Redox induced switching dynamics of a three colour electrochromic metallopolymer film
Energy Technology Data Exchange (ETDEWEB)
Zeng Qiang; McNally, Andrea; Keyes, Tia E. [National Centre for Sensor Research, Biomedical Diagnostics Institute, School of Chemical Sciences, Dublin City University, Dublin 9 (Ireland); Forster, Robert J. [National Centre for Sensor Research, Biomedical Diagnostics Institute, School of Chemical Sciences, Dublin City University, Dublin 9 (Ireland)], E-mail: robert.forster@dcu.ie
2008-10-15
Thin films of a novel Ru-phenolate based metallopolymer, [Ru(terpy)(box)PVP{sub 20}]PF{sub 6}, in which one in every twenty of the 4-vinyl pyridine monomer units is labelled with the ruthenium complex have been formed on glassy carbon electrodes, terpy is 2,2':6',2''-terpyridine, box is 2-(2-hydroxyphenyl)benzoxazole, and PVP is poly(4-vinylpyridine). Cyclic voltammetry and Raman spectroscopy reveal that the Ru{sup 2+/3+} couple is electrochemically reversible but that the phenolate ligand based oxidation is irreversible. These redox processes are associated with reversible colour changes from wine red (reduced) to red orange (mixed composition) then to light green (oxidized) in the visible region and an irreversible change in the near-IR region, respectively. Scanning electron microscopy reveals that repeated switching in LiClO{sub 4} aqueous solution does not induce any significant structural change within the deposit films. Cyclic voltammetry has been used to determine the electrochromic switching rate under semi-infinite linear diffusion conditions. In aqueous LiClO{sub 4}, the homogeneous charge transport diffusion coefficient, D{sub CT}, decreases from 3.6 {+-} 0.3 x 10{sup -13} to 2.7 {+-} 0.2 x 10{sup -13} cm{sup 2} s{sup -1} as the LiClO{sub 4} concentration increases from 0.1 to 1.0 M. This weak dependence of D{sub CT} on electrolyte concentration suggests that counterion availability is not rate-determining and that the overall rate of charge transport through the metallopolymer film is limited by the rate of segmental polymer chain motion necessary to bring adjacent centres sufficiently close to allow electron transfer to occur. Also the impact of changing the identity of the charge compensating anion of the redox electrochromic switching rate has been investigated. Finally, the electronic conductivity has been determined using interdigitated array electrodes (IDAs)
Redox induced switching dynamics of a three colour electrochromic metallopolymer film
Energy Technology Data Exchange (ETDEWEB)
Zeng, Qiang; McNally, Andrea; Keyes, Tia E.; Forster, Robert J. [National Centre for Sensor Research, Biomedical Diagnostics Institute, School of Chemical Sciences, Dublin City University, Dublin 9 (Ireland)
2008-10-15
Thin films of a novel Ru-phenolate based metallopolymer, [Ru(terpy)(box)PVP{sub 20}]PF{sub 6}, in which one in every twenty of the 4-vinyl pyridine monomer units is labelled with the ruthenium complex have been formed on glassy carbon electrodes, terpy is 2,2':6',2''-terpyridine, box is 2-(2-hydroxyphenyl)benzoxazole, and PVP is poly(4-vinylpyridine). Cyclic voltammetry and Raman spectroscopy reveal that the Ru{sup 2+/3+} couple is electrochemically reversible but that the phenolate ligand based oxidation is irreversible. These redox processes are associated with reversible colour changes from wine red (reduced) to red orange (mixed composition) then to light green (oxidized) in the visible region and an irreversible change in the near-IR region, respectively. Scanning electron microscopy reveals that repeated switching in LiClO{sub 4} aqueous solution does not induce any significant structural change within the deposit films. Cyclic voltammetry has been used to determine the electrochromic switching rate under semi-infinite linear diffusion conditions. In aqueous LiClO{sub 4}, the homogeneous charge transport diffusion coefficient, D{sub CT}, decreases from 3.6 {+-} 0.3 x 10{sup -13} to 2.7 {+-} 0.2 x 10{sup -13} cm{sup 2} s{sup -1} as the LiClO{sub 4} concentration increases from 0.1 to 1.0 M. This weak dependence of D{sub CT} on electrolyte concentration suggests that counterion availability is not rate-determining and that the overall rate of charge transport through the metallopolymer film is limited by the rate of segmental polymer chain motion necessary to bring adjacent centres sufficiently close to allow electron transfer to occur. Also the impact of changing the identity of the charge compensating anion of the redox electrochromic switching rate has been investigated. Finally, the electronic conductivity has been determined using interdigitated array electrodes (IDAs). (author)
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.
DEFF Research Database (Denmark)
Nielsen, Søren R.K.
The present textbook has been written for a course on stochastic vibration theory that is being given on the 9th semester at Aalborg University for M.Sc. students in structural engineering.......The present textbook has been written for a course on stochastic vibration theory that is being given on the 9th semester at Aalborg University for M.Sc. students in structural engineering....
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
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...
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
DEFF Research Database (Denmark)
Nielsen, Søren R.K.
This book has been prepared for the course on Computational Dynamics given at the 8th semester at the structural program in civil engineering at Aalborg University.......This book has been prepared for the course on Computational Dynamics given at the 8th semester at the structural program in civil engineering at Aalborg University....
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.
DEFF Research Database (Denmark)
Kejlberg-Rasmussen, Casper
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...... concept we use, throughout this thesis, to solve data structure problems is invariants. In the design of dynamic data structures we have some set of query and update operations which we want our data structure to support, but we do not choose the order that they are performed in. Invariants are logical...... structure is implicit, meaning that we do not use any extra space than that of the input keys. Our data structure is implicitly encoded through the permutation of the input keys. Other dictionaries with the working set property have constant factor overhead in the space usage, our dictionary has no overhead...
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...
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
Microcantilever actuation generated by redox-induced surface stress
Tabard-Cossa, Vincent
Electrochemically-induced changes in surface stress at the solid-liquid interface are measured using a differential cantilever-based sensor. The simultaneous, in situ measurements of the current (charge) and interfacial stress changes are performed by employing an AFM cantilever as both the working electrode (in a conventional three-probe electrochemical cell configuration) and as the mechanical transducer (bending of the cantilever). The custom-built instrument achieves a surface stress sensitivity of 1x10-4 N/m and a dynamic range of 5x105. Combining electrochemistry with cantilever-based sensing provides the extra surface characterization capability essential for the interpretation of the origin of the surface stress. The objective of the present study is to gain a better understanding of the mechanisms responsible for the nanomechanical motion of cantilever sensors during adsorption and absorption processes. The study of these simple model systems will lead to a general understanding of the cantilever-based sensor's response and provide insights into the physical origin of the measured surface stress. The surface stress generated by the electrochemically-controlled absorption of ions into a thin polypyrrole film is investigated. A compressive change in surface stress of about -2 N/m is measured when the polymer is electrochemically switched between its oxidized and neutral (swollen) state. The volume change of the polymer phase with respect to the gold-coated cantilever is shown to be responsible for the mechanical motion observed. The potential-induced surface stress and surface energy change on an Au(111)-textured cantilever, in a 0.1 M HClO4 electrolyte, are simultaneously measured. These measurements revealed that for solid electrodes these two thermodynamic parameters are significantly different. In the double layer region, a surface stress change of -0.55 +/-0.06 N/m is measured during ClO4- adsorption whereas the surface energy variation is smaller by
Structural dynamic modifications via models
Indian Academy of Sciences (India)
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 ...
Distributed Dynamic Condition Response Structures
DEFF Research Database (Denmark)
Hildebrandt, Thomas; Mukkamala, Raghava Rao
We present distributed dynamic condition response structures as a declarative process model inspired by the workflow language employed by our industrial partner and conservatively generalizing labelled event structures. The model adds to event structures the possibility to 1) finitely specify...... as a labelled transition system. Exploration of the relationship between dynamic condition response structures and traditional models for concurrency, application to more complex scenarios, and further extensions of the model is left to future work....
Structure, Reactivity and Dynamics
Indian Academy of Sciences (India)
Oppenheimer approx- imation are also studied. New and improved methodologies have been applied to study multi-surface multi-mode nuclear dynamics. The interesting phenomenon involving the geometric phase which may have important ...
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.
Structural dynamic modification
Indian Academy of Sciences (India)
Abstract. Vibration and acoustic requirements are becoming increasingly im- portant 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.
DEFF Research Database (Denmark)
Nielsen, Søren R.K.
The present textbook has been written for a course on stochastic vibration theory that is being given on the 9th semester at Aalborg University for M.Sc. students in structural engineering.......The present textbook has been written for a course on stochastic vibration theory that is being given on the 9th semester at Aalborg University for M.Sc. students in structural engineering....
DEFF Research Database (Denmark)
Tsakalidis, Konstantinos
multi-versioned indexing database. We ﬁrst present a generic method for making data structures fully persistent in external memory. This method can render any database multi-versioned, as long as its implementation abides by our assumptions. We obtain the result by presenting an implementation of B...
Structural dynamic modification
Indian Academy of Sciences (India)
... 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 ...
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.
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.
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....
Relating structure and dynamics in organisation models
Jonkers, C.M.; Treur, J.
2002-01-01
To understand how an organisational structure relates to dynamics is an interesting fundamental challenge in the area of social modelling. Specifications of organisational structure usually have a diagrammatic form that abstracts from more detailed dynamics. Dynamic properties of agent systems,
Dynamic range majority data structures
DEFF Research Database (Denmark)
Elmasry, Amr Ahmed Abd Elmoneim; He, Meng; Munro, J. Ian
2011-01-01
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......((lg n/(α lglg n)). For constant values of α, 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 ≥ 2, as well as dynamic arrays, in which each entry...
Static and Dynamic Membrane Structures
Directory of Open Access Journals (Sweden)
Sergiu Ivanov
2012-10-01
Full Text Available While originally P systems were defined to contain multiset rewriting rules, it turned out that considering different types of rules may produce important results, such as increasing the computational power of the rules. This paper focuses on factoring out the concept of a membrane structure out of various P system models with the goal of providing useful formalisations. Both static and dynamic membrane structures are considered.
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.
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.
Nucleolus: from structure to dynamics
Hernandez-Verdun, Danièle
2005-01-01
The nucleolus, a large nuclear domain, is the ribosome factory of the cells. Ribosomal RNAs are synthesized, processed and assembled with ribosomal proteins in the nucleolus, and the ribosome subunits are then transported to the cytoplasm. In this review, the structural organization of the nucleolus and the dynamics of the nucleolar proteins are discussed in an attempt to link both information. By electron microscopy, three main nucleolar components corresponding to different steps of ribosom...
Dynamic Response of Concrete and Concrete Structures
1984-01-26
low - . AFOSR-T... 84-0.165 DYNAMIC RESPONSE OF CONCRETE AND CONCRETE STRUCTURES FIRST ANNUAL TECHNICAL REPORT LAWRENCE E. 14ALVERN C. ALLEN ROSS...and Subtitle) S. TYPE OF REPORT I PERIOD COVERED DYNAMIC RESPONSE OF CONCRETE 1 DEC 1982 - 30 NOV 1983 AND CONCRETE STRUCTURES I_____198__-__0_NOV_198...Bar Dynamic Loads Fracture Materials Testing Dynamic Properties Impact Rate Effects Dynamic Testing Hopkinson Bar Reinforced Concrete Structures 20
Surface structure determines dynamic wetting
Shiomi, Junichiro; Wang, Jiayu; Do-Quang, Minh; Cannon, James; Yue, Feng; Suzuki, Yuji; Amberg, Gustav
2014-11-01
Dynamic wetting, the spontaneous spreading process after droplet contacts a solid surface, is important in various engineering processes, such as in printing, coating, and lubrication. In the recent years, experiments and numerical simulations have greatly progressed the understanding in the dynamic wetting particularly on ``flat'' substrates. To gain further insight into the governing physics of the dynamic wetting, we perform droplet-wetting experiments on microstructured surfaces, just a few micrometers in size, with complementary numerical simulations, and investigate the dependence of the spreading rate on the microstructure geometries and fluid properties. We reveal that the influence of microstructures can be quantified in terms of a line friction coefficient for the energy dissipation rate at the contact line, and that this can be described in a simple formula in terms of the geometrical parameters of the roughness and the line-friction coefficient of the planar surface. The systematic study is also of practical importance since structures and roughness are omnipresent and their influence on spreading rate would give us additional degrees of freedom to control the dynamic wetting. This work was financially supported in part by, the Japan Society for the Promotion of Science (J.W., J.C., and J.S) and Swedish Governmental Agency for Innovation Systems (M.D.-Q. and G.A.).
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...
Evolutionary dynamics in structured populations
Nowak, Martin A.; Tarnita, Corina E.; Antal, Tibor
2010-01-01
Evolutionary dynamics shape the living world around us. At the centre of every evolutionary process is a population of reproducing individuals. The structure of that population affects evolutionary dynamics. The individuals can be molecules, cells, viruses, multicellular organisms or humans. Whenever the fitness of individuals depends on the relative abundance of phenotypes in the population, we are in the realm of evolutionary game theory. Evolutionary game theory is a general approach that can describe the competition of species in an ecosystem, the interaction between hosts and parasites, between viruses and cells, and also the spread of ideas and behaviours in the human population. In this perspective, we review the recent advances in evolutionary game dynamics with a particular emphasis on stochastic approaches in finite sized and structured populations. We give simple, fundamental laws that determine how natural selection chooses between competing strategies. We study the well-mixed population, evolutionary graph theory, games in phenotype space and evolutionary set theory. We apply these results to the evolution of cooperation. The mechanism that leads to the evolution of cooperation in these settings could be called ‘spatial selection’: cooperators prevail against defectors by clustering in physical or other spaces. PMID:20008382
Computational Methods for Structural Mechanics and Dynamics
Stroud, W. Jefferson (Editor); Housner, Jerrold M. (Editor); Tanner, John A. (Editor); Hayduk, Robert J. (Editor)
1989-01-01
Topics addressed include: transient dynamics; transient finite element method; transient analysis in impact and crash dynamic studies; multibody computer codes; dynamic analysis of space structures; multibody mechanics and manipulators; spatial and coplanar linkage systems; flexible body simulation; multibody dynamics; dynamical systems; and nonlinear characteristics of joints.
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
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.
Chromatin structure in telomere dynamics
Directory of Open Access Journals (Sweden)
Alessandra eGalati
2013-03-01
Full Text Available The establishment of a specific nucleoprotein structure, the telomere, is required to ensure the protection of chromosome ends from being recognized as DNA damage sites. Telomere shortening below a critical length triggers a DNA damage response that leads to replicative senescence. In normal human somatic cells, characterized by telomere shortening with each cell division, telomere uncapping is a regulated process associated with cell turnover. Nevertheless, telomere dysfunction has also been associated with genomic instability, cell transformation and cancer. Despite the essential role telomeres play in chromosome protection and in tumorigenesis, our knowledge of the chromatin structure involved in telomere maintenance is still limited. Here we review the recent findings on chromatin modifications associated with the dynamic changes of telomeres from protected to de-protected state and their role in telomere functions.
Predictive structural dynamic network analysis.
Chen, Rong; Herskovits, Edward H
2015-04-30
Classifying individuals based on magnetic resonance data is an important task in neuroscience. Existing brain network-based methods to classify subjects analyze data from a cross-sectional study and these methods cannot classify subjects based on longitudinal data. We propose a network-based predictive modeling method to classify subjects based on longitudinal magnetic resonance data. Our method generates a dynamic Bayesian network model for each group which represents complex spatiotemporal interactions among brain regions, and then calculates a score representing that subject's deviation from expected network patterns. This network-derived score, along with other candidate predictors, are used to construct predictive models. We validated the proposed method based on simulated data and the Alzheimer's Disease Neuroimaging Initiative study. For the Alzheimer's Disease Neuroimaging Initiative study, we built a predictive model based on the baseline biomarker characterizing the baseline state and the network-based score which was constructed based on the state transition probability matrix. We found that this combined model achieved 0.86 accuracy, 0.85 sensitivity, and 0.87 specificity. For the Alzheimer's Disease Neuroimaging Initiative study, the model based on the baseline biomarkers achieved 0.77 accuracy. The accuracy of our model is significantly better than the model based on the baseline biomarkers (p-value=0.002). We have presented a method to classify subjects based on structural dynamic network model based scores. This method is of great importance to distinguish subjects based on structural network dynamics and the understanding of the network architecture of brain processes and disorders. Copyright © 2015 Elsevier B.V. All rights reserved.
Lewis Structures Technology, 1988. Volume 1: Structural Dynamics
1988-01-01
The specific purpose of the symposium was to familiarize the engineering structures community with the depth and range of research performed by the Structures Division of the Lewis Research Center and its academic and industrial partners. Sessions covered vibration control, fracture mechanics, ceramic component reliability, parallel computing, nondestructive testing, dynamical systems, fatigue and damage, wind turbines, hot section technology, structural mechanics codes, computational methods for dynamics, structural optimization, and applications of structural dynamics.
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.
Structural dynamic modification using additive damping
Indian Academy of Sciences (India)
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 ...
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...
Structural dynamics branch research and accomplishments
1990-01-01
Summaries are presented of fiscal year 1989 research highlights from the Structural Dynamics Branch at NASA Lewis Research Center. Highlights from the branch's major work areas include aeroelasticity, vibration control, dynamic systems, and computation structural methods. A listing of the fiscal year 1989 branch publications is given.
Transforming Static Data Structures to Dynamic Structures.
1979-09-03
transform. An interesting open problem is to examine other counting schemes (such as Fibonacci counting) for their properties as transforms. 9 9 3 3 1...any strategy which permits such overlapping structures can be improved by omitting the shared elements from all but one of the overlapping structures...also forbid overlapping structures on the grounds that transformations which allow them cannot be optimal for space in the worst case. An even more
Particular Approaches about Symmetrical Structures Dynamics
Aurora Potirniche
2013-01-01
The paper presents some aspects about dynamic behaviour of a rigid structure building insulated on anti-seismic elastic devices. The structure presents symmetries in terms of the geometrical and insulation configurations, and this allows decoupling of the eigenmodes. Thereby, is simpler to evaluate the impact of the dynamic forces transmitted through the terrain-structure path during the earthquake. Based on the vibration isolation theory, it can be evaluated the isolation d...
Structural stability of nonlinear population dynamics
Cenci, Simone; Saavedra, Serguei
2018-01-01
In population dynamics, the concept of structural stability has been used to quantify the tolerance of a system to environmental perturbations. Yet, measuring the structural stability of nonlinear dynamical systems remains a challenging task. Focusing on the classic Lotka-Volterra dynamics, because of the linearity of the functional response, it has been possible to measure the conditions compatible with a structurally stable system. However, the functional response of biological communities is not always well approximated by deterministic linear functions. Thus, it is unclear the extent to which this linear approach can be generalized to other population dynamics models. Here, we show that the same approach used to investigate the classic Lotka-Volterra dynamics, which is called the structural approach, can be applied to a much larger class of nonlinear models. This class covers a large number of nonlinear functional responses that have been intensively investigated both theoretically and experimentally. We also investigate the applicability of the structural approach to stochastic dynamical systems and we provide a measure of structural stability for finite populations. Overall, we show that the structural approach can provide reliable and tractable information about the qualitative behavior of many nonlinear dynamical systems.
Dynamic Discrete Choice Structural Models: A Survey
Victor Aguirregabiria; Pedro mira
2007-01-01
This paper reviews methods for the estimation of dynamic discrete choice structural models and discusses related econometric issues. We consider single agent models, competitive equilibrium models and dynamic games. The methods are illustrated with descriptions of empirical studies which have applied these techniques to problems in different areas of economics. Programming codes for the estimation methods will be available in a companion web page.
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
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).
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 Structural Health Monitoring of Slender Structures Using Optical Sensors
Paulo André; José Jara; Humberto Varum; José Melo; Hugo Rodrigues; Rui Travanca; Paulo Antunes
2012-01-01
In this paper we summarize the research activities at the Instituto de Telecomunicações—Pólo de Aveiro and University of Aveiro, in the field of fiber Bragg grating based sensors and their applications in dynamic measurements for Structural Health Monitoring of slender structures such as towers. In this work we describe the implementation of an optical biaxial accelerometer based on fiber Bragg gratings inscribed on optical fibers. The proof-of-concept was done with the dynamic monitoring of ...
Design optimization applied in structural dynamics
Akcay-Perdahcioglu, Didem; de Boer, Andries; van der Hoogt, Peter; Tiskarna, T
2007-01-01
This paper introduces the design optimization strategies, especially for structures which have dynamic constraints. Design optimization involves first the modeling and then the optimization of the problem. Utilizing the Finite Element (FE) model of a structure directly in an optimization process
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...
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.
Identification of dynamic load for prosthetic structures.
Zhang, Dequan; Han, Xu; Zhang, Zhongpu; Liu, Jie; Jiang, Chao; Yoda, Nobuhiro; Meng, Xianghua; Li, Qing
2017-12-01
Dynamic load exists in numerous biomechanical systems, and its identification signifies a critical issue for characterizing dynamic behaviors and studying biomechanical consequence of the systems. This study aims to identify dynamic load in the dental prosthetic structures, namely, 3-unit implant-supported fixed partial denture (I-FPD) and teeth-supported fixed partial denture. The 3-dimensional finite element models were constructed through specific patient's computerized tomography images. A forward algorithm and regularization technique were developed for identifying dynamic load. To verify the effectiveness of the identification method proposed, the I-FPD and teeth-supported fixed partial denture structures were investigated to determine the dynamic loads. For validating the results of inverse identification, an experimental force-measuring system was developed by using a 3-dimensional piezoelectric transducer to measure the dynamic load in the I-FPD structure in vivo. The computationally identified loads were presented with different noise levels to determine their influence on the identification accuracy. The errors between the measured load and identified counterpart were calculated for evaluating the practical applicability of the proposed procedure in biomechanical engineering. This study is expected to serve as a demonstrative role in identifying dynamic loading in biomedical systems, where a direct in vivo measurement may be rather demanding in some areas of interest clinically. Copyright © 2017 John Wiley & Sons, Ltd.
Dynamic Structural Health Monitoring of slender structures using optical sensors.
Antunes, Paulo; Travanca, Rui; Rodrigues, Hugo; Melo, José; Jara, José; Varum, Humberto; André, Paulo
2012-01-01
In this paper we summarize the research activities at the Instituto de Telecomunicações--Pólo de Aveiro and University of Aveiro, in the field of fiber Bragg grating based sensors and their applications in dynamic measurements for Structural Health Monitoring of slender structures such as towers. In this work we describe the implementation of an optical biaxial accelerometer based on fiber Bragg gratings inscribed on optical fibers. The proof-of-concept was done with the dynamic monitoring of a reinforced concrete structure and a slender metallic telecommunication tower. Those structures were found to be suitable to demonstrate the feasibility of FBG accelerometers to obtain the structures' natural frequencies, which are the key parameters in Structural Health Monitoring and in the calibration of numerical models used to simulate the structure behavior.
Dynamic Structural Health Monitoring of Slender Structures Using Optical Sensors
Antunes, Paulo; Travanca, Rui; Rodrigues, Hugo; Melo, José; Jara, José; Varum, Humberto; André, Paulo
2012-01-01
In this paper we summarize the research activities at the Instituto de Telecomunicações—Pólo de Aveiro and University of Aveiro, in the field of fiber Bragg grating based sensors and their applications in dynamic measurements for Structural Health Monitoring of slender structures such as towers. In this work we describe the implementation of an optical biaxial accelerometer based on fiber Bragg gratings inscribed on optical fibers. The proof-of-concept was done with the dynamic monitoring of a reinforced concrete structure and a slender metallic telecommunication tower. Those structures were found to be suitable to demonstrate the feasibility of FBG accelerometers to obtain the structures' natural frequencies, which are the key parameters in Structural Health Monitoring and in the calibration of numerical models used to simulate the structure behavior. PMID:22778661
Program of Research in Structures and Dynamics
1988-01-01
The Structures and Dynamics Program was first initiated in 1972 with the following two major objectives: to provide a basic understanding and working knowledge of some key areas pertinent to structures, solid mechanics, and dynamics technology including computer aided design; and to provide a comprehensive educational and research program at the NASA Langley Research Center leading to advanced degrees in the structures and dynamics areas. During the operation of the program the research work was done in support of the activities of both the Structures and Dynamics Division and the Loads and Aeroelasticity Division. During the period of 1972 to 1986 the Program provided support for two full-time faculty members, one part-time faculty member, three postdoctoral fellows, one research engineer, eight programmers, and 28 graduate research assistants. The faculty and staff of the program have published 144 papers and reports, and made 70 presentations at national and international meetings, describing their research findings. In addition, they organized and helped in the organization of 10 workshops and national symposia in the structures and dynamics areas. The graduate research assistants and the students enrolled in the program have written 20 masters theses and 2 doctoral dissertations. The overall progress is summarized.
Particular Approaches about Symmetrical Structures Dynamics
Directory of Open Access Journals (Sweden)
Aurora Potirniche
2013-09-01
Full Text Available The paper presents some aspects about dynamic behaviour of a rigid structure building insulated on anti-seismic elastic devices. The structure presents symmetries in terms of the geometrical and insulation configurations, and this allows decoupling of the eigenmodes. Thereby, is simpler to evaluate the impact of the dynamic forces transmitted through the terrain-structure path during the earthquake. Based on the vibration isolation theory, it can be evaluated the isolation degree for the considered structure. It has considered as an excitation factor the complex signal of an earthquake defined through the ground motion acceleration. The analysis that was made in the paper reveals the need to identification and evaluation requirements for the functional correlations between the reference parameters of the considered structure and the characteristics of the isolating and insulating devices.
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.
Simultaneous determination of protein structure and dynamics
DEFF Research Database (Denmark)
Lindorff-Larsen, Kresten; Best, Robert B.; DePristo, M. A.
2005-01-01
at the atomic level about the structural and dynamical features of proteins-with the ability of molecular dynamics simulations to explore a wide range of protein conformations. We illustrate the method for human ubiquitin in solution and find that there is considerable conformational heterogeneity throughout......We present a protocol for the experimental determination of ensembles of protein conformations that represent simultaneously the native structure and its associated dynamics. The procedure combines the strengths of nuclear magnetic resonance spectroscopy-for obtaining experimental information...... the protein structure. The interior atoms of the protein are tightly packed in each individual conformation that contributes to the ensemble but their overall behaviour can be described as having a significant degree of liquid-like character. The protocol is completely general and should lead to significant...
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
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.
Fundamental structures of dynamic social networks
DEFF Research Database (Denmark)
Sekara, Vedran; Stopczynski, Arkadiusz; Jørgensen, Sune Lehmann
2016-01-01
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......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...
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
Structural dynamics of tropical moist forest gaps
Maria O. Hunter; 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...
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.
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.
Ultrafast structural dynamics of VO2
Lysenko, Sergiy; Kumar, Nardeep; Rúa, Armando; Figueroa, José; Lu, Junqiang; Fernández, Félix
2017-08-01
Distinct contribution of acoustic and optical phonons in light-induced lattice transformation was resolved at different time scales by monitoring the insulator-to-metal phase transition in epitaxial and nonepitaxial VO2 films. Applying the ultrafast angle-resolved light scattering technique we demonstrate a significant influence of internal misfit strain in epitaxial films on subpicosecond phase transition dynamics. This technique also allows for observing a contribution of structural defects in the evolution of the transient state. The ultrafast structural phase transition dynamics is discussed in terms of the Ginzburg-Landau formalism. Using a set of experimental data we reconstruct the thermodynamic potential of photoexcited VO2 and provide a phenomenological model of the ultrafast light-induced structural phase transition.
Gradient-based optimization in nonlinear structural dynamics
DEFF Research Database (Denmark)
Dou, Suguang
, frequency stabilization, and disk resonator gyroscope. For advanced design of these structures, it is of considerable value to extend current optimization in linear structural dynamics into nonlinear structural dynamics. In this thesis, we present a framework for modelling, analysis, characterization...
The 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...
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.
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.
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.
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.
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.
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....
The Structure and Dynamics of Jupiter's Magnetosphere
Vogt, Marissa Farland
2012-01-01
Eight spacecraft have now visited the Jovian system and obtained a wealth of information about Jupiter's magnetosphere and aurora, both of which have proved to be very different from what we observe at the Earth. These differences are due in part to unique features such as large magnetospheric scale sizes, an internal plasma source from the moon Io, and a rapid planetary rotation period. These features have important influences on Jupiter's magnetosphere structure and dynamics, which are the ...
Structure and dynamics of GPCR signaling complexes.
Hilger, Daniel; Masureel, Matthieu; Kobilka, Brian K
2018-01-01
G-protein-coupled receptors (GPCRs) relay numerous extracellular signals by triggering intracellular signaling through coupling with G proteins and arrestins. Recent breakthroughs in the structural determination of GPCRs and GPCR-transducer complexes represent important steps toward deciphering GPCR signal transduction at a molecular level. A full understanding of the molecular basis of GPCR-mediated signaling requires elucidation of the dynamics of receptors and their transducer complexes as well as their energy landscapes and conformational transition rates. Here, we summarize current insights into the structural plasticity of GPCR-G-protein and GPCR-arrestin complexes that underlies the regulation of the receptor's intracellular signaling profile.
Structural Dynamics of Chondrocytes during Culturing.
Omelyanenko, N P; Rodionov, S A
2017-12-01
We performed comparative analysis of the morphology of chondrocytes in normal cartilage, after their isolation from the tissue, and at different stages of culturing; structural dynamics of cells during culturing was also studied. Significant morphological differences in chondrocytes at the specified stages of their preparation to in vivo use were revealed. Pronounced structural changes (blebbing and cytoplasm swelling) were found in chondrocytes before their implantation, which can affect the formation of cartilage regenerate. The study was performed using light microscopy methods including time-lapse recording of the cell cultures with differential interference Nomarski contrasting combined with transmission electron microscopy.
Dynamic Analyses Including Joints Of Truss Structures
Belvin, W. Keith
1991-01-01
Method for mathematically modeling joints to assess influences of joints on dynamic response of truss structures developed in study. Only structures with low-frequency oscillations considered; only Coulomb friction and viscous damping included in analysis. Focus of effort to obtain finite-element mathematical models of joints exhibiting load-vs.-deflection behavior similar to measured load-vs.-deflection behavior of real joints. Experiments performed to determine stiffness and damping nonlinearities typical of joint hardware. Algorithm for computing coefficients of analytical joint models based on test data developed to enable study of linear and nonlinear effects of joints on global structural response. Besides intended application to large space structures, applications in nonaerospace community include ground-based antennas and earthquake-resistant steel-framed buildings.
Evolutionary dynamics on any population structure
Allen, Benjamin; Lippner, Gabor; Chen, Yu-Ting; Fotouhi, Babak; Momeni, Naghmeh; Yau, Shing-Tung; Nowak, Martin A.
2017-03-01
Evolution occurs in populations of reproducing individuals. The structure of a population can affect which traits evolve. Understanding evolutionary game dynamics in structured populations remains difficult. Mathematical results are known for special structures in which all individuals have the same number of neighbours. The general case, in which the number of neighbours can vary, has remained open. For arbitrary selection intensity, the problem is in a computational complexity class that suggests there is no efficient algorithm. Whether a simple solution for weak selection exists has remained unanswered. Here we provide a solution for weak selection that applies to any graph or network. Our method relies on calculating the coalescence times of random walks. We evaluate large numbers of diverse population structures for their propensity to favour cooperation. We study how small changes in population structure—graph surgery—affect evolutionary outcomes. We find that cooperation flourishes most in societies that are based on strong pairwise ties.
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.
Structural dynamic analysis of turbine blade
Antony, A. Daniel; Gopalsamy, M.; Viswanadh, Chaparala B. V.; Krishnaraj, R.
2017-10-01
In any gas turbine design cycle, blade design is a crucial element which needs maximum attention to meet the aerodynamic performance, structural safety margins, manufacturing feasibility, material availability etc. In present day gas turbine engines, most of the failures occur during engine development test and in-service, in rotor and stator blades due to fatigue and resonance failures. To address this issue, an extensive structural dynamic analysis is carried out to predict the natural frequencies and mode shapes using FE methods. Using the dynamics characteristics, the Campbell diagram is constructed to study the possibility of resonance at various operating speeds. In this work, the feasibility of using composite material in place of titanium alloy from the structural dynamics point of view. This is being attempted in a Low-pressure compressor where the temperatures are relatively low and fixed with the casings. The analysis will be carried out using FE method for different composite material with different lamina orientations chosen through the survey. This study will focus on the sensitivity of blade mode shapes to different laminae orientations, which will be used to alter the natural frequency and tailor the mode shapes. Campbell diagrams of existing titanium alloy are compared with the composite materials with different laminae at all critical operating conditions. The existing manufacturing methods and the proven techniques for blade profiles will also be discussed in this report.
Controlling Proton Delivery through Catalyst Structural Dynamics
Energy Technology Data Exchange (ETDEWEB)
Cardenas, Allan J.; Ginovska-Pangovska, Bojana; Kumar, Neeraj; Hou, Jianbo; Raugei, Simone; Helm, Monte L.; Appel, Aaron M.; Bullock, R. Morris; O' Hagan, Molly J.
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
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;}
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.
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...
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.
Structural optimization for nonlinear dynamic response
DEFF Research Database (Denmark)
Dou, Suguang; Strachan, B. Scott; Shaw, Steven W.
2015-01-01
by a single vibrating mode, or by a pair of internally resonant modes. The approach combines techniques from nonlinear dynamics, computational mechanics and optimization, and it allows one to relate the geometric and material properties of structural elements to terms in the normal form for a given resonance......Much is known about the nonlinear resonant response of mechanical systems, but methods for the systematic design of structures that optimize aspects of these responses have received little attention. Progress in this area is particularly important in the area of micro-systems, where nonlinear...... resonant behaviour is being used for a variety of applications in sensing and signal conditioning. In this work, we describe a computational method that provides a systematic means for manipulating and optimizing features of nonlinear resonant responses of mechanical structures that are described...
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....
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
Structural Dynamics, Stability, and Control of Helicopters
Meirovitch, L.; Hale, A. L.
1978-01-01
The dynamic synthesis of gyroscopic structures consisting of point-connected substructures is investigated. The objective is to develop a mathematical model capable of an adequate simulation of the modal characteristics of a helicopter using a minimum number of degrees of freedom. The basic approach is to regard the helicopter structure as an assemblage of flexible substructures. The variational equations for the perturbed motion about certain equilibrium solutions are derived. The discretized variational equations can be conveniently exhibited in matrix form, and a great deal of information about the system modal characteristics can be extracted from the coefficient matrices. The derivation of the variational equations requires a monumental amount of algebraic operations. To automate this task a symbolic manipulation program on a digital computer is developed.
Structure and dynamics of amorphous water ice
Laufer, D.; Kochavi, E.; Bar-Nun, A.; Owen, T. (Principal Investigator)
1987-01-01
Further insight into the structure and dynamics of amorphous water ice, at low temperatures, was obtained by trapping in it Ar, Ne, H2, and D2. Ballistic water-vapor deposition results in the growth of smooth, approximately 1 x 0.2 micrometer2, ice needles. The amorphous ice seems to exist in at least two separate forms, at T water hexagons in the ice are wide enough to allow the free penetration of H2 and D2 into the ice matrix even in the relatively compact cubic ice, resulting in H2-(D2-) to-ice ratios (by number) as high as 0.63. The larger Ar atoms can penetrate only into the wider channels of amorphous ice, and Ne is an intermediate case. Dynamic percolation behavior explains the emergence of Ar and Ne (but not H2 and D2) for the ice, upon warming, in small and big gas jets. The big jets, each containing approximately 5 x 10(10) atoms, break and propel the ice needles. Dynamic percolation also explains the collapse of the ice matrix under bombardment by Ar , at a pressure exceeding 2.6 dyn cm-2, and the burial of huge amounts of gas inside the collapsed matrix, up to an Ar-to-ice of 3.3 (by number). The experimental results could be relevant to comets, icy satellites, and icy grain mantles in dense interstellar clouds.
Structural dynamics and ecology of flatfish populations
Bailey, Kevin M.
1997-11-01
The concept of structure in populations of marine fishes is fundamental to how we manage and conduct research on these resources. The degree of population structure ranges widely among flatfishes. Although we know that large populations tend to be subdivided into local populations, based on morphological, meristic and reproductive characteristics, these data often conflict with evidence on genetic stock structure, due to the scale and organization of movement within the metapopulation. Movement of individuals between local subpopulations and colonization events on a macroecological scale are probably important to some flatfish populations. Dispersal of larvae is known to be a major factor affecting population mixing. Some flatfishes have planktonic stages of long duration and for these species there is often, but not always, little population structure; gene flow sometimes may be limited by oceanographic features, such as eddies and fronts. At the juvenile stage dispersal can result in colonization of under-utilized habitats; however, for flatfishes with strong habitat requirements, this type of event may be less likely when suitable habitats are fragmented. Complex population structure has major implications for management, e.g. lumping harvested populations with little gene flow can have detrimental local effects. Moreover, the issue of population structure and movement influences the interpretation of research data, where populations are generally treated as closed systems. There is currently a strong need for a multidisciplinary approach to study fish population dynamics and the structure of their populations. This research should involve molecular geneticists, population geneticists, animal behaviourists and ecologists. Migration mechanisms, colonization and extinction events, gene flow and density-dependent movements are subject areas of great importance to managing large harvested populations, but our understanding of them at ecological scales, at least for
NMR Studies of Protein Structure and Dynamics
Li, Xiang
Available from UMI in association with The British Library. Requires signed TDF. This thesis describes applications of 2D homonuclear NMR techniques to the study of protein structure and dynamics in solution. The sequential assignments for the 3G-residue bovine Pancreatic Polypeptide (bPP) are reported. The secondary and tertiary structure of bPP in solution has been determined from experimental NMR data. bPP has a well defined C-terminal alpha-helix and a rather ordered conformation in the N-terminal region. The two segments are joined by a turn which is poorly defined. Both the N- and the C-terminus are highly disordered. The mean solution structure of bPP is remarkably similar to the crystal structure of avian Pancreatic Polypeptide (aPP). The average conformations of most side-chains from the alpha-helix of bPP in solution are closely similar to those of aPP in the crystalline state. A large number of side-chains of bPP, however, show significant conformational averaging in solution. The 89-residue kringle domain of urokinase from both human and recombinant sources has been investigated. Sequential assignments based primarily on the recombinant sample and the determination of secondary structure are presented. Two helices have been identified; one of these corresponds to that reported for t-PA kringle 2, but does not exist in other kringles with known structures. The second helix is thus far unique to the urokinase kringle. Three antiparallel beta-sheets and three tight turns have also been identified. The tertiary fold of the molecule conforms broadly to that found for other kringles. Three regions in the urokinase kringle exhibit high local mobility; one of these, the Pro56-Pro62 segment, forms part of the proposed binding site. The other two mobile regions are the N- and C-termini which are likely to form the interfaces between the kringle and the other two domains (EGF and protease) in urokinase. The differential dynamic behaviours of the kringle and
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.
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.
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 signatures of dynamic heterogeneities in monolayers of colloidal ellipsoids.
Zheng, Zhongyu; Ni, Ran; Wang, Feng; Dijkstra, Marjolein; Wang, Yuren; Han, Yilong
2014-05-08
When a liquid is supercooled towards the glass transition, its dynamics drastically slows down, whereas its static structure remains relatively unchanged. Finding a structural signature of the dynamic slowing down is a major challenge, yet it is often too subtle to be uncovered. Here we discover the structural signatures for both translational and rotational dynamics in monolayers of colloidal ellipsoids by video microscopy experiments and computer simulations. The correlation lengths of the dynamic slowest-moving clusters, the static glassy clusters, the static local structural entropy and the dynamic heterogeneity follow the same power-law divergence, suggesting that the kinetic slowing down is caused by a decrease in the structural entropy and an increase in the size of the glassy cluster. Ellipsoids with different aspect ratios exhibit single- or double-step glass transitions with distinct dynamic heterogeneities. These findings demonstrate that the particle shape anisotropy has important effects on the structure and dynamics of the glass.
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.
Fundamental structures of dynamic social networks
DEFF Research Database (Denmark)
Sekara, Vedran; Stopczynski, Arkadiusz; Jørgensen, Sune Lehmann
2016-01-01
, 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...... 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...
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).
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.
Indoor footstep localization from structural dynamics instrumentation
Poston, Jeffrey D.; Buehrer, R. Michael; Tarazaga, Pablo A.
2017-05-01
Measurements from accelerometers originally deployed to measure a building's structural dynamics can serve a new role: locating individuals moving within a building. Specifically, this paper proposes measurements of footstep-generated vibrations as a novel source of information for localization. The complexity of wave propagation in a building (e.g., dispersion and reflection) limits the utility of existing algorithms designed to locate, for example, the source of sound in a room or radio waves in free space. This paper develops enhancements for arrival time determination and time difference of arrival localization in order to address the complexities posed by wave propagation within a building's structure. Experiments with actual measurements from an instrumented public building demonstrate the potential of locating footsteps to sub-meter accuracy. Furthermore, this paper explains how to forecast performance in other buildings with different sensor configurations. This localization capability holds the potential to assist public safety agencies in building evacuation and incidence response, to facilitate occupancy-based optimization of heating or cooling and to inform facility security.
Confined Water: Structure, Dynamics, and Thermodynamics.
Chakraborty, Sudip; Kumar, Hemant; Dasgupta, Chandan; Maiti, Prabal K
2017-09-19
Understanding the properties of strongly confined water is important for a variety of applications such as fast flow and desalination devices, voltage generation, flow sensing, and nanofluidics. Confined water also plays an important role in many biological processes such as flow through ion channels. Water in the bulk exhibits many unusual properties that arise primarily from the presence of a network of hydrogen bonds. Strong confinement in structures such as carbon nanotubes (CNTs) substantially modifies the structural, thermodynamic, and dynamic (both translational and orientational) properties of water by changing the structure of the hydrogen bond network. In this Account, we provide an overview of the behavior of water molecules confined inside CNTs and slit pores between graphene and graphene oxide (GO) sheets. Water molecules confined in narrow CNTs are arranged in a single file and exhibit solidlike ordering at room temperature due to strong hydrogen bonding between nearest-neighbor molecules. Although molecules constrained to move along a line are expected to exhibit single-file diffusion in contrast to normal Fickian diffusion, we show, from a combination of molecular dynamics simulations and analytic calculations, that water molecules confined in short and narrow CNTs with open ends exhibit Fickian diffusion because of their collective motion as a single unit due to strong hydrogen bonding. Confinement leads to strong anisotropy in the orientational relaxation of water molecules. The time scale of relaxation of the dipolar correlations of water molecules arranged in a single file becomes ultraslow, of the order of several nanoseconds, compared with the value of 2.5 ps for bulk water. In contrast, the relaxation of the vector that joins the two hydrogens in a water molecule is much faster, with a time scale of about 150 fs, which is about 10 times shorter than the corresponding time scale for bulk water. This is a rare example of confinement leading to
Triplet repeat DNA structures and human genetic disease: dynamic ...
Indian Academy of Sciences (India)
Triplet repeat DNA structures and human genetic disease: dynamic mutations from dynamic DNA. Richard R Sinden Vladimir N ... Different models have been proposed for the expansion of triplet repeats, most of which presume the formation of alternative DNA structures in repeat tracts. One of the most likely structures, ...
Sea anemones possess dynamic mitogenome structures.
Emblem, Åse; Okkenhaug, Siri; Weiss, Emily S; Denver, Dee R; Karlsen, Bård Ove; Moum, Truls; Johansen, Steinar D
2014-06-01
A notable feature of hexacoral mitogenomes is the presence of complex self-catalytic group I introns. We investigated mitogenome structural variations and evolutionary mechanisms in actiniarian sea anemones based on the complete mitogenome sequence of the cold-water sea anemone species Urticina eques, Bolocera tuediae, Hormathia digitata and Metridium senile, and two isolates of the sub-tropical Aiptasia pulchella. Whole genome sequencing at 50 times coverage of B. tuediae and H. digitata indicated low mtDNA copy number of per haploid nuclear genome and presence of rare haplotypes. A group I intron inserted in ND5 was found to host essential mitochondrial protein genes in all species, and an additional truncated copy of ND5 in B. tuediae. A second group I intron (inserted in COI) that contained a homing endonuclease gene (HEG) was present in all mtDNA examined. Different variants of HEGs were observed, and included expressed elements fused in-frame with upstream exons and free-standing HEGs embedded within the intron. A notable hallmark of HEGs was a high extent of overlap with ribozyme structural elements; the U. eques HEG overlapped with the entire intron. We reconstructed the evolutionary history of the COI intron from insertion at unoccupied cognate sites, through HEG degradation, to intron loss. We also identified a novel insertion element in U. eques that contained two expressed protein-coding genes. An evolutionary analysis of the sea anemone mtDNA genes revealed higher substitution rates in the HEG and the insertion sequence as compared to the other loci, indicating relaxed selective pressures in these elements. We conclude that sea anemone mitogenomes are surprisingly dynamic in structure despite the economical organization and low sequence mutation rate. Copyright © 2014 Elsevier Inc. All rights reserved.
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...
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.
Phase space structures governing reaction dynamics in rotating molecules
Ciftci, Unver; Waalkens, Holger
Recently, the phase space structures governing reaction dynamics in Hamiltonian systems have been identified and algorithms for their explicit construction have been developed. These phase space structures are induced by saddle type equilibrium points which are characteristic for reaction type
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
Exploring Ultrafast Structural Dynamics for Energetic Enhancement or Disruption
2016-03-01
processes at ultrafast time scales that follow dynamical stimuli, energy localization and delocalization, changes in lattice structure, decomposition...understand the pathways starting from dynamic stimuli, lattice molecular vibrational and electronic responses, excited-state chemical dynamics, and...public release; distribution is unlimited. 11 12. Glascoe EA, Zaug JM, Armstrong MR, Crowhurst JC , Grant CD, Fried LE. Nanosecond time-resolved and
Structural signatures of dynamic heterogeneities in monolayers of colloidal ellipsoids
Zheng, Zhongyu; Ni, Ran|info:eu-repo/dai/nl/314569227; Wang, Feng; Dijkstra, Marjolein|info:eu-repo/dai/nl/123538807; Wang, Yuren; Han, Yilong
2014-01-01
When a liquid is supercooled towards the glass transition, its dynamics drastically slows down, whereas its static structure remains relatively unchanged. Finding a structural signature of the dynamic slowing down is a major challenge, yet it is often too subtle to be uncovered. Here we discover the
Structural dynamics branch research and accomplishments to FY 1992
Lawrence, Charles
1992-01-01
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.
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.
Structures in dynamics finite dimensional deterministic studies
Broer, HW; van Strien, SJ; Takens, F
1991-01-01
The study of non-linear dynamical systems nowadays is an intricate mixture of analysis, geometry, algebra and measure theory and this book takes all aspects into account. Presenting the contents of its authors' graduate courses in non-linear dynamical systems, this volume aims at researchers who wish to be acquainted with the more theoretical and fundamental subjects in non-linear dynamics and is designed to link the popular literature with research papers and monographs. All of the subjects covered in this book are extensively dealt with and presented in a pedagogic
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.
4th International Conference on Structural Nonlinear Dynamics and Diagnosis
2018-01-01
This book presents contributions on the most active lines of recent advanced research in the field of nonlinear mechanics and physics selected from the 4th International Conference on Structural Nonlinear Dynamics and Diagnosis. It includes fifteen chapters by outstanding scientists, covering various aspects of applications, including road tanker dynamics and stability, simulation of abrasive wear, energy harvesting, modeling and analysis of flexoelectric nanoactuator, periodic Fermi–Pasta–Ulam problems, nonlinear stability in Hamiltonian systems, nonlinear dynamics of rotating composites, nonlinear vibrations of a shallow arch, extreme pulse dynamics in mode-locked lasers, localized structures in a photonic crystal fiber resonator, nonlinear stochastic dynamics, linearization of nonlinear resonances, treatment of a linear delay differential equation, and fractional nonlinear damping. It appeals to a wide range of experts in the field of structural nonlinear dynamics and offers researchers and engineers a...
Structure and dynamics of liquid ethanol
Saiz, L.; Padro Cardenas, Joan Angel; Guàrdia Manuel, Elvira
1997-01-01
Molecular dynamics simulations of liquid ethanol at four thermodynamic states ranging from T = 173 K to T = 348 K were carried out using the transferable OPLS potential model of Jorgensen (J. Phys. Chem. 1986, 90, 1276). Both static and dynamic properties are analyzed. The resulting properties show an overall agreement with available experimental data. Special attention is paid to the hydrogen bonds and to their influence on the molecular behavior. Results for liquid ethanol are compared with...
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.
The dynamic structure of thrombin in solution.
Fuglestad, Brian; Gasper, Paul M; Tonelli, Marco; McCammon, J Andrew; Markwick, Phineus R L; Komives, Elizabeth A
2012-07-03
The backbone dynamics of human α-thrombin inhibited at the active site serine were analyzed using R(1), R(2), and heteronuclear NOE experiments, variable temperature TROSY 2D [(1)H-(15)N] correlation spectra, and R(ex) measurements. The N-terminus of the heavy chain, which is formed upon zymogen activation and inserts into the protein core, is highly ordered, as is much of the double beta-barrel core. Some of the surface loops, by contrast, remain very dynamic with order parameters as low as 0.5 indicating significant motions on the ps-ns timescale. Regions of the protein that were thought to be dynamic in the zymogen and to become rigid upon activation, in particular the γ-loop, the 180s loop, and the Na(+) binding site have order parameters below 0.8. Significant R(ex) was observed in most of the γ-loop, in regions proximal to the light chain, and in the β-sheet core. Accelerated molecular dynamics simulations yielded a molecular ensemble consistent with measured residual dipolar couplings that revealed dynamic motions up to milliseconds. Several regions, including the light chain and two proximal loops, did not appear highly dynamic on the ps-ns timescale, but had significant motions on slower timescales. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.
A framework of DYNAMIC data structures for string processing
DEFF Research Database (Denmark)
Prezza, Nicola
2017-01-01
In this paper we present DYNAMIC, an open-source C++ library implementing dynamic compressed data structures for string manipulation. Our framework includes useful tools such as searchable partial sums, succinct/gap-encoded bitvectors, and entropy/run-length compressed strings and FM indexes. We...... implemented using DYNAMIC with those of stateof-the-art tools performing the same task. Our experiments show that algorithms making use of dynamic compressed data structures can be up to three orders of magnitude more space-efficient (albeit slower) than classical ones performing the same tasks....
Dynamics of cavitation-structure interaction
Wang, Guoyu; Wu, Qin; Huang, Biao
2017-08-01
Cavitation-structure interaction has become one of the major issues for most engineering applications. The present work reviews recent progress made toward developing experimental and numerical investigation for unsteady turbulent cavitating flow and cavitation-structure interaction. The goal of our overall efforts is to (1) summarize the progress made in the experimental and numerical modeling and approaches for unsteady cavitating flow and cavitation-structure interaction, (2) discuss the global multiphase structures for different cavitation regimes, with special emphasis on the unsteady development of cloud cavitation and corresponding cavitating flow-induced vibrations, with a high-speed visualization system and a structural vibration measurement system, as well as a simultaneous sampling system, (3) improve the understanding of the hydroelastic response in cavitating flows via combined physical and numerical analysis, with particular emphasis on the interaction between unsteady cavitation development and structural deformations. Issues including unsteady cavitating flow structures and cavitation-structure interaction mechanism are discussed.
Structural dynamic modification using additive damping
Indian Academy of Sciences (India)
Some current trends for vibration control are also discussed. Keywords. Structural modifications; viscoelastic damping; perturbation; sensitivity analysis; optimization; vibration control. 1. Introduction. Vibrations in machines and structures, if not properly controlled, may cause component fatigue and human discomfort.
Nonlinear structural mechanics theory, dynamical phenomena and modeling
Lacarbonara, Walter
2013-01-01
Nonlinear Structural Mechanics: Theory, Dynamical Phenomena and Modeling offers a concise, coherent presentation of the theoretical framework of nonlinear structural mechanics, computational methods, applications, parametric investigations of nonlinear phenomena and their mechanical interpretation towards design. The theoretical and computational tools that enable the formulation, solution, and interpretation of nonlinear structures are presented in a systematic fashion so as to gradually attain an increasing level of complexity of structural behaviors, under the prevailing assumptions on the geometry of deformation, the constitutive aspects and the loading scenarios. Readers will find a treatment of the foundations of nonlinear structural mechanics towards advanced reduced models, unified with modern computational tools in the framework of the prominent nonlinear structural dynamic phenomena while tackling both the mathematical and applied sciences. Nonlinear Structural Mechanics: Theory, Dynamical Phenomena...
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.
Nonlinear Light Dynamics in Multi-Core Structures
2017-02-27
AFRL-AFOSR-UK-TR-2017-0013 Nonlinear light dynamics in multi-core structures Sergei Turitsyn ASTON UNIVERSITY Final Report 02/27/2017 DISTRIBUTION A...From - To) 30 Sep 2014 to 29 Sep 2016 4. TITLE AND SUBTITLE Nonlinear light dynamics in multi-core structures 5a. CONTRACT NUMBER 5b. GRANT NUMBER...number: FA9550-14-1-0305 Nonlinear light dynamics in multi-core structures Summary. This report presents the results of the research activities
Ab initio theory for ultrafast magnetization dynamics with a dynamic band structure
Energy Technology Data Exchange (ETDEWEB)
Mueller, B.Y.; Haag, M.; Fähnle, M., E-mail: faehnle@is.mpg.de
2016-09-15
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. - Highlights: • The contribution of electron–electron spin-flip scattering to the ultrafast demagnetization of ferromagnets after laser excitation is investigated. • Dynamical change of the band structure is taken into account on an ab initio level. • Large influence of the dynamical band structure on the magnetization dynamics is observed. • We trace electron dynamics and explain the thermalization and relaxation process after laser irradiation. • Treating the dynamical band structure yields a demagnetization comparable to the experimental one.
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...... and show how to characterise the execution of DCR structures and the acceptance condition for infinite runs by giving a map to Bu ̈chi-automata. This is the first step towards automatic verification of processes specified as DCR structures....
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.
Protein dynamics derived from clusters of crystal structures
van Aalten, D.M.F.; Conn, D.A.; de Groot, B.L.; Berendsen, H.J.C.; Findlay, J.B.C.; 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
Dynamic active earth pressure on retaining structures
Indian Academy of Sciences (India)
the attention of researchers through the decades. Even under static conditions this is one of the most critical and complex problems of soil mechanics and geotechnical engineering. So, under dynamic condition and/or under seismic loading, the problem is no doubt challenging. The recent devastating earthquakes in India, ...
Effect of Gold Nanoparticle Conjugation on Peptide Dynamics and Structure
Directory of Open Access Journals (Sweden)
F. Marty Ytreberg
2012-03-01
Full Text Available Molecular dynamics simulations were used to characterize the structure and dynamics for several peptides and the effect of conjugating them to a gold nanoparticle. Peptide structure and dynamics were compared for two cases: unbound peptides in water, and peptides bound to the gold nanoparticle surface in water. The results show that conjugating the peptides to the gold nanoparticle usually decreases conformational entropy, but sometimes increases entropy. Conjugating the peptides can also result in more extended structures or more compact structures depending on the amino acid sequence of the peptide. The results also suggest that if one wishes to use peptide-nanoparticle conjugates for drug delivery it is important that the peptides contain secondary structure in solution because in our simulations the peptides with little to no secondary structure adsorbed to the nanoparticle surface.
Nonstationary and Chaotic Dynamics in Age-Structured Population Models
Directory of Open Access Journals (Sweden)
Arild Wikan
2017-01-01
Full Text Available The dynamics from nonlinear discrete age-structured population models is under consideration. Focus is on bifurcations, as well as nonstationary and chaotic dynamics. We also explore different mechanisms which may lead to periodic phenomena. Some new results are also presented, in particular from models where both fecundity and survival terms contain nonlinear elements.
Quantifying and modeling soil structure dynamics
Characterization of soil structure has been a topic of scientific discussions ever since soil structure has been recognized as an important factor affecting soil physical, mechanical, chemical, and biological processes. Beyond semi-quantitative soil morphology classes, it is a challenge to describe ...
HYDRATION STRUCTURE AND WATER EXCHANGE DYNAMICS ...
African Journals Online (AJOL)
Preferred Customer
was carried out for Fe(II) in water using the 2-body potential and its 3-body correction function to study hydration structure of the Fe(II) ion. Furthermore, the present study investigates the water exchange processes around the Fe(II) ion in the aqueous solution. Emphasis is given on the illumination of the structural changes at ...
Metapopulation Structure and Dynamics of an Endangered Butterfly
2010-01-01
J. Slansky, & J. G. Rodriguez (Eds.), Nutritional ecology of insects, mites, spiders , and related invertebrates (pp. 369–391). New York: John Wiley...structure and dynamics of an endangered butterfly Margaret S. Guineya,∗, David A. Andowb, Timothy T. Wilderc aDepartment of Conservation Biology , 200...Recovery plans for endangered invertebrates will improve with a better understanding of population dynamics and structure. Some spatially distributed
A new method for abrupt change detection in dynamic structures
Directory of Open Access Journals (Sweden)
W. P. He
2008-07-01
Full Text Available Based on Detrended Fluctuation Analysis (DFA, we propose a new method – Moving Detrended Fluctuation Analysis (MDFA – to detect abrupt change in dynamic structures. Application of this technique shows that this method may be of use in detecting time-instants of abrupt change in dynamic structures and we even find that the MDFA results almost do not depend on length of subseries, and are less affected by noise.
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
Controlling flexible structures with second order actuator dynamics
Inman, Daniel J.; Umland, Jeffrey W.; Bellos, John
1989-01-01
The control of flexible structures for those systems with actuators that are modeled by second order dynamics is examined. Two modeling approaches are investigated. First a stability and performance analysis is performed using a low order finite dimensional model of the structure. Secondly, a continuum model of the flexible structure to be controlled, coupled with lumped parameter second order dynamic models of the actuators performing the control is used. This model is appropriate in the modeling of the control of a flexible panel by proof-mass actuators as well as other beam, plate and shell like structural numbers. The model is verified with experimental measurements.
Structure prediction of subtilisin BPN' mutants using molecular dynamics methods
Heiner, Andreas P.; Berendsen, Herman J.C.; van Gunsteren, Wilfred F.
2017-01-01
In this paper we describe the achievements and pitfalls encountered in doing structure predictions of protein mutants using molecular dynamics simulation techniques in which properties of atoms are slowly changed as a function of time. Basically the method consists of a thermodynamic integration (slow growth) calculation used for free energy determination, but aimed at structure prediction; this allows for a fast determination of the mutant structure. We compared the calculated structure of t...
Combustion fume structure and dynamics. Final report
Energy Technology Data Exchange (ETDEWEB)
Flagan, R.C.
1995-06-29
An investigation of the fundamental physical processes that govern the structures of fume particles that are produced from the vapor phase in a wide range of high temperature systems has been conducted. The key objective of this study has been to develop models of the evolution of fine particles of refractory materials that are produced from the vapor phase, with particular emphasis on those processes that govern the evolution of ash fumes produced from volatilized mineral matter during coal combustion. To accomplish this goal, the study has included investigations of a number of fundamental aspects of pyrogenous fumes: Structural characterization of agglomerate particles in terms of fractal structure parameters; the relationship between the structures of agglomerate particles and the aerodynamic drag forces they experience; coagulation kinetics of fractal-like particles; sintering of aerosol agglomerates past the early stage of neck formation and incorporating the simultaneous influences of several transport mechanisms.
On population structure and marriage dynamics
Giolito, Eugenio P.
2010-01-01
I develop an equilibrium, two-sided search model of marriage with endogenous population growth to study the interaction between fertility, the age structure of the population and the age at first marriage of men and women. Within a simple two-period overlapping generation model I show that, given an increase of the desired number of children, age at marriage is affected through two different channels. First, as population growth increases, the age structure of the population produces a thicke...
Partial structure factors reveal atomic dynamics in metallic alloy melts
Nowak, B.; Holland-Moritz, D.; Yang, F.; Voigtmann, Th.; Kordel, T.; Hansen, T. C.; Meyer, A.
2017-07-01
We investigate the dynamical decoupling of the diffusion coefficients of the different components in a metallic alloy melt, using a combination of neutron diffraction, isotopic substitution, and electrostatic levitation in Zr-Ni melts. We show that excess Ni atoms can diffuse more freely in a background of saturated chemical interaction, causing their dynamics to become much faster and thus decoupled than anticipated from the interparticle interactions. Based on the mode-coupling theory of the glass transition, the averaged structure as given by the partial static structure factors is able to explain the observed dynamical behavior.
Structure and dynamics of water inside hydrophobic and hydrophilic nanotubes
Köhler, Mateus Henrique; Bordin, José Rafael; da Silva, Leandro B.; Barbosa, Marcia C.
2018-01-01
We have used Molecular Dynamics simulations to investigate the structure and dynamics of TIP4P/2005 water confined inside nanotubes. The nanotubes have distinct sizes and were built with hydrophilic or hydrophobic sites, and we compare the water behavior inside each nanotube. Our results shows that the structure and dynamics are strongly influenced by polarity inside narrow nanotubes, where water layers were observed, and the influence is negligible for wider nanotubes, where the water has a bulk-like density profile. As well, we show that water at low density can have a smaller diffusion inside nanotubes than water at higher densities. This result is a consequence of water diffusion anomaly.
Ab initio lattice dynamics of complex structures
DEFF Research Database (Denmark)
Voss, Johannes
2008-01-01
atomic coordinates, we have developed a new numerical optimization scheme, which allows for a fast convergence of the coordinate relaxation. Moreover, a method for the efficient calculation of phonon frequencies has been developed, which is based on a combination of density functional theory calculations......, showing that the mobility of hydrogen is limited by high energetic barriers in the intermediate decomposition product Na3AlH6 in particular, and that the effect of titanium as a dopant on the dynamics is negligible. The presented methods and studies demonstrate possibilities for a design of new materials...
The dynamics and control of large flexible space structures
Bainum, P. M.; Kumar, V. K.; Krishna, R.; Reddy, A. S. S. R.; Diarra, C. M.
1983-01-01
Large, flexible orbiting systems proposed for possible use in communications, electronic orbital based mail systems, and solar energy collection are discussed. The size and low weight to area ratio of such systems indicate that system flexibility is now the main consideration in the dynamics and control problem. For such large, flexible systems, both orientation and surface shape control will often be required. A conceptual development plan of a system software capability for use in analysis of the dynamics and control of large space structures technology (LSST) systems is discussed. This concept can be subdivided into four different stages: (1) system dynamics; (2) structural dynamics; (3) application of control algorithms; and (4) simulation of environmental disturbances. Modeling the system dynamics of such systems in orbit is the most fundamental component. Solar radiation pressure effects and orbital and gravity gradient effects are discussed.
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...
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.
Structure and dynamics of magnetic nanoparticles
DEFF Research Database (Denmark)
Clausen, K.N.; Bødker, F.; Hansen, M.F.
2000-01-01
In this paper we present X-ray and neutron diffraction data illustrating aspects of crystal and magnetic structures of ferromagnetic alpha-Fe and antiferromagnetic NiO nanoparticles, as well as inelastic neutron scattering studies of the magnetic fluctuations in NiO and in canted antiferromagnetic...
Studying the dynamics of coronavirus replicative structures
Hagemeijer, Marne C.; De Haan, Cornelis A M
2015-01-01
Coronaviruses (CoVs) generate specialized membrane compartments, which consist of double membrane vesicles connected to convoluted membranes, the so-called replicative structures, where viral RNA synthesis takes place. These sites harbor the CoV replication-transcription complexes (RTCs):
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.
Structural Identifiability of Dynamic Systems Biology Models.
Villaverde, Alejandro F; Barreiro, Antonio; Papachristodoulou, Antonis
2016-10-01
A powerful way of gaining insight into biological systems is by creating a nonlinear differential equation model, which usually contains many unknown parameters. Such a model is called structurally identifiable if it is possible to determine the values of its parameters from measurements of the model outputs. Structural identifiability is a prerequisite for parameter estimation, and should be assessed before exploiting a model. However, this analysis is seldom performed due to the high computational cost involved in the necessary symbolic calculations, which quickly becomes prohibitive as the problem size increases. In this paper we show how to analyse the structural identifiability of a very general class of nonlinear models by extending methods originally developed for studying observability. We present results about models whose identifiability had not been previously determined, report unidentifiabilities that had not been found before, and show how to modify those unidentifiable models to make them identifiable. This method helps prevent problems caused by lack of identifiability analysis, which can compromise the success of tasks such as experiment design, parameter estimation, and model-based optimization. The procedure is called STRIKE-GOLDD (STRuctural Identifiability taKen as Extended-Generalized Observability with Lie Derivatives and Decomposition), and it is implemented in a MATLAB toolbox which is available as open source software. The broad applicability of this approach facilitates the analysis of the increasingly complex models used in systems biology and other areas.
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...
Molecular dynamics of the structure and thermodynamics of dusty ...
African Journals Online (AJOL)
The static structure and thermodynamic properties of two-dimensional dusty plasma are analyzed for some typical values of coupling and screening parameters using classical molecular dynamics. Radial distribution function and static structure factor are computed. The radial distribution functions display the typical ...
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…
Language dynamics in structured form and meaning spaces
de Boer, B.; Verhoef, T.
2012-01-01
This paper reviews how the structure of form and meaning spaces influences the nature and the dynamics of the form-meaning mappings in language. In general, in a structured form or meaning space, not all forms and meanings are equivalent: some forms and some meanings are more easily confused with
Structural and dynamic properties of urea and thiourea inclusion compounds
Harris, Kenneth D. M.
1996-01-01
There is currently considerable interest in the chemistry and physics of solid inclusion compounds as a consequence of the wide range of important physico-chemical properties associated with them. In part, scientific interest in these materials is motivated by the desire to compare the structural, dynamic, and chemical properties of organic "guest" molecules embedded within different crystalline environments, and to investigate how the properties of the guest molecule may be influenced by the structural characteristics of its environment. This paper is focused upon urea and thiourea inclusion compounds containing a variety of different types of organic guest molecule. Aspects of the structural and dynamic properties of these inclusion compounds have been probed using solid-state NMR spectroscopy, X-ray diffraction, EXAFS spectroscopy, incoherent quasielastic neutron scattering, Raman spectroscopy, computer simulation and mathematical modelling. On the basis of the results from these investigations, the current level of understanding of the structural and dynamic properties of these materials is assessed.
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...
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 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.
Structural concerns in dynamic drop loads on transfer lock mechanisms
Energy Technology Data Exchange (ETDEWEB)
Pfeiffer, P.A.; Moran, T.J.; Kulak, R.F. [Argonne National Lab., IL (United States). Reactor Engineering Div.
1997-07-01
Drop loads are usually low probability events that can generate substantial loading to the impacted structures. When the impacted structure contains slender elements, the concern about dynamic buckling must be addressed. The problem of interest here is a structure is also under significant preload, which must be taken into account in the transient analysis. For complex structures, numerical simulations are the only viable option for assessing the transient response to short duration impactive loads. this paper addresses several analysis issues of preloaded structures with slender members subjected to drop loads. A three-dimensional beam element is validated for use in dynamic buckling analysis. the numerical algorithm used to solve the transient response of preloaded structures is discussed. The methodology is applied to an inter-compartment lock that is under significant preloads, and subjected to a drop load.
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.
Information Diversity in Structure and Dynamics of Simulated Neuronal Networks
Directory of Open Access Journals (Sweden)
Tuomo eMäki-Marttunen
2011-06-01
Full Text Available 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 (NCD. 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 behaviours 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.
Structural dynamics of the cell nucleus
Wiegert, Simon; Bading, Hilmar
2011-01-01
Neuronal morphology plays an essential role in signal processing in the brain. Individual neurons can undergo use-dependent changes in their shape and connectivity, which affects how intracellular processes are regulated and how signals are transferred from one cell to another in a neuronal network. Calcium is one of the most important intracellular second messengers regulating cellular morphologies and functions. In neurons, intracellular calcium levels are controlled by ion channels in the plasma membrane such as NMDA receptors (NMDARs), voltage-gated calcium channels (VGCCs) and certain α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) as well as by calcium exchange pathways between the cytosol and internal calcium stores including the endoplasmic reticulum and mitochondria. Synaptic activity and the subsequent opening of ligand and/or voltage-gated calcium channels can initiate cytosolic calcium transients which propagate towards the cell soma and enter the nucleus via its nuclear pore complexes (NPCs) embedded in the nuclear envelope. We recently described the discovery that in hippocampal neurons the morphology of the nucleus affects the calcium dynamics within the nucleus. Here we propose that nuclear infoldings determine whether a nucleus functions as an integrator or detector of oscillating calcium signals. We outline possible ties between nuclear mophology and transcriptional activity and discuss the importance of extending the approach to whole cell calcium signal modeling in order to understand synapse-to-nucleus communication in healthy and dysfunctional neurons. PMID:21738832
Dynamic and structural control utilizing smart materials and structures
Rogers, C. A.; Robertshaw, H. H.
1989-01-01
An account is given of several novel 'smart material' structural control concepts that are currently under development. The thrust of these investigations is the evolution of intelligent materials and structures superceding the recently defined variable-geometry trusses and shape memory alloy-reinforced composites; the substances envisioned will be able to autonomously evaluate emergent environmental conditions and adapt to them, and even change their operational objectives. While until now the primary objective of the developmental efforts presently discussed has been materials that mimic biological functions, entirely novel concepts may be formulated in due course.
The Dynamics and Structures of Adsorbed Surfaces
DEFF Research Database (Denmark)
Nielsen, M; Ellenson, W. D.; McTague, J. P.
1978-01-01
. Elastic neutron diffraction measurements, determining the two-dimensional structural ordering of the adsorbed films, have been performed on layers of N2, Ar, H2, D2, O2, Kr, and He. Measurements on layers of larger molecules such as CD4 and ND3 have also been reported. Inelastic neutron scattering...... of molecules such as NH3 or the internal modes of adsorbed molecules such as C4H10. Neutron scattering measurements where substrates other than graphite products are used as the adsorbents will not be reviewed here. However, the power of the technique will be demonstrated in an example of H2 physisorbed...
Dynamic Identification for Control of Large Space Structures
Ibrahim, S. R.
1985-01-01
This is a compilation of reports by the one author on one subject. It consists of the following five journal articles: (1) A Parametric Study of the Ibrahim Time Domain Modal Identification Algorithm; (2) Large Modal Survey Testing Using the Ibrahim Time Domain Identification Technique; (3) Computation of Normal Modes from Identified Complex Modes; (4) Dynamic Modeling of Structural from Measured Complex Modes; and (5) Time Domain Quasi-Linear Identification of Nonlinear Dynamic Systems.
Dynamic membrane structure induces temporal pattern formation.
Lippoldt, J; Händel, C; Dietrich, U; Käs, J A
2014-10-01
The understanding of temporal pattern formation in biological systems is essential for insights into regulatory processes of cells. Concerning this problem, the present work introduces a model to explain the attachment/detachment cycle of MARCKS and PKC at the cell membrane, which is crucial for signal transduction processes. Our model is novel with regard to its driving mechanism: Structural changes within the membrane fuel an activator-inhibitor based global density oscillation of membrane related proteins. Based on simulated results of our model, phase diagrams were generated to illustrate the interplay of MARCKS and PKC. They predict the oscillatory behavior in the form of the number of peaks, the periodic time, and the damping constant depending on the amounts of MARCKS and PKC, respectively. The investigation of the phase space also revealed an unexpected intermediate state prior to the oscillations for high amounts of MARCKS in the system. The validation of the obtained results was carried out by stability analysis, which also accounts for further enhanced understanding of the studied system. It was shown, that the occurrence of the oscillating behavior is independent of the diffusion and the consumption of the reactants. The diffusion terms in the used reaction-diffusion equations only act as modulating terms and are not required for the oscillation. The hypothesis of our work suggests a new mechanism of temporal pattern formation in biological systems. This mechanism includes a classical activator-inhibitor system, but is based on the modifications of the membrane structure, rather than a reaction-diffusion system. Copyright © 2014 Elsevier B.V. All rights reserved.
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. Copyright © 2011 Elsevier Ltd. All rights reserved.
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.
An optimal dynamic interval stabbing-max data structure?
DEFF Research Database (Denmark)
Agarwal, Pankaj Kumar; Arge, Lars; Yi, Ke
2005-01-01
In this paper we consider the dynamic stabbing-max problem, that is, the problem of dynamically maintaining a set S of n axis-parallel hyper-rectangles in Rd, where each rectangle s ∈ S has a weight w(s) ∈ R, so that the rectangle with the maximum weight containing a query point can be determined...... efficiently. We develop a linear-size structure for the one-dimensional version of the problem, the interval stabbing-max problem, that answers queries in worst-case O(log n) time and supports updates in amortized O(log n) time. Our structure works in the pointer-machine model of computation and utilizes many...... ingredients from recently developed external memory structures. Using standard techniques, our one-dimensional structure can be extended to higher dimensions, while paying a logarithmic factor in space, update time, and query time per dimension. Furthermore, our structure can easily be adapted to external...
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...
Modelling sequences and temporal networks with dynamic community structures.
Peixoto, Tiago P; Rosvall, Martin
2017-09-19
In evolving complex systems such as air traffic and social organisations, collective effects emerge from their many components' dynamic interactions. While the dynamic interactions can be represented by temporal networks with nodes and links that change over time, they remain highly complex. It is therefore often necessary to use methods that extract the temporal networks' large-scale dynamic community structure. However, such methods are subject to overfitting or suffer from effects of arbitrary, a priori-imposed timescales, which should instead be extracted from data. Here we simultaneously address both problems and develop a principled data-driven method that determines relevant timescales and identifies patterns of dynamics that take place on networks, as well as shape the networks themselves. We base our method on an arbitrary-order Markov chain model with community structure, and develop a nonparametric Bayesian inference framework that identifies the simplest such model that can explain temporal interaction data.The description of temporal networks is usually simplified in terms of their dynamic community structures, whose identification however relies on a priori assumptions. Here the authors present a data-driven method that determines relevant timescales for the dynamics and uses it to identify communities.
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.
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.
An Aspect of Dynamic Human-structure Interaction
DEFF Research Database (Denmark)
Pedersen, Lars
2008-01-01
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......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....... 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...
Adaptive mutations alter antibody structure and dynamics during affinity maturation.
Adhikary, Ramkrishna; Yu, Wayne; Oda, Masayuki; Walker, Ross C; Chen, Tingjian; Stanfield, Robyn L; Wilson, Ian A; Zimmermann, Jörg; Romesberg, Floyd E
2015-03-24
While adaptive mutations can bestow new functions on proteins via the introduction or optimization of reactive centers, or other structural changes, a role for the optimization of protein dynamics also seems likely but has been more difficult to evaluate. Antibody (Ab) affinity maturation is an example of adaptive evolution wherein the adaptive mutations may be identified and Abs may be raised to specific targets that facilitate the characterization of protein dynamics. Here, we report the characterization of three affinity matured Abs that evolved from a common germline precursor to bind the chromophoric antigen (Ag), 8-methoxypyrene-1,3,6-trisulfonate (MPTS). In addition to characterizing the sequence, molecular recognition, and structure of each Ab, we characterized the dynamics of each complex by determining their mechanical response to an applied force via three-pulse photon echo peak shift (3PEPS) spectroscopy and deconvoluting the response into elastic, anelastic, and plastic components. We find that for one Ab, affinity maturation was accomplished via the introduction of a single functional group that mediates a direct contact with MPTS and results in a complex with little anelasticity or plasticity. In the other two cases, more mutations were introduced but none directly contact MPTS, and while their effects on structure are subtle, their effects on anelasticity and plasticity are significant, with the level of plasticity correlated with specificity, suggesting that the optimization of protein dynamics may have contributed to affinity maturation. A similar optimization of structure and dynamics may contribute to the evolution of other proteins.
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.
Acetylene structure and dynamics on Pd(111)
Energy Technology Data Exchange (ETDEWEB)
Dunphy, J.C.; Rose, M.; Behler, S.; Ogletree, D.F.; Salmeron, M. [Lawrence Berkeley National Laboratory, Materials Sciences Division, University of California, Berkeley, California 94720 (United States); Sautet, P. [Laboratoire de Chimie Theorique, ENS, 69364Lyon (France)]|[Institut de Recherches sur la Catalyse, CNRS, 69626Villeurbanne (France)
1998-05-01
Acetylene molecules adsorbed onto a Pd(111) crystal surface were imaged by scanning tunneling microscopy (STM) below 70 K. Single C{sub 2}H{sub 2} molecules appeared as a combination of a protrusion and a depression 3.5 {Angstrom} apart. This peculiar shape is due to the molecular {pi} orbital, which is oriented at a shallow angle out of the surface. Six orientations of the molecule with respect to the substrate were observed, indicating two different threefold hollow binding sites each with three possible rotational states. At 44 K, thermally activated rotation of the molecules between the three equivalent states on the same threefold hollow site occurs on the time scale of seconds. Diffusion of molecules between adjacent threefold sites began at {approximately}70K. The findings agree with the structure of the adsorption site determined by total-energy calculations and with the STM image calculated using the electron scattering quantum chemistry method. {copyright} {ital 1998} {ital The American Physical Society}
Map updates in a dynamic Voronoi data structure
DEFF Research Database (Denmark)
Mioc, Darka; Antón Castro, Francesc/François; Gold, C. M.
2006-01-01
algorithms for addition, deletion, and motion of spatial objects) on the dynamic Voronoi data structure. The formalization of map commands led to the development of a spatial language comprising a set of atomic operations or constructs on spatial primitives (points and lines), powerful enough to define...... the complex operations. This resulted in a new formal model for map updates, similar to "cellular encoding", where each update is uniquely characterized by the numbers of newly created and inactivated Voronoi regions. This research shows that the result of the formalization of the operations on the dynamic...... Voronoi data structure is a spatial language or a map grammar that is deterministic and reversible....
Control of Spin Wave Dynamics in Spatially Twisted Magnetic Structures
2017-06-27
AFRL-AFOSR-JP-TR-2017-0053 Control of Spin Wave Dynamics in Spatially Twisted Magnetic Structures Takeshi Seki TOHOKU UNIVERSITY Final Report 06/27...currently valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ORGANIZATION. 1. REPORT DATE (DD-MM-YYYY) 27-06-2017 2. REPORT TYPE Final...3. DATES COVERED (From - To) 12 Jun 2015 to 12 Dec 2016 4. TITLE AND SUBTITLE Control of Spin Wave Dynamics in Spatially Twisted Magnetic Structures
Structural and dynamic characteristics in monolayer square ice.
Zhu, YinBo; Wang, FengChao; Wu, HengAn
2017-07-28
When water is constrained between two sheets of graphene, it becomes an intriguing monolayer solid with a square pattern due to the ultrahigh van der Waals pressure. However, the square ice phase has become a matter of debate due to the insufficient experimental interpretation and the slightly rhomboidal feature in simulated monolayer square-like structures. Here, we performed classical molecular dynamics simulations to reveal monolayer square ice in graphene nanocapillaries from the perspective of structure and dynamic characteristics. Monolayer square-like ice (instantaneous snapshot), assembled square-rhombic units with stacking faults, is a long-range ordered structure, in which the square and rhombic units are assembled in an order of alternative distribution, and the other rhombic unit forms stacking faults (polarized water chains). Spontaneous flipping of water molecules in monolayer square-like ice is intrinsic and induces transformations among different elementary units, resulting in the structural evolution of monolayer square ice in dynamics. The existence of stacking faults should be attributed to the spontaneous flipping behavior of water molecules under ambient temperature. Statistical averaging results (thermal average positions) demonstrate the inherent square characteristic of monolayer square ice. The simulated data and insight obtained here might be significant for understanding the topological structure and dynamic behavior of monolayer square ice.
Higher-order structure and epidemic dynamics in clustered networks.
Ritchie, Martin; Berthouze, Luc; House, Thomas; Kiss, Istvan Z
2014-05-07
Clustering is typically measured by the ratio of triangles to all triples regardless of whether open or closed. Generating clustered networks, and how clustering affects dynamics on networks, is reasonably well understood for certain classes of networks (Volz et al., 2011; Karrer and Newman, 2010), e.g. networks composed of lines and non-overlapping triangles. In this paper we show that it is possible to generate networks which, despite having the same degree distribution and equal clustering, exhibit different higher-order structure, specifically, overlapping triangles and other order-four (a closed network motif composed of four nodes) structures. To distinguish and quantify these additional structural features, we develop a new network metric capable of measuring order-four structure which, when used alongside traditional network metrics, allows us to more accurately describe a network׳s topology. Three network generation algorithms are considered: a modified configuration model and two rewiring algorithms. By generating homogeneous networks with equal clustering we study and quantify their structural differences, and using SIS (Susceptible-Infected-Susceptible) and SIR (Susceptible-Infected-Recovered) dynamics we investigate computationally how differences in higher-order structure impact on epidemic threshold, final epidemic or prevalence levels and time evolution of epidemics. Our results suggest that characterising and measuring higher-order network structure is needed to advance our understanding of the impact of network topology on dynamics unfolding on the networks. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.
Lumped mass modelling for the dynamic analysis of aircraft structures
Abu-Saba, Elias G.; Shen, Ji Yao; Mcginley, William M.; Montgomery, Raymond C.
1992-01-01
Aircraft structures may be modelled by lumping the masses at particular strategic points and the flexibility or stiffness of the structure is obtained with reference to these points. Equivalent moments of inertia for the section at these positions are determined. The lumped masses are calculated based on the assumption that each point will represent the mass spread on one half of the space on each side. Then these parameters are used in the differential equation of motion and the eigen characteristics are determined. A comparison is made with results obtained by other established methods. The lumped mass approach in the dynamic analysis of complicated structures provides an easier means of predicting the dynamic characteristics of these structures. It involves less computer time and avoids computational errors that are inherent in the numerical solution of complicated systems.
Water Determines the Structure and Dynamics of Proteins.
Bellissent-Funel, Marie-Claire; Hassanali, Ali; Havenith, Martina; Henchman, Richard; Pohl, Peter; Sterpone, Fabio; van der Spoel, David; Xu, Yao; Garcia, Angel E
2016-07-13
Water is an essential participant in the stability, structure, dynamics, and function of proteins and other biomolecules. Thermodynamically, changes in the aqueous environment affect the stability of biomolecules. Structurally, water participates chemically in the catalytic function of proteins and nucleic acids and physically in the collapse of the protein chain during folding through hydrophobic collapse and mediates binding through the hydrogen bond in complex formation. Water is a partner that slaves the dynamics of proteins, and water interaction with proteins affect their dynamics. Here we provide a review of the experimental and computational advances over the past decade in understanding the role of water in the dynamics, structure, and function of proteins. We focus on the combination of X-ray and neutron crystallography, NMR, terahertz spectroscopy, mass spectroscopy, thermodynamics, and computer simulations to reveal how water assist proteins in their function. The recent advances in computer simulations and the enhanced sensitivity of experimental tools promise major advances in the understanding of protein dynamics, and water surely will be a protagonist.
Structure and dynamics of aqueous solution of uranyl ions
Energy Technology Data Exchange (ETDEWEB)
Chopra, Manish [Radiation Safety Systems Division, Bhabha Atomic Research Centre, Mumbai-400085 (India); Choudhury, Niharendu, E-mail: nihcho@barc.gov.in [Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai-400085 (India)
2014-04-24
The present work describes a molecular dynamics simulation study of structure and dynamics of aqueous solution of uranyl ions in water. Structural properties of the system in terms of radial distribution functions and dynamical characteristics as obtained through velocity autocorrelation function and mean square displacements have been analyzed. The results for radial distribution functions show the oxygen of water to form the first solvation shell at 2.4 Å around the uranium atom, whereas the hydrogen atoms of water are distributed around the uranium atom with the major peak at around 3.0 Å. Analyses of transport behaviors of ions and water through MSD indicates that the diffusion of the uranyl ion is much less as compared to that of the water molecules. It is also observed that the dynamical behavior of water molecules gets modified due to the presence of uranyl ion. The effect of increase in concentration of uranyl ions on the structure and dynamics of water molecules is also studied.
32nd IMAC Conference and Exposition on Structural Dynamics
Mayes, Randy; Rixen, Daniel; Catbas, Fikret; Atamturktur, H; Moaveni, Babak; Papadimitriou, Costas; Schoenherr, Tyler; Foss, Gary; Niezrecki, Christopher; Allemang, Randall; Kerschen, Gaetan
2014-01-01
This critical collection examines a range of topics in modal analysis, from experimental techniques to acoustics to biodynamics, as presented in early findings and case studies from the Proceedings of the 32nd IMAC, A Conference and Exposition on Structural Dynamics, 2014. The collection includes papers in the following general technical research areas: Experimental Techniques, Processing Modal Data, Rotating Machinery, Acoustics, Adaptive Structures, Biodynamics, Damping
Dynamics and mechanism of structural diffusion in linear hydrogen bond.
Chaiwongwattana, Sermsiri; Phonyiem, Mayuree; Vchirawongkwin, Viwat; Prueksaaroon, Supakit; Sagarik, Kritsana
2012-01-15
Dynamics and mechanism of proton transfer in a protonated hydrogen bond (H-bond) chain were studied, using the CH(3)OH(2)(+)(CH(3)OH)(n) complexes, n = 1-4, as model systems. The present investigations used B3LYP/TZVP calculations and Born-Oppenheimer MD (BOMD) simulations at 350 K to obtain characteristic H-bond structures, energetic and IR spectra of the transferring protons in the gas phase and continuum liquid. The static and dynamic results were compared with the H(3)O(+)(H(2)O)(n) and CH(3)OH(2)(+)(H(2)O)(n) complexes, n = 1-4. It was found that the H-bond chains with n = 1 and 3 represent the most active intermediate states and the CH(3)OH(2)(+)(CH(3)OH)(n) complexes possess the lowest threshold frequency of proton transfer. The IR spectra obtained from BOMD simulations revealed that the thermal energy fluctuation and dynamics help promote proton transfer in the shared-proton structure with n = 3 by lowering the vibrational energy for the interconversion between the oscillatory shuttling and structural diffusion motions, leading to a higher population of the structural diffusion motion than in the shared-proton structure with n = 1. Additional explanation on the previously proposed mechanisms was introduced, with the emphases on the energetic of the transferring proton, the fluctuation of the number of the CH(3)OH molecules in the H-bond chain, and the quasi-dynamic equilibriums between the shared-proton structure (n = 3) and the close-contact structures (n ≥ 4). The latter prohibits proton transfer reaction in the H-bond chain from being concerted, since the rate of the structural diffusion depends upon the lifetime of the shared-proton intermediate state. Copyright © 2011 Wiley Periodicals, Inc.
Unlocking the Structure and Dynamics of Thin Polymeric Films
2016-11-13
librational freedom, branched structures , and in the case of copolymers, monomers of (potentially) differing surface energy along the chain...containing molecules are known to have low surface energy , and to partition to the interfaces in heterogeneous films. In paper 2, the architecture and...AFRL-AFOSR-JP-TR-2016-0092 Unlocking the Structure and Dynamics of Thin Polymeric Films Andrew Whittaker THE UNIVERSITY OF QUEENSLAND Final Report 11
Development of structural health monitoring techniques using dynamics testing
Energy Technology Data Exchange (ETDEWEB)
James, G.H. III [Sandia National Labs., Albuquerque, NM (United States). Experimental Structural Dynamics Dept.
1996-03-01
Today`s society depends upon many structures (such as aircraft, bridges, wind turbines, offshore platforms, buildings, and nuclear weapons) which are nearing the end of their design lifetime. Since these structures cannot be economically replaced, techniques for structural health monitoring must be developed and implemented. Modal and structural dynamics measurements hold promise for the global non-destructive inspection of a variety of structures since surface measurements of a vibrating structure can provide information about the health of the internal members without costly (or impossible) dismantling of the structure. In order to develop structural health monitoring for application to operational structures, developments in four areas have been undertaken within this project: operational evaluation, diagnostic measurements, information condensation, and damage identification. The developments in each of these four aspects of structural health monitoring have been exercised on a broad range of experimental data. This experimental data has been extracted from structures from several application areas which include aging aircraft, wind energy, aging bridges, offshore structures, structural supports, and mechanical parts. As a result of these advances, Sandia National Laboratories is in a position to perform further advanced development, operational implementation, and technical consulting for a broad class of the nation`s aging infrastructure problems.
Upstream trophic structure modulates downstream community dynamics via resource subsidies.
Harvey, Eric; Gounand, Isabelle; Little, Chelsea J; Fronhofer, Emanuel A; Altermatt, Florian
2017-08-01
In many natural systems, the physical structure of the landscape dictates the flow of resources. Despite mounting evidence that communities' dynamics can be indirectly coupled by reciprocal among ecosystem resource flows, our understanding of how directional resource flows might indirectly link biological communities is limited. We here propose that differences in community structure upstream should lead to different downstream dynamics, even in the absence of dispersal of organisms. We report an experimental test of the effect of upstream community structure on downstream community dynamics in a simplified but highly controlled setting, using protist microcosms. We implemented directional flows of resources, without dispersal, from a standard resource pool into upstream communities of contrasting interaction structure and then to further downstream communities of either one or two trophic levels. Our results demonstrate that different types of species interactions in upstream habitats may lead to different population sizes and levels of biomass in these upstream habitats. This, in turn, leads to varying levels of detritus transfer (dead biomass) to the downstream communities, thus influencing their population densities and trophic interactions in predictable ways. Our results suggest that the structure of species interactions in directionally structured ecosystems can be a key mediator of alterations to downstream habitats. Alterations to upstream habitats can thus cascade down to downstream communities, even without dispersal.
Spectroscopic Tools for Quantitative Studies of DNA Structure and Dynamics
DEFF Research Database (Denmark)
Preus, Søren
The main objective of this thesis is to develop quantitative fluorescence-based, spectroscopic tools for probing the 3D structure and dynamics of DNA and RNA. The thesis is founded on six peer-reviewed papers covering mainly the development, characterization and use of fluorescent nucleobase...
Dynamic soil-structure interaction of monopod and polypod foundations
DEFF Research Database (Denmark)
Andersen, Lars Vabbersgaard
2016-01-01
The paper concerns the importance of through–soil coupling for structures having foundations with more footings. First, a model for dynamic analysis of polypod footings is established in the frequency domain, employing Green’s function for wave propagation in a layered half-space. To allow analysis...
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...
Simultaneous dynamic electrical and structural measurements of functional materials
Energy Technology Data Exchange (ETDEWEB)
Vecchini, C.; Stewart, M.; Muñiz-Piniella, A.; Wooldridge, J. [National Physical Laboratory, Hampton Road, Teddington TW11 0LW (United Kingdom); Thompson, P.; McMitchell, S. R. C.; Bouchenoire, L.; Brown, S.; Wermeille, D.; Lucas, C. A. [XMaS, The UK-CRG, ESRF-The European Synchrotron, CS40220, F-38043, Grenoble Cedex 09 (France); Department of Physics, University of Liverpool, Liverpool L69 3BX (United Kingdom); Lepadatu, S. [National Physical Laboratory, Hampton Road, Teddington TW11 0LW (United Kingdom); Jeremiah Horrocks Institute, University of Central Lancashire, Preston PR1 2HE (United Kingdom); Bikondoa, O.; Hase, T. P. A. [XMaS, The UK-CRG, ESRF-The European Synchrotron, CS40220, F-38043, Grenoble Cedex 09 (France); Department of Physics, University of Warwick, Coventry CV4 7AL (United Kingdom); Lesourd, M. [ESRF-The European Synchrotron, CS40220, F-38043, Grenoble Cedex 09 (France); Dontsov, D. [SIOS Meßtechnik GmbH, Am Vogelherd 46, 98693 Ilmenau (Germany); Cain, M. G. [National Physical Laboratory, Hampton Road, Teddington TW11 0LW (United Kingdom); Electrosciences Ltd., Farnham, Surrey GU9 9QT (United Kingdom)
2015-10-15
A new materials characterization system developed at the XMaS beamline, located at the European Synchrotron Radiation Facility in France, is presented. We show that this new capability allows to measure the atomic structural evolution (crystallography) of piezoelectric materials whilst simultaneously measuring the overall strain characteristics and electrical response to dynamically (ac) applied external stimuli.
The stability and dynamic behaviour of fluid-loaded structures
CSIR Research Space (South Africa)
Suliman, Ridhwaan
2015-07-01
Full Text Available volume method for discretisation of the entire domain and a reduced-order modal approach for the structure coupled with a finite volume fluid solver. Strong-coupling is achieved by means of a fixed-point solver with dynamic relaxation. Both approaches...
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
On the use of Stockwell transform in structural dynamic analysis
Indian Academy of Sciences (India)
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 ...
A new dynamic null model for phylogenetic community structure
Pigot, Alex L; Etienne, Rampal S
Phylogenies are increasingly applied to identify the mechanisms structuring ecological communities but progress has been hindered by a reliance on statistical null models that ignore the historical process of community assembly. Here, we address this, and develop a dynamic null model of assembly by
Composition, structure, and dynamics of the Illinois Ozark Hills Forest
Lisa M. Helmig; James S. Fralish
2011-01-01
In the mature oak-hickory ecosystem of the Illinois Ozark Hills, forest community composition, dynamics, and structure were studied to examine the extent of conversion to mesophytic species and eventually predict the broad threshold time of complete conversion. Tree, sapling, and seedling data were collected from 87 plots distributed throughout the region. Data for the...
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.
Structural preablation dynamics of graphite observed by ultrafast electron crystallography
Carbone, Fabrizio; Baum, Peter; Rudolf, Petra; Zewail, Ahmed H.
2008-01-01
By means of time-resolved electron crystallography, we report direct observation of the structural dynamics of graphite, providing new insights into the processes involving coherent lattice motions and ultrafast graphene ablation. When graphite is excited by an ultrashort laser pulse, the excited
Dynamics and control of twisting bi-stable structures
Arrieta, Andres F.; van Gemmeren, Valentin; Anderson, Aaron J.; Weaver, Paul M.
2018-02-01
Compliance-based morphing structures have the potential to offer large shape adaptation, high stiffness and low weight, while reducing complexity, friction, and scalability problems of mechanism based systems. A promising class of structure that enables these characteristics are multi-stable structures given their ability to exhibit large deflections and rotations without the expensive need for continuous actuation, with the latter only required intermittently. Furthermore, multi-stable structures exhibit inherently fast response due to the snap-through instability governing changes between stable states, enabling rapid configuration switching between the discrete number of programmed shapes of the structure. In this paper, the design and utilisation of the inherent nonlinear dynamics of bi-stable twisting I-beam structures for actuation with low strain piezoelectric materials is presented. The I-beam structure consists of three compliant components assembled into a monolithic single element, free of moving parts, and showing large deflections between two stable states. Finite element analysis is utilised to uncover the distribution of strain across the width of the flange, guiding the choice of positioning for piezoelectric actuators. In addition, the actuation authority is maximised by calculating the generalised coupling coefficient for different positions of the piezoelectric actuators. The results obtained are employed to tailor and test I-beam designs exhibiting desired large deflection between stable states, while still enabling the activation of snap-through with the low strain piezoelectric actuators. To this end, the dynamic response of the I-beams to piezoelectric excitation is investigated, revealing that resonant excitations are insufficient to dynamically trigger snap-through. A novel bang–bang control strategy, which exploits the nonlinear dynamics of the structure successfully triggers both single and constant snap-through between the stable
DEFF Research Database (Denmark)
Luczak, Marcin; Peeters, Bart; Kahsin, Maciej
2014-01-01
Aerospace and wind energy structures are extensively using components made of composite materials. Since these structures are subjected to dynamic environments with time-varying loading conditions, it is important to model their dynamic behavior and validate these models by means of vibration...... for uncertainty evaluation in experimentally estimated models. Investigated structures are plates, fuselage panels and helicopter main rotor blades as they represent different complexity levels ranging from coupon, through sub-component up to fully assembled structures made of composite materials. To evaluate...
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.
Structure and dynamics in network-forming materials.
Wilson, Mark
2016-12-21
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.
Size-structure dynamics of mixed versus pure forest stands
Directory of Open Access Journals (Sweden)
Hans Pretzsch
2014-12-01
Full Text Available Mixed species forests are presently on the advance and widely held to provide many ecosystem functions and services better than pure stands. Recent studies well explored species mixing effects at the individual tree or stand level. However, the link between individual and stand level which is represented by the size-structure dynamics of stands, is still hardly understood.Aim of this study: The objective was to analyse how species mixing modifies the size-structure dynamics of mixed compared with pure forest stands. Area of the study: the study was carried out in Southern Germany.Material and Methods: We selected 11long-term experiments comprising 129 plots of un-thinned or just lightly thinned pure and mixed stands of European beech (Fagus sylvatica [ L.] and analysed their size structure dynamics.Main Results: Based on the Gini coefficient, skewness and kurtosis we show how mixing with Norway spruce (Picea abies [L.] Karst and sessile oak (Quercus petraea (Matt. Liebl. modifies the size-structure dynamics of European beech. The size distribution of beech in mixture mostly lags behind the pure stand, is more size-asymmetric, and the mortality shifts from the smaller diameter classes further to the taller trees than in pure stands.Research highlights: The revealed changes of the size-structure dynamics of beech in mixed versus pure stands result from a modification of both growth partitioning and self-thinning. We draw conclusions of the reduced size growth and size equality of beech in mixed versus pure stands for forest management planning and perspectives for forest research.Keywords: species selection effect; true mixing effect; morphological plasticity; size-distribution; growth partitioning between trees; mode of mortality; European beech (Fagus sylvatica [L.]; Norway spruce (Picea abies [L.] Karst; sessile oak (Quercus petraea (Matt. Liebl..
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
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.
Directory of Open Access Journals (Sweden)
Ronak Y. Patel
2011-01-01
Full Text Available Glycolipids are important constituents of biological membranes, and understanding their structure and dynamics in lipid bilayers provides insights into their physiological and pathological roles. Experimental techniques have provided details into their behavior at model and biological membranes; however, computer simulations are needed to gain atomic level insights. This paper summarizes the insights obtained from MD simulations into the conformational and orientational dynamics of glycosphingolipids and their exposure, hydration, and hydrogen-bonding interactions in membrane environment. The organization of glycosphingolipids in raft-like membranes and their modulation of lipid membrane structure are also reviewed.
Dynamic soil-structure interaction of monopod and polypod foundations
DEFF Research Database (Denmark)
Andersen, Lars Vabbersgaard
2016-01-01
The paper concerns the importance of through–soil coupling for structures having foundations with more footings. First, a model for dynamic analysis of polypod footings is established in the frequency domain, employing Green’s function for wave propagation in a layered half-space. To allow analysis...... within the time domain, frequency-independent lumped-parameter models are developed. The paper proposes a decision criterion for determination of which components must be included within a lumped-parameter model in order to account for the structure–soil–structure interaction in an adequate and efficient...... manner. As a computational example, the dynamic response of a plane frame structure with two footings is compared for two cases: one with and one without the cross coupling. Homogeneous as well as layered soil is considered....
Dynamic soil-structure interaction of monopod and polypod foundations
DEFF Research Database (Denmark)
Andersen, Lars Vabbersgaard
2016-01-01
within the time domain, frequency-independent lumped-parameter models are developed. The paper proposes a decision criterion for determination of which components must be included within a lumped-parameter model in order to account for the structure–soil–structure interaction in an adequate and efficient......The paper concerns the importance of through–soil coupling for structures having foundations with more footings. First, a model for dynamic analysis of polypod footings is established in the frequency domain, employing Green’s function for wave propagation in a layered half-space. To allow analysis...... manner. As a computational example, the dynamic response of a plane frame structure with two footings is compared for two cases: one with and one without the cross coupling. Homogeneous as well as layered soil is considered....
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.
Detailed Multidimensional Simulations of the Structure and Dynamics of Flames
Patnaik, G.; Kailasanath, K.
1999-01-01
Numerical simulations in which the various physical and chemical processes can be independently controlled can significantly advance our understanding of the structure, stability, dynamics and extinction of flames. Therefore, our approach has been to use detailed time-dependent, multidimensional, multispecies numerical models to perform carefully designed computational experiments of flames on Earth and in microgravity environments. Some of these computational experiments are complementary to physical experiments performed under the Microgravity Program while others provide a fundamental understanding that cannot be obtained from physical experiments alone. In this report, we provide a brief summary of our recent research highlighting the contributions since the previous microgravity combustion workshop. There are a number of mechanisms that can cause flame instabilities and result in the formation of dynamic multidimensional structures. In the past, we have used numerical simulations to show that it is the thermo-diffusive instability rather than an instability due to preferential diffusion that is the dominant mechanism for the formation of cellular flames in lean hydrogen-air mixtures. Other studies have explored the role of gravity on flame dynamics and extinguishment, multi-step kinetics and radiative losses on flame instabilities in rich hydrogen-air flames, and heat losses on burner-stabilized flames in microgravity. The recent emphasis of our work has been on exploring flame-vortex interactions and further investigating the structure and dynamics of lean hydrogen-air flames in microgravity. These topics are briefly discussed after a brief discussion of our computational approach for solving these problems.
Sensitive Dependence of Optimal Network Dynamics on Network Structure
Directory of Open Access Journals (Sweden)
Takashi Nishikawa
2017-11-01
Full Text Available The relation between network structure and dynamics is determinant for the behavior of complex systems in numerous domains. An important long-standing 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, using diffusively coupled systems as examples, we demonstrate that the stability of a dynamical state can exhibit sensitivity to unweighted structural perturbations (i.e., link removals and node additions for undirected optimal networks and to weighted perturbations (i.e., small changes in link weights for directed optimal networks. As mechanisms underlying this sensitivity, we identify discontinuous transitions occurring in the complement of undirected optimal networks and the prevalence of eigenvector degeneracy in directed optimal networks. These findings establish a unified characterization of networks optimized for dynamical stability, which we illustrate using Turing instability in activator-inhibitor systems, synchronization in power-grid networks, network diffusion, and several other network processes. Our results suggest that the network structure of a complex system operating near an optimum can potentially be fine-tuned for a significantly enhanced stability compared to what one might expect from simple extrapolation. On the other hand, they also suggest constraints on how close to the optimum the system can be in practice. Finally, the results have potential implications for biophysical networks, which have evolved under the competing pressures of optimizing fitness while remaining robust against perturbations.
Dynamic Force Identification for Beamlike Structures Using an Improved Dynamic Stiffness Method
Directory of Open Access Journals (Sweden)
S.L. Chen
1996-01-01
Full Text Available In this study a procedure of dynamic force identification for beamlike structures is developed based on an improved dynamic stiffness method. In this procedure, the entire structure is first divided into substructures according to the excitation locations and the measured response sites. Each substructure is then represented by an equivalent element. The resulting model only retains the degree of freedom (DOF associated with the excitations and the measured responses and the DOF corresponding to the boundaries of the structures. Because the technique partly bypasses the processes of modal parameter extraction, global matrix inversion, and model reduction, it can eliminate many of the approximations and errors that may be introduced during these processes. The principle of the method is described in detail and its efficiency is demonstrated via numerical simulations of three different structures. The sensitivity of the estimated force to random noise is discussed and the limitation of the technique is pointed out.
Structural fluctuation governed dynamic diradical character in pentacene.
Yang, Hongfang; Chen, Mengzhen; Song, Xinyu; Bu, Yuxiang
2015-06-07
We unravel intriguing dynamical diradical behavior governed by structural fluctuation in pentacene using ab initio molecular dynamics simulation. In contrast to static equilibrium configuration of pentacene with a closed-shell ground state without diradical character, due to structural fluctuation, some of its dynamical snapshot configurations exhibit an open-shell broken-symmetry singlet ground state with diradical character, and such diradical character presents irregular pulsing behavior in time evolution. Not all structural changes can lead to diradical character, only those involving the shortening of cross-linking C-C bonds and variations of the C-C bonds in polyacetylene chains are the main contributors. This scenario about diradicalization is distinctly different from that in long acenes. The essence is that structural distortion cooperatively raises the HOMO and lowers the LUMO, efficiently reducing the HOMO-LUMO and singlet-triplet energy gaps, which facilitate the formation of a broken-symmetry open-shell singlet state. The irregular pulsing behavior originates from the mixing of normal vibrations in pentacene. This fascinating behavior suggests the potential application of pentacene as a suitable building block in the design of new electronic devices due to its magnetism-controllability through energy induction. This work provides new insight into inherent electronic property fluctuation in acenes.
Loads and Structural Dynamics Requirements for Spaceflight Hardware
Schultz, Kenneth P.
2011-01-01
The purpose of this document is to establish requirements relating to the loads and structural dynamics technical discipline for NASA and commercial spaceflight launch vehicle and spacecraft hardware. Requirements are defined for the development of structural design loads and recommendations regarding methodologies and practices for the conduct of load analyses are provided. As such, this document represents an implementation of NASA STD-5002. Requirements are also defined for structural mathematical model development and verification to ensure sufficient accuracy of predicted responses. Finally, requirements for model/data delivery and exchange are specified to facilitate interactions between Launch Vehicle Providers (LVPs), Spacecraft Providers (SCPs), and the NASA Technical Authority (TA) providing insight/oversight and serving in the Independent Verification and Validation role. In addition to the analysis-related requirements described above, a set of requirements are established concerning coupling phenomena or other interaction between structural dynamics and aerodynamic environments or control or propulsion system elements. Such requirements may reasonably be considered structure or control system design criteria, since good engineering practice dictates consideration of and/or elimination of the identified conditions in the development of those subsystems. The requirements are included here, however, to ensure that such considerations are captured in the design space for launch vehicles (LV), spacecraft (SC) and the Launch Abort Vehicle (LAV). The requirements in this document are focused on analyses to be performed to develop data needed to support structural verification. As described in JSC 65828, Structural Design Requirements and Factors of Safety for Spaceflight Hardware, implementation of the structural verification requirements is expected to be described in a Structural Verification Plan (SVP), which should describe the verification of each
Evolutionary dynamics of general group interactions in structured populations
Li, Aming; Broom, Mark; Du, Jinming; Wang, Long
2016-02-01
The evolution of populations is influenced by many factors, and the simple classical models have been developed in a number of important ways. Both population structure and multiplayer interactions have been shown to significantly affect the evolution of important properties, such as the level of cooperation or of aggressive behavior. Here we combine these two key factors and develop the evolutionary dynamics of general group interactions in structured populations represented by regular graphs. The traditional linear and threshold public goods games are adopted as models to address the dynamics. We show that for linear group interactions, population structure can favor the evolution of cooperation compared to the well-mixed case, and we see that the more neighbors there are, the harder it is for cooperators to persist in structured populations. We further show that threshold group interactions could lead to the emergence of cooperation even in well-mixed populations. Here population structure sometimes inhibits cooperation for the threshold public goods game, where depending on the benefit to cost ratio, the outcomes are bistability or a monomorphic population of defectors or cooperators. Our results suggest, counterintuitively, that structured populations are not always beneficial for the evolution of cooperation for nonlinear group interactions.
GPS in dynamic monitoring of long-period structures
Celebi, M.
2000-01-01
Global Positioning System (GPS) technology with high sampling rates (??? 10 samples per second) allows scientifically justified and economically feasible dynamic measurements of relative displacements of long-period structures-otherwise difficult to measure directly by other means, such as the most commonly used accelerometers that require post-processing including double integration. We describe an experiment whereby the displacement responses of a simulated tall building are measured clearly and accurately in real-time. Such measurements can be used to assess average drift ratios and changes in dynamic characteristics, and therefore can be used by engineers and building owners or managers to assess the building performance during extreme motions caused by earthquakes and strong winds. By establishing threshold displacements or drift ratios and identifying changing dynamic characteristics, procedures can be developed to use such information to secure public safety and/or take steps to improve the performance of the building. Published by Elsevier Science Ltd.
The ABRAVIBE toolbox for teaching vibration analysis and structural dynamics
DEFF Research Database (Denmark)
Brandt, A.
2013-01-01
Vibration analysis is a subject where students often find it hard to comprehend the fundamental theory. The fact that we have, in general, almost no intuition for dynamic phenomena, means that students need to explore various dynamic phenomena in order to grasp the subject. For this reason......, a MATLAB toolbox (the ABRAVIBE toolbox) has been developed as an accompanying toolbox for the recent book "Noise and Vibration Analysis" by the author. This free, open software, published under GNU Public License, can be used with GNU Octave, if an entirely free software platform is wanted, with a few......). In this paper, an overview of the functionality is given and recommended use in teaching is discussed. It is also shown how the toolbox can be used for general vibration analysis using data from multichannel measurements. Finally, some laboratory exercises for structural dynamics teaching are discussed...
Structural Influence on Excited State Dynamics in Simple Amines
DEFF Research Database (Denmark)
Klein, Liv Bærenholdt
experiments with calculations, provides new insight into the nature of the internal conversion processes that mediate the dynamical evolution between Rydberg states, and how structural variations in simple amine system have a large impact on the non-adiabatic processes. The experimental method of choice......Simple amines are basic model system of nitrogen-containing chromophores that appear widely in nature. They are also ideal systems for detailed investigation of nonadiabatic dynamical processes and ultrafast temporal evolution of electronic states of the Rydberg type. This investigation, combining...... and sensitive collection of photoelectron spectra. In particular, the angleresolved data available from the VMI approach provides highly detailed mechanistic insight about the relaxation pathways. One striking novel nding is that for tertiary amines, the critical factor driving the non-adiabatic dynamics...
IUTAM Symposium on Hamiltonian Dynamics, Vortex Structures, Turbulence
Borisov, Alexey V; Mamaev, Ivan S; Sokolovskiy, Mikhail A; IUTAM BOOKSERIES : Volume 6
2008-01-01
This work brings together previously unpublished notes contributed by participants of the IUTAM Symposium on Hamiltonian Dynamics, Vortex Structures, Turbulence (Moscow, 25-30 August 2006). The study of vortex motion is of great interest to fluid and gas dynamics: since all real flows are vortical in nature, applications of the vortex theory are extremely diverse, many of them (e.g. aircraft dynamics, atmospheric and ocean phenomena) being especially important. The last few decades have shown that serious possibilities for progress in the research of real turbulent vortex motions are essentially related to the combined use of mathematical methods, computer simulation and laboratory experiments. These approaches have led to a series of interesting results which allow us to study these processes from new perspectives. Based on this principle, the papers collected in this proceedings volume present new results on theoretical and applied aspects of the processes of formation and evolution of various flows, wave a...
Sultan, Cornel
2009-05-01
The design of structures for dynamic properties is addressed by placing conditions on the separation between natural frequencies. Additional constraints, like lower and upper bounds on the natural frequencies, are also included. A fast numerical algorithm that exploits the mathematical structure of the resulting problem is developed. Examples of the algorithm's application to tensegrity structures design are presented and the connection between natural frequencies separation and proportional damping approximation is analyzed.
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.
Differentiable dynamical systems an introduction to structural stability and hyperbolicity
Wen, Lan
2016-01-01
This is a graduate text in differentiable dynamical systems. It focuses on structural stability and hyperbolicity, a topic that is central to the field. Starting with the basic concepts of dynamical systems, analyzing the historic systems of the Smale horseshoe, Anosov toral automorphisms, and the solenoid attractor, the book develops the hyperbolic theory first for hyperbolic fixed points and then for general hyperbolic sets. The problems of stable manifolds, structural stability, and shadowing property are investigated, which lead to a highlight of the book, the \\Omega-stability theorem of Smale. While the content is rather standard, a key objective of the book is to present a thorough treatment for some tough material that has remained an obstacle to teaching and learning the subject matter. The treatment is straightforward and hence could be particularly suitable for self-study. Selected solutions are available electronically for instructors only. Please send email to textbooks@ams.org for more informatio...
Dynamic time warping for temperature compensation in structural health monitoring
Douglass, Alexander; Harley, Joel B.
2017-02-01
Guided wave structural health monitoring uses ultrasonic waves to identify changes in structures. To identify these changes, most guided wave methods require a pristine baseline measurement with which other measurements are compared. Damage signatures arise when there is a deviation between the baseline and the recorded measurement. However, temperature significantly complicates this analysis by creating misalignment between the baseline and measurements. This leads to false alarms of damage and significantly reduces the reliability of these systems. Several methods have been created to account for these temperature perturbations. Yet, most of these compensation methods fail in harsh, highly variable temperature conditions or require a prohibitive amount of prior data. In this paper, we use an algorithm known as dynamic time warping to compensate for temperature in these harsh conditions. We demonstrate that dynamic time warping is able to account for temperature variations whereas the more traditional baseline signal stretch method is unable to resolve damage under high temperature fluctuations.
Advanced composite turboprops - Modeling, structural, and dynamic analyses
Aiello, R. A.; Chi, S.
1988-01-01
This paper presents a structural and dynamic analysis of a scaled-down wind tunnel model propfan blade made from fiber composites. This blade is one of a series of propfan blades that have been tested at the NASA Lewis Research Center wind tunnel facilities. The blade is highly swept and twisted and of the spar/shell construction. Due to the complexity of the blade geometry and its high performance, it is subjected to much higher loads and tends to be much less stable than conventional blades. The structural and dynamic analyses of the blade were performed using the NASA-Lewis COBSTRAN computer code. COBSTRAN is designed to generate the mesh and calculate the anisotropic material properties for composite blade analysis. Comparison of analytical and experimental mode shapes and frequencies are shown, verifying the model development and analysis techniques used. The methodologies and programs developed for this analysis are directly applicable to other propfan blades.
Spectroscopic Tools for Quantitative Studies of DNA Structure and Dynamics
DEFF Research Database (Denmark)
Preus, Søren
The main objective of this thesis is to develop quantitative fluorescence-based, spectroscopic tools for probing the 3D structure and dynamics of DNA and RNA. The thesis is founded on six peer-reviewed papers covering mainly the development, characterization and use of fluorescent nucleobase anal...... analogues. In addition, four software packages is presented for the simulation and quantitative analysis of time-resolved and steady-state UV-Vis absorption and fluorescence experiments.......The main objective of this thesis is to develop quantitative fluorescence-based, spectroscopic tools for probing the 3D structure and dynamics of DNA and RNA. The thesis is founded on six peer-reviewed papers covering mainly the development, characterization and use of fluorescent nucleobase...
Hydroxyapatites: Key Structural Questions and Answers from Dynamic Nuclear Polarization.
Leroy, César; Aussenac, Fabien; Bonhomme-Coury, Laure; Osaka, Akiyoshi; Hayakawa, Satoshi; Babonneau, Florence; Coelho-Diogo, Cristina; Bonhomme, Christian
2017-10-03
We demonstrate that NMR/DNP (Dynamic Nuclear Polarization) allows an unprecedented description of carbonate substituted hydroxyapatite (CHAp). Key structural questions related to order/disorder and clustering of carbonates are tackled using distance sensitive DNP experiments using 13 C- 13 C recoupling. Such experiments are easily implemented due to unprecedented DNP gain (orders of magnitude). DNP is efficiently mediated by quasi one-dimensional spin diffusion through the hydroxyl columns present in the CHAp structure (thought of as "highways" for spin diffusion). For spherical nanoparticles and ϕ dynamics and line shape resolution). Finally, all 2D DNP experiments can be interpreted in terms of domains exhibiting well identified types of substitution: local order and carbonate clustering are clearly favored.
Ultrafast Dynamic Pressure Sensors Based on Graphene Hybrid Structure.
Liu, Shanbiao; Wu, Xing; Zhang, Dongdong; Guo, Congwei; Wang, Peng; Hu, Weida; Li, Xinming; Zhou, Xiaofeng; Xu, Hejun; Luo, Chen; Zhang, Jian; Chu, Junhao
2017-07-19
Mechanical flexible electronic skin has been focused on sensing various physical parameters, such as pressure and temperature. The studies of material design and array-accessible devices are the building blocks of strain sensors for subtle pressure sensing. Here, we report a new and facile preparation of a graphene hybrid structure with an ultrafast dynamic pressure response. Graphene oxide nanosheets are used as a surfactant to prevent graphene restacking in aqueous solution. This graphene hybrid structure exhibits a frequency-independent pressure resistive sensing property. Exceeding natural skin, such pressure sensors, can provide transient responses from static up to 10 000 Hz dynamic frequencies. Integrated by the controlling system, the array-accessible sensors can manipulate a robot arm and self-rectify the temperature of a heating blanket. This may pave a path toward the future application of graphene-based wearable electronics.
Letting Structure Emerge: Connectionist and Dynamical Systems Approaches to Cognition
McClelland, James L.; Botvinick, Matthew M.; Noelle, David C.; Plaut, David C.; Rogers, Timothy T.; Seidenberg, Mark S.; Smith, Linda B.
2011-01-01
Connectionist and dynamical systems approaches explain human thought, language and behavior in terms of the emergent consequences of a large number of simple non-cognitive processes. We view the entities that serve as the basis for structured probabilistic approaches as sometimes useful but often misleading abstractions that have no real basis in the actual processes that give rise to linguistic and cognitive abilities or the development of these abilities. While structured probabilistic approaches can be useful in determining what would be optimal under certain assumptions, we suggest that approaches such as the connectionist and dynamical systems approaches, which focus on explaining the mechanisms giving rise to cognition, will be essential in achieving a full understanding of cognition and development. PMID:20598626
A general modeling framework for describing spatially structured population dynamics
Sample, Christine; Fryxell, John; Bieri, Joanna; Federico, Paula; Earl, Julia; Wiederholt, Ruscena; Mattsson, Brady; Flockhart, Tyler; Nicol, Sam; Diffendorfer, James E.; Thogmartin, Wayne E.; Erickson, Richard A.; Norris, D. Ryan
2017-01-01
Variation in movement across time and space fundamentally shapes the abundance and distribution of populations. Although a variety of approaches model structured population dynamics, they are limited to specific types of spatially structured populations and lack a unifying framework. Here, we propose a unified network-based framework sufficiently novel in its flexibility to capture a wide variety of spatiotemporal processes including metapopulations and a range of migratory patterns. It can accommodate different kinds of age structures, forms of population growth, dispersal, nomadism and migration, and alternative life-history strategies. Our objective was to link three general elements common to all spatially structured populations (space, time and movement) under a single mathematical framework. To do this, we adopt a network modeling approach. The spatial structure of a population is represented by a weighted and directed network. Each node and each edge has a set of attributes which vary through time. The dynamics of our network-based population is modeled with discrete time steps. Using both theoretical and real-world examples, we show how common elements recur across species with disparate movement strategies and how they can be combined under a unified mathematical framework. We illustrate how metapopulations, various migratory patterns, and nomadism can be represented with this modeling approach. We also apply our network-based framework to four organisms spanning a wide range of life histories, movement patterns, and carrying capacities. General computer code to implement our framework is provided, which can be applied to almost any spatially structured population. This framework contributes to our theoretical understanding of population dynamics and has practical management applications, including understanding the impact of perturbations on population size, distribution, and movement patterns. By working within a common framework, there is less chance
Leveraging natural dynamical structures to explore multi-body systems
Bosanac, Natasha
Multi-body systems have become the target of an increasing number of mission concepts and observations, supplying further information about the composition, origin and dynamical environment of bodies within the solar system and beyond. In many of these scenarios, identification and characterization of the particular solutions that exist in a circular restricted three-body model is valuable. This insight into the underlying natural dynamical structures is achieved via the application of dynamical systems techniques. One application of such analysis is trajectory design for CubeSats, which are intended to explore cislunar space and other planetary systems. These increasingly complex mission objectives necessitate innovative trajectory design strategies for spacecraft within our solar system, as well as the capability for rapid and well-informed redesign. Accordingly, a trajectory design framework is constructed using dynamical systems techniques and demonstrated for the Lunar IceCube mission. An additional application explored in this investigation involves the motion of an exoplanet near a binary star system. Due to the strong gravitational field near a binary star, physicists have previously leveraged these systems as testbeds for examining the validity of gravitational and relativistic theories. In this investigation, a preliminary analysis into the effect of an additional three-body interaction on the dynamical environment near a large mass ratio binary system is conducted. As demonstrated through both of these sample applications, identification and characterization of the natural particular solutions that exist within a multi-body system supports a well-informed and guided analysis.
Feedback Linearized Aircraft Control Using Dynamic Cell Structure
Jorgensen, C. C.
1998-01-01
A Dynamic Cell Structure (DCS ) Neural Network was developed which learns a topology representing network (TRN) of F-15 aircraft aerodynamic stability and control derivatives. The network is combined with a feedback linearized tracking controller to produce a robust control architecture capable of handling multiple accident and off-nominal flight scenarios. This paper describes network and its performance for accident scenarios including differential stabilator lock, soft sensor failure, control, stability derivative variation, and turbulence.
Sierra Structural Dynamics User's Notes
Energy Technology Data Exchange (ETDEWEB)
Reese, Garth M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
2015-10-19
Sierra/SD provides a massively parallel implementation of structural dynamics finite element analysis, required for high fidelity, validated models used in modal, vibration, static and shock analysis of weapons systems. This document provides a users guide to the input for Sierra/SD. Details of input specifications for the different solution types, output options, element types and parameters are included. The appendices contain detailed examples, and instructions for running the software on parallel platforms.
Yaw control for active damping of structural dynamics
Energy Technology Data Exchange (ETDEWEB)
Ekelund, T. [Chalmers Univ. of Technology, Goeteborg (Sweden). Control Engineering Lab.
1996-12-01
Yaw torque control for reduction of structural dynamic loads in a two-bladed wind turbine is investigated. The models are obtained using rigid-body mechanics. Linear quadratic control theory is utilized for design and analysis. The analysis of two simple examples, where the teeter angle and the tower lateral bending motion are regarded, shows that a time-varying controller has some advantages compared with a time-invariant controller. 6 refs, 9 figs
Phase structure of Causal Dynamical Triangulations in 4D
Gizbert-Studnicki, Jakub
2017-01-01
Causal Dynamical Triangulations (CDT) is a lattice approach to quantum gravity. CDT has rich phase structure, including a semiclassical phase consistent with Einstein's general relativity. Some of the observed phase transitions are second (or higher) order which opens a possibility of investigating the ultraviolet continuum limit. Recently a new phase with intriguing geometric properties has been discovered and the new phase transition is also second (or higher) order.
Doublet vs. FODO structure: beam dynamics and layout
Eshraqi, M; CERN. Geneva. BE Department
2010-01-01
A FoDo (singlet) structure is designed for the CERN Superconducting Proton LINAC. This architecture is compared to the baseline (doublet) architecture of SPL on the basis of its beam dynamics performance and the required investment. The sensitivity of both layouts to quadrupole gradient errors and misalignment is checked and a correction scheme for beam steering is proposed. Finally a single quad beam dilution scheme is studied and designed for the pilot beam dump.
Development of paradigms for the dynamics of structured populations
Energy Technology Data Exchange (ETDEWEB)
1994-10-01
This is a technical progress report on the dynamics of predator-prey systems in a patchy environment. A new phenomenon that might contribute to outbreaks in systems of discrete patches has been determined using a discrete time model with both spatial and age structure. A model for a single species in a patchy environment with migration, local population growth and disasters with in patches has been formulated and a brief description is included.
Directory of Open Access Journals (Sweden)
Sepahvand K.
2016-01-01
Full Text Available Stochastic analysis of structures having nonlinearity by means of sampling methods leads to expensive cost in term of computational time. In contrast, non-sampling methods based on the spectral representation of uncertainty are very efficient with comparable accurate results. In this pa- per, the application of spectral methods to nonlinear dynamics of structures with random parameters is investigated. The impact of the parameter randomness on structural responses has been consid- ered. To this end, uncertain parameters and the structure responses are represented using the gPC expansions with unknown deterministic coefficients and random orthogonal polynomial basis. The deterministic finite element model of the structure is used as black-box and it is executed on a set of random collocation points. As the sample structure responses are estimated, a nonlinear optimization process is employed to calculate the unknown coefficients. The method has this main advantage that can be used for complicated nonlinear structural dynamic problems for which the deterministic FEM model has been already developed. Furthermore, it is very time efficient in comparison with sampling methods, as MC simulations. The application of the method is applied to the nonlinear transient analysis of composite beam structures including uncertain quadratic random damping. The results show that the proposed method can capture the large range of uncertainty in input parameters as well as in structural dynamic responses while it is too time-efficient.
NMR contributions to structural dynamics studies of intrinsically disordered proteins☆
Konrat, Robert
2014-01-01
Intrinsically disordered proteins (IDPs) are characterized by substantial conformational plasticity. Given their inherent structural flexibility X-ray crystallography is not applicable to study these proteins. In contrast, NMR spectroscopy offers unique opportunities for structural and dynamic studies of IDPs. The past two decades have witnessed significant development of NMR spectroscopy that couples advances in spin physics and chemistry with a broad range of applications. This article will summarize key advances in basic physical-chemistry and NMR methodology, outline their limitations and envision future R&D directions. PMID:24656082
Dynamic Capital Structure with Callable Debt and Debt Renegotiations
DEFF Research Database (Denmark)
Christensen, Peter Ove; Flor, Christian Riis; Lando, David
2014-01-01
taxes and bankruptcy costs are the only frictions, violations of the absolute priority rule (APR) are typically optimal. The size of the bankruptcy costs and the equity holders’ bargaining power affect the size of APR violations, but they have only a minor impact on the choice of capital structure.......We consider a dynamic trade-off model of a firm’s capital structure with debt renegotiation. Debt holders only accept restructuring offers from equity holders backed by threats which are in the equity holders’ own interest to execute. Our model shows that in a complete information model in which...
Structure-dynamics relationship in coherent transport through disordered systems
Mostarda, Stefano; Levi, Federico; Prada-Gracia, Diego; Mintert, Florian; Rao, Francesco
2013-08-01
Quantum transport is strongly influenced by interference with phase relations that depend on the scattering medium. As even small changes in the geometry of the medium can turn constructive interference to destructive, a clear relation between structure and fast, efficient transport is difficult to identify. Here we present a complex network analysis of quantum transport through disordered systems to elucidate the relationship between transport efficiency and structural organization. Evidence is provided for the emergence of structural classes with different geometries but similar high efficiency. Specifically, a structural motif characterized by pair sites, which are not actively participating to the dynamics, renders transport properties robust against perturbations. Our results pave the way for a systematic rationalization of the design principles behind highly efficient transport, which is of paramount importance for technological applications as well as to address transport robustness in natural-light-harvesting complexes.
Allosteric Transitions in Myosin V: Structural Basis for the Dynamics
Tehver, Riina; Thirumalai, D.
2010-03-01
The key to understanding the operation of molecular motors lies in deciphering the details of their mechano-chemical coupling, i.e. how nucleotide binding, hydrolysis and release translate into coordinated conformational changes and the resulting mechanical work. We use myosin V to study the details of this coupling. Applying the Structural Perturbation Method (SPM) in conjunction with normal model analysis helps us predict the key structural elements in the transitions. Brownian dynamics simulations, using a coarse-grained Self-Organized Polymer (SOP) model, reveal a hierarchy of local structural changes that occur in the structural elements during the transitions. The combination of methods used here should be of general applicability to describe the fundamental steps in the reaction cycle of other molecular motors.
Structure-dynamics relationship in coherent transport through disordered systems.
Mostarda, Stefano; Levi, Federico; Prada-Gracia, Diego; Mintert, Florian; Rao, Francesco
2013-01-01
Quantum transport is strongly influenced by interference with phase relations that depend on the scattering medium. As even small changes in the geometry of the medium can turn constructive interference to destructive, a clear relation between structure and fast, efficient transport is difficult to identify. Here we present a complex network analysis of quantum transport through disordered systems to elucidate the relationship between transport efficiency and structural organization. Evidence is provided for the emergence of structural classes with different geometries but similar high efficiency. Specifically, a structural motif characterized by pair sites, which are not actively participating to the dynamics, renders transport properties robust against perturbations. Our results pave the way for a systematic rationalization of the design principles behind highly efficient transport, which is of paramount importance for technological applications as well as to address transport robustness in natural-light-harvesting complexes.
Biogenesis and Dynamics of the Coronavirus Replicative Structures
Hagemeijer, Marne C.; Rottier, Peter J.M.; de Haan, Cornelis A.M.
2012-01-01
Coronaviruses are positive-strand RNA viruses that are important infectious agents of both animals and humans. A common feature among positive-strand RNA viruses is their assembly of replication-transcription complexes in association with cytoplasmic membranes. Upon infection, coronaviruses extensively rearrange cellular membranes into organelle-like replicative structures that consist of double-membrane vesicles and convoluted membranes to which the nonstructural proteins involved in RNA synthesis localize. Double-stranded RNA, presumably functioning as replicative intermediate during viral RNA synthesis, has been detected at the double-membrane vesicle interior. Recent studies have provided new insights into the assembly and functioning of the coronavirus replicative structures. This review will summarize the current knowledge on the biogenesis of the replicative structures, the membrane anchoring of the replication-transcription complexes, and the location of viral RNA synthesis, with particular focus on the dynamics of the coronavirus replicative structures and individual replication-associated proteins. PMID:23202524
Dynamic testing of nuclear power plant structures: an evaluation
Energy Technology Data Exchange (ETDEWEB)
Weaver, H.J.
1980-02-01
Lawrence Livermore Laboratory (LLL) evaluated the applications of system identification techniques to the dynamic testing of nuclear power plant structures and subsystems. These experimental techniques involve exciting a structure and measuring, digitizing, and processing the time-history motions that result. The data can be compared to parameters calculated using finite element or other models of the test systems to validate the model and to verify the seismic analysis. This report summarizes work in three main areas: (1) analytical qualification of a set of computer programs developed at LLL to extract model parameters from the time histories; (2) examination of the feasibility of safely exciting nuclear power plant structures and accurately recording the resulting time-history motions; (3) study of how the model parameters that are extracted from the data be used best to evaluate structural integrity and analyze nuclear power plants.
Molecular dynamics simulation studies of structural and dynamical properties of rapidly quenched Al
Energy Technology Data Exchange (ETDEWEB)
Shen, B.; Liu, C. Y.; Jia, Y.; Yue, G. Q.; Ke, F. S.; Zhao, H. B.; Chen, L. Y.; Wang, S. Y.; Wang, C. Z.; Ho, K. M.
2014-01-01
The structural and dynamical properties of rapidly quenched Al are studied by molecular dynamics simulations. The pair-correlation function of high temperature liquid Al agrees well with the experimental results. Different cooling rates are applied with high cooling rates leading to glass formation, while low cooling rates leading to crystallization. The local structures are characterized by Honeycutt–Andersen indices and Voronoi tessellation analysis. The results show that for high cooling rates, the local structures of the liquid and glassy Al are predominated by icosahedral clusters, together with considerable amount of face-centered cubic and hexagonal close packed short-range orders. These short-range order results are further confirmed using the recently developed atomic cluster alignment method. Moreover, the atomic cluster alignment clearly shows the crystal nucleation process in supercooled liquid of Al. Finally, the mean square displacement for the liquid is also analyzed, and the corresponding diffusion coefficient as a function of temperature is calculated.
Nesting of thermodynamic, structural, and dynamic anomalies in liquid silicon.
Vasisht, Vishwas V; Mathew, John; Sengupta, Shiladitya; Sastry, Srikanth
2014-09-28
Anomalous behaviour in density, diffusivity, and structural order is investigated for silicon modeled by the Stillinger-Weber potential by performing molecular dynamics simulations. As previously reported in the case of water [J. R. Errington and P. G. Debenedetti, Nature (London) 409, 318 (2001)] and silica [M. S. Shell, P. G. Debenedetti, and A. Z. Panagiotopoulos, Phys. Rev. E 66, 011202 (2002)], a cascading of thermodynamic, dynamic, and structural anomalous regions is also observed in liquid silicon. The region of structural anomaly includes the region of diffusivity anomaly, which in turn encompasses the region of density anomaly (which is unlike water but similar to silica). In the region of structural anomaly, a tight correlation between the translational and tetrahedrality order parameter is found, but the correlation is weaker when a local orientational order parameter (q3) is used as a measure of tetrahedrality. The total excess entropy and the pair correlation entropy are computed across the phase diagram and the correlation between the excess entropy and the regions of anomalies in the phase diagram of liquid silicon is examined. Scaling relations associating the excess entropy with the diffusion coefficient show considerable deviation from the quasi-universal behaviour observed in hard-sphere and Lennard-Jones liquids and some liquid metals. Excess entropy based criteria for diffusivity and structural anomalies fail to capture the observed regions of anomaly.
Modelling of Spacecraft Dynamics at Deployment of Large Elastic Structure
Directory of Open Access Journals (Sweden)
V. S. Khoroshilov
2012-01-01
Full Text Available In this paper, a new approach to the modelling of the deployment dynamics of a flexible multi-body system with the time dependent configurations is demonstrated in the frame of the study the dynamics of a spacecraft with the gyro-gravitational system of stabilization. Primarily the gravitational stabilizer that is made as a pantograph structure is in a compact form. The deployment of a flexible pantograph structure is performed after placing the spacecraft into orbit and completion of the preliminary damping by a special jet-propelled system, and after uncaging the gyros. After its deployment, the pantograph turns into an elongated structure that serves as a gravitational stabilizer and carrier of solar batteries. The objective of the study is the creation of the generalized mathematical model and the conducting of the computational modelling of the spacecraft dynamics. The equations of motion are derived with the use of the Eulerian-LaGrangian formalism and symbolic computing. Numerical simulations of the typical operational mode of the system are conducted taking into account various control profiles for the deployment. Numerical results indicate that the system used for attitude stabilization ensures the shape of the deployed design and prescribed accuracy of the orientation.
Tools to detect structures in dynamical systems using Jet Transport
Pérez-Palau, Daniel; Masdemont, Josep J.; Gómez, Gerard
2015-11-01
This paper is devoted to the development of some dynamical indicators that allow the determination of regions and structures that separate different dynamic regimes in autonomous and non-autonomous dynamical systems. The underlying idea is closely related to the Lagrangian coherent structures concept introduced by Haller. In the present paper, instead of using the Cauchy-Green tensor, that determines the domains where the flow associated to a differential equation is expanding in the normal direction, the Jet Transport methodology is used. This is a semi-numerical tool, that has as basic ingredients a polynomial algebra package and a numerical integration method, allowing, at each integration step, the propagation under a flow of a neighbourhood U instead of a single initial condition. The output of the procedure is a polynomial in several variables that represents the image of U up to a selected order, containing high order terms of the variational equations. Using these high order representation, the places where the normal direction expands can be easily detected, in a similar manner as the procedures for calculating the Lagrangian coherent structures do. In order to illustrate the methodology, first the results obtained in the determination of the separatrices of the simple and the periodically perturbed pendulum are given. Later, the applications to the circular restricted three body problem are considered, where the aim is the detection of invariant manifolds of libration point orbits, as well as in the non-autonomous vector field defined by the elliptic restricted three body problem.
Age structure and cooperation in coevolutionary games on dynamic network
Qin, Zilong; Hu, Zhenhua; Zhou, Xiaoping; Yi, Jingzhang
2015-04-01
Our proposed model imitates the growth of a population and describes the age structure and the level of cooperation in games on dynamic network with continuous changes of structure and topology. The removal of nodes and links caused by age-dependent attack, together with the nodes addition standing for the newborns of population, badly ruins Matthew effect in this coevolutionary process. Though the network is generated by growth and preferential attachment, it degenerates into random network and it is no longer heterogeneous. When the removal of nodes and links is equal to the addition of nodes and links, the size of dynamic network is maintained in steady-state, so is the low level of cooperation. Severe structure variation, homogeneous topology and continuous invasion of new defection jointly make dynamic network unsuitable for the survival of cooperator even when the probability with which the newborn players initially adopt the strategy cooperation is high, while things change slightly when the connections of newborn players are restricted. Fortunately, moderate interactions in a generation trigger an optimal recovering process to encourage cooperation. The model developed in this paper outlines an explanation of the cohesion changes in the development process of an organization. Some suggestions for cooperative behavior improvement are given in the end.
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.
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.
Yang, Bingen
2005-01-01
Stress, Strain, and Structural Dynamics is a comprehensive and definitive reference to statics and dynamics of solids and structures, including mechanics of materials, structural mechanics, elasticity, rigid-body dynamics, vibrations, structural dynamics, and structural controls. This text integrates the development of fundamental theories, formulas and mathematical models with user-friendly interactive computer programs, written in the powerful and popular MATLAB. This unique merger of technical referencing and interactive computing allows instant solution of a variety of engineering problems
Correlative microscopy for 3D structural analysis of dynamic interactions.
Jun, Sangmi; Zhao, Gongpu; Ning, Jiying; Gibson, Gregory A; Watkins, Simon C; Zhang, Peijun
2013-06-24
Cryo-electron tomography (cryoET) allows 3D visualization of cellular structures at molecular resolution in a close-to-physiological state(1). However, direct visualization of individual viral complexes in their host cellular environment with cryoET is challenging(2), due to the infrequent and dynamic nature of viral entry, particularly in the case of HIV-1. While time-lapse live-cell imaging has yielded a great deal of information about many aspects of the life cycle of HIV-1(3-7), the resolution afforded by live-cell microscopy is limited (~200 nm). Our work was aimed at developing a correlation method that permits direct visualization of early events of HIV-1 infection by combining live-cell fluorescent light microscopy, cryo-fluorescent microscopy, and cryoET. In this manner, live-cell and cryo-fluorescent signals can be used to accurately guide the sampling in cryoET. Furthermore, structural information obtained from cryoET can be complemented with the dynamic functional data gained through live-cell imaging of fluorescent labeled target. In this video article, we provide detailed methods and protocols for structural investigation of HIV-1 and host-cell interactions using 3D correlative high-speed live-cell imaging and high-resolution cryoET structural analysis. HeLa cells infected with HIV-1 particles were characterized first by confocal live-cell microscopy, and the region containing the same viral particle was then analyzed by cryo-electron tomography for 3D structural details. The correlation between two sets of imaging data, optical imaging and electron imaging, was achieved using a home-built cryo-fluorescence light microscopy stage. The approach detailed here will be valuable, not only for study of virus-host cell interactions, but also for broader applications in cell biology, such as cell signaling, membrane receptor trafficking, and many other dynamic cellular processes.
Dynamical simulation of structural multiplicity in grain boundaries
Energy Technology Data Exchange (ETDEWEB)
Majid, I.; Bristowe, P.D.
1987-06-01
Work on a computer simulation study of a low-energy high-angle boundary structure which is not periodic have been recently reported. This result is of interest since grain boundary structures are usually assumed to have a periodicity corresponding to the appropriate coincidence site lattice (CSL) and many experimental observations of the structure of grain boundaries performed using conventional and high-resolution electron microscopy, electron diffraction and x-ray diffraction appear to support this work. However, this work, using empirical interatomic pair potentials and the relaxation method of molecular statics, have simulated a ..sigma.. = 5 36.87/sup 0/ (001) twist boundary and found a low energy structure having a larger repeat cell than the CSL and is composed of two different types of structural unit that are randomly distributed in the boundary plane. This result, which has been termed the multiplicity of grain boundary structures, has also been found in the simulation of tilt boundaries. The multiplicity phenomenon is of special interest in twist boundaries since it is used as a structural model to explain the x-ray scattering from a ..sigma.. = 5 boundary in gold. These scattering patterns had previously remained unexplained using stable structures that had simple CSL periodicity. Also, the effect of having a multiple number of low energy structural units coexisting in the grain boundary is of more general interest since it implies that the boundary structures may be quasi-periodic and, in some circumstances, may even result in a roughening of the boundary plane. This paper extends this work by showing, using molecular dynamics, that a multiplicity of structural units can actually nucleate spontaneously in a high-angle grain boundary at finite temperatures.
Dynamical simulation of structural multiplicity in grain boundaries
Majid, I.; Bristowe, P. D.
1987-06-01
Work on a computer simulation study of a low-energy high-angle boundary structure which is not periodic have been recently reported. This result is of interest since grain boundary structures are usually assumed to have a periodicity corresponding to the appropriate coincidence site lattice (CSL) and many experimental observations of the structure of grain boundaries performed using conventional and high-resolution electron microscopy, electron diffraction and X-ray diffraction appear to support this work. However, this work, using empirical interatomic pair potentials and the relaxation method of molecular statics, have simulated a Sigma=5 (36.87 deg)(001) twist boundary and found a low energy structure having a larger repeat cell than the CSL and is composed of two different types of structural unit randomly distributed in the boundary plane. This result, termed the multiplicity of grain boundary structures, has also been found in the simulation of tilt boundaries. The multiplicity phenomenon is of special interest in twist boundaries since it is used as a structural model to explain the X-ray scattering from a Sigma=5 boundary in gold. These scattering patterns had previously remained unexplained using stable structures that had simple CSL periodicity. Also, the effect of having a multiple number of low energy structural units coexisting in the grain boundary is of more general interest since it implies that the boundary structures may be quasi-periodic and, in some circumstances, may even result in a roughening of the boundary plane. This work is extended by showing, using molecular dynamics, that a multiplicity of structural units can actually nucleate spontaneously in a high-angle grain boundary at finite temperatures.
Crystal structures and dynamical properties of dense CO2
Yong, Xue; Liu, Hanyu; Wu, Min; Yao, Yansun; Tse, John S.; Dias, Ranga; Yoo, Choong-Shik
2016-01-01
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. PMID:27647887
Directory of Open Access Journals (Sweden)
Ratna Juwita
2013-04-01
Full Text Available Cell membranes are composed mainly of phospholipids which are in turn, composed of five major chemical elements: carbon, hydrogen, nitrogen, oxygen, and phosphorus. Recent studies have suggested the possibility of sustaining life if the phosphorus is substituted by arsenic. Although this issue is still controversial, it is of interest to investigate the properties of arsenated-lipid bilayers to evaluate this possibility. In this study, we simulated arsenated-lipid, 1-palmitoyl-2-oleoyl-sn-glycero-3-arsenocholine (POAC, lipid bilayers using all-atom molecular dynamics to understand basic structural and dynamical properties, in particular, the differences from analogous 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, (POPC lipid bilayers. Our simulations showed that POAC lipid bilayers have distinct structural and dynamical properties from those of native POPC lipid bilayers. Relative to POPC lipid bilayers, POAC lipid bilayers have a more compact structure with smaller lateral areas and greater order. The compact structure of POAC lipid bilayers is due to the fact that more inter-lipid salt bridges are formed with arsenate-choline compared to the phosphate-choline of POPC lipid bilayers. These inter-lipid salt bridges bind POAC lipids together and also slow down the head group rotation and lateral diffusion of POAC lipids. Thus, it would be anticipated that POAC and POPC lipid bilayers would have different biological implications.
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.
Self-diagnosis of smart structures based on dynamical properties
Fritzen, C.-P.; Kraemer, P.
2009-08-01
When we talk about "smart structures" we can think about different properties and capabilities which make a structure "intelligent" in a certain sense. Originally, the expression "smart" was used in the context that a structure can react and adapt to certain environmental conditions, such as change of shape, compensation of deformations, active vibration damping, etc. Over the last year, the expression "smart" has been extended to the field of structural health monitoring (SHM), where sensor networks, actuators and computational capabilities are used to enable a structure to perform a self-diagnosis with the goal that this structure can release early warnings about a critical health state, locate and classify damage or even to forecast the remaining life-time. This paper intends to give an overview and point out recent developments of vibration-based methods for SHM. All these methods have in common that a structural change due to a damage results in a more or less significant change of the dynamic behavior. For the diagnosis an inverse problem has to be solved. We discuss the use of modal information as well as the direct use of forced and ambient vibrations in the time and frequency domain. Examples from civil and aerospace engineering as well as off-shore wind energy plants show the applicability of these methods.
High frequency dynamics and structural relaxation process in liquid ammonia
Giura, P.; Angelini, R.; Datchi, F.; Ruocco, G.; Sette, F.
2007-08-01
The dynamic structure factor S(Q,ω) of liquid ammonia has been measured by inelastic x-ray scattering in the terahertz frequency region as a function of the temperature in the range of 220-298K at a pressure P =85bars. The data have been analyzed using the generalized hydrodynamic formalism with a three term memory function to take into account the thermal, the structural, (α) and the microscopic (μ) relaxation processes affecting the dynamics of the liquid. This allows to extract the temperature dependence of the structural relaxation time (τα) and strength (Δα). The former quantity follows an Arrhenius behavior with an activation energy Ea=2.6±0.2kcal/mol, while the latter is temperature independent suggesting that there are no changes in the interparticle potential and arrangement with T. The obtained results, compared with those already existing in liquid water and liquid hydrogen fluoride, suggest the strong influence of the connectivity of the molecular network on the structural relaxation.
Effects of seat structural dynamics on current ride comfort criteria.
Fard, M; Lo, L; Subic, A; Jazar, R
2014-01-01
The ISO 2631-1 ( 1997 ) provides methodologies for assessment of the seated human body comfort in response to vibrations. The standard covers various conditions such as frequency content, direction and location of the transmission of the vibration to the human body. However, the effects of seat structural dynamics mode shapes and corresponding resonances have not been discussed. This study provides important knowledge about the effects of vehicle seat structural vibration modes on discomfort assessment. The occupied seat resonant frequencies and corresponding vibration modes were measured and comfort test was carried out based on the paired comparison test method. The results show that the ISO 2631-1 ( 1997 ) method significantly underestimates the vibration discomfort level around the occupied seat twisting resonant frequencies. This underestimation is mainly due to the ISO suggested location of the accelerometer pad on the seatback. The centre of the seatback is a nodal point at the seat twisting mode. Therefore, it underestimates the total vibration transferred to the occupant body from the seatback. The effects of the vehicle seat structural dynamics have not been discussed in the human body vibration ISO . The results of this research show that the current measurement method suggested by ISO 2631-1 (1997) can significantly underestimate the vibration discomfort level at around the seat structural vibration mode.
DEFF Research Database (Denmark)
Tahavori, Maryamsadat; Shaker, Hamid Reza
A method for model reduction of dynamical systems with the second order structure is proposed in this paper. The proposed technique preserves the second order structure of the system, and also preserves the stability of the original systems. The method uses the controllability and observability...... gramians within the time interval to build the appropriate Petrov-Galerkin projection for dynamical systems within the time interval of interest. The bound on approximation error is also derived. The numerical results are compared with the counterparts from other techniques. The results confirm...
Carr, J. K.; Buchanan, L. E.; Schmidt, J. R.; Zanni, M. T.; Skinner, J. L.
2013-01-01
Urea/water is an archetypical “biological” mixture, and is especially well known for its relevance to protein thermodynamics, as urea acts as a protein denaturant at high concentration. This behavior has given rise to an extended debate concerning urea’s influence on water structure. Based on a variety of methods and of definitions of water structure, urea has been variously described as a structure-breaker, a structure-maker, or as remarkably neutral towards water. Because of its sensitivity to microscopic structure and dynamics, vibrational spectroscopy can help resolve these debates. We report experimental and theoretical spectroscopic results for the OD stretch of HOD/H2O/urea mixtures (linear IR, 2DIR, and pump-probe anisotropy decay) and for the CO stretch of urea-D4/D2O mixtures (linear IR only). Theoretical results are obtained using existing approaches for water, and a modification of a frequency map developed for acetamide. All absorption spectra are remarkably insensitive to urea concentration, consistent with the idea that urea only very weakly perturbs water structure. Both this work and experiments by Rezus and Bakker, however, show that water’s rotational dynamics are slowed down by urea. Analysis of the simulations casts doubt on the suggestion that urea immobilizes particular doubly hydrogen bonded water molecules. PMID:23841646
Linking Carbon Flux Dynamics and Soil Structure in Dryland Soils
DeCarlo, K. F.; Caylor, K. K.
2016-12-01
Biological sources in the form of microbes and plants play a fundamental role in determining the magnitude of carbon flux. However, the geophysical structure of the soil (which the carbon must pass through before entering the atmosphere) often serves as a constraining entity, which has the potential to serve as instigators or mitigators of those carbon and hydrologic flux processes. We characterized soil carbon dynamics in three dryland soil systems: bioturbated soils, biocompacted soils, and undisturbed soils. Carbon fluxes were characterized using a closed-system respiration chamber, with CO2 concentration differences measured using an infrared gas analyzer (IRGA). Structure of the soil systems, with a focus on the macro-crack structure, were characterized using a combined resin-casting/X-ray imaging technique. Results show fundamental differences in carbon dynamics between the different soil systems/structures: control soils have gaussian distributions of carbon flux that decrease with progressive drying of the soil, while biocompacted soils exhibit exponentially distributed fluxes that do not regularly decrease with increased drying of the soil. Bioturbated soils also exhibit an exponential distribution of carbon flux, though at a much higher magnitude. These differences are evaluated in the context of the underlying soil structure: while the control soils exhibit a shallow and narrow crack structure, the biocompacted soils exhibit a "systematic" crack network with moderate cracking intensity and large depth. The deep crack networks of the biocompacted soils may serve to physically enhance an otherwise weak source of carbon via advection and/or convection, inducing fluxes that are equal or greater than an otherwise carbon-rich soil. The bioturbated soils exhibit a "surficial" crack network that is shallow but extensive, but additionally have deep holes known to convectively vent carbon, which may explain their periodically large carbon fluxes. Our results
Dynamic properties of high structural integrity auxetic open cell foam
Scarpa, F.; Ciffo, L. G.; Yates, J. R.
2004-02-01
This paper illustrates various dynamic characteristics of open cell compliant polyurethane foam with auxetic (negative Poisson's ratio) behaviour. The foam is obtained from off-the-shelf open cell polyurethane grey foam with a manufacturing process based on mechanical deformation on a mould in a temperature-controlled oven. The Poisson's ratio is measured with an image processing technique based on edge detection with wavelet methods. Foam samples have been tested in a viscoelastic analyser tensile test machine to determine the Young's modulus and loss factor for small dynamic strains. The same samples have also been tested in an acoustic impedance tube to measure acoustic absorption and specific acoustic resistance and reactance with a transmissibility technique. Another set of tests has been set up on a cam plastometer machine for constant strain rate dynamic crushing analysis. All the tests have been carried out on auxetic and normal foam samples to provide a comparison between the two types of cellular solids. The results from the experimental tests are discussed and interpreted using microstructure models for cellular materials existing in the literature. The negative Poisson's ratio foam presented in this paper shows an overall superiority regarding damping and acoustic properties compared to the original conventional foam. Its dynamic crushing performance is also significantly superior to the normal foam, suggesting a possible use in structural integrity compliant elements.
Revealing the hidden structure of dynamic ecological networks.
Miele, Vincent; Matias, Catherine
2017-06-01
In ecology, recent technological advances and long-term data studies now provide longitudinal interaction data (e.g. between individuals or species). Most often, time is the parameter along which interactions evolve but any other one-dimensional gradient (temperature, altitude, depth, humidity, etc.) can be considered. These data can be modelled through a sequence of different snapshots of an evolving ecological network, i.e. a dynamic network. Here, we present how the dynamic stochastic block model approach developed by Matias & Miele (Matias & Miele In press J. R. Stat. Soc. B (doi:10.1111/rssb.12200)) can capture the complexity and dynamics of these networks. First, we analyse a dynamic contact network of ants and we observe a clear high-level assembly with some variations in time at the individual level. Second, we explore the structure of a food web evolving during a year and we detect a stable predator-prey organization but also seasonal differences in the prey assemblage. Our approach, based on a rigorous statistical method implemented in the R package dynsbm, can pave the way for exploration of evolving ecological networks.
Optical Fibres Contactless Sensor for Dynamic Testing of Lightweight Structures
Directory of Open Access Journals (Sweden)
L. Bregant
2008-01-01
Full Text Available With dynamic testing, engineers describe activities focused on the identification of some properties of vibrating structures. This step requires for the measurements of excitations and responses signals, applying appropriate sensors directly on the test article. These instruments modify the system's mass and stiffness distributions and eventually the eigen-properties of the structure. These errors become unacceptable especially when testing lightweight structures. This paper shows the results of some tests performed on a small compressor with the purpose of identifying the blades’ natural frequencies and modes. It compares the acquisitions performed with standard accelerometers and two different contact-less systems using as exciters either a micro-hammer or a micro inertial shaker. The paper shows how the contact-less sensors provide good quality data and consistent results in the mode identification phase.
Model Reduction in Dynamic Finite Element Analysis of Lightweight Structures
DEFF Research Database (Denmark)
Flodén, Ola; Persson, Kent; Sjöström, Anders
2012-01-01
models may be created by assembling models of floor and wall structures into large models of complete buildings. When assembling the floor and wall models, the number of degrees of freedom quickly increases to exceed the limits of computer capacity, at least in a reasonable amount of computational time....... The objective of the analyses presented in this paper is to evaluate methods for model reduction of detailed finite element models of floor and wall structures and to investigate the influence of reducing the number of degrees of freedom and computational cost on the dynamic response of the models in terms....... The drawback of component mode synthesis compared to modelling with structural elements is the increased computational cost, although the number of degrees of freedom is small in comparison, as a result of the large bandwidth of the system matrices....
Perspective: Structure and ultrafast dynamics of biomolecular hydration shells.
Laage, Damien; Elsaesser, Thomas; Hynes, James T
2017-07-01
The structure and function of biomolecules can be strongly influenced by their hydration shells. A key challenge is thus to determine the extent to which these shells differ from bulk water, since the structural fluctuations and molecular excitations of hydrating water molecules within these shells can cover a broad range in both space and time. Recent progress in theory, molecular dynamics simulations, and ultrafast vibrational spectroscopy has led to new and detailed insight into the fluctuations of water structure, elementary water motions, and electric fields at hydrated biointerfaces. Here, we discuss some central aspects of these advances, focusing on elementary molecular mechanisms and processes of hydration on a femto- to picosecond time scale, with some special attention given to several issues subject to debate.
Mapping Language Networks Using the Structural and Dynamic Brain Connectomes.
Del Gaizo, John; Fridriksson, Julius; Yourganov, Grigori; Hillis, Argye E; Hickok, Gregory; Misic, Bratislav; Rorden, Chris; Bonilha, Leonardo
2017-01-01
Lesion-symptom mapping is often employed to define brain structures that are crucial for human behavior. Even though poststroke deficits result from gray matter damage as well as secondary white matter loss, the impact of structural disconnection is overlooked by conventional lesion-symptom mapping because it does not measure loss of connectivity beyond the stroke lesion. This study describes how traditional lesion mapping can be combined with structural connectome lesion symptom mapping (CLSM) and connectome dynamics lesion symptom mapping (CDLSM) to relate residual white matter networks to behavior. Using data from a large cohort of stroke survivors with aphasia, we observed improved prediction of aphasia severity when traditional lesion symptom mapping was combined with CLSM and CDLSM. Moreover, only CLSM and CDLSM disclosed the importance of temporal-parietal junction connections in aphasia severity. In summary, connectome measures can uniquely reveal brain networks that are necessary for function, improving the traditional lesion symptom mapping approach.
Beyond Membrane Protein Structure: Drug Discovery, Dynamics and Difficulties.
Biggin, Philip C; Aldeghi, Matteo; Bodkin, Michael J; Heifetz, Alexander
2016-01-01
Most of the previous content of this book has focused on obtaining the structures of membrane proteins. In this chapter we explore how those structures can be further used in two key ways. The first is their use in structure based drug design (SBDD) and the second is how they can be used to extend our understanding of their functional activity via the use of molecular dynamics. Both aspects now heavily rely on computations. This area is vast, and alas, too large to consider in depth in a single book chapter. Thus where appropriate we have referred the reader to recent reviews for deeper assessment of the field. We discuss progress via the use of examples from two main drug target areas; G-protein coupled receptors (GPCRs) and ion channels. We end with a discussion of some of the main challenges in the area.
Model Reduction in Dynamic Finite Element Analysis of Lightweight Structures
DEFF Research Database (Denmark)
Flodén, Ola; Persson, Kent; Sjöström, Anders
2012-01-01
. The objective of the analyses presented in this paper is to evaluate methods for model reduction of detailed finite element models of floor and wall structures and to investigate the influence of reducing the number of degrees of freedom and computational cost on the dynamic response of the models in terms....... The drawback of component mode synthesis compared to modelling with structural elements is the increased computational cost, although the number of degrees of freedom is small in comparison, as a result of the large bandwidth of the system matrices.......The application of wood as a construction material when building multi-storey buildings has many advantages, e.g., light weight, sustainability and low energy consumption during the construction and lifecycle of the building. However, compared to heavy structures, it is a greater challenge to build...
Computational and theoretical aspects of biomolecular structure and dynamics
Energy Technology Data Exchange (ETDEWEB)
Garcia, A.E.; Berendzen, J.; Catasti, P., Chen, X. [and others
1996-09-01
This is the final report for a project that sought to evaluate and develop theoretical, and computational bases for designing, performing, and analyzing experimental studies in structural biology. Simulations of large biomolecular systems in solution, hydrophobic interactions, and quantum chemical calculations for large systems have been performed. We have developed a code that implements the Fast Multipole Algorithm (FMA) that scales linearly in the number of particles simulated in a large system. New methods have been developed for the analysis of multidimensional NMR data in order to obtain high resolution atomic structures. These methods have been applied to the study of DNA sequences in the human centromere, sequences linked to genetic diseases, and the dynamics and structure of myoglobin.
Perspective: Structure and ultrafast dynamics of biomolecular hydration shells
Directory of Open Access Journals (Sweden)
Damien Laage
2017-07-01
Full Text Available The structure and function of biomolecules can be strongly influenced by their hydration shells. A key challenge is thus to determine the extent to which these shells differ from bulk water, since the structural fluctuations and molecular excitations of hydrating water molecules within these shells can cover a broad range in both space and time. Recent progress in theory, molecular dynamics simulations, and ultrafast vibrational spectroscopy has led to new and detailed insight into the fluctuations of water structure, elementary water motions, and electric fields at hydrated biointerfaces. Here, we discuss some central aspects of these advances, focusing on elementary molecular mechanisms and processes of hydration on a femto- to picosecond time scale, with some special attention given to several issues subject to debate.
Structure and dynamics of thylakoids in land plants
DEFF Research Database (Denmark)
Pribil, Mathias; Labs, Mathias; Leister, Dario
2014-01-01
Thylakoids of land plants have a bipartite structure, consisting of cylindrical grana stacks, made of membranous discs piled one on top of the other, and stroma lamellae which are helically wound around the cylinders. Protein complexes predominantly located in the stroma lamellae and grana end...... of the granum. Stacking of grana is thought to be due to adhesion between Lhcb proteins (LHCII or CP26) located in opposed thylakoid membranes. The grana margins contain oligomers of CURT1 proteins, which appear to control the size and number of grana discs in a dosage- and phosphorylation-dependent manner....... Depending on light conditions, thylakoid membranes undergo dynamic structural changes that involve alterations in granum diameter and height, vertical unstacking of grana, and swelling of the thylakoid lumen. This plasticity is realized predominantly by reorganization of the supramolecular structure...
Mapping the structural and dynamical features of kinesin motor domains.
Directory of Open Access Journals (Sweden)
Guido Scarabelli
Full Text Available Kinesin motor proteins drive intracellular transport by coupling ATP hydrolysis to conformational changes that mediate directed movement along microtubules. Characterizing these distinct conformations and their interconversion mechanism is essential to determining an atomic-level model of kinesin action. Here we report a comprehensive principal component analysis of 114 experimental structures along with the results of conventional and accelerated molecular dynamics simulations that together map the structural dynamics of the kinesin motor domain. All experimental structures were found to reside in one of three distinct conformational clusters (ATP-like, ADP-like and Eg5 inhibitor-bound. These groups differ in the orientation of key functional elements, most notably the microtubule binding α4-α5, loop8 subdomain and α2b-β4-β6-β7 motor domain tip. Group membership was found not to correlate with the nature of the bound nucleotide in a given structure. However, groupings were coincident with distinct neck-linker orientations. Accelerated molecular dynamics simulations of ATP, ADP and nucleotide free Eg5 indicate that all three nucleotide states could sample the major crystallographically observed conformations. Differences in the dynamic coupling of distal sites were also evident. In multiple ATP bound simulations, the neck-linker, loop8 and the α4-α5 subdomain display correlated motions that are absent in ADP bound simulations. Further dissection of these couplings provides evidence for a network of dynamic communication between the active site, microtubule-binding interface and neck-linker via loop7 and loop13. Additional simulations indicate that the mutations G325A and G326A in loop13 reduce the flexibility of these regions and disrupt their couplings. Our combined results indicate that the reported ATP and ADP-like conformations of kinesin are intrinsically accessible regardless of nucleotide state and support a model where neck
Structure and dynamics of proflavine association around DNA.
Sasikala, Wilbee D; Mukherjee, Arnab
2016-04-21
Proflavine is a small molecule that intercalates into DNA and, thereby, acts as an anticancer agent. Intercalation of proflavine is shown to be a two-step process in which the first step is believed to be the formation of a pre-intercalative outside bound state. Experimental studies so far have been unable to capture the nature of the outside bound state. However, the sub-millisecond timescale observed in fluorescence kinetic experiments is often attributed to the binding of proflavine outside of DNA. Here, we have performed molecular dynamics simulations with multiple proflavine molecules to study the structure and dynamics of the formation of the outside bound state of DNA at different ion concentrations. We observed that the timescale of the outside bound state formation is, at least, five orders of magnitude faster (in nanoseconds) than the experimentally reported timescale (sub-milliseconds) attributed to binding outside DNA. Moreover, we also observed the stacked arrangement of proflavine all around DNA, which is different from the experimentally predicted stacking arrangement perpendicular to the helical axis of DNA in the close vicinity of the phosphate groups. This study, therefore, provides insight into the molecular structure and dynamics of the pre-intercalative outside bound state and will help in understanding the overall intercalation mechanism.
Polyacrylic acids–bovine serum albumin complexation: Structure and dynamics
Energy Technology Data Exchange (ETDEWEB)
Othman, Mohamed; Aschi, Adel, E-mail: aschi13@yahoo.fr; Gharbi, Abdelhafidh
2016-01-01
The study of the mixture of BSA with polyacrylic acids at different masses versus pH allowed highlighting the existence of two regimes of weak and strong complexation. These complexes were studied in diluted regime concentration, by turbidimetry, dynamic light scattering (DLS), zeta-potential measurements and nuclear magnetic resonance (NMR). We have followed the pH effect on the structure and properties of the complex. This allowed refining the interpretation of the phase diagram and understanding the observed phenomena. The NMR measurements allowed probing the dynamics of the constituents versus the pH. The computational method was used to precisely determine the electrostatic potential of BSA and how the polyelectrolyte binds to it at different pH. - Highlights: • Influence of physico-chemical parameters on the electrostatic interactions in the complex system (polyelectrolyte/protein). • Stabilization and encapsulation of biological macromolecules solution by mean of polyelectrolyte. • Properties and structure of mixture obtained by screening the charges of globular protein and at different masses of polyacrylic acids. • Dynamic of the constituents formed by complexes particles. • Evaluation of the electrostatic properties of bovine serum albumin versus pH through solution of the Poisson-Boltzmann equation.
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 driven flow with exclusion in graphenelike structures.
Stinchcombe, R B; de Queiroz, S L A
2015-05-01
We present a mean-field theory for the dynamics of driven flow with exclusion in graphenelike structures, and numerically check its predictions. We treat first a specific combination of bond transmissivity rates, where mean field predicts, and numerics to a large extent confirms, that the sublattice structure characteristic of honeycomb networks becomes irrelevant. Dynamics, in the various regions of the phase diagram set by open boundary injection and ejection rates, is then in general identical to that of one-dimensional systems, although some discrepancies remain between mean-field theory and numerical results, in similar ways for both geometries. However, at the critical point for which the characteristic exponent is z=3/2 in one dimension, the mean-field value z=2 is approached for very large systems with constant (finite) aspect ratio. We also treat a second combination of bond (and boundary) rates where, more typically, sublattice distinction persists. For the two rate combinations, in continuum or late-time limits, respectively, the coupled sets of mean-field dynamical equations become tractable with various techniques and give a two-band spectrum, gapless in the critical phase. While for the second rate combination quantitative discrepancies between mean-field theory and simulations increase for most properties and boundary rates investigated, theory still is qualitatively correct in general, and gives a fairly good quantitative account of features such as the late-time evolution of density profile differences from their steady-state values.
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.
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.
Structural Dynamics Experimental Activities in Ultra-Lightweight and Inflatable Space Structures
Pappa, Richard S.; Lassiter, John O.; Ross, Brian P.
2001-01-01
This paper reports recently completed structural dynamics experimental activities with new ultra-lightweight and inflatable space structures (a.k.a., "Gossamer" spacecraft) at NASA Langley Research Center, NASA Marshall Space Flight Center, and NASA Goddard Space Flight Center. Nine aspects of this work are covered: 1) inflated, rigidized tubes, 2) active control experiments, 3) photogrammetry, 4) laser vibrometry, 5) modal tests of inflatable structures, 6) in-vacuum modal tests, 7) tensioned membranes, 8) deployment tests, and 9) flight experiment support. Structural dynamics will play a major role in the design and eventually in-space deployment and performance of Gossamer spacecraft. Experimental research and development such as this is required to validate new analysis methods. The activities discussed in the paper are pathfinder accomplishments. conducted on unique components and prototypes of future spacecraft systems.
Biomembrane Structure and Dynamics Controlled by Dehydration and Osmotic Stress
Kinnun, Jacob; Mallikarjunaiah, K. J.; Leftin, Avigdor; Petrache, Horia; Brown, Michael
2011-10-01
Membrane deformation and dynamics and their effects on membrane protein function remain mysterious. With osmolytes and dehydration we observe deformation of DMPC-d54 lipid membranes via solid-state ^2H NMR spectroscopy. A unified theoretical framework predicts that membrane osmotic pressure depends inversely on the number waters per lipid. Through temperature variation we find osmotic pressure is generated by membrane undulations and lipid protrusions. We extend this thermodynamic framework via a mean-torque model to analyze the compressibility of the lipids. Under pressure, the area per lipid decreases and hydrocarbon thickness increases as described by a compressibility modulus. Changes in membrane thickness result in hydrophobic mismatch which affect protein-lipid interactions. Our findings show how altering membrane structure and dynamics affect membrane protein function.
Distinguish Dynamic Basic Blocks by Structural Statistical Testing
DEFF Research Database (Denmark)
Petit, Matthieu; Gotlieb, Arnaud
of satisfying a structural coverage criterion for instance. In this paper, we propose a new statistical testing method that generates sequences of random test data that respect the following probabilistic properties: 1) each sequence guarantees the uniform selection of feasible paths only and 2) the uniform...... selection of test data over the subdomain associated with these paths. Baudry et al. present a testing for-diagnosis method where the essential notion of Dynamic Basic Block was identified to be strongly correlated to the effectiveness of fault-localization technique. We show that generating a sequence...... of random test data respecting these properties allows to well-distinguished Dynamic Basic Blocks. Thanks to Constraint programming techniques, we propose an efficient algorithm that uniformly selects feasible paths only by drastically decreasing the number of rejects (test data that activate another...
Dynamical structures of high-frequency financial data
Kim, Kyungsik; Yoon, Seong-Min; Kim, SooYong; Chang, Ki-Ho; Kim, Yup; Hoon Kang, Sang
2007-03-01
We study the dynamical behavior of high-frequency data from the Korean Stock Price Index (KOSPI) using the movement of returns in Korean financial markets. The dynamical behavior of a binarized series of our models is not completely random. In addition, the conditional probability is numerically estimated from a return series of KOSPI tick data. Non-trivial probability structures can be constituted from binary time series of autoregressive (AR), logit, and probit models, for which the Akaike Information Criterion shows a minimum value at the 15th order. From our results, we find that the value of the correct match ratio for the AR model is slightly larger than that derived by other models.
Ultrafast Structural Dynamics in Combustion Relevant Model Systems
Energy Technology Data Exchange (ETDEWEB)
Weber, Peter M. [Brown University
2014-03-31
The research project explored the time resolved structural dynamics of important model reaction system using an array of novel methods that were developed specifically for this purpose. They include time resolved electron diffraction, time resolved relativistic electron diffraction, and time resolved Rydberg fingerprint spectroscopy. Toward the end of the funding period, we also developed time-resolved x-ray diffraction, which uses ultrafast x-ray pulses at LCLS. Those experiments are just now blossoming, as the funding period expired. In the following, the time resolved Rydberg Fingerprint Spectroscopy is discussed in some detail, as it has been a very productive method. The binding energy of an electron in a Rydberg state, that is, the energy difference between the Rydberg level and the ground state of the molecular ion, has been found to be a uniquely powerful tool to characterize the molecular structure. To rationalize the structure sensitivity we invoke a picture from electron diffraction: when it passes the molecular ion core, the Rydberg electron experiences a phase shift compared to an electron in a hydrogen atom. This phase shift requires an adjustment of the binding energy of the electron, which is measurable. As in electron diffraction, the phase shift depends on the molecular, geometrical structure, so that a measurement of the electron binding energy can be interpreted as a measurement of the molecule’s structure. Building on this insight, we have developed a structurally sensitive spectroscopy: the molecule is first elevated to the Rydberg state, and the binding energy is then measured using photoelectron spectroscopy. The molecule’s structure is read out as the binding energy spectrum. Since the photoionization can be done with ultrafast laser pulses, the technique is inherently capable of a time resolution in the femtosecond regime. For the purpose of identifying the structures of molecules during chemical reactions, and for the analysis of
Surface Structure of Hydroxyapatite from Simulated Annealing Molecular Dynamics Simulations.
Wu, Hong; Xu, Dingguo; Yang, Mingli; Zhang, Xingdong
2016-05-10
The surface structure of hydroxyapatite (HAP) is crucial for its bioactivity. Using a molecular dynamics simulated annealing method, we studied the structure and its variation with annealing temperature of the HAP (100) surface. In contrast to the commonly used HAP surface model, which is sliced from HAP crystal and then relaxed at 0 K with first-principles or force-field calculations, a new surface structure with gradual changes from ordered inside to disordered on the surface was revealed. The disordering is dependent on the annealing temperature, Tmax. When Tmax increases up to the melting point, which was usually adopted in experiments, the disordering increases, as reflected by its radial distribution functions, structural factors, and atomic coordination numbers. The disordering of annealed structures does not show significant changes when Tmax is above the melting point. The thickness of disordered layers is about 10 Å. The surface energy of the annealed structures at high temperature is significantly less than that of the crystal structure relaxed at room temperature. A three-layer model of interior, middle, and surface was then proposed to describe the surface structure of HAP. The interior layer retains the atomic configurations in crystal. The middle layer has its atoms moved and its groups rotated about their original locations. In the surface layer, the atomic arrangements are totally different from those in crystal. In particular for the hydroxyl groups, they move outward and cover the Ca(2+) ions, leaving holes occupied by the phosphate groups. Our study suggested a new model with disordered surface structures for studying the interaction of HAP-based biomaterials with other molecules.
Teo, Hui Fen
2014-01-01
Approved for public release; distribution is unlimited With the growing interest in using composites in naval shipbuilding, it is crucial to understand the behavior of structures, especially the Fluid Structural Interaction (FSI) aspect of the composites under dynamic loading, to ensure the survivability of the platform at sea. The objective of this study is to perform displacement-controlled fatigue cyclic loading on quasi-isotropic E-glass laminate, which is commonly used in the shipbuil...
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.
Single-Molecule Spectroscopic Investigations of RNA Structural Dynamics
Fiore, Julie L.; Nesbitt, David J.
2007-03-01
To function properly, catalytic RNAs (ribozymes) fold into specific three-dimensional shapes stabilized by multiple tertiary interactions. However, only limited information is available on the contributions of individual tertiary contacts to RNA conformational dynamics. The Tetrahymena ribozymes's P4--P6 domain forms a hinged, ``candy-cane'' structure with parallel helices clamped by two motifs, the GAAA tetraloop-tetraloop receptor and adenosine (A)-rich bulge--P4 helix interactions. Previously, we characterized RNA folding due to a tetraloop-receptor interaction. In this study, we employ time-resolved single-molecule FRET methods to probe A-rich bulge induced structural dynamics. Specifically, fluorescently labeled RNA constructs excited by a pulsed 532 nm laser are detected in the confocal region of an inverted microscope, with each photon sorted by arrival time, color and polarization. We resolve the kinetic dependence of A-rich bulge-P4 helix docking/undocking on cationic environment (e.g. Na^+ and Mg^2+ concentration.) At saturating [Mg^2+], the docked structure appears only weakly stabilized, while only 50% of the molecules exhibit efficient folding.
Stochastic simulation of structured skin cell population dynamics.
Nakaoka, Shinji; Aihara, Kazuyuki
2013-03-01
The epidermis is the outmost skin tissue. It operates as a first defense system to process inflammatory signals and responds by producing inflammatory mediators that promote the recruitment of immune cells. Various skin diseases such as atopic dermatitis occur as a result of the defect of proper skin barrier function and successive impaired inflammatory responses. The onset of such a skin disease links to the disturbed epidermal homeostasis regulated by appropriate self-renewal and differentiation of epidermal stem cells. The theory of physiologically structured population models provides a versatile framework to formulate mathematical models which describe the growth dynamics of a cell population such as the epidermis. In this paper, we develop an algorithm to implement stochastic simulation for a class of physiologically structured population models. We demonstrate that the developed algorithm is applicable to several cell population models and typical age-structured population models. On the basis of the developed algorithm, we investigate stochastic dynamics of skin cell populations and spread of inflammation. It is revealed that demographic stochasticity can bring considerable impact on the outcome of inflammation spread at the tissue level.
Modeling structured population dynamics using data from unmarked individuals
Grant, Evan H. Campbell; Zipkin, Elise; Thorson, James T.; See, Kevin; Lynch, Heather J.; Kanno, Yoichiro; Chandler, Richard; Letcher, Benjamin H.; Royle, J. Andrew
2014-01-01
The study of population dynamics requires unbiased, precise estimates of abundance and vital rates that account for the demographic structure inherent in all wildlife and plant populations. Traditionally, these estimates have only been available through approaches that rely on intensive mark–recapture data. We extended recently developed N-mixture models to demonstrate how demographic parameters and abundance can be estimated for structured populations using only stage-structured count data. Our modeling framework can be used to make reliable inferences on abundance as well as recruitment, immigration, stage-specific survival, and detection rates during sampling. We present a range of simulations to illustrate the data requirements, including the number of years and locations necessary for accurate and precise parameter estimates. We apply our modeling framework to a population of northern dusky salamanders (Desmognathus fuscus) in the mid-Atlantic region (USA) and find that the population is unexpectedly declining. Our approach represents a valuable advance in the estimation of population dynamics using multistate data from unmarked individuals and should additionally be useful in the development of integrated models that combine data from intensive (e.g., mark–recapture) and extensive (e.g., counts) data sources.
On Cognition, Structured Sequence Processing, and Adaptive Dynamical Systems
Petersson, Karl Magnus
2008-11-01
Cognitive neuroscience approaches the brain as a cognitive system: a system that functionally is conceptualized in terms of information processing. We outline some aspects of this concept and consider a physical system to be an information processing device when a subclass of its physical states can be viewed as representational/cognitive and transitions between these can be conceptualized as a process operating on these states by implementing operations on the corresponding representational structures. We identify a generic and fundamental problem in cognition: sequentially organized structured processing. Structured sequence processing provides the brain, in an essential sense, with its processing logic. In an approach addressing this problem, we illustrate how to integrate levels of analysis within a framework of adaptive dynamical systems. We note that the dynamical system framework lends itself to a description of asynchronous event-driven devices, which is likely to be important in cognition because the brain appears to be an asynchronous processing system. We use the human language faculty and natural language processing as a concrete example through out.
Ricles, James M.
1990-01-01
The development and preliminary assessment of a method for dynamic structural analysis based on load-dependent Ritz vectors are presented. The vector basis is orthogonalized with respect to the mass and structural stiffness in order that the equations of motion can be uncoupled and efficient analysis of large space structure performed. A series of computer programs was developed based on the algorithm for generating the orthogonal load-dependent Ritz vectors. Transient dynamic analysis performed on the Space Station Freedom using the software was found to provide solutions that require a smaller number of vectors than the modal analysis method. Error norm based on the participation of the mass distribution of the structure and spatial distribution of structural loading, respectively, were developed in order to provide an indication of vector truncation. These norms are computed before the transient analysis is performed. An assessment of these norms through a convergence study of the structural response was performed. The results from this assessment indicate that the error norms can provide a means of judging the quality of the vector basis and accuracy of the transient dynamic solution.
Improving the Dynamic Characteristics of Body-in-White Structure Using Structural Optimization
Directory of Open Access Journals (Sweden)
Aizzat S. Yahaya Rashid
2014-01-01
Full Text Available The dynamic behavior of a body-in-white (BIW structure has significant influence on the noise, vibration, and harshness (NVH and crashworthiness of a car. Therefore, by improving the dynamic characteristics of BIW, problems and failures associated with resonance and fatigue can be prevented. The design objectives attempt to improve the existing torsion and bending modes by using structural optimization subjected to dynamic load without compromising other factors such as mass and stiffness of the structure. The natural frequency of the design was modified by identifying and reinforcing the structure at critical locations. These crucial points are first identified by topology optimization using mass and natural frequencies as the design variables. The individual components obtained from the analysis go through a size optimization step to find their target thickness of the structure. The thickness of affected regions of the components will be modified according to the analysis. The results of both optimization steps suggest several design modifications to achieve the target vibration specifications without compromising the stiffness of the structure. A method of combining both optimization approaches is proposed to improve the design modification process.
Structure and Dynamics of Polymer/Polymer grafted nanoparticle composite
Archer, Lynden
Addition of nanoparticles to polymers is a well-practiced methodology for augmenting various properties of the polymer host, including mechanical strength, thermal stability, barrier properties, dimensional stability and wear resistance. Many of these property changes are known to arise from nanoparticle-induced modification of polymer structure and chain dynamics, which are strong functions of the dispersion state of the nanoparticles' and on their relative size (D) to polymer chain dimensions (e.g. Random coil radius Rg or entanglement mesh size a) . This talk will discuss polymer nanocomposites (PNCs) comprised of Polyethylene Glycol (PEG) tethered silica nanoparticles (SiO2-PEG) dispersed in polymers as model systems for investigating phase stability and dynamics of PNCs. On the basis of small-angle X-ray Scattering, it will be shown that favorable enthalpic interactions between particle-tethered chains and a polymer host provides an important mechanism for creating PNCs in which particle aggregation is avoided. The talk will report on polymer and particle scale dynamics in these materials and will show that grafted nanoparticles well dispersed in a polymer host strongly influence the host polymer relaxation dynamics on all timescales and the polymers in turn produce dramatic changes in the nature (from diffusive to hyperdiffusive) and speed of nano particle decorrelation dynamics at the polymer entanglement threshold. A local viscosity model capable of explaining these observations is discussed and the results compared with scaling theories for NP motions in polymers This material is based on work supported by the National Science Foundation Award Nos. DMR-1609125 and CBET-1512297.
Dynamic brain structural changes after left hemisphere subcortical stroke.
Fan, Fengmei; Zhu, Chaozhe; Chen, Hai; Qin, Wen; Ji, Xunming; Wang, Liang; Zhang, Yujin; Zhu, Litao; Yu, Chunshui
2013-08-01
This study aimed to quantify dynamic structural changes in the brain after subcortical stroke and identify brain areas that contribute to motor recovery of affected limbs. High-resolution structural MRI and neurological examinations were conducted at five consecutive time points during the year following stroke in 10 patients with left hemisphere subcortical infarctions involving motor pathways. Gray matter volume (GMV) was calculated using an optimized voxel-based morphometry technique, and dynamic changes in GMV were evaluated using a mixed-effects model. After stroke, GMV was decreased bilaterally in brain areas that directly or indirectly connected with lesions, which suggests the presence of regional damage in these "healthy" brain tissues in stroke patients. Moreover, the GMVs of these brain areas were not correlated with the Motricity Index (MI) scores when controlling for time intervals after stroke, which indicates that these structural changes may reflect an independent process (such as axonal degeneration) but cannot affect the improvement of motor function. In contrast, the GMV was increased in several brain areas associated with motor and cognitive functions after stroke. When controlling for time intervals after stroke, only the GMVs in the cognitive-related brain areas (hippocampus and precuneus) were positively correlated with MI scores, which suggests that the structural reorganization in cognitive-related brain areas may facilitate the recovery of motor function. However, considering the small sample size of this study, further studies are needed to clarify the exact relationships between structural changes and recovery of motor function in stroke patients. Copyright © 2012 Wiley Periodicals, Inc.
An Introduction to the Problem of Dynamic Structural Damping,
1978-01-01
INTRODUCTION TO THE P ROBLEM OF DYNAMIC STRUCTURAL DAMPING by PSa n t ini , A.Castellan i and A.Nappi (stituto di Tecnologia Aerospaziale deIl’Unive rsità di...obtain information s on typical values of ~ to be used in each of the analyses described under Art . 2. It is generally agreed, in fac t , that the...clearly indicate that experimental validation of the results is of vital importance. No safe prediction of the phenomena listed under Art . 2 can be
Soft phonon mode dynamics in Aurivillius-type structures
Maurya, Deepam; Charkhesht, Ali; Nayak, Sanjeev K.; Sun, Fu-Chang; George, Deepu; Pramanick, Abhijit; Kang, Min-Gyu; Song, Hyun-Cheol; Alexander, Marshall M.; Lou, Djamila; Khodaparast, Giti A.; Alpay, S. P.; Vinh, N. Q.; Priya, Shashank
2017-10-01
We report the dynamics of soft phonon modes and their role toward various structural transformations in Aurivillius materials by employing terahertz frequency-domain spectroscopy, atomic pair distribution function analysis, and first-principles calculations. We have chosen B i4T i3O12 as a model system and identified soft phonon modes associated with the paraelectric tetragonal to the ferroelectric monoclinic transition. Three soft phonon modes have been discovered that exhibit a strong temperature dependence. We have determined that the anharmonicity in Bi-O bonds plays a significant role in phonon softening, and that Bi cations play an important role in the emergence of ferroelectricity.
Cache-mesh, a Dynamics Data Structure for Performance Optimization
DEFF Research Database (Denmark)
Nguyen, Tuan T.; Dahl, Vedrana Andersen; Bærentzen, J. Andreas
2017-01-01
This paper proposes the cache-mesh, a dynamic mesh data structure in 3D that allows modifications of stored topological relations effortlessly. The cache-mesh can adapt to arbitrary problems and provide fast retrieval to the most-referred-to topological relations. This adaptation requires trivial...... of the cache-mesh, and the extra work for caching is also trivial. Though it appears that it takes effort for initial implementation, building the cache-mesh is comparable to a traditional mesh in terms of implementation....
SPAR improved structure/fluid dynamic analysis capability
Oden, J. T.; Pearson, M. L.
1983-01-01
The capability of analyzing a coupled dynamic system of flowing fluid and elastic structure was added to the SPAR computer code. A method, developed and adopted for use in SPAR utilizes the existing assumed stress hybrid plan element in SPAR. An operational mode was incorporated in SPAR which provides the capability for analyzing the flaw of a two dimensional, incompressible, viscous fluid within rigid boundaries. Equations were developed to provide for the eventual analysis of the interaction of such fluids with an elastic solid.
Molecular dynamics simulations: from structure function relationships to drug discovery.
Nair, Pramod C; Miners, John O
2014-01-01
Molecular dynamics (MD) simulation is an emerging in silico technique with potential applications in diverse areas of pharmacology. Over the past three decades MD has evolved as an area of importance for understanding the atomic basis of complex phenomena such as molecular recognition, protein folding, and the transport of ions and small molecules across membranes. The application of MD simulations in isolation and in conjunction with experimental approaches have provided an increased understanding of protein structure-function relationships and demonstrated promise in drug discovery.
Structural Dynamics of Insulin Receptor and Transmembrane Signaling.
Tatulian, Suren A
2015-09-15
The insulin receptor (IR) is a (αβ)2-type transmembrane tyrosine kinase that plays a central role in cell metabolism. Each αβ heterodimer consists of an extracellular ligand-binding α-subunit and a membrane-spanning β-subunit that comprises the cytoplasmic tyrosine kinase (TK) domain and the phosphorylation sites. The α- and β-subunits are linked via a single disulfide bridge, and the (αβ)2 tetramer is formed by disulfide bonds between the α-chains. Insulin binding induces conformational changes in IR that reach the intracellular β-subunit followed by a protein phosphorylation and activation cascade. Defects in this signaling process, including IR dysfunction caused by mutations, result in type 2 diabetes. Rational drug design aimed at treatment of diabetes relies on knowledge of the detailed structure of IR and the dynamic structural transformations during transmembrane signaling. Recent X-ray crystallographic studies have provided important clues about the mode of binding of insulin to IR, the resulting structural changes and their transmission to the TK domain, but a complete understanding of the structural basis underlying insulin signaling has not been achieved. This review presents a critical analysis of the current status of the structure-function relationship of IR, with a comparative assessment of the other IR family receptors, and discusses potential advancements that may provide insight into the molecular mechanism of insulin signaling.
Dynamics of a moored structure model in ice
Energy Technology Data Exchange (ETDEWEB)
Williams, F.M.; Duthinh, D.; Valenchon, C.
1992-03-01
The response of a floating, moored offshore structure to loads applied by drifting ice was investigated. Scale model tests of the NEKTON 8000 FPV semisubmersible drilling platform were carred out in an ice tank at two different headings with respect to the ice velocity, and at two ice thicknesses. The tank uses a variant of the fourth generation model ice known as EG/AD/S containing no sugar. The test results show a sawtooth mode in which response is most severe. The sawtooth mode occurred at lower ice velocities and a harmonic mode occurred at higher velocities. The data are examined to determine the conditions under which this mode occurs. From an analysis of a second order system, a dynamic response coefficient is defined which provides a criterion for the sawtooth mode. The analysis is general and also applies to the response of fixed structures. 21 refs., 8 figs., 1 tab.
[Structure and dynamic of the nucleosome core particle].
Bertin, Aurélie; Mangenot, Stéphanie
2008-01-01
In eukaryotic cell, a few meters of DNA are compacted in nuclear compartment of a few microns. This high level of compaction is an important way to regulate gene expression. In the present paper, we present a description of the organization of DNA into its first level of compaction: the nucleosome core particle. The structure of the nucleosome has been described at an atomic resolution more than 10 years ago, where DNA is wrapped around an octamer of histones. Post-translational modifications affecting histone tails have been shown to regulate the chromatin degree of compaction and thus the gene expression and regulation. The structure of the NCP is far from being frozen and is highly dynamic. Remodeling factors can induce DNA sliding around the histones, DNA transaction processes such as transcription and replication.
Dynamics of Localized Structures in Systems with Broken Parity Symmetry
Javaloyes, J; Marconi, M; Giudici, M
2016-01-01
A great variety of nonlinear dissipative systems are known to host structures having a correlation range much shorter than the size of the system. The dynamics of these Localized Structures (LSs) have been investigated so far in situations featuring parity symmetry. In this letter we extend this analysis to systems lacking of this property. We show that the LS drifting speed in a parameter varying landscape is not simply proportional to the parameter gradient, as found in parity preserving situations. The symmetry breaking implies a new contribution to the velocity field which is a function of the parameter value, thus leading to a new paradigm for LSs manipulation. We illustrate this general concept by studying the trajectories of the LSs found in a passively mode-locked laser operated in the localization regime. Moreover, the lack of parity affects significantly LSs interactions which are governed by asymmetrical repulsive forces.
STRUCTURE AND DYNAMICS OF IRREGULAR MULTIARM STAR POLYMERS
Directory of Open Access Journals (Sweden)
D.Vlassopoulos
2002-01-01
Full Text Available Melt properties of highly branched star polymers consisting of a 1,2-polybutadiene core and nearly 270 arms of 1,4-polybutadiene with varying sizes have been investigated using small angle X-ray scattering (SAXS and dynamic rheological measurements in the linear viscoelastic limit. Despite their difference in internal structure compared to the regular stars with 128 arms and spherical dendritic core, these polymers exhibit the same features: a liquid-like ordering resulting from their specific intramolecular monomer density distribution. This leads to a dual terminal viscoelastic relaxation, consisting of a fast arm relaxation and a slow structural relaxation mechanisms. Both modes conform quantitatively to the generic behaviour of multiarm star polymers, suggesting a universality of the behaviour of highly branched macromolecular objects.
A Modal Model to Simulate Typical Structural Dynamic Nonlinearity
Energy Technology Data Exchange (ETDEWEB)
Pacini, Benjamin Robert [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Mayes, Randall L. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Roettgen, Daniel R [Univ. of Wisconsin, Madison, WI (United States)
2015-10-01
Some initial investigations have been published which simulate nonlinear response with almost traditional modal models: instead of connecting the modal mass to ground through the traditional spring and damper, a nonlinear Iwan element was added. This assumes that the mode shapes do not change with amplitude and there are no interactions between modal degrees of freedom. This work expands on these previous studies. An impact experiment is performed on a structure which exhibits typical structural dynamic nonlinear response, i.e. weak frequency dependence and strong damping dependence on the amplitude of vibration. Use of low level modal test results in combination with high level impacts are processed using various combinations of modal filtering, the Hilbert Transform and band-pass filtering to develop response data that are then fit with various nonlinear elements to create a nonlinear pseudo-modal model. Simulations of forced response are compared with high level experimental data for various nonlinear element assumptions.
Dynamic multiprotein assemblies shape the spatial structure of cell signaling.
Nussinov, Ruth; Jang, Hyunbum
2014-01-01
Cell signaling underlies critical cellular decisions. Coordination, efficiency as well as fail-safe mechanisms are key elements. How the cell ensures that these hallmarks are at play are important questions. Cell signaling is often viewed as taking place through discrete and cross-talking pathways; oftentimes these are modularized to emphasize distinct functions. While simple, convenient and clear, such models largely neglect the spatial structure of cell signaling; they also convey inter-modular (or inter-protein) spatial separation that may not exist. Here our thesis is that cell signaling is shaped by a network of multiprotein assemblies. While pre-organized, the assemblies and network are loose and dynamic. They contain transiently-associated multiprotein complexes which are often mediated by scaffolding proteins. They are also typically anchored in the membrane, and their continuum may span the cell. IQGAP1 scaffolding protein which binds proteins including Raf, calmodulin, Mek, Erk, actin, and tens more, with actin shaping B-cell (and likely other) membrane-anchored nanoclusters and allosterically polymerizing in dynamic cytoskeleton formation, and Raf anchoring in the membrane along with Ras, provides a striking example. The multivalent network of dynamic proteins and lipids, with specific interactions forming and breaking, can be viewed as endowing gel-like properties. Collectively, this reasons that efficient, productive and reliable cell signaling takes place primarily through transient, preorganized and cooperative protein-protein interactions spanning the cell rather than stochastic, diffusion-controlled processes. Copyright © 2014 Elsevier Ltd. All rights reserved.
Electrostatic cloaking of surface structure for dynamic wetting
Shiomi, Junichiro; Nita, Satoshi; Do-Quang, Minh; Wang, Jiayu; Chen, Yu-Chung; Suzuki, Yuji; Amberg, Gustav
2017-11-01
Dynamic wetting problems are fundamental to the understanding of the interaction between liquids and solids. Even in a superficially simple experimental situation, such as a droplet spreading over a dry surface, the result may depend not only on the liquid properties but also strongly on the substrate-surface properties; even for macroscopically smooth surfaces, the microscopic geometrical roughness can be important. In addition, as surfaces may often be naturally charged, or electric fields are used to manipulate fluids, electric effects are crucial components that influence wetting phenomena. Here we investigate the interplay between electric forces and surface structures in dynamic wetting. While surface microstructures can significantly hinder the spreading, we find that the electrostatics can ``cloak'' the microstructures, i.e. deactivate the hindering. We identify the physics in terms of reduction in contact-line friction, which makes the dynamic wetting inertial force dominant and insensitive to the substrate properties. This work was financially supported in part by, the Japan Society for the Promotion of Science, Swedish Governmental Agency for Innovation Systems, and the Japan Science and Technology Agency.
Structural and dynamical properties of recombining ultracold neutral plasma
Tiwari, Sanat Kumar; Shaffer, Nathaniel R.; Baalrud, Scott D.
2017-10-01
An ultracold plasma (UCP) is an evolving collection of free charges and bound charges (Rydberg atoms). Over time, bound species concentration increases due to recombination. We present the structural and dynamical properties of an evolving UCP using classical molecular dynamics simulation. Coulomb collapse is avoided using a repulsive core with the attractive Coulomb potential. The repulsive core size controls the concentration of bound states, as it determines the depth of the potential well between opposite charges. We vary the repulsive core size to emulate the quasi-static state of plasma at different time during the evolution. Binary, chain and ring-like bound states are observed in the simulation carried out at different coupling strengths and repulsive core size. The effect of bound states can be seen as molecular peaks in the radial distribution function (RDF). The thermodynamic properties associated with the free charges can be analyzed from RDF by separating free from bound states. These bound states also change the dynamical properties of the plasma. The electron velocity auto-correlation displays oscillations due to the orbital motion in bound states. These bound states act like a neutral species, damping electron plasmon modes and broadening the ion acoustic mode. This work is supported by AFOSR Grant Number FA9550-16-1-0221. It used computational resources by XSEDE, which is supported by NSF Grant Number ACI-1053575.
Dynamics of a Duopoly Game with Two Different Delay Structures
Directory of Open Access Journals (Sweden)
Shumin Jiang
2017-01-01
Full Text Available Two different time delay structures for the dynamical Cournot game with two heterogeneous players are considered in this paper, in which a player is assumed to make decision via his marginal profit with time delay and another is assumed to adjust strategy according to the delayed price. The dynamics of both players output adjustments are analyzed and simulated. The time delay for the marginal profit has more influence on the dynamical behaviors of the system while the market price delay has less effect, and an intermediate level of the delay weight for the marginal profit can expand the stability region and thus promote the system stability. It is also shown that the system may lose stability due to either a period-doubling bifurcation or a Neimark-Sacker bifurcation. Numerical simulations show that the chaotic behaviors can be stabilized by the time-delayed feedback control, and the two different delays play different roles on the system controllability: the delay of the marginal profit has more influence on the system control than the delay of the market price.
Automatic anatomical structures location based on dynamic shape measurement
Witkowski, Marcin; Rapp, Walter; Sitnik, Robert; Kujawinska, Malgorzata; Vander Sloten, Jos; Haex, Bart; Bogaert, Nico; Heitmann, Kjell
2005-09-01
New image processing methods and active photonics apparatus have made possible the development of relatively inexpensive optical systems for complex shape and object measurements. We present dynamic 360° scanning method for analysis of human lower body biomechanics, with an emphasis on the analysis of the knee joint. The anatomical structure (of high medical interest) that is possible to scan and analyze, is patella. Tracking of patella position and orientation under dynamic conditions may lead to detect pathological patella movements and help in knee joint disease diagnosis. The processed data is obtained from a dynamic laser triangulation surface measurement system, able to capture slow to normal movements with a scan frequency between 15 and 30 Hz. These frequency rates are enough to capture controlled movements used e.g. for medical examination purposes. The purpose of the work presented is to develop surface analysis methods that may be used as support of diagnosis of motoric abilities of lower limbs. The paper presents algorithms used to process acquired lower limbs surface data in order to find the position and orientation of patella. The algorithms implemented include input data preparation, curvature description methods, knee region discrimination and patella assumed position/orientation calculation. Additionally, a method of 4D (3D + time) medical data visualization is proposed. Also some exemplary results are presented.
Energy Technology Data Exchange (ETDEWEB)
Demontis, Pierfranco; Suffritti, Giuseppe B. [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari (Italy); Gulín-González, Jorge [Grupo de Matemática y Física Computacionales, Universidad de las Ciencias Informáticas (UCI), Carretera a San Antonio de los Baños, Km 21/2, La Lisa, La Habana (Cuba); Masia, Marco [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari (Italy); Istituto Officina dei Materiali del CNR, UOS SLACS, Via Vienna 2, 07100 Sassari (Italy); Sant, Marco [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy)
2015-06-28
In order to study the interplay between dynamical heterogeneities and structural properties of bulk liquid water in the temperature range 130–350 K, thus including the supercooled regime, we use the explicit trend of the distribution functions of some molecular properties, namely, the rotational relaxation constants, the atomic mean-square displacements, the relaxation of the cross correlation functions between the linear and squared displacements of H and O atoms of each molecule, the tetrahedral order parameter q and, finally, the number of nearest neighbors (NNs) and of hydrogen bonds (HBs) per molecule. Two different potentials are considered: TIP4P-Ew and a model developed in this laboratory for the study of nanoconfined water. The results are similar for the dynamical properties, but are markedly different for the structural characteristics. In particular, for temperatures higher than that of the dynamic crossover between “fragile” (at higher temperatures) and “strong” (at lower temperatures) liquid behaviors detected around 207 K, the rotational relaxation of supercooled water appears to be remarkably homogeneous. However, the structural parameters (number of NNs and of HBs, as well as q) do not show homogeneous distributions, and these distributions are different for the two water models. Another dynamic crossover between “fragile” (at lower temperatures) and “strong” (at higher temperatures) liquid behaviors, corresponding to the one found experimentally at T{sup ∗} ∼ 315 ± 5 K, was spotted at T{sup ∗} ∼ 283 K and T{sup ∗} ∼ 276 K for the TIP4P-Ew and the model developed in this laboratory, respectively. It was detected from the trend of Arrhenius plots of dynamic quantities and from the onset of a further heterogeneity in the rotational relaxation. To our best knowledge, it is the first time that this dynamical crossover is detected in computer simulations of bulk water. On the basis of the simulation results, the possible
Ultrafast Structural Dynamics by X-Ray Diffraction and Structural Spectroscopy
Weber, Peter M.
2015-05-01
The ability to observe molecular reactions in real time is expected to aid the exploration of new reaction mechanisms, the development of catalysts, the understanding of biomolecular processes and the control of chemical reactions and material properties on a molecular level. To reach this goal, we have developed a gas-phase x-ray diffraction experiment that uses the ultrashort x-ray pulses from the Linac Coherent Light Source (LCLS) to capture atomic motions within molecules in a dilute gas (movie'' of the observed dynamics is constructed by comparing ab initio quantum molecular dynamics simulations with the experimental diffraction signal to derive weighted trajectories that provide a good representation of the structural dynamics, with the weighted ensemble of trajectories corresponding to the nuclear flux during the chemical reaction. The x-ray structural data thus provide reaction pathways for which ionization energies can be calculated at each step. We use ultrafast time-resolved multiphoton - ionization photoelectron spectroscopy to measure the travel time required for the molecule to reach certain resonance windows to Rydberg states. By so combining the results from the ultrafast x-ray diffraction with observations from ultrafast (structural) spectroscopy, it appears that we can make significant progress towards the ultimate goal: a comprehensive understanding of the spatially resolved photochemical reaction dynamics.
Li, Cheng-Peng; Chen, Jing; Liu, Chun-Sen; Du, Miao
2015-02-18
Reactions in the solid state, especially single-crystal-to-single-crystal (SC-SC) transformations, provide an appealing pathway to obtain target crystalline materials with modified properties via a solvent-free green chemistry approach. This feature article focuses on the progress to date in the context of coordination supramolecular systems (CSSs), especially coordination polymers (CPs) or metal-organic frameworks (MOFs), which show interesting dynamic natures upon exposure to various exogenous stimuli, including concentration, temperature, light and mechanical force, as well as their synergic effect. In essence, dynamic CSSs normally possess crucial crystalline-reactive characteristics: (i) metal ions or clusters with unstable or metastable electronic configurations and coordination geometries; (ii) organic ligands bearing physicochemically active functional groups for subsequent reactions; (iii) polymeric networks of high flexibility for structural bending, rotation, swelling, or shrinking; (iv) guest moieties to be freely exchanged or eliminated by varying the environmental conditions. The significant changes in catalytic, sorption, magnetic, or luminescent properties accompanied by the structural transformations will also be discussed, which reveal the proof-of-concept thereof in designing new functional crystalline materials.
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.
Deformation, Ecosystem Structure, and Dynamics of Ice (DESDynI)
Donnellan, Andrea; Rosen, Paul; Ranson, Jon; Zebker, Howard
2008-01-01
The National Research Council Earth Science Decadal Survey, Earth Science Applications from Space, recommends that DESDynI (Deformation, Ecosystem Structure, and Dynamics of Ice), an integrated L-band InSAR and multibeam Lidar mission, launch in the 2010- 2013 timeframe. The mission will measure surface deformation for solid Earth and cryosphere objectives and vegetation structure for understanding the carbon cycle. InSAR has been used to study surface deformation of the solid Earth and cryosphere and more recently vegetation structure for estimates of biomass and ecosystem function. Lidar directly measures topography and vegetation structure and is used to estimate biomass and detect changes in surface elevation. The goal of DESDynI is to take advantage of the spatial continuity of InSAR and the precision and directness of Lidar. There are several issues related to the design of the DESDynI mission, including combining the two instruments into a single platform, optimizing the coverage and orbit for the two techniques, and carrying out the science modeling to define and maximize the scientific output of the mission.
Dynamic protein interaction networks and new structural paradigms in signaling
Csizmok, Veronika; Follis, Ariele Viacava; Kriwacki, Richard W.; Forman-Kay, Julie D.
2017-01-01
Understanding signaling and other complex biological processes requires elucidating the critical roles of intrinsically disordered proteins and regions (IDPs/IDRs), which represent ~30% of the proteome and enable unique regulatory mechanisms. In this review we describe the structural heterogeneity of disordered proteins that underpins these mechanisms and the latest progress in obtaining structural descriptions of ensembles of disordered proteins that are needed for linking structure and dynamics to function. We describe the diverse interactions of IDPs that can have unusual characteristics such as “ultrasensitivity” and “regulated folding and unfolding”. We also summarize the mounting data showing that large-scale assembly and protein phase separation occurs within a variety of signaling complexes and cellular structures. In addition, we discuss efforts to therapeutically target disordered proteins with small molecules. Overall, we interpret the remodeling of disordered state ensembles due to binding and post-translational modifications within an expanded framework for allostery that provides significant insights into how disordered proteins transmit biological information. PMID:26922996
Structure and dynamics of the M3 muscarinic acetylcholine receptor
Energy Technology Data Exchange (ETDEWEB)
Kruse, Andrew C.; Hu, Jianxin; Pan, Albert C.; Arlow, Daniel H.; Rosenbaum, Daniel M.; Rosemond, Erica; Green, Hillary F.; Liu, Tong; Chae, Pil Seok; Dror, Ron O.; Shaw, David E.; Weis, William I.; Wess, Jürgen; Kobilka, Brian K. (Stanford); (NIH); (D.E. Shaw); (Hanyang); (UTSMC)
2012-03-01
Acetylcholine, the first neurotransmitter to be identified, exerts many of its physiological actions via activation of a family of G-protein-coupled receptors (GPCRs) known as muscarinic acetylcholine receptors (mAChRs). Although the five mAChR subtypes (M1-M5) share a high degree of sequence homology, they show pronounced differences in G-protein coupling preference and the physiological responses they mediate. Unfortunately, despite decades of effort, no therapeutic agents endowed with clear mAChR subtype selectivity have been developed to exploit these differences. We describe here the structure of the G{sub q/11}-coupled M3 mAChR ('M3 receptor', from rat) bound to the bronchodilator drug tiotropium and identify the binding mode for this clinically important drug. This structure, together with that of the G{sub i/o}-coupled M2 receptor, offers possibilities for the design of mAChR subtype-selective ligands. Importantly, the M3 receptor structure allows a structural comparison between two members of a mammalian GPCR subfamily displaying different G-protein coupling selectivities. Furthermore, molecular dynamics simulations suggest that tiotropium binds transiently to an allosteric site en route to the binding pocket of both receptors. These simulations offer a structural view of an allosteric binding mode for an orthosteric GPCR ligand and provide additional opportunities for the design of ligands with different affinities or binding kinetics for different mAChR subtypes. Our findings not only offer insights into the structure and function of one of the most important GPCR families, but may also facilitate the design of improved therapeutics targeting these critical receptors.
PCI-SS: MISO dynamic nonlinear protein secondary structure prediction
Directory of Open Access Journals (Sweden)
Aboul-Magd Mohammed O
2009-07-01
Full Text Available Abstract Background Since the function of a protein is largely dictated by its three dimensional configuration, determining a protein's structure is of fundamental importance to biology. Here we report on a novel approach to determining the one dimensional secondary structure of proteins (distinguishing α-helices, β-strands, and non-regular structures from primary sequence data which makes use of Parallel Cascade Identification (PCI, a powerful technique from the field of nonlinear system identification. Results Using PSI-BLAST divergent evolutionary profiles as input data, dynamic nonlinear systems are built through a black-box approach to model the process of protein folding. Genetic algorithms (GAs are applied in order to optimize the architectural parameters of the PCI models. The three-state prediction problem is broken down into a combination of three binary sub-problems and protein structure classifiers are built using 2 layers of PCI classifiers. Careful construction of the optimization, training, and test datasets ensures that no homology exists between any training and testing data. A detailed comparison between PCI and 9 contemporary methods is provided over a set of 125 new protein chains guaranteed to be dissimilar to all training data. Unlike other secondary structure prediction methods, here a web service is developed to provide both human- and machine-readable interfaces to PCI-based protein secondary structure prediction. This server, called PCI-SS, is available at http://bioinf.sce.carleton.ca/PCISS. In addition to a dynamic PHP-generated web interface for humans, a Simple Object Access Protocol (SOAP interface is added to permit invocation of the PCI-SS service remotely. This machine-readable interface facilitates incorporation of PCI-SS into multi-faceted systems biology analysis pipelines requiring protein secondary structure information, and greatly simplifies high-throughput analyses. XML is used to represent the input
Structural evolution and atomic dynamics in Ni-Nb metallic glasses: A molecular dynamics study
Xu, T. D.; Wang, X. D.; Zhang, H.; Cao, Q. P.; Zhang, D. X.; Jiang, J. Z.
2017-10-01
The composition and temperature dependence of static and dynamic structures in NixNb1-x (x = 50-70 at. %) were systematically studied using molecular dynamics with a new-released semi-empirical embedded atom method potential by Mendelev. The calculated pair correlation functions and the structure factor match well with the experimental data, demonstrating the reliability of the potential within relatively wide composition and temperature ranges. The local atomic structures were then characterized by bond angle distributions and Voronoi tessellation methods, demonstrating that the icosahedral ⟨0,0,12,0⟩ is only a small fraction in the liquid state but increases significantly during cooling and becomes dominant at 300 K. The most abundant clusters are identified as ⟨0,0,12,0⟩ and distorted icosahedron ⟨0,2,8,2⟩. The large fraction of these two clusters hints that the relatively good glass forming ability is near the eutectic point. Unlike Cu-Zr alloys, both the self-diffusion coefficient and shear viscosity are insensitive to compositions upon cooling in Ni-Nb alloys. The breakdown of the Stokes-Einstein relation happens at around 1.6Tg (Tg: glass transition temperature). In the amorphous state, the solid and liquid-like atoms can be distinguished based on the Debye-Waller factor ⟨u2⟩. The insensitivity of the dynamic properties of Ni-Nb alloys to compositions may result from the relatively simple solidification process in the phase diagram, in which only one eutectic point exists in the studied composition range.
Gao, Q.; Yao, W. A.; Wu, F.; Zhang, H. W.; Lin, J. H.; Zhong, W. X.; Howson, W. P.; Williams, F. W.
2013-09-01
This paper proposes an efficient algorithm for computing the dynamic responses of one-dimensional periodic structures and periodic structures with defects. It uses the symmetric property of the periodic structure and the energy propagation feature of the dynamic system to analyze the algebraic structure of the matrix exponential corresponding to one-dimensional periodic structures and periodic structures with defects. By using the special algebraic structure of this matrix exponential and the precise integration method, an efficient and accurate algorithm is proposed for computing the matrix exponential corresponding to one-dimensional periodic structures or periodic structures with defects. Hence an efficient method is presented for computing the dynamic responses of one-dimensional periodic structures and periodic structures with defects. It is accurate, efficient and saves memory.
Tyrosine aminotransferase: biochemical and structural properties and molecular dynamics simulations
Energy Technology Data Exchange (ETDEWEB)
Mehere, P.; Robinson, H.; Han, Q.; Lemkul, J. A.; Vavricka, C. J.; Bevan, D. R.; Li, J.
2010-11-01
Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using {alpha}-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 {angstrom} resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.
Tyrosine Aminotransferase: Biochemical and Structural Properties and Molecular Dynamics Simulations
Energy Technology Data Exchange (ETDEWEB)
P Mehere; Q Han; J Lemkul; C Vavricka; H Robinson; D Bevan; J Li
2011-12-31
Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using {alpha}-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 {angstrom} resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.
Postnatal brain development: Structural imaging of dynamic neurodevelopmental processes
Jernigan, Terry L.; Baaré, William F. C.; Stiles, Joan; Madsen, Kathrine Skak
2013-01-01
After birth, there is striking biological and functional development of the brain’s fiber tracts as well as remodeling of cortical and subcortical structures. Behavioral development in children involves a complex and dynamic set of genetically guided processes by which neural structures interact constantly with the environment. This is a protracted process, beginning in the third week of gestation and continuing into early adulthood. Reviewed here are studies using structural imaging techniques, with a special focus on diffusion weighted imaging, describing age-related brain maturational changes in children and adolescents, as well as studies that link these changes to behavioral differences. Finally, we discuss evidence for effects on the brain of several factors that may play a role in mediating these brain–behavior associations in children, including genetic variation, behavioral interventions, and hormonal variation associated with puberty. At present longitudinal studies are few, and we do not yet know how variability in individual trajectories of biological development in specific neural systems map onto similar variability in behavioral trajectories. PMID:21489384
Brain connectivity dynamics during social interaction reflect social network structure.
Schmälzle, Ralf; Brook O'Donnell, Matthew; Garcia, Javier O; Cascio, Christopher N; Bayer, Joseph; Bassett, Danielle S; Vettel, Jean M; Falk, Emily B
2017-05-16
Social ties are crucial for humans. Disruption of ties through social exclusion has a marked effect on our thoughts and feelings; however, such effects can be tempered by broader social network resources. Here, we use fMRI data acquired from 80 male adolescents to investigate how social exclusion modulates functional connectivity within and across brain networks involved in social pain and understanding the mental states of others (i.e., mentalizing). Furthermore, using objectively logged friendship network data, we examine how individual variability in brain reactivity to social exclusion relates to the density of participants' friendship networks, an important aspect of social network structure. We find increased connectivity within a set of regions previously identified as a mentalizing system during exclusion relative to inclusion. These results are consistent across the regions of interest as well as a whole-brain analysis. Next, examining how social network characteristics are associated with task-based connectivity dynamics, we find that participants who showed greater changes in connectivity within the mentalizing system when socially excluded by peers had less dense friendship networks. This work provides insight to understand how distributed brain systems respond to social and emotional challenges and how such brain dynamics might vary based on broader social network characteristics.
The Influence of Knitting Structure on Heating and Cooling Dynamic
Directory of Open Access Journals (Sweden)
Daiva MIKUČIONIENĖ
2013-05-01
Full Text Available The comfort provided by clothing depends on several factors, one of them being thermal comfort. Human thermal comfort depends on a combination of clothing, climate, and physical activity. It is known, the fibre type, yarn properties, fabric structure, finishing are the main factors affecting thermo-physiological comfort. The thermal property of knitted fabric is very important not only for its thermal comfort but also for protection against cross weather conditions. Most of the studies carried out have been devoted to measure static thermal properties. But it is very important not only amount of the heat released to the environment but also the dynamics of the heat transmission. The main goal of this work was to investigate the dynamic of the heat and cool transfer through the fabrics with different knitting pattern and different type of the yarns. Three different types of knitted fabrics were developed for this experimental work.DOI: http://dx.doi.org/10.5755/j01.ms.19.2.4434
The Dynamical Structure of HR 8799's Inner Debris Disk.
Contro, B; Wittenmyer, Robert A; Horner, J; Marshall, Jonathan P
2015-06-01
The HR 8799 system, with its four giant planets and two debris belts, has an architecture closely mirroring that of our Solar system where the inner, warm asteroid belt and outer, cool Edgeworth-Kuiper belt bracket the giant planets. As such, it is a valuable laboratory for examining exoplanetary dynamics and debris disk-exoplanet interactions. Whilst the outer debris belt of HR 8799 has been well resolved by previous observations, the spatial extent of the inner disk remains unknown. This leaves a significant question mark over both the location of the planetesimals responsible for producing the belt's visible dust and the physical properties of those grains. We have performed the most extensive simulations to date of the inner, unresolved debris belt around HR 8799, using UNSW Australia's Katana supercomputing facility to follow the dynamical evolution of a model inner disk comprising 300,298 particles for a period of 60 Ma. These simulations have enabled the characterisation of the extent and structure of the inner disk in detail, and will in future allow us to provide a first estimate of the small-body impact rate and water delivery prospects for possible (as-yet undetected) terrestrial planet (s) in the inner system.
Free vibration and dynamic response analysis of spinning structures
1986-01-01
The proposed effort involved development of numerical procedures for efficient solution of free vibration problems of spinning structures. An eigenproblem solution procedure, based on a Lanczos method employing complex arithmetic, was successfully developed. This task involved formulation of the numerical procedure, FORTRAN coding of the algorithm, checking and debugging of software, and implementation of the routine in the STARS program. A graphics package for the E/S PS 300 as well as for the Tektronix terminals was successfully generated and consists of the following special capabilities: (1) a dynamic response plot for the stresses and displacements as functions of time; and (2) a menu driven command module enabling input of data on an interactive basis. Finally, the STARS analysis capability was further improved by implementing the dynamic response analysis package that provides information on nodal deformations and element stresses as a function of time. A number of test cases were run utilizing the currently developed algorithm implemented in the STARS program and such results indicate that the newly generated solution technique is significantly more efficient than other existing similar procedures.
The Fine Structure of Equity-Index Option Dynamics
DEFF Research Database (Denmark)
Andersen, Torben G.; Bondarenko, Oleg; Todorov, Viktor
We analyze the high-frequency dynamics of S&P 500 equity-index option prices by constructing an assortment of implied volatility measures. This allows us to infer the underlying fine structure behind the innovations in the latent state variables driving the movements of the volatility surface....... In particular, we focus attention on implied volatilities covering a wide range of moneyness (strike/underlying stock price), which load differentially on the different latent state variables. We conduct a similar analysis for high-frequency observations on the VIX volatility index as well as on futures written...... on it. We find that the innovations in the risk-neutral intensity of the negative jumps in the S&P 500 index over small time scales are best described via non-Gaussian shocks, i.e., jumps. On the other hand, the innovations over small time scales of the diffusive volatility are best modeled as Gaussian...
Direct Adaptive Aircraft Control Using Dynamic Cell Structure Neural Networks
Jorgensen, Charles C.
1997-01-01
A Dynamic Cell Structure (DCS) Neural Network was developed which learns topology representing networks (TRNS) of F-15 aircraft aerodynamic stability and control derivatives. The network is integrated into a direct adaptive tracking controller. The combination produces a robust adaptive architecture capable of handling multiple accident and off- nominal flight scenarios. This paper describes the DCS network and modifications to the parameter estimation procedure. The work represents one step towards an integrated real-time reconfiguration control architecture for rapid prototyping of new aircraft designs. Performance was evaluated using three off-line benchmarks and on-line nonlinear Virtual Reality simulation. Flight control was evaluated under scenarios including differential stabilator lock, soft sensor failure, control and stability derivative variations, and air turbulence.
The landscape of nonlinear structural dynamics: an introduction.
Butlin, T; Woodhouse, J; Champneys, A R
2015-09-28
Nonlinear behaviour is ever-present in vibrations and other dynamical motions of engineering structures. Manifestations of nonlinearity include amplitude-dependent natural frequencies, buzz, squeak and rattle, self-excited oscillation and non-repeatability. This article primarily serves as an extended introduction to a theme issue in which such nonlinear phenomena are highlighted through diverse case studies. More ambitiously though, there is another goal. Both the engineering context and the mathematical techniques that can be used to identify, analyse, control or exploit these phenomena in practice are placed in the context of a mind-map, which has been created through expert elicitation. This map, which is available in software through the electronic supplementary material, attempts to provide a practitioner's guide to what hitherto might seem like a vast and complex research landscape. © 2015 The Authors.
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.
Coding considerations for standalone molecular dynamics simulations of atomistic structures
Ocaya, R. O.; Terblans, J. J.
2017-10-01
The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.
Applications of Asymptotic Sampling on High Dimensional Structural Dynamic Problems
DEFF Research Database (Denmark)
Sichani, Mahdi Teimouri; Nielsen, Søren R.K.; Bucher, Christian
2011-01-01
The paper represents application of the asymptotic sampling on various structural models subjected to random excitations. A detailed study on the effect of different distributions of the so-called support points is performed. This study shows that the distribution of the support points has...... 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...... 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...
Growth, structure and lattice dynamics of rare earth silicide nanostructures
Energy Technology Data Exchange (ETDEWEB)
Seiler, Anja
2015-07-13
In the present thesis the epitaxial growth, crystal structure, stoichiometry, thermal stability and lattice dynamics of self-organized EuSi{sub 2} and DySi{sub 2} films, nanoislands and nanowires are investigated. The rare earth silicide (RESi) nanostructures have attracted considerable interest due to their high conductivity, very low Schottky barrier heights, remarkable chemical stability, self-organization in high area density and defects-free nano-objects with tunable size and shape, and the direct integration into the Si technology. The extensive research is driven by the continuous downscaling of the CMOS electronics that require new approaches in the devices architecture and circuits interconnects. Although RESi nanostructures attracted a lot of interest already several years ago and a lot of research has been done in this field, the lattice dynamics of these materials are still unknown. Recent developments at third generation synchrotron radiation sources have brought their performance to a stage where phonon spectroscopy of nanostructures and thin layers became feasible using nuclear inelastic X-ray scattering. This novel experimental technique is based on the process of phonon-assisted nuclear resonant absorption/emission of X-rays from the nuclei of Moessbauer-active isotopes. The method provides direct access to the phonon density of states (DOS) of the investigated element. Together with the ab initio calculations it was possible to get a comprehensive understanding of the lattice dynamics. EuSi{sub 2} films and nanoislands and DySi{sub 2} films, nanoislands and nanowires have been grown on the vicinal Si(001) surface by molecular beam epitaxy. While DySi{sub 2} was grown following known growth procedures, the growth conditions for EuSi{sub 2} had to be established first. EuSi{sub 2} was grown at two different growth conditions to study the influence of crystal structure and morphology upon different growth temperatures. The structure has been
The Structure and Dynamics of the Solar Corona
Mikic, Zoran
2000-01-01
This report covers technical progress during the third year of the NASA Space Physics Theory contract "The Structure and Dynamics of the Solar Corona," between NASA and Science Applications International Corporation, and covers the period June 16, 1998 to August 15, 1999. This is also the final report for this contract. Under this contract SAIC, the University of California, Irvine (UCI), and the Jet Propulsion Laboratory (JPL), have conducted research into theoretical modeling of active regions, the solar corona, and the inner heliosphere, using the MHD model. During the three-year duration of this contract we have published 49 articles in the scientific literature. These publications are listed in Section 3 of this report. In the Appendix we have attached reprints of selected articles. We summarize our progress during the third year of the contract. Full descriptions of our work can be found in the cited publications, a few of which are attached to this report.
Guiding lead optimization with GPCR structure modeling and molecular dynamics.
Heifetz, Alexander; James, Tim; Morao, Inaki; Bodkin, Michael J; Biggin, Philip C
2016-10-01
G-protein coupled receptor (GPCR) modeling approaches are widely used in the hit-to-lead and lead optimization stages of drug discovery. Modern protocols that involve molecular dynamics simulation can address key issues such as the free energy of binding (affinity), ligand-induced GPCR flexibility, ligand binding kinetics, conserved water positions and their role in ligand binding and the effects of mutations. The goals of these calculations are to predict the structures of the complexes between existing ligands and their receptors, to understand the key interactions and to utilize these insights in the design of new molecules with improved binding, selectivity or other pharmacological properties. In this review we present a brief survey of various computational approaches illustrated through a hierarchical GPCR modeling protocol and its prospective application in three industrial drug discovery projects. Copyright © 2016 Elsevier Ltd. All rights reserved.
Develop Infrared Structural Biology for Probing Structural Dynamics of Protein Functions
Xie, Aihua; Kang, Zhouyang; Causey, Oliver; Liu, Charle
2015-03-01
Protein functions are carried out through a series of structural transitions. Lack of knowledge on functionally important structural motions of proteins impedes our understanding of protein functions. Infrared structural biology is an emerging technology with powerful applications for protein structural dynamics. One key element of infrared structural biology is the development of vibrational structural marker (VSM) database library that translates infrared spectroscopic signals into specific structural information. We report the development of VSM for probing the type, geometry and strength of hydrogen bonding interactions of buried COO- side chains of Asp and Glu in proteins. Quantum theory based first principle computational studies combined with bioinformatic hydrogen bond analysis are employed in this study. We will discuss the applications of VSM in mechanistic studies of protein functions. Infrared structural biology is expected to emerge as a powerful technique for elucidating the functional mechanism of a broad range of proteins, including water soluble and membrane proteins. This work is supported by OCAST HR10-078 and NSF DBI1338097.
Solution structure and dynamics of ADF from Toxoplasma gondii.
Yadav, Rahul; Pathak, Prem Prakash; Shukla, Vaibhav Kumar; Jain, Anupam; Srivastava, Shubhra; Tripathi, Sarita; Krishna Pulavarti, S V S R; Mehta, Simren; Sibley, L David; Arora, Ashish
2011-10-01
Toxoplasma gondii ADF (TgADF) belongs to a functional subtype characterized by strong G-actin sequestering activity and low F-actin severing activity. Among the characterized ADF/cofilin proteins, TgADF has the shortest length and is missing a C-terminal helix implicated in F-actin binding. In order to understand its characteristic properties, we have determined the solution structure of TgADF and studied its backbone dynamics from ¹⁵N-relaxation measurements. TgADF has conserved ADF/cofilin fold consisting of a central mixed β-sheet comprised of six β-strands that are partially surrounded by three α-helices and a C-terminal helical turn. The high G-actin sequestering activity of TgADF relies on highly structurally and dynamically optimized interactions between G-actin and G-actin binding surface of TgADF. The equilibrium dissociation constant for TgADF and rabbit muscle G-actin was 23.81 nM, as measured by ITC, which reflects very strong affinity of TgADF and G-actin interactions. The F-actin binding site of TgADF is partially formed, with a shortened F-loop that does not project out of the ellipsoid structure and a C-terminal helical turn in place of the C-terminal helix α4. Yet, it is more rigid than the F-actin binding site of Leishmania donovani cofilin. Experimental observations and structural features do not support the interaction of PIP2 with TgADF, and PIP2 does not affect the interaction of TgADF with G-actin. Overall, this study suggests that conformational flexibility of G-actin binding sites enhances the affinity of TgADF for G-actin, while conformational rigidity of F-actin binding sites of conventional ADF/cofilins is necessary for stable binding to F-actin. Copyright © 2011 Elsevier Inc. All rights reserved.
The Three Dimensional Structure and Dynamics of Magnetotail Reconnection
Walker, Raymond; Lapenta, Giovanni; Liang, Haoming; El Alaoui, Mostafa; Berchem, Jean; Goldstein, Melvyn
2017-04-01
Magnetic reconnection is a fundamental process by which magnetic energy is dissipated and converted into particle energy. In the next few months the Magnetosphere Multi-Scale Mission (MMS) will provide high resolution observations of reconnection and its consequences in the magnetotail. Of high priority will be observations of the electron diffusion region (EDR) where the actual process of reconnection is thought to occur. In preparation for the MMS observations we have investigated tail reconnection in a realistic magnetospheric configuration by using a new approach that combines a global magnetohydrodynamic simulation of the solar wind, magnetosphere and ionosphere system with a large scale (30X12X12RE) implicit particle-in-cell (iPic3D) simulation (see Lapenta et al., 2016 Geophys. Res. Lett. 43, 515-524, doi:10.1002/2015GL066689 for a discussion of the technique). In particular we have investigated the three dimensional structure and dynamics of tail reconnection during a substorm on February 15, 2008. We found that just earthward of the reconnection site the tail becomes highly structured in the Y direction in the GSM coordinate system. The structures result from an instability associated with strong shear flows in the Y direction within the current sheet. In particular we found that the work done by the magnetic field J•E in the electron frame alternated between positive and negative although the net J•E was positive. We used several methods for identifying the EDR (non-gyrotropy, slippage, the non-ideal terms in OHM's law as well as J•E) and found that all gave false positive results in some regions of the tail. However all of the approaches gave positive results in some of the small structures with J•E positive. These putative EDRs extended ( 2di, >1di, 1di) in the X, Y and Z directions.
Electrophoretic dynamics of self-assembling branched DNA structures
Heuer, Daniel Milton
This study advances our understanding of the electrophoretic dynamics of branched biopolymers and explores technologies designed to exploit their unique properties. New self-assembly techniques were developed to create branched DNA for visualization via fluorescence microscopy. Experiments in fixed gel networks reveal a distinct trapping behavior, in contrast with linear topologies. The finding that detection can be achieved by introducing a branch point contributes significantly to the field of separation science and can be exploited to develop new applications. Results obtained in polymer solutions point to identical mobilities for branched and linear topologies, despite large differences in their dynamics. This finding led to a new description of electrophoresis based on non-Newtonian viscoelastic effects in the electric double layer surrounding a charged object. This new theoretical framework presents a new outlook important not only to the electrophoretic physics of nucleic acids, but all charged objects including proteins, colloids, and nanoparticles. To study the behavior of smaller biopolymers, such as restriction fragments and recombination intermediates, a library of symmetrically branched DNA was synthesized followed by characterization in gels. The experimental results contribute a large body of information relating molecular architecture and the dynamics of rigid structures in an electric field. The findings allow us to create new separation technologies based on topology. These contributions can also be utilized in a number of different applications including the study of recombination intermediates and the separation of proteins according to structure. To demonstrate the importance of these findings, a sequence and mutation detection technique was envisioned and applied for genetic analysis. Restriction fragments from mutation "hotspots" in the p53 tumor suppressor gene, known to play a role in cancer development, were analyzed with this technique
Femtosecond structural dynamics on the atomic length scale
Energy Technology Data Exchange (ETDEWEB)
Zhang, Dongfang
2014-03-15
This thesis reports on the development and application of two different but complementary ultrafast electron diffraction setups built at the Max Planck Research Department for Structural Dynamics. One is an ultra-compact femtosecond electron diffraction (FED) setup (Egun300), which is currently operational (with a maximum electron energy of 150 keV) and provides ultrashort (∝300 fs) and bright (∝10 e/μm{sup 2}) electron bunches. The other one, named as Relativistic Electron Gun for Atomic Exploration (REGAE) is a radio frequency driven 2 to 5 MeV FED setup built in collaboration with different groups from DESY. REGAE was developed as a facility that will provide high quality diffraction with sufficient coherence to even address structural protein dynamics and with electron pulses as short as 20 fs (FWHM). As one of the first students in Prof. R.J. Dwayne Miller's group, I led the femtosecond (fs) laser sub-group at REGAE being responsible for the construction of different key optical elements required to drive both of aforementioned FED systems. A third harmonic generation (THG) and a nonlinear optical parametric amplifier (NOPA) have been used for the photo-generation of ultrashort electron bursts as well as sample laser excitation. Different diagnostic tools have been constructed to monitor the performance of the fs optical system. A fast autocorrelator was developed to provide on the fly pulse duration correction. A transient-grating frequency-resolved optical gating (TG-FROG) was built to obtain detail information about the characteristics of fs optical pulse, i.e. phase and amplitude of its spectral components. In addition to these optical setups, I developed a fs optical pump-probe system, which supports broadband probe pulses. This setup was successfully applied to investigate the semiconductor-to-metal photoinduced phase transition in VO{sub 2} and the ultrafast photo-reduction mechanism of graphene oxide. In regard to FED setups, I have been
Analysis of Dynamic Properties of Piezoelectric Structure under Impact Load
Directory of Open Access Journals (Sweden)
Taotao Zhang
2015-10-01
Full Text Available An analytical model of the dynamic properties is established for a piezoelectric structure under impact load, without considering noise and perturbations in this paper. Based on the general theory of piezo-elasticity and impact mechanics, the theoretical solutions of the mechanical and electrical fields of the smart structure are obtained with the standing and traveling wave methods, respectively. The comparisons between the two methods have shown that the standing wave method is better for studying long-time response after an impact load. In addition, good agreements are found between the theoretical and the numerical results. To simulate the impact load, both triangle and step pulse loads are used and comparisons are given. Furthermore, the influence of several parameters is discussed so as to provide some advices for practical use. It can be seen that the proposed analytical model would benefit, to some extent, the design and application (especially the airport runway of the related smart devices by taking into account their impact load performance.
Structural improvements on hydrodynamic separators: a computational fluid dynamics approach.
Mendoza, Joseph Albert; Lee, Dong Hoon; Lee, Sang-Il; Kang, Joo-Hyon
2016-12-01
Hydrodynamic separators (HDSs) have been used extensively to reduce stormwater pollutants from urbanized areas before entering the receiving water bodies. They primarily remove particulates and associated pollutants using gravity settling. Two types of HDSs with different structural configurations of the inner vortex-inducing components were presented in this study. One configuration consisted of a dip cylindrical plate with a center shaft while the other one has a hollow screen inside. With the help of computational fluid dynamics, the performance of these different types of HDSs have been evaluated and comparatively analyzed. The results showed that the particle removal efficiency was better with the cylindrical plate type HDSs than the screen type HDSs because of the larger swirling flow regime formed inside the device. Plate type HDSs were found more effective in removing fine particles (∼50 μm) than the screen type HDSs that were only efficient in removing large particles (≥250 μm). Structural improvements in a HDS such as increase in diameter and angle of the inlet pipe can enhance the removal efficiencies by up to 20% for plate type HDS while increase in the screen diameter can increase removal efficiencies of the screen type HDS.
The relevance of network micro-structure for neural dynamics
Directory of Open Access Journals (Sweden)
Volker ePernice
2013-06-01
Full Text Available The activity of cortical neurons is determined by the input they receive from presynaptic neurons. Many previousstudies have investigated how specific aspects of the statistics of the input affect the spike trains of single neurons and neuronsin recurrent networks. However, typically very simple random network models are considered in such studies. Here weuse a recently developed algorithm to construct networks based on a quasi-fractal probability measure which are much morevariable than commonly used network models, and which therefore promise to sample the space of recurrent networks ina more exhaustive fashion than previously possible. We use the generated graphs as the underlying network topology insimulations of networks of integrate-and-fire neurons in an asynchronous and irregular state. Based on an extensive datasetof networks and neuronal simulations we assess statistical relations between features of the network structure and the spikingactivity. Our results highlight the strong influence that some details of the network structure have on the activity dynamics ofboth single neurons and populations, even if some global network parameters are kept fixed. We observe specific and consistentrelations between activity characteristics like spike-train irregularity or correlations and network properties, for example thedistributions of the numbers of in- and outgoing connections or clustering. Exploiting these relations, we demonstrate that itis possible to estimate structural characteristics of the network from activity data. We also assess higher order correlationsof spiking activity in the various networks considered here, and find that their occurrence strongly depends on the networkstructure. These results provide directions for further theoretical studies on recurrent networks, as well as new ways to interpretspike train recordings from neural circuits.
Building a Data Store with the Dynamic Structure
Directory of Open Access Journals (Sweden)
Yu. N. Artamonov
2016-01-01
Full Text Available This article presents the analysis of approaches to data warehouse construction based on relational and NoSQL solutions and lists the limitations of the relational approach to data mining. The contradiction between data presentation in the real subject domain and the model of data presentation in the relational and NoSQL approaches is revealed. The revealed contradiction is related to the temporality of the values of individual data attributes, the variability of the composition of these attributes, and structure of connections between them. A new logical model of the data warehouse with dynamic structure is proposed. The model is based on the concept of the object as a container for properties storage. Each property of the object includes the property name and two property values without reference and with reference, that are relevant at a given time. The reference property value points to an object whose name is interpreted as the value of the property at a given time. A formal description of the model with allocation of the necessary functionality to manipulate objects and their properties (selectors, predicates, constructors is given and the necessary control structures are introduced. Substantiation of the proposed model, called an OP-model is given on the basis of compliance with the logical ER data model. It is proved that any ER data model can be implemented in the OP-model. At the same time, the advantages of the OP-model are indicated, they are associated with the possibility of changing connections between entities due to changes in the reference value at a particular time. The potential for scalability of data warehouse due to the unique identification of each object is noted.
Gas structure and dynamics towards bipolar infrared bubble
Xu, Jin-Long; Yu, Naiping; Zhang, Chuan-Peng; Liu, Xiao-Lan
2017-09-01
We present multi-wavelength analysis for four bipolar bubbles (G045.386-0.726, G049.998-0.125, G050.489+0.993, and G051.610-0.357) to probe the structure and dynamics of their surrounding gas. The 12CO J=1-0, 13CO J=1-0 and C18O J=1-0 observations are made with the Purple Mountain Observation (PMO) 13.7 m radio telescope. For the four bipolar bubbles, the bright 8.0 μm emission shows the bipolar structure. Each bipolar bubble is associated with an H ii region. From CO observations we find that G045.386-0.726 is composed of two bubbles with different distances, not a bipolar bubble. Each of G049.998-0.125 and G051.610-0.357 is associated with a filament. The filaments in CO emission divide G049.998-0.125 and G051.610-0.357 into two lobes. We suggest that the exciting stars of both G049.998-0.125 and G051.610-0.357 form in a sheet-like structure clouds. Furthermore, G050.489+0.993 is associated with a clump, which shows a triangle-like shape with a steep integrated intensity gradient towards the two lobes of G050.489+0.993. We suggest that the two lobes of G050.489+0.993 have simultaneously expanded into the clump.
Structure and Dynamics of Nonionic Surfactant Aggregates in Layered Materials.
Guégan, Régis; Veron, Emmanuel; Le Forestier, Lydie; Ogawa, Makoto; Cadars, Sylvian
2017-09-26
The aggregation of surfactants on solid surfaces as they are adsorbed from solution is the basis of numerous technological applications such as colloidal stabilization, ore flotation, and floor cleaning. The understanding of both the structure and the dynamics of surfactant aggregates applies to the development of alternative ways of preparing hybrid layered materials. For this purpose, we study the adsorption of the triethylene glycol mono n-decyl ether (C10E3) nonionic surfactant onto a synthetic montmorillonite (Mt), an aluminosilicate clay mineral for organoclay preparation with important applications in materials sciences, catalysis, wastewater treatment, or as drug delivery. The aggregation mechanisms follow those observed in an analogous natural Mt, with the condensation of C10E3 in a bilayer arrangement once the surfactant self-assembles in a lamellar phase beyond the critical micelle concentration, underlining the importance of the surfactant state in solution. Solid-state 1H nuclear magnetic resonance (NMR) at fast magic-angle spinning (MAS) and high magnetic field combined with1H-13C correlation experiments and different types of 13C NMR experiments selectively probes mobile or rigid moieties of C10E3 in three different aggregate organizations: (i) a lateral monolayer, (ii) a lateral bilayer, and (iii) a normal bilayer. High-resolution 1H{27Al} CP-1H-1H spin diffusion experiments shed light on the proximities and dynamics of the different fragments and fractions of the intercalated surfactant molecules with respect to the Mt surface. 23Na and 1H NMR measurements combined with complementary NMR data, at both molecular and nanometer scales, precisely pointed out the location of the C10E3 ethylene oxide hydrophilic group in close contact with the Mt surface interacting through ion-dipole or van der Waals interactions.
Structure, dynamics, and reactivity of hydrated electrons by ab initio molecular dynamics.
Marsalek, Ondrej; Uhlig, Frank; VandeVondele, Joost; Jungwirth, Pavel
2012-01-17
Understanding the properties of hydrated electrons, which were first observed using pulse radiolysis of water in 1962, is crucial because they are key species in many radiation chemistry processes. Although time-resolved spectroscopic studies and molecular simulations have shown that an electron in water (prepared, for example, by water photoionization) relaxes quickly to a localized, cavity-like structure ∼2.5 Å in radius, this picture has recently been questioned. In another experimental approach, negatively charged water clusters of increasing size were studied with photoelectron and IR spectroscopies. Although small water clusters can bind an excess electron, their character is very different from bulk hydrated species. As data on electron binding in liquid water have become directly accessible experimentally, the cluster-to-bulk extrapolations have become a topic of lively debate. Quantum electronic structure calculations addressing experimental measurables have, until recently, been largely limited to small clusters; extended systems were approached mainly with pseudopotential calculations combining a classical description of water with a quantum mechanical treatment of the excess electron. In this Account, we discuss our investigations of electrons solvated in water by means of ab initio molecular dynamics simulations. This approach, applied to a model system of a negatively charged cluster of 32 water molecules, allows us to characterize structural, dynamical, and reactive aspects of the hydrated electron using all of the system's valence electrons. We show that under ambient conditions, the electron localizes into a cavity close to the surface of the liquid cluster. This cavity is, however, more flexible and accessible to water molecules than an analogous area around negatively charged ions. The dynamical process of electron attachment to a neutral water cluster is strongly temperature dependent. Under ambient conditions, the electron relaxes in the
National Research Council Canada - National Science Library
Yingchun Zhang; Xiandong Liu; Chi Zhang; Mengjia He; Xiancai Lu
2017-01-01
In this study, by using first principles simulation techniques, we explored the basal spacings, interlayer structures, and dynamics of arsenite and arsenate intercalated Layered double hydroxides (LDHs...
Direct Integration of Dynamic Emissive Displays into Knitted Fabric Structures
Bellingham, Alyssa
Smart textiles are revolutionizing the textile industry by combining technology into fabric to give clothing new abilities including communication, transformation, and energy conduction. The advent of electroluminescent fibers, which emit light in response to an applied electric field, has opened the door for fabric-integrated emissive displays in textiles. This thesis focuses on the development of a flexible and scalable emissive fabric display with individually addressable pixels disposed within a fabric matrix. The pixels are formed in areas where a fiber supporting the dielectric and phosphor layers of an electroluminescent structure contacts a conductive surface. This conductive surface can be an external conductive fiber, yarn or wire, or a translucent conductive material layer deposited at set points along the electroluminescent fibers. Different contacting methods are introduced and the different ways the EL yarns can be incorporated into the knitted fabric are discussed. EL fibers were fabricated using a single yarn coating system with a custom, adjustable 3D printed slot die coater for even distribution of material onto the supporting fiber substrates. These fibers are mechanically characterized inside of and outside of a knitted fabric matrix to determine their potential for various applications, including wearables. A 4-pixel dynamic emissive display prototype is fabricated and characterized. This is the first demonstration of an all-knit emissive display with individually controllable pixels. The prototype is composed of a grid of fibers supporting the dielectric and phosphor layers of an electroluminescent (EL) device structure, called EL fibers, and conductive fibers acting as the top electrode. This grid is integrated into a biaxial weft knit structure where the EL fibers make up the rows and conductive fibers make up the columns of the reinforcement yarns inside the supporting weft knit. The pixels exist as individual segments of
Structure and Dynamics of Humpback Whales Competitive Groups in Ecuador
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Fernando Félix
2015-02-01
Full Text Available We assessed the social structure and behavior of humpback whale (Megaptera novaeangliae competitive groups off Ecuador between July and August 2010. During this time we followed 185 whales in 22 competitive groups for 41.45 hr. The average group size was 8.4 animals (SD = 2.85. The average sighting time was 113.05 min/group (SD = 47.1. We used photographs of dorsal fins and video to record interactions and estimate an association index (AI between each pair of whales within the groups. Sightings were divided into periods, which were defined by changes in group membership. On average, group composition changed every 30.2 min, which confirms that the structure of competitive groups is highly dynamic. Interactions between escorts characterized by low level of aggression. At least 60% of escorts joined or left together the group in small subunits between two and five animals, suggesting some type of cooperative association. Although singletons, as well as pairs or trios were able to join competitive groups at any moment, escorts that joined together were able to stay longer with the group and displace dominant escorts. Genetic analysis showed that in three occasions more than one female was present within a competitive group, suggesting either males are herding females or large competitive groups are formed by subunits. Males and females performed similar surface displays. We propose that competition and cooperation are interrelated in humpback whales’ competitive groups and that male cooperation would be an adaptive strategy either to displace dominant escorts or to fend off challengers.
Structural and economic dynamics in diversified Italian farms
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Cristina Salvioni
2013-12-01
Full Text Available Objective of this work is to investigate the structural change and economic dynamics of farms pursuing diversification and differentiation strategies in Italy. The analysis was performed on a panel of data built on the basis of information collected by the Italian FADN between 2003-2009. For the purpose of the analysis, we divided the population of commercial Italian farms into a five-fold farm typology based on size and the extent of diversification and differentiation strategies adopted by the farms. In detail, farms are defined as differentiated when they make use of a system of quality certification, while they are defined as diversified when they take up non farming activities (agritourism, social farms etc.. The findings show that conventional farms remain by far the largest category within the population of Italian commercial farms, while only 13% of the total commercial farms are classified as differentiated and/or diversified. Farms adopting product differentiation strategies are found to have an income growth path similar to that of conventional farms. Yet the category of diversified farms is the only one showing an upward trend with regard to income per worker in the observed years, while farms relying entirely on agricultural products appear to perform poorly in terms of labour productivity.
Biomolecular Deuteration for Neutron Structural Biology and Dynamics.
Haertlein, Michael; Moulin, Martine; Devos, Juliette M; Laux, Valerie; Dunne, Orla; Forsyth, V Trevor
2016-01-01
Neutron scattering studies provide important information in structural biology that is not accessible using other approaches. The uniqueness of the technique, and its complementarity with X-ray scattering, is greatest when full use is made of deuterium labeling. The ability to produce tailor-made deuterium-labeled biological macromolecules allows neutron studies involving solution scattering, crystallography, reflection, and dynamics to be optimized in a manner that has major impact on the scope, quality, and throughput of work in these areas. Deuteration facilities have now been developed at many neutron centres throughout the world; these are having a crucial effect on neutron studies in the life sciences and on biologically related studies in soft matter. This chapter describes methods that have been developed for the efficient production of deuterium-labeled samples for a wide range of neutron scattering applications. Examples are given that illustrate the use of these samples for each of the main techniques. Perspectives for biological deuterium labeling are discussed in relation to developments at current facilities and those that are planned in the future. © 2016 Elsevier Inc. All rights reserved.
Dynamical structure and risk assessment of 20th Century Windstorms
Varino, Filipa; Philippe, Arbogast; Bruno, Joly; Gwendal, Rivière; Marie-Laure, Fandeur; Henry, Bovy; Jean-Baptiste, Granier; Mitchell-Wallace, Kirsten
2017-04-01
Windstorms play an important role in weather variability over western Europe. Strong winds associated with fronts and sting jets can lead to several social and economic damages. However, in addition to wind intensity, the displacement speed of the storm, its area and position are also important factors in determining loss. In this study we focus on windstorms associated with the highest damages of the 20th century, and we analyse whether the dynamical structure of the storm is related to its impact. First, we apply an extra-tropical storm tracking algorithm to the ECMWF ERA-20C reanalysis that covers the whole twentieth century and for the whole Northern Hemisphere. Secondly, using the same data, we compute the 3-hourly Loss and Meteorological index for 18 different European countries as in Pinto et al. (2012) with a 25km grid resolution. Thirdly, we develop a High-Loss Tracking Method that matches information from the Loss Index results and the trajectories tracked to systematically associate damages over a particular country to a particular storm. Such a combination provides information on the typical life cycle of storms that create strong damages over a particular country. Finally, only storms hitting France are considered. More than 1500 storms are detected over the whole period and their evolution is analyzed by performing various composites depending on their position relative to the jet stream and their region of impact.
Degeneracy-Driven Self-Structuring Dynamics in Selective Repertoires
Atamas, Sergei P.; Bell, Jonathan
2013-01-01
Numerous biological interactions, such as interactions between T cell receptors or antibodies with antigens, interactions between enzymes and substrates, or interactions between predators and prey are often not strictly specific. In such less specific, or “sloppy,” systems, referred to here as degenerate systems, a given unit of a diverse resource (antigens, enzymatic substrates, prey) is at risk of being recognized and consumed by multiple consumers (lymphocytes, enzymes, predators). In this study, we model generalized degenerate consumer-resource systems of Lotka–Volterra and Verhulst types. In the degenerate systems of Lotka–Volterra, there is a continuum of types of consumer and resource based on variation of a single trait (characteristic, or preference). The consumers experience competition for a continuum of resource types. This non-local interaction system is modeled with partial differential-integral equations and shows spontaneous self-structuring of the consumer population that depends on the degree of interaction degeneracy between resource and consumer, but does not mirror the distribution of resource. We also show that the classical Verhulst (i.e. logistic) single population model can be generalized to a degenerate model, which shows qualitative behavior similar to that in the degenerate Lotka–Volterra model. These results provide better insight into the dynamics of selective systems in biology, suggesting that adaptation of degenerate repertoires is not a simple “mirroring” of the environment by the “fittest” elements of population. PMID:19337776
Technical Tools for Studying Structure and Dynamics of Water Masses
Directory of Open Access Journals (Sweden)
V.Z. Dykman
2016-12-01
Full Text Available The article gives a review of the technical tools designed to study structure and dynamics of water masses in the surface, bottom and deep-water sea layers, where the acting processes are not connected with wind waves. The process of adapting the measuring equipment to the requirements resulting from the expanding notions on physics of the marine environment phenomena is shown. Almost all the major designs are patented in the USSR, Ukraine and Russia. The experience in the development of different instruments enable adequately respond to the need for new methods and technical means intended for the organization of operational observations of the marine environment and land and sea interface zone. CTD-system experimental samples having a high degree of miniaturization and extremely low power consumption have already been created. They possess the necessary metrological characteristics and are intended for use in the drifters and lost (disposable probes. According to its metrological and operating characteristics, the autonomous electromagnetic current meter is able to provide reliable data in a variety of conditions (including collapse area of wind waves both being installed on a fixed base and hung on buoy stations. For wide manufacture of the new measurement tools it is necessary to create a complete set of design documentation on the basis of existing sketches, as well as to find the production base, equipped with machine tools of the corresponding class.
Goddard Space Flight Center's Structural Dynamics Data Acquisition System
McLeod, Christopher
2004-01-01
Turnkey Commercial Off The Shelf (COTS) data acquisition systems typically perform well and meet most of the objectives of the manufacturer. The problem is that they seldom meet most of the objectives of the end user. The analysis software, if any, is unlikely to be tailored to the end users specific application; and there is seldom the chance of incorporating preferred algorithms to solve unique problems. Purchasing a customized system allows the end user to get a system tailored to the actual application, but the cost can be prohibitive. Once the system has been accepted, future changes come with a cost and response time that's often not workable. When it came time to replace the primary digital data acquisition system used in the Goddard Space Flight Center's Structural Dynamics Test Section, the decision was made to use a combination of COTS hardware and in-house developed software. The COTS hardware used is the DataMAX II Instrumentation Recorder built by R.C. Electronics Inc. and a desktop Pentium 4 computer system. The in-house software was developed using MATLAF3 from The Mathworks. This paper will describe the design and development of the new data acquisition and analysis system.
Chaotic features of nuclear structure and dynamics: selected topics
Zelevinsky, Vladimir; Volya, Alexander
2016-03-01
Quantum chaos has become an important element of our knowledge about physics of complex systems. In typical mesoscopic systems of interacting particles the dynamics invariably become chaotic when the level density, growing by combinatorial reasons, leads to the increasing probability of mixing simple mean-field (particle-hole) configurations. The resulting stationary states have exceedingly complicated structures that are comparable to those in random matrix theory. We discuss the main properties of mesoscopic quantum chaos and show that it can serve as a justification for application of statistical mechanics to mesoscopic systems. We show that quantum chaos becomes a powerful instrument for experimental, theoretical and computational work. The generalization to open systems and effects in the continuum are discussed with the help of the effective non-Hermitian Hamiltonian; it is shown how to formulate this approach for numerous problems of quantum signal transmission. The artificially introduced randomness can also be helpful for a deeper understanding of physics. We indicate the problems that require more investigation so as to be understood further.
KInetic Effect on Dynamics of Plasma Coherent Structures
Ishiguro, Seiji; Hasegawa, Hiroki
2013-10-01
Kinetic effects on plasma blob dynamics have been studied by means of a three dimensional electrostatic plasma particle simulation code with particle absorbing boundaries. In the particle simulation, an external magnetic field B is pointing into the z direction (corresponding to the toroidal direction). The strength of magnetic field increases in the positive x direction (corresponding to the counter radial direction), i.e., ∂B / ∂x > 0 . A coherent structure is initially set as a column along the external magnetic field and propagates in the - x direction. In this study, we have investigated the dependence of blob propagation on the ion-to-electron temperature ratio and the magnetic field strength. When the magnetic field strength is decreased (or the ion-to-electron temperature ratio is increased), we have found that the symmetry breaking in a blob profile occurs. This fact is thought to indicate that the effect of gyro motion of plasma particles induces the symmetry breaking. Supported by NIFS Collaboration Research programs (NIFS13KNSS038 and NIFS13KNXN258) and a Grant-in-Aid for Scientific Research from Japan Society for the Promotion of Science (KAKENHI 23740411).
Crystal structure and encapsulation dynamics of ice II-structured neon hydrate.
Yu, Xiaohui; Zhu, Jinlong; Du, Shiyu; Xu, Hongwu; Vogel, Sven C; Han, Jiantao; Germann, Timothy C; Zhang, Jianzhong; Jin, Changqing; Francisco, Joseph S; Zhao, Yusheng
2014-07-22
Neon hydrate was synthesized and studied by in situ neutron diffraction at 480 MPa and temperatures ranging from 260 to 70 K. For the first time to our knowledge, we demonstrate that neon atoms can be enclathrated in water molecules to form ice II-structured hydrates. The guest Ne atoms occupy the centers of D2O channels and have substantial freedom of movement owing to the lack of direct bonding between guest molecules and host lattices. Molecular dynamics simulation confirms that the resolved structure where Ne dissolved in ice II is thermodynamically stable at 480 MPa and 260 K. The density distributions indicate that the vibration of Ne atoms is mainly in planes perpendicular to D2O channels, whereas their distributions along the channels are further constrained by interactions between adjacent Ne atoms.
Leydesdorff, L.; Schank, T.
2008-01-01
The dynamic analysis of structural change in the organization of the sciences requires, methodologically, the integration of multivariate and time-series analysis. Structural change - for instance, interdisciplinary development - is often an objective of government interventions. Recent developments
Equilibration of experimentally determined protein structures for molecular dynamics simulation.
Walton, Emily B; Vanvliet, Krystyn J
2006-12-01
Preceding molecular dynamics simulations of biomolecular interactions, the molecule of interest is often equilibrated with respect to an initial configuration. This so-called equilibration stage is required because the input structure is typically not within the equilibrium phase space of the simulation conditions, particularly in systems as complex as proteins, which can lead to artifactual trajectories of protein dynamics. The time at which nonequilibrium effects from the initial configuration are minimized-what we will call the equilibration time-marks the beginning of equilibrium phase-space exploration. Note that the identification of this time does not imply exploration of the entire equilibrium phase space. We have found that current equilibration methodologies contain ambiguities that lead to uncertainty in determining the end of the equilibration stage of the trajectory. This results in equilibration times that are either too long, resulting in wasted computational resources, or too short, resulting in the simulation of molecular trajectories that do not accurately represent the physical system. We outline and demonstrate a protocol for identifying the equilibration time that is based on the physical model of Normal Mode Analysis. We attain the computational efficiency required of large-protein simulations via a stretched exponential approximation that enables an analytically tractable and physically meaningful form of the root-mean-square deviation of atoms comprising the protein. We find that the fitting parameters (which correspond to physical properties of the protein) fluctuate initially but then stabilize for increased simulation time, independently of the simulation duration or sampling frequency. We define the end of the equilibration stage--and thus the equilibration time--as the point in the simulation when these parameters attain constant values. Compared to existing methods, our approach provides the objective identification of the time at
Woodrow Whitlow, Jr. (Editor); Todd, Emily N. (Editor)
1999-01-01
These proceedings represent a collection of the latest advances in aeroelasticity and structural dynamics from the world community. Research in the areas of unsteady aerodynamics and aeroelasticity, structural modeling and optimization, active control and adaptive structures, landing dynamics, certification and qualification, and validation testing are highlighted in the collection of papers. The wide range of results will lead to advances in the prediction and control of the structural response of aircraft and spacecraft.
Structure and dynamics of a Gay-Berne liquid crystal confined in cylindrical nanopores.
Ji, Qing; Lefort, Ronan; Busselez, Rémi; Morineau, Denis
2009-06-21
Gay-Berne liquid crystals confined in two cylindrical nanopores with different pore sizes were studied by molecular dynamics simulation. Their structure and dynamics properties were obtained and compared with those of the bulk. Our data show that confinement changes the bulk isotropic-to-nematic transition to a continuous ordering from a paranematic to a nematic phase. Moreover, confinement strongly hinders the smectic translational order. The molecular dynamics is characterized by the translational diffusion coefficients and the first-rank reorientational correlation times. Very different characteristic times and temperature variations in the dynamics are observed in confinement. Spatially resolved quantities illustrate that confinement induces predominant structural and dynamical heterogeneities.
Condensation and Wetting Dynamics on Micro/Nano-Structured Surfaces
Olceroglu, Emre
-condensable gases (NCGs), a novel characterization technique has been developed based on image tracking of droplet growth rates. The full-field dynamic characterization of superhydrophobic surfaces during condensation has been achieved using high-speed microscopy coupled with image-processing algorithms. This method is able to resolve heat fluxes as low as 20 W/m 2 and heat transfer coefficients of up to 1000 kW/m2, across an array of 1000's of microscale droplets simultaneously. Nanostructured surfaces with mixed wettability have been used to demonstrate delayed flooding during superhydrophobic condensation. These surfaces have been optimized and characterized using optical and electron microscopy, leading to the observation of self-organizing microscale droplets. The self-organization of small droplets effectively delays the onset of surface flooding, allowing the superhydrophobic surfaces to operate at higher supersaturations. Additionally, hierarchical surfaces have been fabricated and characterized showing enhanced droplet growth rates as compared to existing models. This enhancement has been shown to be derived from the presence of small feeder droplets nucleating within the microscale unit cells of the hierarchical surfaces. Based on the experimental observations, a mechanistic model for growth rates has been developed for superhydrophobic hierarchical surfaces. While superhydrophobic surfaces exhibit high heat transfer rates they are inherently unstable due to the necessity to maintain a non-wetted state in a condensing environment. As an alternative condensation surface, a novel design is introduced here using ambiphilic structures to promote the formation of a thin continuous liquid film across the surface which can still provide the benefits of superhydrophobic condensation. Preliminary results show that the ambiphilic structures restrain the film thickness, thus maintaining a low thermal resistance while simultaneously maximizing the liquid-vapor interface available for
Structural Modeling and Analysis on Dynamic Characteristics of Antenna Pedestal in Airborne SAR
Directory of Open Access Journals (Sweden)
He Li-ping
2012-06-01
Full Text Available Finite element modeling and structural dynamic characteristics of antenna pedestal in airborne SAR were studied in this paper. The Finite element model of antenna pedestal in airborne SAR was set up on the basis of structural dynamic theory, then, the key technologies of dynamic simulation were pointed out, and the modal analysis and transient analysis were carried out. Simulation results show that the dynamic characteristics of antenna pedestal in airborne SAR can meet the requirements of servo bandwidth and structural strength. The fast finite element modeling and simulation method proposed in this paper are of great significance to the weight reducing design of antenna pedestal in airborne SAR.
Villaverde, Alejandro F; Banga, Julio R
2017-11-01
The concept of dynamical compensation has been recently introduced to describe the ability of a biological system to keep its output dynamics unchanged in the face of varying parameters. However, the original definition of dynamical compensation amounts to lack of structural identifiability. This is relevant if model parameters need to be estimated, as is often the case in biological modelling. Care should we taken when using an unidentifiable model to extract biological insight: the estimated values of structurally unidentifiable parameters are meaningless, and model predictions about unmeasured state variables can be wrong. Taking this into account, we explore alternative definitions of dynamical compensation that do not necessarily imply structural unidentifiability. Accordingly, we show different ways in which a model can be made identifiable while exhibiting dynamical compensation. Our analyses enable the use of the new concept of dynamical compensation in the context of parameter identification, and reconcile it with the desirable property of structural identifiability.
Taylor, Lawrence W., Jr.; Rajiyah, H.
1991-01-01
Partial differential equations for modeling the structural dynamics and control systems of flexible spacecraft are applied here in order to facilitate systems analysis and optimization of these spacecraft. Example applications are given, including the structural dynamics of SCOLE, the Solar Array Flight Experiment, the Mini-MAST truss, and the LACE satellite. The development of related software is briefly addressed.
A report of advancements in structural dynamic technology resulting from Saturn 5 programs
1970-01-01
Two volume report on practical aspects of structural dynamic analysis in Saturn 5 program is described. Volume 1 is oriented toward program managers of future structural dynamic programs. Volume 2, oriented toward technical leaders of programs, discusses methods and procedures used in Saturn 5 program.
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,…
Assessment of bacterial and structural dynamics in aerobic granular biofilms
Directory of Open Access Journals (Sweden)
David G. Weissbrodt
2013-07-01
Full Text Available Aerobic granular sludge is based on self-granulated flocs forming mobile biofilms with a gel-like consistence. Bacterial and structural dynamics from flocs to granules were followed in anaerobic-aerobic sequencing batch reactors fed with synthetic wastewater, namely a bubble column (BC-SBR operated under wash-out conditions for fast granulation, and two stirred-tank enrichments of Accumulibacter (PAO-SBR and Competibacter (GAO-SBR operated at steady-state. In the BC-SBR, granules formed within two weeks by swelling of Zoogloea colonies around flocs, developing subsequently smooth zoogloeal biofilms. However, Zoogloea predominance (37-79% led to deteriorated nutrient removal during the first months of reactor operation. Upon maturation, improved nitrification (80-100%, nitrogen removal (43-83%, and high but unstable dephosphatation (75-100% were obtained. Proliferation of dense clusters of nitrifiers, Accumulibacter, and Competibacter from granule cores outwards resulted in heterogeneous bioaggregates, inside which only low abundance Zoogloea (<5% were detected in biofilm interstices. The presence of different extracellular glycoconjugates detected by fluorescence lectin-binding analysis showed the complex nature of the intracellular matrix of these granules. In the PAO-SBR, granulation occurred within two months with abundant and active Accumulibacter populations (56±10% that were selected under full anaerobic uptake of volatile fatty acids and that aggregated as dense clusters within heterogeneous granules. Flocs self-granulated in the GAO-SBR after 480 days during a period of over-aeration caused by biofilm growth on the oxygen sensor. Granules were dominated by heterogeneous clusters of Competibacter (37±11%. Zoogloea were never abundant in biomass of both PAO- and GAO-SBRs. This study showed that Zoogloea, Accumulibacter, and Competibacter affiliates can form granules, and that the granulation mechanisms rely on the dominant population
Dynamic compressibility of air in porous structures at audible frequencies
DEFF Research Database (Denmark)
Lafarge, Denis; Lemarinier, Pavel; Allard, Jean F.
1997-01-01
Measurements of dynamic compressibility of air-filled porous sound-absorbing materials are compared with predictions involving two parametere, the static thermal permeability k'_0 and the thermal characteristic dimension GAMMA'. Emphasis on the notion of dynamic and static thermal permeability...... of the viscous forces. Using both parameters, a simple model is constructed for the dynamic thermal permeability k', which is completely analogous to the Johnson et al. [J. Fluid Mech. vol. 176, 379 (1987)] model of dynamic viscous permeability k. The resultant modeling of dynamic compressibility provides...... predictions which are closer to the experimental results than the previously used simpler model where the compressibility is the same as in identical circular cross-sectional shaped pores, or distributions of slits, related to a given GAMMA'....
Hellyer, Peter J.; Scott, Gregory; Shanahan, Murray; Sharp, David J.
2015-01-01
Current theory proposes that healthy neural dynamics operate in a metastable regime, where brain regions interact to simultaneously maximize integration and segregation. Metastability may confer important behavioral properties, such as cognitive flexibility. It is increasingly recognized that neural dynamics are constrained by the underlying structural connections between brain regions. An important challenge is, therefore, to relate structural connectivity, neural dynamics, and behavior. Traumatic brain injury (TBI) is a pre-eminent structural disconnection disorder whereby traumatic axonal injury damages large-scale connectivity, producing characteristic cognitive impairments, including slowed information processing speed and reduced cognitive flexibility, that may be a result of disrupted metastable dynamics. Therefore, TBI provides an experimental and theoretical model to examine how metastable dynamics relate to structural connectivity and cognition. Here, we use complementary empirical and computational approaches to investigate how metastability arises from the healthy structural connectome and relates to cognitive performance. We found reduced metastability in large-scale neural dynamics after TBI, measured with resting-state functional MRI. This reduction in metastability was associated with damage to the connectome, measured using diffusion MRI. Furthermore, decreased metastability was associated with reduced cognitive flexibility and information processing. A computational model, defined by empirically derived connectivity data, demonstrates how behaviorally relevant changes in neural dynamics result from structural disconnection. Our findings suggest how metastable dynamics are important for normal brain function and contingent on the structure of the human connectome. PMID:26085630
Structure and Dynamics of Polymers in Cylindrical Nanoconfinement: A Molecular Dynamics Study
Pressly, James; Riggleman, Robert; Winey, Karen
The structure and dynamics of polymers under nanoconfinement is critical for understanding how polymers behave in applications from hydraulic fracking to fabricating integrated circuits. We previously used simulations to explore the effect of the diameter of cylindrical pores (d = 10-40 σ, where σ is the unit length in reduced units) on polymer end-to-end distance (Ree,perp, Ree,par) , entanglement density, melt diffusion coefficient (D), and local relaxation time (τperp, τpar) at fixed polymer chain length (N = 350). These studies found D, Ree,par, and τperp increased with increasing confinement while entanglement density, Ree,perp, and τpar decreased. Experiments also found that D increased but to a lesser extent. Here, we examine the molecular weight dependence of these properties using N = 25, 50, 100, 200, 350, and 500 confined to pores of diameter 14 σ to examine a range of confinements. Our preliminary results show that as N increases D and Ree,par, increase as well, relative to the unconfined state, while entanglement density and Ree,perp decrease, consistent with our previous work. Interestingly, τ is shown to be independent of chain length indicating the impact of confinement imposed by reducing pore diameter is distinct from that imposed by increasing chain length.
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.
Simulation and Experimental Investigation of Structural Dynamic Frequency Characteristics Control
Directory of Open Access Journals (Sweden)
Bing Li
2012-04-01
Full Text Available In general, mechanical equipment such as cars, airplanes, and machine tools all operate with constant frequency characteristics. These constant working characteristics should be controlled if the dynamic performance of the equipment demands improvement or the dynamic characteristics is intended to change with different working conditions. Active control is a stable and beneficial method for this, but current active control methods mainly focus on vibration control for reducing the vibration amplitudes in the time domain or frequency domain. In this paper, a new method of dynamic frequency characteristics active control (DFCAC is presented for a flat plate, which can not only accomplish vibration control but also arbitrarily change the dynamic characteristics of the equipment. The proposed DFCAC algorithm is based on a neural network including two parts of the identification implement and the controller. The effectiveness of the DFCAC method is verified by several simulation and experiments, which provide desirable results.
Dynamics of homegarden structure and function in Kerala, India
Peyre, A.; Guidal, A.; Wiersum, K.F.; Bongers, F.J.J.M.
2006-01-01
Homegardens in Kerala have long been important multi-purpose agroforestry systems that combine ecological and socioeconomical sustainability. However, traditional homegardens are subject to different conversion processes linked to socioeconomic changes. These dynamics were studied in a survey of 30
Parametric dynamic structural components for prefabricated reinforced concrete elements
Česnik, Jure
2012-01-01
Advanced 3D modelling computer programs for authoring of building projects are gaining on popularity among civil engineers and architects and are thus developing with lightning speed. One of the main areas of development are parametric dynamic components and their use in BIM environments. The first part of the presented work deals with the development and use of parametric dynamic components in BIM software, focusing on prefabricated construction elements. It also explains how ...
Dynamical Mean Field Theory and Electronic Structure Calculations
Chitra, R.; Kotliar, G.
1999-01-01
We formulate the dynamical mean field theory directly in the continuum. For a given definition of the local Green's function, we show the existence of a unique functional, whose stationary point gives the physical local Green's function of the solid. We present the diagrammatic rules to calculate it perturbatively in the interaction. Inspired by the success of dynamical mean field calculations for model Hamiltonian systems, we present approximations to the exact saddle point equations which m...
Posokhov, Yevgen O; Kyrychenko, Alexander
2013-10-01
The modulation of the properties and function of cell membranes by small volatile substances is important for many biomedical applications. Despite available experimental results, molecular mechanisms of action of inhalants and organic solvents, such as acetone, on lipid membranes remain not well understood. To gain a better understanding of how acetone interacts with membranes, we have performed a series of molecular dynamics (MD) simulations of a POPC bilayer in aqueous solution in the presence of acetone, whose concentration was varied from 2.8 to 11.2 mol%. The MD simulations of passive distribution of acetone between a bulk water phase and a lipid bilayer show that acetone favors partitioning into the water-free region of the bilayer, located near the carbonyl groups of the phospholipids and at the beginning of the hydrocarbon core of the lipid membrane. Using MD umbrella sampling, we found that the permeability barrier of ~0.5 kcal/mol exists for acetone partitioning into the membrane. In addition, a Gibbs free energy profile of the acetone penetration across a bilayer demonstrates a favorable potential energy well of -3.6 kcal/mol, located at 15-16Å from the bilayer center. The analysis of the structural and dynamics properties of the model membrane revealed that the POPC bilayer can tolerate the presence of acetone in the concentration range of 2.8-5.6 mol%. The accumulation of the higher acetone concentration of 11.2 mol% results, however, in drastic disordering of phospholipid packing and the increase in the membrane fluidity. The acetone molecules push the lipid heads apart and, hence, act as spacers in the headgroup region. This effect leads to the increase in the average headgroup area per molecule. In addition, the acyl tail region of the membrane also becomes less dense. We suggest, therefore, that the molecular mechanism of acetone action on the phospholipid bilayer has many common features with the effects of short chain alcohols, DMSO, and
Pande, Vineet; Nilsson, Lennart
2008-01-01
Locked nucleic acid (LNA) is a chemically modified nucleic acid with its sugar ring locked in an RNA-like (C3′-endo) conformation. LNAs show extraordinary thermal stabilities when hybridized with DNA, RNA or LNA itself. We performed molecular dynamics simulations on five isosequential duplexes (LNA–DNA, LNA–LNA, LNA–RNA, RNA–DNA and RNA–RNA) in order to characterize their structure, dynamics and hydration. Structurally, the LNA–DNA and LNA–RNA duplexes are found to be similar to regular RNA–D...
Pressure effects on structure and dynamics of metallic glass-forming liquid
Hu, Yuan-Chao; Guan, Peng-Fei; Wang, Qing; Yang, Yong; Bai, Hai-Yang; Wang, Wei-Hua
2017-01-01
Although the structure and dynamics of metallic glass-forming liquids have been extensively investigated, studies of the pressure effects are rare. In the present study, the structural and dynamical properties of a ternary metallic liquid are systematically studied via extensive molecular dynamics simulations. Our results clearly show that, like isobaric cooling, isothermal compression could also slow down the dynamics of metallic liquid, leading to glass formation. However, the temperature- and pressure-induced glass transitions differ in the formation of local coordination structures and the variation of fragility. The increase of the kinetic fragility with increasing pressure is also accompanied by a monotonic structural fragility change. These findings may suggest a link between dynamics and structure. In addition, with increasing pressure, the dynamics becomes more heterogeneous, as revealed by the non-Gaussian parameter and dynamic correlation length. Here the length scales of both slow and fast domains are examined and discussed by analyzing the four-point dynamic structure factor associated with spatial correlations of atomic mobility. These correlation lengths coexist in the metallic liquids and grow comparatively in the considered temperature and pressure ranges. Finally, the scaling relation between the relaxation times and correlation lengths is discussed, which is found to be consistent with the spirit of Adam-Gibbs and random first-order transition theories.
DEFF Research Database (Denmark)
Zhang, H.W.; Luo, Z.P.; Hansen, Niels
2015-01-01
The structural heterogeneity of a polycrystalline Ni subjected to dynamic plastic deformation to a strain of 2.3 was characterized, and its influence on the structural coarsening behaviour during post annealing was investigated. Structural heterogeneity on the large scale manifests itself...... orientation. In contrast HMRs contain both low and high angle boundaries (>15o) and the texture is mixed with close to the compression axis. During annealing, LMRs coarsen uniformly and recrystallization nucleation is difficult to form. In HMRs, the structural evolution is heterogeneous...... and recrystallization nuclei are readily formed. The importance of structural heterogeneity during structural design for high performance nanostructure was highlighted....
Ground Reaction Forces Generated During Rhythmical Squats as a Dynamic Loads of the Structure
Pantak, Marek
2017-10-01
Dynamic forces generated by moving persons can lead to excessive vibration of the long span, slender and lightweight structure such as floors, stairs, stadium stands and footbridges. These dynamic forces are generated during walking, running, jumping and rhythmical body swaying in vertical or horizontal direction etc. In the paper the mathematical models of the Ground Reaction Forces (GRFs) generated during squats have been presented. Elaborated models was compared to the GRFs measured during laboratory tests carried out by author in wide range of frequency using force platform. Moreover, the GRFs models were evaluated during dynamic numerical analyses and dynamic field tests of the exemplary structure (steel footbridge).
Complex dynamic and static structures in interconnected particle systems
Energy Technology Data Exchange (ETDEWEB)
Kristiansen, Kai de Lange
2004-07-01
Observations in the magnetic hole system under different conditions have generated many different patterns and dynamical phenomena which have generated even more ideas on how to attack and analyze them on a firm physical basis. Some of these problems are described in paper 4. In this thesis we have studied the dynamics of the few body system. The braid theory provides a compact description of this motion and enables a better real-time analysis with a minimum of information needed for computation. Also the amount of data to store on disks can then be reduced. Another aspect is that braid theory provides new topological invariants which can bring new light on the phenomena under study. The world lines from the few body system can also be closed into a knot. In knot theory several invariant quantities have been developed the last two decades, where the Jones polynomial is one powerful invariant, as pointed out in Appendix B. The diffusive processes of a few body systems can take super diffusive behaviour, as shown in paper 3. Apparently intermittent states of the same system display a large variety of different modes. By analyzing these modes using rank-ordering statistics, we find that they obey the so-called Zipf-Mandelbrot relation, as discussed in papers 1, 2, 3 and 4. Numerical calculations based on Stokes' drag and magnetic dipole-dipole interactions resemble the behaviour of the experiments well. In sections 3.2 and A.1 we presented a possible derivation of the exponent {gamma} in the Zipf-Mandelbrot relation. The derived values of {gamma} are within the same order of magnitude as the values of {gamma} obtained in the experiments. However, the derived values of {gamma} have high uncertainties. These uncertainties may be reduced with a more refined definition of the work of a mode. This refinement has to take into account the correlation between the modes. The physical meaning behind the exponent {gamma} and the correction term {zeta} in the Zipf
Camp, Piet
1985-01-01
The 1984 Advanced Study Institute on "Electronic Structure, Dynamics and Quantum Structural Properties of Condensed Matter" took place at the Corsendonk Conference Center, close to the City of Antwerpen, from July 16 till 27, 1984. This NATO Advanced Study Institute was motivated by the research in my Institute, where, in 1971, a project was started on "ab-initio" phonon calculations in Silicon. I~ is my pleasure to thank several instances and people who made this ASI possible. First of all, the sponsor of the Institute, the NATO Scientific Committee. Next, the co-sponsors: Agfa-Gevaert, Bell Telephone Mfg. Co. N.V., C & A, Esso Belgium·, CDC Belgium, Janssens Pharmaceutica, Kredietbank and the Scientific Office of the U.S. Army. Special thanks are due to Dr. P. Van Camp and Drs. H. Nachtegaele, who, over several months, prepared the practical aspects of the ASI with the secretarial help of Mrs. R.-M. Vandekerkhof. I also like to. thank Mrs. M. Cuyvers who prepared and organized the subject and material ...
McGowan, Anna-Maria Rivas; Wilkie, W. Keats; Moses, Robert W.; Lake, Renee C.; Florance, Jennifer Pinkerton; Wieseman, Carol D.; Reaves, Mercedes C.; Taleghani, Barmac K.; Mirick, Paul H.; Wilbur, Mathew L.
1997-01-01
An overview of smart structures research currently underway at the NASA Langley Research Center in the areas of aeroservoelasticity and structural dynamics is presented. Analytical and experimental results, plans, potential technology pay-offs, and challenges are discussed. The goal of this research is to develop the enabling technologies to actively and passively control aircraft and rotorcraft vibration and loads using smart devices. These enabling technologies and related research efforts include developing experimentally-validated finite element and aeroservoelastic modeling techniques; conducting bench experimental tests to assess feasibility and understand system trade-offs; and conducting large-scale wind tunnel tests to demonstrate system performance. The key aeroservoelastic applications of this research include: active twist control of rotor blades using interdigitated electrode piezoelectric composites and active control of flutter, and gust and buffeting responses using discrete piezoelectric patches. In addition, NASA Langley is an active participant in the DARPA/Air Force Research Laboratory/NASA/Northrop Grumman Smart Wing program which is assessing aerodynamic performance benefits using smart materials.
Structural dynamics in complex liquids studied with multidimensional vibrational spectroscopy
Energy Technology Data Exchange (ETDEWEB)
Tokmakoff, Andrei [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)
2013-08-31
The development of new sustainable energy sources is linked to our understanding of the molecular properties of water and aqueous solutions. Energy conversion, storage, and transduction processes, particularly those that occur in biology, fuel cells, and batteries, make use of water for the purpose of moving energy in the form of charges and mediating the redox chemistry that allows this energy to be stored as and released from chemical bonds. To build our fundamental knowledge in this area, this project supports work in the Tokmakoff group to investigate the molecular dynamics of water’s hydrogen bond network, and how these dynamics influence its solutes and the mechanism of proton transport in water. To reach the goals of this grant, we developed experiments to observe molecular dynamics in water as directly as possible, using ultrafast multidimensional vibrational spectroscopy. We excite and probe broad vibrational resonances of water, molecular solutes, and protons in water. By correlating how molecules evolve from an initial excitation frequency to a final frequency, we can describe the underlying molecular dynamics. Theoretical modeling of the data with the help of computational spectroscopy coupled with molecular dynamics simulations provided the atomistic insight in these studies.
Dynamics Modelling of Tensegrity Structures with Expanding Properties
Abdulkareem, Musa; Mahfouf, M.; Theilliol, D.
Given the prestress level of a tensegrity structural system obtained from any form-finding method, an important step in the design process is to develop mathematical models that describe the behaviour of the system. Moreover, tensegrity structures are strongly dependent on their geometric, or kinematic, configurations. As such, except for small scale tensegrity structures with a few structural members, resorting to the use of computational techniques for analysis is a necessity. Because tensegrity structures are kinematically and statically indeterminate structures, a free standing tensegrity structure has at least one rigid body mode apart from the six rigid body modes that can be eliminated, for example, by applying boundary conditions assuming the structure is attached to a base. In this paper, a new general tool (applicable to small and large systems) for systematic and efficient formulation of structural models for tensegrity systems is proposed. Current tools are limited to structures with a few degrees of freedom (DOF), however, this new tool simplifies the analyses of tensegrity structures with several DOFs and provides a new insight into the behaviour of these interesting and yet challenging structures, at least from a control systems' viewpoint.
Xu, Kuangyi; Li, Kun; Cong, Rui; Wang, Long
2017-02-01
In the framework of the evolutionary game theory, two fundamentally different mechanisms, the imitation process and the aspiration-driven dynamics, can be adopted by players to update their strategies. In the former case, individuals imitate the strategy of a more successful peer, while in the latter case individuals change their strategies based on a comparison of payoffs they collect in the game to their own aspiration levels. Here we explore how cooperation evolves for the coexistence of these two dynamics. Intriguingly, cooperation reaches its lowest level when a certain moderate fraction of individuals pick aspiration-level-driven rule while the others choose pairwise comparison rule. Furthermore, when individuals can adjust their update rules besides their strategies, either imitation dynamics or aspiration-driven dynamics will finally take over the entire population, and the stationary cooperation level is determined by the outcome of competition between these two dynamics. We find that appropriate synergetic effects and moderate aspiration level boost the fixation probability of aspiration-driven dynamics most effectively. Our work may be helpful in understanding the cooperative behavior induced by the coexistence of imitation dynamics and aspiration dynamics in the society.
A novel dynamics combination model reveals the hidden information of community structure
Li, Hui-Jia; Li, Huiying; Jia, Chuanliang
2015-09-01
The analysis of the dynamic details of community structure is an important question for scientists from many fields. In this paper, we propose a novel Markov-Potts framework to uncover the optimal community structures and their stabilities across multiple timescales. Specifically, we model the Potts dynamics to detect community structure by a Markov process, which has a clear mathematical explanation. Then the local uniform behavior of spin values revealed by our model is shown that can naturally reveal the stability of hierarchical community structure across multiple timescales. To prove the validity, phase transition of stochastic dynamic system is used to indicate that the stability of community structure we proposed is able to describe the significance of community structure based on eigengap theory. Finally, we test our framework on some example networks and find it does not have resolute limitation problem at all. Results have shown the model we proposed is able to uncover hierarchical structure in different scales effectively and efficiently.
Basu, Sohini; Sen, Srikanta
2013-02-25
Structure and dynamics both are known to be important for the activity of a protein. A fundamental question is whether a thermophilic protein and its mesophilic homologue exhibit similar dynamics at their respective optimal growth temperatures. We have addressed this question by performing molecular dynamics (MD) simulations of a natural mesophilic-thermophilic homologue pair at their respective optimal growth temperatures to compare their structural, dynamical, and solvent properties. The MD simulations were done in explicit aqueous solvent under periodic boundary and constant pressure and temperature (CPT) conditions and continued for 10.0 ns using the same protocol for the two proteins, excepting the temperatures. The trajectories were analyzed to compare the properties of the two proteins. Results indicated that the dynamical behaviors of the two proteins at the respective optimal growth temperatures were remarkably similar. For the common residues in the thermophilic protein, the rms fluctuations have a general trend to be slightly higher compared to that in the mesophilic counterpart. Lindemann parameter values indicated that only a few residues exhibited solid-like dynamics while the protein as a whole appeared as a molten globule in each case. Interestingly, the water-water interaction was found to be strikingly similar in spite of the difference in temperatures while, the protein-water interaction was significantly different in the two simulations.
Bedrov, Dmitry; Borodin, Oleg; Li, Zhe; Smith, Grant D
2010-04-22
Utilizing the transferable, quantum-chemistry-based, Atomistic Polarizable Potential for Liquids, Electrolytes, & Polymers (APPLE&P) force field, we have systematically investigated the influence of polarization effects on the accuracy of properties predicted from molecular dynamics simulations of various room temperature ionic liquids (ILs). Simulations of ILs in which the atom-based polarizability was set to zero for all atoms (nonpolarizable APPLE&P potential) resulted in changes in thermodynamic and dynamic properties from those predicted by the polarizable APPLE&P potential that are qualitatively different from changes observed for nonionic liquids. Investigation of structural and dynamical correlations using both the polarizable and nonpolarizable versions of APPLE&P allowed us to obtain a mechanistic understanding of the influence of polarization on dynamics in the ILs investigated. Additionally, the Force Matching (FM) approach was employed to systematically obtain nonpolarizable two-body force fields for several ILs that reproduce as accurately as possible intermolecular forces predicted by the polarizable model. Unlike water, for which the FM approach was found to yield an accurate representation of the liquid phase structure predicted by a polarizable model, the FM approach does not result in a two-body potential that accurately reproduces either structure or dynamics predicted by the polarizable IL model.
Crossing the Logarithmic Barrier for Dynamic Boolean Data Structure Lower Bounds
Larsen, Kasper Green; Weinstein, Omri; Yu, Huacheng
2017-01-01
This paper proves the first super-logarithmic lower bounds on the cell probe complexity of dynamic boolean (a.k.a. decision) data structure problems, a long-standing milestone in data structure lower bounds. We introduce a new method for proving dynamic cell probe lower bounds and use it to prove a $\\tilde{\\Omega}(\\log^{1.5} n)$ lower bound on the operational time of a wide range of boolean data structure problems, most notably, on the query time of dynamic range counting over $\\mathbb{F}_2$ ...
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.
Structure and Dynamics of the tRNA-like Structure Domain of Brome Mosaic Virus
Vieweger, Mario; Nesbitt, David
2014-03-01
Conformational switching is widely accepted as regulatory mechanism in gene expression in bacterial systems. More recently, similar regulation mechanisms are emerging for viral systems. One of the most abundant and best studied systems is the tRNA-like structure domain that is found in a number of plant viruses across eight genera. In this work, the folding dynamics of the tRNA-like structure domain of Brome Mosaic Virus are investigated using single-molecule Fluorescence Resonance Energy Transfer techniques. In particular, Burst fluorescence is applied to observe metal-ion induced folding in freely diffusing RNA constructs resembling the 3'-terminal 169nt of BMV RNA3. Histograms of EFRET probabilities reveal a complex equilibrium of three distinct populations. A step-wise kinetic model for TLS folding is developed in accord with the evolution of conformational populations and structural information in the literature. In this mechanism, formation of functional TLS domains from unfolded RNAs requires two consecutive steps; 1) hybridization of a long-range stem interaction followed by 2) formation of a 3' pseudoknot. This three-state equilibrium is well described by step-wise dissociation constants K1(328(30) μM) and K2(1092(183) μM) for [Mg2+] and K1(74(6) mM) and K2(243(52) mM) for [Na+]-induced folding. The kinetic model is validated by oligo competition with the STEM interaction. Implications of this conformational folding mechanism are discussed in regards to regulation of virus replication.
Dynamic stiffness and damping of foundations for jacket structures
DEFF Research Database (Denmark)
Latini, Chiara; Zania, Varvara; Johannesson, Björn
2015-01-01
resistance as defined by Nogami & Novak (1977) is determined, considering 3D wave propagation within linear soil layer with hysteretic damping. Thereafter, the dynamic response of the pile is estimated assuming soil pressure equal to the soil resistance and imposing displacement compatibility. A parametric...... study clarifies the role of the parameters involved i.e. the depth of the soil layer, the pile diameter and the soil layer shear wave velocity. Results are presented in terms of dimensionless graphs which highlight the frequency dependency of the dynamic stiffness and damping....
Scarpelli, Francesco
2009-01-01
Proteins and enzymes play a key role in all biological systems. Understanding the mechanism of biological functions and reactions in which proteins and enzymes are involved requires a detailed characterization of protein structure and dynamics. Structure refers to geometrical structure, as a result
Hydration structure and water exchange dynamics of Fe(II) ion in ...
African Journals Online (AJOL)
Computer simulation studies of the hydration structure and water exchange dynamics in the first hydration shell for Fe(II) in water are presented. The structure of the hydrated ion is discussed in terms of radial distribution functions, coordination numbers, and angular distributions. The average first-shell hydration structure is ...
Organizational and Spatial Dynamics of Attentional Focusing in Hierarchically Structured Objects
Yeari, Menahem; Goldsmith, Morris
2011-01-01
Is the focusing of visual attention object-based, space-based, both, or neither? Attentional focusing latencies in hierarchically structured compound-letter objects were examined, orthogonally manipulating global size (larger vs. smaller) and organizational complexity (two-level structure vs. three-level structure). In a dynamic focusing task,…
The Dynamics in the Structure of Sugarcane Job Market
Directory of Open Access Journals (Sweden)
Roselis Natalina Mazzuchetti
2015-12-01
Full Text Available Esta pesquisa teve como propósito averiguar a estrutura do mercado de trabalho na atividade de cultivo de cana-de-açúcar, à luz das mudanças recentes ocorridas no setor sucroalcooleiro, levando-se em conta os principais estados produtores de cana. Para tanto, realizou-se uma análise estatística descritiva e uma análise de regressão linear simples, com base nos dados da PNAD, de 1997 a 2009. Como corolário, constatou-se que houve uma redução da informalidade no mercado de trabalho em questão, sendo que esta redução foi mais expressiva em Alagoas. Confirmou-se, também, mudanças recentes nas ocupações do setor, com acréscimos nas atividades técnicas, representadas por tratoristas e operadores de máquinas. Evidenciou-se que o mercado de trabalho do setor em questão tem sua dinâmica diretamente ligada aos fatores que ocorrem na cadeia produtiva do setor sucroalcooleiro como um todo. Palavras-Chave: Mercado de Trabalho, Tecnologia, Agronegócios e Produção de cana-de-açúcar. *** Abstract: This research aims to verify the structure of sugarcane cultivation’s job market, considering the recent changes in this sector and the states with the major production. For that, descriptive and statistical analysis were made, as well as a simplified line regression analysis, based on the Pesquisa Nacional por Amostra de Domicílios - PNAD data, for the 1997-2009 period. As corollary, it was stated that there was a reduction in the informal jobs in the sugarcane production market, showing more expressivity in the state of Alagoas. Recent changes in the sector occupation were confirmed, as an increase in technical activities, represented by tractors and machinery operators. It was evidenced that this sector’s job market has its dynamics closely linked to the sugarcane production chain as a whole. Keywords: Job Market, Agribusiness, Technology, Sugarcane production. *** Sumario: Esta investigación tuvo como objetivo investigar la
Topological effects of network structure on long-term social network dynamics in a wild mammal.
Ilany, Amiyaal; Booms, Andrew S; Holekamp, Kay E
2015-07-01
Social structure influences ecological processes such as dispersal and invasion, and affects survival and reproductive success. Recent studies have used static snapshots of social networks, thus neglecting their temporal dynamics, and focused primarily on a limited number of variables that might be affecting social structure. Here, instead we modelled effects of multiple predictors of social network dynamics in the spotted hyena, using observational data collected during 20 years of continuous field research in Kenya. We tested the hypothesis that the current state of the social network affects its long-term dynamics. We employed stochastic agent-based models that allowed us to estimate the contribution of multiple factors to network changes. After controlling for environmental and individual effects, we found that network density and individual centrality affected network dynamics, but that social bond transitivity consistently had the strongest effects. Our results emphasise the significance of structural properties of networks in shaping social dynamics. © 2015 John Wiley & Sons Ltd/CNRS.
Structural and dynamic heterogeneity of interfacial water on chemically modified polymer surfaces
Bekele, Selemon; Tsige, Mesfin
Using molecular dynamics (MD) simulations, we investigate the structural and dynamical properties of water molecules in a slab of water in contact with atactic polystyrene surfaces of varying polarity. We find that the dynamics of water molecules in the interfacial region slows down with increasing polarity of the polystyrene surface. In addition, the interfacial water molecules exhibit structural and dynamic heterogeneity with respect to diffusion, hydrogen bond distribution and relaxation of the hydrogen bond network. The results obtained enhance our understanding of water structure and dynamics at the polymer/water interface with important implications for such desired functional properties as lubrication, adhesion and friction. Interfacial properties of water at hydrophobic and hydrophilic SAM (Self Assembled Monolayers) surfaces will also be presented for comparison. This work was supported by NSF Grant DMR1410290.
Dielectric properties and structural dynamics of melt compounded ...
Indian Academy of Sciences (India)
dispersed OMMT nano-platelets in PEO matrix governs the PEO segmental dynamics. A.C. conductivity of these nanocomposites increases by two orders of magnitude in the experimental frequency range. Keywords. PEO–OMMT nanocomposites; dielectric relaxation; electrical conductivity; impedance spectroscopy. 1.
A Molecular Dynamics Approach to Grain Boundary Structure and Migration
DEFF Research Database (Denmark)
Cotterill, R. M. J.; Leffers, Torben; Lilholt, Hans
1974-01-01
It has been demonstrated that grain boundary formation from the melt can be simulated by the molecular dynamics method. The space between two mutually-misoriented crystal slabs was filled with atoms in a random manner and this liquid was then cooled until crystallization occurred. The general...
The formation of cosmic structure with modified Newtonian dynamics
Sanders, R. H.
2001-01-01
I consider the growth of inhomogeneities in a low-density, baryonic, vacuum energy-dominated universe in the context of modified Newtonian dynamics (MOND). I first write down a two-field Langrangian-based theory of MOND (nonrelativistic) that embodies several assumptions, such as constancy of the
Chain length effect on dynamical structure of poly (vinyl pyrrolidone ...
Indian Academy of Sciences (India)
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 ...
Size-structured interactions and the dynamics of aquatic systems
Persson, L.; de Roos, A.M.
2006-01-01
Size variation within species as a result of individual growth and development over the life cycle is a ubiquitous feature of many aquatic organisms. We review the implications of this size variation for the dynamics of aquatic systems. Ontogenetic development results in differences in size
Rural Poverty Dynamics in Kenya: Structural Declines and Stochastic Escapes
Radeny, M.A.O.; Berg, van den M.M.; Schipper, R.A.
2012-01-01
We use panel survey data and household event-histories to explore patterns of rural poverty dynamics in Kenya over the period 2000–2009. We find substantial mobility across poverty categories using economic transition matrices. Drawing on asset-based approaches, we distinguish stochastic from
Retinal vascular and structural dynamics during acute hyperglycaemia
DEFF Research Database (Denmark)
Klefter, Oliver N; Lauritsen, Tina Vilsbøll; Knop, Filip K
2015-01-01
PURPOSE: To compare retinal vascular dynamics during acute hyperglycaemia in patients with type 2 diabetes and healthy volunteers. METHODS: Twenty-one patients with type 2 diabetes and 27 healthy controls were examined with fundus photographic measurement of retinal vessel diameters, retinal...
Geometrical Models of the Phase Space Structures Governing Reaction Dynamics
2009-08-01
conductor physics [Jacucci et al.(1984), Eckhardt(1995)], stud- ies of diffusion dynamics in materials [Voter et al.(2002)], cosmology [de Oliveira et al...Sciences. Springer-Verlag, Berlin, Heidelberg, New York. [Miller(1998)] Miller, W. H. (1998). Spiers Memorial Lecture . Quantum and semiclassical theory of
TOPSAN: a dynamic web database for structural genomics.
Ellrott, Kyle; Zmasek, Christian M; Weekes, Dana; Sri Krishna, S; Bakolitsa, Constantina; Godzik, Adam; Wooley, John
2011-01-01
The Open Protein Structure Annotation Network (TOPSAN) is a web-based collaboration platform for exploring and annotating structures determined by structural genomics efforts. Characterization of those structures presents a challenge since the majority of the proteins themselves have not yet been characterized. Responding to this challenge, the TOPSAN platform facilitates collaborative annotation and investigation via a user-friendly web-based interface pre-populated with automatically generated information. Semantic web technologies expand and enrich TOPSAN's content through links to larger sets of related databases, and thus, enable data integration from disparate sources and data mining via conventional query languages. TOPSAN can be found at http://www.topsan.org.
McEwan, Iain J; Nardulli, Ann M
2009-12-31
Nuclear hormone receptors (NHRs) represent a large and diverse family of ligand-activated transcription factors involved in regulating development, metabolic homeostasis, salt balance and reproductive health. The ligands for these receptors are typically small hydrophobic molecules such as steroid hormones, thyroid hormone, vitamin D3 and fatty acid derivatives. The first NHR structural information appeared approximately 20 years ago with the solution and crystal structures of the DNA binding domains and was followed by the structure of the agonist and antagonist bound ligand binding domains of different NHR members. Interestingly, in addition to these defined structural features, it has become clear that NHRs also possess significant structural plasticity. Thus, the dynamic structure of the NHRs was the topic of a recent stimulating and informative FASEB Summer Research Conference held in Vermont.
Weaver, D. L.
1982-01-01
Theoretical methods and solutions of the dynamics of protein folding, protein aggregation, protein structure, and the origin of life are discussed. The elements of a dynamic model representing the initial stages of protein folding are presented. The calculation and experimental determination of the model parameters are discussed. The use of computer simulation for modeling protein folding is considered.
The rise and fall of small worlds : Exploring the dynamics of social structure
Gulati, R.; Sytch, M.; Tatarynowicz, A.
2012-01-01
This paper explores the interplay between social structure and economic action by examining some of the evolutionary dynamics of an emergent network that coalesces into a small-world system. The study highlights the small-world system's evolutionary dynamics at both the macro level of the network
Ultrafast structural and vibrational dynamics of the hydration shell around DNA
Directory of Open Access Journals (Sweden)
Szyc Ł
2013-03-01
Full Text Available Two-dimensional infrared spectroscopy in the frequency range of OH- and NH stretch excitations serves for a direct mapping of hydration dynamics around DNA. A moderate slowing down of structural dynamics and resonant OH stretch energy transfer is observed in the DNA water shell compared to bulk water.
Krapp, Andreas
2002-01-01
Presents a collection of theoretical concepts and models that can be used to describe and explore structural and dynamic aspects of interest development from an ontogenic research perspective. Outlines basic ideas of an educational-psychological conceptualization of interest that is based on a dynamic theory of personality. (SLD)
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…
Robust Generation of Dynamic Data Structure Visualizations with Multiple Interaction Approaches
Cross, James H., II; Hendrix, T. Dean; Umphress, David A.; Barowski, Larry A.; Jain, Jhilmil; Montgomery, Lacey N.
2009-01-01
jGRASP has three integrated approaches for interacting with its dynamic viewers for data structures: debugger, workbench, and text-based interactions that allow individual Java statements and expressions to be executed/evaluated. These approaches can be used together to provide a complementary set of interactions with the dynamic viewers. Data…
Dynamic Stability of a #D Tensegrity Structure Carrying a Top Mass: Simulations and Experiments
Michielsen, Joris; Fey, Rob H. B.; Nijmeijer, Henk
2012-07-01
The static and dynamic stability of a 3D tensegrity structure carrying a top mass is investigated both theoretically and experimentally by studying static and linear dynamic responses, (nonlinear) frequency-amplitude plots, and Poincaré maps. A good correspondence between numerical and experimental results is obtained for the eigenfrequencies, FRFs, and frequency-amplitude plots.
Hensen, Ulf; Meyer, Tim; Haas, Jürgen; Rex, René; Vriend, Gert; Grubmüller, Helmut
2012-01-01
Proteins are usually described and classified according to amino acid sequence, structure or function. Here, we develop a minimally biased scheme to compare and classify proteins according to their internal mobility patterns. This approach is based on the notion that proteins not only fold into recurring structural motifs but might also be carrying out only a limited set of recurring mobility motifs. The complete set of these patterns, which we tentatively call the dynasome, spans a multi-dimensional space with axes, the dynasome descriptors, characterizing different aspects of protein dynamics. The unique dynamic fingerprint of each protein is represented as a vector in the dynasome space. The difference between any two vectors, consequently, gives a reliable measure of the difference between the corresponding protein dynamics. We characterize the properties of the dynasome by comparing the dynamics fingerprints obtained from molecular dynamics simulations of 112 proteins but our approach is, in principle, not restricted to any specific source of data of protein dynamics. We conclude that: 1. the dynasome consists of a continuum of proteins, rather than well separated classes. 2. For the majority of proteins we observe strong correlations between structure and dynamics. 3. Proteins with similar function carry out similar dynamics, which suggests a new method to improve protein function annotation based on protein dynamics. PMID:22606222
Simulation of the Zero-Gravity Environment for Dynamic Testing of Structures
National Research Council Canada - National Science Library
Kienholz, David A
1996-01-01
.... A multipoint, six degree of freedom suspension system for dynamic testing is described. Intended primarily for highly flexible space structures, it uses a combination of passive pneumatic and active electromagnetic subsystems...
National Research Council Canada - National Science Library
Behrman, Robert; Carley, Kathleen
2003-01-01
This paper describes the Dynamic Information Flow Simulation (DIFS), an abstract model for analyzing the structure and function of intelligence support organizations and the activities of entities within them...
Structural and Dynamic Heterogeneity of Capillary Wave Fronts at Aqueous Interfaces.
Zhou, Tiecheng; McCue, Alex; Ghadar, Yasaman; Bakó, Imre; Clark, Aurora E
2017-09-28
Using a unique combination of slab-layering analyses and identification of truly interfacial molecules, this work examines water/vapor and water/n-hexane interfaces, specifically the structural and dynamic perturbations of the interfacial water molecules at different locations within the surface capillary waves. From both the structural and dynamic properties analyzed, it is found that these interfacial water molecules dominate the perturbations within the interfacial region, which can extend deep into the water phase relative to the Gibbs dividing surface. Of more importance is the demonstration of structural and dynamic heterogeneity of the interfacial water molecules at the capillary wave front, as indicated by the dipole orientation and the structural and dynamic behavior of hydrogen bonds and their networks.
Yang, Zhijian; Liu, Zhiming
2017-03-01
The paper investigates the well-posedness and the longtime dynamics of the quasilinear wave equations with structural damping and supercritical nonlinearities: {{u}tt}- Δ u+{{≤ft(- Δ \\right)}α}{{u}t}-\
Structural Transformation in Africa : Static gains, Dynamic losses
de Vries, Gaaitzen J.; Timmer, Marcel; de Vries, Klaas
2015-01-01
This paper places recent growth and structural transformation in 11 Sub-Saharan African countries in historical and international perspective. During the early post-independence period, resources were reallocated to manufacturing activities with high productivity growth. Structural change stalled in
Accuracy of Dynamic and Acoustic Analysis of Lightweight Panel Structures
DEFF Research Database (Denmark)
Kirkegaard, Poul Henning; Dickow, Kristoffer Ahrens; Andersen, Lars Vabbersgaard
2012-01-01
in such buildings is important. In the lowfrequency range, prediction of sound and vibration in building structures may be achieved by finite-element analysis (FEA). The aim of this paper is to compare the two commercial codes ABAQUS and ANSYS for FEA of an acoustic-structural coupling in a timber lightweight panel...
Influences of Family Structure Dynamics on Sexual Debut in Africa ...
African Journals Online (AJOL)
There is no research on the timing, sequencing and number of changes in family environment and their influences on sexual and reproductive health outcomes in Africa. Using a population-based survey with data on family structure at three points in the life course, this paper examines the influences of these family structure ...
Dynamic Error Analysis Method for Vibration Shape Reconstruction of Smart FBG Plate Structure
Directory of Open Access Journals (Sweden)
Hesheng Zhang
2016-01-01
Full Text Available Shape reconstruction of aerospace plate structure is an important issue for safe operation of aerospace vehicles. One way to achieve such reconstruction is by constructing smart fiber Bragg grating (FBG plate structure with discrete distributed FBG sensor arrays using reconstruction algorithms in which error analysis of reconstruction algorithm is a key link. Considering that traditional error analysis methods can only deal with static data, a new dynamic data error analysis method are proposed based on LMS algorithm for shape reconstruction of smart FBG plate structure. Firstly, smart FBG structure and orthogonal curved network based reconstruction method is introduced. Then, a dynamic error analysis model is proposed for dynamic reconstruction error analysis. Thirdly, the parameter identification is done for the proposed dynamic error analysis model based on least mean square (LMS algorithm. Finally, an experimental verification platform is constructed and experimental dynamic reconstruction analysis is done. Experimental results show that the dynamic characteristics of the reconstruction performance for plate structure can be obtained accurately based on the proposed dynamic error analysis method. The proposed method can also be used for other data acquisition systems and data processing systems as a general error analysis method.
Dynamics and structure of water-bitumen mixtures
DEFF Research Database (Denmark)
Lemarchand, Claire; Greenfield, Michael L.; Hansen, Jesper Schmidt
2016-01-01
Systems of Cooee bitumen and water up to 4% mass are studied by molecular dynamics simulations. The cohesive energy density of the system is shown to decrease with an increasing water content. This decrease is due mainly to an increase in the interaction energy which is not high enough...... to counterbalance the increase in volume due to the addition of water. It is not due to a decrease of interaction energy between the slightly polar asphaltene molecules. The water molecules tend to form a droplet in bitumen. The size and the distribution of sizes of the droplets are quantified, with multiple...... droplets being more stable at the highest temperature simulated. The droplet is mainly located close to the saturates molecules in bitumen. Finally, it is shown that the water dynamics is much slower in bitumen than in pure water because it is governed by the diffusion of the droplet and not of the single...
Insights into Chromatin Structure and Dynamics in Plants
Directory of Open Access Journals (Sweden)
Stefanie Rosa
2013-11-01
Full Text Available The packaging of chromatin into the nucleus of a eukaryotic cell requires an extraordinary degree of compaction and physical organization. In recent years, it has been shown that this organization is dynamically orchestrated to regulate responses to exogenous stimuli as well as to guide complex cell-type-specific developmental programs. Gene expression is regulated by the compartmentalization of functional domains within the nucleus, by distinct nucleosome compositions accomplished via differential modifications on the histone tails and through the replacement of core histones by histone variants. In this review, we focus on these aspects of chromatin organization and discuss novel approaches such as live cell imaging and photobleaching as important tools likely to give significant insights into our understanding of the very dynamic nature of chromatin and chromatin regulatory processes. We highlight the contribution plant studies have made in this area showing the potential advantages of plants as models in understanding this fundamental aspect of biology.
Controlling the dynamics of a self-organized structure using a rf-field
Energy Technology Data Exchange (ETDEWEB)
Talasman, S.J.; Ignat, M
2004-03-15
We investigate the influence of an external rf-field upon a plasma self-organized structure. We show that depending on the intensity of this field, though it is at very low values, the dynamics of the structure can be easily controlled over a wide range of the state parameters values. This could be considered as a non-feedback method of dynamics control.
Effect of Infills in Influencing the Dynamic Responses of Multistoried Structures
E. Rahmathulla Noufal
2015-01-01
Investigating the dynamic responses of high rise structures under the effect of siesmic ground motion is extremely important for the proper analysis and design of multitoried structures. Since the presence of infilled walls strongly influences the behaviour of frame systems in multistoried buildings, there is an increased need for developing guidelines for the analysis and design of infilled frames under the effect of dynamic loads for safe and proper design of buildings....
Finite-time rotation number: A fast indicator for chaotic dynamical structures
Energy Technology Data Exchange (ETDEWEB)
Szezech, J.D., E-mail: jds98@fisica.ufpr.br [Instituto de Física, Universidade de São Paulo, 5315-970, São Paulo, São Paulo (Brazil); Departamento de Matemática e Estatística, Universidade Estadual de Ponta Grossa, 84033-240, Ponta Grossa, Paraná (Brazil); Schelin, A.B., E-mail: schelin@if.usp.br [Instituto de Física, Universidade de São Paulo, 5315-970, São Paulo, São Paulo (Brazil); Departamento de Física, Universidade Tecnológica Federal do Paraná, 80230-901, Curitiba, Paraná (Brazil); Caldas, I.L., E-mail: ibere@if.usp.br [Instituto de Física, Universidade de São Paulo, 5315-970, São Paulo, São Paulo (Brazil); Lopes, S.R., E-mail: lopes@fisica.ufpr.br [Departamento de Física, Universidade Federal do Paraná, 81531-990, Curitiba, Paraná (Brazil); Morrison, P.J., E-mail: morrison@physics.utexas.edu [Department of Physics, The University of Texas at Austin, Austin, TX 78712 (United States); Viana, R.L., E-mail: rlv640@gmail.com [Departamento de Física, Universidade Federal do Paraná, 81531-990, Curitiba, Paraná (Brazil)
2013-02-04
Lagrangian coherent structures are effective barriers, sticky regions, that separate chaotic phase space regions of different dynamical behavior. The usual way to detect such structures is by calculating finite-time Lyapunov exponents. We show that similar results can be obtained for time-periodic systems by calculating finite-time rotation numbers, which are faster to compute. We illustrate our claim by considering examples of continuous- and discrete-time dynamical systems of physical interest.
H-Adaptive Methods for Nonlinear Dynamic Analysis of Shell Structures
Directory of Open Access Journals (Sweden)
Sang-Ho Lee
1995-01-01
Full Text Available The implementation and application of h-adaptivity in an explicit finite element program for nonlinear structural dynamics is described. Particular emphasis is placed on developing procedures for general purpose structural dynamics programs and efficiently handling adaptivity in shell elements. New projection techniques for error estimation and projecting variables on new meshes after fission or fusion are described. Several problems of severe impact are described.
[The significance of structural dynamics for a theory of neurosis and personality disorders].
Frommer, J
2003-01-01
Following the psychopathological approach of Janzarik (structural dynamics), this paper develops a two-dimensional theory for the understanding of neuroses and personality disorders. The dynamic dimension serves to describe the symptomatology between the two poles of anxiety and depression. The structural dimension differs according to the maturity of the personal identity between mature neurotic personality organization on the one hand and severe personality disorder on the other.
Molecular dynamics simulation of nanocrystalline nickel: structure and mechanical properties
Energy Technology Data Exchange (ETDEWEB)
Swygenhoven, H. van [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Caro, A. [Comision Nacional de Energia Atomica, San Carlos de Bariloche (Argentina). Centro Atomico Bariloche
1997-09-01
Molecular dynamics computer simulations of low temperature elastic and plastic deformation of Ni nanophase samples (3-7 nm) are performed. The samples are polycrystals nucleated from different seeds, with random locations and orientations. Bulk and Young`s modulus, onset of plastic deformation and mechanism responsible for the plastic behaviour are studied and compared with the behaviour of coarse grained samples. (author) 1 fig., 3 refs.
Surface-hopping dynamics and decoherence with quantum equilibrium structure.
Grunwald, Robbie; Kim, Hyojoon; Kapral, Raymond
2008-04-28
In open quantum systems, decoherence occurs through interaction of a quantum subsystem with its environment. The computation of expectation values requires a knowledge of the quantum dynamics of operators and sampling from initial states of the density matrix describing the subsystem and bath. We consider situations where the quantum evolution can be approximated by quantum-classical Liouville dynamics and examine the circumstances under which the evolution can be reduced to surface-hopping dynamics, where the evolution consists of trajectory segments exclusively evolving on single adiabatic surfaces, with probabilistic hops between these surfaces. The justification for the reduction depends on the validity of a Markovian approximation on a bath averaged memory kernel that accounts for quantum coherence in the system. We show that such a reduction is often possible when initial sampling is from either the quantum or classical bath initial distributions. If the average is taken only over the quantum dispersion that broadens the classical distribution, then such a reduction is not always possible.
Covariance of dynamic strain responses for structural damage detection
Li, X. Y.; Wang, L. X.; Law, S. S.; Nie, Z. H.
2017-10-01
A new approach to address the practical problems with condition evaluation/damage detection of structures is proposed based on the distinct features of a new damage index. The covariance of strain response function (CoS) is a function of modal parameters of the structure. A local stiffness reduction in structure would cause monotonous increase in the CoS. Its sensitivity matrix with respect to local damages of structure is negative and narrow-banded. The damage extent can be estimated with an approximation to the sensitivity matrix to decouple the identification equations. The CoS sensitivity can be calibrated in practice from two previous states of measurements to estimate approximately the damage extent of a structure. A seven-storey plane frame structure is numerically studied to illustrate the features of the CoS index and the proposed method. A steel circular arch in the laboratory is tested. Natural frequencies changed due to damage in the arch and the damage occurrence can be judged. However, the proposed CoS method can identify not only damage happening but also location, even damage extent without need of an analytical model. It is promising for structural condition evaluation of selected components.
Local Structure and Dynamics of Hydration Water in Intrinsically Disordered Proteins.
Rani, Pooja; Biswas, Parbati
2015-08-27
Hydration water around protein surface plays a key role in structure, folding and dynamics of proteins. Intrinsically disordered proteins lack secondary and/or tertiary structure in their native state. Thus, characterizing the local structure and dynamics of hydration water around disordered proteins is challenging for both experimentalists and theoreticians. The local structure, orientation and dynamics of hydration water in the vicinity of intrinsically disordered proteins is investigated through molecular dynamics simulations. The analysis of the hydration capacity reveals that the disordered proteins have much larger binding capacity for hydration water than globular proteins. The surface and radial distribution of water molecules around the disordered proteins depict a similar trend. The local structure of the hydration water evaluated in terms of the tetrahedral order parameter, shows a higher order among the water molecules surrounding disordered proteins/regions. The residence time of water molecules clearly exhibits slow dynamics of hydration water around the surface of disordered proteins/regions as compared to globular proteins. The orientation of water molecules is found to be distinctly different for ordered and disordered proteins/regions. This analysis provides a better insight into the structure and dynamics of hydration water around disordered proteins.
Computing the Ediz eccentric connectivity index of discrete dynamic structures
Directory of Open Access Journals (Sweden)
Wu Hualong
2017-06-01
Full Text Available From the earlier studies in physical and chemical sciences, it is found that the physico-chemical characteristics of chemical compounds are internally connected with their molecular structures. As a theoretical basis, it provides a new way of thinking by analyzing the molecular structure of the compounds to understand their physical and chemical properties. In our article, we study the physico-chemical properties of certain molecular structures via computing the Ediz eccentric connectivity index from mathematical standpoint. The results we yielded mainly apply to the techniques of distance and degree computation of mathematical derivation, and the conclusions have guiding significance in physical engineering.
Computing the Ediz eccentric connectivity index of discrete dynamic structures
Wu, Hualong; Kamran Siddiqui, Muhammad; Zhao, Bo; Gan, Jianhou; Gao, Wei
2017-06-01
From the earlier studies in physical and chemical sciences, it is found that the physico-chemical characteristics of chemical compounds are internally connected with their molecular structures. As a theoretical basis, it provides a new way of thinking by analyzing the molecular structure of the compounds to understand their physical and chemical properties. In our article, we study the physico-chemical properties of certain molecular structures via computing the Ediz eccentric connectivity index from mathematical standpoint. The results we yielded mainly apply to the techniques of distance and degree computation of mathematical derivation, and the conclusions have guiding significance in physical engineering.
An Updating Method for Structural Dynamics Models with Uncertainties
Directory of Open Access Journals (Sweden)
B. Faverjon
2008-01-01
Full Text Available One challenge in the numerical simulation of industrial structures is model validation based on experimental data. Among the indirect or parametric methods available, one is based on the “mechanical” concept of constitutive relation error estimator introduced in order to quantify the quality of finite element analyses. In the case of uncertain measurements obtained from a family of quasi-identical structures, parameters need to be modeled randomly. In this paper, we consider the case of a damped structure modeled with stochastic variables. Polynomial chaos expansion and reduced bases are used to solve the stochastic problems involved in the calculation of the error.
Structure of local interactions in complex financial dynamics
Jiang, X. F.; Chen, T. T.; Zheng, B.
2014-06-01
With the network methods and random matrix theory, we investigate the interaction structure of communities in financial markets. In particular, based on the random matrix decomposition, we clarify that the local interactions between the business sectors (subsectors) are mainly contained in the sector mode. In the sector mode, the average correlation inside the sectors is positive, while that between the sectors is negative. Further, we explore the time evolution of the interaction structure of the business sectors, and observe that the local interaction structure changes dramatically during a financial bubble or crisis.
D3-Tree: A Dynamic Distributed Deterministic Load - Balancer for decentralized tree structures
Sourla, Efrosini; Sioutas, Spyros; Tsichlas, Kostas; Zaroliagis, Christos
2015-01-01
In this work, we propose D3-Tree, a dynamic distributed deterministic structure for data management in decentralized networks. We present in brief the theoretical algorithmic analysis, in which our proposed structure is based on, and we describe thoroughly the key aspects of the implementation. Conducting experiments, we verify that the implemented structure outperforms other well-known hierarchical tree-based structures, since it provides better complexities regarding load-balancing operatio...
Structure and Dynamic Properties of Membrane Proteins using NMR
DEFF Research Database (Denmark)
Rösner, Heike; Kragelund, Birthe
2012-01-01
conformational changes. Their structural and functional decoding is challenging and has imposed demanding experimental development. Solution nuclear magnetic resonance (NMR) spectroscopy is one of the techniques providing the capacity to make a significant difference in the deciphering of the membrane protein...... structure-function paradigm. The method has evolved dramatically during the last decade resulting in a plethora of new experiments leading to a significant increase in the scientific repertoire for studying membrane proteins. Besides solving the three-dimensional structures using state-of-the-art approaches......-populated states, this review seeks to introduce the vast possibilities solution NMR can offer to the study of membrane protein structure-function analyses with special focus on applicability. © 2012 American Physiological Society. Compr Physiol 2:1491-1539, 2012....
Simulating Nonlinear Dynamics of Deployable Space Structures Project
National Aeronautics and Space Administration — To support NASA's vital interest in developing much larger solar array structures over the next 20 years, MotionPort LLC's Phase I SBIR project will strengthen...
Structural parameter identifiability analysis for dynamic reaction networks
DEFF Research Database (Denmark)
Davidescu, Florin Paul; Jørgensen, Sten Bay
2008-01-01
where for a given set of measured variables it is desirable to investigate which parameters may be estimated prior to spending computational effort on the actual estimation. This contribution addresses the structural parameter identifiability problem for the typical case of reaction network models....... The proposed analysis is performed in two phases. The first phase determines the structurally identifiable reaction rates based on reaction network stoichiometry. The second phase assesses the structural parameter identifiability of the specific kinetic rate expressions using a generating series expansion...... method based on Lie derivatives. The proposed systematic two phase methodology is illustrated on a mass action based model for an enzymatically catalyzed reaction pathway network where only a limited set of variables is measured. The methodology clearly pinpoints the structurally identifiable parameters...
The Social Structure of Chinese Society: Stratification Dynamics
Directory of Open Access Journals (Sweden)
- Wong Syodi
2011-12-01
Full Text Available Since the foundation of the Chinese People's Republic, in the course of over 60 years - from 1949 to 2011, substantial transformations have occurred in the social structure of Chinese society. Rapid economic, political and cultural development of China has resulted in deep social transformations. The article reveals the logic, reasons and consequences of these transformations; the author identifies the qualitative and quantitative features of the structure of Chinese society in a wide historical perspective of half a century.
Structural constraints and dynamics of bacterial cell wall architecture
Directory of Open Access Journals (Sweden)
Miguel Angel De Pedro
2015-05-01
Full Text Available The peptidoglycan wall (PG is a unique structure which confers physical strength and defined shape to bacteria. It consists of a net-like macromolecule of peptide interlinked glycan chains overlying the cell membrane. The structure and layout of the PG dictates that the wall has to be continuously modified as bacteria go through division, morphological differentiation and adaptive responses. The PG is poorly known in structural terms. However, to understand morphogenesis a precise knowledge of glycan strand arrangement and of local effects of the different kinds of subunits is essential. The scarcity of data led to a conception of the PG as a regular, highly ordered structure which strongly influenced growth models. Here, we review the structure of the PG to define a more realistic conceptual framework. We discuss the consequences of the plasticity of murein architecture in morphogenesis and try to define a set of minimal structural constraints that must be fulfilled by any model to be compatible with present day information.
35th IMAC, A Conference and Exposition on Structural Dynamics 2017
Niezrecki, Christopher; Maio, Dario; Castellini, Paolo; Mains, Michael; Blough, JR; Kerschen, Gaetan; Caicedo, Juan; Pakzad, Shamim; Barthorpe, Robert; Platz, Roland; Lopez, Israel; Moaveni, Babak; Papadimitriou, Costas; v.1 Nonlinear dynamics; v.2 Dynamics of civil structures; v.3 Model validation and uncertainty quantification; v.4 Dynamics of coupled structures; v.5 Sensors and instrumentation; v.6 Special topics in structural dynamics; v.7 Structural health monitoring & damage detection; v.8 Rotating machinery, hybrid test methods, vibro-acoustics & laser vibrometry; v.9 Shock & vibration, aircraft/aerospace, energy harvesting, acoustics & optics; v.10 Topics in modal analysis & testing
2017-01-01
Nonlinear Dynamics, Volume 1: Proceedings of the 35th IMAC, A Conference and Exposition on Structural Dynamics, 2017, the first volume of ten 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 Nonlinear Dynamics, including papers on: Nonlinear System Identification Nonlinear Modeling & Simulation Nonlinear Reduced-order Modeling Nonlinearity in Practice Nonlinearity in Aerospace Systems Nonlinearity in Multi-Physics Systems Nonlinear Modes and Modal Interactions Experimental Nonlinear Dynamics.
Development of a finite dynamic element for free vibration analysis of two-dimensional structures
Gupta, K. K.
1978-01-01
The paper develops an efficient free-vibration analysis procedure of two-dimensional structures. This is achieved by employing a discretization technique based on a recently developed concept of finite dynamic elements, involving higher order dynamic correction terms in the associated stiffness and inertia matrices. A plane rectangular dynamic element is developed in detail. Numerical solution results of free-vibration analysis presented herein clearly indicate that these dynamic elements combined with a suitable quadratic matrix eigenproblem solution technique effect a most economical and efficient solution for such an analysis when compared with the usual finite element method.
Impact of methionine oxidation on calmodulin structural dynamics
Energy Technology Data Exchange (ETDEWEB)
McCarthy, Megan R.; Thompson, Andrew R.; Nitu, Florentin [Biochemistry, Molecular Biology and Biophysics Department, University of Minnesota, Minneapolis, MN 55455 (United States); Moen, Rebecca J. [Chemistry and Geology Department, Minnesota State University, Mankato, MN 56001 (United States); Olenek, Michael J. [Biology Department, University of Wisconsin, La Crosse, WI 54601 (United States); Klein, Jennifer C., E-mail: jklein@uwlax.edu [Biology Department, University of Wisconsin, La Crosse, WI 54601 (United States); Thomas, David D., E-mail: ddt@umn.edu [Biochemistry, Molecular Biology and Biophysics Department, University of Minnesota, Minneapolis, MN 55455 (United States)
2015-01-09
Highlights: • We measured the distance distribution between two spin labels on calmodulin by DEER. • Two structural states, open and closed, were resolved at both low and high Ca. • Ca shifted the equilibrium toward the open state by a factor of 13. • Methionine oxidation, simulated by glutamine substitution, decreased the Ca effect. • These results have important implications for aging in muscle and other tissues. - Abstract: We have used electron paramagnetic resonance (EPR) to examine the structural impact of oxidizing specific methionine (M) side chains in calmodulin (CaM). It has been shown that oxidation of either M109 or M124 in CaM diminishes CaM regulation of the muscle calcium release channel, the ryanodine receptor (RyR), and that mutation of M to Q (glutamine) in either case produces functional effects identical to those of oxidation. Here we have used site-directed spin labeling and double electron–electron resonance (DEER), a pulsed EPR technique that measures distances between spin labels, to characterize the structural changes resulting from these mutations. Spin labels were attached to a pair of introduced cysteine residues, one in the C-lobe (T117C) and one in the N-lobe (T34C) of CaM, and DEER was used to determine the distribution of interspin distances. Ca binding induced a large increase in the mean distance, in concert with previous X-ray crystallography and NMR data, showing a closed structure in the absence of Ca and an open structure in the presence of Ca. DEER revealed additional information about CaM’s structural heterogeneity in solution: in both the presence and absence of Ca, CaM populates both structural states, one with probes separated by ∼4 nm (closed) and another at ∼6 nm (open). Ca shifts the structural equilibrium constant toward the open state by a factor of 13. DEER reveals the distribution of interprobe distances, showing that each of these states is itself partially disordered, with the width of each
Structure and dynamics of water in nanoscopic spheres and tubes.
van der Loop, Tibert H; Ottosson, Niklas; Lotze, Stephan; Kentzinger, Emmanuel; Vad, Thomas; Sager, Wiebke F C; Bakker, Huib J; Woutersen, Sander
2014-11-14
We study the reorientation dynamics of liquid water confined in nanometer-sized reverse micelles of spherical and cylindrical shape. The size and shape of the micelles are characterized in detail using small-angle x-ray scattering, and the reorientation dynamics of the water within the micelles is investigated using GHz dielectric relaxation spectroscopy and polarization-resolved infrared pump-probe spectroscopy on the OD-stretch mode of dilute HDO:H2O mixtures. We find that the GHz dielectric response of both the spherical and cylindrical reverse micelles can be well described as a sum of contributions from the surfactant, the water at the inner surface of the reversed micelles, and the water in the core of the micelles. The Debye relaxation time of the core water increases from the bulk value τ(H2O) of 8.2 ± 0.1 ps for the largest reverse micelles with a radius of 3.2 nm to 16.0 ± 0.4 ps for the smallest micelles with a radius of 0.7 nm. For the nano-spheres the dielectric response of the water is approximately ∼6 times smaller than expected from the water volume fraction and the bulk dielectric relaxation of water. We find that the dielectric response of nano-spheres is more attenuated than that of nano-tubes of identical composition (water-surfactant ratio), whereas the reorientation dynamics of the water hydroxyl groups is identical for the two geometries. We attribute the attenuation of the dielectric response compared to bulk water to a local anti-parallel ordering of the molecular dipole moments. The difference in attenuation between nano-spheres and nano-cylinders indicates that the anti-parallel ordering of the water dipoles is more pronounced upon spherical than upon cylindrical nanoconfinement.
Physical relativity space-time structure from a dynamical perspective
Brown, Harvey R
2005-01-01
Physical Relativity explores the nature of the distinction at the heart of Einstein's 1905 formulation of his special theory of relativity: that between kinematics and dynamics. Einstein himself became increasingly uncomfortable with this distinction, and with the limitations of what he called the 'principle theory' approach inspired by the logic of thermodynamics. A handful of physicists and philosophers have over the last century likewise expressed doubts about Einstein'streatment of the relativistic behaviour of rigid bodies and clocks in motion in the kinematical part of his great paper, a
An Optimal Dynamic Data Structure for Stabbing-Semigroup Queries
DEFF Research Database (Denmark)
Agarwal, Pankaj K.; Arge, Lars; Kaplan, Haim
2012-01-01
Let S be a set of n intervals in $\\mathbb{R}$, and let $(\\mathbf{S}, +)$ be any commutative semigroup. We assign a weight $\\omega(s) \\in \\mathbf{S}$ to each interval in S. For a point $x \\in \\mathbb{R}$, let $S(x) \\subseteq S$ be the set of intervals that contain x. Given a point $q \\in \\mathbb{R....... For the restricted case of a nested family of intervals (either every pair of intervals is disjoint or one contains the other), we present a simpler solution based on dynamic trees...
Studies on Nucleic Acids – Structure and Dynamics
Isaksson, Johan
2005-01-01
This thesis is based on six papers, Papers I-VI, focusing on the interplay between the stabilizing elements of nucleic acids self-assembly; hydrogen bonding, stacking and solvent effects. In Paper I we investigate how the substitution of the O4' for CH2 in the sugar moiety of adenosine (2'-deoxyaristeromycin) at the A6 position of the Dickerson-Drew dodecamer makes the two modified bases exist in a dynamic equilibrium between Hoogsteen and Watson-Crick base pairing in the NMR time scale. Pape...
SPECTROSCOPIC STUDIES OF STRUCTURE, DYNAMICS AND REACTIVITY IN IONIC LIQUIDS.
Energy Technology Data Exchange (ETDEWEB)
WISHART,J.F.
2007-11-30
Ionic liquids (ILs) are a rapidly expanding family of condensed-phase media with important applications in energy production, nuclear fuel and waste processing, improving the efficiency and safety of industrial chemical processes, and pollution prevention. ILs are generally nonvolatile, noncombustible, highly conductive, recyclable and capable of dissolving a wide variety of materials. They are finding new uses in chemical synthesis, catalysis, separations chemistry, electrochemistry and other areas. Ionic liquids have dramatically different properties compared to conventional molecular solvents, and they provide a new and unusual environment to test our theoretical understanding of charge transfer and other reactions. We are interested in how IL properties influence physical and dynamical processes that determine the stability and lifetimes of reactive intermediates and thereby affect the courses of chemical reactions and product distributions. Successful use of ionic liquids in radiation-filled environments, where their safety advantages could be significant, requires an understanding of ionic liquid radiation chemistry. For example, characterizing the primary steps of IL radiolysis will reveal radiolytic degradation pathways and suggest ways to prevent them or mitigate their effects on the properties of the material. An understanding of ionic liquid radiation chemistry will also facilitate pulse radiolysis studies of general chemical reactivity in ILs, which will aid in the development of applications listed above. Very early in our radiolysis studies it became evident that slow solvation dynamics of the excess electron in ILs (which vary over a wide viscosity range) increases the importance of pre-solvated electron reactivity and consequently alters product distributions. Parallel studies of IL solvation phenomena using coumarin-153 dynamic Stokes shifts and polarization anisotropy decay rates are done to compare with electron solvation studies and to evaluate
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...... 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...... 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...
Borah, Sangkha; Padma Kumar, P
2016-06-07
Microscopic investigation of solvation of selenic acid (H2SeO4) in the aqueous environment has been carried out using the Car-Parrinello molecular dynamics simulation technique. The species deprotonates to HSeO4(-) in a few picoseconds owing to its low pKa1 value of -3.0. A dynamic equilibrium between HSeO4(-) and SeO4(2-), is observed in qualitative agreement with the reported pKa2 value of 1.70. The governing deprotonation mechanism and the structural and dynamic evolutions of the system, particularly the nature of hydrogen bonding, their strengths and lifetimes are investigated comprehensively. A comparison of the vibrational spectra of the species recorded in the gas phase and in the aqueous environment provides further insights on the nature of the interaction between the solute species and water. The results are in good agreement with the available experimental data and other recent computational studies.
Structural Dynamics Verification of Rotorcraft Comprehensive Analysis System (RCAS)
Energy Technology Data Exchange (ETDEWEB)
Bir, G. S.
2005-02-01
The Rotorcraft Comprehensive Analysis System (RCAS) was acquired and evaluated as part of an ongoing effort by the U.S Department of Energy (DOE) and the National Renewable Energy Laboratory (NREL) to provide state-of-the-art wind turbine modeling and analysis technology for Government and industry. RCAS is an interdisciplinary tool offering aeroelastic modeling and analysis options not supported by current codes. RCAS was developed during a 4-year joint effort among the U.S. Army's Aeroflightdynamics Directorate, Advanced Rotorcraft Technology Inc., and the helicopter industry. The code draws heavily from its predecessor 2GCHAS (Second Generation Comprehensive Helicopter Analysis System), which required an additional 14 years to develop. Though developed for the rotorcraft industry, its general-purpose features allow it to model or analyze a general dynamic system. Its key feature is a specialized finite element that can model spinning flexible parts. The code, therefore, appears particularly suited for wind turbines whose dynamics is dominated by massive flexible spinning rotors. In addition to the simulation capability of the existing codes, RCAS [1-3] offers a range of unique capabilities, including aeroelastic stability analysis, trim, state-space modeling, operating modes, modal reduction, multi-blade coordinate transformation, periodic-system-specific analysis, choice of aerodynamic models, and a controls design/implementation graphical interface.
Atmospheric dynamics InfraStructure in Europe: The ARISE project
Blanc, Elisabeth
2013-04-01
ARISE proposes to design a new infrastructure that integrates different station networks in order to provide a new "3D" image of the atmospheric dynamics from the ground up to the mesosphere with unprecedented spatio-temporal resolution. The implied networks are: - the International infrasound network developed for the verification of the Comprehensive nuclear Test Ban Treaty (CTBT). This system is unique by its quality for infrasound and atmospheric wave observations, - the Network for the Detection of Atmospheric Composition Changes (NDACC) which uses Lidar to measure stratospheric dynamics, - the Network for the Detection of Mesopause Changes (NDMC), dedicated to airglow layer measurements in the mesosphere, and additional complementary stations and satellite data. The infrastructure extends across Europe and outlying regions, including polar and equatorial regions. The measurements will be used to improve the parameterization of gravity waves in the stratosphere to better resolve climate models. Such description is crucial to estimate the impact of stratospheric climate forcing on the troposphere. In the long term, data will be used for monitoring changes in the occurrence of extreme events and trends in the middle atmosphere climate. The project impact also concerns civil applications related to monitoring of natural hazards as volcanoes. The presentation will focus on the first results obtained using three technologies during specific events as stratospheric warming, volcanic eruptions and severe weather. The benefits of using the three technologies will be discussed.
Structural basis for catalytically restrictive dynamics of a high-energy enzyme state
Kovermann, Michael; Ådén, Jörgen; Grundström, Christin; Elisabeth Sauer-Eriksson, A.; Sauer, Uwe H.; Wolf-Watz, Magnus
2015-07-01
An emerging paradigm in enzymology is that transient high-energy structural states play crucial roles in enzymatic reaction cycles. Generally, these high-energy or `invisible' states cannot be studied directly at atomic resolution using existing structural and spectroscopic techniques owing to their low populations or short residence times. Here we report the direct NMR-based detection of the molecular topology and conformational dynamics of a catalytically indispensable high-energy state of an adenylate kinase variant. On the basis of matching energy barriers for conformational dynamics and catalytic turnover, it was found that the enzyme's catalytic activity is governed by its dynamic interconversion between the high-energy state and a ground state structure that was determined by X-ray crystallography. Our results show that it is possible to rationally tune enzymes' conformational dynamics and hence their catalytic power--a key aspect in rational design of enzymes catalysing novel reactions.
Cheng, Ching-An; Huang, Han-Pang; Hsu, Huan-Kun; Lai, Wei-Zh; Cheng, Chih-Chun
2016-07-01
We investigate the modeling of inverse dynamics without prior kinematic information for holonomic rigid-body robots. Despite success in compensating robot dynamics and friction, general inverse dynamics models are nontrivial. Rigid-body models are restrictive or inefficient; learning-based models are generalizable yet require large training data. The structured kernels address the dilemma by embedding the robot dynamics in reproducing kernel Hilbert space. The proposed kernels autonomously converge to rigid-body models but require fewer samples; with a semi-parametric framework that incorporates additional parametric basis for friction, the structured kernels can efficiently model general rigid-body robots. We tested the proposed scheme in simulations and experiments; the models that consider the structure of function space are more accurate.
The basic approach to age-structured population dynamics models, methods and numerics
Iannelli, Mimmo
2017-01-01
This book provides an introduction to age-structured population modeling which emphasises the connection between mathematical theory and underlying biological assumptions. Through the rigorous development of the linear theory and the nonlinear theory alongside numerics, the authors explore classical equations that describe the dynamics of certain ecological systems. Modeling aspects are discussed to show how relevant problems in the fields of demography, ecology, and epidemiology can be formulated and treated within the theory. In particular, the book presents extensions of age-structured modelling to the spread of diseases and epidemics while also addressing the issue of regularity of solutions, the asymptotic behaviour of solutions, and numerical approximation. With sections on transmission models, non-autonomous models and global dynamics, this book fills a gap in the literature on theoretical population dynamics. The Basic Approach to Age-Structured Population Dynamics will appeal to graduate students an...
Structure and Dynamics of Low-Density and High-Density Liquid Water at High Pressure.
Fanetti, Samuele; Lapini, Andrea; Pagliai, Marco; Citroni, Margherita; Di Donato, Mariangela; Scandolo, Sandro; Righini, Roberto; Bini, Roberto
2014-01-02
Liquid water has a primary role in ruling life on Earth in a wide temperature and pressure range as well as a plethora of chemical, physical, geological, and environmental processes. Nevertheless, a full understanding of its dynamical and structural properties is still lacking. Water molecules are associated through hydrogen bonds, with the resulting extended network characterized by a local tetrahedral arrangement. Two different local structures of the liquid, called low-density (LDW) and high-density (HDW) water, have been identified to potentially affect many different chemical, biological, and physical processes. By combining diamond anvil cell technology, ultrafast pump-probe infrared spectroscopy, and classical molecular dynamics simulations, we show that the liquid structure and orientational dynamics are intimately connected, identifying the P-T range of the LDW and HDW regimes. The latter are defined in terms of the speeding up of the orientational dynamics, caused by the increasing probability of breaking and reforming the hydrogen bonds.
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.
2012-01-01
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. PMID:22113029
Cryo-electron microscopy for structural analysis of dynamic biological macromolecules.
Murata, Kazuyoshi; Wolf, Matthias
2018-02-01
Since the introduction of what became today's standard for cryo-embedding of biological macromolecules at native conditions more than 30years ago, techniques and equipment have been drastically improved and the structure of biomolecules can now be studied at near atomic resolution by cryo-electron microscopy (cryo-EM) while capturing multiple dynamic states. Here we review the recent progress in cryo-EM for structural studies of dynamic biological macromolecules. We provide an overview of the cryo-EM method and introduce contemporary studies to investigate biomolecular structure and dynamics, including examples from the recent literature. Cryo-EM is a powerful tool for the investigation of biological macromolecular structures including analysis of their dynamics by using advanced image-processing algorithms. The method has become even more widely applicable with present-day single particle analysis and electron tomography. The cryo-EM method can be used to determine the three-dimensional structure of biomacromolecules in near native condition at close to atomic resolution, and has the potential to reveal conformations of dynamic molecular complexes. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.
Dynamic Analysis of Wind Turbines Including Soil-Structure Interaction
DEFF Research Database (Denmark)
Harte, M.; Basu, B.; Nielsen, Søren R.K.
2012-01-01
blades and includes the effect of centrifugal stiffening due to rotation. The foundation of the structure is modeled as a rigid gravity based foundation with two DOF whose movement is related to the surrounding soil by means of complex impedance functions generated using cone model. Transfer functions...... for displacement of the turbine system are obtained and the modal frequencies of the combined turbine-foundation system are estimated. Simulations are presented for the MDOF turbine structure subjected to wind loading for different soil stiffness conditions. Steady state and turbulent wind loading, developed using...... blade element momentum theory and the Kaimal spectrum, have been considered. Soil stiffness and damping properties acquired from DNV/Risø standards are used as a comparison. The soil-structure interaction is shown to affect the response of the wind turbine. This is examined in terms of the turbine...
Vesicles and vesicle gels - structure and dynamics of formation
Gradzielski, M
2003-01-01
Vesicles constitute an interesting morphology formed by self-aggregating amphiphilic molecules. They exhibit a rich structural variety and are of interest both from a fundamental point of view (for studying closed bilayer systems) and from a practical point of view (whenever one is interested in the encapsulation of active molecules). In many circumstances vesicular structures have to be formed by external forces, but of great interest are amphiphilic systems, where they form spontaneously. Here the question arises of whether this means that they are also thermodynamically stable structures, which at least in some systems appears to be the case. If such vesicles are well defined in size, it is possible to pack them densely and thereby form vesicle gels that possess highly elastic properties even for relatively low volume fractions of amphiphile. Conditions for the formation and the microstructure of such vesicle gels have been studied in some detail for the case of unilamellar vesicles. Another important and ...
Dynamic response of nonuniform structures to classes of pressure fields
Cottis, M. G.
1971-01-01
A semi-analytical method is developed for the calculation of the response of nonuniform structures to deterministic and random excitation. The method is based on parametric representations of the impulse response and input functions. With these representations, a class of structures of specified geometry and a class of pressure fields of practical concern can be considered simultaneously in a single analytical calculation of structural response. In engineering applications, the parameters in the impulse response function can be fixed once the numerical solution of the associated eigenvalue problem is available; the input function parameters can be specified given a particular input function or pressure field data. This methodology is applied to nonuniform beams and circular cylindrical shells for which parametric response solutions are derived. The computerized version of these solutions is also presented.
Deco, Gustavo; Ponce-Alvarez, Adrián; Mantini, Dante; Romani, Gian Luca; Hagmann, Patric; Corbetta, Maurizio
2013-07-03
Brain fluctuations at rest are not random but are structured in spatial patterns of correlated activity across different brain areas. The question of how resting-state functional connectivity (FC) emerges from the brain's anatomical connections has motivated several experimental and computational studies to understand structure-function relationships. However, the mechanistic origin of resting state is obscured by large-scale models' complexity, and a close structure-function relation is still an open problem. Thus, a realistic but simple enough description of relevant brain dynamics is needed. Here, we derived a dynamic mean field model that consistently summarizes the realistic dynamics of a detailed spiking and conductance-based synaptic large-scale network, in which connectivity is constrained by diffusion imaging data from human subjects. The dynamic mean field approximates the ensemble dynamics, whose temporal evolution is dominated by the longest time scale of the system. With this reduction, we demonstrated that FC emerges as structured linear fluctuations around a stable low firing activity state close to destabilization. Moreover, the model can be further and crucially simplified into a set of motion equations for statistical moments, providing a direct analytical link between anatomical structure, neural network dynamics, and FC. Our study suggests that FC arises from noise propagation and dynamical slowing down of fluctuations in an anatomically constrained dynamical system. Altogether, the reduction from spiking models to statistical moments presented here provides a new framework to explicitly understand the building up of FC through neuronal dynamics underpinned by anatomical connections and to drive hypotheses in task-evoked studies and for clinical applications.
Sadykova, S P; Tkachenko, I M
2010-01-01
The $e-e$, $e-i$, $i-i$ and charge-charge static structure factors are calculated for alkali and Be$^{2+}$ plasmas using the method described by Gregori et al. in \\cite{bibGreg2006}. The dynamic structure factors for alkali plasmas are calculated using the method of moments \\cite{bibAdam83}, \\cite{bibAdam93}. In both methods the screened Hellmann-Gurskii-Krasko potential, obtained on the basis of Bogolyubov's method, has been used taking into account not only the quantum-mechanical effects but also the ion structure \\cite{bib73}. PACS: 52.27.Aj (Alkali and alkaline earth plasmas, Static and dynamic structure factors), 52.25.Kn (Thermodynamics of plasmas), 52.38.Ph (X-ray scattering)
Orellana, Liliana; Rotnitzky, Andrea; Robins, James M
2010-01-01
Dynamic treatment regimes are set rules for sequential decision making based on patient covariate history. Observational studies are well suited for the investigation of the effects of dynamic treatment regimes because of the variability in treatment decisions found in them. This variability exists because different physicians make different decisions in the face of similar patient histories. In this article we describe an approach to estimate the optimal dynamic treatment regime among a set of enforceable regimes. This set is comprised by regimes defined by simple rules based on a subset of past information. The regimes in the set are indexed by a Euclidean vector. The optimal regime is the one that maximizes the expected counterfactual utility over all regimes in the set. We discuss assumptions under which it is possible to identify the optimal regime from observational longitudinal data. Murphy et al. (2001) developed efficient augmented inverse probability weighted estimators of the expected utility of one fixed regime. Our methods are based on an extension of the marginal structural mean model of Robins (1998, 1999) which incorporate the estimation ideas of Murphy et al. (2001). Our models, which we call dynamic regime marginal structural mean models, are specially suitable for estimating the optimal treatment regime in a moderately small class of enforceable regimes of interest. We consider both parametric and semiparametric dynamic regime marginal structural models. We discuss locally efficient, double-robust estimation of the model parameters and of the index of the optimal treatment regime in the set. In a companion paper in this issue of the journal we provide proofs of the main results.
Cheng, I-Chung; Chen, Ya-Jyun; Ku, Chia-Wei; Huang, Yu-Wen; Yang, Chia-Ning
2015-10-26
Keap1 is an adaptor protein that regulates Nrf2 in response to oxidative stress. Under basal conditions, Nrf2 is negatively regulated through ubiquitination by Keap1. However, upon exposure to oxidative stress, the ubiquitination of Nrf2 is inhibited, resulting in an increased steady-state level of Nrf2 in the nucleus and increased transcription of cytoprotective genes. A gene variant G364C and somatic mutation G430C on Keap1 have recently been reported to substantially impair the Keap1-Nrf2 interaction and to be associated with lung cancer. By contrast, alanine scanning experiments have shown that the mutations S363A, S508A, S555A, and S602A do not affect the ability of Keap1 to bind to Nrf2, regardless of the fact that G364 and G430 are not in contact with Nrf2 whereas the four serine residues are involved in the accommodation of Nrf2 with their hydroxy groups. In this study, molecular dynamics simulations were performed to investigate the structural and dynamic variances among wild-type (WT) Keap1 and the six mutants in unbound form. Principal component analysis of the collected MD trajectories was performed to provide dynamic diversity. Our dynamic and structural observations suggest that the G364C and G430C mutants possess a mobile D385 that moves toward R380, an anchor residue to accommodate an acidic residue in Nrf2, thereby hampering the Keap1-Nrf2 recognition of an electrostatic nature. By contrast, none of the four serine-to-alanine mutants alters the H-bond network formed by the serine backbone to its partner; accordingly, these mutants are almost as intact as the WT structurally and dynamically.
STRUCTURE AND DYNAMICS OF THE GLOBULAR CLUSTER PALOMAR 13
Energy Technology Data Exchange (ETDEWEB)
Bradford, J. D. [Department of Physics, Central Connecticut State University, 1615 Stanley Street, New Britain, CT 06050 (United States); Geha, M.; Munoz, R. R.; Santana, F. A. [Astronomy Department, Yale University, New Haven, CT 06520 (United States); Simon, J. D. [The Observatories of the Carnegie Institution of Washington, 813 Santa Barbara Street, Pasadena, CA 91101 (United States); Cote, P.; Stetson, P. B. [National Research Council of Canada, Herzberg Institute of Astrophysics, 5071 West Saanich Road, Victoria, BC V9E 2E7 (Canada); Kirby, E.; Djorgovski, S. G., E-mail: jeremydbradford@gmail.com, E-mail: marla.geha@yale.edu [California Institute of Technology, Department of Astronomy, MS 249-17, Pasadena, CA 91106 (United States)
2011-12-20
We present Keck/DEIMOS spectroscopy and Canada-France-Hawaii Telescope/MegaCam photometry for the Milky Way globular cluster Palomar 13. We triple the number of spectroscopically confirmed members, including many repeat velocity measurements. Palomar 13 is the only known globular cluster with possible evidence for dark matter, based on a Keck/High Resolution Echelle Spectrometer 21 star velocity dispersion of {sigma} = 2.2 {+-} 0.4 km s{sup -1}. We reproduce this measurement, but demonstrate that it is inflated by unresolved binary stars. For our sample of 61 stars, the velocity dispersion is {sigma} = 0.7{sup +0.6}{sub -0.5} km s{sup -1}. Combining our DEIMOS data with literature values, our final velocity dispersion is {sigma} = 0.4{sup +0.4}{sub -0.3} km s{sup -1}. We determine a spectroscopic metallicity of [Fe/H] = -1.6 {+-} 0.1 dex, placing a 1{sigma} upper limit of {sigma}{sub [Fe/H]} {approx} 0.2 dex on any internal metallicity spread. We determine Palomar 13's total luminosity to be M{sub V} = -2.8 {+-} 0.4, making it among the least luminous known globular clusters. The photometric isophotes are regular out to the half-light radius and mildly irregular outside this radius. The outer surface brightness profile slope is shallower than typical globular clusters ({Sigma}{proportional_to}r{sup {eta}}, {eta} = -2.8 {+-} 0.3). Thus at large radius, tidal debris is likely affecting the appearance of Palomar 13. Combining our luminosity with the intrinsic velocity dispersion, we find a dynamical mass of M{sub 1/2} = 1.3{sup +2:7}{sub -1.3} Multiplication-Sign 10{sup 3} M{sub Sun} and a mass-to-light ratio of M/L{sub V} = 2.4{sup +5.0}{sub -2.4} M{sub Sun }/L{sub Sun }. Within our measurement errors, the mass-to-light ratio agrees with the theoretical predictions for a single stellar population. We conclude that, while there is some evidence for tidal stripping at large radius, the dynamical mass of Palomar 13 is consistent with its stellar mass and neither
Structural transformation in Africa : Static gains, dynamic losses
Vries, Gaaitzen J. de; Timmer, Marcel P.; Vries, Klaas de
2013-01-01
This paper studies structural transformation in Africa and its implications for productivity growth during the past fifty years, extending the work by McMillan and Rodrik (2011). We present the Africa Sector Database including time series of value added and employment by sector for eleven
Structure and dynamics of demersal fish assemblages over three ...
African Journals Online (AJOL)
In this study, we analysed data from scientific trawl surveys carried out on the continental shelf off Guinea between 1985 and 2012. We performed factorial analyses and calculated biodiversity indices to characterise the changes in the structure and composition of fish communities that occurred over the 28-year period in this ...
Assessment of dynamic analyses for deploying space truss structures
Weidman, D.; Housner, J.
1984-01-01
A selected list of references on the analysis of the deployment concepts for large space truss structures are reviewed. The stability of the deployment process is discussed, and stable methods of deployment mentioned. Analytical and experimental needs to assess feasibility and performance of proposed deployment concepts are outlined.
Dynamic fracture modeling in shell structures based on XFEM
Larsson, R.; Mediavilla, J.; Fagerström, M.
2011-01-01
Through-the-thickness crack propagation in thin-walled structures is dealt with in this paper. The formulation is based on the cohesive zone concept applied to a kinematically consistent shell model enhanced with an XFEM-based discontinuous kinematical representation. The resulting formulation
Zooplankton community structure and dynamics during the transition ...
African Journals Online (AJOL)
Canonical Correspondence Analysis was used to determine correlation between the physicochemical parameters and the zooplankton species abundance. The transition from ... Zooplankton community structure showed that species diversity and abundance decreased during the transition from 24 in March to 16 in June.
Robust time-optimal control of uncertain structural dynamic systems
Wie, Bong; Sinha, Ravi; Liu, Qiang
1993-01-01
A time-optimal open-loop control problem of flexible spacecraft in the presence of modeling uncertainty has been investigated. The results indicate that the proposed approach significantly reduces the residual structural vibrations caused by modeling uncertainty. The results also indicate the importance of proper jet placement for practical tradeoffs among the maneuvering time, fuel consumption, and performance robustness.
Information Propagation in Complex Networks : Structures and Dynamics
Märtens, M.
2018-01-01
This thesis is a contribution to a deeper understanding of how information propagates and what this process entails. At its very core is the concept of the network: a collection of nodes and links, which describes the structure of the systems under investigation. The network is a mathematical model
Dynamic response analysis of a 24-story damped steel structure
Feng, Demin; Miyama, Takafumi
2017-10-01
In Japanese and Chinese building codes, a two-stage design philosophy, damage limitation (small earthquake, Level 1) and life safety (extreme large earthquake, Level 2), is adopted. It is very interesting to compare the design method of a damped structure based on the two building codes. In the Chinese code, in order to be consistent with the conventional seismic design method, the damped structure is also designed at the small earthquake level. The effect of damper systems is considered by the additional damping ratio concept. The design force will be obtained from the damped design spectrum considering the reduction due to the additional damping ratio. The additional damping ratio by the damper system is usually calculated by a time history analysis method at the small earthquake level. The velocity dependent type dampers such as viscous dampers can function well even in the small earthquake level. But, if steel damper is used, which usually remains elastic in the small earthquake, there will be no additional damping ratio achieved. On the other hand, a time history analysis is used in Japan both for small earthquake and extreme large earthquake level. The characteristics of damper system and ductility of the structure can be modelled well. An existing 24-story steel frame is modified to demonstrate the design process of the damped structure based on the two building codes. Viscous wall type damper and low yield steel panel dampers are studied as the damper system.
The dynamics of age structures on Agropyron michnoi and Leymus ...
African Journals Online (AJOL)
In this study, the method of unit sampling was adopted for two years to investigate and analyze the age structure of clonal tillers and seedlings of Agropyron michnoi and Leymus chinensis in the secondary succession process of Hulunbeier sandy vegetation in north China. The results indicate that in single and mixed ...
Dynamics of bacterial community structure in a fullscale wastewater ...
African Journals Online (AJOL)
The 16S rDNA sequence analysis indicated that the. DGGE bands of dominant bacterial from this plant harbored sequences of possible nitrogen remover with potential aerobic denitrification / heterotrophic nitrification. Key words: Community structure, PCR-DGGE, 16S ribosomal DNA, wastewater treatment plant (WWTP); ...
Monte Carlo filters for identification of nonlinear structural dynamical ...
Indian Academy of Sciences (India)
relevance in structural engineering has not yet been explored in the existing literature. Accord- ingly, in the present work, we apply three simulation-based filtering strategies to the problem of system parameter identification in two typical nonlinear oscillators, namely, the Duffing oscillator and the Coulomb oscillator.
DEFF Research Database (Denmark)
Koivuniemi, A.; Vattulainen, I.
2012-01-01
The structure and function of high density lipoprotein (HDL) particles have intrigued the scientific community for decades because of their crucial preventive role in coronary heart disease. However, it has been a taunting task to reveal the precise molecular structure and dynamics of HDL. Further...