is understood in terms of an evolving network of long time metastable cooperative domains of particles.
Excitonic dynamical Franz-Keldysh effect
DEFF Research Database (Denmark)
Nordstrøm, K.B.; Johnsen, Kristinn; Allen, S.J.
1998-01-01
The dynamical Franz-Keldysh effect is exposed by exploring near-band-gap absorption in the presence of intense THz electric fields. It bridges the gap between the de Franz-Keldysh effect and multiphoton absorption and competes with the THz ac Stark effect in shifting the energy of the excitonic...... resonance. A theoretical model which includes the strong THz field nonperturbatively via a nonequilibrium Green functions technique is able to describe the dynamical Franz-Keldysh effect in the presence of excitonic absorption....