Structural stability of nonlinear population dynamics

NASA Astrophysics Data System (ADS)

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.

Structural Stability of Mathematical Models of National Economy

NASA Astrophysics Data System (ADS)

Ashimov, Abdykappar A.; Sultanov, Bahyt T.; Borovskiy, Yuriy V.; Adilov, Zheksenbek M.; Ashimov, Askar A.

2011-12-01

In the paper we test robustness of particular dynamic systems in a compact regions of a plane and a weak structural stability of one dynamic system of high order in a compact region of its phase space. The test was carried out based on the fundamental theory of dynamical systems on a plane and based on the conditions for weak structural stability of high order dynamic systems. A numerical algorithm for testing the weak structural stability of high order dynamic systems has been proposed. Based on this algorithm we assess the weak structural stability of one computable general equilibrium model.

Disconnecting structure and dynamics in glassy thin films

PubMed Central

Sussman, Daniel M.; Cubuk, Ekin D.; Liu, Andrea J.

2017-01-01

Nanometrically thin glassy films depart strikingly from the behavior of their bulk counterparts. We investigate whether the dynamical differences between a bulk and thin film polymeric glass former can be understood by differences in local microscopic structure. Machine learning methods have shown that local structure can serve as the foundation for successful, predictive models of particle rearrangement dynamics in bulk systems. By contrast, in thin glassy films, we find that particles at the center of the film and those near the surface are structurally indistinguishable despite exhibiting very different dynamics. Next, we show that structure-independent processes, already present in bulk systems and demonstrably different from simple facilitated dynamics, are crucial for understanding glassy dynamics in thin films. Our analysis suggests a picture of glassy dynamics in which two dynamical processes coexist, with relative strengths that depend on the distance from an interface. One of these processes depends on local structure and is unchanged throughout most of the film, while the other is purely Arrhenius, does not depend on local structure, and is strongly enhanced near the free surface of a film. PMID:28928147

Lewis Structures Technology, 1988. Volume 2: Structural Mechanics

NASA Technical Reports Server (NTRS)

1988-01-01

Lewis Structures Div. performs and disseminates results of research conducted in support of aerospace engine structures. These results have a wide range of applicability to practitioners of structural engineering mechanics beyond the aerospace arena. The engineering community was familiarized with the depth and range of research performed by the division and its academic and industrial partners. Sessions covered vibration control, fracture mechanics, ceramic component reliability, parallel computing, nondestructive evaluation, constitutive models and experimental capabilities, dynamic systems, fatigue and damage, wind turbines, hot section technology (HOST), aeroelasticity, structural mechanics codes, computational methods for dynamics, structural optimization, and applications of structural dynamics, and structural mechanics computer codes.

Structure and Dynamics of Hydroxyl-Functionalized Protic Ammonium Carboxylate Ionic Liquids.

PubMed

Thummuru, Dhileep Nagi Reddy; Mallik, Bhabani S

2017-10-26

We performed classical molecular dynamics simulations to investigate the structure and dynamics of protic ionic liquids, 2-hydroxy ethylammonium acetate, ethylammonium hydroxyacetate, and 2-hydroxyethylammonium hydroxyacetate at ambient conditions. Structural properties such as density, radial distribution functions, spatial distribution functions, and structure factors have been calculated. Dynamic properties such as mean square displacements, as well as residence and hydrogen bond dynamics have also been calculated. Hydrogen bond lifetimes and residence times change with the addition of hydroxyl groups. We observe that when a hydroxyl group is present on the cation, dynamics become very slow and it forms a strong hydrogen bond with carboxylate oxygen atoms of the anion. The hydroxyl functionalized ILs show more dynamic diversity than structurally similar ILs.

Structural failure; International Symposium on Structural Crashworthiness, 2nd, Massachusetts Institute of Technology, Cambridge, June 6-8, 1988, Invited Lectures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wierzbicki, T.; Jones, N.

1989-01-01

The book discusses the fragmentation of solids under dynamic loading, the debris-impact protection of space structures, the controlled fracturing of structures by shock-wave interaction and focusing, the tearing of thin metal sheets, and the dynamic inelastic failure of beams, and dynamic rupture of shells. Consideration is also given to investigations of the failure of brittle and composite materials by numerical methods, the energy absorption of polymer matrix composite structures (frictional effects), the mechanics of deep plastic collapse of thin-walled structures, the denting and bending of tubular beams under local loads, the dynamic bending collapse of strain-softening cantilever beams, and themore » failure of bar structures under repeated loading. Other topics discussed are on the behavior of composite and metallic superstructures under blast loading, the catastrophic failure modes of marine structures, and industrial experience with structural failure.« less

Development of an Aeroelastic Modeling Capability for Transient Nozzle Side Load Analysis

NASA Technical Reports Server (NTRS)

Wang, Ten-See; Zhao, Xiang; Zhang, Sijun; Chen, Yen-Sen

2013-01-01

Lateral nozzle forces are known to cause severe structural damage to any new rocket engine in development during test. While three-dimensional, transient, turbulent, chemically reacting computational fluid dynamics methodology has been demonstrated to capture major side load physics with rigid nozzles, hot-fire tests often show nozzle structure deformation during major side load events, leading to structural damages if structural strengthening measures were not taken. The modeling picture is incomplete without the capability to address the two-way responses between the structure and fluid. The objective of this study is to develop a coupled aeroelastic modeling capability by implementing the necessary structural dynamics component into an anchored computational fluid dynamics methodology. The computational fluid dynamics component is based on an unstructured-grid, pressure-based computational fluid dynamics formulation, while the computational structural dynamics component is developed in the framework of modal analysis. Transient aeroelastic nozzle startup analyses of the Block I Space Shuttle Main Engine at sea level were performed. The computed results from the aeroelastic nozzle modeling are presented.

Lewis Structures Technology, 1988. Volume 3: Structural Integrity Fatigue and Fracture Wind Turbines HOST

NASA Technical Reports Server (NTRS)

1988-01-01

The charter of the Structures Division is to perform and disseminate results of research conducted in support of aerospace engine structures. These results have a wide range of applicability to practioners of structural engineering mechanics beyond the aerospace arena. The specific purpose of the symposium was to familiarize the engineering structures community with the depth and range of research performed by the division and its academic and industrial partners. Sessions covered vibration control, fracture mechanics, ceramic component reliability, parallel computing, nondestructive evaluation, constitutive models and experimental capabilities, dynamic systems, fatigue and damage, wind turbines, hot section technology (HOST), aeroelasticity, structural mechanics codes, computational methods for dynamics, structural optimization, and applications of structural dynamics, and structural mechanics computer codes.

Multiscale regression modeling in mouse supraspinatus tendons reveals that dynamic processes act as mediators in structure-function relationships.

PubMed

Connizzo, Brianne K; Adams, Sheila M; Adams, Thomas H; Jawad, Abbas F; Birk, David E; Soslowsky, Louis J

2016-06-14

Recent advances in technology have allowed for the measurement of dynamic processes (re-alignment, crimp, deformation, sliding), but only a limited number of studies have investigated their relationship with mechanical properties. The overall objective of this study was to investigate the role of composition, structure, and the dynamic response to load in predicting tendon mechanical properties in a multi-level fashion mimicking native hierarchical collagen structure. Multiple linear regression models were investigated to determine the relationships between composition/structure, dynamic processes, and mechanical properties. Mediation was then used to determine if dynamic processes mediated structure-function relationships. Dynamic processes were strong predictors of mechanical properties. These predictions were location-dependent, with the insertion site utilizing all four dynamic responses and the midsubstance responding primarily with fibril deformation and sliding. In addition, dynamic processes were moderately predicted by composition and structure in a regionally-dependent manner. Finally, dynamic processes were partial mediators of the relationship between composition/structure and mechanical function, and results suggested that mediation is likely shared between multiple dynamic processes. In conclusion, the mechanical properties at the midsubstance of the tendon are controlled primarily by fibril structure and this region responds to load via fibril deformation and sliding. Conversely, the mechanical function at the insertion site is controlled by many other important parameters and the region responds to load via all four dynamic mechanisms. Overall, this study presents a strong foundation on which to design future experimental and modeling efforts in order to fully understand the complex structure-function relationships present in tendon. Copyright © 2016 Elsevier Ltd. All rights reserved.

PDEMOD: Software for control/structures optimization

NASA Technical Reports Server (NTRS)

Taylor, Lawrence W., Jr.; Zimmerman, David

1991-01-01

Because of the possibility of adverse interaction between the control system and the structural dynamics of large, flexible spacecraft, great care must be taken to ensure stability and system performance. Because of the high cost of insertion of mass into low earth orbit, it is prudent to optimize the roles of structure and control systems simultaneously. Because of the difficulty and the computational burden in modeling and analyzing the control structure system dynamics, the total problem is often split and treated iteratively. It would aid design if the control structure system dynamics could be represented in a single system of equations. With the use of the software PDEMOD (Partial Differential Equation Model), it is now possible to optimize structure and control systems simultaneously. The distributed parameter modeling approach enables embedding the control system dynamics into the same equations for the structural dynamics model. By doing this, the current difficulties involved in model order reduction are avoided. The NASA Mini-MAST truss is used an an example for studying integrated control structure design.

Research in structures, structural dynamics and materials, 1989

NASA Technical Reports Server (NTRS)

Hunter, William F. (Compiler); Noor, Ahmed K. (Compiler)

1989-01-01

Topics addressed include: composite plates; buckling predictions; missile launch tube modeling; structural/control systems design; optimization of nonlinear R/C frames; error analysis for semi-analytic displacement; crack acoustic emission; and structural dynamics.

Nouvelles techniques pratiques pour la modelisation du comportement dynamique des systèmes eau-structure

NASA Astrophysics Data System (ADS)

Miquel, Benjamin

The dynamic or seismic behavior of hydraulic structures is, as for conventional structures, essential to assure protection of human lives. These types of analyses also aim at limiting structural damage caused by an earthquake to prevent rupture or collapse of the structure. The particularity of these hydraulic structures is that not only the internal displacements are caused by the earthquake, but also by the hydrodynamic loads resulting from fluid-structure interaction. This thesis reviews the existing complex and simplified methods to perform such dynamic analysis for hydraulic structures. For the complex existing methods, attention is placed on the difficulties arising from their use. Particularly, interest is given in this work on the use of transmitting boundary conditions to simulate the semi infinity of reservoirs. A procedure has been developed to estimate the error that these boundary conditions can introduce in finite element dynamic analysis. Depending on their formulation and location, we showed that they can considerably affect the response of such fluid-structure systems. For practical engineering applications, simplified procedures are still needed to evaluate the dynamic behavior of structures in contact with water. A review of the existing simplified procedures showed that these methods are based on numerous simplifications that can affect the prediction of the dynamic behavior of such systems. One of the main objectives of this thesis has been to develop new simplified methods that are more accurate than those existing. First, a new spectral analysis method has been proposed. Expressions for the fundamental frequency of fluid-structure systems, key parameter of spectral analysis, have been developed. We show that this new technique can easily be implemented in a spreadsheet or program, and that its calculation time is near instantaneous. When compared to more complex analytical or numerical method, this new procedure yields excellent prediction of the dynamic behavior of fluid-structure systems. Spectral analyses ignore the transient and oscillatory nature of vibrations. When such dynamic analyses show that some areas of the studied structure undergo excessive stresses, time history analyses allow a better estimate of the extent of these zones as well as a time notion of these excessive stresses. Furthermore, the existing spectral analyses methods for fluid-structure systems account only for the static effect of higher modes. Thought this can generally be sufficient for dams, for flexible structures the dynamic effect of these modes should be accounted for. New methods have been developed for fluid-structure systems to account for these observations as well as the flexibility of foundations. A first method was developed to study structures in contact with one or two finite or infinite water domains. This new technique includes flexibility of structures and foundations as well as the dynamic effect of higher vibration modes and variations of the levels of the water domains. Extension of this method was performed to study beam structures in contact with fluids. These new developments have also allowed extending existing analytical formulations of the dynamic properties of a dry beam to a new formulation that includes effect of fluid-structure interaction. The method yields a very good estimate of the dynamic behavior of beam-fluid systems or beam like structures in contact with fluid. Finally, a Modified Accelerogram Method (MAM) has been developed to modify the design earthquake into a new accelerogram that directly accounts for the effect of fluid-structure interaction. This new accelerogram can therefore be applied directly to the dry structure (i.e. without water) in order to calculate the dynamic response of the fluid-structure system. This original technique can include numerous parameters that influence the dynamic response of such systems and allows to treat analytically the fluid-structure interaction while keeping the advantages of finite element modeling.

An Unstructured Finite Volume Approach for Structural Dynamics in Response to Fluid Motions.

PubMed

Xia, Guohua; Lin, Ching-Long

2008-04-01

A new cell-vortex unstructured finite volume method for structural dynamics is assessed for simulations of structural dynamics in response to fluid motions. A robust implicit dual-time stepping method is employed to obtain time accurate solutions. The resulting system of algebraic equations is matrix-free and allows solid elements to include structure thickness, inertia, and structural stresses for accurate predictions of structural responses and stress distributions. The method is coupled with a fluid dynamics solver for fluid-structure interaction, providing a viable alternative to the finite element method for structural dynamics calculations. A mesh sensitivity test indicates that the finite volume method is at least of second-order accuracy. The method is validated by the problem of vortex-induced vibration of an elastic plate with different initial conditions and material properties. The results are in good agreement with existing numerical data and analytical solutions. The method is then applied to simulate a channel flow with an elastic wall. The effects of wall inertia and structural stresses on the fluid flow are investigated.

Modelling and enhanced molecular dynamics to steer structure-based drug discovery.

PubMed

Kalyaanamoorthy, Subha; Chen, Yi-Ping Phoebe

2014-05-01

The ever-increasing gap between the availabilities of the genome sequences and the crystal structures of proteins remains one of the significant challenges to the modern drug discovery efforts. The knowledge of structure-dynamics-functionalities of proteins is important in order to understand several key aspects of structure-based drug discovery, such as drug-protein interactions, drug binding and unbinding mechanisms and protein-protein interactions. This review presents a brief overview on the different state of the art computational approaches that are applied for protein structure modelling and molecular dynamics simulations of biological systems. We give an essence of how different enhanced sampling molecular dynamics approaches, together with regular molecular dynamics methods, assist in steering the structure based drug discovery processes. Copyright © 2013 Elsevier Ltd. All rights reserved.

Structural dynamics verification facility study

NASA Technical Reports Server (NTRS)

Kiraly, L. J.; Hirchbein, M. S.; Mcaleese, J. M.; Fleming, D. P.

1981-01-01

The need for a structural dynamics verification facility to support structures programs was studied. Most of the industry operated facilities are used for highly focused research, component development, and problem solving, and are not used for the generic understanding of the coupled dynamic response of major engine subsystems. Capabilities for the proposed facility include: the ability to both excite and measure coupled structural dynamic response of elastic blades on elastic shafting, the mechanical simulation of various dynamical loadings representative of those seen in operating engines, and the measurement of engine dynamic deflections and interface forces caused by alternative engine mounting configurations and compliances.

Fracture of Structural Materials under Dynamic Loading

DTIC Science & Technology

1981-03-25

in character- izing the dynamic fracture resistance of materials, and in designing equipment and procedures for measuring dynamic fracture toughness...useful in assessing the safety of structures under dynamic loads, in characterizing the dyraamic fracture resistance of materials, and in designing ...I INTRODUCTION Structures used by the United States Air Force must be designed to resist catastrophic fracture when subjected ti dynamic loads. For

NASA Workshop on Computational Structural Mechanics 1987, part 3

NASA Technical Reports Server (NTRS)

Sykes, Nancy P. (Editor)

1989-01-01

Computational Structural Mechanics (CSM) topics are explored. Algorithms and software for nonlinear structural dynamics, concurrent algorithms for transient finite element analysis, computational methods and software systems for dynamics and control of large space structures, and the use of multi-grid for structural analysis are discussed.

Integrating protein structural dynamics and evolutionary analysis with Bio3D.

PubMed

Skjærven, Lars; Yao, Xin-Qiu; Scarabelli, Guido; Grant, Barry J

2014-12-10

Popular bioinformatics approaches for studying protein functional dynamics include comparisons of crystallographic structures, molecular dynamics simulations and normal mode analysis. However, determining how observed displacements and predicted motions from these traditionally separate analyses relate to each other, as well as to the evolution of sequence, structure and function within large protein families, remains a considerable challenge. This is in part due to the general lack of tools that integrate information of molecular structure, dynamics and evolution. Here, we describe the integration of new methodologies for evolutionary sequence, structure and simulation analysis into the Bio3D package. This major update includes unique high-throughput normal mode analysis for examining and contrasting the dynamics of related proteins with non-identical sequences and structures, as well as new methods for quantifying dynamical couplings and their residue-wise dissection from correlation network analysis. These new methodologies are integrated with major biomolecular databases as well as established methods for evolutionary sequence and comparative structural analysis. New functionality for directly comparing results derived from normal modes, molecular dynamics and principal component analysis of heterogeneous experimental structure distributions is also included. We demonstrate these integrated capabilities with example applications to dihydrofolate reductase and heterotrimeric G-protein families along with a discussion of the mechanistic insight provided in each case. The integration of structural dynamics and evolutionary analysis in Bio3D enables researchers to go beyond a prediction of single protein dynamics to investigate dynamical features across large protein families. The Bio3D package is distributed with full source code and extensive documentation as a platform independent R package under a GPL2 license from http://thegrantlab.org/bio3d/ .

Relations between structural and dynamic thermal characteristics of building walls

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kossecka, E.; Kosny, J.

1996-10-01

The effect of internal thermal structure on dynamic characteristics of walls is analyzed. The concept of structure factors is introduced and the conditions they impose on response factors are given. Simple examples of multilayer walls, representing different types of thermal resistance and capacity distribution, are analyzed to illustrate general relations between structure factors and response factors. The idea of the ``thermally equivalent wall``, a plane multilayer structure, with dynamic characteristics similar to those of a complex structure, in which three-dimensional heat flow occurs, is presented.

Recent developments in structural proteomics for protein structure determination.

PubMed

Liu, Hsuan-Liang; Hsu, Jyh-Ping

2005-05-01

The major challenges in structural proteomics include identifying all the proteins on the genome-wide scale, determining their structure-function relationships, and outlining the precise three-dimensional structures of the proteins. Protein structures are typically determined by experimental approaches such as X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. However, the knowledge of three-dimensional space by these techniques is still limited. Thus, computational methods such as comparative and de novo approaches and molecular dynamic simulations are intensively used as alternative tools to predict the three-dimensional structures and dynamic behavior of proteins. This review summarizes recent developments in structural proteomics for protein structure determination; including instrumental methods such as X-ray crystallography and NMR spectroscopy, and computational methods such as comparative and de novo structure prediction and molecular dynamics simulations.

Structural Dynamic Behavior of Wind Turbines

NASA Technical Reports Server (NTRS)

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).

Cognitive Flexibility through Metastable Neural Dynamics Is Disrupted by Damage to the Structural Connectome.

PubMed

Hellyer, Peter J; Scott, Gregory; Shanahan, Murray; Sharp, David J; Leech, Robert

2015-06-17

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. Copyright © 2015 the authors 0270-6474/15/359050-14$15.00/0.

Accurate Structural Correlations from Maximum Likelihood Superpositions

PubMed Central

Theobald, Douglas L; Wuttke, Deborah S

2008-01-01

The cores of globular proteins are densely packed, resulting in complicated networks of structural interactions. These interactions in turn give rise to dynamic structural correlations over a wide range of time scales. Accurate analysis of these complex correlations is crucial for understanding biomolecular mechanisms and for relating structure to function. Here we report a highly accurate technique for inferring the major modes of structural correlation in macromolecules using likelihood-based statistical analysis of sets of structures. This method is generally applicable to any ensemble of related molecules, including families of nuclear magnetic resonance (NMR) models, different crystal forms of a protein, and structural alignments of homologous proteins, as well as molecular dynamics trajectories. Dominant modes of structural correlation are determined using principal components analysis (PCA) of the maximum likelihood estimate of the correlation matrix. The correlations we identify are inherently independent of the statistical uncertainty and dynamic heterogeneity associated with the structural coordinates. We additionally present an easily interpretable method (“PCA plots”) for displaying these positional correlations by color-coding them onto a macromolecular structure. Maximum likelihood PCA of structural superpositions, and the structural PCA plots that illustrate the results, will facilitate the accurate determination of dynamic structural correlations analyzed in diverse fields of structural biology. PMID:18282091

Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation.

PubMed

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.

CEAS/AIAA/ICASE/NASA Langley International Forum on Aeroelasticity and Structural Dynamics 1999. Pt. 1

NASA Technical Reports Server (NTRS)

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.

Linking models and data on vegetation structure

NASA Astrophysics Data System (ADS)

Hurtt, G. C.; Fisk, J.; Thomas, R. Q.; Dubayah, R.; Moorcroft, P. R.; Shugart, H. H.

2010-06-01

For more than a century, scientists have recognized the importance of vegetation structure in understanding forest dynamics. Now future satellite missions such as Deformation, Ecosystem Structure, and Dynamics of Ice (DESDynI) hold the potential to provide unprecedented global data on vegetation structure needed to reduce uncertainties in terrestrial carbon dynamics. Here, we briefly review the uses of data on vegetation structure in ecosystem models, develop and analyze theoretical models to quantify model-data requirements, and describe recent progress using a mechanistic modeling approach utilizing a formal scaling method and data on vegetation structure to improve model predictions. Generally, both limited sampling and coarse resolution averaging lead to model initialization error, which in turn is propagated in subsequent model prediction uncertainty and error. In cases with representative sampling, sufficient resolution, and linear dynamics, errors in initialization tend to compensate at larger spatial scales. However, with inadequate sampling, overly coarse resolution data or models, and nonlinear dynamics, errors in initialization lead to prediction error. A robust model-data framework will require both models and data on vegetation structure sufficient to resolve important environmental gradients and tree-level heterogeneity in forest structure globally.

Dynamic Structural Health Monitoring of slender structures using optical sensors.

PubMed

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.

Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement.

PubMed

Calhoun, Jennifer R; Liu, Weixia; Spiegel, Katrin; Dal Peraro, Matteo; Klein, Michael L; Valentine, Kathleen G; Wand, A Joshua; DeGrado, William F

2008-02-01

We report the solution NMR structure of a designed dimetal-binding protein, di-Zn(II) DFsc, along with a secondary refinement step employing molecular dynamics techniques. Calculation of the initial NMR structural ensemble by standard methods led to distortions in the metal-ligand geometries at the active site. Unrestrained molecular dynamics using a nonbonded force field for the metal shell, followed by quantum mechanical/molecular mechanical dynamics of DFsc, were used to relax local frustrations at the dimetal site that were apparent in the initial NMR structure and provide a more realistic description of the structure. The MD model is consistent with NMR restraints, and in good agreement with the structural and functional properties expected for DF proteins. This work demonstrates that NMR structures of metalloproteins can be further refined using classical and first-principles molecular dynamics methods in the presence of explicit solvent to provide otherwise unavailable insight into the geometry of the metal center.

Network structure shapes spontaneous functional connectivity dynamics.

PubMed

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

2015-04-08

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

Hamiltonian dynamics for complex food webs

NASA Astrophysics Data System (ADS)

Kozlov, Vladimir; Vakulenko, Sergey; Wennergren, Uno

2016-03-01

We investigate stability and dynamics of large ecological networks by introducing classical methods of dynamical system theory from physics, including Hamiltonian and averaging methods. Our analysis exploits the topological structure of the network, namely the existence of strongly connected nodes (hubs) in the networks. We reveal new relations between topology, interaction structure, and network dynamics. We describe mechanisms of catastrophic phenomena leading to sharp changes of dynamics and hence completely altering the ecosystem. We also show how these phenomena depend on the structure of interaction between species. We can conclude that a Hamiltonian structure of biological interactions leads to stability and large biodiversity.

Structural dynamics branch research and accomplishments

NASA Technical Reports Server (NTRS)

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.

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

PubMed Central

Moffatt, Ryan; Ma, Buyong; Nussinov, Ruth

2016-01-01

Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts. PMID:27124275

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.

PubMed

Maximova, Tatiana; Moffatt, Ryan; Ma, Buyong; Nussinov, Ruth; Shehu, Amarda

2016-04-01

Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts.

Structure and dynamics of complex liquid water: Molecular dynamics simulation

NASA Astrophysics Data System (ADS)

S, Indrajith V.; Natesan, Baskaran

2015-06-01

We have carried out detailed structure and dynamical studies of complex liquid water using molecular dynamics simulations. Three different model potentials, namely, TIP3P, TIP4P and SPC-E have been used in the simulations, in order to arrive at the best possible potential function that could reproduce the structure of experimental bulk water. All the simulations were performed in the NVE micro canonical ensemble using LAMMPS. The radial distribution functions, gOO, gOH and gHH and the self diffusion coefficient, Ds, were calculated for all three models. We conclude from our results that the structure and dynamical parameters obtained for SPC-E model matched well with the experimental values, suggesting that among the models studied here, the SPC-E model gives the best structure and dynamics of bulk water.

Combined electromechanical impedance and fiber optic diagnosis of aerospace structures

NASA Astrophysics Data System (ADS)

Schlavin, Jon; Zagrai, Andrei; Clemens, Rebecca; Black, Richard J.; Costa, Joey; Moslehi, Behzad; Patel, Ronak; Sotoudeh, Vahid; Faridian, Fereydoun

2014-03-01

Electromechanical impedance is a popular diagnostic method for assessing structural conditions at high frequencies. It has been utilized, and shown utility, in aeronautic, space, naval, civil, mechanical, and other types of structures. By contrast, fiber optic sensing initially found its niche in static strain measurement and low frequency structural dynamic testing. Any low frequency limitations of the fiber optic sensing, however, are mainly governed by its hardware elements. As hardware improves, so does the bandwidth (frequency range * number of sensors) provided by the appropriate enabling fiber optic sensor interrogation system. In this contribution we demonstrate simultaneous high frequency measurements using fiber optic and electromechanical impedance structural health monitoring technologies. A laboratory specimen imitating an aircraft wing structure, incorporating surfaces with adjustable boundary conditions, was instrumented with piezoelectric and fiber optic sensors. Experiments were conducted at different structural boundary conditions associated with deterioration of structural health. High frequency dynamic responses were collected at multiple locations on a laboratory wing specimen and conclusions were drawn about correspondence between structural damage and dynamic signatures as well as correlation between electromechanical impedance and fiber optic sensors spectra. Theoretical investigation of the effect of boundary conditions on electromechanical impedance spectra is presented and connection to low frequency structural dynamics is suggested. It is envisioned that acquisition of high frequency structural dynamic responses with multiple fiber optic sensors may open new diagnostic capabilities for fiber optic sensing technologies.

Minimal complexity control law synthesis

NASA Technical Reports Server (NTRS)

Bernstein, Dennis S.; Haddad, Wassim M.; Nett, Carl N.

1989-01-01

A paradigm for control law design for modern engineering systems is proposed: Minimize control law complexity subject to the achievement of a specified accuracy in the face of a specified level of uncertainty. Correspondingly, the overall goal is to make progress towards the development of a control law design methodology which supports this paradigm. Researchers achieve this goal by developing a general theory of optimal constrained-structure dynamic output feedback compensation, where here constrained-structure means that the dynamic-structure (e.g., dynamic order, pole locations, zero locations, etc.) of the output feedback compensation is constrained in some way. By applying this theory in an innovative fashion, where here the indicated iteration occurs over the choice of the compensator dynamic-structure, the paradigm stated above can, in principle, be realized. The optimal constrained-structure dynamic output feedback problem is formulated in general terms. An elegant method for reducing optimal constrained-structure dynamic output feedback problems to optimal static output feedback problems is then developed. This reduction procedure makes use of star products, linear fractional transformations, and linear fractional decompositions, and yields as a byproduct a complete characterization of the class of optimal constrained-structure dynamic output feedback problems which can be reduced to optimal static output feedback problems. Issues such as operational/physical constraints, operating-point variations, and processor throughput/memory limitations are considered, and it is shown how anti-windup/bumpless transfer, gain-scheduling, and digital processor implementation can be facilitated by constraining the controller dynamic-structure in an appropriate fashion.

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

PubMed Central

Yoo, Jejoong; Aksimentiev, Aleksei

2013-01-01

The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects. PMID:24277840

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

PubMed

Yoo, Jejoong; Aksimentiev, Aleksei

2013-12-10

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

Dynamic GSCA (Generalized Structured Component Analysis) with Applications to the Analysis of Effective Connectivity in Functional Neuroimaging Data

ERIC Educational Resources Information Center

Jung, Kwanghee; Takane, Yoshio; Hwang, Heungsun; Woodward, Todd S.

2012-01-01

We propose a new method of structural equation modeling (SEM) for longitudinal and time series data, named Dynamic GSCA (Generalized Structured Component Analysis). The proposed method extends the original GSCA by incorporating a multivariate autoregressive model to account for the dynamic nature of data taken over time. Dynamic GSCA also…

Instability-driven frequency decoupling between structure dynamics and wake fluctuations

NASA Astrophysics Data System (ADS)

Jin, Yaqing; Kim, Jin-Tae; Chamorro, Leonardo P.

2018-04-01

Flow-induced dynamics of flexible structures is, in general, significantly modulated by periodic vortex shedding. Experiments and numerical simulations suggest that the frequencies associated with the dominant motions of structures are highly coupled with those of the wake under low-turbulence uniform flow. Here we present experimental evidence that demonstrates a significant decoupling between the dynamics of simple structures and wake fluctuations for various geometries, Reynolds numbers, and mass ratios. High-resolution particle tracking velocimetry and hot-wire anemometry are used to quantitatively characterize the dynamics of the structures and wake fluctuations; a complementary planar particle image velocimetry measurement is conducted to illustrate distinctive flow patterns. Results show that for structures with directional stiffness, von Kármán vortex shedding might dominate the wake of bodies governed by natural-frequency motion. This phenomenon can be a consequence of Kelvin-Helmholtz instability, where the structural characteristics of the body dominate the oscillations.

Dynamic Structural Health Monitoring of Slender Structures Using Optical Sensors

PubMed Central

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

Advanced solid-state NMR techniques for characterization of membrane protein structure and dynamics: Application to Anabaena Sensory Rhodopsin

NASA Astrophysics Data System (ADS)

Ward, Meaghan E.; Brown, Leonid S.; Ladizhansky, Vladimir

2015-04-01

Studies of the structure, dynamics, and function of membrane proteins (MPs) have long been considered one of the main applications of solid-state NMR (SSNMR). Advances in instrumentation, and the plethora of new SSNMR methodologies developed over the past decade have resulted in a number of high-resolution structures and structural models of both bitopic and polytopic α-helical MPs. The necessity to retain lipids in the sample, the high proportion of one type of secondary structure, differential dynamics, and the possibility of local disorder in the loop regions all create challenges for structure determination. In this Perspective article we describe our recent efforts directed at determining the structure and functional dynamics of Anabaena Sensory Rhodopsin, a heptahelical transmembrane (7TM) protein. We review some of the established and emerging methods which can be utilized for SSNMR-based structure determination, with a particular focus on those used for ASR, a bacterial protein which shares its 7TM architecture with G-protein coupled receptors.

Structural Dynamics Branch research and accomplishments for FY 1990

NASA Technical Reports Server (NTRS)

1991-01-01

Presented here is a collection of FY 1990 research highlights from the Structural Dynamics Branch at the NASA Lewis Research Center. Highlights are from the branch's major work areas: aeroelasticity, vibration control, dynamic systems, and computational structural methods. A listing is given of FY 1990 branch publications.

Molecular dynamics simulations: advances and applications

PubMed Central

Hospital, Adam; Goñi, Josep Ramon; Orozco, Modesto; Gelpí, Josep L

2015-01-01

Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed. PMID:26604800

Dynamic Spectral Structure Specifies Vowels for Adults and Children

PubMed Central

Nittrouer, Susan; Lowenstein, Joanna H.

2014-01-01

The dynamic specification account of vowel recognition suggests that formant movement between vowel targets and consonant margins is used by listeners to recognize vowels. This study tested that account by measuring contributions to vowel recognition of dynamic (i.e., time-varying) spectral structure and coarticulatory effects on stationary structure. Adults and children (four-and seven-year-olds) were tested with three kinds of consonant-vowel-consonant syllables: (1) unprocessed; (2) sine waves that preserved both stationary coarticulated and dynamic spectral structure; and (3) vocoded signals that primarily preserved that stationary, but not dynamic structure. Sections of two lengths were removed from syllable middles: (1) half the vocalic portion; and (2) all but the first and last three pitch periods. Adults performed accurately with unprocessed and sine-wave signals, as long as half the syllable remained; their recognition was poorer for vocoded signals, but above chance. Seven-year-olds performed more poorly than adults with both sorts of processed signals, but disproportionately worse with vocoded than sine-wave signals. Most four-year-olds were unable to recognize vowels at all with vocoded signals. Conclusions were that both dynamic and stationary coarticulated structures support vowel recognition for adults, but children attend to dynamic spectral structure more strongly because early phonological organization favors whole words. PMID:25536845

Application of design sensitivity analysis for greater improvement on machine structural dynamics

NASA Technical Reports Server (NTRS)

Yoshimura, Masataka

1987-01-01

Methodologies are presented for greatly improving machine structural dynamics by using design sensitivity analyses and evaluative parameters. First, design sensitivity coefficients and evaluative parameters of structural dynamics are described. Next, the relations between the design sensitivity coefficients and the evaluative parameters are clarified. Then, design improvement procedures of structural dynamics are proposed for the following three cases: (1) addition of elastic structural members, (2) addition of mass elements, and (3) substantial charges of joint design variables. Cases (1) and (2) correspond to the changes of the initial framework or configuration, and (3) corresponds to the alteration of poor initial design variables. Finally, numerical examples are given for demonstrating the availability of the methods proposed.

Analysis of the structure and dynamics of human serum albumin.

PubMed

Guizado, T R Cuya

2014-10-01

Human serum albumin (HSA) is a biologically relevant protein that binds a variety of drugs and other small molecules. No less than 50 structures are deposited in the RCSB Protein Data Bank (PDB). Based on these structures, we first performed a clustering analysis. Despite the diversity of ligands, only two well defined conformations are detected, with a deviation of 0.46 nm between the average structures of the two clusters, while deviations within each cluster are smaller than 0.08 nm. Those two conformations are representative of the apoprotein and the HSA-myristate complex already identified in previous literature. Considering the structures within each cluster as a representative sample of the dynamical states of the corresponding conformation, we scrutinize the structural and dynamical differences between both conformations. Analysis of the fluctuations within each cluster set reveals that domain II is the most rigid one and better matches both structures. Then, taking this domain as reference, we show that the structural difference between both conformations can be expressed in terms of twist and hinge motions of domains I and III, respectively. We also characterize the dynamical difference between conformations by computing correlations and principal components for each set of dynamical states. The two conformations display different collective motions. The results are compared with those obtained from the trajectories of short molecular dynamics simulations, giving consistent outcomes. Let us remark that, beyond the relevance of the results for the structural and dynamical characterization of HAS conformations, the present methodology could be extended to other proteins in the PDB archive.

Model-Based Heterogeneous Data Fusion for Reliable Force Estimation in Dynamic Structures under Uncertainties

PubMed Central

Khodabandeloo, Babak; Melvin, Dyan; Jo, Hongki

2017-01-01

Direct measurements of external forces acting on a structure are infeasible in many cases. The Augmented Kalman Filter (AKF) has several attractive features that can be utilized to solve the inverse problem of identifying applied forces, as it requires the dynamic model and the measured responses of structure at only a few locations. But, the AKF intrinsically suffers from numerical instabilities when accelerations, which are the most common response measurements in structural dynamics, are the only measured responses. Although displacement measurements can be used to overcome the instability issue, the absolute displacement measurements are challenging and expensive for full-scale dynamic structures. In this paper, a reliable model-based data fusion approach to reconstruct dynamic forces applied to structures using heterogeneous structural measurements (i.e., strains and accelerations) in combination with AKF is investigated. The way of incorporating multi-sensor measurements in the AKF is formulated. Then the formulation is implemented and validated through numerical examples considering possible uncertainties in numerical modeling and sensor measurement. A planar truss example was chosen to clearly explain the formulation, while the method and formulation are applicable to other structures as well. PMID:29149088

Structural dynamics of lipid bilayers using ultrafast electron crystallography

NASA Astrophysics Data System (ADS)

Chen, Songye; Seidel, Marco; Zewail, Ahmed

2007-03-01

The structures and dynamics of bilayers of crystalline fatty acids and phospholipids were studied using ultrafast electron crystallography (UEC). The systems investigated are arachidic (eicosanoic) acid and dimyristoyl phosphatidic acid (DMPA), deposited on a substrate by the Langmuir-Blodgett technique. The atomic structures under different preparation conditions were determined. The structural dynamics following a temperature jump induced by femtosecond laser on the substrates were obtained and compared to the equilibrium temperature dependence.

Unlocking the Structure and Dynamics of Thin Polymeric Films

DTIC Science & Technology

2016-11-13

AFRL-AFOSR-JP-TR-2016-0092 Unlocking the Structure and Dynamics of Thin Polymeric Films Andrew Whittaker THE UNIVERSITY OF QUEENSLAND Final Report 11...Final 3. DATES COVERED (From - To)  15 Jun 2015 to 16 Jun 2016 4. TITLE AND SUBTITLE Unlocking the Structure and Dynamics of Thin Polymeric Films 5a...the interfacial structure that are inherent in thin films affects how polymers behave. A number of technically relevant polymeric systems were

Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation

PubMed Central

2017-01-01

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. PMID:29186132

Computational Methods for Structural Mechanics and Dynamics

NASA Technical Reports Server (NTRS)

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 End-to-End Loop Formation of the Penta-Peptide Cys-Ala-Gly-Gln-Trp in Implicit Solvents

DTIC Science & Technology

2009-01-01

implicit solvents on peptide structure and dynamics , we performed extensive molecular dynamics simulations on the penta-peptide Cys-Ala-Gly-Gln-Trp. Two...end-to-end distances and dihedral angles obtained from molecular dynamics simulations with implicit solvent models were in a good agreement with those...to maintain the temperature of the systems. Introduction Molecular dynamics (MD) simulation techniques are widely used to study structure and

Sparse dynamical Boltzmann machine for reconstructing complex networks with binary dynamics

NASA Astrophysics Data System (ADS)

Chen, Yu-Zhong; Lai, Ying-Cheng

2018-03-01

Revealing the structure and dynamics of complex networked systems from observed data is a problem of current interest. Is it possible to develop a completely data-driven framework to decipher the network structure and different types of dynamical processes on complex networks? We develop a model named sparse dynamical Boltzmann machine (SDBM) as a structural estimator for complex networks that host binary dynamical processes. The SDBM attains its topology according to that of the original system and is capable of simulating the original binary dynamical process. We develop a fully automated method based on compressive sensing and a clustering algorithm to construct the SDBM. We demonstrate, for a variety of representative dynamical processes on model and real world complex networks, that the equivalent SDBM can recover the network structure of the original system and simulates its dynamical behavior with high precision.

Sparse dynamical Boltzmann machine for reconstructing complex networks with binary dynamics.

PubMed

Chen, Yu-Zhong; Lai, Ying-Cheng

2018-03-01

Revealing the structure and dynamics of complex networked systems from observed data is a problem of current interest. Is it possible to develop a completely data-driven framework to decipher the network structure and different types of dynamical processes on complex networks? We develop a model named sparse dynamical Boltzmann machine (SDBM) as a structural estimator for complex networks that host binary dynamical processes. The SDBM attains its topology according to that of the original system and is capable of simulating the original binary dynamical process. We develop a fully automated method based on compressive sensing and a clustering algorithm to construct the SDBM. We demonstrate, for a variety of representative dynamical processes on model and real world complex networks, that the equivalent SDBM can recover the network structure of the original system and simulates its dynamical behavior with high precision.

Organizational and Spatial Dynamics of Attentional Focusing in Hierarchically Structured Objects

ERIC Educational Resources Information Center

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,…

Modelling fungal growth in heterogeneous soil: analyses of the effect of soil physical structure on fungal community dynamics

NASA Astrophysics Data System (ADS)

Falconer, R.; Radoslow, P.; Grinev, D.; Otten, W.

2009-04-01

Fungi play a pivital role in soil ecosystems contributing to plant productivity. The underlying soil physical and biological processes responsible for community dynamics are interrelated and, at present, poorly understood. If these complex processes can be understood then this knowledge can be managed with an aim to providing more sustainable agriculture. Our understanding of microbial dynamics in soil has long been hampered by a lack of a theoretical framework and difficulties in observation and quantification. We will demonstrate how the spatial and temporal dynamics of fungi in soil can be understood by linking mathematical modelling with novel techniques that visualise the complex structure of the soil. The combination of these techniques and mathematical models opens up new possibilities to understand how the physical structure of soil affects fungal colony dynamics and also how fungal dynamics affect soil structure. We will quantify, using X ray tomography, soil structure for a range of artificially prepared microcosms. We characterise the soil structures using soil metrics such as porosity, fractal dimension, and the connectivity of the pore volume. Furthermore we will use the individual based fungal colony growth model of Falconer et al. 2005, which is based on the physiological processes of fungi, to assess the effect of soil structure on microbial dynamics by qualifying biomass abundances and distributions. We demonstrate how soil structure can critically affect fungal species interactions with consequences for biological control and fungal biodiversity.

Structural dynamics branch research and accomplishments to FY 1992

NASA Technical Reports Server (NTRS)

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.

Analysis of dynamic accumulative damage about the lining structure of high speed railway’s tunnel based on ultrasonic testing technology

NASA Astrophysics Data System (ADS)

Wang, Xiang-qiu; Zhang, Huojun; Xie, Wen-xi

2017-08-01

Based on the similar material model test of full tunnel, the theory of elastic wave propagation and the testing technology of intelligent ultrasonic wave had been used to research the dynamic accumulative damage characteristics of tunnel’s lining structure under the dynamic loads of high speed train. For the more, the dynamic damage variable of lining structure of high speed railway’s tunnel was obtained. The results shown that the dynamic cumulative damage of lining structure increases nonlinearly with the times of cumulative vibration, the weakest part of dynamic cumulative damage is the arch foot of tunnel. Much more attention should be paid to the design and operation management of high speed railway’s tunnel.

Somatic Hypermutation-Induced Changes in the Structure and Dynamics of HIV-1 Broadly Neutralizing Antibodies.

PubMed

Davenport, Thaddeus M; Gorman, Jason; Joyce, M Gordon; Zhou, Tongqing; Soto, Cinque; Guttman, Miklos; Moquin, Stephanie; Yang, Yongping; Zhang, Baoshan; Doria-Rose, Nicole A; Hu, Shiu-Lok; Mascola, John R; Kwong, Peter D; Lee, Kelly K

2016-08-02

Antibody somatic hypermutation (SHM) and affinity maturation enhance antigen recognition by modifying antibody paratope structure to improve its complementarity with the target epitope. SHM-induced changes in paratope dynamics may also contribute to antibody maturation, but direct evidence of this is limited. Here, we examine two classes of HIV-1 broadly neutralizing antibodies (bNAbs) for SHM-induced changes in structure and dynamics, and delineate the effects of these changes on interactions with the HIV-1 envelope glycoprotein (Env). In combination with new and existing structures of unmutated and affinity matured antibody Fab fragments, we used hydrogen/deuterium exchange with mass spectrometry to directly measure Fab structural dynamics. Changes in antibody structure and dynamics were positioned to improve complementarity with Env, with changes in dynamics primarily observed at the paratope peripheries. We conclude that SHM optimizes paratope complementarity to conserved HIV-1 epitopes and restricts the mobility of paratope-peripheral residues to minimize clashes with variable features on HIV-1 Env. Copyright © 2016 Elsevier Ltd. All rights reserved.

Structure and Dynamics of Ionic Block Copolymer Melts: Computational Study

DOE PAGES

Aryal, Dipak; Agrawal, Anupriya; Perahia, Dvora; ...

2017-09-06

Structure and dynamics of melts of copolymers with an ABCBA topology, where C is an ionizable block, have been studied by fully atomistic molecular dynamics (MD) simulations. Introducing an ionizable block for functionality adds a significant element to the coupled set of interactions that determine the structure and dynamics of the macromolecule. The polymer consists of a randomly sulfonated polystyrene C block tethered to a flexible poly(ethylene-r-propylene) bridge B and end-capped with poly(tert-butylstyrene) A. The chemical structure and topology of these polymers constitute a model for incorporation of ionic blocks within a framework that provides tactility and mechanical stability. Heremore » in this paper we resolve the structure and dynamics of a structured polymer on the nanoscale constrained by ionic clusters. We find that the melts form intertwined networks of the A and C blocks independent of the degree of sulfonation of the C block with no long-range order. The cluster cohesiveness and morphology affect both macroscopic translational motion and segmental dynamics of all the blocks.« less

Structure and Dynamics of Ionic Block Copolymer Melts: Computational Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aryal, Dipak; Agrawal, Anupriya; Perahia, Dvora

Structure and dynamics of melts of copolymers with an ABCBA topology, where C is an ionizable block, have been studied by fully atomistic molecular dynamics (MD) simulations. Introducing an ionizable block for functionality adds a significant element to the coupled set of interactions that determine the structure and dynamics of the macromolecule. The polymer consists of a randomly sulfonated polystyrene C block tethered to a flexible poly(ethylene-r-propylene) bridge B and end-capped with poly(tert-butylstyrene) A. The chemical structure and topology of these polymers constitute a model for incorporation of ionic blocks within a framework that provides tactility and mechanical stability. Heremore » in this paper we resolve the structure and dynamics of a structured polymer on the nanoscale constrained by ionic clusters. We find that the melts form intertwined networks of the A and C blocks independent of the degree of sulfonation of the C block with no long-range order. The cluster cohesiveness and morphology affect both macroscopic translational motion and segmental dynamics of all the blocks.« less

Molecular dynamics simulation of the structure and dynamics of 5-HT3 serotonin receptor

NASA Astrophysics Data System (ADS)

Antonov, M. Yu.; Popinako, A. V.; Prokopiev, G. A.

2016-10-01

In this work, we investigated structure, dynamics and ion transportation in transmembrane domain of the 5-HT3 serotonin receptor. High-resolution (0.35 nm) structure of the 5-HT3 receptor in complex with stabilizing nanobodies was determined by protein crystallography in 2014 (Protein data bank (PDB) code 4PIR). Transmembrane domain of the structure was prepared in complex with explicit membrane environment (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC)) and solvent (TIP3P water model). Molecular dynamics protocols for simulation and stabilization of the transmembrane domain of the 5-HT3 receptor model were developed and 60 ns simulation of the structure was conducted in order to explore structural parameters of the system. We estimated the mean force profile for Na+ ions using umbrella sampling method.

AB INITIO Molecular Dynamics Simulations on Local Structure and Electronic Properties in Liquid MgxBi1-x Alloys

NASA Astrophysics Data System (ADS)

Hao, Qing-Hai; You, Yu-Wei; Kong, Xiang-Shan; Liu, C. S.

2013-03-01

The microscopic structure and dynamics of liquid MgxBi1-x(x = 0.5, 0.6, 0.7) alloys together with pure liquid Mg and Bi metals were investigated by means of ab initio molecular dynamics simulations. We present results of structure properties including pair correlation function, structural factor, bond-angle distribution function and bond order parameter, and their composition dependence. The dynamical and electronic properties have also been studied. The structure factor and pair correlation function are in agreement with the available experimental data. The calculated bond-angle distribution function and bond order parameter suggest that the stoichiometric composition Mg3Bi2 exhibits a different local structure order compared with other concentrations, which help us understand the appearance of the minimum electronic conductivity at this composition observed in previous experiments.

Linking extinction-colonization dynamics to genetic structure in a salamander metapopulation.

PubMed

Cosentino, Bradley J; Phillips, Christopher A; Schooley, Robert L; Lowe, Winsor H; Douglas, Marlis R

2012-04-22

Theory predicts that founder effects have a primary role in determining metapopulation genetic structure. However, ecological factors that affect extinction-colonization dynamics may also create spatial variation in the strength of genetic drift and migration. We tested the hypothesis that ecological factors underlying extinction-colonization dynamics influenced the genetic structure of a tiger salamander (Ambystoma tigrinum) metapopulation. We used empirical data on metapopulation dynamics to make a priori predictions about the effects of population age and ecological factors on genetic diversity and divergence among 41 populations. Metapopulation dynamics of A. tigrinum depended on wetland area, connectivity and presence of predatory fish. We found that newly colonized populations were more genetically differentiated than established populations, suggesting that founder effects influenced genetic structure. However, ecological drivers of metapopulation dynamics were more important than age in predicting genetic structure. Consistent with demographic predictions from metapopulation theory, genetic diversity and divergence depended on wetland area and connectivity. Divergence was greatest in small, isolated wetlands where genetic diversity was low. Our results show that ecological factors underlying metapopulation dynamics can be key determinants of spatial genetic structure, and that habitat area and isolation may mediate the contributions of drift and migration to divergence and evolution in local populations.

Protein flexibility in the light of structural alphabets

PubMed Central

Craveur, Pierrick; Joseph, Agnel P.; Esque, Jeremy; Narwani, Tarun J.; Noël, Floriane; Shinada, Nicolas; Goguet, Matthieu; Leonard, Sylvain; Poulain, Pierre; Bertrand, Olivier; Faure, Guilhem; Rebehmed, Joseph; Ghozlane, Amine; Swapna, Lakshmipuram S.; Bhaskara, Ramachandra M.; Barnoud, Jonathan; Téletchéa, Stéphane; Jallu, Vincent; Cerny, Jiri; Schneider, Bohdan; Etchebest, Catherine; Srinivasan, Narayanaswamy; Gelly, Jean-Christophe; de Brevern, Alexandre G.

2015-01-01

Protein structures are valuable tools to understand protein function. Nonetheless, proteins are often considered as rigid macromolecules while their structures exhibit specific flexibility, which is essential to complete their functions. Analyses of protein structures and dynamics are often performed with a simplified three-state description, i.e., the classical secondary structures. More precise and complete description of protein backbone conformation can be obtained using libraries of small protein fragments that are able to approximate every part of protein structures. These libraries, called structural alphabets (SAs), have been widely used in structure analysis field, from definition of ligand binding sites to superimposition of protein structures. SAs are also well suited to analyze the dynamics of protein structures. Here, we review innovative approaches that investigate protein flexibility based on SAs description. Coupled to various sources of experimental data (e.g., B-factor) and computational methodology (e.g., Molecular Dynamic simulation), SAs turn out to be powerful tools to analyze protein dynamics, e.g., to examine allosteric mechanisms in large set of structures in complexes, to identify order/disorder transition. SAs were also shown to be quite efficient to predict protein flexibility from amino-acid sequence. Finally, in this review, we exemplify the interest of SAs for studying flexibility with different cases of proteins implicated in pathologies and diseases. PMID:26075209

Communication: On the origin of the non-Arrhenius behavior in water reorientation dynamics.

PubMed

Stirnemann, Guillaume; Laage, Damien

2012-07-21

We combine molecular dynamics simulations and analytic modeling to determine the origin of the non-Arrhenius temperature dependence of liquid water's reorientation and hydrogen-bond dynamics between 235 K and 350 K. We present a quantitative model connecting hydrogen-bond exchange dynamics to local structural fluctuations, measured by the asphericity of Voronoi cells associated with each water molecule. For a fixed local structure the regular Arrhenius behavior is recovered, and the global anomalous temperature dependence is demonstrated to essentially result from a continuous shift in the unimodal structure distribution upon cooling. The non-Arrhenius behavior can thus be explained without invoking an equilibrium between distinct structures. In addition, the large width of the homogeneous structural distribution is shown to cause a growing dynamical heterogeneity and a non-exponential relaxation at low temperature.

Analysis of the dynamic behavior of structures using the high-rate GNSS-PPP method combined with a wavelet-neural model: Numerical simulation and experimental tests

NASA Astrophysics Data System (ADS)

Kaloop, Mosbeh R.; Yigit, Cemal O.; Hu, Jong W.

2018-03-01

Recently, the high rate global navigation satellite system-precise point positioning (GNSS-PPP) technique has been used to detect the dynamic behavior of structures. This study aimed to increase the accuracy of the extraction oscillation properties of structural movements based on the high-rate (10 Hz) GNSS-PPP monitoring technique. A developmental model based on the combination of wavelet package transformation (WPT) de-noising and neural network prediction (NN) was proposed to improve the dynamic behavior of structures for GNSS-PPP method. A complicated numerical simulation involving highly noisy data and 13 experimental cases with different loads were utilized to confirm the efficiency of the proposed model design and the monitoring technique in detecting the dynamic behavior of structures. The results revealed that, when combined with the proposed model, GNSS-PPP method can be used to accurately detect the dynamic behavior of engineering structures as an alternative to relative GNSS method.

Understanding the impact of nanoscale aggregation on charge transport and structural dynamics in room temperature ionic liquids

NASA Astrophysics Data System (ADS)

Griffin, Philip; Holt, Adam; Wang, Yangyang; Sokolov, Alexei

2015-03-01

Amphiphilic room temperature ionic liquids (ILs) segregate on the nanoscale, forming intricate networks of charge-rich ionic domains intercalated with charge-poor aliphatic domains. While this structural phenomenon has been well established through x-ray diffraction studies and atomistic MD simulations, the precise effects of nanophase segregation on ion transport and structural dynamics in ILs remains poorly understood. Using a combination of broadband dielectric spectroscopy, light scattering spectroscopy, and rheology, we have characterized the ionic conductivity, structural dynamics, and shear viscosity of a homologous series of quaternary ammonium ionic liquids over a wide temperature range. Upon increasing the length and volume fraction of the alkyl side chains of these quaternary ammonium ILs, ionic conductivity decreases precipitously, although no corresponding slowing of the structural dynamics is observed. Instead, we identify the dynamical signature of supramolecular aggregates. Our results directly demonstrate the role that chemical structure and ionic aggregation plays in determining the charge transport properties of amphiphilic ILs.

Free Vibration Response Comparison of Composite Beams with Fluid Structure Interaction

DTIC Science & Technology

2012-09-01

fluid damping to vibrating structures when in contact with a fluid medium such as water . The added mass effect changes the dynamic responses of the...200 words) The analysis of the dynamic response of a vibrating structure in contact with a fluid medium can be interpreted as an added mass effect...INTENTIONALLY LEFT BLANK v ABSTRACT The analysis of the dynamic response of a vibrating structure in contact with a fluid medium can be interpreted as

Recent Progress in Heliogyro Solar Sail Structural Dynamics

NASA Technical Reports Server (NTRS)

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.

NASA Dryden Flight Loads Laboratory

NASA Technical Reports Server (NTRS)

Horn, Tom

2008-01-01

This viewgraph presentation reviews the work of the Dryden Flight Loads Laboratory. The capabilities and research interests of the lab are: Structural, thermal, & dynamic analysis; Structural, thermal, & dynamic ground-test techniques; Advanced structural instrumentation; and Flight test support.

FLEXAN (version 2.0) user's guide

NASA Technical Reports Server (NTRS)

Stallcup, Scott S.

1989-01-01

The FLEXAN (Flexible Animation) computer program, Version 2.0 is described. FLEXAN animates 3-D wireframe structural dynamics on the Evans and Sutherland PS300 graphics workstation with a VAX/VMS host computer. Animation options include: unconstrained vibrational modes, mode time histories (multiple modes), delta time histories (modal and/or nonmodal deformations), color time histories (elements of the structure change colors through time), and rotational time histories (parts of the structure rotate through time). Concurrent color, mode, delta, and rotation, time history animations are supported. FLEXAN does not model structures or calculate the dynamics of structures; it only animates data from other computer programs. FLEXAN was developed to aid in the study of the structural dynamics of spacecraft.

Advances and trends in structures and dynamics; Proceedings of the Symposium, Washington, DC, October 22-25, 1984

NASA Technical Reports Server (NTRS)

Noor, A. K. (Editor); Hayduk, R. J. (Editor)

1985-01-01

Among the topics discussed are developments in structural engineering hardware and software, computation for fracture mechanics, trends in numerical analysis and parallel algorithms, mechanics of materials, advances in finite element methods, composite materials and structures, determinations of random motion and dynamic response, optimization theory, automotive tire modeling methods and contact problems, the damping and control of aircraft structures, and advanced structural applications. Specific topics covered include structural design expert systems, the evaluation of finite element system architectures, systolic arrays for finite element analyses, nonlinear finite element computations, hierarchical boundary elements, adaptive substructuring techniques in elastoplastic finite element analyses, automatic tracking of crack propagation, a theory of rate-dependent plasticity, the torsional stability of nonlinear eccentric structures, a computation method for fluid-structure interaction, the seismic analysis of three-dimensional soil-structure interaction, a stress analysis for a composite sandwich panel, toughness criterion identification for unidirectional composite laminates, the modeling of submerged cable dynamics, and damping synthesis for flexible spacecraft structures.

Molecular Dynamic Simulation of Space and Earth-Grown Crystal Structures of Thermostable T1 Lipase Geobacillus zalihae Revealed a Better Structure.

PubMed

Ishak, Siti Nor Hasmah; Aris, Sayangku Nor Ariati Mohamad; Halim, Khairul Bariyyah Abd; Ali, Mohd Shukuri Mohamad; Leow, Thean Chor; Kamarudin, Nor Hafizah Ahmad; Masomian, Malihe; Rahman, Raja Noor Zaliha Raja Abd

2017-09-25

Less sedimentation and convection in a microgravity environment has become a well-suited condition for growing high quality protein crystals. Thermostable T1 lipase derived from bacterium Geobacillus zalihae has been crystallized using the counter diffusion method under space and earth conditions. Preliminary study using YASARA molecular modeling structure program for both structures showed differences in number of hydrogen bond, ionic interaction, and conformation. The space-grown crystal structure contains more hydrogen bonds as compared with the earth-grown crystal structure. A molecular dynamics simulation study was used to provide insight on the fluctuations and conformational changes of both T1 lipase structures. The analysis of root mean square deviation (RMSD), radius of gyration, and root mean square fluctuation (RMSF) showed that space-grown structure is more stable than the earth-grown structure. Space-structure also showed more hydrogen bonds and ion interactions compared to the earth-grown structure. Further analysis also revealed that the space-grown structure has long-lived interactions, hence it is considered as the more stable structure. This study provides the conformational dynamics of T1 lipase crystal structure grown in space and earth condition.

Assessing intra- and inter-regional climate effects on Douglas-fir biomass dynamics in Oregon and Washington, USA

Treesearch

David M. Bell; Andrew N. Gray

2016-01-01

While ecological succession shapes contemporary forest structure and dynamics, other factors like forest structure (dense vs. sparse canopies) and climate may alter structural trajectories. To assess potential sources of variation in structural trajectories, we examined proportional biomass change for a regionally dominant tree species, Douglas-fir (...

Tribute to the contribution of Gerard Lallenment to structural dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Los Alamos National Laboratory

The Society for Experimental Mechanics and the International Modal Analysis Conference recognize the remarkable contribution to experimental mechanics, mechanical engineering and structural dynamics of Professor Gerard Lallement, from the University of Franche-Comte, France. A special session is organized during the IMAC-XX to outline the many achievements of Gerard Lallement in the fields of modal analysis, structural system identification, the theory and practice of structural modification, component mode synthesis and finite element model updating. The purpose of this publication is not to provide an exhaustive account of Gerard Lallement's contribution to structural dynamics. Numerous references are provided that should help themore » interested reader learn more about the many aspects of his work. Instead, the significance of this work is illustrated by discussing the role of structural dynamics in industrial applications and its future challenges. The technical aspects of Gerard Lallement's work are illustrated with a discussion of structural modification, modeling error localization and model updating.« less

Improving the Dynamic Characteristics of Body-in-White Structure Using Structural Optimization

PubMed Central

Yahaya Rashid, Aizzat S.; Mohamed Haris, Sallehuddin; Alias, Anuar

2014-01-01

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. PMID:25101312

Dynamic response of underpasses for high-speed train lines

NASA Astrophysics Data System (ADS)

Vega, J.; Fraile, A.; Alarcon, E.; Hermanns, L.

2012-11-01

Underpasses are common in modern railway lines. Wildlife corridors and drainage conduits often fall into this category of partially buried structures. Their dynamic behavior has received far less attention than that of other structures such as bridges, but their large number makes their study an interesting challenge from the viewpoint of safety and cost savings. Here, we present a complete study of a culvert, including on-site measurements and numerical modeling. The studied structure belongs to the high-speed railway line linking Segovia and Valladolid in Spain. The line was opened to traffic in 2004. On-site measurements were performed for the structure by recording the dynamic response at selected points of the structure during the passage of high-speed trains at speeds ranging between 200 and 300 km/h. The measurements provide not only reference values suitable for model fitting, but also a good insight into the main features of the dynamic behavior of this structure. Finite element techniques were used to model the dynamic behavior of the structure and its key features. Special attention is paid to vertical accelerations, the values of which should be limited to avoid track instability according to Eurocode. This study furthers our understanding of the dynamic response of railway underpasses to train loads.

Structural Dynamics of Education Reforms and Quality of Primary Education in Uganda

ERIC Educational Resources Information Center

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,…

| NREL

Science.gov Websites

of NREL's Computational Science Center, where he uses electronic structure calculations and other introductory chemistry and physical chemistry. Research Interests Electronic structure and dynamics in the quantum/classical molecular dynamics simulation|Coupling of molecular electronic structure to

Influence of Structural Flexibility on the Dynamic Precision of a Vehicle-Mounted Equipment System

DTIC Science & Technology

2015-05-12

Paramsothy Jayakumar , Dave Mechergui, Ronald Renke U.S.Army RDECOM TARDEC INFLUENCE OF STRUCTURAL FLEXIBILITY ON THE DYNAMIC PRECISION OF A...COVERED 00-00-2015 to 00-00-2015 4. TITLE AND SUBTITLE INFLUENCE OF STRUCTURAL FLEXIBILITY ON THE DYNAMIC PRECISION OF A VEHICLE-MOUNTED EQUIPMENT...Equipment Enclosure CMS Results 23 12. Influence of CMS Method on the Vehicle Dynamics 24 13. Influence of Flexibility on the Vehicle

Modeling and molecular dynamics simulations of the V33 variant of the integrin subunit β3: Structural comparison with the L33 (HPA-1a) and P33 (HPA-1b) variants.

PubMed

Jallu, Vincent; Poulain, Pierre; Fuchs, Patrick F J; Kaplan, Cecile; de Brevern, Alexandre G

2014-10-01

The human platelet alloantigen (HPA)-1 system, the first cause of alloimmune thrombocytopenia in Caucasians, results from leucine-to-proline substitution (alleles 1a and 1b) of residue 33 in β3 subunit of the integrin αIIbβ3. A third variant with a valine (V33) has been described. Although leucine and valine share similar physicochemical properties, sera containing alloantibodies to the HPA-1a antigen variably reacted with V33-β3, suggesting structural alterations of β3. To analyze the effect of the L33V transition, molecular dynamics simulations were performed on a 3D structural model of the V33 form of the whole β3 extracellular domain (690 residues). Dynamics of the PSI (carrying residue 33), I-EGF-1, and I-EGF-2 domains of β3 were compared to previously obtained dynamics of HPA-1a structure and HPA-1b structural model using classical and innovative developments (a structural alphabet). Clustering approach and local structure analysis showed that L33-β3 and V33-β3 mostly share common structures co-existing in different dynamic equilibria. The L33V substitution mainly displaces the equilibrium between common structures. These observations can explain the variable reactivity of anti-HPA-1a alloantibodies suggesting that molecular dynamic plays a key role in the binding of these alloantibodies. Unlike the L33P substitution, the L33V transition would not affect the structure flexibility of the β3 knee, and consequently the functions of αIIbβ3. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

On the coherency of dynamic load estimates for vehicles on flexible structures

NASA Astrophysics Data System (ADS)

Mitra, Mainak; Gordon, Timothy

2014-05-01

This paper develops a novel form of a well-known signal processing technique, so as to be applicable to the interaction between a heavy truck and a supporting bridge structure. Motivated by the problem of structural health monitoring of bridges, a new modal coherency function is defined. This relates the input action of moving wheel loads to the dynamic response of the bridge, including the effects of unevenness of the road surface and the vertical dynamics of the truck suspension. The analysis here is specifically aimed at future experimental testing - the validation of axle load estimators obtained from sensors on the truck. It is applicable even when no independent 'ground truth' for the dynamic loads is available. The approach can be more widely used in the analysis of dynamic interactions involving suspended moving loads on deformable structures, e.g. for structural vibrations due to high-speed trains.

Sequence, Structural Analysis and Metrics to Define the Unique Dynamic Features of the Flap Regions Among Aspartic Proteases.

PubMed

McGillewie, Lara; Ramesh, Muthusamy; Soliman, Mahmoud E

2017-10-01

Aspartic proteases are a class of hydrolytic enzymes that have been implicated in a number of diseases such as HIV, malaria, cancer and Alzheimer's. The flap region of aspartic proteases is a characteristic unique structural feature of these enzymes; and found to have a profound impact on protein overall structure, function and dynamics. Flap dynamics also plays a crucial role in drug binding and drug resistance. Therefore, understanding the structure and dynamic behavior of this flap regions is crucial in the design of potent and selective inhibitors against aspartic proteases. Defining metrics that can describe the flap motion/dynamics has been a challenging topic in literature. This review is the first attempt to compile comprehensive information on sequence, structure, motion and metrics used to assess the dynamics of the flap region of different aspartic proteases in "one pot". We believe that this review would be of critical importance to the researchers from different scientific domains.

Cluster Morphology-Polymer Dynamics Correlations in Sulfonated Polystyrene Melts: Computational Study

DOE PAGES

Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S.

2016-04-11

Reaching exceptionally long times up to 500 ns in equilibrium and nonequilibrium molecular dynamics simulations studies, we have attained a fundamental molecular understanding of the correlation of ionomer clusters structure and multiscale dynamics, providing new insight into one critical, long-standing challenge in ionic polymer physics. The cluster structure in melts of sulfonated polystyrene with Na + and Mg 2+ counterions are resolved and correlated with the dynamics on multiple length and time scales extracted from measurements of the dynamic structure factor and shear rheology. We find that as the morphology of the ionic clusters changes from ladderlike for Na +more » to disordered structures for Mg 2+, the dynamic structure factor is affected on the length scale corresponding to the ionic clusters. Lastly, rheology studies show that the viscosity for Mg 2+ melts is higher than for Na + ones for all shear rates, which is well correlated with the larger ionic clusters’ size for the Mg 2+ melts.« less

Dynamic fiber Bragg gratings based health monitoring system of composite aerospace structures

NASA Astrophysics Data System (ADS)

Panopoulou, A.; Loutas, T.; Roulias, D.; Fransen, S.; Kostopoulos, V.

2011-09-01

The main purpose of the current work is to develop a new system for structural health monitoring of composite aerospace structures based on real-time dynamic measurements, in order to identify the structural state condition. Long-gauge Fibre Bragg Grating (FBG) optical sensors were used for monitoring the dynamic response of the composite structure. The algorithm that was developed for structural damage detection utilizes the collected dynamic response data, analyzes them in various ways and through an artificial neural network identifies the damage state and its location. Damage was simulated by slightly varying locally the mass of the structure (by adding a known mass) at different zones of the structure. Lumped masses in different locations upon the structure alter the eigen-frequencies in a way similar to actual damage. The structural dynamic behaviour has been numerically simulated and experimentally verified by means of modal testing on two different composite aerospace structures. Advanced digital signal processing techniques, e.g. the wavelet transform (WT), were used for the analysis of the dynamic response for feature extraction. WT's capability of separating the different frequency components in the time domain without loosing frequency information makes it a versatile tool for demanding signal processing applications. The use of WT is also suggested by the no-stationary nature of dynamic response signals and the opportunity of evaluating the temporal evolution of their frequency contents. Feature extraction is the first step of the procedure. The extracted features are effective indices of damage size and location. The classification step comprises of a feed-forward back propagation network, whose output determines the simulated damage location. Finally, dedicated training and validation activities were carried out by means of numerical simulations and experimental procedures. Experimental validation was performed initially on a flat stiffened panel, representing a section of a typical aeronautical structure, manufactured and tested in the lab and, as a second step, on a scaled up space oriented structure, which is a composite honeycomb plate, used as a deployment base for antenna arrays. An integrated FBG sensor network, based on the advantage of multiplexing, was mounted on both structures and different excitation positions and boundary conditions were used. The analysis of operational dynamic responses was employed to identify both the damage and its position. The system that was designed and tested initially on the thin composite panel, was successfully validated on the larger honeycomb structure. Numerical simulation of both structures was used as a support tool at all the steps of the work providing among others the location of the optical sensors used. The proposed work will be the base for the whole system qualification and validation on an antenna reflector in future work.

Damage of composite structures: Detection technique, dynamic response and residual strength

NASA Astrophysics Data System (ADS)

Lestari, Wahyu

2001-10-01

Reliable and accurate health monitoring techniques can prevent catastrophic failures of structures. Conventional damage detection methods are based on visual or localized experimental methods and very often require prior information concerning the vicinity of the damage or defect. The structure must also be readily accessible for inspections. The techniques are also labor intensive. In comparison to these methods, health-monitoring techniques that are based on the structural dynamic response offers unique information on failure of structures. However, systematic relations between the experimental data and the defect are not available and frequently, the number of vibration modes needed for an accurate identification of defects is much higher than the number of modes that can be readily identified in the experiment. These motivated us to develop an experimental data based detection method with systematic relationships between the experimentally identified information and the analytical or mathematical model representing the defective structures. The developed technique use changes in vibrational curvature modes and natural frequencies. To avoid misinterpretation of the identified information, we also need to understand the effects of defects on the structural dynamic response prior to developing health-monitoring techniques. In this thesis work we focus on two type of defects in composite structures, namely delamination and edge notch like defect. Effects of nonlinearity due to the presence of defect and due to the axial stretching are studied for beams with delamination. Once defects are detected in a structure, next concern is determining the effects of the defects on the strength of the structure and its residual stiffness under dynamic loading. In this thesis, energy release rate due to dynamic loading in a delaminated structure is studied, which will be a foundation toward determining the residual strength of the structure.

Effects of temperature on bridge dynamic properties : final report.

DOT National Transportation Integrated Search

2015-12-01

Structural health monitoring (SHM) using ambient vibration has become a valuable tool in : evaluating and assessing the condition of civil structures. For bridge structures, a vibrationbased : SHM system uses the dynamic response of a bridge to measu...

Mid-frequency Band Dynamics of Large Space Structures

NASA Technical Reports Server (NTRS)

Coppolino, Robert N.; Adams, Douglas S.

2004-01-01

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

Dynamics of satellites, asteroids, and rings

NASA Technical Reports Server (NTRS)

Dermott, Stanley F.

1987-01-01

Work is reported on: (1) the shapes and the internal structures of satellites; (2) the tidal heating of Miranda; (3) the dynamics of arc-like rings; and (4) the structure of the zodiacal cloud that was revealed by the Infrared Astronomy Satellite. Significant progress was made in determining the shape and internal structure of Mimas and in understanding the dynamical evolution of Miranda's orbit.

Test facilities of the structural dynamics branch of NASA Lewis Research Center

NASA Technical Reports Server (NTRS)

Montague, Gerald T.; Kielb, Robert E.

1988-01-01

The NASA Lewis Research Center Structural Dynamics Branch conducts experimental and analytical research related to the structural dynamics of aerospace propulsion and power systems. The experimental testing facilities of the branch are examined. Presently there are 10 research rigs and 4 laboratories within the branch. These facilities are described along with current and past research work.

The Shock and Vibration Bulletin. Part 2. Invited Papers, Structural Dynamics

DTIC Science & Technology

1974-08-01

VIKING LANDER DYNAMICS 41 Mr. Joseph C. Pohlen, Martin Marietta Aerospace, Denver, Colorado Structural Dynamics PERFORMANCE OF STATISTICAL ENERGY ANALYSIS 47...aerospace structures. Analytical prediction of these environments is beyond the current scope of classical modal techniques. Statistical energy analysis methods...have been developed that circumvent the difficulties of high-frequency nodal analysis. These statistical energy analysis methods are evaluated

Structural Mechanics and Dynamics Branch

NASA Technical Reports Server (NTRS)

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.

Control of complex networks requires both structure and dynamics

NASA Astrophysics Data System (ADS)

Gates, Alexander J.; Rocha, Luis M.

2016-04-01

The study of network structure has uncovered signatures of the organization of complex systems. However, there is also a need to understand how to control them; for example, identifying strategies to revert a diseased cell to a healthy state, or a mature cell to a pluripotent state. Two recent methodologies suggest that the controllability of complex systems can be predicted solely from the graph of interactions between variables, without considering their dynamics: structural controllability and minimum dominating sets. We demonstrate that such structure-only methods fail to characterize controllability when dynamics are introduced. We study Boolean network ensembles of network motifs as well as three models of biochemical regulation: the segment polarity network in Drosophila melanogaster, the cell cycle of budding yeast Saccharomyces cerevisiae, and the floral organ arrangement in Arabidopsis thaliana. We demonstrate that structure-only methods both undershoot and overshoot the number and which sets of critical variables best control the dynamics of these models, highlighting the importance of the actual system dynamics in determining control. Our analysis further shows that the logic of automata transition functions, namely how canalizing they are, plays an important role in the extent to which structure predicts dynamics.

Program of Research in Structures and Dynamics

NASA Technical Reports Server (NTRS)

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.

Combining protein sequence, structure, and dynamics: A novel approach for functional evolution analysis of PAS domain superfamily.

PubMed

Dong, Zheng; Zhou, Hongyu; Tao, Peng

2018-02-01

PAS domains are widespread in archaea, bacteria, and eukaryota, and play important roles in various functions. In this study, we aim to explore functional evolutionary relationship among proteins in the PAS domain superfamily in view of the sequence-structure-dynamics-function relationship. We collected protein sequences and crystal structure data from RCSB Protein Data Bank of the PAS domain superfamily belonging to three biological functions (nucleotide binding, photoreceptor activity, and transferase activity). Protein sequences were aligned and then used to select sequence-conserved residues and build phylogenetic tree. Three-dimensional structure alignment was also applied to obtain structure-conserved residues. The protein dynamics were analyzed using elastic network model (ENM) and validated by molecular dynamics (MD) simulation. The result showed that the proteins with same function could be grouped by sequence similarity, and proteins in different functional groups displayed statistically significant difference in their vibrational patterns. Interestingly, in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues. In addition, the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function. This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics. This is a new attempt to delineate functional evolution of proteins using the integrated information of sequence, structure, and dynamics. © 2017 The Protein Society.

From structure to function, via dynamics

NASA Astrophysics Data System (ADS)

Stetter, O.; Soriano, J.; Geisel, T.; Battaglia, D.

2013-01-01

Neurons in the brain are wired into a synaptic network that spans multiple scales, from local circuits within cortical columns to fiber tracts interconnecting distant areas. However, brain function require the dynamic control of inter-circuit interactions on time-scales faster than synaptic changes. In particular, strength and direction of causal influences between neural populations (described by the so-called directed functional connectivity) must be reconfigurable even when the underlying structural connectivity is fixed. Such directed functional influences can be quantified resorting to causal analysis of time-series based on tools like Granger Causality or Transfer Entropy. The ability to quickly reorganize inter-areal interactions is a chief requirement for performance in a changing natural environment. But how can manifold functional networks stem "on demand" from an essentially fixed structure? We explore the hypothesis that the self-organization of neuronal synchronous activity underlies the control of brain functional connectivity. Based on simulated and real recordings of critical neuronal cultures in vitro, as well as on mean-field and spiking network models of interacting brain areas, we have found that "function follows dynamics", rather than structure. Different dynamic states of a same structural network, characterized by different synchronization properties, are indeed associated to different functional digraphs (functional multiplicity). We also highlight the crucial role of dynamics in establishing a structure-to-function link, by showing that whenever different structural topologies lead to similar dynamical states, than the associated functional connectivities are also very similar (structural degeneracy).

Controlling flexible structures with second order actuator dynamics

NASA Technical Reports Server (NTRS)

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.

An Investigation of G-Quadruplex Structural Polymorphism in the Human Telomere Using a Combined Approach of Hydrodynamic Bead Modeling and Molecular Dynamics Simulation

PubMed Central

2015-01-01

Guanine-rich oligonucleotides can adopt noncanonical tertiary structures known as G-quadruplexes, which can exist in different forms depending on experimental conditions. High-resolution structural methods, such as X-ray crystallography and NMR spectroscopy, have been of limited usefulness in resolving the inherent structural polymorphism associated with G-quadruplex formation. The lack of, or the ambiguous nature of, currently available high-resolution structural data, in turn, has severely hindered investigations into the nature of these structures and their interactions with small-molecule inhibitors. We have used molecular dynamics in conjunction with hydrodynamic bead modeling to study the structures of the human telomeric G-quadruplex-forming sequences at the atomic level. We demonstrated that molecular dynamics can reproduce experimental hydrodynamic measurements and thus can be a powerful tool in the structural study of existing G-quadruplex sequences or in the prediction of new G-quadruplex structures. PMID:24779348

Revealing the Link between Structural Relaxation and Dynamic Heterogeneity in Glass-Forming Liquids

NASA Astrophysics Data System (ADS)

Wang, Lijin; Xu, Ning; Wang, W. H.; Guan, Pengfei

2018-03-01

Despite the use of glasses for thousands of years, the nature of the glass transition is still mysterious. On approaching the glass transition, the growth of dynamic heterogeneity has long been thought to play a key role in explaining the abrupt slowdown of structural relaxation. However, it still remains elusive whether there is an underlying link between structural relaxation and dynamic heterogeneity. Here, we unravel the link by introducing a characteristic time scale hiding behind an identical dynamic heterogeneity for various model glass-forming liquids. We find that the time scale corresponds to the kinetic fragility of liquids. Moreover, it leads to scaling collapse of both the structural relaxation time and dynamic heterogeneity for all liquids studied, together with a characteristic temperature associated with the same dynamic heterogeneity. Our findings imply that studying the glass transition from the viewpoint of dynamic heterogeneity is more informative than expected.

Towards a true protein movie: a perspective on the potential impact of the ensemble-based structure determination using exact NOEs.

PubMed

Vögeli, Beat; Orts, Julien; Strotz, Dean; Chi, Celestine; Minges, Martina; Wälti, Marielle Aulikki; Güntert, Peter; Riek, Roland

2014-04-01

Confined by the Boltzmann distribution of the energies of the states, a multitude of structural states are inherent to biomolecules. For a detailed understanding of a protein's function, its entire structural landscape at atomic resolution and insight into the interconversion between all the structural states (i.e. dynamics) are required. Whereas dedicated trickery with NMR relaxation provides aspects of local dynamics, and 3D structure determination by NMR is well established, only recently have several attempts been made to formulate a more comprehensive description of the dynamics and the structural landscape of a protein. Here, a perspective is given on the use of exact NOEs (eNOEs) for the elucidation of structural ensembles of a protein describing the covered conformational space. Copyright © 2013 Elsevier Inc. All rights reserved.

Effects of Fluid-Structure Interaction on Dynamic Response of Composite Structures: Experimental and Numerical Studies

DTIC Science & Technology

2013-08-01

STRUCTURES: EXPERIMENTAL AND NUMERICAL STUDIES by Young W. Kwon August 1, 2013 Approved for public release; distribution is unlimited Prepared...failing to comply with a collection of information if it does not display a currently valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO THE...AND SUBTITLE Effects of Fluid-Structure Interaction on Dynamic Responses of Composite Structures: Experimental and Numerical Studies 5a. CONTRACT

Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation

NASA Astrophysics Data System (ADS)

Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

2012-12-01

We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation.

PubMed

Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

2012-12-07

We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

Correlations between dynamics and atomic structures in Cu64.5Zr35.5 metallic glass

NASA Astrophysics Data System (ADS)

Wang, C. Z.; Zhang, Y.; Zhang, F.; Mendelev, M. I.; Kramer, M. J.; Ho, K. M.

2015-03-01

The atomic structure of Cu-Zr metallic glasses (MGs) has been widely accepted to be heterogeneous and dominated by icosahedral short range order (ISRO). However, the correlations between dynamics and atomic structures in Cu-Zr MGs remain an enigma. Using molecular dynamics (MD) simulations, we investigated the correlations between dynamics and atomic structures in Cu64.5Zr35.5 MG. The atomic structures are characterized using ISRO and the Bergman-type medium range order (BMRO). The simulation and analysis results show that the majority of the mobile atoms are not involved in ISRO or BMRO, indicating that the dynamical heterogeneity has a strong correlation to structural heterogeneity. Moreover, we found that the localized soft vibration modes below 1.0 THz are mostly concentrated on the mobile atoms. The diffusion was studied using the atomic trajectory collected in an extended time interval of 1.2 μs at 700 K in MD simulations. It was found that the long range diffusion in MGs is highly heterogeneous, which is confined to the liquid-like regions and strongly avoids the ISRO and the Bergman-type MRO. All These results clearly demonstrate strong correlations between dynamics (in terms of dynamical heterogeneity and diffusion) and atomic structures in Cu64.5Zr35.5 MGs. This work was supported by the U.S. Department of Energy, Basic Energy Sciences, Division of Materials Science and Engineering under the Contract No. DE-AC02-07CH11358.

Simulating Vibrations in a Complex Loaded Structure

NASA Technical Reports Server (NTRS)

Cao, Tim T.

2005-01-01

The Dynamic Response Computation (DIRECT) computer program simulates vibrations induced in a complex structure by applied dynamic loads. Developed to enable rapid analysis of launch- and landing- induced vibrations and stresses in a space shuttle, DIRECT also can be used to analyze dynamic responses of other structures - for example, the response of a building to an earthquake, or the response of an oil-drilling platform and attached tanks to large ocean waves. For a space-shuttle simulation, the required input to DIRECT includes mathematical models of the space shuttle and its payloads, and a set of forcing functions that simulates launch and landing loads. DIRECT can accommodate multiple levels of payload attachment and substructure as well as nonlinear dynamic responses of structural interfaces. DIRECT combines the shuttle and payload models into a single structural model, to which the forcing functions are then applied. The resulting equations of motion are reduced to an optimum set and decoupled into a unique format for simulating dynamics. During the simulation, maximum vibrations, loads, and stresses are monitored and recorded for subsequent analysis to identify structural deficiencies in the shuttle and/or payloads.

Dynamic Structure of a Molecular Liquid S0.5Cl0.5: Ab initio Molecular-Dynamics Simulations

NASA Astrophysics Data System (ADS)

Ohmura, Satoshi; Shimakura, Hironori; Kawakita, Yukinobu; Shimojo, Fuyuki; Yao, Makoto

2013-07-01

The static and dynamic structures of a molecular liquid S0.5Cl0.5 consisting of Cl--S--S--Cl (S2Cl2) type molecules are studied by means of ab initio molecular dynamics simulations. Both the calculated static and dynamic structure factors are in good agreement with experimental results. The dynamic structures are discussed based on van-Hove distinct correlation functions, molecular translational mean-square displacements (TMSD) and rotational mean-square displacements (RMSD). In the TMSD and RMSD, there are ballistic and diffusive regimes in the sub-picosecond and picosecond time regions, respectively. These time scales are consistent with the decay time observed experimentally. The interaction between molecules in the liquid is also discussed in comparison with that in another liquid chalcogen--halogen system Se0.5Cl0.5.

Dynamic condensation of non-classically damped structures using the method of Maclaurin expansion of the frequency response function in Laplace domain

NASA Astrophysics Data System (ADS)

Esmaeilzad, Armin; Khanlari, Karen

2018-07-01

As the number of degrees of freedom (DOFs) in structural dynamic problems becomes larger, the analyzing complexity and CPU usage of computers increase drastically. Condensation (or reduction) method is an efficient technique to reduce the size of the full model or the dimension of the structural matrices by eliminating the unimportant DOFs. After the first presentation of condensation method by Guyan in 1965 for undamped structures, which ignores the dynamic effects of the mass term, various forms of dynamic condensation methods were presented to overcome this issue. Moreover, researchers have tried to expand the dynamic condensation method to non-classically damped structures. Dynamic reduction of such systems is far more complicated than undamped systems. The proposed non-iterative method in this paper is introduced as 'Maclaurin Expansion of the frequency response function in Laplace Domain' (MELD) applied for dynamic reduction of non-classically damped structures. The present approach is implemented in four numerical examples of 2D bending-shear-axial frames with various numbers of stories and spans and also a floating raft isolation system. The results of natural frequencies and dynamic responses of models are compared with each other before and after the dynamic reduction. It is shown that the result accuracy has acceptable convergence in both cases. In addition, it is indicated that the result of the proposed method is more accurate than the results of some other existing condensation methods.

Network structure of SiO2 and MgSiO3 in amorphous and liquid States

NASA Astrophysics Data System (ADS)

Lan, Mai Thi; Thuy Duong, Tran; Viet Huy, Nguyen; Van Hong, Nguyen

2017-03-01

Network structure of SiO2 and MgSiO3 at 300 K and 3200 K is investigated by molecular dynamics simulation and visualization of simulation data. Structural organization of SiO2 and MgSiO3 is clarified via analysis the short range order (SRO) and intermediate range order (IRO). Network topology is determined via analyzing the bond between structural units, the cluster of structural units as well as spatial distribution of structural units. The polyamorphism as well as structural and dynamic heterogeneities are also discussed in this work.

Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity

PubMed Central

Mustoe, Anthony M.; Brooks, Charles L.; Al-Hashimi, Hashim M.

2014-01-01

Recent studies have shown that basic steric and connectivity constraints encoded at the secondary structure level are key determinants of 3D structure and dynamics in simple two-way RNA junctions. However, the role of these topological constraints in higher order RNA junctions remains poorly understood. Here, we use a specialized coarse-grained molecular dynamics model to directly probe the thermodynamic contributions of topological constraints in defining the 3D architecture and dynamics of transfer RNA (tRNA). Topological constraints alone restrict tRNA's allowed conformational space by over an order of magnitude and strongly discriminate against formation of non-native tertiary contacts, providing a sequence independent source of folding specificity. Topological constraints also give rise to long-range correlations between the relative orientation of tRNA's helices, which in turn provides a mechanism for encoding thermodynamic cooperativity between distinct tertiary interactions. These aspects of topological constraints make it such that only several tertiary interactions are needed to confine tRNA to its native global structure and specify functionally important 3D dynamics. We further show that topological constraints are conserved across tRNA's different naturally occurring secondary structures. Taken together, our results emphasize the central role of secondary-structure-encoded topological constraints in defining RNA 3D structure, dynamics and folding. PMID:25217593

Adaptive dynamical networks

NASA Astrophysics Data System (ADS)

Maslennikov, O. V.; Nekorkin, V. I.

2017-10-01

Dynamical networks are systems of active elements (nodes) interacting with each other through links. Examples are power grids, neural structures, coupled chemical oscillators, and communications networks, all of which are characterized by a networked structure and intrinsic dynamics of their interacting components. If the coupling structure of a dynamical network can change over time due to nodal dynamics, then such a system is called an adaptive dynamical network. The term ‘adaptive’ implies that the coupling topology can be rewired; the term ‘dynamical’ implies the presence of internal node and link dynamics. The main results of research on adaptive dynamical networks are reviewed. Key notions and definitions of the theory of complex networks are given, and major collective effects that emerge in adaptive dynamical networks are described.

Structural Dynamics Analysis and Research for FEA Modeling Method of a Light High Resolution CCD Camera

NASA Astrophysics Data System (ADS)

Sun, Jiwen; Wei, Ling; Fu, Danying

2002-01-01

resolution and wide swath. In order to assure its high optical precision smoothly passing the rigorous dynamic load of launch, it should be of high structural rigidity. Therefore, a careful study of the dynamic features of the camera structure should be performed. Pro/E. An interference examination is performed on the precise CAD model of the camera for mending the structural design. for the first time in China, and the analysis of structural dynamic of the camera is accomplished by applying the structural analysis code PATRAN and NASTRAN. The main research programs include: 1) the comparative calculation of modes analysis of the critical structure of the camera is achieved by using 4 nodes and 10 nodes tetrahedral elements respectively, so as to confirm the most reasonable general model; 2) through the modes analysis of the camera from several cases, the inherent frequencies and modes are obtained and further the rationality of the structural design of the camera is proved; 3) the static analysis of the camera under self gravity and overloads is completed and the relevant deformation and stress distributions are gained; 4) the response calculation of sine vibration of the camera is completed and the corresponding response curve and maximum acceleration response with corresponding frequencies are obtained. software technique is accurate and efficient. sensitivity, the dynamic design and engineering optimization of the critical structure of the camera are discussed. fundamental technology in design of forecoming space optical instruments.

Piezoceramic devices and PVDF films as sensors and actuators for intelligent structures

NASA Astrophysics Data System (ADS)

Hanagud, S.; Obal, M. W.; Calise, A. G.

The use of bonded piezoceramic sensors and piezoceramic actuators to control vibrations in structural dynamic systems is discussed. Equations for developing optimum control strategies are derived. An example of a cantilever beam is considered to illustrate the development procedure for optimal vibration control of structures by the use of piezoceramic sensors, actuators, and rate feedbacks with appropriate gains. Research areas and future directions are outlined, including dynamic coupling and constitutive equations; load and energy transfer; composite structures; optimal dynamic compensation; estimation and identification; and distributed control.

Dynamic Programming for Structured Continuous Markov Decision Problems

NASA Technical Reports Server (NTRS)

Dearden, Richard; Meuleau, Nicholas; Washington, Richard; Feng, Zhengzhu

2004-01-01

We describe an approach for exploiting structure in Markov Decision Processes with continuous state variables. At each step of the dynamic programming, the state space is dynamically partitioned into regions where the value function is the same throughout the region. We first describe the algorithm for piecewise constant representations. We then extend it to piecewise linear representations, using techniques from POMDPs to represent and reason about linear surfaces efficiently. We show that for complex, structured problems, our approach exploits the natural structure so that optimal solutions can be computed efficiently.

Fine-scale population dynamics in a marine fish species inferred from dynamic state-space models.

PubMed

Rogers, Lauren A; Storvik, Geir O; Knutsen, Halvor; Olsen, Esben M; Stenseth, Nils C

2017-07-01

Identifying the spatial scale of population structuring is critical for the conservation of natural populations and for drawing accurate ecological inferences. However, population studies often use spatially aggregated data to draw inferences about population trends and drivers, potentially masking ecologically relevant population sub-structure and dynamics. The goals of this study were to investigate how population dynamics models with and without spatial structure affect inferences on population trends and the identification of intrinsic drivers of population dynamics (e.g. density dependence). Specifically, we developed dynamic, age-structured, state-space models to test different hypotheses regarding the spatial structure of a population complex of coastal Atlantic cod (Gadus morhua). Data were from a 93-year survey of juvenile (age 0 and 1) cod sampled along >200 km of the Norwegian Skagerrak coast. We compared two models: one which assumes all sampled cod belong to one larger population, and a second which assumes that each fjord contains a unique population with locally determined dynamics. Using the best supported model, we then reconstructed the historical spatial and temporal dynamics of Skagerrak coastal cod. Cross-validation showed that the spatially structured model with local dynamics had better predictive ability. Furthermore, posterior predictive checks showed that a model which assumes one homogeneous population failed to capture the spatial correlation pattern present in the survey data. The spatially structured model indicated that population trends differed markedly among fjords, as did estimates of population parameters including density-dependent survival. Recent biomass was estimated to be at a near-record low all along the coast, but the finer scale model indicated that the decline occurred at different times in different regions. Warm temperatures were associated with poor recruitment, but local changes in habitat and fishing pressure may have played a role in driving local dynamics. More generally, we demonstrated how state-space models can be used to test evidence for population spatial structure based on survey time-series data. Our study shows the importance of considering spatially structured dynamics, as the inferences from such an approach can lead to a different ecological understanding of the drivers of population declines, and fundamentally different management actions to restore populations. © 2017 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.

Inverse Analysis of Cavitation Impact Phenomena on Structures

DTIC Science & Technology

2007-07-02

can occur within different types of dynamic water environments of structures. Case study analyses using experimental data are used to demonstrate the...cavitation impact phenomena, and ultimately, with cavitation erosion of structures within turbulent water environments. 02-07-2007 Memorandum Report...of dynamic water environments of structures. Case study analyses using experimental data are used to demonstrate the fundamentals of various aspects

154. Photocopy of drawing (1963 structural drawing by General Dynamics/Astronautics) ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

154. Photocopy of drawing (1963 structural drawing by General Dynamics/Astronautics) STRUCTURAL PLANS FOR MST STATION 30, SHEET S84 - Vandenberg Air Force Base, Space Launch Complex 3, Launch Pad 3 East, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

Application of partial differential equation modeling of the control/structural dynamics of flexible spacecraft

NASA Technical Reports Server (NTRS)

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.

More Than Filaments and Cores: Statistical Study of Structure Formation and Dynamics in Nearby Molecular Clouds

NASA Astrophysics Data System (ADS)

Chen, How-Huan; Goodman, Alyssa

2018-01-01

In the past decade, multiple attempts at understanding the connection between filaments and star forming cores have been made using observations across the entire epectrum. However, the filaments and the cores are usually treated as predefined--and well-defined--entities, instead of structures that often come at different sizes, shapes, with substantially different dynamics, and inter-connected at different scales. In my dissertation, I present an array of studies using different statistical methods, including the dendrogram and the probability distribution function (PDF), of structures at different size scales within nearby molecular clouds. These structures are identified using observations of different density tracers, and where possible, in the multi-dimensional parameter space of key dynamic properties--the LSR velocity, the velocity dispersion, and the column density. The goal is to give an overview of structure formation in nearby star-forming clouds, as well as of the dynamics in these structures. I find that the overall statistical properties of a larger structure is often the summation/superposition of sub-structures within, and that there could be significant variations due to local physical processes. I also find that the star formation process within molecular clouds could in fact take place in a non-monolithic manner, connecting potentially merging and/or transient structures, at different scales.

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

PubMed

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

2017-05-19

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

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

PubMed Central

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

2017-01-01

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

Resting-state functional connectivity emerges from structurally and dynamically shaped slow linear fluctuations.

PubMed

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.

A Model Structure for the Heterodimer apoA-IMilano–apoA-II Supports Its Peculiar Susceptibility to Proteolysis

PubMed Central

Rocco, Alessandro Guerini; Mollica, Luca; Gianazza, Elisabetta; Calabresi, Laura; Franceschini, Guido; Sirtori, Cesare R.; Eberini, Ivano

2006-01-01

In this study, we propose a structure for the heterodimer between apolipoprotein A-IMilano and apolipoprotein A-II (apoA-IM–apoA-II) in a synthetic high-density lipoprotein (HDL) containing L-α-palmitoyloleoyl phosphatidylcholine. We applied bioinformatics/computational tools and procedures, such as molecular docking, molecular and essential dynamics, starting from published crystal structures for apolipoprotein A-I and apolipoprotein A-II. Structural and energetic analyses onto the simulated system showed that the molecular dynamics produced a stabilized synthetic HDL. The essential dynamic analysis showed a deviation from the starting belt structure. Our structural results were validated by limited proteolysis experiments on HDL from apoA-IM carriers in comparison with control HDL. The high sensitivity of apoA-IM–apoA-II to proteases was in agreement with the high root mean-square fluctuation values and the reduction in secondary structure content from molecular dynamics data. Circular dichroism on synthetic HDL containing apoA-IM–apoA-II was consistent with the α-helix content computed on the proposed model. PMID:16891368

Current Progress of a Finite Element Computational Fluid Dynamics Prediction of Flutter for the AeroStructures Test Wing

NASA Technical Reports Server (NTRS)

Arena, Andrew S., Jr.

2002-01-01

This progress report focuses on the use of the STructural Analysis RoutineS suite program, SOLIDS, input for the AeroStructures Test Wing. The AeroStructures Test Wing project as a whole is described. The use of the SOLIDS code to find the mode shapes of a structure is discussed. The frequencies, and the structural dynamics to which they relate are examined. The results of the CFD predictions are compared to experimental data from a Ground Vibration Test.

Modal Response of Trapezoidal Wing Structures Using Second Order Shape Sensitivities

NASA Technical Reports Server (NTRS)

Liu, Youhua; Kapania, Rakesh K.

2000-01-01

The modal response of wing structures is very important for assessing their dynamic response including dynamic aeroelastic instabilities. Moreover, in a recent study an efficient structural optimization approach was developed using structural modes to represent the static aeroelastic wing response (both displacement and stress). In this paper, the modal response of general trapezoidal wing structures is approximated using shape sensitivities up to the 2nd order. Also different approaches of computing the derivatives are investigated.

Identifying forest patterns from space to explore dynamics across the circumpolar boreal

NASA Astrophysics Data System (ADS)

Montesano, P. M.; Neigh, C. S. R.; Feng, M.; Channan, S.; Sexton, J. O.; Wagner, W.; Wooten, M.; Poulter, B.; Wang, L.

2017-12-01

A variety of forest patterns are the result of interactions between broad-scale climate and local-scale site factors and history across the northernmost portion of the circumpolar boreal. Patterns of forest extent, height, and cover help describe forest structure transitions that influence future and reflect past dynamics. Coarse spaceborne observations lack structural detail at forest transitions, which inhibits understanding of these dynamics. We highlight: (1) the use of sub-meter spaceborne stereogrammetry for deriving structure estimates in boreal forests; (2) its potential to complement other spaceborne estimates of forest structure at critical scales; and (3) the potential of these sub-meter and other Landsat-derived structure estimates for improving understanding of broad-scale boreal dynamics such as carbon flux and albedo, capturing the spatial variability of the boreal-tundra biome boundary, and assessing its potential for change.

Flexible Virtual Structure Consideration in Dynamic Modeling of Mobile Robots Formation

NASA Astrophysics Data System (ADS)

El Kamel, A. Essghaier; Beji, L.; Lerbet, J.; Abichou, A.

2009-03-01

In cooperative mobile robotics, we look for formation keeping and maintenance of a geometric configuration during movement. As a solution to these problems, the concept of a virtual structure is considered. Based on this idea, we have developed an efficient flexible virtual structure, describing the dynamic model of n vehicles in formation and where the whole formation is kept dependant. Notes that, for 2D and 3D space navigation, only a rigid virtual structure was proposed in the literature. Further, the problem was limited to a kinematic behavior of the structure. Hence, the flexible virtual structure in dynamic modeling of mobile robots formation presented in this paper, gives more capabilities to the formation to avoid obstacles in hostile environment while keeping formation and avoiding inter-agent collision.

Opinion dynamics in a group-based society

NASA Astrophysics Data System (ADS)

Gargiulo, F.; Huet, S.

2010-09-01

Many models have been proposed to analyze the evolution of opinion structure due to the interaction of individuals in their social environment. Such models analyze the spreading of ideas both in completely interacting backgrounds and on social networks, where each person has a finite set of interlocutors. In this paper we analyze the reciprocal feedback between the opinions of the individuals and the structure of the interpersonal relationships at the level of community structures. For this purpose we define a group-based random network and we study how this structure co-evolves with opinion dynamics processes. We observe that the adaptive network structure affects the opinion dynamics process helping the consensus formation. The results also show interesting behaviors in regards to the size distribution of the groups and their correlation with opinion structure.

Self organization of exotic oil-in-oil phases driven by tunable electrohydrodynamics

PubMed Central

Varshney, Atul; Ghosh, Shankar; Bhattacharya, S.; Yethiraj, Anand

2012-01-01

Self organization of large-scale structures in nature - either coherent structures like crystals, or incoherent dynamic structures like clouds - is governed by long-range interactions. In many problems, hydrodynamics and electrostatics are the source of such long-range interactions. The tuning of electrostatic interactions has helped to elucidate when coherent crystalline structures or incoherent amorphous structures form in colloidal systems. However, there is little understanding of self organization in situations where both electrostatic and hydrodynamic interactions are present. We present a minimal two-component oil-in-oil model system where we can control the strength and lengthscale of the electrohydrodynamic interactions by tuning the amplitude and frequency of the imposed electric field. As a function of the hydrodynamic lengthscale, we observe a rich phenomenology of exotic structure and dynamics, from incoherent cloud-like structures and chaotic droplet dynamics, to polyhedral droplet phases, to coherent droplet arrays. PMID:23071902

Self-organization in suspensions of end-functionalized semiflexible polymers under shear flow

NASA Astrophysics Data System (ADS)

Myung, Jin Suk; Winkler, Roland G.; Gompper, Gerhard

2015-12-01

The nonequilibrium dynamical behavior and structure formation of end-functionalized semiflexible polymer suspensions under flow are investigated by mesoscale hydrodynamic simulations. The hybrid simulation approach combines the multiparticle collision dynamics method for the fluid, which accounts for hydrodynamic interactions, with molecular dynamics simulations for the semiflexible polymers. In equilibrium, various kinds of scaffold-like network structures are observed, depending on polymer flexibility and end-attraction strength. We investigate the flow behavior of the polymer networks under shear and analyze their nonequilibrium structural and rheological properties. The scaffold structure breaks up and densified aggregates are formed at low shear rates, while the structural integrity is completely lost at high shear rates. We provide a detailed analysis of the shear- rate-dependent flow-induced structures. The studies provide a deeper understanding of the formation and deformation of network structures in complex materials.

NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1†

PubMed Central

Parkesh, Raman; Fountain, Matthew; Disney, Matthew D.

2011-01-01

The NMR structure of an RNA with a copy of the 5′CUG/3′GUC motif found in the triplet repeating disorder myotonic dystrophy type 1 (DM1) is disclosed. The lowest energy conformation of the UU pair is a single hydrogen bonded structure; however, the UU protons undergo exchange indicating structural dynamics. Molecular dynamics simulations show that the single hydrogen bonded structure is the most populated one but the UU pair interconverts between 0, 1, and 2 hydrogen bonded pairs. These studies have implications for the recognition of the DM1 RNA by small molecules and proteins. PMID:21204525

Dynamic Testing of a Subscale Sunshield for the Next Generation Space Telescope (NGST)

NASA Technical Reports Server (NTRS)

Lienard, Sebastien; Johnston, John D.; Ross, Brian; Smith, James; Brodeur, Steve (Technical Monitor)

2001-01-01

The NGST sunshield is a lightweight, flexible structure consisting of multiple layers of pretensioned, thin-film membranes supported by deployable booms. The structural dynamic behavior of the sunshield must be well understood in order to predict its influence on observatory performance. Ground tests were carried out in a vacuum environment to characterize the structural dynamic behavior of a one-tenth scale model of the sunshield. Results from the tests will be used to validate analytical modeling techniques that can be used in conjunction with scaling laws to predict the performance of the full-sized structure. This paper summarizes the ground tests and presents representative results for the dynamic behavior of the sunshield.

Dynamic soft variable structure control of singular systems

NASA Astrophysics Data System (ADS)

Liu, Yunlong; Zhang, Caihong; Gao, Cunchen

2012-08-01

The dynamic soft variable structure control (VSC) of singular systems is discussed in this paper. The definition of soft VSC and the design of its controller modes are given. The stability of singular systems with the dynamic soft VSC is proposed. The dynamic soft variable structure controller is designed, and the concrete algorithm on the dynamic soft VSC is given. The dynamic soft VSC of singular systems which was developed for the purpose of intentionally precluding chattering, achieving high regulation rates and shortening settling times enhanced the dynamic quality of the systems. It is illustrated the feasibility and validity of the proposed strategy by a simulation example, and an outlook on its auspicious further development is presented.

Revealing Hidden Structural Order Controlling Both Fast and Slow Glassy Dynamics in Supercooled Liquids

NASA Astrophysics Data System (ADS)

Tong, Hua; Tanaka, Hajime

2018-01-01

The dynamics of a supercooled liquid near the glass transition is characterized by two-step relaxation, fast β and slow α relaxations. Because of the apparently disordered nature of glassy structures, there have been long debates over whether the origin of drastic slowing-down of the α relaxation accompanied by heterogeneous dynamics is thermodynamic or dynamic. Furthermore, it has been elusive whether there is any deep connection between fast β and slow α modes. To settle these issues, here we introduce a set of new structural order parameters characterizing sterically favored structures with high local packing capability, and then access structure-dynamics correlation by a novel nonlocal approach. We find that the particle mobility is under control of the static order parameter field. The fast β process is controlled by the instantaneous order parameter field locally, resulting in short-time particle-scale dynamics. Then the mobility field progressively develops with time t , following the initial order parameter field from disorder to more ordered regions. As is well known, the heterogeneity in the mobility field (dynamic heterogeneity) is maximized with a characteristic length ξ4, when t reaches the relaxation time τα. We discover that this mobility pattern can be predicted solely by a spatial coarse graining of the initial order parameter field at t =0 over a length ξ without any dynamical information. Furthermore, we find a relation ξ ˜ξ4, indicating that the static length ξ grows coherently with the dynamic one ξ4 upon cooling. This further suggests an intrinsic link between τα and ξ : the growth of the static length ξ is the origin of dynamical slowing-down. These we confirm for the first time in binary glass formers both in two and three spatial dimensions. Thus, a static structure has two intrinsic characteristic lengths, particle size and ξ , which control dynamics in local and nonlocal manners, resulting in the emergence of the two key relaxation modes, fast β and slow α processes, respectively. Because the two processes share a common structural origin, we can even predict a dynamic propensity pattern at long timescale from the fast β pattern. The presence of such intrinsic structure-dynamics correlation strongly indicates a thermodynamic nature of glass transition.

Landscape Pattern Determines Neighborhood Size and Structure within a Lizard Population

PubMed Central

Ryberg, Wade A.; Hill, Michael T.; Painter, Charles W.; Fitzgerald, Lee A.

2013-01-01

Although defining population structure according to discrete habitat patches is convenient for metapopulation theories, taking this approach may overlook structure within populations continuously distributed across landscapes. For example, landscape features within habitat patches direct the movement of organisms and define the density distribution of individuals, which can generate spatial structure and localized dynamics within populations as well as among them. Here, we use the neighborhood concept, which describes population structure relative to the scale of individual movements, to illustrate how localized dynamics within a population of lizards (Sceloporus arenicolus) arise in response to variation in landscape pattern within a continuous habitat patch. Our results emphasize links between individual movements at small scales and the emergence of spatial structure within populations which resembles metapopulation dynamics at larger scales. We conclude that population dynamics viewed in a landscape context must consider the explicit distribution and movement of individuals within continuous habitat as well as among habitat patches. PMID:23441217

Dynamics and control of diseases in networks with community structure.

PubMed

Salathé, Marcel; Jones, James H

2010-04-08

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 spectral structure specifies vowels for children and adultsa

PubMed Central

Nittrouer, Susan

2008-01-01

When it comes to making decisions regarding vowel quality, adults seem to weight dynamic syllable structure more strongly than static structure, although disagreement exists over the nature of the most relevant kind of dynamic structure: spectral change intrinsic to the vowel or structure arising from movements between consonant and vowel constrictions. Results have been even less clear regarding the signal components children use in making vowel judgments. In this experiment, listeners of four different ages (adults, and 3-, 5-, and 7-year-old children) were asked to label stimuli that sounded either like steady-state vowels or like CVC syllables which sometimes had middle sections masked by coughs. Four vowel contrasts were used, crossed for type (front/back or closed/open) and consonant context (strongly or only slightly constraining of vowel tongue position). All listeners recognized vowel quality with high levels of accuracy in all conditions, but children were disproportionately hampered by strong coarticulatory effects when only steady-state formants were available. Results clarified past studies, showing that dynamic structure is critical to vowel perception for all aged listeners, but particularly for young children, and that it is the dynamic structure arising from vocal-tract movement between consonant and vowel constrictions that is most important. PMID:17902868

Ab initio study of the structure and dynamics of bulk liquid Fe

NASA Astrophysics Data System (ADS)

Marqués, M.; González, L. E.; González, D. J.

2015-10-01

Several static and dynamic properties of bulk liquid Fe at a thermodynamic state near its triple point have been evaluated by ab initio molecular dynamics simulations. The calculated static structure shows very good agreement with the available experimental data, including an asymmetric second peak in the structure factor which underlines a substantial local icosahedral short-range order in the liquid. The dynamical structure reveals propagating density fluctuations, with an associated dispersion relation which closely follows the experimental data. The dynamic structure factors S (q ,ω ) show a good agreement with their experimental counterparts which have been recently measured by an inelastic x-ray scattering experiment. The dynamical processes behind the S (q ,ω ) have been analyzed by using a model with two decay channels (a fast and a slow) associated with the relaxations of the collective excitations. The recent finding of transverselike excitation modes in the IXS data is analyzed by using the present ab initio simulation results. Several transport coefficients have been evaluated and the results are compared with the available experimental data.

Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC).

PubMed

Galindo-Murillo, Rodrigo; Roe, Daniel R; Cheatham, Thomas E

2015-05-01

The structure and dynamics of DNA are critically related to its function. Molecular dynamics simulations augment experiment by providing detailed information about the atomic motions. However, to date the simulations have not been long enough for convergence of the dynamics and structural properties of DNA. Molecular dynamics simulations performed with AMBER using the ff99SB force field with the parmbsc0 modifications, including ensembles of independent simulations, were compared to long timescale molecular dynamics performed with the specialized Anton MD engine on the B-DNA structure d(GCACGAACGAACGAACGC). To assess convergence, the decay of the average RMSD values over longer and longer time intervals was evaluated in addition to assessing convergence of the dynamics via the Kullback-Leibler divergence of principal component projection histograms. These molecular dynamics simulations-including one of the longest simulations of DNA published to date at ~44μs-surprisingly suggest that the structure and dynamics of the DNA helix, neglecting the terminal base pairs, are essentially fully converged on the ~1-5μs timescale. We can now reproducibly converge the structure and dynamics of B-DNA helices, omitting the terminal base pairs, on the μs time scale with both the AMBER and CHARMM C36 nucleic acid force fields. Results from independent ensembles of simulations starting from different initial conditions, when aggregated, match the results from long timescale simulations on the specialized Anton MD engine. With access to large-scale GPU resources or the specialized MD engine "Anton" it is possible for a variety of molecular systems to reproducibly and reliably converge the conformational ensemble of sampled structures. This article is part of a Special Issue entitled: Recent developments of molecular dynamics. Copyright © 2014. Published by Elsevier B.V.

The analysis of dynamic characteristics and wind-induced displacement response of space Beam String Structure

NASA Astrophysics Data System (ADS)

Chen, Yong Jian; Feng, Zhen Fa; Qi, Ai; Huang, Ying

2018-06-01

The Beam String Structure structural system, also called BSS, has the advantages of lighter dead weight and greater flexibility. The wind load is the main design control factor. The dynamic characteristics and wind-induced displacement response of BSS are studied by the finite element method. The roof structure of the stadium roof of the Fuzhou Olympic Sports Center is the engineering background. 1)The numerical model was built by ANSYS, by shape finding, determine the initial stress state of structural members such as external cables; 2)From the analysis of dynamic characteristics, the main mode of vibration is the vibration of cables; 3)The wind speed spectrum of MATLAB generation structure is obtained by AR method, the structural response of the structure under static wind load and fluctuating wind load is calculated. From the analysis result, considering the equivalent static wind load of BSS , the design of adverse wind is not safe, and the fluctuating wind load should be taken into account.

Ion-ion dynamic structure factor of warm dense mixtures

DOE PAGES

Gill, N. M.; Heinonen, R. A.; Starrett, C. E.; ...

2015-06-25

In this study, the ion-ion dynamic structure factor of warm dense matter is determined using the recently developed pseudoatom molecular dynamics method [Starrett et al., Phys. Rev. E 91, 013104 (2015)]. The method uses density functional theory to determine ion-ion pair interaction potentials that have no free parameters. These potentials are used in classical molecular dynamics simulations. This constitutes a computationally efficient and realistic model of dense plasmas. Comparison with recently published simulations of the ion-ion dynamic structure factor and sound speed of warm dense aluminum finds good to reasonable agreement. Using this method, we make predictions of the ion-ionmore » dynamical structure factor and sound speed of a warm dense mixture—equimolar carbon-hydrogen. This material is commonly used as an ablator in inertial confinement fusion capsules, and our results are amenable to direct experimental measurement.« less

On the relationship between the dynamic behavior and nanoscale staggered structure of the bone

NASA Astrophysics Data System (ADS)

Qwamizadeh, Mahan; Zhang, Zuoqi; Zhou, Kun; Zhang, Yong Wei

2015-05-01

Bone, a typical load-bearing biological material, composed of ordinary base materials such as organic protein and inorganic mineral arranged in a hierarchical architecture, exhibits extraordinary mechanical properties. Up to now, most of previous studies focused on its mechanical properties under static loading. However, failure of the bone occurs often under dynamic loading. An interesting question is: Are the structural sizes and layouts of the bone related or even adapted to the functionalities demanded by its dynamic performance? In the present work, systematic finite element analysis was performed on the dynamic response of nanoscale bone structures under dynamic loading. It was found that for a fixed mineral volume fraction and unit cell area, there exists a nanoscale staggered structure at some specific feature size and layout which exhibits the fastest attenuation of stress waves. Remarkably, these specific feature sizes and layouts are in excellent agreement with those experimentally observed in the bone at the same scale, indicating that the structural size and layout of the bone at the nanoscale are evolutionarily adapted to its dynamic behavior. The present work points out the importance of dynamic effect on the biological evolution of load-bearing biological materials.

Dynamic Investigation of Static Divergence: Analysis and Testing

NASA Technical Reports Server (NTRS)

Heeg, Jennifer

2000-01-01

The phenomenon known as aeroelastic divergence is the focus of this work. The analyses and experiment presented here show that divergence can occur without a structural dynamic mode losing its oscillatory nature. Aeroelastic divergence occurs when the structural restorative capability or stiffness of a structure is overwhelmed by the static aerodynamic moment. This static aeroelastic coupling does not require the structural dynamic system behavior to cease, however. Aeroelastic changes in the dynamic mode behavior are governed not only by the stiffness, but by damping and inertial properties. The work presented here supports these fundamental assertions by examining a simple system: a typical section airfoil with only a rotational structural degree of freedom. Analytical results identified configurations that exhibit different types of dynamic mode behavior as the system encounters divergence. A wind tunnel model was designed and tested to examine divergence experimentally. The experimental results validate the analytical calculations and explicitly examine the divergence phenomenon where the dynamic mode persists. Three configurations of the wind tunnel model were tested. The experimental results agree very well with the analytical predictions of subcritical characteristics, divergence velocity, and behavior of the noncritical dynamic mode at divergence.

Insights into structural and dynamical features of water at halloysite interfaces probed by DFT and classical molecular dynamics simulations.

PubMed

Presti, Davide; Pedone, Alfonso; Mancini, Giordano; Duce, Celia; Tiné, Maria Rosaria; Barone, Vincenzo

2016-01-21

Density functional theory calculations and classical molecular dynamics simulations have been used to investigate the structure and dynamics of water molecules on kaolinite surfaces and confined in the interlayer of a halloysite model of nanometric dimension. The first technique allowed us to accurately describe the structure of the tetrahedral-octahedral slab of kaolinite in vacuum and in interaction with water molecules and to assess the performance of two widely employed empirical force fields to model water/clay interfaces. Classical molecular dynamics simulations were used to study the hydrogen bond network structure and dynamics of water adsorbed on kaolinite surfaces and confined in the halloysite interlayer. The results are in nice agreement with the few experimental data available in the literature, showing a pronounced ordering and reduced mobility of water molecules at the hydrophilic octahedral surfaces of kaolinite and confined in the halloysite interlayer, with respect to water interacting with the hydrophobic tetrahedral surfaces and in the bulk. Finally, this investigation provides new atomistic insights into the structural and dynamical properties of water-clay interfaces, which are of fundamental importance for both natural processes and industrial applications.

Dynamics and control of twisting bi-stable structures

NASA Astrophysics Data System (ADS)

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

2018-02-01

Compliance-based morphing structures have the potential to offer large shape adaptation, high stiffness and low weight, while reducing complexity, friction, and scalability problems of mechanism based systems. A promising class of structure that enables these characteristics are multi-stable structures given their ability to exhibit large deflections and rotations without the expensive need for continuous actuation, with the latter only required intermittently. Furthermore, multi-stable structures exhibit inherently fast response due to the snap-through instability governing changes between stable states, enabling rapid configuration switching between the discrete number of programmed shapes of the structure. In this paper, the design and utilisation of the inherent nonlinear dynamics of bi-stable twisting I-beam structures for actuation with low strain piezoelectric materials is presented. The I-beam structure consists of three compliant components assembled into a monolithic single element, free of moving parts, and showing large deflections between two stable states. Finite element analysis is utilised to uncover the distribution of strain across the width of the flange, guiding the choice of positioning for piezoelectric actuators. In addition, the actuation authority is maximised by calculating the generalised coupling coefficient for different positions of the piezoelectric actuators. The results obtained are employed to tailor and test I-beam designs exhibiting desired large deflection between stable states, while still enabling the activation of snap-through with the low strain piezoelectric actuators. To this end, the dynamic response of the I-beams to piezoelectric excitation is investigated, revealing that resonant excitations are insufficient to dynamically trigger snap-through. A novel bang-bang control strategy, which exploits the nonlinear dynamics of the structure successfully triggers both single and constant snap-through between the stable states of the bi-stable twisting I-beam structures. The obtained optimal piezoelectric actuator positioning is not necessarily intuitive and when used with the proposed dynamic actuation strategy serve as a blueprint for the actuation of such multi-stable compliant structures to produce fast and large deflections with highly embeddable actuators. This class of structures has potential applications in aerospace systems and soft/compliant robotics.

Modeling, Analysis, and Optimization Issues for Large Space Structures

NASA Technical Reports Server (NTRS)

Pinson, L. D. (Compiler); Amos, A. K. (Compiler); Venkayya, V. B. (Compiler)

1983-01-01

Topics concerning the modeling, analysis, and optimization of large space structures are discussed including structure-control interaction, structural and structural dynamics modeling, thermal analysis, testing, and design.

Advances in engineering science, volume 2

NASA Technical Reports Server (NTRS)

1976-01-01

Papers are presented dealing with structural dynamics; structural synthesis; and the nonlinear analysis of structures, structural members, and composite structures and materials. Applications of mathematics and computer science are included.

Structures to Resist the Effects of Accidental Explosions. Volume 3. Principles of Dynamic Analysis

DTIC Science & Technology

1984-06-01

multi-degree-of-freedom systems) is presented. A step-by-step numerical integration of an element’s motion under dynamic loads using the...structural arrangements; providing closures, and preventing damage to interior portions of structures due to structual motion , shock, and fragment...an element’s motion under dynamic loads utilizing the Acceleration-Impulse- Extrapolation Method or the Average Acceleration Method and design charts

In Silico Design of Smart Binders to Anthrax PA

DTIC Science & Technology

2012-09-01

nanosecond(ns) molecular dynamics simulation in the NPT ensemble (constant particle number, pressure, and temperature) at 300K, with the CHARMM force...protective antigen (PA). Before the docking runs, the DS23 peptide was simulated using molecular dynamics to generate an ensemble of structures...structure), we do not see a large amount of structural change when using molecular dynamics after Rosetta docking. We note that this RMSD does not take

Coupling of electromagnetics and structural/fluid dynamics - application to the dual coolant blanket subjected to plasma disruptions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jordan, T.

Some aspects concerning the coupling of quasi-stationary electromagnetics and the dynamics of structure and fluid are investigated. The necessary equations are given in a dimensionless form. The dimensionless parameters in these equations are used to evaluate the importance of the different coupling effects. A finite element formulation of the eddy-current damping in solid structures is developed. With this formulation, an existing finite element method (FEM) structural dynamics code is extended and coupled to an FEM eddy-current code. With this program system, the influence of the eddy-current damping on the dynamic loading of the dual coolant blanket during a centered plasmamore » disruption is determined. The analysis proves that only in loosely fixed or soft structures will eddy-current damping considerably reduce the resulting stresses. Additionally, the dynamic behavior of the liquid metal in the blankets` poloidal channels is described with a simple two-dimensional magnetohydrodynamic approach. The analysis of the dimensionless parameters shows that for small-scale experiments, which are designed to model the coupled electromagnetic and structural/fluid dynamic effects in such a blanket, the same magnetic fields must be applied as in the real fusion device. This will be the easiest way to design experiments that produce transferable results. 10 refs., 7 figs.« less

Recent Advances in Heliogyro Solar Sail Structural Dynamics, Stability, and Control Research

NASA Technical Reports Server (NTRS)

Wilkie, W. Keats; Warren, Jerry E.; Horta, Lucas G.; Lyle, Karen H.; Juang, Jer-Nan; Gibbs, S. Chad; Dowell, Earl H.; Guerrant, Daniel V.; Lawrence, Dale

2015-01-01

Results from recent NASA sponsored research on the structural dynamics, stability, 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, and solarelastic stability analysis of heliogyro solar sails, including stability during blade deployment. Recent results from terrestrial 1-g blade dynamics and control experiments on "rope ladder" membrane blade analogs, and small-scale in vacuo system identification experiments with hanging and spinning high-aspect ratio membranes will also be presented. A low-cost, rideshare payload heliogyro technology demonstration mission concept is used as a mission context for these heliogyro structural dynamics and solarelasticity investigations, and is also described. Blade torsional dynamic response and control are also shown to be significantly improved through the use of edge stiffening structural features or inclusion of modest tip masses to increase centrifugal stiffening of the blade structure. An output-only system identification procedure suitable for on-orbit blade dynamics investigations is also developed and validated using ground tests of spinning sub-scale heliogyro blade models. Overall, analytical and experimental investigations to date indicate no intractable stability or control issues for the heliogyro solar sail concept.

Protic ammonium carboxylate ionic liquids: insight into structure, dynamics and thermophysical properties by alkyl group functionalization.

PubMed

Reddy, Th Dhileep N; Mallik, Bhabani S

2017-04-19

This study is aimed at characterising the structure, dynamics and thermophysical properties of five alkylammonium carboxylate ionic liquids (ILs) from classical molecular dynamics simulations. The structural features of these ILs were characterised by calculating the site-site radial distribution functions, g(r), spatial distribution functions and structure factors. The structural properties demonstrate that ILs show greater interaction between cations and anions when alkyl chain length increases on the cation or anion. In all ILs, spatial distribution functions show that the anion is close to the acidic hydrogen atoms of the ammonium cation. We determined the role of alkyl group functionalization of the charged entities, cations and anions, in the dynamical behavior and the transport coefficients of this family of ionic liquids. The dynamics of ILs are described by studying the mean square displacement (MSD) of the centres of mass of the ions, diffusion coefficients, ionic conductivities and hydrogen bonds as well as residence dynamics. The diffusion coefficients and ionic conductivity decrease with an increase in the size of the cation or anion. The effect of alkyl chain length on ionic conductivity calculated in this article is consistent with the findings of other experimental studies. Hydrogen bond lifetimes and residence times along with structure factors were also calculated, and are related to alkyl chain length.

152. Photocopy of drawing (1963 structural drawing by General Dynamics/Astronautics) ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

152. Photocopy of drawing (1963 structural drawing by General Dynamics/Astronautics) STRUCTURAL DETAILS FOR MST STATIONS 21, 30, 39, AND 48, SHEET S98 - Vandenberg Air Force Base, Space Launch Complex 3, Launch Pad 3 East, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

SPAR improved structure-fluid dynamic analysis capability, phase 2

NASA Technical Reports Server (NTRS)

Pearson, M. L.

1984-01-01

An efficient and general method of analyzing a coupled dynamic system of fluid flow and elastic structures is investigated. The improvement of Structural Performance Analysis and Redesign (SPAR) code is summarized. All error codes are documented and the SPAR processor/subroutine cross reference is included.

Advanced structures technology and aircraft safety

NASA Technical Reports Server (NTRS)

Mccomb, H. G., Jr.

1983-01-01

NASA research and development on advanced aeronautical structures technology related to flight safety is reviewed. The effort is categorized as research in the technology base and projects sponsored by the Aircraft Energy Efficiency (ACEE) Project Office. Base technology research includes mechanics of composite structures, crash dynamics, and landing dynamics. The ACEE projects involve development and fabrication of selected composite structural components for existing commercial transport aircraft. Technology emanating from this research is intended to result in airframe structures with improved efficiency and safety.

Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms

PubMed Central

Ding, Feng; Sharma, Shantanu; Chalasani, Poornima; Demidov, Vadim V.; Broude, Natalia E.; Dokholyan, Nikolay V.

2008-01-01

RNA molecules with novel functions have revived interest in the accurate prediction of RNA three-dimensional (3D) structure and folding dynamics. However, existing methods are inefficient in automated 3D structure prediction. Here, we report a robust computational approach for rapid folding of RNA molecules. We develop a simplified RNA model for discrete molecular dynamics (DMD) simulations, incorporating base-pairing and base-stacking interactions. We demonstrate correct folding of 150 structurally diverse RNA sequences. The majority of DMD-predicted 3D structures have <4 Å deviations from experimental structures. The secondary structures corresponding to the predicted 3D structures consist of 94% native base-pair interactions. Folding thermodynamics and kinetics of tRNAPhe, pseudoknots, and mRNA fragments in DMD simulations are in agreement with previous experimental findings. Folding of RNA molecules features transient, non-native conformations, suggesting non-hierarchical RNA folding. Our method allows rapid conformational sampling of RNA folding, with computational time increasing linearly with RNA length. We envision this approach as a promising tool for RNA structural and functional analyses. PMID:18456842

A continuum model for dynamic analysis of the Space Station

NASA Technical Reports Server (NTRS)

Thomas, Segun

1989-01-01

Dynamic analysis of the International Space Station using MSC/NASTRAN had 1312 rod elements, 62 beam elements, 489 nodes and 1473 dynamic degrees of freedom. A realtime, man-in-the-loop simulation of such a model is impractical. This paper discusses the mathematical model for realtime dynamic simulation of the Space Station. Several key questions in structures and structural dynamics are addressed. First, to achieve a significant reduction in the number of dynamic degrees of freedom, a continuum equivalent representation of the Space Station truss structure which accounted for the unsymmetry of the basic configuration and resulted in the coupling of extensional and transverse deformation, is developed. Next, dynamic equations for the continuum equivalent of the Space Station truss structure are formulated using a matrix version of Kane's dynamical equations. Flexibility is accounted for by using a theory that accommodates extension, bending in two principal planes and shear displacement. Finally, constraint equations suitable for dynamic analysis of flexible bodies with closed loop configuration are developed and solution of the resulting system of equations is based on the zero eigenvalue theorem.

Space truss zero gravity dynamics

NASA Technical Reports Server (NTRS)

Swanson, Andy

1989-01-01

The Structural Dynamics Branch of the Air Force Flight Dynamics Laboratory in cooperation with the Reduced Gravity Office of the NASA Lyndon B. Johnson Space Center (JSC) plans to perform zero-gravity dynamic tests of a 12-meter truss structure. This presentation describes the program and presents all results obtained to date.

Mastodon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coleman, Justin Leigh; Veeraraghavan, Swetha; Bolisetti, Chandrakanth

MASTODON has the capability to model stochastic nonlinear soil-structure interaction (NLSSI) in a dynamic probabilistic risk assessment framework. The NLSSI simulations include structural dynamics, time integration, dynamic porous media flow, nonlinear hysteretic soil constitutive models, geometric nonlinearities (gapping, sliding, and uplift). MASTODON is also the MOOSE based master application for dynamic PRA of external hazards.

Structural anomaly and dynamic heterogeneity in cycloether/water binary mixtures: Signatures from composition dependent dynamic fluorescence measurements and computer simulations

NASA Astrophysics Data System (ADS)

Indra, Sandipa; Guchhait, Biswajit; Biswas, Ranjit

2016-03-01

We have performed steady state UV-visible absorption and time-resolved fluorescence measurements and computer simulations to explore the cosolvent mole fraction induced changes in structural and dynamical properties of water/dioxane (Diox) and water/tetrahydrofuran (THF) binary mixtures. Diox is a quadrupolar solvent whereas THF is a dipolar one although both are cyclic molecules and represent cycloethers. The focus here is on whether these cycloethers can induce stiffening and transition of water H-bond network structure and, if they do, whether such structural modification differentiates the chemical nature (dipolar or quadrupolar) of the cosolvent molecules. Composition dependent measured fluorescence lifetimes and rotation times of a dissolved dipolar solute (Coumarin 153, C153) suggest cycloether mole-fraction (XTHF/Diox) induced structural transition for both of these aqueous binary mixtures in the 0.1 ≤ XTHF/Diox ≤ 0.2 regime with no specific dependence on the chemical nature. Interestingly, absorption measurements reveal stiffening of water H-bond structure in the presence of both the cycloethers at a nearly equal mole-fraction, XTHF/Diox ˜ 0.05. Measurements near the critical solution temperature or concentration indicate no role for the solution criticality on the anomalous structural changes. Evidences for cycloether aggregation at very dilute concentrations have been found. Simulated radial distribution functions reflect abrupt changes in respective peak heights at those mixture compositions around which fluorescence measurements revealed structural transition. Simulated water coordination numbers (for a dissolved C153) and number of H-bonds also exhibit minima around these cosolvent concentrations. In addition, several dynamic heterogeneity parameters have been simulated for both the mixtures to explore the effects of structural transition and chemical nature of cosolvent on heterogeneous dynamics of these systems. Simulated four-point dynamic susceptibility suggests formation of clusters inducing local heterogeneity in the solution structure.

Structural behavior and dynamics of an anomalous fluid between attractive and repulsive walls: Templating, molding, and superdiffusion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leoni, Fabio; Franzese, Giancarlo

2014-11-07

Confinement can modify the dynamics, the thermodynamics, and the structural properties of liquid water, the prototypical anomalous liquid. By considering a generic model for anomalous liquids, suitable for describing solutions of globular proteins, colloids, or liquid metals, we study by molecular dynamics simulations the effect that an attractive wall with structure and a repulsive wall without structure have on the phases, the crystal nucleation, and the dynamics of the fluid. We find that at low temperatures the large density of the attractive wall induces a high-density, high-energy structure in the first layer (“templating” effect). In turn, the first layer inducesmore » a “molding” effect on the second layer determining a structure with reduced energy and density, closer to the average density of the system. This low-density, low-energy structure propagates further through the layers by templating effect and can involve all the existing layers at the lowest temperatures investigated. Therefore, although the high-density, high-energy structure does not self-reproduce further than the first layer, the structured wall can have a long-range influence thanks to a sequence of templating, molding, and templating effects through the layers. We find that the walls also have an influence on the dynamics of the liquid, with a stronger effect near the attractive wall. In particular, we observe that the dynamics is largely heterogeneous (i) among the layers, as a consequence of the sequence of structures caused by the walls presence, and (ii) within the same layer, due to superdiffusive liquid veins within a frozen matrix of particles near the walls at low temperature and high density. Hence, the partial freezing of the first layer does not correspond necessarily to an effective reduction of the channel's section in terms of transport properties, as suggested by other authors.« less

An application of holographic interferometry for dynamic vibration analysis of a jet engine turbine compressor rotor

NASA Astrophysics Data System (ADS)

Fein, Howard

2003-09-01

Holographic Interferometry has been successfully employed to characterize the materials and behavior of diverse types of structures under dynamic stress. Specialized variations of this technology have also been applied to define dynamic and vibration related structural behavior. Such applications of holographic technique offer some of the most effective methods of modal and dynamic analysis available. Real-time dynamic testing of the modal and mechanical behavior of jet engine turbine, rotor, vane, and compressor structures has always required advanced instrumentation for data collection in either simulated flight operation test or computer-based modeling and simulations. Advanced optical holography techniques are alternate methods which result in actual full-field behavioral data in a noninvasive, noncontact environment. These methods offer significant insight in both the development and subsequent operational test and modeling of advanced jet engine turbine and compressor rotor structures and their integration with total vehicle system dynamics. Structures and materials can be analyzed with very low amplitude excitation and the resultant data can be used to adjust the accuracy of mathematically derived structural and behavioral models. Holographic Interferometry offers a powerful tool to aid in the developmental engineering of turbine rotor and compressor structures for high stress applications. Aircraft engine applications in particular most consider operational environments where extremes in vibration and impulsive as well as continuous mechanical stress can affect both operation and structural stability. These considerations present ideal requisites for analysis using advanced holographic methods in the initial design and test of turbine rotor components. Holographic techniques are nondestructive, real-time, and definitive in allowing the identification of vibrational modes, displacements, and motion geometries. Such information can be crucial to the determination of mechanical configurations and designs as well as critical operational parameters of turbine structural components or unit turbine components fabricated from advanced and exotic new materials or using new fabrication methods. Anomalous behavioral characteristics can be directly related to hidden structural or mounting anomalies and defects.

Structural behavior and dynamics of an anomalous fluid between attractive and repulsive walls: templating, molding, and superdiffusion.

PubMed

Leoni, Fabio; Franzese, Giancarlo

2014-11-07

Confinement can modify the dynamics, the thermodynamics, and the structural properties of liquid water, the prototypical anomalous liquid. By considering a generic model for anomalous liquids, suitable for describing solutions of globular proteins, colloids, or liquid metals, we study by molecular dynamics simulations the effect that an attractive wall with structure and a repulsive wall without structure have on the phases, the crystal nucleation, and the dynamics of the fluid. We find that at low temperatures the large density of the attractive wall induces a high-density, high-energy structure in the first layer ("templating" effect). In turn, the first layer induces a "molding" effect on the second layer determining a structure with reduced energy and density, closer to the average density of the system. This low-density, low-energy structure propagates further through the layers by templating effect and can involve all the existing layers at the lowest temperatures investigated. Therefore, although the high-density, high-energy structure does not self-reproduce further than the first layer, the structured wall can have a long-range influence thanks to a sequence of templating, molding, and templating effects through the layers. We find that the walls also have an influence on the dynamics of the liquid, with a stronger effect near the attractive wall. In particular, we observe that the dynamics is largely heterogeneous (i) among the layers, as a consequence of the sequence of structures caused by the walls presence, and (ii) within the same layer, due to superdiffusive liquid veins within a frozen matrix of particles near the walls at low temperature and high density. Hence, the partial freezing of the first layer does not correspond necessarily to an effective reduction of the channel's section in terms of transport properties, as suggested by other authors.

MD simulations of papillomavirus DNA-E2 protein complexes hints at a protein structural code for DNA deformation.

PubMed

Falconi, M; Oteri, F; Eliseo, T; Cicero, D O; Desideri, A

2008-08-01

The structural dynamics of the DNA binding domains of the human papillomavirus strain 16 and the bovine papillomavirus strain 1, complexed with their DNA targets, has been investigated by modeling, molecular dynamics simulations, and nuclear magnetic resonance analysis. The simulations underline different dynamical features of the protein scaffolds and a different mechanical interaction of the two proteins with DNA. The two protein structures, although very similar, show differences in the relative mobility of secondary structure elements. Protein structural analyses, principal component analysis, and geometrical and energetic DNA analyses indicate that the two transcription factors utilize a different strategy in DNA recognition and deformation. Results show that the protein indirect DNA readout is not only addressable to the DNA molecule flexibility but it is finely tuned by the mechanical and dynamical properties of the protein scaffold involved in the interaction.

Dynamic New World: Refining Our View of Protein Structure, Function and Evolution

PubMed Central

Mannige, Ranjan V.

2014-01-01

Proteins are crucial to the functioning of all lifeforms. Traditional understanding posits that a single protein occupies a single structure (“fold”), which performs a single function. This view is radically challenged with the recognition that high structural dynamism—the capacity to be extra “floppy”—is more prevalent in functional proteins than previously assumed. As reviewed here, this dynamic take on proteins affects our understanding of protein “structure”, function, and evolution, and even gives us a glimpse into protein origination. Specifically, this review will discuss historical developments concerning protein structure, and important new relationships between dynamism and aspects of protein sequence, structure, binding modes, binding promiscuity, evolvability, and origination. Along the way, suggestions will be provided for how key parts of textbook definitions—that so far have excluded membership to intrinsically disordered proteins (IDPs)—could be modified to accommodate our more dynamic understanding of proteins. PMID:28250374

Environmental structure and competitive scoring advantages in team competitions.

PubMed

Merritt, Sears; Clauset, Aaron

2013-10-29

In most professional sports, playing field structure is kept neutral so that scoring imbalances may be attributed to differences in team skill. It thus remains unknown what impact environmental heterogeneities can have on scoring dynamics or competitive advantages. Applying a novel generative model of scoring dynamics to roughly 10 million team competitions drawn from an online game, we quantify the relationship between the structure within a competition and its scoring dynamics, while controlling the impact of chance. Despite wide structural variations, we observe a common three-phase pattern in the tempo of events. Tempo and balance are highly predictable from a competition's structural features alone and teams exploit environmental heterogeneities for sustained competitive advantage. Surprisingly, the most balanced competitions are associated with specific environmental heterogeneities, not from equally skilled teams. These results shed new light on the design principles of balanced competition, and illustrate the potential of online game data for investigating social dynamics and competition.

Structural and dynamical properties of the V(3+) ion in dilute aqueous solution: An ab initio QM/MM molecular dynamics simulation.

PubMed

Kritayakornupong, Chinapong

2009-12-01

A hybrid ab initio QM/MM molecular dynamics simulation at the Hartree-Fock level has been performed to investigate structural and dynamical parameters of the V(3+) ion in dilute aqueous solution. A distorted octahedral structure with the average V(3+)-O distance of 1.99 A is evaluated from the QM/MM simulation, which is in good agreement with the X-ray data. Several structural parameters such as angular distribution functions, theta- and tilt-angle distributions have been determined to obtain the full description of the hydration structure of the hydrated V(3+). The Jahn-Teller distortions of the V(3+) ion are pronounced in the QM/MM simulation. The mean residence time of 14.5 ps is estimated for the ligand exchange processes in the second hydration shell. (c) 2009 Wiley Periodicals, Inc.

Dynamically variable negative stiffness structures.

PubMed

Churchill, Christopher B; Shahan, David W; Smith, Sloan P; Keefe, Andrew C; McKnight, Geoffrey P

2016-02-01

Variable stiffness structures that enable a wide range of efficient load-bearing and dexterous activity are ubiquitous in mammalian musculoskeletal systems but are rare in engineered systems because of their complexity, power, and cost. We present a new negative stiffness-based load-bearing structure with dynamically tunable stiffness. Negative stiffness, traditionally used to achieve novel response from passive structures, is a powerful tool to achieve dynamic stiffness changes when configured with an active component. Using relatively simple hardware and low-power, low-frequency actuation, we show an assembly capable of fast (<10 ms) and useful (>100×) dynamic stiffness control. This approach mitigates limitations of conventional tunable stiffness structures that exhibit either small (<30%) stiffness change, high friction, poor load/torque transmission at low stiffness, or high power active control at the frequencies of interest. We experimentally demonstrate actively tunable vibration isolation and stiffness tuning independent of supported loads, enhancing applications such as humanoid robotic limbs and lightweight adaptive vibration isolators.

Theoretical and software considerations for nonlinear dynamic analysis

NASA Technical Reports Server (NTRS)

Schmidt, R. J.; Dodds, R. H., Jr.

1983-01-01

In the finite element method for structural analysis, it is generally necessary to discretize the structural model into a very large number of elements to accurately evaluate displacements, strains, and stresses. As the complexity of the model increases, the number of degrees of freedom can easily exceed the capacity of present-day software system. Improvements of structural analysis software including more efficient use of existing hardware and improved structural modeling techniques are discussed. One modeling technique that is used successfully in static linear and nonlinear analysis is multilevel substructuring. This research extends the use of multilevel substructure modeling to include dynamic analysis and defines the requirements for a general purpose software system capable of efficient nonlinear dynamic analysis. The multilevel substructuring technique is presented, the analytical formulations and computational procedures for dynamic analysis and nonlinear mechanics are reviewed, and an approach to the design and implementation of a general purpose structural software system is presented.

Global Dynamics of Proteins: Bridging Between Structure and Function

PubMed Central

Bahar, Ivet; Lezon, Timothy R.; Yang, Lee-Wei; Eyal, Eran

2010-01-01

Biomolecular systems possess unique, structure-encoded dynamic properties that underlie their biological functions. Recent studies indicate that these dynamic properties are determined to a large extent by the topology of native contacts. In recent years, elastic network models used in conjunction with normal mode analyses have proven to be useful for elucidating the collective dynamics intrinsically accessible under native state conditions, including in particular the global modes of motions that are robustly defined by the overall architecture. With increasing availability of structural data for well-studied proteins in different forms (liganded, complexed, or free), there is increasing evidence in support of the correspondence between functional changes in structures observed in experiments and the global motions predicted by these coarse-grained analyses. These observed correlations suggest that computational methods may be advantageously employed for assessing functional changes in structure and allosteric mechanisms intrinsically favored by the native fold. PMID:20192781

Global dynamics of proteins: bridging between structure and function.

PubMed

Bahar, Ivet; Lezon, Timothy R; Yang, Lee-Wei; Eyal, Eran

2010-01-01

Biomolecular systems possess unique, structure-encoded dynamic properties that underlie their biological functions. Recent studies indicate that these dynamic properties are determined to a large extent by the topology of native contacts. In recent years, elastic network models used in conjunction with normal mode analyses have proven to be useful for elucidating the collective dynamics intrinsically accessible under native state conditions, including in particular the global modes of motions that are robustly defined by the overall architecture. With increasing availability of structural data for well-studied proteins in different forms (liganded, complexed, or free), there is increasing evidence in support of the correspondence between functional changes in structures observed in experiments and the global motions predicted by these coarse-grained analyses. These observed correlations suggest that computational methods may be advantageously employed for assessing functional changes in structure and allosteric mechanisms intrinsically favored by the native fold.

Similitude design for the vibration problems of plates and shells: A review

NASA Astrophysics Data System (ADS)

Zhu, Yunpeng; Wang, You; Luo, Zhong; Han, Qingkai; Wang, Deyou

2017-06-01

Similitude design plays a vital role in the analysis of vibration and shock problems encountered in large engineering equipment. Similitude design, including dimensional analysis and governing equation method, is founded on the dynamic similitude theory. This study reviews the application of similitude design methods in engineering practice and summarizes the major achievements of the dynamic similitude theory in structural vibration and shock problems in different fields, including marine structures, civil engineering structures, and large power equipment. This study also reviews the dynamic similitude design methods for thin-walled and composite material plates and shells, including the most recent work published by the authors. Structure sensitivity analysis is used to evaluate the scaling factors to attain accurate distorted scaling laws. Finally, this study discusses the existing problems and the potential of the dynamic similitude theory for the analysis of vibration and shock problems of structures.

Environmental structure and competitive scoring advantages in team competitions

NASA Astrophysics Data System (ADS)

Merritt, Sears; Clauset, Aaron

2013-10-01

In most professional sports, playing field structure is kept neutral so that scoring imbalances may be attributed to differences in team skill. It thus remains unknown what impact environmental heterogeneities can have on scoring dynamics or competitive advantages. Applying a novel generative model of scoring dynamics to roughly 10 million team competitions drawn from an online game, we quantify the relationship between the structure within a competition and its scoring dynamics, while controlling the impact of chance. Despite wide structural variations, we observe a common three-phase pattern in the tempo of events. Tempo and balance are highly predictable from a competition's structural features alone and teams exploit environmental heterogeneities for sustained competitive advantage. Surprisingly, the most balanced competitions are associated with specific environmental heterogeneities, not from equally skilled teams. These results shed new light on the design principles of balanced competition, and illustrate the potential of online game data for investigating social dynamics and competition.

PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks

PubMed Central

Craveur, Pierrick; Joseph, Agnel Praveen; Jallu, Vincent

2017-01-01

This paper describes the development and application of a suite of tools, called PBxplore, to analyze the dynamics and deformability of protein structures using Protein Blocks (PBs). Proteins are highly dynamic macromolecules, and a classical way to analyze their inherent flexibility is to perform molecular dynamics simulations. The advantage of using small structural prototypes such as PBs is to give a good approximation of the local structure of the protein backbone. More importantly, by reducing the conformational complexity of protein structures, PBs allow analysis of local protein deformability which cannot be done with other methods and had been used efficiently in different applications. PBxplore is able to process large amounts of data such as those produced by molecular dynamics simulations. It produces frequencies, entropy and information logo outputs as text and graphics. PBxplore is available at https://github.com/pierrepo/PBxplore and is released under the open-source MIT license. PMID:29177113

Visualization of Dynamic Vortex Structures in Magnetic Films with Uniaxial Anisotropy (Micromagnetic Simulation)

NASA Astrophysics Data System (ADS)

Zverev, V. V.; Izmozherov, I. M.; Filippov, B. N.

2018-02-01

Three-dimensional computer simulation of dynamic processes in a moving domain boundary separating domains in a soft magnetic uniaxial film with planar anisotropy is performed by numerical solution of Landau-Lifshitz-Gilbert equations. The developed visualization methods are used to establish the connection between the motion of surface vortices and antivortices, singular (Bloch) points, and core lines of intrafilm vortex structures. A relation between the character of magnetization dynamics and the film thickness is found. The analytical models of spatial vortex structures for imitation of topological properties of the structures observed in micromagnetic simulation are constructed.

The dynamics, structure, and conformational free energy of proline-containing antifreeze glycoprotein.

PubMed Central

Nguyen, Dat H; Colvin, Michael E; Yeh, Yin; Feeney, Robert E; Fink, William H

2002-01-01

Recent NMR studies of the solution structure of the 14-amino acid antifreeze glycoprotein AFGP-8 have concluded that the molecule lacks long-range order. The implication that an apparently unstructured molecule can still have a very precise function as a freezing inhibitor seems startling at first consideration. To gain insight into the nature of conformations and motions in AFGP-8, we have undertaken molecular dynamics simulations augmented with free energy calculations using a continuum solvation model. Starting from 10 different NMR structures, 20 ns of dynamics of AFGP were explored. The dynamics show that AFGP structure is composed of four segments, joined by very flexible pivots positioned at alanine 5, 8, and 11. The dynamics also show that the presence of prolines in this small AFGP structure facilitates the adoption of the poly-proline II structure as its overall conformation, although AFGP does adopt other conformations during the course of dynamics as well. The free energies calculated using a continuum solvation model show that the lowest free energy conformations, while being energetically equal, are drastically different in conformations. In other words, this AFGP molecule has many structurally distinct and energetically equal minima in its energy landscape. In addition, conformational, energetic, and hydrogen bond analyses suggest that the intramolecular hydrogen bonds between the N-acetyl group and the protein backbone are an important integral part of the overall stability of the AFGP molecule. The relevance of these findings to the mechanism of freezing inhibition is discussed. PMID:12023212

The dynamics, structure, and conformational free energy of proline-containing antifreeze glycoprotein.

PubMed

Nguyen, Dat H; Colvin, Michael E; Yeh, Yin; Feeney, Robert E; Fink, William H

2002-06-01

Recent NMR studies of the solution structure of the 14-amino acid antifreeze glycoprotein AFGP-8 have concluded that the molecule lacks long-range order. The implication that an apparently unstructured molecule can still have a very precise function as a freezing inhibitor seems startling at first consideration. To gain insight into the nature of conformations and motions in AFGP-8, we have undertaken molecular dynamics simulations augmented with free energy calculations using a continuum solvation model. Starting from 10 different NMR structures, 20 ns of dynamics of AFGP were explored. The dynamics show that AFGP structure is composed of four segments, joined by very flexible pivots positioned at alanine 5, 8, and 11. The dynamics also show that the presence of prolines in this small AFGP structure facilitates the adoption of the poly-proline II structure as its overall conformation, although AFGP does adopt other conformations during the course of dynamics as well. The free energies calculated using a continuum solvation model show that the lowest free energy conformations, while being energetically equal, are drastically different in conformations. In other words, this AFGP molecule has many structurally distinct and energetically equal minima in its energy landscape. In addition, conformational, energetic, and hydrogen bond analyses suggest that the intramolecular hydrogen bonds between the N-acetyl group and the protein backbone are an important integral part of the overall stability of the AFGP molecule. The relevance of these findings to the mechanism of freezing inhibition is discussed.

Structural Dynamics Experimental Activities in Ultra-Lightweight and Inflatable Space Structures

NASA Technical Reports Server (NTRS)

Pappa, Richard S.; Lassiter, John O.; Ross, Brian P.

2001-01-01

This paper reports recently completed structural dynamics experimental activities with new ultralightweight 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, as follows: 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 eventual in-space deployment and performance of Gossamer spacecraft, and experimental R&D work such as this is required now to validate new analytical prediction methods. The activities discussed in the paper are pathfinder accomplishments, conducted on unique components and prototypes of future spacecraft systems.

A dynamic social systems model for considering structural factors in HIV prevention and detection

PubMed Central

Latkin, Carl; Weeks, Margaret; Glasman, Laura; Galletly, Carol; Albarracin, Dolores

2010-01-01

We present a model for HIV-related behaviors that emphasizes the dynamic and social nature of the structural factors that influence HIV prevention and detection. Key structural dimensions of the model include resources, science and technology, formal social control, informal social influences and control, social interconnectedness, and settings. These six dimensions can be conceptualized on macro, meso, and micro levels. Given the inherent complexity of structural factors and their interrelatedness, HIV prevention interventions may focus on different levels and dimensions. We employ a systems perspective to describe the interconnected and dynamic processes of change among social systems and their components. The topics of HIV testing and safer injection facilities are analyzed using this structural framework. Finally, we discuss methodological issues in the development and evaluation of structural interventions for HIV prevention and detection. PMID:20838871

Dynamic model updating based on strain mode shape and natural frequency using hybrid pattern search technique

NASA Astrophysics Data System (ADS)

Guo, Ning; Yang, Zhichun; Wang, Le; Ouyang, Yan; Zhang, Xinping

2018-05-01

Aiming at providing a precise dynamic structural finite element (FE) model for dynamic strength evaluation in addition to dynamic analysis. A dynamic FE model updating method is presented to correct the uncertain parameters of the FE model of a structure using strain mode shapes and natural frequencies. The strain mode shape, which is sensitive to local changes in structure, is used instead of the displacement mode for enhancing model updating. The coordinate strain modal assurance criterion is developed to evaluate the correlation level at each coordinate over the experimental and the analytical strain mode shapes. Moreover, the natural frequencies which provide the global information of the structure are used to guarantee the accuracy of modal properties of the global model. Then, the weighted summation of the natural frequency residual and the coordinate strain modal assurance criterion residual is used as the objective function in the proposed dynamic FE model updating procedure. The hybrid genetic/pattern-search optimization algorithm is adopted to perform the dynamic FE model updating procedure. Numerical simulation and model updating experiment for a clamped-clamped beam are performed to validate the feasibility and effectiveness of the present method. The results show that the proposed method can be used to update the uncertain parameters with good robustness. And the updated dynamic FE model of the beam structure, which can correctly predict both the natural frequencies and the local dynamic strains, is reliable for the following dynamic analysis and dynamic strength evaluation.

A model structure for identification of linear models of the UH-60 helicopter in hover and forward flight

DOT National Transportation Integrated Search

1995-08-01

A linear model structure applicable to identification of the UH-60 flight : dynamics in hover and forward flight without rotor-state data is developed. The : structure of the model is determined through consideration of the important : dynamic modes ...

Dynamic loads during failure risk assessment of bridge crane structures

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Dynamic and Structural Gas Turbine Engine Modeling

NASA Technical Reports Server (NTRS)

Turso, James A.

2003-01-01

Model the interactions between the structural dynamics and the performance dynamics of a gas turbine engine. Generally these two aspects are considered separate, unrelated phenomena and are studied independently. For diagnostic purposes, it is desirable to bring together as much information as possible, and that involves understanding how performance is affected by structural dynamics (if it is) and vice versa. This can involve the relationship between thrust response and the excitation of structural modes, for instance. The job will involve investigating and characterizing these dynamical relationships, generating a model that incorporates them, and suggesting and/or developing diagnostic and prognostic techniques that can be incorporated in a data fusion system. If no coupling is found, at the least a vibration model should be generated that can be used for diagnostics and prognostics related to blade loss, for instance.

Complexity and dynamics of topological and community structure in complex networks

NASA Astrophysics Data System (ADS)

Berec, Vesna

2017-07-01

Complexity is highly susceptible to variations in the network dynamics, reflected on its underlying architecture where topological organization of cohesive subsets into clusters, system's modular structure and resulting hierarchical patterns, are cross-linked with functional dynamics of the system. Here we study connection between hierarchical topological scales of the simplicial complexes and the organization of functional clusters - communities in complex networks. The analysis reveals the full dynamics of different combinatorial structures of q-th-dimensional simplicial complexes and their Laplacian spectra, presenting spectral properties of resulting symmetric and positive semidefinite matrices. The emergence of system's collective behavior from inhomogeneous statistical distribution is induced by hierarchically ordered topological structure, which is mapped to simplicial complex where local interactions between the nodes clustered into subcomplexes generate flow of information that characterizes complexity and dynamics of the full system.

Structural dynamic analysis of the Space Shuttle Main Engine

NASA Technical Reports Server (NTRS)

Scott, L. P.; Jamison, G. T.; Mccutcheon, W. A.; Price, J. M.

1981-01-01

This structural dynamic analysis supports development of the SSME by evaluating components subjected to critical dynamic loads, identifying significant parameters, and evaluating solution methods. Engine operating parameters at both rated and full power levels are considered. Detailed structural dynamic analyses of operationally critical and life limited components support the assessment of engine design modifications and environmental changes. Engine system test results are utilized to verify analytic model simulations. The SSME main chamber injector assembly is an assembly of 600 injector elements which are called LOX posts. The overall LOX post analysis procedure is shown.

Interfacial ionic 'liquids': connecting static and dynamic structures

DOE PAGES

Uysal, Ahmet; Zhou, Hua; Feng, Guang; ...

2014-12-05

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

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

PubMed

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

2015-01-28

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

NMR studies of a channel protein without membranes: structure and dynamics of water-solubilized KcsA.

PubMed

Ma, Dejian; Tillman, Tommy S; Tang, Pei; Meirovitch, Eva; Eckenhoff, Roderic; Carnini, Anna; Xu, Yan

2008-10-28

Structural studies of polytopic membrane proteins are often hampered by the vagaries of these proteins in membrane mimetic environments and by the difficulties in handling them with conventional techniques. Designing and creating water-soluble analogues with preserved native structures offer an attractive alternative. We report here solution NMR studies of WSK3, a water-soluble analogue of the potassium channel KcsA. The WSK3 NMR structure (PDB ID code 2K1E) resembles the KcsA crystal structures, validating the approach. By more stringent comparison criteria, however, the introduction of several charged residues aimed at improving water solubility seems to have led to the possible formations of a few salt bridges and hydrogen bonds not present in the native structure, resulting in slight differences in the structure of WSK3 relative to KcsA. NMR dynamics measurements show that WSK3 is highly flexible in the absence of a lipid environment. Reduced spectral density mapping and model-free analyses reveal dynamic characteristics consistent with an isotropically tumbling tetramer experiencing slow (nanosecond) motions with unusually low local ordering. An altered hydrogen-bond network near the selectivity filter and the pore helix, and the intrinsically dynamic nature of the selectivity filter, support the notion that this region is crucial for slow inactivation. Our results have implications not only for the design of water-soluble analogues of membrane proteins but also for our understanding of the basic determinants of intrinsic protein structure and dynamics.

An ab initio study of the structure and dynamics of bulk liquid Ag and its liquid-vapor interface

NASA Astrophysics Data System (ADS)

Gonzalez Del Rio, Beatriz; Gonzalez Tesedo, Luis Enrique; Gonzalez Fernandez, David Jose

Several static and dynamic properties of bulk liquid Ag at a thermodynamic state near its triple point have been calculated by means of ab initio molecular dynamics simulations. The calculated static structure shows a very good agreement with the available experimental data. The dynamical structure reveals collective density excitations with an associated dispersion relation which points to a small positive dispersion. Results are also reported at a slightly higher temperature in order to study the structure of the free liquid surface. The ionic density profile shows an oscillatory behaviour with two different wavelenghts, as the spacing between the outer and first inner layer is different from that between the other inner layers.

Tunable dynamic response of magnetic gels: Impact of structural properties and magnetic fields

NASA Astrophysics Data System (ADS)

Tarama, Mitsusuke; Cremer, Peet; Borin, Dmitry Y.; Odenbach, Stefan; Löwen, Hartmut; Menzel, Andreas M.

2014-10-01

Ferrogels and magnetic elastomers feature mechanical properties that can be reversibly tuned from outside through magnetic fields. Here we concentrate on the question of how their dynamic response can be adjusted. The influence of three factors on the dynamic behavior is demonstrated using appropriate minimal models: first, the orientational memory imprinted into one class of the materials during their synthesis; second, the structural arrangement of the magnetic particles in the materials; and third, the strength of an external magnetic field. To illustrate the latter point, structural data are extracted from a real experimental sample and analyzed. Understanding how internal structural properties and external influences impact the dominant dynamical properties helps to design materials that optimize the requested behavior.

Butterflies, Black swans and Dragon kings: How to use the Dynamical Systems Theory to build a "zoology" of mid-latitude circulation atmospheric extremes?

NASA Astrophysics Data System (ADS)

Faranda, D.; Yiou, P.; Alvarez-Castro, M. C. M.

2015-12-01

A combination of dynamical systems and statistical techniques allows for a robust assessment of the dynamical properties of the mid-latitude atmospheric circulation. Extremes at different spatial and time scales are not only associated to exceptionally intense weather structures (e.g. extra-tropical cyclones) but also to rapid changes of circulation regimes (thunderstorms, supercells) or the extreme persistence of weather structure (heat waves, cold spells). We will show how the dynamical systems theory of recurrence combined to the extreme value theory can take into account the spatial and temporal dependence structure of the mid-latitude circulation structures and provide information on the statistics of extreme events.

Dynamics of Structures in Configuration Space and Phase Space: An Introductory Tutorial

NASA Astrophysics Data System (ADS)

Diamond, P. H.; Kosuga, Y.; Lesur, M.

2015-12-01

Some basic ideas relevant to the dynamics of phase space and real space structures are presented in a pedagogical fashion. We focus on three paradigmatic examples, namely; G. I. Taylor's structure based re-formulation of Rayleigh's stability criterion and its implications for zonal flow momentum balance relations; Dupree's mechanism for nonlinear current driven ion acoustic instability and its implication for anomalous resistivity; and the dynamics of structures in drift and gyrokinetic turbulence and their relation to zonal flow physics. We briefly survey the extension of mean field theory to calculate evolution in the presence of localized structures for regimes where Kubo number K ≃ 1 rather than K ≪ 1, as is usual for quasilinear theory.

An overview of the crash dynamics failure behavior of metal and composite aircraft structures

NASA Technical Reports Server (NTRS)

Carden, Huey D.; Boitnott, Richard L.; Fasanella, Edwin L.; Jones, Lisa E.

1991-01-01

An overview of failure behavior results is presented from some of the crash dynamics research conducted with concepts of aircraft elements and substructure not necessarily designed or optimized for energy absorption or crash loading considerations. Experimental and analytical data are presented that indicate some general trends in the failure behavior of a class of composite structures that includes fuselage panels, individual fuselage sections, fuselage frames, skeleton subfloors with stringers and floor beams without skin covering, and subfloors with skin added to the frame stringer structure. Although the behavior is complex, a strong similarity in the static/dynamic failure behavior among these structures is illustrated through photographs of the experimental results and through analytical data of generic composite structural models.

Laser-Induced Fluorescence Photogrammetry for Dynamic Characterization of Transparent and Aluminized Membrane Structures

NASA Technical Reports Server (NTRS)

Dorrington, Adrian A.; Jones, Thomas W.; Danehy, Paul M.; Pappa, Richard S.

2003-01-01

Photogrammetry has proven to be a valuable tool for static and dynamic profiling of membrane based inflatable and ultra-lightweight space structures. However, the traditional photogrammetric targeting techniques used for solid structures, such as attached retro-reflective targets and white-light dot projection, have some disadvantages and are not ideally suited for measuring highly transparent or reflective membrane structures. In this paper, we describe a new laser-induced fluorescence based target generation technique that is more suitable for these types of structures. We also present several examples of non-contact non-invasive photogrammetric measurements of laser-dye doped polymers, including the dynamic measurement and modal analysis of a 1m-by-1m aluminized solar sail style membrane.

Structural metatransition of energetically tangled crystalline phases.

PubMed

Zhou, Dan; Li, Quan; Zheng, Weitao; Ma, Yanming; Chen, Changfeng

2017-02-08

We solve the longstanding puzzle of pressure induced structural evolution of SnSe using a swarm structure search method combined with first-principles phonon and kinetic barrier calculations. Our results identify a dynamic set of nearly degenerate crystalline SnSe phases that are separated by low kinetic barriers and undergo an unusual type of structural transitions characterized by a dynamically changing mix of the constituent phases. We introduce a new concept of structural metatransition to highlight the transitional nature of such phase transitions. Our theoretical prediction is corroborated by X-ray diffraction measurements, and this intriguing phenomenon offers insights into the enigmatic property variations of SnSe under pressure. This work raises prospects of considerably improving characterization and understanding of intrinsic multiphase crystals and their dynamic evolution.

Dynamics of endoglucanase catalytic domains: implications towards thermostability

USDA-ARS?s Scientific Manuscript database

The function of proteins is controlled by their dynamics inherently determined by their structure. Exploring the protein structure-dynamics relationship is important to develop an understanding of protein function that allows tapping the potential of economically important proteins, such as endogluc...

The Aerodynamic and Dynamic Loading of a Slender Structure by an Impacting Tornado-Like Vortex: The Influence of Relative Vortex-to-Structure Size on Structural Loading

NASA Astrophysics Data System (ADS)

Strasser, Matthew N.

Structural loading produced by an impacting vortex is a hazardous phenomenon that is encountered in numerous applications ranging from the destruction of residences by tornados to the chopping of tip vortices by rotors. Adequate design of structures to resist vortex-induced structural loading necessitates study of the phenomenon that control the structural loading produced by an impacting vortex. This body of work extends the current knowledge base of vortex-structure interaction by evaluating the influence of the relative vortex-to-structure size on the structural loading that the vortex produces. A computer model is utilized to directly simulate the two-dimensional impact of an impinging vortex with a slender, cylindrical structure. The vortex's tangential velocity profile (TVP) is defined by a normalization of the Vatistas analytical (TVP) which realistically replicates the documented spectrum of measured vortex TVPs. The impinging vortex's maximum tangential velocity is fixed, and the vortex's critical radius is incremented from one to one-hundred times the structure's diameter. When the impinging vortex is small, it interacts with vortices produced on the structure by the free stream, and maximum force coefficient amplitudes vary by more than 400% when the impinging vortex impacts the structure at different times. Maximum drag and lift force coefficient amplitudes reach asymptotic values as the impinging vortex's size increases that are respectively 94.77% and 10.66% less than maximum force coefficients produced by an equivalent maximum velocity free stream. The vortex produces maximum structural loading when its path is shifted above the structure's centerline, and maximum drag and lift force coefficients are respectively up to 4.80% and 34.07% greater than maximum force coefficients produced by an equivalent-velocity free stream. Finally, the dynamic load factor (DLF) concept is used to develop a generalized methodology to assess the dynamic amplification of a structure's response to vortex loading and to assess the dynamic loading threat that tornados pose. Typical civil and residential structures will not experience significant response amplification, but responses of very flexible structures may be amplified by up to 2.88 times.

Coherent structures: Comments on mechanisms

NASA Technical Reports Server (NTRS)

Hunt, J. C. R.

1987-01-01

There is now overwhelming evidence that in most turbulent flows there exist regions moving with the flow where the velocity and vorticity have a characteristic structure. These regions are called coherent structures because within them the large-scale distributions of velocity and/or vorticity remain coherent even as these structures move through the flow and interact with other structures. Since the flow enters and leaves the bounding surfaces of these structures, a useful definition for coherent structures is that they are open volumes with distinctive large-scale vorticity distributions. Possible fruitful directions for the study of the dynamics of coherent structures are suggested. Most coherent structures research to data was concentrated on measurement and kinematical analysis; there is now a welcome move to examine the dynamics of coherent structures, by a variety of different methods. A few of them will be described.

Structural studies on choline-carboxylate bio-ionic liquids by x-ray scattering and molecular dynamics.

PubMed

Tanzi, Luana; Ramondo, Fabio; Caminiti, Ruggero; Campetella, Marco; Di Luca, Andrea; Gontrani, Lorenzo

2015-09-21

We report a X-ray diffraction and molecular dynamics study on three choline-based bio-ionic liquids, choline formate, [Ch] [For], choline propanoate, [Ch][Pro], and choline butanoate, [Ch][But]. For the first time, this class of ionic liquids has been investigated by X-ray diffraction. Experimental and theoretical structure factors have been compared for each term of the series. Local structural organization has been obtained from ab initio calculations through static models of isolated ion pairs and dynamic simulations of small portions of liquids through twelve, ten, and nine ion pairs for [Ch][For], [Ch][Pro], and [Ch][But], respectively. All the theoretical models indicate that cations and anions are connected by strong hydrogen bonding and form stable ion pairs in the liquid that are reminiscent of the static ab initio ion pairs. Different structural aspects may affect the radial distribution function, like the local structure of ion pairs and the conformation of choline. When small portions of liquids have been simulated by dynamic quantum chemical methods, some key structural features of the X-ray radial distribution function were well reproduced whereas the classical force fields here applied did not entirely reproduce all the observed structural features.

Structural studies on choline-carboxylate bio-ionic liquids by x-ray scattering and molecular dynamics

NASA Astrophysics Data System (ADS)

Tanzi, Luana; Ramondo, Fabio; Caminiti, Ruggero; Campetella, Marco; Di Luca, Andrea; Gontrani, Lorenzo

2015-09-01

We report a X-ray diffraction and molecular dynamics study on three choline-based bio-ionic liquids, choline formate, [Ch] [For], choline propanoate, [Ch][Pro], and choline butanoate, [Ch][But]. For the first time, this class of ionic liquids has been investigated by X-ray diffraction. Experimental and theoretical structure factors have been compared for each term of the series. Local structural organization has been obtained from ab initio calculations through static models of isolated ion pairs and dynamic simulations of small portions of liquids through twelve, ten, and nine ion pairs for [Ch][For], [Ch][Pro], and [Ch][But], respectively. All the theoretical models indicate that cations and anions are connected by strong hydrogen bonding and form stable ion pairs in the liquid that are reminiscent of the static ab initio ion pairs. Different structural aspects may affect the radial distribution function, like the local structure of ion pairs and the conformation of choline. When small portions of liquids have been simulated by dynamic quantum chemical methods, some key structural features of the X-ray radial distribution function were well reproduced whereas the classical force fields here applied did not entirely reproduce all the observed structural features.

Impedance measures in analysis and characterization of multistable structures subjected to harmonic excitation

NASA Astrophysics Data System (ADS)

Harne, Ryan L.; Goodpaster, Benjamin A.

2018-01-01

Structural components susceptible to adverse, post-buckled dynamic behaviors have long challenged the success of applications requiring lightweight, slender curved structures, while researchers have begun to leverage such bistable systems in emerging applications for novel energy attenuation and shape-changing properties. To expedite development and deployment of these built-up platforms containing post-buckled constituents, efficient approaches are required to complement time-consuming full-field models in the prediction of the near- and far-from-equilibrium dynamics. This research meets the need by introducing a semi-analytical model framework to enable the characterization of steady-state responses in multi degree-of-freedom (DOF) and multistable structural systems subjected to harmonic excitation. In so doing, the pathway for assessing impedance measures is created here so as to identify how energy travels and returns within built-up multistable structures. Verified by simulations and qualitatively validated by experiments, the analysis is shown to accurately reproduce both near- and far-from-equilibrium responses including different classes of energetic snap-through dynamics that only exist in such multistable structures. A first look at the impedance measures of different dynamic regimes reveals a connection between damping in multistable structures and the sustainability of far-from-equilibrium oscillations.

The use of experimental structures to model protein dynamics.

PubMed

Katebi, Ataur R; Sankar, Kannan; Jia, Kejue; Jernigan, Robert L

2015-01-01

The number of solved protein structures submitted in the Protein Data Bank (PDB) has increased dramatically in recent years. For some specific proteins, this number is very high-for example, there are over 550 solved structures for HIV-1 protease, one protein that is essential for the life cycle of human immunodeficiency virus (HIV) which causes acquired immunodeficiency syndrome (AIDS) in humans. The large number of structures for the same protein and its variants include a sample of different conformational states of the protein. A rich set of structures solved experimentally for the same protein has information buried within the dataset that can explain the functional dynamics and structural mechanism of the protein. To extract the dynamics information and functional mechanism from the experimental structures, this chapter focuses on two methods-Principal Component Analysis (PCA) and Elastic Network Models (ENM). PCA is a widely used statistical dimensionality reduction technique to classify and visualize high-dimensional data. On the other hand, ENMs are well-established simple biophysical method for modeling the functionally important global motions of proteins. This chapter covers the basics of these two. Moreover, an improved ENM version that utilizes the variations found within a given set of structures for a protein is described. As a practical example, we have extracted the functional dynamics and mechanism of HIV-1 protease dimeric structure by using a set of 329 PDB structures of this protein. We have described, step by step, how to select a set of protein structures, how to extract the needed information from the PDB files for PCA, how to extract the dynamics information using PCA, how to calculate ENM modes, how to measure the congruency between the dynamics computed from the principal components (PCs) and the ENM modes, and how to compute entropies using the PCs. We provide the computer programs or references to software tools to accomplish each step and show how to use these programs and tools. We also include computer programs to generate movies based on PCs and ENM modes and describe how to visualize them.

The Use of Experimental Structures to Model Protein Dynamics

PubMed Central

Katebi, Ataur R.; Sankar, Kannan; Jia, Kejue; Jernigan, Robert L.

2014-01-01

Summary The number of solved protein structures submitted in the Protein Data Bank (PDB) has increased dramatically in recent years. For some specific proteins, this number is very high – for example, there are over 550 solved structures for HIV-1 protease, one protein that is essential for the life cycle of human immunodeficiency virus (HIV) which causes acquired immunodeficiency syndrome (AIDS) in humans. The large number of structures for the same protein and its variants include a sample of different conformational states of the protein. A rich set of structures solved experimentally for the same protein has information buried within the dataset that can explain the functional dynamics and structural mechanism of the protein. To extract the dynamics information and functional mechanism from the experimental structures, this chapter focuses on two methods – Principal Component Analysis (PCA) and Elastic Network Models (ENM). PCA is a widely used statistical dimensionality reduction technique to classify and visualize high-dimensional data. On the other hand, ENMs are well-established simple biophysical method for modeling the functionally important global motions of proteins. This chapter covers the basics of these two. Moreover, an improved ENM version that utilizes the variations found within a given set of structures for a protein is described. As a practical example, we have extracted the functional dynamics and mechanism of HIV-1 protease dimeric structure by using a set of 329 PDB structures of this protein. We have described, step by step, how to select a set of protein structures, how to extract the needed information from the PDB files for PCA, how to extract the dynamics information using PCA, how to calculate ENM modes, how to measure the congruency between the dynamics computed from the principal components (PCs) and the ENM modes, and how to compute entropies using the PCs. We provide the computer programs or references to software tools to accomplish each step and show how to use these programs and tools. We also include computer programs to generate movies based on PCs and ENM modes and describe how to visualize them. PMID:25330965

Nano-confined water in the interlayers of hydrocalumite: Reorientational dynamics probed by neutron spectroscopy and molecular dynamics computer simulations

NASA Astrophysics Data System (ADS)

Kalinichev, A. G.; Faraone, A.; Udovic, T.; Kolesnikov, A. I.; de Souza, N. R.; Reinholdt, M. X.; Kirkpatrick, R.

2008-12-01

Layered double hydroxides (LDHs, anionic clays) represent excellent model systems for detailed molecular- level studies of the structure, dynamics, and energetics of nano-confined water in mineral interlayers and nano-pores, because LDH interlayers can have a well-defined structures and contain H2O molecules and a wide variety of anions in structurally well-defined positions and coordinations. [Ca2Al(OH)6]Cl·2H2O, also known as hydrocalumite or Friedel's salt, has a well- ordered Ca,Al distribution in the hydroxide layer and a very high degree of H2O,Cl ordering in the interlayer. It is also one of the only LDH phase for which a single crystal structure refinement is available. Thus, it is currently the best model compound for understanding the structure and dynamical behavior of interlayer and surface species in other, less-ordered, LDHs. We investigated the structural and dynamic behavior of water in the interlayers of hydrocalumite using inelastic (INS) and quasielastic (QENS) neutron scattering and molecular dynamics computer simulations. The comperehensive neutron scattering studies were performed for one fully hydrated and one dehydrated sample of hydrocalumite using several complementary instruments (HFBS, DCS and FANS at NCNR; HRMECS and QENS at IPNS) at temperatures above and below the previously discovered order-disorder interlayer phase transition. Together the experimental and molecular modeling results capture the important details of the dynamics of nano-confined water and the effects of the orientational ordering of H2O molecules above and below the phase transition. They provide otherwise unobtainable experimental information about the transformation of H2O librational and diffusional modes across the order-disorder phase transition and significantly add to our current understanding of the structure and dynamics of water in LDH phases based on the earlier NMR, IR, X-ray, and calorimetric measurements. The approach can now be extended to probe the dynamics of nano-confined and interfacial water in more disordered phases (LDH, clays, cement, etc.), for which much less initial structural information is available.

Structural evolution dynamics in fusion of sumanenes and corannulenes: defects formation and self-healing mechanism

NASA Astrophysics Data System (ADS)

Sorkin, Anastassia; Su, Haibin

2018-06-01

The fusion processes of structures consisting of various combinations between sumanene and corannulene, leading to the formation of graphene nanoribbons (GNRs) under heating are simulated by density-functional-based tight-binding molecular dynamics. Distinct stages are unraveled in the course of GNR formation. Firstly, the carbon fragments coalescence into highly strained framework. Secondly, structural reconstruction invokes breaking most strained bonds to form a GNR structure containing numerous defects. Lastly, defects are remedied by the delicate ‘edge-facilitated self-healing’ process through two synergized edge-related effects: elevated mobility of defects and promoted structure reconstructions owing to the remarkable dynamics associated with edges. Importantly, detailed dynamics in the course of forming GNRs with defects and grain boundaries simulated in this work is valuable to provide better understanding at the atomistic scale of defect formation as well as self-healing in the context of the sp2 carbon network. In particular, edges play important roles in not only generating Stone–Wales (SW), 5-8-5 types of defects, 8-5-5-8 and pentagon–heptagon grain boundaries. In addition, our simulations predict the existence of one novel defect, coined as the Inverse SW defect, which is to be confirmed in future experimental studies. This study of dynamic structural evolution reveals that edges are prone to intrinsic and extrinsic modifications such as atomic-scale defects, structural distortions and inhomogeneity.

Modeling the Effect of Fluid-Structure Interaction on the Impact Dynamics of Pressurized Tank Cars

DOT National Transportation Integrated Search

2009-11-13

This paper presents a computational framework that : analyzes the effect of fluid-structure interaction (FSI) on the : impact dynamics of pressurized commodity tank cars using the : nonlinear dynamic finite element code ABAQUS/Explicit. : There exist...

Study on model design and dynamic similitude relations of vibro-acoustic experiment for elastic cavity

NASA Astrophysics Data System (ADS)

Shi, Ao; Lu, Bo; Yang, Dangguo; Wang, Xiansheng; Wu, Junqiang; Zhou, Fangqi

2018-05-01

Coupling between aero-acoustic noise and structural vibration under high-speed open cavity flow-induced oscillation may bring about severe random vibration of the structure, and even cause structure to fatigue destruction, which threatens the flight safety. Carrying out the research on vibro-acoustic experiments of scaled down model is an effective means to clarify the effects of high-intensity noise of cavity on structural vibration. Therefore, in allusion to the vibro-acoustic experiments of cavity in wind tunnel, taking typical elastic cavity as the research object, dimensional analysis and finite element method were adopted to establish the similitude relations of structural inherent characteristics and dynamics for distorted model, and verifying the proposed similitude relations by means of experiments and numerical simulation. Research shows that, according to the analysis of scale-down model, the established similitude relations can accurately simulate the structural dynamic characteristics of actual model, which provides theoretic guidance for structural design and vibro-acoustic experiments of scaled down elastic cavity model.

Effect of node attributes on the temporal dynamics of network structure

NASA Astrophysics Data System (ADS)

Momeni, Naghmeh; Fotouhi, Babak

2017-03-01

Many natural and social networks evolve in time and their structures are dynamic. In most networks, nodes are heterogeneous, and their roles in the evolution of structure differ. This paper focuses on the role of individual attributes on the temporal dynamics of network structure. We focus on a basic model for growing networks that incorporates node attributes (which we call "quality"), and we focus on the problem of forecasting the structural properties of the network in arbitrary times for an arbitrary initial network. That is, we address the following question: If we are given a certain initial network with given arbitrary structure and known node attributes, then how does the structure change in time as new nodes with given distribution of attributes join the network? We solve the model analytically and obtain the quality-degree joint distribution and degree correlations. We characterize the role of individual attributes in the position of individual nodes in the hierarchy of connections. We confirm the theoretical findings with Monte Carlo simulations.

Structural kinematics based damage zone prediction in gradient structures using vibration database

NASA Astrophysics Data System (ADS)

Talha, Mohammad; Ashokkumar, Chimpalthradi R.

2014-05-01

To explore the applications of functionally graded materials (FGMs) in dynamic structures, structural kinematics based health monitoring technique becomes an important problem. Depending upon the displacements in three dimensions, the health of the material to withstand dynamic loads is inferred in this paper, which is based on the net compressive and tensile displacements that each structural degree of freedom takes. These net displacements at each finite element node predicts damage zones of the FGM where the material is likely to fail due to a vibration response which is categorized according to loading condition. The damage zone prediction of a dynamically active FGMs plate have been accomplished using Reddy's higher-order theory. The constituent material properties are assumed to vary in the thickness direction according to the power-law behavior. The proposed C0 finite element model (FEM) is applied to get net tensile and compressive displacement distributions across the structures. A plate made of Aluminum/Ziconia is considered to illustrate the concept of structural kinematics-based health monitoring aspects of FGMs.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rodriguez, Mario E.

An area in earthquake risk reduction that needs an urgent examination is the selection of earthquake records for nonlinear dynamic analysis of structures. An often-mentioned shortcoming from results of nonlinear dynamic analyses of structures is that these results are limited to the type of records that these analyses use as input data. This paper proposes a procedure for selecting earthquake records for nonlinear dynamic analysis of structures. This procedure uses a seismic damage index evaluated using the hysteretic energy dissipated by a Single Degree of Freedom System (SDOF) representing a multi-degree-of freedom structure responding to an earthquake record, and themore » plastic work capacity of the system at collapse. The type of structural system is considered using simple parameters. The proposed method is based on the evaluation of the damage index for a suite of earthquake records and a selected type of structural system. A set of 10 strong ground motion records is analyzed to show an application of the proposed procedure for selecting earthquake records for structural design.« less

Response of Metals and Metallic Structures to Dynamic Loading

DTIC Science & Technology

1978-05-01

materials for service by testing under high rates of loading. Impact tests such as the Charpy test, the drop-weight tear test, and the dynamic tear...have clearly shown this for precracked charpy specimens and for the drop-weight tear test. Hence, there is a strong need for additional dynamic...dynamic fracture resistance ( Charpy , dynamic-tear, drop-weight tear test, etc.), normally assures that fracture in dynamically loaded structures is

Counteracting structural errors in ensemble forecast of influenza outbreaks.

PubMed

Pei, Sen; Shaman, Jeffrey

2017-10-13

For influenza forecasts generated using dynamical models, forecast inaccuracy is partly attributable to the nonlinear growth of error. As a consequence, quantification of the nonlinear error structure in current forecast models is needed so that this growth can be corrected and forecast skill improved. Here, we inspect the error growth of a compartmental influenza model and find that a robust error structure arises naturally from the nonlinear model dynamics. By counteracting these structural errors, diagnosed using error breeding, we develop a new forecast approach that combines dynamical error correction and statistical filtering techniques. In retrospective forecasts of historical influenza outbreaks for 95 US cities from 2003 to 2014, overall forecast accuracy for outbreak peak timing, peak intensity and attack rate, are substantially improved for predicted lead times up to 10 weeks. This error growth correction method can be generalized to improve the forecast accuracy of other infectious disease dynamical models.Inaccuracy of influenza forecasts based on dynamical models is partly due to nonlinear error growth. Here the authors address the error structure of a compartmental influenza model, and develop a new improved forecast approach combining dynamical error correction and statistical filtering techniques.

2D-HB-Network at the air-water interface: A structural and dynamical characterization by means of ab initio and classical molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Pezzotti, Simone; Serva, Alessandra; Gaigeot, Marie-Pierre

2018-05-01

Following our previous work where the existence of a special 2-Dimensional H-Bond (2D-HB)-Network was revealed at the air-water interface [S. Pezzotti et al., J. Phys. Chem. Lett. 8, 3133 (2017)], we provide here a full structural and dynamical characterization of this specific arrangement by means of both Density Functional Theory based and Force Field based molecular dynamics simulations. We show in particular that water at the interface with air reconstructs to maximize H-Bonds formed between interfacial molecules, which leads to the formation of an extended and non-interrupted 2-Dimensional H-Bond structure involving on average ˜90% of water molecules at the interface. We also show that the existence of such an extended structure, composed of H-Bonds all oriented parallel to the surface, constrains the reorientional dynamics of water that is hence slower at the interface than in the bulk. The structure and dynamics of the 2D-HB-Network provide new elements to possibly rationalize several specific properties of the air-water interface, such as water surface tension, anisotropic reorientation of interfacial water under an external field, and proton hopping.

Visualizing the dynamic structure of the plant photosynthetic membrane.

PubMed

Ruban, Alexander V; Johnson, Matthew P

2015-11-03

The chloroplast thylakoid membrane is the site for the initial steps of photosynthesis that convert solar energy into chemical energy, ultimately powering almost all life on earth. The heterogeneous distribution of protein complexes within the membrane gives rise to an intricate three-dimensional structure that is nonetheless extremely dynamic on a timescale of seconds to minutes. These dynamics form the basis for the regulation of photosynthesis, and therefore the adaptability of plants to different environments. High-resolution microscopy has in recent years begun to provide new insights into the structural dynamics underlying a number of regulatory processes such as membrane stacking, photosystem II repair, photoprotective energy dissipation, state transitions and alternative electron transfer. Here we provide an overview of the essentials of thylakoid membrane structure in plants, and consider how recent advances, using a range of microscopies, have substantially increased our knowledge of the thylakoid dynamic structure. We discuss both the successes and limitations of the currently available techniques and highlight newly emerging microscopic methods that promise to move the field beyond the current 'static' view of membrane organization based on frozen snapshots to a 'live' view of functional membranes imaged under native aqueous conditions at ambient temperature and responding dynamically to external stimuli.

Structural versus dynamical origins of mean-field behavior in a self-organized critical model of neuronal avalanches

NASA Astrophysics Data System (ADS)

Moosavi, S. Amin; Montakhab, Afshin

2015-11-01

Critical dynamics of cortical neurons have been intensively studied over the past decade. Neuronal avalanches provide the main experimental as well as theoretical tools to consider criticality in such systems. Experimental studies show that critical neuronal avalanches show mean-field behavior. There are structural as well as recently proposed [Phys. Rev. E 89, 052139 (2014), 10.1103/PhysRevE.89.052139] dynamical mechanisms that can lead to mean-field behavior. In this work we consider a simple model of neuronal dynamics based on threshold self-organized critical models with synaptic noise. We investigate the role of high-average connectivity, random long-range connections, as well as synaptic noise in achieving mean-field behavior. We employ finite-size scaling in order to extract critical exponents with good accuracy. We conclude that relevant structural mechanisms responsible for mean-field behavior cannot be justified in realistic models of the cortex. However, strong dynamical noise, which can have realistic justifications, always leads to mean-field behavior regardless of the underlying structure. Our work provides a different (dynamical) origin than the conventionally accepted (structural) mechanisms for mean-field behavior in neuronal avalanches.

How the Dynamics of a Supramolecular Polymer Determines Its Dynamic Adaptivity and Stimuli-Responsiveness: Structure-Dynamics-Property Relationships From Coarse-Grained Simulations.

PubMed

Torchi, Andrea; Bochicchio, Davide; Pavan, Giovanni M

2018-04-12

The rational design of supramolecular polymers that can adapt or respond in time to specific stimuli in a controlled way is interesting for many applications, but this requires understanding the molecular factors that make the material faster or slower in responding to the stimulus. To this end, it is necessary to study the dynamic adaptive properties at submolecular resolution, which is difficult at an experimental level. Here we show coarse-grained molecular dynamics simulations (<5 Å resolution) demonstrating how the dynamic adaptivity and stimuli responsiveness of a supramolecular polymer is controlled by the intrinsic dynamics of the assembly, which is in turn determined by the structure of the monomers. As a representative case, we focus on a water-soluble 1,3,5-benzenetricarboxamide (BTA) supramolecular polymer incorporating (charged) receptor monomers, experimentally seen to undergo dynamic clustering following the superselective binding to a multivalent recruiter. Our simulations show that the dynamic reorganization of the supramolecular structure proceeds via monomer diffusion on the dynamic fiber surface (exchange within the fiber). Rationally changing the structure of the monomers to make the fiber surface more or less dynamic allows tuning the rate of response to the stimulus and of supramolecular reconfiguration. Simple in silico experiments draw a structure-dynamics-property relationship revealing the key factors underpinning the dynamic adaptivity and stimuli-responsiveness of these supramolecular polymers. We come out with clear evidence that to master the bioinspired properties of these fibers, it is necessary to control their intrinsic dynamics, while the high-resolution of our molecular models permits us to show how.

Research in Structures, Structural Dynamics and Materials, 1990

NASA Technical Reports Server (NTRS)

Barthelemy, Jean-Francois M. (Compiler); Noor, Ahmed K. (Compiler)

1990-01-01

The Structural Dynamics and Materials (SDM) Conference was held on April 2 to 4, 1990 in Long Beach, California. This publication is a compilation of presentations of the work-in-progress sessions and does not contain papers from the regular sessions since those papers are published by AIAA in the conference proceedings.

Introducing Students to Structural Dynamics and Earthquake Engineering

ERIC Educational Resources Information Center

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…

Structural Dynamics and Control Interaction of Flexible Structures

NASA Technical Reports Server (NTRS)

Ryan, Robert S. (Editor); Scofield, Harold N. (Editor)

1987-01-01

A Workshop was held to promote technical exchange between the structural dynamic and control disciplines, foster joint technology, and provide a forum for discussing and focusing critical issues in the separate and combined areas. The workshop was closed by a panel meeting. Panel members' viewpoints and their responses to questions are included.

Finite element modeling of truss structures with frequency-dependent material damping

NASA Technical Reports Server (NTRS)

Lesieutre, George A.

1991-01-01

A physically motivated modelling technique for structural dynamic analysis that accommodates frequency dependent material damping was developed. Key features of the technique are the introduction of augmenting thermodynamic fields (AFT) to interact with the usual mechanical displacement field, and the treatment of the resulting coupled governing equations using finite element analysis methods. The AFT method is fully compatible with current structural finite element analysis techniques. The method is demonstrated in the dynamic analysis of a 10-bay planar truss structure, a structure representative of those contemplated for use in future space systems.

Multiple tuned mass damper based vibration mitigation of offshore wind turbine considering soil-structure interaction

NASA Astrophysics Data System (ADS)

Hussan, Mosaruf; Sharmin, Faria; Kim, Dookie

2017-08-01

The dynamics of jacket supported offshore wind turbine (OWT) in earthquake environment is one of the progressing focuses in the renewable energy field. Soil-structure interaction (SSI) is a fundamental principle to analyze stability and safety of the structure. This study focuses on the performance of the multiple tuned mass damper (MTMD) in minimizing the dynamic responses of the structures objected to seismic loads combined with static wind and wave loads. Response surface methodology (RSM) has been applied to design the MTMD parameters. The analyses have been performed under two different boundary conditions: fixed base (without SSI) and flexible base (with SSI). Two vibration modes of the structure have been suppressed by multi-mode vibration control principle in both cases. The effectiveness of the MTMD in reducing the dynamic response of the structure is presented. The dynamic SSI plays an important role in the seismic behavior of the jacket supported OWT, especially resting on the soft soil deposit. Finally, it shows that excluding the SSI effect could be the reason of overestimating the MTMD performance.

Dynamic analysis of a 5-MW tripod offshore wind turbine by considering fluid-structure interaction

NASA Astrophysics Data System (ADS)

Zhang, Li-wei; Li, Xin

2017-10-01

Fixed offshore wind turbines usually have large underwater supporting structures. The fluid influences the dynamic characteristics of the structure system. The dynamic model of a 5-MW tripod offshore wind turbine considering the pile-soil system and fluid structure interaction (FSI) is established, and the structural modes in air and in water are obtained by use of ANSYS. By comparing low-order natural frequencies and mode shapes, the influence of sea water on the free vibration characteristics of offshore wind turbine is analyzed. On basis of the above work, seismic responses under excitation by El-Centro waves are calculated by the time-history analysis method. The results reveal that the dynamic responses such as the lateral displacement of the foundation and the section bending moment of the tubular piles increase substantially under the influence of the added-mass and hydrodynamic pressure of sea water. The method and conclusions presented in this paper can provide a theoretical reference for structure design and analysis of offshore wind turbines fixed in deep seawater.

Shockwave dynamics: a comparison between stochastic and periodic porous architectures

NASA Astrophysics Data System (ADS)

Branch, Brittany; Ionite, Axinte; Clements, Bradford; Montgomery, David; Schmalzer, Andrew; Patterson, Brian; Mueller, Alexander; Jensen, Brian; Dattelbaum, Dana

Polymeric foams are used extensively as structural supports and load mitigating materials in which they are subjected to compressive loading at a range of strain rates, up to the high strain rates encountered in blast and shockwave loading. To date, there have been few insights into compaction phenomena in porous structures at the mesoscale, and the influence of structure on shockwave localization. Of particular interest is when the properties of the inherent mesoscopic, periodic structure begin to emerge, versus the discrete behavior of the individual cell. Here, we illustrate, for the first time, modulation of shockwave dynamics controlled at micron-length scales in additively manufactured periodic porous structures measured using in situ, time-resolved x-ray phase contrast imaging at the Advanced Photon Source. Further, we demonstrate how the shockwave dynamics in periodic structures differ from stochastic foams of similar density and we conclude that microstructural control in elastomer foams has a dramatic effect on shockwave dynamics and can be tailored towards a variety of applications. Laboratory Directed Research and Development (LDRD) program at Los Alamos National Laboratory (project# 20160103DR) and DOE/NNSA Campaign 2.

Integrated dynamic analysis simulation of space stations with controllable solar array

NASA Technical Reports Server (NTRS)

Heinrichs, J. A.; Fee, J. J.

1972-01-01

A methodology is formulated and presented for the integrated structural dynamic analysis of space stations with controllable solar arrays and non-controllable appendages. The structural system flexibility characteristics are considered in the dynamic analysis by a synthesis technique whereby free-free space station modal coordinates and cantilever appendage coordinates are inertially coupled. A digital simulation of this analysis method is described and verified by comparison of interaction load solutions with other methods of solution. Motion equations are simulated for both the zero gravity and artificial gravity (spinning) orbital conditions. Closed loop controlling dynamics for both orientation control of the arrays and attitude control of the space station are provided in the simulation by various generic types of controlling systems. The capability of the simulation as a design tool is demonstrated by utilizing typical space station and solar array structural representations and a specific structural perturbing force. Response and interaction load solutions are presented for this structural configuration and indicate the importance of using an integrated type analysis for the predictions of structural interactions.

Analyses and tests of the B-1 aircraft structural mode control system

NASA Technical Reports Server (NTRS)

Wykes, J. H.; Byar, T. R.; Macmiller, C. J.; Greek, D. C.

1980-01-01

Analyses and flight tests of the B-1 structural mode control system (SMCS) are presented. Improvements in the total dynamic response of a flexible aircraft and the benefits to ride qualities, handling qualities, crew efficiency, and reduced dynamic loads on the primary structures, were investigated. The effectiveness and the performance of the SMCS, which uses small aerodynamic surfaces at the vehicle nose to provide damping to the structural modes, were evaluated.

Ordered water structure at hydrophobic graphite interfaces observed by 4D, ultrafast electron crystallography

PubMed Central

Yang, Ding-Shyue; Zewail, Ahmed H.

2009-01-01

Interfacial water has unique properties in various functions. Here, using 4-dimensional (4D), ultrafast electron crystallography with atomic-scale spatial and temporal resolution, we report study of structure and dynamics of interfacial water assembly on a hydrophobic surface. Structurally, vertically stacked bilayers on highly oriented pyrolytic graphite surface were determined to be ordered, contrary to the expectation that the strong hydrogen bonding of water on hydrophobic surfaces would dominate with suppressed interfacial order. Because of its terrace morphology, graphite plays the role of a template. The dynamics is also surprising. After the excitation of graphite by an ultrafast infrared pulse, the interfacial ice structure undergoes nonequilibrium “phase transformation” identified in the hydrogen-bond network through the observation of structural isosbestic point. We provide the time scales involved, the nature of ice-graphite structural dynamics, and relevance to properties related to confined water. PMID:19246378

Inferring Biological Structures from Super-Resolution Single Molecule Images Using Generative Models

PubMed Central

Maji, Suvrajit; Bruchez, Marcel P.

2012-01-01

Localization-based super resolution imaging is presently limited by sampling requirements for dynamic measurements of biological structures. Generating an image requires serial acquisition of individual molecular positions at sufficient density to define a biological structure, increasing the acquisition time. Efficient analysis of biological structures from sparse localization data could substantially improve the dynamic imaging capabilities of these methods. Using a feature extraction technique called the Hough Transform simple biological structures are identified from both simulated and real localization data. We demonstrate that these generative models can efficiently infer biological structures in the data from far fewer localizations than are required for complete spatial sampling. Analysis at partial data densities revealed efficient recovery of clathrin vesicle size distributions and microtubule orientation angles with as little as 10% of the localization data. This approach significantly increases the temporal resolution for dynamic imaging and provides quantitatively useful biological information. PMID:22629348

Multilevel Dynamic Generalized Structured Component Analysis for Brain Connectivity Analysis in Functional Neuroimaging Data.

PubMed

Jung, Kwanghee; Takane, Yoshio; Hwang, Heungsun; Woodward, Todd S

2016-06-01

We extend dynamic generalized structured component analysis (GSCA) to enhance its data-analytic capability in structural equation modeling of multi-subject time series data. Time series data of multiple subjects are typically hierarchically structured, where time points are nested within subjects who are in turn nested within a group. The proposed approach, named multilevel dynamic GSCA, accommodates the nested structure in time series data. Explicitly taking the nested structure into account, the proposed method allows investigating subject-wise variability of the loadings and path coefficients by looking at the variance estimates of the corresponding random effects, as well as fixed loadings between observed and latent variables and fixed path coefficients between latent variables. We demonstrate the effectiveness of the proposed approach by applying the method to the multi-subject functional neuroimaging data for brain connectivity analysis, where time series data-level measurements are nested within subjects.

Elucidation of kinematical and dynamical structure of the Galactic bulge

NASA Astrophysics Data System (ADS)

Yano, T.; Gouda, N.; Ueda, H.; Koyama, H.; Kan-ya, Y.; Taruya, A.

2008-07-01

Future space mission of astrometric satellite, GAIA and JASMINE (Japan Astrometry Satellite Mission for Infrared Exploration), will produce astrometric parameter, such as positions, parallaxes, and proper motions of stars in the Galactic bulge. Then kinematical information will be obtained in the future. Accordingly it is expected that our understanding of the dynamical structure will be greatly improved. Therefore it is important to make a method to construct a kinematical and dynamical structure of the Galactic bulge immediately.

Characterization of Local Carrier Dynamics in AlN and AlGaN Films using High Spatial- and Time-resolution Cathodoluminescence Spectroscopy

DTIC Science & Technology

2012-10-12

21/2012 Abstract: In order to assess the impacts of structural and point defects on the local carrier (exciton) recombination dynamics in...quantitatively understood as functions of structural / point defect and impurity concentrations (crystal imperfections). However, only few papers [5...NOTES 14. ABSTRACT In order to assess the impacts of structural and point defects on the local carrier (exciton) recombination dynamics in wide bandgap

Structure-Functional Basis of Ion Transport in Sodium–Calcium Exchanger (NCX) Proteins

PubMed Central

Giladi, Moshe; Shor, Reut; Lisnyansky, Michal; Khananshvili, Daniel

2016-01-01

The membrane-bound sodium–calcium exchanger (NCX) proteins shape Ca2+ homeostasis in many cell types, thus participating in a wide range of physiological and pathological processes. Determination of the crystal structure of an archaeal NCX (NCX_Mj) paved the way for a thorough and systematic investigation of ion transport mechanisms in NCX proteins. Here, we review the data gathered from the X-ray crystallography, molecular dynamics simulations, hydrogen–deuterium exchange mass-spectrometry (HDX-MS), and ion-flux analyses of mutants. Strikingly, the apo NCX_Mj protein exhibits characteristic patterns in the local backbone dynamics at particular helix segments, thereby possessing characteristic HDX profiles, suggesting structure-dynamic preorganization (geometric arrangements of catalytic residues before the transition state) of conserved α1 and α2 repeats at ion-coordinating residues involved in transport activities. Moreover, dynamic preorganization of local structural entities in the apo protein predefines the status of ion-occlusion and transition states, even though Na+ or Ca2+ binding modifies the preceding backbone dynamics nearby functionally important residues. Future challenges include resolving the structural-dynamic determinants governing the ion selectivity, functional asymmetry and ion-induced alternating access. Taking into account the structural similarities of NCX_Mj with the other proteins belonging to the Ca2+/cation exchanger superfamily, the recent findings can significantly improve our understanding of ion transport mechanisms in NCX and similar proteins. PMID:27879668

Odd–even structural sensitivity on dynamics in network-forming ionic liquids

DOE PAGES

Yang, Ke; Cai, Zhikun; Tyagi, Madhusudan; ...

2016-04-13

Understanding structural sensitivity on properties of materials is an important step toward the rational design of materials. As a compelling case of sensitive structure-property relationship, an odd-even effect refers to the alternating trend of physical or chemical properties on odd/even number of repeating structural units. In crystalline or semi-crystalline materials, such odd-even variations of macroscopic properties emerge as manifestations of differences in the periodic packing patterns of molecules. Therefore, due to the lack of long-range order, such odd-even phenomenon is not expected in liquids. Herein, we report the discovery of a remarkable odd-even effect of the dynamical properties in themore » liquid phase, which challenges the traditional periodic packing explanations. In a class of network-forming ionic liquid (NIL), using incoherent quasi-elastic neutron scattering measurements, we measured the dynamical properties including the diffusion coefficient and the rotational relaxation time. These dynamical properties showed pronounced alternating trends with increased number of methylene (–CH 2– ) groups in the backbone. Meanwhile, the structure factor S(Q) showed no long-range periodic packing of molecules, while the pair distribution function g(r) revealed subtle differences in the local molecular morphology. As a result, the observed dynamical odd-even phenomenon in liquids showed that profound dynamical changes originate from subtle local structural differences.« less

Structure-Functional Basis of Ion Transport in Sodium-Calcium Exchanger (NCX) Proteins.

PubMed

Giladi, Moshe; Shor, Reut; Lisnyansky, Michal; Khananshvili, Daniel

2016-11-22

The membrane-bound sodium-calcium exchanger (NCX) proteins shape Ca 2+ homeostasis in many cell types, thus participating in a wide range of physiological and pathological processes. Determination of the crystal structure of an archaeal NCX (NCX_Mj) paved the way for a thorough and systematic investigation of ion transport mechanisms in NCX proteins. Here, we review the data gathered from the X-ray crystallography, molecular dynamics simulations, hydrogen-deuterium exchange mass-spectrometry (HDX-MS), and ion-flux analyses of mutants. Strikingly, the apo NCX_Mj protein exhibits characteristic patterns in the local backbone dynamics at particular helix segments, thereby possessing characteristic HDX profiles, suggesting structure-dynamic preorganization (geometric arrangements of catalytic residues before the transition state) of conserved α₁ and α₂ repeats at ion-coordinating residues involved in transport activities. Moreover, dynamic preorganization of local structural entities in the apo protein predefines the status of ion-occlusion and transition states, even though Na⁺ or Ca 2+ binding modifies the preceding backbone dynamics nearby functionally important residues. Future challenges include resolving the structural-dynamic determinants governing the ion selectivity, functional asymmetry and ion-induced alternating access. Taking into account the structural similarities of NCX_Mj with the other proteins belonging to the Ca 2+ /cation exchanger superfamily, the recent findings can significantly improve our understanding of ion transport mechanisms in NCX and similar proteins.

Stabilities and Dynamics of Protein Folding Nuclei by Molecular Dynamics Simulation

NASA Astrophysics Data System (ADS)

Song, Yong-Shun; Zhou, Xin; Zheng, Wei-Mou; Wang, Yan-Ting

2017-07-01

To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics (MD) simulation in aqueous solution four fragments cut out of a protein G, including one α-helix (seqB: KVFKQYAN), two β-turns (seqA: LNGKTLKG and seqC: YDDATKTF), and one β-strand (seqD: DGEWTYDD). The Markov State Model clustering method combined with the coarse-grained conformation letters method are employed to analyze the data sampled from 2-μs equilibrium MD simulation trajectories. We find that seqA and seqB have more stable structures than their native structures which become metastable when cut out of the protein structure. As expected, seqD alone is flexible and does not have a stable structure. Throughout our simulations, the native structure of seqC is stable but cannot be reached if starting from a structure other than the native one, implying a funnel-shape free energy landscape of seqC in aqueous solution. All the above results suggest that different nuclei have different formation dynamics during protein folding, which may have a major contribution to the hierarchy of protein folding dynamics. Supported by the National Basic Research Program of China under Grant No. 2013CB932804, the National Natural Science Foundation of China under Grant No. 11421063, and the CAS Biophysics Interdisciplinary Innovation Team Project

Application of holographic interferometry for analysis of the dynamic and modal characteristics of an advanced exotic metal airfoil structure

NASA Astrophysics Data System (ADS)

Fein, Howard

1999-03-01

Holographic Interferometry has been successfully employed to characterize the materials and behavior of diverse types of structures under stress. Specialized variations of this technology have also been applied to define dynamic and vibration related structural behavior. Such applications of holographic technique offer some of the most effective methods of modal and dynamic analysis available. Real-time dynamic testing of the modal and mechanical behavior of aerodynamic control and airfoil structures for advanced aircraft has always required advanced instrumentation for data collection in either actual flight test or wind-tunnel simulations. Advanced optical holography techniques are alternate methods which result in actual full-field behavioral data on the ground in a noninvasive environment. These methods offer significant insight in both the development and subsequent operational test and modeling of advanced exotic metal control structures and their integration with total vehicle system dynamics. Structures and materials can be analyzed with very low amplitude excitation and the resultant data can be used to adjust the accuracy mathematically derived structural and behavioral models. Holographic Interferometry offers a powerful tool to aid in the developmental engineering of exotic metal structures for high stress applications. Advanced Titanium alloy is a significant example of these sorts of materials which has found continually increased use in advanced aerodynamic, undersea, and other highly mobil platforms. Aircraft applications in particular must consider environments where extremes in vibration and impulsive mechanical stress can affect both operation and structural stability. These considerations present ideal requisites for analysis using advanced holographic methods in the initial design and test of structures made with such advanced materials. Holographic techniques are nondestructive, real- time, and definitive in allowing the identification of vibrational modes, displacements, and motion geometries. Such information can be crucial to the determination of mechanical configurations and designs as well as operational parameters of structural components fabricated from advanced and exotic materials. Anomalous behavioral characteristics can be directly related to hidden structural or mounting anomalies and defects. Deriving such information can be crucial to the determination of mechanical configurations and designs, as well as critical operational parameters of structural components fabricated from advanced and exotic materials.

Liquid li structure and dynamics: A comparison between OFDFT and second nearest-neighbor embedded-atom method

DOE PAGES

Chen, Mohan; Vella, Joseph R.; Panagiotopoulos, Athanassios Z.; ...

2015-04-08

The structure and dynamics of liquid lithium are studied using two simulation methods: orbital-free (OF) first-principles molecular dynamics (MD), which employs OF density functional theory (DFT), and classical MD utilizing a second nearest-neighbor embedded-atom method potential. The properties we studied include the dynamic structure factor, the self-diffusion coefficient, the dispersion relation, the viscosity, and the bond angle distribution function. Our simulation results were compared to available experimental data when possible. Each method has distinct advantages and disadvantages. For example, OFDFT gives better agreement with experimental dynamic structure factors, yet is more computationally demanding than classical simulations. Classical simulations can accessmore » a broader temperature range and longer time scales. The combination of first-principles and classical simulations is a powerful tool for studying properties of liquid lithium.« less

Dynamic nuclear polarization methods in solids and solutions to explore membrane proteins and membrane systems.

PubMed

Cheng, Chi-Yuan; Han, Songi

2013-01-01

Membrane proteins regulate vital cellular processes, including signaling, ion transport, and vesicular trafficking. Obtaining experimental access to their structures, conformational fluctuations, orientations, locations, and hydration in membrane environments, as well as the lipid membrane properties, is critical to understanding their functions. Dynamic nuclear polarization (DNP) of frozen solids can dramatically boost the sensitivity of current solid-state nuclear magnetic resonance tools to enhance access to membrane protein structures in native membrane environments. Overhauser DNP in the solution state can map out the local and site-specific hydration dynamics landscape of membrane proteins and lipid membranes, critically complementing the structural and dynamics information obtained by electron paramagnetic resonance spectroscopy. Here, we provide an overview of how DNP methods in solids and solutions can significantly increase our understanding of membrane protein structures, dynamics, functions, and hydration in complex biological membrane environments.

NASTRAN analysis of the 1/8-scale space shuttle dynamic model

NASA Technical Reports Server (NTRS)

Bernstein, M.; Mason, P. W.; Zalesak, J.; Gregory, D. J.; Levy, A.

1973-01-01

The space shuttle configuration has more complex structural dynamic characteristics than previous launch vehicles primarily because of the high model density at low frequencies and the high degree of coupling between the lateral and longitudinal motions. An accurate analytical representation of these characteristics is a primary means for treating structural dynamics problems during the design phase of the shuttle program. The 1/8-scale model program was developed to explore the adequacy of available analytical modeling technology and to provide the means for investigating problems which are more readily treated experimentally. The basic objectives of the 1/8-scale model program are: (1) to provide early verification of analytical modeling procedures on a shuttle-like structure, (2) to demonstrate important vehicle dynamic characteristics of a typical shuttle design, (3) to disclose any previously unanticipated structural dynamic characteristics, and (4) to provide for development and demonstration of cost effective prototype testing procedures.

Effect of structural mount dynamics on a pair of operating Stirling Convertors

NASA Astrophysics Data System (ADS)

Goodnight, Thomas W.; Suárez, Vicente J.; Hughes, William O.; Samorezov, Sergey

2002-01-01

The U.S. Department of Energy (DOE), in conjunction with NASA John H. Glenn Research Center and Stirling Technology Company, are currently developing a Stirling convertor for a Stirling Radioisotope Generator (SRG). NASA Headquarters and DOE have identified the SRG for potential use as an advanced spacecraft power system for future NASA deep-space and Mars surface missions. Low-level dynamic base-shake tests were conducted on a dynamic simulation of the structural mount for a pair of Operating Stirling Convertors. These tests were conducted at NASA Glenn Research Center's Structural Dynamics Laboratory as part of the development of this technology. The purpose of these tests was to identify the changes in transmissibility and the effect on structural dynamic response on a pair of operating Stirling Technology Demonstration Convertors (TDCs). This paper addresses the base-shake test, setup, procedure and results conducted on the Stirling TDC mount simulator in April 2001. .

Time, space, and disorder in the expanding proteome universe.

PubMed

Minde, David-Paul; Dunker, A Keith; Lilley, Kathryn S

2017-04-01

Proteins are highly dynamic entities. Their myriad functions require specific structures, but proteins' dynamic nature ranges all the way from the local mobility of their amino acid constituents to mobility within and well beyond single cells. A truly comprehensive view of the dynamic structural proteome includes: (i) alternative sequences, (ii) alternative conformations, (iii) alternative interactions with a range of biomolecules, (iv) cellular localizations, (v) alternative behaviors in different cell types. While these aspects have traditionally been explored one protein at a time, we highlight recently emerging global approaches that accelerate comprehensive insights into these facets of the dynamic nature of protein structure. Computational tools that integrate and expand on multiple orthogonal data types promise to enable the transition from a disjointed list of static snapshots to a structurally explicit understanding of the dynamics of cellular mechanisms. © 2017 The Authors. Proteomics Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ultrafast Dynamics of 1,3-Cyclohexadiene in Highly Excited States

DOE PAGES

Bühler, Christine C.; Minitti, Michael P.; Deb, Sanghamitra; ...

2011-01-01

The ultrafast dynamics of 1,3-cyclohexadiene has been investigated via structurally sensitive Rydberg electron binding energies and shown to differ upon excitation to the 1B state and the 3p Rydberg state. Excitation of the molecule with 4.63 eV photons into the ultrashort-lived 1B state yields the well-known ring opening to 1,3,5-hexatriene, while a 5.99 eV photon lifts the molecule directly into the 3p-Rydberg state. Excitation to 3p does not induce ring opening. In both experiments, time-dependent shifts of the Rydberg electron binding energy reflect the structural dynamics of the molecular core. Structural distortions associated with 3p-excitation cause a dynamical shift in the -more » and -binding energies by 10 and 26 meV/ps, respectively, whereas after excitation into 1B, more severe structural transformations along the ring-opening coordinate produce shifts at a rate of 40 to 60 meV/ps. The experiment validates photoionization-photoelectron spectroscopy via Rydberg states as a powerful technique to observe structural dynamics of polyatomic molecules.« less

Joint nonlinearity effects in the design of a flexible truss structure control system

NASA Technical Reports Server (NTRS)

Mercadal, Mathieu

1986-01-01

Nonlinear effects are introduced in the dynamics of large space truss structures by the connecting joints which are designed with rather important tolerances to facilitate the assembly of the structures in space. The purpose was to develop means to investigate the nonlinear dynamics of the structures, particularly the limit cycles that might occur when active control is applied to the structures. An analytical method was sought and derived to predict the occurrence of limit cycles and to determine their stability. This method is mainly based on the quasi-linearization of every joint using describing functions. This approach was proven successful when simple dynamical systems were tested. Its applicability to larger systems depends on the amount of computations it requires, and estimates of the computational task tend to indicate that the number of individual sources of nonlinearity should be limited. Alternate analytical approaches, which do not account for every single nonlinearity, or the simulation of a simplified model of the dynamical system should, therefore, be investigated to determine a more effective way to predict limit cycles in large dynamical systems with an important number of distributed nonlinearities.

Characterizing RNA Dynamics at Atomic Resolution Using Solution-state NMR Spectroscopy

PubMed Central

Bothe, Jameson R.; Nikolova, Evgenia N.; Eichhorn, Catherine D.; Chugh, Jeetender; Hansen, Alexandar L.; Al-Hashimi, Hashim M.

2012-01-01

Many recently discovered non-coding RNAs do not fold into a single native conformation, but rather, sample many different conformations along their free energy landscape to carry out their biological function. Unprecedented insights into the RNA dynamic structure landscape are provided by solution-state NMR techniques that measure the structural, kinetic, and thermodynamic characteristics of motions spanning picosecond to second timescales at atomic resolution. From these studies a basic description of the RNA dynamic structure landscape is emerging, bringing new insights into how RNA structures change to carry out their function as well as applications in RNA-targeted drug discovery and RNA bioengineering. PMID:22036746

Structural dynamics of the mitochondrial compartment.

PubMed

Thorsness, P E

1992-09-01

The metabolic activities of mitochondria have been extensively characterized. However, there is much less known about the morphogenic changes of the mitochondrial compartment during growth, development and aging of the cell and the consequences of those structural changes on cellular metabolism. There is a growing body of evidence for interactions of mitochondria with cytoskeletal components and changes of mitochondrial structure during development and in response to changing environmental conditions. Segregation and recombination of mitochondrial genomes are also processes dependent upon the dynamic nature of the mitochondrial compartment. These regulatory and structural aspects of mitochondrial compartment dynamics will play an important role in the analysis of mitochondrial function and pathology.

POPULATION DYNAMICS OF HISPID COTTON RATS (SIGMODON HISPIDUS) ACROSS A NITROGEN AMENDED LANDSCAPE

EPA Science Inventory

Population dynamics of some small-mammal species appear to be regulated by plant-community structure, vegetative cover, plant diversity, and food quality. Thus, plant community changes associated with nitrogen additions would likely impact dynamics and structure of small-mammal ...

Dynamic tests of composite panels of an aircraft wing

NASA Astrophysics Data System (ADS)

Splichal, Jan; Pistek, Antonin; Hlinka, Jiri

2015-10-01

The paper describes the analysis of aerospace composite structures under dynamic loading. Today, it is common to use design procedures based on assumption of static loading only, and dynamic loading is rarely assumed and applied in design and certification of aerospace structures. The paper describes the application of dynamic loading for the design of aircraft structures, and the validation of the procedure on a selected structure. The goal is to verify the possibility of reducing the weight through improved design/modelling processes using dynamic loading instead of static loading. The research activity focuses on the modelling and testing of a composite panel representing a local segment of an aircraft wing section, investigating in particular the buckling behavior under dynamic loading. Finite Elements simulation tools are discussed, as well as the advantages of using a digital optical measurement system for the evaluation of the tests. The comparison of the finite element simulations with the results of the tests is presented.

Dynamical interpretation of conditional patterns

NASA Technical Reports Server (NTRS)

Adrian, R. J.; Moser, R. D.; Moin, P.

1988-01-01

While great progress is being made in characterizing the 3-D structure of organized turbulent motions using conditional averaging analysis, there is a lack of theoretical guidance regarding the interpretation and utilization of such information. Questions concerning the significance of the structures, their contributions to various transport properties, and their dynamics cannot be answered without recourse to appropriate dynamical governing equations. One approach which addresses some of these questions uses the conditional fields as initial conditions and calculates their evolution from the Navier-Stokes equations, yielding valuable information about stability, growth, and longevity of the mean structure. To interpret statistical aspects of the structures, a different type of theory which deals with the structures in the context of their contributions to the statistics of the flow is needed. As a first step toward this end, an effort was made to integrate the structural information from the study of organized structures with a suitable statistical theory. This is done by stochastically estimating the two-point conditional averages that appear in the equation for the one-point probability density function, and relating the structures to the conditional stresses. Salient features of the estimates are identified, and the structure of the one-point estimates in channel flow is defined.

Age or stage structure? A comparison of dynamic outcomes from discrete age- and stage-structured population models.

PubMed

Wikan, Arild

2012-06-01

Discrete stage-structured density-dependent and discrete age-structured density-dependent population models are considered. Regarding the former, we prove that the model at hand is permanent (i.e., that the population will neither go extinct nor exhibit explosive oscillations) and given density dependent fecundity terms we also show that species with delayed semelparous life histories tend to be more stable than species which possess precocious semelparous life histories. Moreover, our findings together with results obtained from other stage-structured models seem to illustrate a fairly general ecological principle, namely that iteroparous species are more stable than semelparous species. Our analysis of various age-structured models does not necessarily support the conclusions above. In fact, species with precocious life histories now appear to possess better stability properties than species with delayed life histories, especially in the iteroparous case. We also show that there are dynamical outcomes from semelparous age-structured models which we are not able to capture in corresponding stage-structured cases. Finally, both age- and stage-structured population models may generate periodic dynamics of low period (either exact or approximate). The important prerequisite is to assume density-dependent survival probabilities.

The universality of β-hairpin misfolding indicated by molecular dynamics simulations.

PubMed

Shao, Qiang; Wang, Jinan; Shi, Jiye; Zhu, Weiliang

2013-10-28

Previous molecular dynamics simulations showed that besides the experimentally measured folded structures, several β-structured polypeptides could also have misfolded "out-of-register" structures. Through the enhanced sampling molecular dynamics simulations on a series of polypeptides using either implicit or explicit solvent model, the present study systematically investigated the universality of β-hairpin misfolding and its determinants. It was observed that the misfolding could take place for almost all polypeptides under study, especially in the presence of weak side chain hydrophobicity. Moreover, the observed misfolded structures for various polypeptides share the following common features: (1) the turn length in misfolded structure is one-residue shorter than that in folded structure; (2) the hydrophobic side chains on the two strands are pointed to the opposite directions instead of packing in the same direction to form hydrophobic core cluster in the folded structure; and (3) the misfolded structure is one-residue-shifted asymmetric β-hairpin structure. The detailed analysis suggested that the misfolding of β-hairpin is the result of the competition between the formation of the alterable turn configurations and the inter-strand hydrophobic interactions. These predictions are desired to be tested by experiments.

The universality of β-hairpin misfolding indicated by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Shao, Qiang; Wang, Jinan; Shi, Jiye; Zhu, Weiliang

2013-10-01

Previous molecular dynamics simulations showed that besides the experimentally measured folded structures, several β-structured polypeptides could also have misfolded "out-of-register" structures. Through the enhanced sampling molecular dynamics simulations on a series of polypeptides using either implicit or explicit solvent model, the present study systematically investigated the universality of β-hairpin misfolding and its determinants. It was observed that the misfolding could take place for almost all polypeptides under study, especially in the presence of weak side chain hydrophobicity. Moreover, the observed misfolded structures for various polypeptides share the following common features: (1) the turn length in misfolded structure is one-residue shorter than that in folded structure; (2) the hydrophobic side chains on the two strands are pointed to the opposite directions instead of packing in the same direction to form hydrophobic core cluster in the folded structure; and (3) the misfolded structure is one-residue-shifted asymmetric β-hairpin structure. The detailed analysis suggested that the misfolding of β-hairpin is the result of the competition between the formation of the alterable turn configurations and the inter-strand hydrophobic interactions. These predictions are desired to be tested by experiments.

Shock-driven fluid-structure interaction for civil design

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wood, Stephen L; Deiterding, Ralf

The multiphysics fluid-structure interaction simulation of shock-loaded structures requires the dynamic coupling of a shock-capturing flow solver to a solid mechanics solver for large deformations. The Virtual Test Facility combines a Cartesian embedded boundary approach with dynamic mesh adaptation in a generic software framework of flow solvers using hydrodynamic finite volume upwind schemes that are coupled to various explicit finite element solid dynamics solvers (Deiterding et al., 2006). This paper gives a brief overview of the computational approach and presents first simulations that utilize the general purpose solid dynamics code DYNA3D for complex 3D structures of interest in civil engineering.more » Results from simulations of a reinforced column, highway bridge, multistory building, and nuclear reactor building are presented.« less

Synchronization in dynamical networks with unconstrained structure switching

NASA Astrophysics Data System (ADS)

del Genio, Charo I.; Romance, Miguel; Criado, Regino; Boccaletti, Stefano

2015-12-01

We provide a rigorous solution to the problem of constructing a structural evolution for a network of coupled identical dynamical units that switches between specified topologies without constraints on their structure. The evolution of the structure is determined indirectly from a carefully built transformation of the eigenvector matrices of the coupling Laplacians, which are guaranteed to change smoothly in time. In turn, this allows one to extend the master stability function formalism, which can be used to assess the stability of a synchronized state. This approach is independent from the particular topologies that the network visits, and is not restricted to commuting structures. Also, it does not depend on the time scale of the evolution, which can be faster than, comparable to, or even secular with respect to the dynamics of the units.

X-ray Scattering Combined with Coordinate-Based Analyses for Applications in Natural and Artificial Photosynthesis

PubMed Central

Tiede, David M.; Mardis, Kristy L.; Zuo, Xiaobing

2009-01-01

Advances in x-ray light sources and detectors have created opportunities for advancing our understanding of structure and structural dynamics for supramolecular assemblies in solution by combining x-ray scattering measurement with coordinate-based modeling methods. In this review the foundations for x-ray scattering are discussed and illustrated with selected examples demonstrating the ability to correlate solution x-ray scattering measurements to molecular structure, conformation, and dynamics. These approaches are anticipated to have a broad range of applications in natural and artificial photosynthesis by offering possibilities for structure resolution for dynamic supramolecular assemblies in solution that can not be fully addressed with crystallographic techniques, and for resolving fundamental mechanisms for solar energy conversion by mapping out structure in light-excited reaction states. PMID:19636808

Mechanical properties of multifunctional structure with viscoelastic components based on FVE model

NASA Astrophysics Data System (ADS)

Hao, Dong; Zhang, Lin; Yu, Jing; Mao, Daiyong

2018-02-01

Based on the models of Lion and Kardelky (2004) and Hofer and Lion (2009), a finite viscoelastic (FVE) constitutive model, considering the predeformation-, frequency- and amplitude-dependent properties, has been proposed in our earlier paper [1]. FVE model is applied to investigating the dynamic characteristics of the multifunctional structure with the viscoelastic components. Combing FVE model with the finite element theory, the dynamic model of the multifunctional structure could be obtained. Additionally, the parametric identification and the experimental verification are also given via the frequency-sweep tests. The results show that the computational data agree well with the experimental data. FVE model has made a success of expressing the dynamic characteristics of the viscoelastic materials utilized in the multifunctional structure. The multifunctional structure technology has been verified by in-orbit experiments.

CEAS/AIAA/ICASE/NASA Langley International Forum on Aeroelasticity and Structural Dynamics 1999. Pt. 2

NASA Technical Reports Server (NTRS)

Whitlow, Jr., Woodrow (Editor); Todd, Emily N. (Editor)

1999-01-01

The proceedings of a workshop sponsored by the Confederation of European Aerospace Societies (CEAS), the American Institute of Aeronautics and Astronautics (AIAA), the National Aeronautics and Space Administration (NASA), Washington, D.C., and the Institute for Computer Applications in Science and Engineering (ICASE), Hampton, Virginia, and held in Williamsburg, Virginia June 22-25, 1999 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.

Partial structure factors reveal atomic dynamics in metallic alloy melts

NASA Astrophysics Data System (ADS)

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.

Quantitative Analysis of Cellular Metabolic Dissipative, Self-Organized Structures

PubMed Central

de la Fuente, Ildefonso Martínez

2010-01-01

One of the most important goals of the postgenomic era is understanding the metabolic dynamic processes and the functional structures generated by them. Extensive studies during the last three decades have shown that the dissipative self-organization of the functional enzymatic associations, the catalytic reactions produced during the metabolite channeling, the microcompartmentalization of these metabolic processes and the emergence of dissipative networks are the fundamental elements of the dynamical organization of cell metabolism. Here we present an overview of how mathematical models can be used to address the properties of dissipative metabolic structures at different organizational levels, both for individual enzymatic associations and for enzymatic networks. Recent analyses performed with dissipative metabolic networks have shown that unicellular organisms display a singular global enzymatic structure common to all living cellular organisms, which seems to be an intrinsic property of the functional metabolism as a whole. Mathematical models firmly based on experiments and their corresponding computational approaches are needed to fully grasp the molecular mechanisms of metabolic dynamical processes. They are necessary to enable the quantitative and qualitative analysis of the cellular catalytic reactions and also to help comprehend the conditions under which the structural dynamical phenomena and biological rhythms arise. Understanding the molecular mechanisms responsible for the metabolic dissipative structures is crucial for unraveling the dynamics of cellular life. PMID:20957111

Multiscale structure in eco-evolutionary dynamics

NASA Astrophysics Data System (ADS)

Stacey, Blake C.

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

Analysis on pseudo excitation of random vibration for structure of time flight counter

NASA Astrophysics Data System (ADS)

Wu, Qiong; Li, Dapeng

2015-03-01

Traditional computing method is inefficient for getting key dynamical parameters of complicated structure. Pseudo Excitation Method(PEM) is an effective method for calculation of random vibration. Due to complicated and coupling random vibration in rocket or shuttle launching, the new staging white noise mathematical model is deduced according to the practical launch environment. This deduced model is applied for PEM to calculate the specific structure of Time of Flight Counter(ToFC). The responses of power spectral density and the relevant dynamic characteristic parameters of ToFC are obtained in terms of the flight acceptance test level. Considering stiffness of fixture structure, the random vibration experiments are conducted in three directions to compare with the revised PEM. The experimental results show the structure can bear the random vibration caused by launch without any damage and key dynamical parameters of ToFC are obtained. The revised PEM is similar with random vibration experiment in dynamical parameters and responses are proved by comparative results. The maximum error is within 9%. The reasons of errors are analyzed to improve reliability of calculation. This research provides an effective method for solutions of computing dynamical characteristic parameters of complicated structure in the process of rocket or shuttle launching.

Structural and dynamic characteristics in monolayer square ice.

PubMed

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.

Integral projection models for finite populations in a stochastic environment.

PubMed

Vindenes, Yngvild; Engen, Steinar; Saether, Bernt-Erik

2011-05-01

Continuous types of population structure occur when continuous variables such as body size or habitat quality affect the vital parameters of individuals. These structures can give rise to complex population dynamics and interact with environmental conditions. Here we present a model for continuously structured populations with finite size, including both demographic and environmental stochasticity in the dynamics. Using recent methods developed for discrete age-structured models we derive the demographic and environmental variance of the population growth as functions of a continuous state variable. These two parameters, together with the expected population growth rate, are used to define a one-dimensional diffusion approximation of the population dynamics. Thus, a substantial reduction in complexity is achieved as the dynamics of the complex structured model can be described by only three population parameters. We provide methods for numerical calculation of the model parameters and demonstrate the accuracy of the diffusion approximation by computer simulation of specific examples. The general modeling framework makes it possible to analyze and predict future dynamics and extinction risk of populations with various types of structure, and to explore consequences of changes in demography caused by, e.g., climate change or different management decisions. Our results are especially relevant for small populations that are often of conservation concern.

Characterization of local complex structures in a recurrence plot to improve nonlinear dynamic discriminant analysis.

PubMed

Ding, Hang

2014-01-01

Structures in recurrence plots (RPs), preserving the rich information of nonlinear invariants and trajectory characteristics, have been increasingly analyzed in dynamic discrimination studies. The conventional analysis of RPs is mainly focused on quantifying the overall diagonal and vertical line structures through a method, called recurrence quantification analysis (RQA). This study extensively explores the information in RPs by quantifying local complex RP structures. To do this, an approach was developed to analyze the combination of three major RQA variables: determinism, laminarity, and recurrence rate (DLR) in a metawindow moving over a RP. It was then evaluated in two experiments discriminating (1) ideal nonlinear dynamic series emulated from the Lorenz system with different control parameters and (2) data sets of human heart rate regulations with normal sinus rhythms (n = 18) and congestive heart failure (n = 29). Finally, the DLR was compared with seven major RQA variables in terms of discriminatory power, measured by standardized mean difference (DSMD). In the two experiments, DLR resulted in the highest discriminatory power with DSMD = 2.53 and 0.98, respectively, which were 7.41 and 2.09 times the best performance from RQA. The study also revealed that the optimal RP structures for the discriminations were neither typical diagonal structures nor vertical structures. These findings indicate that local complex RP structures contain some rich information unexploited by RQA. Therefore, future research to extensively analyze complex RP structures would potentially improve the effectiveness of the RP analysis in dynamic discrimination studies.

Dynamic Stiffness Modeling of Composite Plate and Shell Assemblies

DTIC Science & Technology

2013-12-09

FA8655-10-1-3084 Report 6 Dynamic Stiffness Modelling of Plate and Shell Assemblies 4 Introduction Aerospace structures are generally made up of thin ...Sound and Vibration, 294(1- 2):131–161, 2006. [23] Y. F. Xing and B. Liu. New exact solutions for free vibrations of thin orthotropic rectangular plates ...Structures, 89(5–6):467–475, 2011. [80] A.Y.T. Leung. Dynamic stiffness analysis of laminated composite plates . Thin - Walled Structures, 25:109–133, 1996

Computational and experimental studies of microvascular void features for passive-adaptation of structural panel dynamic properties

NASA Astrophysics Data System (ADS)

Sears, Nicholas C.; Harne, Ryan L.

2018-01-01

The performance, integrity, and safety of built-up structural systems are critical to their effective employment in diverse engineering applications. In conflict with these goals, harmonic or random excitations of structural panels may promote large amplitude oscillations that are particularly harmful when excitation energies are concentrated around natural frequencies. This contributes to fatigue concerns, performance degradation, and failure. While studies have considered active or passive damping treatments that adapt material characteristics and configurations for structural control, it remains to be understood how vibration properties of structural panels may be tailored via internal material transitions. Motivated to fill this knowledge gap, this research explores an idea of adapting the static and dynamic material distribution of panels through embedded microvascular channels and strategically placed voids that permit the internal movement of fluids within the panels for structural dynamic control. Finite element model and experimental investigations probe how redistributing material in the form of microscale voids influences the global vibration modes and natural frequencies of structural panels. Through parameter studies, the relationships among void shape, number, size, and location are quantified towards their contribution to the changing structural dynamics. For the panel composition and boundary conditions considered in this report, the findings reveal that transferring material between strategically placed voids may result in eigenfrequency changes as great as 10.0, 5.0, and 7.4% for the first, second, and third modes, respectively.

G-quadruplex dynamics.

PubMed

Harkness, Robert W; Mittermaier, Anthony K

2017-11-01

G-quadruplexes (GQs) are four-stranded nucleic acid secondary structures formed by guanosine (G)-rich DNA and RNA sequences. It is becoming increasingly clear that cellular processes including gene expression and mRNA translation are regulated by GQs. GQ structures have been extensively characterized, however little attention to date has been paid to their conformational dynamics, despite the fact that many biological GQ sequences populate multiple structures of similar free energies, leading to an ensemble of exchanging conformations. The impact of these dynamics on biological function is currently not well understood. Recently, structural dynamics have been demonstrated to entropically stabilize GQ ensembles, potentially modulating gene expression. Transient, low-populated states in GQ ensembles may additionally regulate nucleic acid interactions and function. This review will underscore the interplay of GQ dynamics and biological function, focusing on several dynamic processes for biological GQs and the characterization of GQ dynamics by nuclear magnetic resonance (NMR) spectroscopy in conjunction with other biophysical techniques. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

Overlapping community detection based on link graph using distance dynamics

NASA Astrophysics Data System (ADS)

Chen, Lei; Zhang, Jing; Cai, Li-Jun

2018-01-01

The distance dynamics model was recently proposed to detect the disjoint community of a complex network. To identify the overlapping structure of a network using the distance dynamics model, an overlapping community detection algorithm, called L-Attractor, is proposed in this paper. The process of L-Attractor mainly consists of three phases. In the first phase, L-Attractor transforms the original graph to a link graph (a new edge graph) to assure that one node has multiple distances. In the second phase, using the improved distance dynamics model, a dynamic interaction process is introduced to simulate the distance dynamics (shrink or stretch). Through the dynamic interaction process, all distances converge, and the disjoint community structure of the link graph naturally manifests itself. In the third phase, a recovery method is designed to convert the disjoint community structure of the link graph to the overlapping community structure of the original graph. Extensive experiments are conducted on the LFR benchmark networks as well as real-world networks. Based on the results, our algorithm demonstrates higher accuracy and quality than other state-of-the-art algorithms.

A Computer Code for Dynamic Stress Analysis of Media-Structure Problems with Nonlinearities (SAMSON). Volume III. User’s Manual.

DTIC Science & Technology

NONLINEAR SYSTEMS, LINEAR SYSTEMS, SUBROUTINES , SOIL MECHANICS, INTERFACES, DYNAMICS, LOADS(FORCES), FORCE(MECHANICS), DAMPING, ACCELERATION, ELASTIC...PROPERTIES, PLASTIC PROPERTIES, CRACKS , REINFORCING MATERIALS , COMPOSITE MATERIALS , FAILURE(MECHANICS), MECHANICAL PROPERTIES, INSTRUCTION MANUALS, DIGITAL COMPUTERS...STRESSES, *COMPUTER PROGRAMS), (*STRUCTURES, STRESSES), (*DATA PROCESSING, STRUCTURAL PROPERTIES), SOILS , STRAIN(MECHANICS), MATHEMATICAL MODELS

A Neural Network Model of the Structure and Dynamics of Human Personality

ERIC Educational Resources Information Center

Read, Stephen J.; Monroe, Brian M.; Brownstein, Aaron L.; Yang, Yu; Chopra, Gurveen; Miller, Lynn C.

2010-01-01

We present a neural network model that aims to bridge the historical gap between dynamic and structural approaches to personality. The model integrates work on the structure of the trait lexicon, the neurobiology of personality, temperament, goal-based models of personality, and an evolutionary analysis of motives. It is organized in terms of two…

Ground Reaction Forces Generated During Rhythmical Squats as a Dynamic Loads of the Structure

NASA Astrophysics Data System (ADS)

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).

Dynamic loading and stress life analysis of permanent space station modules

NASA Astrophysics Data System (ADS)

Anisimov, A. V.; Krokhin, I. A.; Likhoded, A. I.; Malinin, A. A.; Panichkin, N. G.; Sidorov, V. V.; Titov, V. A.

2016-11-01

Some methodological approaches to solving several key problems of dynamic loading and structural strength analysis of Permanent Space Station (PSS)modules developed on the basis of the working experience of Soviet and Russian PSS and the International Space station (ISS) are presented. The solutions of the direct and semi-inverse problems of PSS structure dynamics are mathematically stated. Special attention is paid to the use of the results of ground structural strength tests of space station modules and the data on the actual flight actions on the station and its dynamic responses in the orbital operation regime. The procedure of determining the dynamics and operation life parameters of elements of the PSS modules is described.

Toward the fourth dimension of membrane protein structure: insight into dynamics from spin-labeling EPR spectroscopy.

PubMed

McHaourab, Hassane S; Steed, P Ryan; Kazmier, Kelli

2011-11-09

Trapping membrane proteins in the confines of a crystal lattice obscures dynamic modes essential for interconversion between multiple conformations in the functional cycle. Moreover, lattice forces could conspire with detergent solubilization to stabilize a minor conformer in an ensemble thus confounding mechanistic interpretation. Spin labeling in conjunction with electron paramagnetic resonance (EPR) spectroscopy offers an exquisite window into membrane protein dynamics in the native-like environment of a lipid bilayer. Systematic application of spin labeling and EPR identifies sequence-specific secondary structures, defines their topology and their packing in the tertiary fold. Long range distance measurements (60 Å-80 Å) between pairs of spin labels enable quantitative analysis of equilibrium dynamics and triggered conformational changes. This review highlights the contribution of spin labeling to bridging structure and mechanism. Efforts to develop methods for determining structures from EPR restraints and to increase sensitivity and throughput promise to expand spin labeling applications in membrane protein structural biology. Copyright © 2011 Elsevier Ltd. All rights reserved.

Fluid-structure interaction dynamic simulation of spring-loaded pressure relief valves under seismic wave

NASA Astrophysics Data System (ADS)

Lv, Dongwei; Zhang, Jian; Yu, Xinhai

2018-05-01

In this paper, a fluid-structure interaction dynamic simulation method of spring-loaded pressure relief valve was established. The dynamic performances of the fluid regions and the stress and strain of the structure regions were calculated at the same time by accurately setting up the contact pairs between the solid parts and the coupling surfaces between the fluid regions and the structure regions. A two way fluid-structure interaction dynamic simulation of a simplified pressure relief valve model was carried out. The influence of vertical sinusoidal seismic waves on the performance of the pressure relief valve was preliminarily investigated by loading sine waves. Under vertical seismic waves, the pressure relief valve will flutter, and the reseating pressure was affected by the amplitude and frequency of the seismic waves. This simulation method of the pressure relief valve under vertical seismic waves can provide effective means for investigating the seismic performances of the valves, and make up for the shortcomings of the experiment.

Spontaneous scale-free structure in adaptive networks with synchronously dynamical linking

NASA Astrophysics Data System (ADS)

Yuan, Wu-Jie; Zhou, Jian-Fang; Li, Qun; Chen, De-Bao; Wang, Zhen

2013-08-01

Inspired by the anti-Hebbian learning rule in neural systems, we study how the feedback from dynamical synchronization shapes network structure by adding new links. Through extensive numerical simulations, we find that an adaptive network spontaneously forms scale-free structure, as confirmed in many real systems. Moreover, the adaptive process produces two nontrivial power-law behaviors of deviation strength from mean activity of the network and negative degree correlation, which exists widely in technological and biological networks. Importantly, these scalings are robust to variation of the adaptive network parameters, which may have meaningful implications in the scale-free formation and manipulation of dynamical networks. Our study thus suggests an alternative adaptive mechanism for the formation of scale-free structure with negative degree correlation, which means that nodes of high degree tend to connect, on average, with others of low degree and vice versa. The relevance of the results to structure formation and dynamical property in neural networks is briefly discussed as well.

Dynamically variable negative stiffness structures

PubMed Central

Churchill, Christopher B.; Shahan, David W.; Smith, Sloan P.; Keefe, Andrew C.; McKnight, Geoffrey P.

2016-01-01

Variable stiffness structures that enable a wide range of efficient load-bearing and dexterous activity are ubiquitous in mammalian musculoskeletal systems but are rare in engineered systems because of their complexity, power, and cost. We present a new negative stiffness–based load-bearing structure with dynamically tunable stiffness. Negative stiffness, traditionally used to achieve novel response from passive structures, is a powerful tool to achieve dynamic stiffness changes when configured with an active component. Using relatively simple hardware and low-power, low-frequency actuation, we show an assembly capable of fast (<10 ms) and useful (>100×) dynamic stiffness control. This approach mitigates limitations of conventional tunable stiffness structures that exhibit either small (<30%) stiffness change, high friction, poor load/torque transmission at low stiffness, or high power active control at the frequencies of interest. We experimentally demonstrate actively tunable vibration isolation and stiffness tuning independent of supported loads, enhancing applications such as humanoid robotic limbs and lightweight adaptive vibration isolators. PMID:26989771

Control Augmented Structural Synthesis

NASA Technical Reports Server (NTRS)

Lust, Robert V.; Schmit, Lucien A.

1988-01-01

A methodology for control augmented structural synthesis is proposed for a class of structures which can be modeled as an assemblage of frame and/or truss elements. It is assumed that both the plant (structure) and the active control system dynamics can be adequately represented with a linear model. The structural sizing variables, active control system feedback gains and nonstructural lumped masses are treated simultaneously as independent design variables. Design constraints are imposed on static and dynamic displacements, static stresses, actuator forces and natural frequencies to ensure acceptable system behavior. Multiple static and dynamic loading conditions are considered. Side constraints imposed on the design variables protect against the generation of unrealizable designs. While the proposed approach is fundamentally more general, here the methodology is developed and demonstrated for the case where: (1) the dynamic loading is harmonic and thus the steady state response is of primary interest; (2) direct output feedback is used for the control system model; and (3) the actuators and sensors are collocated.

Modeling the Dynamics of Soil Structure and Water in Agricultural Soil

NASA Astrophysics Data System (ADS)

Weller, U.; Lang, B.; Rabot, E.; Stössel, B.; Urbanski, L.; Vogel, H. J.; Wiesmeier, M.; Wollschlaeger, U.

2017-12-01

The impact of agricultural management on soil functions is manifold and severe. It has both positive and adverse influence. Our goal is to develop model tools quantifying the agricultural impact on soil functions based on a mechanistic understanding of soil processes to support farmers and decision makers. The modeling approach is based on defining relevant soil components, i.e. soil matrix, macropores, organisms, roots and organic matter. They interact and form the soil's macroscopic properties and functions including water and gas dynamics, and biochemical cycles. Based on existing literature information we derive functional interaction processes and combine them in a network of dynamic soil components. In agricultural soils, a major issue is linked to changes in soil structure and their influence on water dynamics. Compaction processes are well studied in literature, but for the resilience due to root growth and activity of soil organisms the information is scarcer. We implement structural dynamics into soil water and gas simulations using a lumped model that is both coarse enough to allow extensive model runs while still preserving some important, yet rarely modeled phenomenons like preferential flow, hysteretic and dynamic behavior. For simulating water dynamics, at each depth, the model assumes water at different binding energies depending on soil structure, i.e. the pore size distribution. Non-equilibrium is postulated, meaning that free water may occur even if the soil is not fully saturated. All energy levels are interconnected allowing water to move, both within a spatial node, and between neighboring nodes (adding gravity). Structure dynamics alters the capacity of this water compartments, and the conductance of its connections. Connections are switched on and off depending on whether their sources contain water or their targets have free capacity. This leads to piecewise linear system behavior that allows fast calculation for extended time steps. Based on this concept, the dynamics of soil structure can be directly linked to soil water dynamics as a main driver for other soil processes. Further steps will include integration of temperature and solute leaching as well as defining the feedback of the water regime on the structure forming processes.

Incorporating modeling and simulations in undergraduate biophysical chemistry course to promote understanding of structure-dynamics-function relationships in proteins.

PubMed

Hati, Sanchita; Bhattacharyya, Sudeep

2016-01-01

A project-based biophysical chemistry laboratory course, which is offered to the biochemistry and molecular biology majors in their senior year, is described. In this course, the classroom study of the structure-function of biomolecules is integrated with the discovery-guided laboratory study of these molecules using computer modeling and simulations. In particular, modern computational tools are employed to elucidate the relationship between structure, dynamics, and function in proteins. Computer-based laboratory protocols that we introduced in three modules allow students to visualize the secondary, super-secondary, and tertiary structures of proteins, analyze non-covalent interactions in protein-ligand complexes, develop three-dimensional structural models (homology model) for new protein sequences and evaluate their structural qualities, and study proteins' intrinsic dynamics to understand their functions. In the fourth module, students are assigned to an authentic research problem, where they apply their laboratory skills (acquired in modules 1-3) to answer conceptual biophysical questions. Through this process, students gain in-depth understanding of protein dynamics-the missing link between structure and function. Additionally, the requirement of term papers sharpens students' writing and communication skills. Finally, these projects result in new findings that are communicated in peer-reviewed journals. © 2016 The International Union of Biochemistry and Molecular Biology.

Investigation of the redox-dependent modulation of structure and dynamics in human cytochrome c

DOE Office of Scientific and Technical Information (OSTI.GOV)

Imai, Mizue; Saio, Tomohide; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810

2016-01-22

Redox-dependent changes in the structure and dynamics of human cytochrome c (Cyt c) were investigated by solution NMR. We found significant structural changes in several regions, including residues 23–28 (loop 3), which were further corroborated by chemical shift differences between the reduced and oxidized states of Cyt c. These differences are essential for discriminating redox states in Cyt c by cytochrome c oxidase (CcO) during electron transfer reactions. Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments identified that the region around His33 undergoes conformational exchanges on the μs-ms timescale, indicating significant redox-dependent structural changes. Because His33 is not part of the interaction sitemore » for CcO, our data suggest that the dynamic properties of the region, which is far from the interaction site for CcO, contribute to conformational changes during electron transfer to CcO. - Highlights: • Solution structure and dynamics analysis for human Cyt c by NMR. • Structural changes responsible for the discrimination of the redox state in Cyt c. • Conformational exchange in the region outside of the interaction site for CcO. • Less flexibility and rigid structure of the interaction site on Cyt c for CcO.« less

Structure and Dynamics of Urea/Water Mixtures Investigated by Vibrational Spectroscopy and Molecular Dynamics Simulation

PubMed Central

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

A new modal-based approach for modelling the bump foil structure in the simultaneous solution of foil-air bearing rotor dynamic problems

NASA Astrophysics Data System (ADS)

Bin Hassan, M. F.; Bonello, P.

2017-05-01

Recently-proposed techniques for the simultaneous solution of foil-air bearing (FAB) rotor dynamic problems have been limited to a simple bump foil model in which the individual bumps were modelled as independent spring-damper (ISD) subsystems. The present paper addresses this limitation by introducing a modal model of the bump foil structure into the simultaneous solution scheme. The dynamics of the corrugated bump foil structure are first studied using the finite element (FE) technique. This study is experimentally validated using a purpose-made corrugated foil structure. Based on the findings of this study, it is proposed that the dynamics of the full foil structure, including bump interaction and foil inertia, can be represented by a modal model comprising a limited number of modes. This full foil structure modal model (FFSMM) is then adapted into the rotordynamic FAB problem solution scheme, instead of the ISD model. Preliminary results using the FFSMM under static and unbalance excitation conditions are proven to be reliable by comparison against the corresponding ISD foil model results and by cross-correlating different methods for computing the deflection of the full foil structure. The rotor-bearing model is also validated against experimental and theoretical results in the literature.

Structural studies on choline-carboxylate bio-ionic liquids by x-ray scattering and molecular dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tanzi, Luana; Ramondo, Fabio, E-mail: fabio.ramondo@univaq.it; Caminiti, Ruggero

2015-09-21

We report a X-ray diffraction and molecular dynamics study on three choline-based bio-ionic liquids, choline formate, [Ch] [For], choline propanoate, [Ch][Pro], and choline butanoate, [Ch][But]. For the first time, this class of ionic liquids has been investigated by X-ray diffraction. Experimental and theoretical structure factors have been compared for each term of the series. Local structural organization has been obtained from ab initio calculations through static models of isolated ion pairs and dynamic simulations of small portions of liquids through twelve, ten, and nine ion pairs for [Ch][For], [Ch][Pro], and [Ch][But], respectively. All the theoretical models indicate that cations andmore » anions are connected by strong hydrogen bonding and form stable ion pairs in the liquid that are reminiscent of the static ab initio ion pairs. Different structural aspects may affect the radial distribution function, like the local structure of ion pairs and the conformation of choline. When small portions of liquids have been simulated by dynamic quantum chemical methods, some key structural features of the X-ray radial distribution function were well reproduced whereas the classical force fields here applied did not entirely reproduce all the observed structural features.« less

Structural Properties of Human IAPP Dimer in Membrane Environment Studied by All-Atom Molecular Dynamics Simulations.

PubMed

Liu, Na; Duan, Mojie; Yang, Minghui

2017-08-11

The aggregation of human islet amyloid polypeptide (hIAPP) can damage the membrane of the β-cells in the pancreatic islets and induce type 2 diabetes (T2D). Growing evidences indicated that the major toxic species are small oligomers of IAPP. Due to the fast aggregation nature, it is hard to characterize the structures of IAPP oligomers by experiments, especially in the complex membrane environment. On the other side, molecular dynamics simulation can provide atomic details of the structure and dynamics of the aggregation of IAPP. In this study, all-atom bias-exchange metadynamics (BE-Meta) and unbiased molecular dynamics simulations were employed to study the structural properties of IAPP dimer in the membranes environments. A number of intermediates, including α-helical states, β-sheet states, and fully disordered states, are identified. The formation of N-terminal β-sheet structure is prior to the C-terminal β-sheet structure towards the final fibril-like structures. The α-helical intermediates have lower propensity in the dimeric hIAPP and are off-pathway intermediates. The simulations also demonstrate that the β-sheet intermediates induce more perturbation on the membrane than the α-helical and disordered states and thus pose higher disruption ability.

An improved EMD method for modal identification and a combined static-dynamic method for damage detection

NASA Astrophysics Data System (ADS)

Yang, Jinping; Li, Peizhen; Yang, Youfa; Xu, Dian

2018-04-01

Empirical mode decomposition (EMD) is a highly adaptable signal processing method. However, the EMD approach has certain drawbacks, including distortions from end effects and mode mixing. In the present study, these two problems are addressed using an end extension method based on the support vector regression machine (SVRM) and a modal decomposition method based on the characteristics of the Hilbert transform. The algorithm includes two steps: using the SVRM, the time series data are extended at both endpoints to reduce the end effects, and then, a modified EMD method using the characteristics of the Hilbert transform is performed on the resulting signal to reduce mode mixing. A new combined static-dynamic method for identifying structural damage is presented. This method combines the static and dynamic information in an equilibrium equation that can be solved using the Moore-Penrose generalized matrix inverse. The combination method uses the differences in displacements of the structure with and without damage and variations in the modal force vector. Tests on a four-story, steel-frame structure were conducted to obtain static and dynamic responses of the structure. The modal parameters are identified using data from the dynamic tests and improved EMD method. The new method is shown to be more accurate and effective than the traditional EMD method. Through tests with a shear-type test frame, the higher performance of the proposed static-dynamic damage detection approach, which can detect both single and multiple damage locations and the degree of the damage, is demonstrated. For structures with multiple damage, the combined approach is more effective than either the static or dynamic method. The proposed EMD method and static-dynamic damage detection method offer improved modal identification and damage detection, respectively, in structures.

Molecular dynamics simulations on the local order of liquid and amorphous ZnTe

NASA Astrophysics Data System (ADS)

Rino, José Pedro; Borges, Denilson; Mota, Rita C.; Silva, Maurício A. P.

2008-05-01

Molecular dynamics studies of structural and dynamical correlations of molten and vitreous states under several conditions of density and temperature were performed. We use an effective recently proposed interatomic potential, consisting of two- and three-body covalent interactions which has successfully described the structural, dynamical, and structural phase transformation induced by pressure in ZnTe [D. S. Borges and J. P. Rino, Phys. Rev. B 72, 014107 (2005)]. The two-body term of the interaction potential consists of Coulomb interaction resulting from charge transfer, steric repulsion due to atomic sizes, charge-dipole interaction to include the effect of electronic polarizability of anions, and dipole-dipole (van der Waals) interactions. The three-body covalent term is a modification of the Stillinger-Weber potential. Molecular dynamics simulations in isobaric-isenthalpic ensemble have been performed for systems amounting to 4096 and 64 000 particles. Starting from a crystalline zinc-blende (ZB) structure, the system is initially heated until a very homogeneous liquid is obtained. The vitreous zinc telluride phase is attained by cooling the liquid at sufficiently fast cooling rates, while slower cooling rates lead to a disordered ZB crystalline structure. Two- and three-body correlations for the liquid and vitreous phases are analyzed through pair distribution functions, static structure factors, and bond angle distributions. In particular, the neutron static structure factor for the liquid phase is in very good agreement with both the reported experimental data and first-principles simulations.

Structure and Dynamics of Interacting Nanoparticles in Semidilute Polymer Solutions

DOE PAGES

Pollng-Skutvik, Ryan; Mongcopa, Katrina Irene S.; Faraone, Antonio; ...

2016-08-17

We investigate the structure and dynamics of silica nanoparticles and polymer chains in semidilute solutions of high molecular weight polystyrene in 2-butanone to determine the effect of long-range interparticle interactions on the coupling between particle and polymer dynamics. Particles at concentrations of 1–10 wt % are well dispersed in the semidilute polymer solutions and exhibit long-range electrostatic repulsions between particles. Because the particles are comparably sized to the radius of gyration of the polymer, the particle dynamics is predicted to couple to that of the polymer. We verify that the polymer structure and dynamics are not significantly affected by themore » particles, indicating that the particle–polymer coupling does not change with increasing particle loading. We find that the coupling between the dynamics of comparably sized particles and polymer results in subdiffusive particle dynamics, as expected. Over the interparticle distance, however, the particle dynamics is hindered and not fully described by the relaxation of the surrounding polymer chains. Instead, the particle dynamics is inversely related to the structure factor, suggesting that physical particle–polymer coupling on short length scales and interparticle interactions on long length scales both present energetic barriers to particle motion that lead to subdiffusive dynamics and de Gennes narrowing, respectively.« less

Simulating forest management and its effect on landscape pattern

Treesearch

Eric J. Gustafson

2017-01-01

Landscapes are characterized by their structure (the spatial arrangement of landscape elements), their ecological function (how ecological processes operate within that structure), and the dynamics of change (disturbance and recovery). Thus, understanding the dynamic nature of landscapes and predicting their future dynamics are of particular emphasis. Landscape change...

Finite Element Model Development For Aircraft Fuselage Structures

NASA Technical Reports Server (NTRS)

Buehrle, Ralph D.; Fleming, Gary A.; Pappa, Richard S.; Grosveld, Ferdinand W.

2000-01-01

The ability to extend the valid frequency range for finite element based structural dynamic predictions using detailed models of the structural components and attachment interfaces is examined for several stiffened aircraft fuselage structures. This extended dynamic prediction capability is needed for the integration of mid-frequency noise control technology. Beam, plate and solid element models of the stiffener components are evaluated. Attachment models between the stiffener and panel skin range from a line along the rivets of the physical structure to a constraint over the entire contact surface. The finite element models are validated using experimental modal analysis results.

Molecular dynamics simulation of water at mineral surfaces: Structure, dynamics, energetics and hydrogen bonding

NASA Astrophysics Data System (ADS)

Kalinichev, A. G.; Wang, J.; Kirkpatrick, R.

2006-05-01

Fundamental molecular-level understanding of the properties of aqueous mineral interfaces is of great importance for many geochemical and environmental systems. Interaction between water and mineral surfaces substantially affects the properties of both phases, including the reactivity and functionality of the substrate surface, and the structure, dynamics, and energetics of the near surface aqueous phase. Experimental studies of interfacial water structure and dynamics using surface-sensitive techniques such as sum-frequency vibrational spectroscopy or X-ray and neutron reflectivity are not always possible for many practically important substrates, and their results often require interpretation concerning the atomistic mechanisms responsible for the observed behavior. Molecular computer simulations can provide new insight into the underlying molecular- level relationships between the inorganic substrate structure and composition and the structure, ordering, and dynamics of interfacial water. We have performed a series of molecular dynamics (MD) computer simulations of aqueous interfaces with several silicates (quartz, muscovite, and talc) and hydroxides (brucite, portlandite, gibbsite, Ca/Al and Mg/Al double hydroxides) to quantify the effects of the substrate mineral structure and composition on the structural, transport, and thermodynamic properties of water on these mineral surfaces. Due to the prevalent effects of the development of well-interconnected H-bonding networks across the mineral- water interfaces, all the hydroxide surfaces (including a fully hydroxylated quartz surface) show very similar H2O density profiles perpendicular to the interface. However, the predominant orientations of the interfacial H2O molecules and their detailed 2-dimensional near-surface structure and dynamics parallel to the interface are quite different reflecting the differences in the substrate structural charge distribution and the density and orientations of the surface OH groups. The H2O density profiles and other structural and dynamic characteristics of water at the two siloxane surfaces are very different from each other and from the hydroxide surfaces, since the muscovite surface is negatively charged and hydrophilic, while the talc surface is electrostatically neutral and hydrophobic. In general, at hydrophilic neutral surfaces both donating and accepting H-bonds from the H2O molecules are contributing to the development of the interfacial H-bond network, whereas at hydrophilic but charged surfaces only accepting or donating H-bonds with H2O molecules are possible. At the hydrophobic talc surface H-bonds among H2O molecules dominate the interfacial H-bond network and the water-surface interactions are very weak. The first water layer at all substrates is well ordered parallel to the surface, reflecting substrate crystal structures and indicating the reduced translational and orientational mobility of interfacial H2O molecules. At longer time scale (~100ps) their dynamics can be decomposed into a slow, virtually frozen, regime due to the substrate- bound H2O and a faster regime of almost free water reflecting the dynamics far from the surface. At shorter times (>10ps) the two dynamical regimes are superimposed. The much higher ordering of interfacial water (compared to bulk liquid) can not be adequately described as simply "ice-like". To some extent, it rather resembles the behavior of supercooled water.

Dynamic (Vibration) Testing: Design-Certification of Aerospace System

NASA Technical Reports Server (NTRS)

Aggarwal, Pravin K.

2010-01-01

Various types of dynamic testing of structures for certification purposes are described, including vibration, shock and acoustic testing. Modal testing is discussed as it frequently complements dynamic testing and is part of the structural verification/validation process leading up to design certification. Examples of dynamic and modal testing are presented as well as the common practices, procedures and standards employed.

14 CFR 23.307 - Proof of structure.

Code of Federal Regulations, 2011 CFR

2011-01-01

.... Dynamic tests, including structural flight tests, are acceptable if the design load conditions have been... critical load condition. Structural analysis may be used only if the structure conforms to those for which...

Effects of non-structural components and soil-structure interaction on the seismic response of framed structures

NASA Astrophysics Data System (ADS)

Ditommaso, Rocco; Auletta, Gianluca; Iacovino, Chiara; Nigro, Antonella; Carlo Ponzo, Felice

2017-04-01

In this paper, several nonlinear numerical models of reinforced concrete framed structures have been defined in order to evaluate the effects of non-structural elements and soil-structure interaction on the elastic dynamic behaviour of buildings. In the last few years, many and various studies have highlighted the significant effects derived from the interaction between structural and non-structural components on the main dynamic characteristics of a building. Usually, structural and non-structural elements act together, adding both masses and stiffness. The presence of infill panels is generally neglected in the design process of structural elements, although these elements can significantly increase the lateral stiffness of a structure leading to a modification in the dynamic properties. Particularly, at the Damage Limit State (where an elastic behaviour is expected), soil-structure interaction effects and non-structural elements may further affect the elastic natural period of buildings, changing the spectral accelerations compared with those provided by seismic codes in case of static analyses. In this work, a parametric study has been performed in order to evaluate the elastic fundamental period of vibration of buildings as a function of structural morphology (height, plan area, ratio between plan dimensions), infills presence and distribution and soil characteristics. Acknowledgements This study was partially funded by the Italian Department of Civil Protection within the project DPC-RELUIS 2016 - RS4 ''Seismic observatory of structures and health monitoring'' and by the "Centre of Integrated Geomorphology for the Mediterranean Area - CGIAM" within the Framework Agreement with the University of Basilicata "Study, Research and Experimentation in the Field of Analysis and Monitoring of Seismic Vulnerability of Strategic and Relevant Buildings for the purposes of Civil Protection and Development of Innovative Strategies of Seismic Reinforcement".

Structures composing protein domains.

PubMed

Kubrycht, Jaroslav; Sigler, Karel; Souček, Pavel; Hudeček, Jiří

2013-08-01

This review summarizes available data concerning intradomain structures (IS) such as functionally important amino acid residues, short linear motifs, conserved or disordered regions, peptide repeats, broadly occurring secondary structures or folds, etc. IS form structural features (units or elements) necessary for interactions with proteins or non-peptidic ligands, enzyme reactions and some structural properties of proteins. These features have often been related to a single structural level (e.g. primary structure) mostly requiring certain structural context of other levels (e.g. secondary structures or supersecondary folds) as follows also from some examples reported or demonstrated here. In addition, we deal with some functionally important dynamic properties of IS (e.g. flexibility and different forms of accessibility), and more special dynamic changes of IS during enzyme reactions and allosteric regulation. Selected notes concern also some experimental methods, still more necessary tools of bioinformatic processing and clinically interesting relationships. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Coastal oceanography sets the pace of rocky intertidal community dynamics.

PubMed

Menge, B A; Lubchenco, J; Bracken, M E S; Chan, F; Foley, M M; Freidenburg, T L; Gaines, S D; Hudson, G; Krenz, C; Leslie, H; Menge, D N L; Russell, R; Webster, M S

2003-10-14

The structure of ecological communities reflects a tension among forces that alter populations. Marine ecologists previously emphasized control by locally operating forces (predation, competition, and disturbance), but newer studies suggest that inputs from large-scale oceanographically modulated subsidies (nutrients, particulates, and propagules) can strongly influence community structure and dynamics. On New Zealand rocky shores, the magnitude of such subsidies differs profoundly between contrasting oceanographic regimes. Community structure, and particularly the pace of community dynamics, differ dramatically between intermittent upwelling regimes compared with relatively persistent down-welling regimes. We suggest that subsidy rates are a key determinant of the intensity of species interactions, and thus of structure in marine systems, and perhaps also nonmarine communities.

Verification of nonlinear dynamic structural test results by combined image processing and acoustic analysis

NASA Astrophysics Data System (ADS)

Tene, Yair; Tene, Noam; Tene, G.

1993-08-01

An interactive data fusion methodology of video, audio, and nonlinear structural dynamic analysis for potential application in forensic engineering is presented. The methodology was developed and successfully demonstrated in the analysis of heavy transportable bridge collapse during preparation for testing. Multiple bridge elements failures were identified after the collapse, including fracture, cracks and rupture of high performance structural materials. Videotape recording by hand held camcorder was the only source of information about the collapse sequence. The interactive data fusion methodology resulted in extracting relevant information form the videotape and from dynamic nonlinear structural analysis, leading to full account of the sequence of events during the bridge collapse.

Dynamic and fluid-structure interaction simulations of bioprosthetic heart valves using parametric design with T-splines and Fung-type material models

NASA Astrophysics Data System (ADS)

Hsu, Ming-Chen; Kamensky, David; Xu, Fei; Kiendl, Josef; Wang, Chenglong; Wu, Michael C. H.; Mineroff, Joshua; Reali, Alessandro; Bazilevs, Yuri; Sacks, Michael S.

2015-06-01

This paper builds on a recently developed immersogeometric fluid-structure interaction (FSI) methodology for bioprosthetic heart valve (BHV) modeling and simulation. It enhances the proposed framework in the areas of geometry design and constitutive modeling. With these enhancements, BHV FSI simulations may be performed with greater levels of automation, robustness and physical realism. In addition, the paper presents a comparison between FSI analysis and standalone structural dynamics simulation driven by prescribed transvalvular pressure, the latter being a more common modeling choice for this class of problems. The FSI computation achieved better physiological realism in predicting the valve leaflet deformation than its standalone structural dynamics counterpart.

Recent Developments in Smart Adaptive Structures for Solar Sailcraft

NASA Technical Reports Server (NTRS)

Whorton, M. S.; Kim, Y. K.; Oakley, J.; Adetona, O.; Keel, L. H.

2007-01-01

The "Smart Adaptive Structures for Solar Sailcraft" development activity at MSFC has investigated issues associated with understanding how to model and scale the subsystem and multi-body system dynamics of a gossamer solar sailcraft with the objective of designing sailcraft attitude control systems. This research and development activity addressed three key tasks that leveraged existing facilities and core competencies of MSFC to investigate dynamics and control issues of solar sails. Key aspects of this effort included modeling and testing of a 30 m deployable boom; modeling of the multi-body system dynamics of a gossamer sailcraft; investigation of control-structures interaction for gossamer sailcraft; and development and experimental demonstration of adaptive control technologies to mitigate control-structures interaction.

Structure, Dynamics and Environment of Galaxies

NASA Astrophysics Data System (ADS)

Combes, Francoise; Terlevich, Roberto

This contribution presents a summary of the discussion on structure, dynamics and environment of Galaxies, held on Friday May 26 evening, after the Sherry/Coffee interval and the oral presentation of two dozen posters papers.

Structural properties of CuAu nanoparticles with different type. Molecular dynamic simulations

NASA Astrophysics Data System (ADS)

Chepkasov, I. V.; Baidyshev, V. S.; Baev, A. Y.

2018-05-01

The paper is devoted to the thermal stability of a CuAu nanoparticles structure (D=5 nm) of various type (binary alloy, core-shell, "Janus" type) and of various percentage of copper atoms. The simulation was carried out with molecular dynamics, using the embedded atom potential. The authors defined the most preferable structural options from the standpoint of thermodynamics, as well as studied in detail the influence of different temperatures on the structural stability of CuAu nanoparticles.

Structured population dynamics: continuous size and discontinuous stage structures.

PubMed

Buffoni, Giuseppe; Pasquali, Sara

2007-04-01

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

Modeling and tachometer feedback in the control of an experimental single link flexible structure

NASA Technical Reports Server (NTRS)

Garcia, Ephrahim; Inman, Daniel J.

1990-01-01

In this work a formulation for the modeling of a single link flexible structure will be introduced that includes the effects of dynamic interaction between the actuator and structure. These effects are the rotational modal participation factors for the structure's vibratory motion that occurs at the slewing axis. It will be shown, both theoretically and experimentally, that this dynamic interaction can be advantageous for vibration suppression of the flexible modes of the system during slewing positioning maneuvers.

Stress-strain state of the structure in the service area of underground railway

NASA Astrophysics Data System (ADS)

Barabash, M.; Bashinsky, Y.; Korjakins, A.

2017-10-01

The paper focuses on numerical study how vibration due to underground trains influences the load-bearing building structures. Diagrams of vibration levels for monolithic floor slab depending on frequency are obtained. Levels of vibrations on floor slabs and columns are measured. The simulation of dynamic load from underground railway onto load-bearing building structures is presented as an example with account of load transmission through the soil. Recommendations for generation of design model in dynamic analysis of structure are provided.

Structures and dynamics in a two-dimensional dipolar dust particle system

NASA Astrophysics Data System (ADS)

Hou, X. N.; Liu, Y. H.; Kravchenko, O. V.; Lapushkina, T. A.; Azarova, O. A.; Chen, Z. Y.; Huang, F.

2018-05-01

The effects of electric dipole moment, the number of dipolar particles, and system temperature on the structures and dynamics of a dipolar dust particle system are studied by molecular dynamics simulations. The results show that the larger electric dipole moment is favorable for the formation of a long-chain structure, the larger number of dipolar dust particles promotes the formation of the multi-chain structure, and the higher system temperature can cause higher rotation frequency. The trajectories, mean square displacement (MSD), and the corresponding spectrum functions of the MSDs are also calculated to illustrate the dynamics of the dipolar dust particle system, which is also closely related to the growth of dust particles. Some simulations are qualitatively in agreement with our experiments and can provide a guide for the study on dust growth, especially on the large-sized particles.

Integrative, Dynamic Structural Biology at Atomic Resolution—It’s About Time

PubMed Central

van den Bedem, Henry; Fraser, James S.

2015-01-01

Biomolecules adopt a dynamic ensemble of conformations, each with the potential to interact with binding partners or perform the chemical reactions required for a multitude of cellular functions. Recent advances in X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, and other techniques are helping us realize the dream of seeing—in atomic detail—how different parts of biomolecules exchange between functional sub-states using concerted motions. Integrative structural biology has advanced our understanding of the formation of large macromolecular complexes and how their components interact in assemblies by leveraging data from many low-resolution methods. Here, we review the growing opportunities for integrative, dynamic structural biology at the atomic scale, contending there is increasing synergistic potential between X-ray crystallography, NMR, and computer simulations to reveal a structural basis for protein conformational dynamics at high resolution. PMID:25825836

Relationship between local structure and relaxation in out-of-equilibrium glassy systems

DOE PAGES

Schoenholz, Samuel S.; Cubuk, Ekin D.; Kaxiras, Efthimios; ...

2016-12-27

The dynamical glass transition is typically taken to be the temperature at which a glassy liquid is no longer able to equilibrate on experimental timescales. Consequently, the physical properties of these systems just above or below the dynamical glass transition, such as viscosity, can change by many orders of magnitude over long periods of time following external perturbation. During this progress toward equilibrium, glassy systems exhibit a history dependence that has complicated their study. In previous work, we bridged the gap between structure and dynamics in glassy liquids above their dynamical glass transition temperatures by introducing a scalar field calledmore » “softness,” a quantity obtained using machine-learning methods. Softness is designed to capture the hidden patterns in relative particle positions that correlate strongly with dynamical rearrangements of particle positions. Here we show that the out-of-equilibrium behavior of a model glass-forming system can be understood in terms of softness. We first demonstrate that the evolution of behavior following a temperature quench is a primarily structural phenomenon: The structure changes considerably, but the relationship between structure and dynamics remains invariant. We then show that the relaxation time can be robustly computed from structure as quantified by softness, with the same relation holding both in equilibrium and as the system ages. Together, these results show that the history dependence of the relaxation time in glasses requires knowledge only of the softness in addition to the usual state variables.« less

Structural relaxation of polydisperse hard spheres: comparison of the mode-coupling theory to a Langevin dynamics simulation.

PubMed

Weysser, F; Puertas, A M; Fuchs, M; Voigtmann, Th

2010-07-01

We analyze the slow glassy structural relaxation as measured through collective and tagged-particle density correlation functions obtained from Brownian dynamics simulations for a polydisperse system of quasi-hard spheres in the framework of the mode-coupling theory (MCT) of the glass transition. Asymptotic analyses show good agreement for the collective dynamics when polydispersity effects are taken into account in a multicomponent calculation, but qualitative disagreement at small q when the system is treated as effectively monodisperse. The origin of the different small-q behavior is attributed to the interplay between interdiffusion processes and structural relaxation. Numerical solutions of the MCT equations are obtained taking properly binned partial static structure factors from the simulations as input. Accounting for a shift in the critical density, the collective density correlation functions are well described by the theory at all densities investigated in the simulations, with quantitative agreement best around the maxima of the static structure factor and worst around its minima. A parameter-free comparison of the tagged-particle dynamics however reveals large quantitative errors for small wave numbers that are connected to the well-known decoupling of self-diffusion from structural relaxation and to dynamical heterogeneities. While deviations from MCT behavior are clearly seen in the tagged-particle quantities for densities close to and on the liquid side of the MCT glass transition, no such deviations are seen in the collective dynamics.

A computer lab exploring evolutionary aspects of chromatin structure and dynamics for an undergraduate chromatin course*.

PubMed

Eirín-López, José M

2013-01-01

The study of chromatin constitutes one of the most active research fields in life sciences, being subject to constant revisions that continuously redefine the state of the art in its knowledge. As every other rapidly changing field, chromatin biology requires clear and straightforward educational strategies able to efficiently translate such a vast body of knowledge to the classroom. With this aim, the present work describes a multidisciplinary computer lab designed to introduce undergraduate students to the dynamic nature of chromatin, within the context of the one semester course "Chromatin: Structure, Function and Evolution." This exercise is organized in three parts including (a) molecular evolutionary biology of histone families (using the H1 family as example), (b) histone structure and variation across different animal groups, and (c) effect of histone diversity on nucleosome structure and chromatin dynamics. By using freely available bioinformatic tools that can be run on common computers, the concept of chromatin dynamics is interactively illustrated from a comparative/evolutionary perspective. At the end of this computer lab, students are able to translate the bioinformatic information into a biochemical context in which the relevance of histone primary structure on chromatin dynamics is exposed. During the last 8 years this exercise has proven to be a powerful approach for teaching chromatin structure and dynamics, allowing students a higher degree of independence during the processes of learning and self-assessment. Copyright © 2013 International Union of Biochemistry and Molecular Biology, Inc.

Relationship between local structure and relaxation in out-of-equilibrium glassy systems.

PubMed

Schoenholz, Samuel S; Cubuk, Ekin D; Kaxiras, Efthimios; Liu, Andrea J

2017-01-10

The dynamical glass transition is typically taken to be the temperature at which a glassy liquid is no longer able to equilibrate on experimental timescales. Consequently, the physical properties of these systems just above or below the dynamical glass transition, such as viscosity, can change by many orders of magnitude over long periods of time following external perturbation. During this progress toward equilibrium, glassy systems exhibit a history dependence that has complicated their study. In previous work, we bridged the gap between structure and dynamics in glassy liquids above their dynamical glass transition temperatures by introducing a scalar field called "softness," a quantity obtained using machine-learning methods. Softness is designed to capture the hidden patterns in relative particle positions that correlate strongly with dynamical rearrangements of particle positions. Here we show that the out-of-equilibrium behavior of a model glass-forming system can be understood in terms of softness. To do this we first demonstrate that the evolution of behavior following a temperature quench is a primarily structural phenomenon: The structure changes considerably, but the relationship between structure and dynamics remains invariant. We then show that the relaxation time can be robustly computed from structure as quantified by softness, with the same relation holding both in equilibrium and as the system ages. Together, these results show that the history dependence of the relaxation time in glasses requires knowledge only of the softness in addition to the usual state variables.

Effect of Material Ion Exchanges on the Mechanical Stiffness Properties and Shear Deformation of Hydrated Cement Material Chemistry Structure C-S-H Jennite -- A Computational Modeling Study

NASA Astrophysics Data System (ADS)

Adebiyi, Babatunde Mattew

Material properties and performance are governed by material molecular chemistry structures and molecular level interactions. Methods to understand relationships between the material properties and performance and their correlation to the molecular level chemistry and morphology, and thus find ways of manipulating and adjusting matters at the atomistic level in order to improve material performance, are required. A computational material modeling methodology is investigated and demonstrated for a key cement hydrated component material chemistry structure of Calcium-Silicate-Hydrate (C-S-H) Jennite in this work. The effect of material ion exchanges on the mechanical stiffness properties and shear deformation behavior of hydrated cement material chemistry structure of Calcium Silicate Hydrate (C-S-H) Jennite was studied. Calcium ions were replaced with Magnesium ions in Jennite structure of the C-S-H gel. Different level of substitution of the ions was used. The traditional Jennite structure was obtained from the American Mineralogist Crystal Structure Database and super cells of the structures were created using a Molecular Dynamics Analyzer and Visualizer Material Studio. Molecular dynamics parameters used in the modeling analysis were determined by carrying out initial dynamic studies. 64 unit cell of C-S-H Jennite was used in material modeling analysis studies based on convergence results obtained from the elastic modulus and total energies. NVT forcite dynamics using COMPASS force field based on 200 ps dynamics time was used to determine mechanical modulus of the traditional C-S-H gel and the Magnesium ion modified structures. NVT Discover dynamics using COMPASS forcefield was used in the material modeling studies to investigate the influence of ionic exchange on the shear deformation of the associated material chemistry structures. A prior established quasi-static deformation method to emulate shear deformation of C-S-H material chemistry structure that is based on a triclinic crystal structure was used, by deforming the triclinic crystal structure at 0.2 degree per time step for 75 steps of deformation. It was observed that there is a decrease in the total energies of the systems as the percentage of magnesium ion increases in the C-S-H Jennite molecular structure systems. Investigation of effect of ion exchange on the elastic modulus shows that the elastic stiffness modulus tends to decrease as the amount of Mg in the systems increases, using either COMPASS or universal force field. On the other hand, shear moduli obtained after deforming the structures computed from the stress-strain curve obtained from material modeling increases as the amount of Mg increases in the system. The present investigations also showed that ultimate shear stress obtained from predicted shear stress---strain also increases with amount of Mg in the chemistry structure. Present study clearly demonstrates that computational material modeling following molecular dynamics analysis methodology is an effective way to predict and understand the effective material chemistry and additive changes on the stiffness and deformation characteristics in cementitious materials, and the results suggest that this method can be extended to other materials.

Dynamic/Jitter Assessment of Multiple Potential HabEx Structural Designs

NASA Technical Reports Server (NTRS)

Knight, J. Brent; Stahl, H. Philip; Singleton, Andy; Hunt, Ron; Therrell, Melissa; Caldwell, Kate; Garcia, Jay; Baysinger, Mike

2017-01-01

One of the driving structural requirements of the Habitable Exo-Planet (HabEx) telescope is to maintain Line Of Sight (LOS) stability between the Primary Mirror (PM) and Secondary Mirror (SM) of = 5 mas. Dynamic analyses of two configurations of a proposed (HabEx) 4 meter off-axis telescope structure were performed to predict effects of jitter on primary/secondary mirror alignment. The dynamic disturbance used as the forcing function was the James Webb Space Telescope reaction wheel assembly vibration emission specification level. The objective of these analyses was to predict "order-of-magnitude" performance for various structural configurations which will roll into efforts to define the HabEx structural design's global architecture. Two variations of the basic architectural design were analyzed. Relative motion between the PM and the SM for each design configuration are reported.

Structure, Dynamic Cracking Resistance, and Crack Growth Micromechanism in Pipe Billets after Thermomechanical Treatment

NASA Astrophysics Data System (ADS)

Simonov, M. Yu.; Simonov, Yu. N.; Shaimanov, G. S.

2018-01-01

The structure, dynamic cracking resistance, and micromechanisms of crack growth in initially highly tempered pipe billets made of structural carbon steel are studied after thermomechanical treatment, including cold plastic deformation by radial forging followed by annealing, under various conditions. The strength is found to be maximum after cold radial forging followed by annealing at 300°C. Cold radial forging and annealing at 600°C are shown to cause the formation of an ultrafine-grained structure with an average grain/subgrain size of 900 nm. The structural features formed in both the axial and the transverse direction after cold radial forging have been revealed. The mechanism of crack growth after heat treatment and thermomechanical treatment has been studied. The fracture surface elements formed during dynamic-crackingresistance tests have been qualitatively analyzed.

Dynamic/jitter assessment of multiple potential HabEx structural designs

NASA Astrophysics Data System (ADS)

Knight, J. Brent; Stahl, H. Philip; Singleton, Andy; Hunt, Ron; Therrell, Melissa; Caldwell, Kate; Garcia, Jay; Baysinger, Mike

2017-09-01

One of the driving structural requirements of the Habitable Exo-Planet (HabEx) telescope is to maintain Line Of Sight (LOS) stability between the Primary Mirror (PM) and Secondary Mirror (SM) of <= 5 milli-arc seconds (mas). Dynamic analyses of two configurations of a proposed HabEx 4 meter off-axis telescope structure were performed to predict effects of a vibration input on primary/secondary mirror alignment. The dynamic disturbance used as the forcing function was the James Webb Space Telescope reaction wheel assembly vibration emission specification level. The objective of these analyses was to predict "order-of-magnitude" performance for various structural configurations which contribute to efforts in defining the HabEx structural design's global architecture. Two variations of the basic architectural design were analyzed. Relative motion between the PM and the SM for each design configuration are reported.

Structure and dynamics of stock market in times of crisis

NASA Astrophysics Data System (ADS)

Zhao, Longfeng; Li, Wei; Cai, Xu

2016-02-01

Daily correlations among 322 S&P 500 constituent stocks are investigated by means of correlation-based (CB) network. By using the heterogeneous time scales, we identify global expansion and local clustering market behaviors during crises, which are mainly caused by community splits and inter-sector edge number decreases. The CB networks display distinctive community and sector structures. Graph edit distance is applied to capturing the dynamics of CB networks in which drastic structure reconfigurations can be observed during crisis periods. Edge statistics reveal the power-law nature of edges' duration time distribution. Despite the networks' strong structural changes during crises, we still find some long-duration edges that serve as the backbone of the stock market. Finally the dynamical change of network structure has shown its capability in predicting the implied volatility index (VIX).

A curved piezo-structure model: implications on active structural acoustic control.

PubMed

Henry, J K; Clark, R L

1999-09-01

Current research in Active Structural Acoustic Control (ASAC) relies heavily upon accurately capturing the application physics associated with the structure being controlled. The application of ASAC to aircraft interior noise requires a greater understanding of the dynamics of the curved panels which compose the skin of an aircraft fuselage. This paper presents a model of a simply supported curved panel with attached piezoelectric transducers. The model is validated by comparison to previous work. Further, experimental results for a simply supported curved panel test structure are presented in support of the model. The curvature is shown to affect substantially the dynamics of the panel, the integration of transducers, and the bandwidth required for structural acoustic control.

Detection of internal cracks in rubber composite structures using an impact acoustic modality

NASA Astrophysics Data System (ADS)

Shen, Q.; Kurfess, T. R.; Omar, M.; Gramling, F.

2014-01-01

The objective of this study is to investigate the use of impact acoustic signals to non-intrusively inspect rubber composite structures for the presence of internal cracks, such as those found in an automobile tyre. Theoretical contact dynamic models for both integral and defective rubber structures are developed based on Hertz's impact model, further modified for rubber composite materials. The model generates the prediction of major impact dynamic quantities, namely the maximum impact force, impact duration and contact deformation; such parameters are also theoretically proven to be correlated with the presence of internal cracks. The tyre structures are simplified into cubic rubber blocks, to mitigate complexity for analytical modelling. Both impact force and impact sound signals are measured experimentally, and extraction of useful features from both signals for defect identification is achieved. The impact force produces two direct measurements of theoretical impact dynamic quantities. A good correlation between these experimental discriminators and the theoretical dynamic quantities provide validation for the contact dynamics models. Defect discriminators extracted from the impact sound are dependent on both time- and frequency-domain analyses. All the discriminators are closely connected with the theoretical dynamic quantities and experimentally verified as good indicators of internal cracks in rubber composite structures.

Measuring and comparing structural fluctuation patterns in large protein datasets.

PubMed

Fuglebakk, Edvin; Echave, Julián; Reuter, Nathalie

2012-10-01

The function of a protein depends not only on its structure but also on its dynamics. This is at the basis of a large body of experimental and theoretical work on protein dynamics. Further insight into the dynamics-function relationship can be gained by studying the evolutionary divergence of protein motions. To investigate this, we need appropriate comparative dynamics methods. The most used dynamical similarity score is the correlation between the root mean square fluctuations (RMSF) of aligned residues. Despite its usefulness, RMSF is in general less evolutionarily conserved than the native structure. A fundamental issue is whether RMSF is not as conserved as structure because dynamics is less conserved or because RMSF is not the best property to use to study its conservation. We performed a systematic assessment of several scores that quantify the (dis)similarity between protein fluctuation patterns. We show that the best scores perform as well as or better than structural dissimilarity, as assessed by their consistency with the SCOP classification. We conclude that to uncover the full extent of the evolutionary conservation of protein fluctuation patterns, it is important to measure the directions of fluctuations and their correlations between sites. Nathalie.Reuter@mbi.uib.no Supplementary data are available at Bioinformatics Online.

Ser/Thr Motifs in Transmembrane Proteins: Conservation Patterns and Effects on Local Protein Structure and Dynamics

PubMed Central

del Val, Coral; White, Stephen H.

2014-01-01

We combined systematic bioinformatics analyses and molecular dynamics simulations to assess the conservation patterns of Ser and Thr motifs in membrane proteins, and the effect of such motifs on the structure and dynamics of α-helical transmembrane (TM) segments. We find that Ser/Thr motifs are often present in β-barrel TM proteins. At least one Ser/Thr motif is present in almost half of the sequences of α-helical proteins analyzed here. The extensive bioinformatics analyses and inspection of protein structures led to the identification of molecular transporters with noticeable numbers of Ser/Thr motifs within the TM region. Given the energetic penalty for burying multiple Ser/Thr groups in the membrane hydrophobic core, the observation of transporters with multiple membrane-embedded Ser/Thr is intriguing and raises the question of how the presence of multiple Ser/Thr affects protein local structure and dynamics. Molecular dynamics simulations of four different Ser-containing model TM peptides indicate that backbone hydrogen bonding of membrane-buried Ser/Thr hydroxyl groups can significantly change the local structure and dynamics of the helix. Ser groups located close to the membrane interface can hydrogen bond to solvent water instead of protein backbone, leading to an enhanced local solvation of the peptide. PMID:22836667

Structure Calculation and Reconstruction of Discrete-State Dynamics from Residual Dipolar Couplings.

PubMed

Cole, Casey A; Mukhopadhyay, Rishi; Omar, Hanin; Hennig, Mirko; Valafar, Homayoun

2016-04-12

Residual dipolar couplings (RDCs) acquired by nuclear magnetic resonance (NMR) spectroscopy are an indispensable source of information in investigation of molecular structures and dynamics. Here, we present a comprehensive strategy for structure calculation and reconstruction of discrete-state dynamics from RDC data that is based on the singular value decomposition (SVD) method of order tensor estimation. In addition to structure determination, we provide a mechanism of producing an ensemble of conformations for the dynamical regions of a protein from RDC data. The developed methodology has been tested on simulated RDC data with ±1 Hz of error from an 83 residue α protein (PDB ID 1A1Z ) and a 213 residue α/β protein DGCR8 (PDB ID 2YT4 ). In nearly all instances, our method reproduced the structure of the protein including the conformational ensemble to within less than 2 Å. On the basis of our investigations, arc motions with more than 30° of rotation are identified as internal dynamics and are reconstructed with sufficient accuracy. Furthermore, states with relative occupancies above 20% are consistently recognized and reconstructed successfully. Arc motions with a magnitude of 15° or relative occupancy of less than 10% are consistently unrecognizable as dynamical regions within the context of ±1 Hz of error.

Virtual-pulse time integral methodology: A new explicit approach for computational dynamics - Theoretical developments for general nonlinear structural dynamics

NASA Technical Reports Server (NTRS)

Chen, Xiaoqin; Tamma, Kumar K.; Sha, Desong

1993-01-01

The present paper describes a new explicit virtual-pulse time integral methodology for nonlinear structural dynamics problems. The purpose of the paper is to provide the theoretical basis of the methodology and to demonstrate applicability of the proposed formulations to nonlinear dynamic structures. Different from the existing numerical methods such as direct time integrations or mode superposition techniques, the proposed methodology offers new perspectives and methodology of development, and possesses several unique and attractive computational characteristics. The methodology is tested and compared with the implicit Newmark method (trapezoidal rule) through a nonlinear softening and hardening spring dynamic models. The numerical results indicate that the proposed explicit virtual-pulse time integral methodology is an excellent alternative for solving general nonlinear dynamic problems.

Structural dynamics of Casein Kinase I (CKI) from malarial parasite Plasmodium falciparum (Isolate 3D7): Insights from theoretical modelling and molecular simulations.

PubMed

Dehury, Budheswar; Behera, Santosh Kumar; Mahapatra, Namita

2017-01-01

The protein kinases (PKs), belonging to serine/threonine kinase (STKs), are important drug targets for a wide spectrum of diseases in human. Among protein kinases, the Casein Kinases (CKs) are vastly expanded in various organisms, where, the malarial parasite Plasmodium falciparum possesses a single member i.e., PfCKI, which can phosphorylate various proteins in parasite extracts in vitro condition. But, the structure-function relationship of PfCKI and dynamics of ATP binding is yet to be understood. Henceforth, an attempt was made to study the dynamics, stability, and ATP binding mechanisms of PfCKI through computational modelling, docking, molecular dynamics (MD) simulations, and MM/PBSA binding free energy estimation. Bi-lobed catalytic domain of PfCKI shares a high degree of secondary structure topology with CKI domains of rice, human, and mouse indicating co-evolution of these kinases. Molecular docking study revealed that ATP binds to the active site where the glycine-rich ATP-binding motif (G16-X-G18-X-X-G21) along with few conserved residues plays a crucial role maintaining stability of the complex. Structural superposition of PfCKI with close structural homologs depicted that the location and length of important loops are different, indicating the dynamic properties of these loops among CKIs, which is consistent with principal component analysis (PCA). PCA displayed that the overall global motion of ATP-bound form is comparatively higher than that of apo form. The present study provides insights into the structural features of PfCKI, which could contribute towards further understanding of related protein structures, dynamics of catalysis and phosphorylation mechanism in these important STKs from malarial parasite in near future. Copyright © 2016 Elsevier Inc. All rights reserved.

Deciphering complex dynamics of water counteraction around secondary structural elements of allosteric protein complex: Case study of SAP-SLAM system in signal transduction cascade

NASA Astrophysics Data System (ADS)

Samanta, Sudipta; Mukherjee, Sanchita

2018-01-01

The first hydration shell of a protein exhibits heterogeneous behavior owing to several attributes, majorly local polarity and structural flexibility as revealed by solvation dynamics of secondary structural elements. We attempt to recognize the change in complex water counteraction generated due to substantial alteration in flexibility during protein complex formation. The investigation is carried out with the signaling lymphocytic activation molecule (SLAM) family of receptors, expressed by an array of immune cells, and interacting with SLAM-associated protein (SAP), composed of one SH2 domain. All atom molecular dynamics simulations are employed to the aqueous solutions of free SAP and SLAM-peptide bound SAP. We observed that water dynamics around different secondary structural elements became highly affected as well as nicely correlated with the SLAM-peptide induced change in structural rigidity obtained by thermodynamic quantification. A few instances of contradictory dynamic features of water to the change in structural flexibility are explained by means of occluded polar residues by the peptide. For βD, EFloop, and BGloop, both structural flexibility and solvent accessibility of the residues confirm the obvious contribution. Most importantly, we have quantified enhanced restriction in water dynamics around the second Fyn-binding site of the SAP due to SAP-SLAM complexation, even prior to the presence of Fyn. This observation leads to a novel argument that SLAM induced more restricted water molecules could offer more water entropic contribution during the subsequent Fyn binding and provide enhanced stability to the SAP-Fyn complex in the signaling cascade. Finally, SLAM induced water counteraction around the second binding site of the SAP sheds light on the allosteric property of the SAP, which becomes an integral part of the underlying signal transduction mechanism.

Dynamics of psychological crisis experience with psychological consulting by gestalt therapy methods.

PubMed

Fahrutdinova, Liliya Raifovna; Nugmanova, Dzhamilia Renatovna

2015-01-01

Dynamics of experience as such and its corporeal, emotional and cognitive elements in the situation of psychological consulting provisioning is covered. The aim of research was to study psychological crisis experience dynamics in the situation when psychological consulting by gestalt therapy methods is provided. Theoretical analysis of the problem of crisis situations, phenomenon and structural, and dynamic organization of experience of the subject of consulting have been carried out. To fulfill research project test subjects experience crisis situation have been selected, studied in the situation when they provided psychological consulting by methods of gestalt therapy, and methodology of study of crisis situations experience has been prepared. Specifics of psychological crisis experience have been revealed and its elements in different stages of psychological consulting by gestalt therapy methods. Dynamics of experience of psychological crisis and its structural elements have been revealed and reliable changes in it have been revealed. Dynamics of psychological crisis experience and its structural elements have been revealed and reliable changes in it have been revealed. "Desiccation" of experience is being observed, releasing its substantiality of negative impression to the end of consulting and development of the new experience of control over crisis situation. Interrelations of structural elements of experience in the process of psychological consulting have been shown. Effecting one structure causes reliable changes in all others structural elements of experience. Giving actual psychological help to clients in crisis situation by methods of gestalt therapy is possible as it was shown in psychological consulting sessions. Structure of client's request has been revealed - problems of personal sense are fixed as the most frequent cause of clients' applications, as well as absence of choices, obtrusiveness of negative thoughts, tend to getting stuck on events took place in the past, drawing into oneself, etc.

Deciphering complex dynamics of water counteraction around secondary structural elements of allosteric protein complex: Case study of SAP-SLAM system in signal transduction cascade.

PubMed

Samanta, Sudipta; Mukherjee, Sanchita

2018-01-28

The first hydration shell of a protein exhibits heterogeneous behavior owing to several attributes, majorly local polarity and structural flexibility as revealed by solvation dynamics of secondary structural elements. We attempt to recognize the change in complex water counteraction generated due to substantial alteration in flexibility during protein complex formation. The investigation is carried out with the signaling lymphocytic activation molecule (SLAM) family of receptors, expressed by an array of immune cells, and interacting with SLAM-associated protein (SAP), composed of one SH2 domain. All atom molecular dynamics simulations are employed to the aqueous solutions of free SAP and SLAM-peptide bound SAP. We observed that water dynamics around different secondary structural elements became highly affected as well as nicely correlated with the SLAM-peptide induced change in structural rigidity obtained by thermodynamic quantification. A few instances of contradictory dynamic features of water to the change in structural flexibility are explained by means of occluded polar residues by the peptide. For βD, EFloop, and BGloop, both structural flexibility and solvent accessibility of the residues confirm the obvious contribution. Most importantly, we have quantified enhanced restriction in water dynamics around the second Fyn-binding site of the SAP due to SAP-SLAM complexation, even prior to the presence of Fyn. This observation leads to a novel argument that SLAM induced more restricted water molecules could offer more water entropic contribution during the subsequent Fyn binding and provide enhanced stability to the SAP-Fyn complex in the signaling cascade. Finally, SLAM induced water counteraction around the second binding site of the SAP sheds light on the allosteric property of the SAP, which becomes an integral part of the underlying signal transduction mechanism.

Salmonella Typhimurium and Staphylococcus aureus dynamics in/on variable (micro)structures of fish-based model systems at suboptimal temperatures.

PubMed

Baka, Maria; Verheyen, Davy; Cornette, Nicolas; Vercruyssen, Stijn; Van Impe, Jan F

2017-01-02

The limited knowledge concerning the influence of food (micro)structure on microbial dynamics decreases the accuracy of the developed predictive models, as most studies have mainly been based on experimental data obtained in liquid microbiological media or in/on real foods. The use of model systems has a great potential when studying this complex factor. Apart from the variability in (micro)structural properties, model systems vary in compositional aspects, as a consequence of their (micro)structural variation. In this study, different experimental food model systems, with compositional and physicochemical properties similar to fish patés, are developed to study the influence of food (micro)structure on microbial dynamics. The microbiological safety of fish products is of major importance given the numerous cases of salmonellosis and infections attributed to staphylococcus toxins. The model systems understudy represent food (micro)structures of liquids, aqueous gels, emulsions and gelled emulsions. The growth/inactivation dynamics and a modelling approach of combined growth and inactivation of Salmonella Typhimurium and Staphylococcus aureus, related to fish products, are investigated in/on these model systems at temperatures relevant to fish products' common storage (4°C) and to abuse storage temperatures (8 and 12°C). ComBase (http://www.combase.cc/) predictions compared with the maximum specific growth rate (μ max ) values estimated by the Baranyi and Roberts model in the current study indicated that the (micro)structure influences the microbial dynamics. Overall, ComBase overestimated microbial growth at the same pH, a w and storage temperature. Finally, the storage temperature had also an influence on how much each model system affected the microbial dynamics. Copyright © 2016. Published by Elsevier B.V.

Nonlinear Dynamics and Control of Flexible Structures

DTIC Science & Technology

1991-03-01

of which might be used for space applications. This project was a collaborative one involving structural, electrical and mechanical engineers and...methods for vibration analysis and new models to analyze chaotic dynamics in nonlinear structures with large deformations and friction forces. Finally... electrical and mechanical engineers and resulted in nine doctoral dissertations and two masters theses wholly or partially supported by this grant

Dynamic mesh adaption for triangular and tetrahedral grids

NASA Technical Reports Server (NTRS)

Biswas, Rupak; Strawn, Roger

1993-01-01

The following topics are discussed: requirements for dynamic mesh adaption; linked-list data structure; edge-based data structure; adaptive-grid data structure; three types of element subdivision; mesh refinement; mesh coarsening; additional constraints for coarsening; anisotropic error indicator for edges; unstructured-grid Euler solver; inviscid 3-D wing; and mesh quality for solution-adaptive grids. The discussion is presented in viewgraph form.

Elucidating Peptide and Protein Structure and Dynamics: UV Resonance Raman Spectroscopy

PubMed Central

Oladepo, Sulayman A.; Xiong, Kan; Hong, Zhenmin; Asher, Sanford A.

2011-01-01

UV resonance Raman spectroscopy (UVRR) is a powerful method that has the requisite selectivity and sensitivity to incisively monitor biomolecular structure and dynamics in solution. In this perspective, we highlight applications of UVRR for studying peptide and protein structure and the dynamics of protein and peptide folding. UVRR spectral monitors of protein secondary structure, such as the Amide III3 band and the Cα-H band frequencies and intensities can be used to determine Ramachandran Ψ angle distributions for peptide bonds. These incisive, quantitative glimpses into conformation can be combined with kinetic T-jump methodologies to monitor the dynamics of biomolecular conformational transitions. The resulting UVRR structural insight is impressive in that it allows differentiation of, for example, different α-helix-like states that enable differentiating π- and 310- states from pure α-helices. These approaches can be used to determine the Gibbs free energy landscape of individual peptide bonds along the most important protein (un)folding coordinate. Future work will find spectral monitors that probe peptide bond activation barriers that control protein (un)folding mechanisms. In addition, UVRR studies of sidechain vibrations will probe the role of side chains in determining protein secondary, tertiary and quaternary structures. PMID:21379371

Aeroelastic Analysis Of Joined Wing Of High Altitude Long Endurance (HALE) Aircraft Based On The Sensor-Craft Configuration

NASA Astrophysics Data System (ADS)

Marisarla, Soujanya; Ghia, Urmila; "Karman" Ghia, Kirti

2002-11-01

Towards a comprehensive aeroelastic analysis of a joined wing, fluid dynamics and structural analyses are initially performed separately. Steady flow calculations are currently performed using 3-D compressible Navier-Stokes equations. Flow analysis of M6-Onera wing served to validate the software for the fluid dynamics analysis. The complex flow field of the joined wing is analyzed and the prevailing fluid dynamic forces are computed using COBALT software. Currently, these forces are being transferred as fluid loads on the structure. For the structural analysis, several test cases were run considering the wing as a cantilever beam; these served as validation cases. A nonlinear structural analysis of the wing is being performed using ANSYS software to predict the deflections and stresses on the joined wing. Issues related to modeling, and selecting appropriate mesh for the structure were addressed by first performing a linear analysis. The frequencies and mode shapes of the deformed wing are obtained from modal analysis. Both static and dynamic analyses are carried out, and the results obtained are carefully analyzed. Loose coupling between the fluid and structural analyses is currently being examined.

Application of Dynamic Mode Decomposition: Temporal Evolution of Flow Structures in an Aneurysm

NASA Astrophysics Data System (ADS)

Conlin, William; Yu, Paulo; Durgesh, Vibhav

2017-11-01

An aneurysm is an enlargement of a weakened arterial wall that can be fatal or debilitating on rupture. Aneurysm hemodynamics is integral to developing an understanding of aneurysm formation, growth, and rupture. The flow in an aneurysm exhibits complex fluid dynamics behavior due to an inherent unsteady inflow condition and its interactions with large-scale flow structures present in the aneurysm. The objective of this study is to identify the large-scale structures in the aneurysm, study temporal behavior, and quantify their interaction with the inflow condition. For this purpose, detailed Particle Image Velocimetry (PIV) measurements were performed at the center plane of an idealized aneurysm model for a range of inflow conditions. Inflow conditions were precisely controlled using a ViVitro SuperPump system. Dynamic Modal Decomposition (DMD) of the velocity field was used to identify coherent structures and their temporal behavior. DMD was successful in capturing the large-scale flow structures and their temporal behavior. A low dimensional approximation to the flow field was obtained with the most relevant dynamic modes and was used to obtain temporal information about the coherent structures and their interaction with the inflow, formation, evolution, and growth.

Effects of local vibrations on the dynamics of space truss structures

NASA Technical Reports Server (NTRS)

Warnaar, Dirk B.; Mcgowan, Paul E.

1987-01-01

The paper discusses the influence of local member vibrations on the dynamics of repetitive space truss structures. Several focus problems wherein local member vibration modes are in the frequency range of the global truss modes are discussed. Special attention is given to defining methods that can be used to identify the global modes of a truss structure amidst many local modes. Significant interactions between the motions of local member vibrations and the global behavior are shown to occur in truss structures when: (1) the natural frequencies of the individual members for clamped-clamped boundary conditions are in the vicinity of the global truss frequency; and (2) the total mass of the individual members represents a large portion of the mass of the whole structure. The analysis is carried out with a structural analysis code which uses exact member theory. The modeling detail required using conventional finite element codes to adequately represent such a class of problems is examined. The paper concludes with some practical considerations for the design and dynamic testing of structures which might exhibit such behavior.

How relevant are assembled equilibrium samples in understanding structure formation during lipid digestion?

PubMed

Phan, Stephanie; Salentinig, Stefan; Hawley, Adrian; Boyd, Ben J

2015-10-01

Lipid-based formulations are gaining interest for use as drug delivery systems for poorly water-soluble drug compounds. During digestion, the lipolysis products self-assemble with endogenous surfactants in the gastrointestinal tract to form colloidal structures, enabling enhanced drug solubilisation. Although earlier studies in the literature focus on assembled equilibrium systems, little is known about structure formation under dynamic lipolysis conditions. The purpose of this study was to investigate the likely colloidal structure formation in the small intestine after the ingestion of lipids, under equilibrium and dynamic conditions. The structural aspects were studied using small angle X-ray scattering and dynamic light scattering, and were found to depend on lipid composition, lipid chain length, prandial state and emulsification. Incorporation of phospholipids and lipolysis products into bile salt micelles resulted in swelling of the structure. At insufficient bile salt concentrations, a co-existing lamellar phase was observed, due to a reduction in the solubilisation capacity for lipolysis products. Emulsification accelerated the rate of lipolysis and structure formation. Copyright © 2015 Elsevier B.V. All rights reserved.

Study on embedding fiber Bragg grating sensor into the 3D printing structure for health monitoring

NASA Astrophysics Data System (ADS)

Li, Ruiya; Tan, Yuegang; Zhou, Zude; Fang, Liang; Chen, Yiyang

2016-10-01

3D printing technology is a rapidly developing manufacturing technology, which is known as a core technology in the third industrial revolution. With the continuous improvement of the application of 3D printing products, the health monitoring of the 3D printing structure is particularly important. Fiber Bragg grating (FBG) sensing technology is a new type of optical sensing technology with unique advantages comparing to traditional sensing technology, and it has great application prospects in structural health monitoring. In this paper, the FBG sensors embedded in the internal structure of the 3D printing were used to monitor the static and dynamic strain variation of 3D printing structure during loading process. The theoretical result and experimental result has good consistency and the characteristic frequency detected by FBG sensor is consistent with the testing results of traditional accelerator in the dynamic experiment. The results of this paper preliminary validate that FBG embedded in the 3D printing structure can effectively detecting the static and dynamic stain change of the 3D printing structure, which provide some guidance for the health monitoring of 3D printing structure.

Folding molecular dynamics simulations accurately predict the effect of mutations on the stability and structure of a vammin-derived peptide.

PubMed

Koukos, Panagiotis I; Glykos, Nicholas M

2014-08-28

Folding molecular dynamics simulations amounting to a grand total of 4 μs of simulation time were performed on two peptides (with native and mutated sequences) derived from loop 3 of the vammin protein and the results compared with the experimentally known peptide stabilities and structures. The simulations faithfully and accurately reproduce the major experimental findings and show that (a) the native peptide is mostly disordered in solution, (b) the mutant peptide has a well-defined and stable structure, and (c) the structure of the mutant is an irregular β-hairpin with a non-glycine β-bulge, in excellent agreement with the peptide's known NMR structure. Additionally, the simulations also predict the presence of a very small β-hairpin-like population for the native peptide but surprisingly indicate that this population is structurally more similar to the structure of the native peptide as observed in the vammin protein than to the NMR structure of the isolated mutant peptide. We conclude that, at least for the given system, force field, and simulation protocol, folding molecular dynamics simulations appear to be successful in reproducing the experimentally accessible physical reality to a satisfactory level of detail and accuracy.

Time scale of dynamic heterogeneity in model ionic liquids and its relation to static length scale and charge distribution.

PubMed

Park, Sang-Won; Kim, Soree; Jung, YounJoon

2015-11-21

We study how dynamic heterogeneity in ionic liquids is affected by the length scale of structural relaxation and the ionic charge distribution by the molecular dynamics simulations performed on two differently charged models of ionic liquid and their uncharged counterpart. In one model of ionic liquid, the charge distribution in the cation is asymmetric, and in the other it is symmetric, while their neutral counterpart has no charge with the ions. It is found that all the models display heterogeneous dynamics, exhibiting subdiffusive dynamics and a nonexponential decay of structural relaxation. We investigate the lifetime of dynamic heterogeneity, τ(dh), in these systems by calculating the three-time correlation functions to find that τ(dh) has in general a power-law behavior with respect to the structural relaxation time, τ(α), i.e., τ(dh) ∝ τ(α)(ζ(dh)). Although the dynamics of the asymmetric-charge model is seemingly more heterogeneous than that of the symmetric-charge model, the exponent is found to be similar, ζ(dh) ≈ 1.2, for all the models studied in this work. The same scaling relation is found regardless of interactions, i.e., with or without Coulomb interaction, and it holds even when the length scale of structural relaxation is long enough to become the Fickian diffusion. This fact indicates that τ(dh) is a distinctive time scale from τ(α), and the dynamic heterogeneity is mainly affected by the short-range interaction and the molecular structure.

Superfluid in a shaken optical lattice: quantum critical dynamics and topological defect engineering

NASA Astrophysics Data System (ADS)

Gaj, Anita; Feng, Lei; Clark, Logan W.; Chin, Cheng

2017-04-01

We present our recent studies of non-equilibrium dynamics in Bose-Einstein condensates using the shaken optical lattice. By increasing the shaking amplitude we observe a quantum phase transition from an ordinary superfluid to an effectively ferromagnetic superfluid composed of discrete domains with different quasi-momentum. We investigate the critical dynamics during which the domain structure and domain walls emerge. We demonstrate the use of a digital micromirror device to deterministically create desired domain structure. Using this technique we develop a clearer picture of the quantum critical dynamics at early times and its impact on the domain structure long after the transition.

A Molecular Dynamics Study of the Structure-Dynamics Relationships of Supercooled Liquids and Glasses

NASA Astrophysics Data System (ADS)

Soklaski, Ryan

Central to the field of condensed matter physics is a decades old outstanding problem in the study of glasses -- namely explaining the extreme slowing of dynamics in a liquid as it is supercooled towards the so-called glass transition. Efforts to universally describe the stretched relaxation processes and heterogeneous dynamics that characteristically develop in supercooled liquids remain divided in both their approaches and successes. Towards this end, a consensus on the role that atomic and molecular structures play in the liquid is even more tenuous. However, mounting material science research efforts have culminated to reveal that the vast diversity of metallic glass species and their properties are rooted in an equally-broad set of structural archetypes. Herein lies the motivation of this dissertation: the detailed information available regarding the structure-property relationships of metallic glasses provides a new context in which one can study the evolution of a supercooled liquid by utilizing a structural motif that is known to dominate the glass. Cu64Zr36 is a binary alloy whose good glass-forming ability and simple composition makes it a canonical material to both empirical and numerical studies. Here, we perform classical molecular dynamics simulations and conduct a comprehensive analysis of the dynamical regimes of liquid Cu64Zr36, while focusing on the roles played by atomic icosahedral ordering -- a structural motif which ultimately percolates the glass' structure. Large data analysis techniques are leveraged to obtain uniquely detailed structural and dynamical information in this context. In doing so, we develop the first account of the origin of icosahedral order in this alloy, revealing deep connections between this incipient structural ordering, frustration-limited domain theory, and recent important empirical findings that are relevant to the nature of metallic liquids at large. Furthermore, important dynamical landmarks such as the breakdown of the Stokes-Einstein relationship, the decoupling of particle diffusivities, and the development of general "glassy" relaxation features are found to coincide with successive manifestation of icosahedral ordering that arise as the liquid is supercooled. Remarkably, we detect critical-like features in the growth of the icosahedron network, with signatures that suggest that a liquid-liquid phase transition may occur in the deeply supercooled regime to precede glass formation. Such a transition is predicted to occur in many supercooled liquids, although explicit evidence of this phenomenon in realistic systems is scarce. Ultimately this work concludes that icosahedral order characterizes all dynamical regimes of Cu64Zr 36, demonstrating the importance and utility of studying supercooled liquids in the context of locally-preferred structure. More broadly, it serves to confirm and inform recent theoretical and empirical findings that are central to understanding the physics underlying the glass transition.

Proteins with Novel Structure, Function and Dynamics

NASA Technical Reports Server (NTRS)

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.

The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery.

PubMed

Papaleo, Elena; Saladino, Giorgio; Lambrughi, Matteo; Lindorff-Larsen, Kresten; Gervasio, Francesco Luigi; Nussinov, Ruth

2016-06-08

Proteins are dynamic entities that undergo a plethora of conformational changes that may take place on a wide range of time scales. These changes can be as small as the rotation of one or a few side-chain dihedral angles or involve concerted motions in larger portions of the three-dimensional structure; both kinds of motions can be important for biological function and allostery. It is becoming increasingly evident that "connector regions" are important components of the dynamic personality of protein structures. These regions may be either disordered loops, i.e., poorly structured regions connecting secondary structural elements, or linkers that connect entire protein domains. Experimental and computational studies have, however, revealed that these regions are not mere connectors, and their role in allostery and conformational changes has been emerging in the last few decades. Here we provide a detailed overview of the structural properties and classification of loops and linkers, as well as a discussion of the main computational methods employed to investigate their function and dynamical properties. We also describe their importance for protein dynamics and allostery using as examples key proteins in cellular biology and human diseases such as kinases, ubiquitinating enzymes, and transcription factors.

Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions.

PubMed

Baltoumas, Fotis A; Theodoropoulou, Margarita C; Hamodrakas, Stavros J

2016-06-01

A significant amount of experimental evidence suggests that G-protein coupled receptors (GPCRs) do not act exclusively as monomers but also form biologically relevant dimers and oligomers. However, the structural determinants, stoichiometry and functional importance of GPCR oligomerization remain topics of intense speculation. In this study we attempted to evaluate the nature and dynamics of GPCR oligomeric interactions. A representative set of GPCR homodimers were studied through Coarse-Grained Molecular Dynamics simulations, combined with interface analysis and concepts from network theory for the construction and analysis of dynamic structural networks. Our results highlight important structural determinants that seem to govern receptor dimer interactions. A conserved dynamic behavior was observed among different GPCRs, including receptors belonging in different GPCR classes. Specific GPCR regions were highlighted as the core of the interfaces. Finally, correlations of motion were observed between parts of the dimer interface and GPCR segments participating in ligand binding and receptor activation, suggesting the existence of mechanisms through which dimer formation may affect GPCR function. The results of this study can be used to drive experiments aimed at exploring GPCR oligomerization, as well as in the study of transmembrane protein-protein interactions in general.

Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions

NASA Astrophysics Data System (ADS)

Baltoumas, Fotis A.; Theodoropoulou, Margarita C.; Hamodrakas, Stavros J.

2016-06-01

A significant amount of experimental evidence suggests that G-protein coupled receptors (GPCRs) do not act exclusively as monomers but also form biologically relevant dimers and oligomers. However, the structural determinants, stoichiometry and functional importance of GPCR oligomerization remain topics of intense speculation. In this study we attempted to evaluate the nature and dynamics of GPCR oligomeric interactions. A representative set of GPCR homodimers were studied through Coarse-Grained Molecular Dynamics simulations, combined with interface analysis and concepts from network theory for the construction and analysis of dynamic structural networks. Our results highlight important structural determinants that seem to govern receptor dimer interactions. A conserved dynamic behavior was observed among different GPCRs, including receptors belonging in different GPCR classes. Specific GPCR regions were highlighted as the core of the interfaces. Finally, correlations of motion were observed between parts of the dimer interface and GPCR segments participating in ligand binding and receptor activation, suggesting the existence of mechanisms through which dimer formation may affect GPCR function. The results of this study can be used to drive experiments aimed at exploring GPCR oligomerization, as well as in the study of transmembrane protein-protein interactions in general.

Emergent dynamic structures and statistical law in spherical lattice gas automata.

PubMed

Yao, Zhenwei

2017-12-01

Various lattice gas automata have been proposed in the past decades to simulate physics and address a host of problems on collective dynamics arising in diverse fields. In this work, we employ the lattice gas model defined on the sphere to investigate the curvature-driven dynamic structures and analyze the statistical behaviors in equilibrium. Under the simple propagation and collision rules, we show that the uniform collective movement of the particles on the sphere is geometrically frustrated, leading to several nonequilibrium dynamic structures not found in the planar lattice, such as the emergent bubble and vortex structures. With the accumulation of the collision effect, the system ultimately reaches equilibrium in the sense that the distribution of the coarse-grained speed approaches the two-dimensional Maxwell-Boltzmann distribution despite the population fluctuations in the coarse-grained cells. The emergent regularity in the statistical behavior of the system is rationalized by mapping our system to a generalized random walk model. This work demonstrates the capability of the spherical lattice gas automaton in revealing the lattice-guided dynamic structures and simulating the equilibrium physics. It suggests the promising possibility of using lattice gas automata defined on various curved surfaces to explore geometrically driven nonequilibrium physics.

Atomic-scale structural signature of dynamic heterogeneities in metallic liquids

NASA Astrophysics Data System (ADS)

Pasturel, Alain; Jakse, Noel

2017-08-01

With sufficiently high cooling rates, liquids will cross their equilibrium melting temperatures and can be maintained in a metastable undercooled state before solidifying. Studies of undercooled liquids reveal several intriguing dynamic phenomena and because explicit connections between liquid structure and liquids dynamics are difficult to identify, it remains a major challenge to capture the underlying structural link to these phenomena. Ab initio molecular dynamics (AIMD) simulations are yet especially powerful in providing atomic-scale details otherwise not accessible in experiments. Through the AIMD-based study of Cr additions in Al-based liquids, we evidence for the first time a close relationship between the decoupling of component diffusion and the emergence of dynamic heterogeneities in the undercooling regime. In addition, we demonstrate that the origin of both phenomena is related to a structural heterogeneity caused by a strong interplay between chemical short-range order (CSRO) and local fivefold topology (ISRO) at the short-range scale in the liquid phase that develops into an icosahedral-based medium-range order (IMRO) upon undercooling. Finally, our findings reveal that this structural signature is also captured in the temperature dependence of partial pair-distribution functions which opens up the route to more elaborated experimental studies.

Temperature-driven regime shifts in the dynamics of size-structured populations.

PubMed

Ohlberger, Jan; Edeline, Eric; Vøllestad, Leif Asbjørn; Stenseth, Nils C; Claessen, David

2011-02-01

Global warming impacts virtually all biota and ecosystems. Many of these impacts are mediated through direct effects of temperature on individual vital rates. Yet how this translates from the individual to the population level is still poorly understood, hampering the assessment of global warming impacts on population structure and dynamics. Here, we study the effects of temperature on intraspecific competition and cannibalism and the population dynamical consequences in a size-structured fish population. We use a physiologically structured consumer-resource model in which we explicitly model the temperature dependencies of the consumer vital rates and the resource population growth rate. Our model predicts that increased temperature decreases resource density despite higher resource growth rates, reflecting stronger intraspecific competition among consumers. At a critical temperature, the consumer population dynamics destabilize and shift from a stable equilibrium to competition-driven generation cycles that are dominated by recruits. As a consequence, maximum age decreases and the proportion of younger and smaller-sized fish increases. These model predictions support the hypothesis of decreasing mean body sizes due to increased temperatures. We conclude that in size-structured fish populations, global warming may increase competition, favor smaller size classes, and induce regime shifts that destabilize population and community dynamics.

Emergent dynamic structures and statistical law in spherical lattice gas automata

NASA Astrophysics Data System (ADS)

Yao, Zhenwei

2017-12-01

Various lattice gas automata have been proposed in the past decades to simulate physics and address a host of problems on collective dynamics arising in diverse fields. In this work, we employ the lattice gas model defined on the sphere to investigate the curvature-driven dynamic structures and analyze the statistical behaviors in equilibrium. Under the simple propagation and collision rules, we show that the uniform collective movement of the particles on the sphere is geometrically frustrated, leading to several nonequilibrium dynamic structures not found in the planar lattice, such as the emergent bubble and vortex structures. With the accumulation of the collision effect, the system ultimately reaches equilibrium in the sense that the distribution of the coarse-grained speed approaches the two-dimensional Maxwell-Boltzmann distribution despite the population fluctuations in the coarse-grained cells. The emergent regularity in the statistical behavior of the system is rationalized by mapping our system to a generalized random walk model. This work demonstrates the capability of the spherical lattice gas automaton in revealing the lattice-guided dynamic structures and simulating the equilibrium physics. It suggests the promising possibility of using lattice gas automata defined on various curved surfaces to explore geometrically driven nonequilibrium physics.

Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses.

PubMed

Sarti, Edoardo; Gladich, Ivan; Zamuner, Stefano; Correia, Bruno E; Laio, Alessandro

2016-09-01

The prediction of protein-protein interactions and their structural configuration remains a largely unsolved problem. Most of the algorithms aimed at finding the native conformation of a protein complex starting from the structure of its monomers are based on searching the structure corresponding to the global minimum of a suitable scoring function. However, protein complexes are often highly flexible, with mobile side chains and transient contacts due to thermal fluctuations. Flexibility can be neglected if one aims at finding quickly the approximate structure of the native complex, but may play a role in structure refinement, and in discriminating solutions characterized by similar scores. We here benchmark the capability of some state-of-the-art scoring functions (BACH-SixthSense, PIE/PISA and Rosetta) in discriminating finite-temperature ensembles of structures corresponding to the native state and to non-native configurations. We produce the ensembles by running thousands of molecular dynamics simulations in explicit solvent starting from poses generated by rigid docking and optimized in vacuum. We find that while Rosetta outperformed the other two scoring functions in scoring the structures in vacuum, BACH-SixthSense and PIE/PISA perform better in distinguishing near-native ensembles of structures generated by molecular dynamics in explicit solvent. Proteins 2016; 84:1312-1320. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Nickel-aluminum alloy clusters -- structural and dynamical properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jellinek, J.; Krissinel, E.B.

1997-08-01

Structural and dynamical properties of mixed Ni{sub n}Al{sub m} alloy clusters mimicked by a many-body potential are studied computationally for all the possible compositions n and m such that n + m = 13. It is shown that the manifold of the usually very large number of the different possible structural forms can be systematized by introducing classes of structures corresponding to the same concentration of the components, geometry and type of the central atom. General definitions of mixing energy and mixing coefficient are introduced, and it is shown that the energy ordering of the structural forms within each classmore » is governed by the mixing coefficient. The peculiarities of the solid-to-liquid-like transition are described as a function of the concentration of the two types of atoms. These peculiarities are correlated with and explained in terms of the energy spectra of the structural forms. Class-dependent features of the dynamics are described and analyzed.« less

Development of an Aeroelastic Modeling Capability for Transient Nozzle Side Load Analysis

NASA Technical Reports Server (NTRS)

Wang, Ten-See; Zhao, Xiang; Zhang, Sijun; Chen, Yen-Sen

2013-01-01

Lateral nozzle forces are known to cause severe structural damage to any new rocket engine in development. Currently there is no fully coupled computational tool to analyze this fluid/structure interaction process. The objective of this study was to develop a fully coupled aeroelastic modeling capability to describe the fluid/structure interaction process during the transient nozzle operations. The aeroelastic model composes of three components: the computational fluid dynamics component based on an unstructured-grid, pressure-based computational fluid dynamics formulation, the computational structural dynamics component developed in the framework of modal analysis, and the fluid-structural interface component. The developed aeroelastic model was applied to the transient nozzle startup process of the Space Shuttle Main Engine at sea level. The computed nozzle side loads and the axial nozzle wall pressure profiles from the aeroelastic nozzle are compared with those of the published rigid nozzle results, and the impact of the fluid/structure interaction on nozzle side loads is interrogated and presented.

Measuring the dynamic structure factor of a quantum gas undergoing a structural phase transition

PubMed Central

Landig, Renate; Brennecke, Ferdinand; Mottl, Rafael; Donner, Tobias; Esslinger, Tilman

2015-01-01

The dynamic structure factor is a central quantity describing the physics of quantum many-body systems, capturing structure and collective excitations of a material. In condensed matter, it can be measured via inelastic neutron scattering, which is an energy-resolving probe for the density fluctuations. In ultracold atoms, a similar approach could so far not be applied because of the diluteness of the system. Here we report on a direct, real-time and nondestructive measurement of the dynamic structure factor of a quantum gas exhibiting cavity-mediated long-range interactions. The technique relies on inelastic scattering of photons, stimulated by the enhanced vacuum field inside a high finesse optical cavity. We extract the density fluctuations, their energy and lifetime while the system undergoes a structural phase transition. We observe an occupation of the relevant quasi-particle mode on the level of a few excitations, and provide a theoretical description of this dissipative quantum many-body system. PMID:25944151

Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?

PubMed

Cossio, Pilar; Laio, Alessandro; Pietrucci, Fabio

2011-06-14

An important step in the computer simulation of the dynamics of biomolecules is the comparison of structures in a trajectory by exploiting a measure of distance. This allows distinguishing structures which are geometrically similar from those which are different. By analyzing microseconds-long all-atom molecular dynamics simulations of a polypeptide, we find that a distance based on backbone dihedral angles performs very well in distinguishing structures that are kinetically correlated from those that are not, while the widely used C(α) root mean square distance performs more poorly. The root mean square difference between contact matrices turns out instead to be the metric providing the highest clustering coefficient, namely, according to this similarity measure, the neighbors of a structure are also, on average, neighbors among themselves. We also propose a combined distance measure which, for the system considered here, performs well both for distinguishing structures which are distant in time and for giving a consistent cluster analysis. This journal is © the Owner Societies 2011

Characterizing highly dynamic conformational states: The transcription bubble in RNAP-promoter open complex as an example

NASA Astrophysics Data System (ADS)

Lerner, Eitan; Ingargiola, Antonino; Weiss, Shimon

2018-03-01

Bio-macromolecules carry out complicated functions through structural changes. To understand their mechanism of action, the structure of each step has to be characterized. While classical structural biology techniques allow the characterization of a few "structural snapshots" along the enzymatic cycle (usually of stable conformations), they do not cover all (and often fast interconverting) structures in the ensemble, where each may play an important functional role. Recently, several groups have demonstrated that structures of different conformations in solution could be solved by measuring multiple distances between different pairs of residues using single-molecule Förster resonance energy transfer (smFRET) and using them as constrains for hybrid/integrative structural modeling. However, this approach is limited in cases where the conformational dynamics is faster than the technique's temporal resolution. In this study, we combine existing tools that elucidate sub-millisecond conformational dynamics together with hybrid/integrative structural modeling to study the conformational states of the transcription bubble in the bacterial RNA polymerase-promoter open complex (RPo). We measured microsecond alternating laser excitation-smFRET of differently labeled lacCONS promoter dsDNA constructs. We used a combination of burst variance analysis, photon-by-photon hidden Markov modeling, and the FRET-restrained positioning and screening approach to identify two conformational states for RPo. The experimentally derived distances of one conformational state match the known crystal structure of bacterial RPo. The experimentally derived distances of the other conformational state have characteristics of a scrunched RPo. These findings support the hypothesis that sub-millisecond dynamics in the transcription bubble are responsible for transcription start site selection.

The structure of aqueous sodium hydroxide solutions: a combined solution x-ray diffraction and simulation study.

PubMed

Megyes, Tünde; Bálint, Szabolcs; Grósz, Tamás; Radnai, Tamás; Bakó, Imre; Sipos, Pál

2008-01-28

To determine the structure of aqueous sodium hydroxide solutions, results obtained from x-ray diffraction and computer simulation (molecular dynamics and Car-Parrinello) have been compared. The capabilities and limitations of the methods in describing the solution structure are discussed. For the solutions studied, diffraction methods were found to perform very well in describing the hydration spheres of the sodium ion and yield structural information on the anion's hydration structure. Classical molecular dynamics simulations were not able to correctly describe the bulk structure of these solutions. However, Car-Parrinello simulation proved to be a suitable tool in the detailed interpretation of the hydration sphere of ions and bulk structure of solutions. The results of Car-Parrinello simulations were compared with the findings of diffraction experiments.

Predation risk suppresses the positive feedback between size structure and cannibalism.

PubMed

Kishida, Osamu; Trussell, Geoffrey C; Ohno, Ayaka; Kuwano, Shinya; Ikawa, Takuya; Nishimura, Kinya

2011-11-01

1. Cannibalism can play a prominent role in the structuring and dynamics of ecological communities. Previous studies have emphasized the importance of size structure and density of cannibalistic species in shaping short- and long-term cannibalism dynamics, but our understanding of how predators influence cannibalism dynamics is limited. This is despite widespread evidence that many prey species exhibit behavioural and morphological adaptations in response to predation risk. 2. This study examined how the presence and absence of predation risk from larval dragonflies Aeshna nigroflava affected cannibalism dynamics in its prey larval salamanders Hynobius retardatus. 3. We found that feedback dynamics between size structure and cannibalism depended on whether dragonfly predation risk was present. In the absence of dragonfly risk cues, a positive feedback between salamander size structure and cannibalism through time occurred because most of the replicates in this treatment contained at least one salamander larvae having an enlarged gape (i.e. cannibal). In contrast, this feedback and the emergence of cannibalism were rarely observed in the presence of the dragonfly risk cues. Once salamander size divergence occurred, experimental reversals of the presence or absence of dragonfly risk cues did not alter existing cannibalism dynamics as the experiment progressed. Thus, the effects of risk on the mechanisms driving cannibalism dynamics likely operated during the early developmental period of the salamander larvae. 4. The effects of dragonfly predation risk on behavioural aspects of cannibalistic interactions among hatchlings may prohibit the initiation of dynamics between size structure and cannibalism. Our predation trials clearly showed that encounter rates among hatchlings and biting and ingestion rates of prospective prey by prospective cannibals were significantly lower in the presence vs. absence of dragonfly predation risk even though the size asymmetry between cannibals and victims was similar in both risk treatments. These results suggest that dragonfly risk cues first suppress cannibalism among hatchlings and then prevent size variation from increasing through time. 5. We suggest that the positive feedback dynamics between size structure and cannibalism and their modification by predation risk may also operate in other systems to shape the population dynamics of cannibalistic prey species as well as overall community dynamics. © 2011 The Authors. Journal of Animal Ecology © 2011 British Ecological Society.

A molecular dynamics study of ethanol-water hydrogen bonding in binary structure I clathrate hydrate with CO2

NASA Astrophysics Data System (ADS)

Alavi, Saman; Ohmura, Ryo; Ripmeester, John A.

2011-02-01

Guest-host hydrogen bonding in clathrate hydrates occurs when in addition to the hydrophilic moiety which causes the molecule to form hydrates under high pressure-low temperature conditions, the guests contain a hydrophilic, hydrogen bonding functional group. In the presence of carbon dioxide, ethanol clathrate hydrate has been synthesized with 10% of large structure I (sI) cages occupied by ethanol. In this work, we use molecular dynamics simulations to study hydrogen bonding structure and dynamics in this binary sI clathrate hydrate in the temperature range of 100-250 K. We observe that ethanol forms long-lived (>500 ps) proton-donating and accepting hydrogen bonds with cage water molecules from both hexagonal and pentagonal faces of the large cages while maintaining the general cage integrity of the sI clathrate hydrate. The presence of the nondipolar CO2 molecules stabilizes the hydrate phase, despite the strong and prevalent alcohol-water hydrogen bonding. The distortions of the large cages from the ideal form, the radial distribution functions of the guest-host interactions, and the ethanol guest dynamics are characterized in this study. In previous work through dielectric and NMR relaxation time studies, single crystal x-ray diffraction, and molecular dynamics simulations we have observed guest-water hydrogen bonding in structure II and structure H clathrate hydrates. The present work extends the observation of hydrogen bonding to structure I hydrates.

The role of structural dynamics in the design and operations of space systems: The history, the lessons, the technical challenges of the future

NASA Technical Reports Server (NTRS)

Ryan, Robert S.

1994-01-01

Structural dynamics and its auxiliary fields are the most progressive and challenging areas space system engineering design and operations face. Aerospace systems are dependent on structural dynamicists for their success. Past experiences (history) are colored with many dynamic issues, some producing ground or flight test failures. The innovation and creativity that was brought to these issues and problems are the aura from the past that lights the path to the future. Using this illumination to guide understanding of the dynamic phenomena and designing for its potential occurrence are the keys to successful space systems. Our great paradox, or challenge, is how we remain in depth specialists, yet become generalists to the degree that we make good team members and set the right priorities. This paper will deal with how we performed with acclaim in the past, the basic characteristics of structural dynamics (loads cycle, for example), and the challenges of the future.

Use of the dynamic stiffness method to interpret experimental data from a nonlinear system

NASA Astrophysics Data System (ADS)

Tang, Bin; Brennan, M. J.; Gatti, G.

2018-05-01

The interpretation of experimental data from nonlinear structures is challenging, primarily because of dependency on types and levels of excitation, and coupling issues with test equipment. In this paper, the use of the dynamic stiffness method, which is commonly used in the analysis of linear systems, is used to interpret the data from a vibration test of a controllable compressed beam structure coupled to a test shaker. For a single mode of the system, this method facilitates the separation of mass, stiffness and damping effects, including nonlinear stiffness effects. It also allows the separation of the dynamics of the shaker from the structure under test. The approach needs to be used with care, and is only suitable if the nonlinear system has a response that is predominantly at the excitation frequency. For the structure under test, the raw experimental data revealed little about the underlying causes of the dynamic behaviour. However, the dynamic stiffness approach allowed the effects due to the nonlinear stiffness to be easily determined.

Noise-induced relations between network connectivity and dynamics

NASA Astrophysics Data System (ADS)

Ching, Emily Sc

Many biological systems of interest can be represented as networks of many nodes that are interacting with one another. Often these systems are subject to external influence or noise. One of the central issues is to understand the relation between dynamics and the interaction pattern of the system or the connectivity structure of the network. In particular, a challenging problem is to infer the network connectivity structure from the dynamics. In this talk, we show that for stochastic dynamical systems subjected to noise, the presence of noise gives rise to mathematical relations between the network connectivity structure and quantities that can be calculated using solely the time-series measurements of the dynamics of the nodes. We present these relations for both undirected networks with bidirectional coupling and directed networks with directional coupling and discuss how such relations can be utilized to infer the network connectivity structure of the systems. Work supported by the Hong Kong Research Grants Council under Grant No. CUHK 14300914.

Dynamic analysis of geometrically non-linear three-dimensional beams under moving mass

NASA Astrophysics Data System (ADS)

Zupan, E.; Zupan, D.

2018-01-01

In this paper, we present a coupled dynamic analysis of a moving particle on a deformable three-dimensional frame. The presented numerical model is capable of considering arbitrary curved and twisted initial geometry of the beam and takes into account geometric non-linearity of the structure. Coupled with dynamic equations of the structure, the equations of moving particle are solved. The moving particle represents the dynamic load and varies the mass distribution of the structure and at the same time its path is adapting due to deformability of the structure. A coupled geometrically non-linear behaviour of beam and particle is studied. The equation of motion of the particle is added to the system of the beam dynamic equations and an additional unknown representing the coordinate of the curvilinear path of the particle is introduced. The specially designed finite-element formulation of the three-dimensional beam based on the weak form of consistency conditions is employed where only the boundary conditions are affected by the contact forces.

Pressure dependence of excited-state charge-carrier dynamics in organolead tribromide perovskites

NASA Astrophysics Data System (ADS)

Liu, X. C.; Han, J. H.; Zhao, H. F.; Yan, H. C.; Shi, Y.; Jin, M. X.; Liu, C. L.; Ding, D. J.

2018-05-01

Excited-state charge-carrier dynamics governs the performance of organometal trihalide perovskites (OTPs) and is strongly influenced by the crystal structure. Characterizing the excited-state charge-carrier dynamics in OTPs under high pressure is imperative for providing crucial insights into structure-property relations. Here, we conduct in situ high-pressure femtosecond transient absorption spectroscopy experiments to study the excited-state carrier dynamics of CH3NH3PbBr3 (MAPbBr3) under hydrostatic pressure. The results indicate that compression is an effective approach to modulate the carrier dynamics of MAPbBr3. Across each pressure-induced phase, carrier relaxation, phonon scattering, and Auger recombination present different pressure-dependent properties under compression. Responsiveness is attributed to the pressure-induced variation in the lattice structure, which also changes the electronic band structure. Specifically, simultaneous prolongation of carrier relaxation and Auger recombination is achieved in the ambient phase, which is very valuable for excess energy harvesting. Our discussion provides clues for optimizing the photovoltaic performance of OTPs.

Active influence in dynamical models of structural balance in social networks

NASA Astrophysics Data System (ADS)

Summers, Tyler H.; Shames, Iman

2013-07-01

We consider a nonlinear dynamical system on a signed graph, which can be interpreted as a mathematical model of social networks in which the links can have both positive and negative connotations. In accordance with a concept from social psychology called structural balance, the negative links play a key role in both the structure and dynamics of the network. Recent research has shown that in a nonlinear dynamical system modeling the time evolution of “friendliness levels” in the network, two opposing factions emerge from almost any initial condition. Here we study active external influence in this dynamical model and show that any agent in the network can achieve any desired structurally balanced state from any initial condition by perturbing its own local friendliness levels. Based on this result, we also introduce a new network centrality measure for signed networks. The results are illustrated in an international-relations network using United Nations voting record data from 1946 to 2008 to estimate friendliness levels amongst various countries.

The Impact of Structural Heterogeneity on Excitation-Inhibition Balance in Cortical Networks.

PubMed

Landau, Itamar D; Egger, Robert; Dercksen, Vincent J; Oberlaender, Marcel; Sompolinsky, Haim

2016-12-07

Models of cortical dynamics often assume a homogeneous connectivity structure. However, we show that heterogeneous input connectivity can prevent the dynamic balance between excitation and inhibition, a hallmark of cortical dynamics, and yield unrealistically sparse and temporally regular firing. Anatomically based estimates of the connectivity of layer 4 (L4) rat barrel cortex and numerical simulations of this circuit indicate that the local network possesses substantial heterogeneity in input connectivity, sufficient to disrupt excitation-inhibition balance. We show that homeostatic plasticity in inhibitory synapses can align the functional connectivity to compensate for structural heterogeneity. Alternatively, spike-frequency adaptation can give rise to a novel state in which local firing rates adjust dynamically so that adaptation currents and synaptic inputs are balanced. This theory is supported by simulations of L4 barrel cortex during spontaneous and stimulus-evoked conditions. Our study shows how synaptic and cellular mechanisms yield fluctuation-driven dynamics despite structural heterogeneity in cortical circuits. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

A comparative assessment of different frequency based damage detection in unidirectional composite plates using MFC sensors

NASA Astrophysics Data System (ADS)

de Medeiros, Ricardo; Sartorato, Murilo; Vandepitte, Dirk; Tita, Volnei

2016-11-01

The basic concept of the vibration based damage identification methods is that the dynamic behaviour of a structure can change if damage occurs. Damage in a structure can alter the structural integrity, and therefore, the physical properties like stiffness, mass and/or damping may change. The dynamic behaviour of a structure is a function of these physical properties and will, therefore, directly be affected by the damage. The dynamic behaviour can be described in terms of time, frequency and modal domain parameters. The changes in these parameters (or properties derived from these parameters) are used as indicators of damage. Hence, this work has two main objectives. The first one is to provide an overview of the structural vibration based damage identification methods. For this purpose, a fundamental description of the structural vibration based damage identification problem is given, followed by a short literature overview of the damage features, which are commonly addressed. The second objective is to create a damage identification method for detection of the damage in composite structures. To aid in this process, two basic principles are discussed, namely the effect of the potential damage case on the dynamic behaviour, and the consequences involved with the information reduction in the signal processing. Modal properties from the structural dynamic output response are obtained. In addition, experimental and computational results are presented for the application of modal analysis techniques applied to composite specimens with and without damage. The excitation of the structures is performed using an impact hammer and, for measuring the output data, accelerometers as well as piezoelectric sensors. Finite element models are developed by shell elements, and numerical results are compared to experimental data, showing good correlation for the response of the specimens in some specific frequency range. Finally, FRFs are analysed using suitable metrics, including a new one, which are compared in terms of their capability for damage identification. The experimental and numerical results show that the vibration-based damage methods combined to the metrics can be used in Structural Health Monitoring (SHM) systems to identify the damage in the structure.

Structures and Dynamics of Social Networks: Selection, Influence, and Self-Organization

ERIC Educational Resources Information Center

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…

Structural and Dynamic Aspects of Interest Development: Theoretical Considerations from an Ontogenetic Perspective.

ERIC Educational Resources Information Center

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)

Matrix Perturbation Techniques in Structural Dynamics

NASA Technical Reports Server (NTRS)

Caughey, T. K.

1973-01-01

Matrix perturbation are developed techniques which can be used in the dynamical analysis of structures where the range of numerical values in the matrices extreme or where the nature of the damping matrix requires that complex valued eigenvalues and eigenvectors be used. The techniques can be advantageously used in a variety of fields such as earthquake engineering, ocean engineering, aerospace engineering and other fields concerned with the dynamical analysis of large complex structures or systems of second order differential equations. A number of simple examples are included to illustrate the techniques.

The Shock and Vibration Bulletin. Part 3: Structure Medium Interaction, Case Studies in Dynamics

NASA Technical Reports Server (NTRS)

1979-01-01

Structure and medium interactions topics are addressed. Topics include: a failure analysis of underground concrete structures subjected to blast loadings, an optimization design procedure for concrete slabs, and a discussion of the transient response of a cylindrical shell submerged in a fluid. Case studies in dynamics are presented which include an examination of a shock isolation platform for a seasparrow launcher, a discussion of hydrofoil fatigue load environments, and an investigation of the dynamic characteristics of turbine generators and low tuned foundations.

Dynamic analysis of space structures including elastic, multibody, and control behavior

NASA Technical Reports Server (NTRS)

Pinson, Larry; Soosaar, Keto

1989-01-01

The problem is to develop analysis methods, modeling stategies, and simulation tools to predict with assurance the on-orbit performance and integrity of large complex space structures that cannot be verified on the ground. The problem must incorporate large reliable structural models, multi-body flexible dynamics, multi-tier controller interaction, environmental models including 1g and atmosphere, various on-board disturbances, and linkage to mission-level performance codes. All areas are in serious need of work, but the weakest link is multi-body flexible dynamics.

Stability and free energy calculation of LNA modified quadruplex: a molecular dynamics study

NASA Astrophysics Data System (ADS)

Chaubey, Amit Kumar; Dubey, Kshatresh Dutta; Ojha, Rajendra Prasad

2012-03-01

Telomeric ends of chromosomes, which comprise noncoding repeat sequences of guanine-rich DNA, which are the fundamental in protecting the cell from recombination and degradation. Telomeric DNA sequences can form four stranded quadruplex structures, which are involved in the structure of telomere ends. The formation and stabilization of telomeric quadruplexes has been shown to inhibit the activity of telomerase, thus establishing telomeric DNA quadrulex as an attractive target for cancer therapeutic intervention. Molecular dynamic simulation offers the prospects of detailed description of the dynamical structure with ion and water at molecular level. In this work we have taken a oligomeric part of human telomeric DNA, d(TAGGGT) to form different monomeric quadruplex structures d(TAGGGT)4. Here we report the relative stabilities of these structures under K+ ion conditions and binding interaction between the strands, as determined by molecular dynamic simulations followed by energy calculation. We have taken locked nucleic acid (LNA) in this study. The free energy molecular mechanics Poission Boltzman surface area calculations are performed for the determination of most stable complex structure between all modified structures. We calculated binding free energy for the combination of different strands as the ligand and receptor for all structures. The energetic study shows that, a mixed hybrid type quadruplex conformation in which two parallel strands are bind with other two antiparallel strands, are more stable than other conformations. The possible mechanism for the inhibition of the cancerous growth has been discussed. Such studies may be helpful for the rational drug designing.

Nonlinear problems in flight dynamics

NASA Technical Reports Server (NTRS)

Chapman, G. T.; Tobak, M.

1984-01-01

A comprehensive framework is proposed for the description and analysis of nonlinear problems in flight dynamics. Emphasis is placed on the aerodynamic component as the major source of nonlinearities in the flight dynamic system. Four aerodynamic flows are examined to illustrate the richness and regularity of the flow structures and the nature of the flow structures and the nature of the resulting nonlinear aerodynamic forces and moments. A framework to facilitate the study of the aerodynamic system is proposed having parallel observational and mathematical components. The observational component, structure is described in the language of topology. Changes in flow structure are described via bifurcation theory. Chaos or turbulence is related to the analogous chaotic behavior of nonlinear dynamical systems characterized by the existence of strange attractors having fractal dimensionality. Scales of the flow are considered in the light of ideas from group theory. Several one and two degree of freedom dynamical systems with various mathematical models of the nonlinear aerodynamic forces and moments are examined to illustrate the resulting types of dynamical behavior. The mathematical ideas that proved useful in the description of fluid flows are shown to be similarly useful in the description of flight dynamic behavior.

Dynamical, structural and chemical heterogeneities in a binary metallic glass-forming liquid

NASA Astrophysics Data System (ADS)

Puosi, F.; Jakse, N.; Pasturel, A.

2018-04-01

As it approaches the glass transition, particle motion in liquids becomes highly heterogeneous and regions with virtually no mobility coexist with liquid-like domains. This complex dynamic is believed to be responsible for different phenomena including non-exponential relaxation and the breakdown of the Stokes-Einstein relation. Understanding the relationships between dynamical heterogeneities and local structure in metallic liquids and glasses is a major scientific challenge. Here we use classical molecular dynamics simulations to study the atomic dynamics and microscopic structure of Cu50Zr50 alloy in the supercooling regime. Dynamical heterogeneities are identified via an isoconfigurational analysis. We demonstrate the transition from isolated to clustering low mobility with decreasing temperature. These slow clusters, whose sizes grow upon cooling, are also associated with concentration fluctuations, characterized by a Zr-enriched phase, with a composition CuZr2 . In addition, a structural analysis of slow clusters based on Voronoi tessellation evidences an increase with respect of the bulk system of the fraction of Cu atoms having a local icosahedral order. These results are in agreement with the consolidated scenario of the relevant role played by icosahedral order in the dynamic slowing-down in supercooled metal alloys.

Recursive formulae and performance comparisons for first mode dynamics of periodic structures

NASA Astrophysics Data System (ADS)

Hobeck, Jared D.; Inman, Daniel J.

2017-05-01

Periodic structures are growing in popularity especially in the energy harvesting and metastructures communities. Common types of these unique structures are referred to in the literature as zigzag, orthogonal spiral, fan-folded, and longitudinal zigzag structures. Many of these studies on periodic structures have two competing goals in common: (a) minimizing natural frequency, and (b) minimizing mass or volume. These goals suggest that no single design is best for all applications; therefore, there is a need for design optimization and comparison tools which first require efficient easy-to-implement models. All available structural dynamics models for these types of structures do provide exact analytical solutions; however, they are complex requiring tedious implementation and providing more information than necessary for practical applications making them computationally inefficient. This paper presents experimentally validated recursive models that are able to very accurately and efficiently predict the dynamics of the four most common types of periodic structures. The proposed modeling technique employs a combination of static deflection formulae and Rayleigh’s Quotient to estimate the first mode shape and natural frequency of periodic structures having any number of beams. Also included in this paper are the results of an extensive experimental validation study which show excellent agreement between model prediction and measurement. Lastly, the proposed models are used to evaluate the performance of each type of structure. Results of this performance evaluation reveal key advantages and disadvantages associated with each type of structure.

Mixture models for protein structure ensembles.

PubMed

Hirsch, Michael; Habeck, Michael

2008-10-01

Protein structure ensembles provide important insight into the dynamics and function of a protein and contain information that is not captured with a single static structure. However, it is not clear a priori to what extent the variability within an ensemble is caused by internal structural changes. Additional variability results from overall translations and rotations of the molecule. And most experimental data do not provide information to relate the structures to a common reference frame. To report meaningful values of intrinsic dynamics, structural precision, conformational entropy, etc., it is therefore important to disentangle local from global conformational heterogeneity. We consider the task of disentangling local from global heterogeneity as an inference problem. We use probabilistic methods to infer from the protein ensemble missing information on reference frames and stable conformational sub-states. To this end, we model a protein ensemble as a mixture of Gaussian probability distributions of either entire conformations or structural segments. We learn these models from a protein ensemble using the expectation-maximization algorithm. Our first model can be used to find multiple conformers in a structure ensemble. The second model partitions the protein chain into locally stable structural segments or core elements and less structured regions typically found in loops. Both models are simple to implement and contain only a single free parameter: the number of conformers or structural segments. Our models can be used to analyse experimental ensembles, molecular dynamics trajectories and conformational change in proteins. The Python source code for protein ensemble analysis is available from the authors upon request.

Aeroelastic, CFD, and Dynamic Computation and Optimization for Buffet and Flutter Application

NASA Technical Reports Server (NTRS)

Kandil, Osama A.

1997-01-01

The work presented in this paper include: 'Coupled and Uncoupled Bending-Torsion Responses of Twin-Tail Buffet'; 'Fluid/Structure Twin Tail Buffet Response Over a Wide Range of Angles of Attack'; 'Resent Advances in Multidisciplinary Aeronautical Problems of Fluids/Structures/Dynamics Interaction'; and'Development of a Coupled Fluid/Structure Aeroelastic Solver with Applications to Vortex Breakdown induced Twin Tail Buffeting.

Computational methods and software systems for dynamics and control of large space structures

NASA Technical Reports Server (NTRS)

Park, K. C.; Felippa, C. A.; Farhat, C.; Pramono, E.

1990-01-01

Two key areas of crucial importance to the computer-based simulation of large space structures are discussed. The first area involves multibody dynamics (MBD) of flexible space structures, with applications directed to deployment, construction, and maneuvering. The second area deals with advanced software systems, with emphasis on parallel processing. The latest research thrust in the second area involves massively parallel computers.

49 CFR Appendix F to Part 238 - Alternative Dynamic Performance Requirements for Front End Structures of Cab Cars and MU Locomotives

Code of Federal Regulations, 2010 CFR

2010-10-01

... Front End Structures of Cab Cars and MU Locomotives F Appendix F to Part 238 Transportation Other... Performance Requirements for Front End Structures of Cab Cars and MU Locomotives As specified in § 238.209(b... and allow for the application of dynamic performance criteria to cab cars and MU locomotives as an...

Transport induced by large scale convective structures in a dipole-confined plasma.

PubMed

Grierson, B A; Mauel, M E; Worstell, M W; Klassen, M

2010-11-12

Convective structures characterized by E×B motion are observed in a dipole-confined plasma. Particle transport rates are calculated from density dynamics obtained from multipoint measurements and the reconstructed electrostatic potential. The calculated transport rates determined from the large-scale dynamics and local probe measurements agree in magnitude, show intermittency, and indicate that the particle transport is dominated by large-scale convective structures.

Structures and Dynamics Division research and technology plans for FY 1894 and accomplishments for FY 1982

NASA Technical Reports Server (NTRS)

Bales, K. S.

1984-01-01

The Objectives, Expected Results, Approach, and Fiscal Year FY 1984 Milestones for the Structures and Dynamics Division's research programs are examined. The FY 1983 Accomplishments are presented where applicable.

Structure and Dynamics of Bimodal Colloidal Dispersions in a Low-Molecular-Weight Polymer Solution

DOE PAGES

Zhang, Fan; Allen, Andrew J.; Levine, Lyle E.; ...

2017-02-24

We present an experimental study of the structural and dynamical properties of bimodal, micrometersized colloidal dispersions (size ratio ≈ 2) in an aqueous solution of low-molecular weight polymer (polyethylene glycol 2000) using synchrotron ultra-small angle X-ray scattering (USAXS) and USAXSbased X-ray photon correlation spectroscopy. We fixed the volume fraction of the large particles at 5 % and systematically increased the volume fraction of the small particles from 0 % to 5 % to evaluate its effect on the structure and dynamics. The bimodal dispersions were homogenous through the investigated parameter space. We found that the partial structure factors can bemore » satisfactorily retrieved for the bimodal colloidal dispersions using a Percus-Yevick hard sphere potential when the particle size distributions of the particles were taken into account. We also found that the partial structure factor between the large particles does not exhibit significant variation with increasing volume fraction of small particles, whereas the isothermal compressibility of the binary mixture was found to decrease with increasing volume fraction of small particles. The dynamics of single-component large particle dispersion obey the principles of de Gennes narrowing, where the wave vector dependence of the interparticle diffusion coefficient is inversely proportional to the interparticle structure factor. The dynamics of the bimodal dispersions demonstrate strong dependence on the fraction of small particles. As a result, we also made a comparison between the experimental effective dynamic viscosity of the bimodal dispersion with theoretical predictions, which suggest that the complex mutual interactions between large and small particles have a strong effect on the dynamic behaviors of bimodal dispersions.« less

Structure and Dynamics of Bimodal Colloidal Dispersions in a Low-Molecular-Weight Polymer Solution.

PubMed

Zhang, Fan; Allen, Andrew J; Levine, Lyle E; Tsai, De-Hao; Ilavsky, Jan

2017-03-21

We present an experimental study of the structural and dynamical properties of bimodal, micrometer-sized colloidal dispersions (size ratio ≈ 2) in an aqueous solution of low-molecular-weight polymer (polyethylene glycol 2000) using synchrotron ultra-small angle X-ray scattering (USAXS) and USAXS-based X-ray photon correlation spectroscopy. We fixed the volume fraction of the large particles at 5% and systematically increased the volume fraction of the small particles from 0 to 5% to evaluate their effects on the structure and dynamics. The bimodal dispersions were homogenous through the investigated parameter space. We found that the partial structure factors can be satisfactorily retrieved for the bimodal colloidal dispersions using a Percus-Yevick hard-sphere potential when the size distributions of the particles were taken into account. We also found that the partial structure factor between the large particles did not exhibit a significant variation with increasing volume fraction of the small particles, whereas the isothermal compressibility of the binary mixture was found to decrease with increasing volume fraction of the small particles. The dynamics of single-component large-particle dispersion obey the principles of de Gennes narrowing, where the wave vector dependence of the interparticle diffusion coefficient is inversely proportional to the interparticle structure factor. The dynamics of the bimodal dispersions demonstrate a strong dependence on the fraction of small particles. We also made a comparison between the experimental effective dynamic viscosity of the bimodal dispersion with the theoretical predictions, which suggest that the complex mutual interactions between the large and small particles have a strong effect on the dynamic behaviors of bimodal dispersions.

Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)

PubMed Central

Galindo-Murillo, Rodrigo; Roe, Daniel R.; Cheatham, Thomas E.

2014-01-01

Background The structure and dynamics of DNA are critically related to its function. Molecular dynamics (MD) simulations augment experiment by providing detailed information about the atomic motions. However, to date the simulations have not been long enough for convergence of the dynamics and structural properties of DNA. Methods MD simulations performed with AMBER using the ff99SB force field with the parmbsc0 modifications, including ensembles of independent simulations, were compared to long timescale MD performed with the specialized Anton MD engine on the B-DNA structure d(GCACGAACGAACGAACGC). To assess convergence, the decay of the average RMSD values over longer and longer time intervals was evaluated in addition to assessing convergence of the dynamics via the Kullback-Leibler divergence of principal component projection histograms. Results These MD simulations —including one of the longest simulations of DNA published to date at ~44 μs—surprisingly suggest that the structure and dynamics of the DNA helix, neglecting the terminal base pairs, are essentially fully converged on the ~1–5 μs timescale. Conclusions We can now reproducibly converge the structure and dynamics of B-DNA helices, omitting the terminal base pairs, on the μs time scale with both the AMBER and CHARMM C36 nucleic acid force fields. Results from independent ensembles of simulations starting from different initial conditions, when aggregated, match the results from long timescale simulations on the specialized Anton MD engine. General Significance With access to large-scale GPU resources or the specialized MD engine “Anton” it is possibly for a variety of molecular systems to reproducibly and reliably converge the conformational ensemble of sampled structures. PMID:25219455

Adaptive control of structural balance for complex dynamical networks based on dynamic coupling of nodes

NASA Astrophysics Data System (ADS)

Gao, Zilin; Wang, Yinhe; Zhang, Lili

2018-02-01

In the existing research results of the complex dynamical networks controlled, the controllers are mainly used to guarantee the synchronization or stabilization of the nodes’ state, and the terms coupled with connection relationships may affect the behaviors of nodes, this obviously ignores the dynamic common behavior of the connection relationships between the nodes. In fact, from the point of view of large-scale system, a complex dynamical network can be regarded to be composed of two time-varying dynamic subsystems, which can be called the nodes subsystem and the connection relationships subsystem, respectively. Similar to the synchronization or stabilization of the nodes subsystem, some characteristic phenomena can be also emerged in the connection relationships subsystem. For example, the structural balance in the social networks and the synaptic facilitation in the biological neural networks. This paper focuses on the structural balance in dynamic complex networks. Generally speaking, the state of the connection relationships subsystem is difficult to be measured accurately in practical applications, and thus it is not easy to implant the controller directly into the connection relationships subsystem. It is noted that the nodes subsystem and the relationships subsystem are mutually coupled, which implies that the state of the connection relationships subsystem can be affected by the controllable state of nodes subsystem. Inspired by this observation, by using the structural balance theory of triad, the controller with the parameter adaptive law is proposed for the nodes subsystem in this paper, which may ensure the connection relationship matrix to approximate a given structural balance matrix in the sense of the uniformly ultimately bounded (UUB). That is, the structural balance may be obtained by employing the controlling state of the nodes subsystem. Finally, the simulations are used to show the validity of the method in this paper.

Structural domains and main-chain flexibility in prion proteins.

PubMed

Blinov, N; Berjanskii, M; Wishart, D S; Stepanova, M

2009-02-24

In this study we describe a novel approach to define structural domains and to characterize the local flexibility in both human and chicken prion proteins. The approach we use is based on a comprehensive theory of collective dynamics in proteins that was recently developed. This method determines the essential collective coordinates, which can be found from molecular dynamics trajectories via principal component analysis. Under this particular framework, we are able to identify the domains where atoms move coherently while at the same time to determine the local main-chain flexibility for each residue. We have verified this approach by comparing our results for the predicted dynamic domain systems with the computed main-chain flexibility profiles and the NMR-derived random coil indexes for human and chicken prion proteins. The three sets of data show excellent agreement. Additionally, we demonstrate that the dynamic domains calculated in this fashion provide a highly sensitive measure of protein collective structure and dynamics. Furthermore, such an analysis is capable of revealing structural and dynamic properties of proteins that are inaccessible to the conventional assessment of secondary structure. Using the collective dynamic simulation approach described here along with a high-temperature simulations of unfolding of human prion protein, we have explored whether locations of relatively low stability could be identified where the unfolding process could potentially be facilitated. According to our analysis, the locations of relatively low stability may be associated with the beta-sheet formed by strands S1 and S2 and the adjacent loops, whereas helix HC appears to be a relatively stable part of the protein. We suggest that this kind of structural analysis may provide a useful background for a more quantitative assessment of potential routes of spontaneous misfolding in prion proteins.

Structure and Dynamics of Bimodal Colloidal Dispersions in a Low-Molecular-Weight Polymer Solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Fan; Allen, Andrew J.; Levine, Lyle E.

We present an experimental study of the structural and dynamical properties of bimodal, micrometersized colloidal dispersions (size ratio ≈ 2) in an aqueous solution of low-molecular weight polymer (polyethylene glycol 2000) using synchrotron ultra-small angle X-ray scattering (USAXS) and USAXSbased X-ray photon correlation spectroscopy. We fixed the volume fraction of the large particles at 5 % and systematically increased the volume fraction of the small particles from 0 % to 5 % to evaluate its effect on the structure and dynamics. The bimodal dispersions were homogenous through the investigated parameter space. We found that the partial structure factors can bemore » satisfactorily retrieved for the bimodal colloidal dispersions using a Percus-Yevick hard sphere potential when the particle size distributions of the particles were taken into account. We also found that the partial structure factor between the large particles does not exhibit significant variation with increasing volume fraction of small particles, whereas the isothermal compressibility of the binary mixture was found to decrease with increasing volume fraction of small particles. The dynamics of single-component large particle dispersion obey the principles of de Gennes narrowing, where the wave vector dependence of the interparticle diffusion coefficient is inversely proportional to the interparticle structure factor. The dynamics of the bimodal dispersions demonstrate strong dependence on the fraction of small particles. As a result, we also made a comparison between the experimental effective dynamic viscosity of the bimodal dispersion with theoretical predictions, which suggest that the complex mutual interactions between large and small particles have a strong effect on the dynamic behaviors of bimodal dispersions.« less

A Model Comparison for Characterizing Protein Motions from Structure

NASA Astrophysics Data System (ADS)

David, Charles; Jacobs, Donald

2011-10-01

A comparative study is made using three computational models that characterize native state dynamics starting from known protein structures taken from four distinct SCOP classifications. A geometrical simulation is performed, and the results are compared to the elastic network model and molecular dynamics. The essential dynamics is quantified by a direct analysis of a mode subspace constructed from ANM and a principal component analysis on both the FRODA and MD trajectories using root mean square inner product and principal angles. Relative subspace sizes and overlaps are visualized using the projection of displacement vectors on the model modes. Additionally, a mode subspace is constructed from PCA on an exemplar set of X-ray crystal structures in order to determine similarly with respect to the generated ensembles. Quantitative analysis reveals there is significant overlap across the three model subspaces and the model independent subspace. These results indicate that structure is the key determinant for native state dynamics.

An ab initio study of the structure and dynamics of bulk liquid Cd and its liquid-vapor interface.

PubMed

Calderín, L; González, L E; González, D J

2013-02-13

Several static and dynamic properties of bulk liquid Cd at a thermodynamic state near its triple point have been calculated by means of ab initio molecular dynamics simulations. The calculated static structure shows a very good agreement with the available experimental data. The dynamical structure reveals collective density excitations with an associated dispersion relation which points to a small positive dispersion. Results are also reported for several transport coefficients. Additional simulations have also been performed at a slightly higher temperature in order to study the structure of the free liquid surface. The ionic density profile shows an oscillatory behavior with two different wavelengths, as the spacing between the outer and first inner layer is different from that between the other inner layers. The calculated reflectivity shows a marked maximum whose origin is related to the surface layering, along with a shoulder located at a much smaller wavevector transfer.

Dynamics of Opinion Forming in Structurally Balanced Social Networks

PubMed Central

Altafini, Claudio

2012-01-01

A structurally balanced social network is a social community that splits into two antagonistic factions (typical example being a two-party political system). The process of opinion forming on such a community is most often highly predictable, with polarized opinions reflecting the bipartition of the network. The aim of this paper is to suggest a class of dynamical systems, called monotone systems, as natural models for the dynamics of opinion forming on structurally balanced social networks. The high predictability of the outcome of a decision process is explained in terms of the order-preserving character of the solutions of this class of dynamical systems. If we represent a social network as a signed graph in which individuals are the nodes and the signs of the edges represent friendly or hostile relationships, then the property of structural balance corresponds to the social community being splittable into two antagonistic factions, each containing only friends. PMID:22761667

Robust, nonlinear, high angle-of-attack control design for a supermaneuverable vehicle

NASA Technical Reports Server (NTRS)

Adams, Richard J.

1993-01-01

High angle-of-attack flight control laws are developed for a supermaneuverable fighter aircraft. The methods of dynamic inversion and structured singular value synthesis are combined into an approach which addresses both the nonlinearity and robustness problems of flight at extreme operating conditions. The primary purpose of the dynamic inversion control elements is to linearize the vehicle response across the flight envelope. Structured singular value synthesis is used to design a dynamic controller which provides robust tracking to pilot commands. The resulting control system achieves desired flying qualities and guarantees a large margin of robustness to uncertainties for high angle-of-attack flight conditions. The results of linear simulation and structured singular value stability analysis are presented to demonstrate satisfaction of the design criteria. High fidelity nonlinear simulation results show that the combined dynamics inversion/structured singular value synthesis control law achieves a high level of performance in a realistic environment.

Site-Mutation of Hydrophobic Core Residues Synchronically Poise Super Interleukin 2 for Signaling: Identifying Distant Structural Effects through Affordable Computations.

PubMed

Mei, Longcan; Zhou, Yanping; Zhu, Lizhe; Liu, Changlin; Wu, Zhuo; Wang, Fangkui; Hao, Gefei; Yu, Di; Yuan, Hong; Cui, Yanfang

2018-03-20

A superkine variant of interleukin-2 with six site mutations away from the binding interface developed from the yeast display technique has been previously characterized as undergoing a distal structure alteration which is responsible for its super-potency and provides an elegant case study with which to get insight about how to utilize allosteric effect to achieve desirable protein functions. By examining the dynamic network and the allosteric pathways related to those mutated residues using various computational approaches, we found that nanosecond time scale all-atom molecular dynamics simulations can identify the dynamic network as efficient as an ensemble algorithm. The differentiated pathways for the six core residues form a dynamic network that outlines the area of structure alteration. The results offer potentials of using affordable computing power to predict allosteric structure of mutants in knowledge-based mutagenesis.

Multiscale polar theory of microtubule and motor-protein assemblies

DOE PAGES

Gao, Tong; Blackwell, Robert; Glaser, Matthew A.; ...

2015-01-27

Microtubules and motor proteins are building blocks of self-organized subcellular biological structures such as the mitotic spindle and the centrosomal microtubule array. These same ingredients can form new “bioactive” liquid-crystalline fluids that are intrinsically out of equilibrium and which display complex flows and defect dynamics. It is not yet well understood how microscopic activity, which involves polarity-dependent interactions between motor proteins and microtubules, yields such larger-scale dynamical structures. In our multiscale theory, Brownian dynamics simulations of polar microtubule ensembles driven by cross-linking motors allow us to study microscopic organization and stresses. Polarity sorting and cross-link relaxation emerge as two polar-specificmore » sources of active destabilizing stress. On larger length scales, our continuum Doi-Onsager theory captures the hydrodynamic flows generated by polarity-dependent active stresses. Finally, the results connect local polar structure to flow structures and defect dynamics.« less

Thermal modal analysis of novel non-pneumatic mechanical elastic wheel based on FEM and EMA

NASA Astrophysics Data System (ADS)

Zhao, Youqun; Zhu, Mingmin; Lin, Fen; Xiao, Zhen; Li, Haiqing; Deng, Yaoji

2018-01-01

A combination of Finite Element Method (FEM) and Experiment Modal Analysis (EMA) have been employed here to characterize the structural dynamic response of mechanical elastic wheel (ME-Wheel) operating under a specific thermal environment. The influence of high thermal condition on the structural dynamic response of ME-Wheel is investigated. The obtained results indicate that the EMA results are in accordance with those obtained using the proposed Finite Element (FE) model, indicting the high reliability of this FE model applied in analyzing the modal of ME-Wheel working under practical thermal environment. It demonstrates that the structural dynamic response of ME-Wheel operating under a specific thermal condition can be predicted and evaluated using the proposed analysis method, which is beneficial for the dynamic optimization design of the wheel structure to avoid tire temperature related vibration failure and improve safety of tire.

Relevance of Internal Friction and Structural Constraints for the Dynamics of Denatured Bovine Serum Albumin.

PubMed

Ameseder, Felix; Radulescu, Aurel; Holderer, Olaf; Falus, Peter; Richter, Dieter; Stadler, Andreas M

2018-05-17

A general property of disordered proteins is their structural expansion that results in a high molecular flexibility. The structure and dynamics of bovine serum albumin (BSA) denatured by guanidinium hydrochloride (GndCl) were investigated using small-angle neutron scattering (SANS) and neutron spin-echo spectroscopy (NSE). SANS experiments demonstrated the relevance of intrachain interactions for structural expansion. Using NSE experiments, we observed a high internal flexibility of denatured BSA in addition to center-of-mass diffusion detected by dynamic light scattering. Internal motions measured by NSE were described using concepts based on polymer theory. The contribution of residue-solvent friction was accounted for using the Zimm model including internal friction (ZIF). Disulfide bonds forming loops of amino acids of the peptide backbone have a major impact on internal dynamics that can be interpreted with a reduced set of Zimm modes.

Studying the Structure and Dynamics of Biomolecules by Using Soluble Paramagnetic Probes

PubMed Central

Hocking, Henry G; Zangger, Klaus; Madl, Tobias

2013-01-01

Characterisation of the structure and dynamics of large biomolecules and biomolecular complexes by NMR spectroscopy is hampered by increasing overlap and severe broadening of NMR signals. As a consequence, the number of available NMR spectroscopy data is often sparse and new approaches to provide complementary NMR spectroscopy data are needed. Paramagnetic relaxation enhancements (PREs) obtained from inert and soluble paramagnetic probes (solvent PREs) provide detailed quantitative information about the solvent accessibility of NMR-active nuclei. Solvent PREs can be easily measured without modification of the biomolecule; are sensitive to molecular structure and dynamics; and are therefore becoming increasingly powerful for the study of biomolecules, such as proteins, nucleic acids, ligands and their complexes in solution. In this Minireview, we give an overview of the available solvent PRE probes and discuss their applications for structural and dynamic characterisation of biomolecules and biomolecular complexes. PMID:23836693

Brownian dynamics of sterically-stabilized colloidal suspensions

DOE Office of Scientific and Technical Information (OSTI.GOV)

TeGrotenhuis, W.E.; Radke, C.J.; Denn, M.M.

1994-02-01

One application where microstructure plays a critical role is in the production of specialty ceramics, where colloidal suspensions act as precursors; here the microstructure influences the structural, thermal, optical and electrical properties of the ceramic products. Using Brownian dynamics, equilibrium and dynamic properties are calculated for colloidal suspensions that are stabilized through the Milner, Witten and Cates (1988) steric potential. Results are reported for osmotic pressures, radial distributions functions, static structure factors, and self-diffusion coefficients. The sterically-stabilized systems are also approximated by equivalent hard spheres, with good agreement for osmotic pressure and long-range structure. The suitability of the potential tomore » model the behavior of a real system is explored by comparing static structure factors calculated from Brownian dynamics simulations to those measured using SANS. Finally, the effects of Hamaker and hydrodynamic forces on calculated properties are investigated.« less

Structure and Liquid Fragility in Sodium Carbonate.

PubMed

Wilson, Mark; Ribeiro, Mauro C C; Wilding, Martin C; Benmore, Chris; Weber, J K R; Alderman, Oliver; Tamalonis, Anthony; Parise, J B

2018-02-01

The relationship between local structure and dynamics is explored for molten sodium carbonate. A flexible fluctuating-charge model, which allows for changes in the shape and charge distribution of the carbonate molecular anion, is developed. The system shows the evolution of highly temperature-dependent complex low-dimensional structures which control the dynamics (and hence the liquid fragility). By varying the molecular anion charge distribution, the key interactions responsible for the formation of these structures can be identified and rationalized. An increase in the mean charge separation within the carbonate ions increases the connectivity of the emerging structures and leads to an increase in the system fragility.

Analysis of passive damping in thick composite structures

NASA Technical Reports Server (NTRS)

Saravanos, D. A.

1993-01-01

Computational mechanics for the prediction of damping and other dynamic characteristics in composite structures of general thicknesses and laminations are presented. Discrete layer damping mechanics that account for the representation of interlaminar shear effects in the material are summarized. Finite element based structural mechanics for the analysis of damping are described, and a specialty finite element is developed. Applications illustrate the quality of the discrete layer damping mechanics in predicting the damped dynamic characteristics of composite structures with thicker sections and/or laminate configurations that induce interlaminar shear. The results also illustrate and quantify the significance of interlaminar shear damping in such composite structures.

Search for Length Dependent Stable Structures of Polyglutamaine Proteins with Replica Exchange Molecular Dynamic

NASA Astrophysics Data System (ADS)

Kluber, Alexander; Hayre, Robert; Cox, Daniel

2012-02-01

Motivated by the need to find beta-structure aggregation nuclei for the polyQ diseases such as Huntington's, we have undertaken a search for length dependent structure in model polyglutamine proteins. We use the Onufriev-Bashford-Case (OBC) generalized Born implicit solvent GPU based AMBER11 molecular dynamics with the parm96 force field coupled with a replica exchange method to characterize monomeric strands of polyglutamine as a function of chain length and temperature. This force field and solvation method has been shown among other methods to accurately reproduce folded metastability in certain small peptides, and to yield accurately de novo folded structures in a millisecond time-scale protein. Using GPU molecular dynamics we can sample out into the microsecond range. Additionally, explicit solvent runs will be used to verify results from the implicit solvent runs. We will assess order using measures of secondary structure and hydrogen bond content.

Comparative characterization of short monomeric polyglutamine peptides by replica exchange molecular dynamics simulation.

PubMed

Nakano, Miki; Watanabe, Hirofumi; Rothstein, Stuart M; Tanaka, Shigenori

2010-05-27

Polyglutamine (polyQ) diseases are caused by an abnormal expansion of CAG repeats. While their detailed structure remains unclear, polyQ peptides assume beta-sheet structures when they aggregate. To investigate the conformational ensemble of short, monomeric polyQ peptides, which consist of 15 glutamine residues (Q(15)), we performed replica exchange molecular dynamics (REMD) simulations. We found that Q(15) can assume multiple configurations due to all of the residues affecting the formation of side-chain hydrogen bonds. Analysis of the free energy landscape reveals that Q(15) has a basin for random-coil structures and another for alpha-helix or beta-turn structures. To investigate properties of aggregated polyQ peptides, we performed multiple molecular dynamics (MMD) simulations for monomeric and oligomeric Q(15). MMD revealed that the formation of oligomers stabilizes the beta-turn structure by increasing the number of hydrogen bonds between the main chains.

Maintenance of a functional higher order chromatin structure: The role of the nuclear matrix in normal and disease states

PubMed Central

Linnemann, Amelia K.; Krawetz, Stephen A.

2010-01-01

Summary The ordered packaging of DNA within the nucleus of somatic cells reflects a dynamic supportive structure that facilitates stable transcription interrupted by intermittent cycles of extreme condensation. This dynamic mode of packing and unpacking chromatin is intimately linked to the ability of the genome to specifically complex with both histones and non-histone proteins. Understanding the underlying mechanism that governs the formation of higher order chromatin structures is a key to understanding how local architecture modulates transcription. In part, the formation of these structures appears to be regulated through genomic looping that is dynamically mediated by attachment to the nuclear scaffold/matrix at S/MARs, i.e., Scaffold/Matrix Attachment Regions. Although the mechanism guiding the formation and use of these higher-ordered structures remains unknown, S/MARs continue to reveal a multitude of roles in development and the pathogenesis of disease. PMID:20948980

Maintenance of a functional higher order chromatin structure: The role of the nuclear matrix in normal and disease states.

PubMed

Linnemann, Amelia K; Krawetz, Stephen A

2009-01-01

The ordered packaging of DNA within the nucleus of somatic cells reflects a dynamic supportive structure that facilitates stable transcription interrupted by intermittent cycles of extreme condensation. This dynamic mode of packing and unpacking chromatin is intimately linked to the ability of the genome to specifically complex with both histones and non-histone proteins. Understanding the underlying mechanism that governs the formation of higher order chromatin structures is a key to understanding how local architecture modulates transcription. In part, the formation of these structures appears to be regulated through genomic looping that is dynamically mediated by attachment to the nuclear scaffold/matrix at S/MARs, i.e., Scaffold/Matrix Attachment Regions. Although the mechanism guiding the formation and use of these higher-ordered structures remains unknown, S/MARs continue to reveal a multitude of roles in development and the pathogenesis of disease.

Creating a Test Validated Structural Dynamic Finite Element Model of the Multi-Utility Technology Test Bed Aircraft

NASA Technical Reports Server (NTRS)

Pak, Chan-Gi; Truong, Samson S.

2014-01-01

Small modeling errors in the finite element model will eventually induce errors in the structural flexibility and mass, thus propagating into unpredictable errors in the unsteady aerodynamics and the control law design. One of the primary objectives of Multi Utility Technology Test Bed, X-56A, aircraft is the flight demonstration of active flutter suppression, and therefore in this study, the identification of the primary and secondary modes for the structural model tuning based on the flutter analysis of X-56A. The ground vibration test validated structural dynamic finite element model of the X-56A is created in this study. The structural dynamic finite element model of the X-56A is improved using a model tuning tool. In this study, two different weight configurations of the X-56A have been improved in a single optimization run.

A Nonlinear Modal Aeroelastic Solver for FUN3D

NASA Technical Reports Server (NTRS)

Goldman, Benjamin D.; Bartels, Robert E.; Biedron, Robert T.; Scott, Robert C.

2016-01-01

A nonlinear structural solver has been implemented internally within the NASA FUN3D computational fluid dynamics code, allowing for some new aeroelastic capabilities. Using a modal representation of the structure, a set of differential or differential-algebraic equations are derived for general thin structures with geometric nonlinearities. ODEPACK and LAPACK routines are linked with FUN3D, and the nonlinear equations are solved at each CFD time step. The existing predictor-corrector method is retained, whereby the structural solution is updated after mesh deformation. The nonlinear solver is validated using a test case for a flexible aeroshell at transonic, supersonic, and hypersonic flow conditions. Agreement with linear theory is seen for the static aeroelastic solutions at relatively low dynamic pressures, but structural nonlinearities limit deformation amplitudes at high dynamic pressures. No flutter was found at any of the tested trajectory points, though LCO may be possible in the transonic regime.

Ab initio study on structural stability of uranium carbide

NASA Astrophysics Data System (ADS)

Sahoo, B. D.; Joshi, K. D.; Gupta, Satish C.

2013-06-01

First principles calculations have been performed using plane wave pseudopotential and full potential linearized augmented plane wave (FP-LAPW) methods to analyze structural, elastic and dynamic stability of UC under hydrostatic compression. Our calculations within pseudopotential method suggest that the rocksalt (B1) structure will transform to body centered orthorhombic (bco) structure at ˜21.5 GPa. The FP-LAPW calculations put this transition at 23 GPa. The transition pressures determined from our calculations though agree reasonably with the experimental value of 27 GPa, the high pressure bco structure suggested by theory differs slightly from the experimentally reported pseudo bco phase. The elastic stability analysis of B1 phase suggests that the B1 to bco transition is driven by the failure of C44 modulus. This finding is further substantiated by the lattice dynamic calculations which demonstrate that the B1 phase becomes dynamically unstable around the transition pressure and the instability is of long wavelength nature.

From Sequence and Forces to Structure, Function and Evolution of Intrinsically Disordered Proteins

PubMed Central

Forman-Kay, Julie D.; Mittag, Tanja

2015-01-01

Intrinsically disordered proteins (IDPs), which lack persistent structure, are a challenge to structural biology due to the inapplicability of standard methods for characterization of folded proteins as well as their deviation from the dominant structure/function paradigm. Their widespread presence and involvement in biological function, however, has spurred the growing acceptance of the importance of IDPs and the development of new tools for studying their structure, dynamics and function. The interplay of folded and disordered domains or regions for function and the existence of a continuum of protein states with respect to conformational energetics, motional timescales and compactness is shaping a unified understanding of structure-dynamics-disorder/function relationships. On the 20th anniversary of this journal, Structure, we provide a historical perspective on the investigation of IDPs and summarize the sequence features and physical forces that underlie their unique structural, functional and evolutionary properties. PMID:24010708

From sequence and forces to structure, function, and evolution of intrinsically disordered proteins.

PubMed

Forman-Kay, Julie D; Mittag, Tanja

2013-09-03

Intrinsically disordered proteins (IDPs), which lack persistent structure, are a challenge to structural biology due to the inapplicability of standard methods for characterization of folded proteins as well as their deviation from the dominant structure/function paradigm. Their widespread presence and involvement in biological function, however, has spurred the growing acceptance of the importance of IDPs and the development of new tools for studying their structure, dynamics, and function. The interplay of folded and disordered domains or regions for function and the existence of a continuum of protein states with respect to conformational energetics, motional timescales, and compactness are shaping a unified understanding of structure-dynamics-disorder/function relationships. In the 20(th) anniversary of Structure, we provide a historical perspective on the investigation of IDPs and summarize the sequence features and physical forces that underlie their unique structural, functional, and evolutionary properties. Copyright © 2013 Elsevier Ltd. All rights reserved.

Control of Flexible Structures (COFS) Flight Experiment Background and Description

NASA Technical Reports Server (NTRS)

Hanks, B. R.

1985-01-01

A fundamental problem in designing and delivering large space structures to orbit is to provide sufficient structural stiffness and static configuration precision to meet performance requirements. These requirements are directly related to control requirements and the degree of control system sophistication available to supplement the as-built structure. Background and rationale are presented for a research study in structures, structural dynamics, and controls using a relatively large, flexible beam as a focus. This experiment would address fundamental problems applicable to large, flexible space structures in general and would involve a combination of ground tests, flight behavior prediction, and instrumented orbital tests. Intended to be multidisciplinary but basic within each discipline, the experiment should provide improved understanding and confidence in making design trades between structural conservatism and control system sophistication for meeting static shape and dynamic response/stability requirements. Quantitative results should be obtained for use in improving the validity of ground tests for verifying flight performance analyses.

STITCHER: Dynamic assembly of likely amyloid and prion β-structures from secondary structure predictions

PubMed Central

Bryan, Allen W; O’Donnell, Charles W; Menke, Matthew; Cowen, Lenore J; Lindquist, Susan; Berger, Bonnie

2012-01-01

The supersecondary structure of amyloids and prions, proteins of intense clinical and biological interest, are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid fibrils. Previous work has demonstrated that probability-based prediction of discrete β-strand pairs can offer insight into these structures. Here, we devise a system of energetic rules that can be used to dynamically assemble these discrete β-strand pairs into complete amyloid β-structures. The STITCHER algorithm progressively ‘stitches’ strand-pairs into full β-sheets based on a novel free-energy model, incorporating experimentally observed amino-acid side-chain stacking contributions, entropic estimates, and steric restrictions for amyloidal parallel β-sheet construction. A dynamic program computes the top 50 structures and returns both the highest scoring structure and a consensus structure taken by polling this list for common discrete elements. Putative structural heterogeneity can be inferred from sequence regions that compose poorly. Predictions show agreement with experimental models of Alzheimer’s amyloid beta peptide and the Podospora anserina Het-s prion. Predictions of the HET-s homolog HET-S also reflect experimental observations of poor amyloid formation. We put forward predicted structures for the yeast prion Sup35, suggesting N-terminal structural stability enabled by tyrosine ladders, and C-terminal heterogeneity. Predictions for the Rnq1 prion and alpha-synuclein are also given, identifying a similar mix of homogenous and heterogeneous secondary structure elements. STITCHER provides novel insight into the energetic basis of amyloid structure, provides accurate structure predictions, and can help guide future experimental studies. Proteins 2012. © 2011 Wiley Periodicals, Inc. PMID:22095906

STITCHER: Dynamic assembly of likely amyloid and prion β-structures from secondary structure predictions.

PubMed

Bryan, Allen W; O'Donnell, Charles W; Menke, Matthew; Cowen, Lenore J; Lindquist, Susan; Berger, Bonnie

2012-02-01

The supersecondary structure of amyloids and prions, proteins of intense clinical and biological interest, are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid fibrils. Previous work has demonstrated that probability-based prediction of discrete β-strand pairs can offer insight into these structures. Here, we devise a system of energetic rules that can be used to dynamically assemble these discrete β-strand pairs into complete amyloid β-structures. The STITCHER algorithm progressively 'stitches' strand-pairs into full β-sheets based on a novel free-energy model, incorporating experimentally observed amino-acid side-chain stacking contributions, entropic estimates, and steric restrictions for amyloidal parallel β-sheet construction. A dynamic program computes the top 50 structures and returns both the highest scoring structure and a consensus structure taken by polling this list for common discrete elements. Putative structural heterogeneity can be inferred from sequence regions that compose poorly. Predictions show agreement with experimental models of Alzheimer's amyloid beta peptide and the Podospora anserina Het-s prion. Predictions of the HET-s homolog HET-S also reflect experimental observations of poor amyloid formation. We put forward predicted structures for the yeast prion Sup35, suggesting N-terminal structural stability enabled by tyrosine ladders, and C-terminal heterogeneity. Predictions for the Rnq1 prion and alpha-synuclein are also given, identifying a similar mix of homogenous and heterogeneous secondary structure elements. STITCHER provides novel insight into the energetic basis of amyloid structure, provides accurate structure predictions, and can help guide future experimental studies. Copyright © 2011 Wiley Periodicals, Inc.

Key Structures and Interactions for Binding of Mycobacterium tuberculosis Protein Kinase B Inhibitors from Molecular Dynamics Simulation.

PubMed

Punkvang, Auradee; Kamsri, Pharit; Saparpakorn, Patchreenart; Hannongbua, Supa; Wolschann, Peter; Irle, Stephan; Pungpo, Pornpan

2015-07-01

Substituted aminopyrimidine inhibitors have recently been introduced as antituberculosis agents. These inhibitors show impressive activity against protein kinase B, a Ser/Thr protein kinase that is essential for cell growth of M. tuberculosis. However, up to now, X-ray structures of the protein kinase B enzyme complexes with the substituted aminopyrimidine inhibitors are currently unavailable. Consequently, structural details of their binding modes are questionable, prohibiting the structural-based design of more potent protein kinase B inhibitors in the future. Here, molecular dynamics simulations, in conjunction with molecular mechanics/Poisson-Boltzmann surface area binding free-energy analysis, were employed to gain insight into the complex structures of the protein kinase B inhibitors and their binding energetics. The complex structures obtained by the molecular dynamics simulations show binding free energies in good agreement with experiment. The detailed analysis of molecular dynamics results shows that Glu93, Val95, and Leu17 are key residues responsible to the binding of the protein kinase B inhibitors. The aminopyrazole group and the pyrimidine core are the crucial moieties of substituted aminopyrimidine inhibitors for interaction with the key residues. Our results provide a structural concept that can be used as a guide for the future design of protein kinase B inhibitors with highly increased antagonistic activity. © 2014 John Wiley & Sons A/S.

Dynamic structure mediates halophilic adaptation of a DNA polymerase from the deep-sea brines of the Red Sea.

PubMed

Takahashi, Masateru; Takahashi, Etsuko; Joudeh, Luay I; Marini, Monica; Das, Gobind; Elshenawy, Mohamed M; Akal, Anastassja; Sakashita, Kosuke; Alam, Intikhab; Tehseen, Muhammad; Sobhy, Mohamed A; Stingl, Ulrich; Merzaban, Jasmeen S; Di Fabrizio, Enzo; Hamdan, Samir M

2018-01-24

The deep-sea brines of the Red Sea are remote and unexplored environments characterized by high temperatures, anoxic water, and elevated concentrations of salt and heavy metals. This environment provides a rare system to study the interplay between halophilic and thermophilic adaptation in biologic macromolecules. The present article reports the first DNA polymerase with halophilic and thermophilic features. Biochemical and structural analysis by Raman and circular dichroism spectroscopy showed that the charge distribution on the protein's surface mediates the structural balance between stability for thermal adaptation and flexibility for counteracting the salt-induced rigid and nonfunctional hydrophobic packing. Salt bridge interactions via increased negative and positive charges contribute to structural stability. Salt tolerance, conversely, is mediated by a dynamic structure that becomes more fixed and functional with increasing salt concentration. We propose that repulsive forces among excess negative charges, in addition to a high percentage of negatively charged random coils, mediate this structural dynamism. This knowledge enabled us to engineer a halophilic version of KOD DNA polymerase.-Takahashi, M., Takahashi, E., Joudeh, L. I., Marini, M., Das, G., Elshenawy, M. M., Akal, A., Sakashita, K., Alam, I., Tehseen, M., Sobhy, M. A., Stingl, U., Merzaban, J. S., Di Fabrizio, E., Hamdan, S. M. Dynamic structure mediates halophilic adaptation of a DNA polymerase from the deep-sea brines of the Red Sea.

Revisiting structure and dynamics of preferential solvation of K(I) ion in aqueous ammonia using QMCF-MD simulation

NASA Astrophysics Data System (ADS)

Hidayat, Yuniawan; Pranowo, Harno Dwi; Armunanto, Ria

2018-05-01

Structure and dynamics of preferential solvation of K(I) ion in aqueous ammonia have been reinvestigated using ab initio quantum mechanical charge field (QMCF) molecular dynamics (MD) simulation. The average coordination number of the first solvation consists of 2 ammonia and 4 waters. The mean residence time is less than 2 ps confirming the rapid mobility of ligands. The distance evolution data shows the frequent of ligand exchanges. The second solvation shell shows a more labile structure. The NBO analysis of the first shell structure emphasizes that interaction of K(I)-H2O is stronger than K(I)-NH3. The Wiberg bond confirms a weak electrostatic of ion-ligand interaction.

Dynamic and fluid–structure interaction simulations of bioprosthetic heart valves using parametric design with T-splines and Fung-type material models

PubMed Central

Kamensky, David; Xu, Fei; Kiendl, Josef; Wang, Chenglong; Wu, Michael C. H.; Mineroff, Joshua; Reali, Alessandro; Bazilevs, Yuri; Sacks, Michael S.

2015-01-01

This paper builds on a recently developed immersogeometric fluid–structure interaction (FSI) methodology for bioprosthetic heart valve (BHV) modeling and simulation. It enhances the proposed framework in the areas of geometry design and constitutive modeling. With these enhancements, BHV FSI simulations may be performed with greater levels of automation, robustness and physical realism. In addition, the paper presents a comparison between FSI analysis and standalone structural dynamics simulation driven by prescribed transvalvular pressure, the latter being a more common modeling choice for this class of problems. The FSI computation achieved better physiological realism in predicting the valve leaflet deformation than its standalone structural dynamics counterpart. PMID:26392645

Computational methods and software systems for dynamics and control of large space structures

NASA Technical Reports Server (NTRS)

Park, K. C.; Felippa, C. A.; Farhat, C.; Pramono, E.

1990-01-01

This final report on computational methods and software systems for dynamics and control of large space structures covers progress to date, projected developments in the final months of the grant, and conclusions. Pertinent reports and papers that have not appeared in scientific journals (or have not yet appeared in final form) are enclosed. The grant has supported research in two key areas of crucial importance to the computer-based simulation of large space structure. The first area involves multibody dynamics (MBD) of flexible space structures, with applications directed to deployment, construction, and maneuvering. The second area deals with advanced software systems, with emphasis on parallel processing. The latest research thrust in the second area, as reported here, involves massively parallel computers.

Hierarchical structure and dynamics of oligocarbonate-functionalized PEG block copolymer gels

NASA Astrophysics Data System (ADS)

Prabhu, Vivek; Wei, Guangmin; Ali, Samim; Venkataraman, Shrinivas; Yang, Yi Yan; Hedrick, James

Hierarchical, self-assembled block copolymers in aqueous solutions provide advanced materials for biomaterial applications. Recent advancements in the synthesis of aliphatic polycarbonates have shown nontraditional micellar and hierarchical structures driven by the supramolecular assembly of the carbonate block functionality that includes cholesterol, vitamin D, and fluorene. This presentation shall describe the supramolecular assembly structure and dynamics observed by static and dynamic light scattering, small-angle neutron scattering and transmission electron microscopy in a model pi-pi stacking driven fluorene system. The combination of real-space and reciprocal space methods to develop appropriate models that quantify the structure from the micelle to transient gel network will be discussed. 1) Biomedical Research Council, Agency for Science, Technology and Research, Singapore, 2) NIST Materials Genome Initiative.

Mutations in actin used for structural studies partially disrupt β-thymosin/WH2 domains interaction.

PubMed

Deville, Célia; Girard-Blanc, Christine; Assrir, Nadine; Nhiri, Naïma; Jacquet, Eric; Bontems, François; Renault, Louis; Petres, Stéphane; van Heijenoort, Carine

2016-10-01

Understanding the structural basis of actin cytoskeleton remodeling requires stabilization of actin monomers, oligomers, and filaments in complex with partner proteins, using various biochemical strategies. Here, we report a dramatic destabilization of the dynamic interaction with a model β-thymosin/WH2 domain induced by mutations in actin. This result underlines that mutant actins should be used with prudence to characterize interactions with intrinsically disordered partners as destabilization of dynamic interactions, although identifiable by NMR, may be invisible to other structural techniques. It also highlights how both β-thymosin/WH2 domains and actin tune local structure and dynamics in regulatory processes involving intrinsically disordered domains. © 2016 Federation of European Biochemical Societies.

Wasp waist or beer belly? Modeling food web structure and energetic control in Alaskan marine ecosystems, with implications for fishing and environmental forcing

NASA Astrophysics Data System (ADS)

Gaichas, Sarah; Aydin, Kerim; Francis, Robert C.

2015-11-01

The Eastern Bering Sea (EBS) and Gulf of Alaska (GOA) continental shelf ecosystems show some similar and some distinctive groundfish biomass dynamics. Given that similar species occupy these regions and fisheries management is also comparable, similarities might be expected, but to what can we attribute the differences? Different types of ecosystem structure and control (e.g. top-down, bottom-up, mixed) can imply different ecosystem dynamics and climate interactions. Further, the structural type identified for a given ecosystem may suggest optimal management for sustainable fishing. Here, we use information on the current system state derived from food web models of both the EBS and the GOA combined with dynamic ecosystem models incorporating uncertainty to classify each ecosystem by its structural type. We then suggest how this structure might be generally related to dynamics and predictability. We find that the EBS and GOA have fundamentally different food web structures both overall, and when viewed from the perspective of the same commercially and ecologically important species in each system, walleye pollock (Gadus chalcogrammus). EBS food web structure centers on a large mass of pollock, which appears to contribute to relative system stability and predictability. In contrast, GOA food web structure features high predator biomass, which contributes to a more dynamic, less predictable ecosystem. Mechanisms for climate influence on pollock production in the EBS are increasingly understood, while climate forcing mechanisms contributing to the potentially destabilizing high predator biomass in the GOA remain enigmatic. We present results of identical pollock fishing and climate-driven pollock recruitment simulations in the EBS and GOA which show different system responses, again with less predictable response in the GOA. Overall, our results suggest that identifying structural properties of fished food webs is as important for sustainable fisheries management as attempting to predict climate and fisheries effects within each ecosystem.

Prediction of new high pressure structural sequence in thorium carbide: A first principles study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sahoo, B. D., E-mail: bdsahoo@barc.gov.in; Joshi, K. D.; Gupta, Satish C.

2015-05-14

In the present work, we report the detailed electronic band structure calculations on thorium monocarbide. The comparison of enthalpies, derived for various phases using evolutionary structure search method in conjunction with first principles total energy calculations at several hydrostatic compressions, yielded a high pressure structural sequence of NaCl type (B1) → Pnma → Cmcm → CsCl type (B2) at hydrostatic pressures of ∼19 GPa, 36 GPa, and 200 GPa, respectively. However, the two high pressure experimental studies by Gerward et al. [J. Appl. Crystallogr. 19, 308 (1986); J. Less-Common Met. 161, L11 (1990)] one up to 36 GPa and other up to 50 GPa, onmore » substoichiometric thorium carbide samples with carbon deficiency of ∼20%, do not report any structural transition. The discrepancy between theory and experiment could be due to the non-stoichiometry of thorium carbide samples used in the experiment. Further, in order to substantiate the results of our static lattice calculations, we have determined the phonon dispersion relations for these structures from lattice dynamic calculations. The theoretically calculated phonon spectrum reveal that the B1 phase fails dynamically at ∼33.8 GPa whereas the Pnma phase appears as dynamically stable structure around the B1 to Pnma transition pressure. Similarly, the Cmcm structure also displays dynamic stability in the regime of its structural stability. The B2 phase becomes dynamically stable much below the Cmcm to B2 transition pressure. Additionally, we have derived various thermophysical properties such as zero pressure equilibrium volume, bulk modulus, its pressure derivative, Debye temperature, thermal expansion coefficient and Gruneisen parameter at 300 K and compared these with available experimental data. Further, the behavior of zero pressure bulk modulus, heat capacity and Helmholtz free energy has been examined as a function temperature and compared with the experimental data of Danan [J. Nucl. Mater. 57, 280 (1975)].« less

Exploring Protein Dynamics Space: The Dynasome as the Missing Link between Protein Structure and Function

PubMed Central

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

Functional connectivity dynamically evolves on multiple time-scales over a static structural connectome: Models and mechanisms.

PubMed

Cabral, Joana; Kringelbach, Morten L; Deco, Gustavo

2017-10-15

Over the last decade, we have observed a revolution in brain structural and functional Connectomics. On one hand, we have an ever-more detailed characterization of the brain's white matter structural connectome. On the other, we have a repertoire of consistent functional networks that form and dissipate over time during rest. Despite the evident spatial similarities between structural and functional connectivity, understanding how different time-evolving functional networks spontaneously emerge from a single structural network requires analyzing the problem from the perspective of complex network dynamics and dynamical system's theory. In that direction, bottom-up computational models are useful tools to test theoretical scenarios and depict the mechanisms at the genesis of resting-state activity. Here, we provide an overview of the different mechanistic scenarios proposed over the last decade via computational models. Importantly, we highlight the need of incorporating additional model constraints considering the properties observed at finer temporal scales with MEG and the dynamical properties of FC in order to refresh the list of candidate scenarios. Copyright © 2017 Elsevier Inc. All rights reserved.

Dynamic Structure Factor: An Introduction

NASA Astrophysics Data System (ADS)

Sturm, K.

1993-02-01

The doubly differential cross-section for weak inelastic scattering of waves or particles by manybody systems is derived in Born approximation and expressed in terms of the dynamic structure factor according to van Hove. The application of this very general scheme to scattering of neutrons, x-rays and high-energy electrons is discussed briefly. The dynamic structure factor, which is the space and time Fourier transform of the density-density correlation function, is a property of the many-body system independent of the external probe and carries information on the excitation spectrum of the system. The relation of the electronic structure factor to the density-density response function defined in linear-response theory is shown using the fluctuation-dissipation theorem. This is important for calculations, since the response function can be calculated approximately from the independent-particle response function in self-consistent field approximations, such as the random-phase approximation or the local-density approximation of the density functional theory. Since the density-density response function also determines the dielectric function, the dynamic structure can be expressed by the dielectric function.

Molecular Dynamics Visualization (MDV): Stereoscopic 3D Display of Biomolecular Structure and Interactions Using the Unity Game Engine.

PubMed

Wiebrands, Michael; Malajczuk, Chris J; Woods, Andrew J; Rohl, Andrew L; Mancera, Ricardo L

2018-06-21

Molecular graphics systems are visualization tools which, upon integration into a 3D immersive environment, provide a unique virtual reality experience for research and teaching of biomolecular structure, function and interactions. We have developed a molecular structure and dynamics application, the Molecular Dynamics Visualization tool, that uses the Unity game engine combined with large scale, multi-user, stereoscopic visualization systems to deliver an immersive display experience, particularly with a large cylindrical projection display. The application is structured to separate the biomolecular modeling and visualization systems. The biomolecular model loading and analysis system was developed as a stand-alone C# library and provides the foundation for the custom visualization system built in Unity. All visual models displayed within the tool are generated using Unity-based procedural mesh building routines. A 3D user interface was built to allow seamless dynamic interaction with the model while being viewed in 3D space. Biomolecular structure analysis and display capabilities are exemplified with a range of complex systems involving cell membranes, protein folding and lipid droplets.

An evolutionary game approach for determination of the structural conflicts in signed networks

PubMed Central

Tan, Shaolin; Lü, Jinhu

2016-01-01

Social or biochemical networks can often divide into two opposite alliances in response to structural conflicts between positive (friendly, activating) and negative (hostile, inhibiting) interactions. Yet, the underlying dynamics on how the opposite alliances are spontaneously formed to minimize the structural conflicts is still unclear. Here, we demonstrate that evolutionary game dynamics provides a felicitous possible tool to characterize the evolution and formation of alliances in signed networks. Indeed, an evolutionary game dynamics on signed networks is proposed such that each node can adaptively adjust its choice of alliances to maximize its own fitness, which yet leads to a minimization of the structural conflicts in the entire network. Numerical experiments show that the evolutionary game approach is universally efficient in quality and speed to find optimal solutions for all undirected or directed, unweighted or weighted signed networks. Moreover, the evolutionary game approach is inherently distributed. These characteristics thus suggest the evolutionary game dynamic approach as a feasible and effective tool for determining the structural conflicts in large-scale on-line signed networks. PMID:26915581

Bias field tunable magnetic configuration and magnetization dynamics in Ni80Fe20 nano-cross structures with varying arm length

NASA Astrophysics Data System (ADS)

Adhikari, K.; Choudhury, S.; Mandal, R.; Barman, S.; Otani, Y.; Barman, A.

2017-01-01

Ferromagnetic nano-cross structures promise exotic static magnetic configurations and very rich and tunable magnetization dynamics leading towards potential applications in magnetic logic and communication devices. Here, we report an experimental study of external magnetic field tunable static magnetic configurations and magnetization dynamics in Ni80Fe20 nano-cross structures with varying arm lengths (L). Broadband ferromagnetic resonance measurements showed a strong variation in the number of spin-wave (SW) modes and mode frequencies (f) with bias field magnitude (H). Simulated static magnetic configurations and SW mode profiles explain the rich variation of the SW spectra, including mode softening, mode crossover, mode splitting, and mode merging. Such variation of SW spectra is further modified by the size of the nano-cross. Remarkably, with decreasing arm length of nano-cross structures, the onion magnetization ground state becomes more stable. Calculated magnetostatic field distributions support the above observations and revealed the non-collective nature of the dynamics in closely packed nano-cross structures. The latter is useful for their possible applications in magnetic storage and memory devices.

Large Angle Transient Dynamics (LATDYN) user's manual

NASA Technical Reports Server (NTRS)

Abrahamson, A. Louis; Chang, Che-Wei; Powell, Michael G.; Wu, Shih-Chin; Bingel, Bradford D.; Theophilos, Paula M.

1991-01-01

A computer code for modeling the large angle transient dynamics (LATDYN) of structures was developed to investigate techniques for analyzing flexible deformation and control/structure interaction problems associated with large angular motions of spacecraft. This type of analysis is beyond the routine capability of conventional analytical tools without simplifying assumptions. In some instances, the motion may be sufficiently slow and the spacecraft (or component) sufficiently rigid to simplify analyses of dynamics and controls by making pseudo-static and/or rigid body assumptions. The LATDYN introduces a new approach to the problem by combining finite element structural analysis, multi-body dynamics, and control system analysis in a single tool. It includes a type of finite element that can deform and rotate through large angles at the same time, and which can be connected to other finite elements either rigidly or through mechanical joints. The LATDYN also provides symbolic capabilities for modeling control systems which are interfaced directly with the finite element structural model. Thus, the nonlinear equations representing the structural model are integrated along with the equations representing sensors, processing, and controls as a coupled system.

Atomistic Structure and Dynamics of the Solvation Shell Formed by Organic Carbonates around Lithium Ions via Infrared Spectroscopies

NASA Astrophysics Data System (ADS)

Kuroda, Daniel; Fufler, Kristen

Lithium-ion batteries have become ubiquitous to the portable energy storage industry, but efficiency issues still remain. Currently, most technological and scientific efforts are focused on the electrodes with little attention on the electrolyte. For example, simple fundamental questions about the lithium ion solvation shell composition in commercially used electrolytes have not been answered. Using a combination of linear and non-linear IR spectroscopies and theoretical calculations, we have carried out a thorough investigation of the solvation structure and dynamics of the lithium ion in various linear and cyclic carbonates at common battery electrolyte concentrations. Our studies show that carbonates coordinate the lithium ion tetrahedrally. They also reveal that linear and cyclic carbonates have contrasting dynamics in which cyclic carbonates present the most ordered structure. Finally, our experiments demonstrate that simple structural modifications in the linear carbonates impact significantly the microscopic interactions of the system. The stark differences in the solvation structure and dynamics among different carbonates reveal previously unknown details about the molecular level picture of these systems.

Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase

PubMed Central

Mittag, Tanja; Marsh, Joseph; Grishaev, Alexander; Orlicky, Stephen; Lin, Hong; Sicheri, Frank; Tyers, Mike; Forman-Kay, Julie D.

2010-01-01

Summary Intrinsically disordered proteins can form highly dynamic complexes with partner proteins. One such dynamic complex involves the intrinsically disordered Sic1 with its partner Cdc4 in regulation of yeast cell cycle progression. Phosphorylation of six N-terminal Sic1 sites leads to equilibrium engagement of each phosphorylation site with the primary binding pocket in Cdc4, the substrate recognition subunit of a ubiquitin ligase. ENSEMBLE calculations utilizing experimental NMR and small-angle x-ray scattering data reveal significant transient structure in both phosphorylation states of the isolated ensembles (Sic1 and pSic1) that modulates their electrostatic potential, suggesting a structural basis for the proposed strong contribution of electrostatics to binding. A structural model of the dynamic pSic1-Cdc4 complex demonstrates the spatial arrangements in the ubiquitin ligase complex. These results provide a physical picture of a protein that is predominantly disordered in both its free and bound states, enabling aspects of its structure/function relationship to be elucidated. PMID:20399186

Dynamics of representational change: entropy, action, and cognition.

PubMed

Stephen, Damian G; Dixon, James A; Isenhower, Robert W

2009-12-01

Explaining how the cognitive system can create new structures has been a major challenge for cognitive science. Self-organization from the theory of nonlinear dynamics offers an account of this remarkable phenomenon. Two studies provide an initial test of the hypothesis that the emergence of new cognitive structure follows the same universal principles as emergence in other domains (e.g., fluids, lasers). In both studies, participants initially solved gear-system problems by manually tracing the force across a system of gears. Subsequently, they discovered that the gears form an alternating sequence, thereby demonstrating a new cognitive structure. In both studies, dynamical analyses of action during problem solving predicted the spontaneous emergence of the new cognitive structure. Study 1 showed that a peak in entropy, followed by negentropy, key indicators of self-organization, predicted discovery of alternation. Study 2 replicated these effects, and showed that increasing environmental entropy accelerated discovery, a classic prediction from dynamics. Additional analyses based on the relationship between phase transitions and power-law behavior provide converging evidence. The studies provide an initial demonstration of the emergence of cognitive structure through self-organization.

"Structure and dynamics in complex chemical systems: Gaining new insights through recent advances in time-resolved spectroscopies.” ACS Division of Physical Chemistry Symposium presented at the Fall National ACS Meeting in Boston, MA, August 2015

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crawford, Daniel

8-Session Symposium on STRUCTURE AND DYNAMICS IN COMPLEX CHEMICAL SYSTEMS: GAINING NEW INSIGHTS THROUGH RECENT ADVANCES IN TIME-RESOLVED SPECTROSCOPIES. The intricacy of most chemical, biochemical, and material processes and their applications are underscored by the complex nature of the environments in which they occur. Substantial challenges for building a global understanding of a heterogeneous system include (1) identifying unique signatures associated with specific structural motifs within the heterogeneous distribution, and (2) resolving the significance of each of multiple time scales involved in both small- and large-scale nuclear reorganization. This symposium focuses on the progress in our understanding of dynamics inmore » complex systems driven by recent innovations in time-resolved spectroscopies and theoretical developments. Such advancement is critical for driving discovery at the molecular level facilitating new applications. Broad areas of interest include: Structural relaxation and the impact of structure on dynamics in liquids, interfaces, biochemical systems, materials, and other heterogeneous environments.« less

AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics, and Materials Conference, 34th and AIAA/ASME Adaptive Structures Forum, La Jolla, CA, Apr. 19-22, 1993, Technical Papers. Pts. 1-6

NASA Astrophysics Data System (ADS)

Topics addressed include the prediction of helicopter component loads using neural networks, spacecraft on-orbit coupled loads analysis, hypersonic flutter of a curved shallow panel with aerodynamic heating, thermal-acoustic fatigue of ceramic matrix composite materials, transition elements based on transfinite interpolation, damage progression in stiffened composite panels, a direct treatment of min-max dynamic response optimization problems, and sources of helicopter rotor hub inplane shears. Also discussed are dynamics of a layered elastic system, confidence bounds on structural reliability, mixed triangular space-time finite elements, advanced transparency development for USAF aircraft, a low-velocity impact on a graphite/PEEK, an automated mode-tracking strategy, transonic flutter suppression by a passive flap, a nonlinear response of composite panels to random excitation, an optimal placement of elastic supports on a simply supported plate, a probabilistic assessment of composite structures, a model for mode I failure of laminated composites, a residual flexibility approach to multibody dynamics,and multilayer piezoelectric actuators.

New multirate sampled-data control law structure and synthesis algorithm

NASA Technical Reports Server (NTRS)

Berg, Martin C.; Mason, Gregory S.; Yang, Gen-Sheng

1992-01-01

A new multirate sampled-data control law structure is defined and a new parameter-optimization-based synthesis algorithm for that structure is introduced. The synthesis algorithm can be applied to multirate, multiple-input/multiple-output, sampled-data control laws having a prescribed dynamic order and structure, and a priori specified sampling/update rates for all sensors, processor states, and control inputs. The synthesis algorithm is applied to design two-input, two-output tip position controllers of various dynamic orders for a sixth-order, two-link robot arm model.

Structure Analysis of Jungle-Gym-Type Gels by Brownian Dynamics Simulation

NASA Astrophysics Data System (ADS)

Ohta, Noriyoshi; Ono, Kohki; Takasu, Masako; Furukawa, Hidemitsu

2008-02-01

We investigated the structure and the formation process of two kinds of gels by Brownian dynamics simulation. The effect of flexibility of main chain oligomer was studied. From our results, hard gel with rigid main chain forms more homogeneous network structure than soft gel with flexible main chain. In soft gel, many small loops are formed, and clusters tend to shrink. This heterogeneous network structure may be caused by microgels. In the low density case, soft gel shows more heterogeneity than the high density case.

Probing the structural and dynamical properties of liquid water with models including non-local electron correlation

NASA Astrophysics Data System (ADS)

Del Ben, Mauro; Hutter, Jürg; VandeVondele, Joost

2015-08-01

Water is a ubiquitous liquid that displays a wide range of anomalous properties and has a delicate structure that challenges experiment and simulation alike. The various intermolecular interactions that play an important role, such as repulsion, polarization, hydrogen bonding, and van der Waals interactions, are often difficult to reproduce faithfully in atomistic models. Here, electronic structure theories including all these interactions at equal footing, which requires the inclusion of non-local electron correlation, are used to describe structure and dynamics of bulk liquid water. Isobaric-isothermal (NpT) ensemble simulations based on the Random Phase Approximation (RPA) yield excellent density (0.994 g/ml) and fair radial distribution functions, while various other density functional approximations produce scattered results (0.8-1.2 g/ml). Molecular dynamics simulation in the microcanonical (NVE) ensemble based on Møller-Plesset perturbation theory (MP2) yields dynamical properties in the condensed phase, namely, the infrared spectrum and diffusion constant. At the MP2 and RPA levels of theory, ice is correctly predicted to float on water, resolving one of the anomalies as resulting from a delicate balance between van der Waals and hydrogen bonding interactions. For several properties, obtaining quantitative agreement with experiment requires correction for nuclear quantum effects (NQEs), highlighting their importance, for structure, dynamics, and electronic properties. A computed NQE shift of 0.6 eV for the band gap and absorption spectrum illustrates the latter. Giving access to both structure and dynamics of condensed phase systems, non-local electron correlation will increasingly be used to study systems where weak interactions are of paramount importance.

Proposed Assessment of Dynamic Resistance of the Existing Industrial Portal Frame Building Structures to the Impact of Mining Tremors

NASA Astrophysics Data System (ADS)

Rusek, Janusz; Kocot, Wojciech

2017-10-01

The article presents the method for assessing dynamic resistance of the existing industrial portal frame building structures subjected to mining tremors. The study was performed on two industrial halls of a reinforced concrete structure and a steel structure. In order to determine the dynamic resistances of these objects, static and dynamic numerical analysis in the FEA environment was carried out. The scope of numerical calculations was adapted to the guidelines contained in the former and current design standards. This allowed to formulate the criteria, on the basis of which the maximum permissible value of the horizontal ground acceleration was obtained, constituting resistance of the analyzed objects. The permissible range of structural behaviour was determined by comparing the effects of load combinations adopted at the design stage with a seismic combination recognized in Eurocode 8. The response spectrum method was used in the field of dynamic analysis, taking into account the guidelines contained in Eurocode 8 and the guidelines of National. Finally, in accordance with the established procedure, calculations were carried out and the results for the two model portal frame buildings of reinforced concrete and steel structures were presented. The results allowed for the comparison of the dynamic resistance of two different types of material and design, and a sensitivity analysis with respect to their constituent bearing elements. The conclusions drawn from these analyses helped to formulate the thesis for the next stage of the research, in which it is expected to analyze a greater number of objects using a parametric approach, in relation to the geometry and material properties.

Identification of dynamic load for prosthetic structures.

PubMed

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.

Nonlinear dynamics of solitary and optically injected two-element laser arrays with four different waveguide structures: a numerical study.

PubMed

Li, Nianqiang; Susanto, H; Cemlyn, B R; Henning, I D; Adams, M J

2018-02-19

We study the nonlinear dynamics of solitary and optically injected two-element laser arrays with a range of waveguide structures. The analysis is performed with a detailed direct numerical simulation, where high-resolution dynamic maps are generated to identify regions of dynamic instability in the parameter space of interest. Our combined one- and two-parameter bifurcation analysis uncovers globally diverse dynamical regimes (steady-state, oscillation, and chaos) in the solitary laser arrays, which are greatly influenced by static design waveguiding structures, the amplitude-phase coupling factor of the electric field, i.e. the linewidth-enhancement factor, as well as the control parameter, e.g. the pump rate. When external optical injection is introduced to one element of the arrays, we show that the whole system can be either injection-locked simultaneously or display rich, different dynamics outside the locking region. The effect of optical injection is to significantly modify the nature and the regions of nonlinear dynamics from those found in the solitary case. We also show similarities and differences (asymmetry) between the oscillation amplitude of the two elements of the array in specific well-defined regions, which hold for all the waveguiding structures considered. Our findings pave the way to a better understanding of dynamic instability in large arrays of lasers.

Gyrodampers for large space structures

NASA Technical Reports Server (NTRS)

Aubrun, J. N.; Margulies, G.

1979-01-01

The problem of controlling the vibrations of a large space structures by the use of actively augmented damping devices distributed throughout the structure is addressed. The gyrodamper which consists of a set of single gimbal control moment gyros which are actively controlled to extract the structural vibratory energy through the local rotational deformations of the structure, is described and analyzed. Various linear and nonlinear dynamic simulations of gyrodamped beams are shown, including results on self-induced vibrations due to sensor noise and rotor imbalance. The complete nonlinear dynamic equations are included. The problem of designing and sizing a system of gyrodampers for a given structure, or extrapolating results for one gyrodamped structure to another is solved in terms of scaling laws. Novel scaling laws for gyro systems are derived, based upon fundamental physical principles, and various examples are given.

Futurepath: The Story of Research and Technology at NASA Lewis Research Center. Structures for Flight Propulsion, ARC Sprayed Monotape, National Aero-Space Plane

NASA Technical Reports Server (NTRS)

1989-01-01

The story of research and technology at NASA Lewis Research Center's Structures Division is presented. The job and designs of the Structures Division needed for flight propulsion is described including structural mechanics, structural dynamics, fatigue, and fracture. The video briefly explains why properties of metals used in structural mechanics need to be tested. Examples of tests and simulations used in structural dynamics (bodies in motion) are briefly described. Destructive and non-destructive fatigue/fracture analysis is also described. The arc sprayed monotape (a composite material) is explained, as are the programs in which monotape plays a roll. Finally, the National Aero-Space Plane (NASP or x-30) is introduced, including the material development and metal matrix as well as how NASP will reduce costs for NASA.

Active Polymers — Emergent Conformational and Dynamical Properties: A Brief Review

NASA Astrophysics Data System (ADS)

Winkler, Roland G.; Elgeti, Jens; Gompper, Gerhard

2017-10-01

Active matter exhibits a wealth of emerging nonequilibrium behaviours. A paradigmatic example is the interior of cells, where active components, such as the cytoskeleton, are responsible for its structural organization and the dynamics of the various components. Of particular interest are the properties of polymers and filaments. The intimate coupling of thermal and active noise, hydrodynamic interactions, and polymer conformations implies the emergence of novel structural and dynamical features. In this article, we review recent theoretical and simulation developments and results for the structural and dynamical properties of polymers exposed to activity. Two- and three-dimensional filaments are considered propelled by different mechanisms such as active Brownian particles or hydrodynamically-coupled force dipoles.

Querying databases of trajectories of differential equations: Data structures for trajectories

NASA Technical Reports Server (NTRS)

Grossman, Robert

1989-01-01

One approach to qualitative reasoning about dynamical systems is to extract qualitative information by searching or making queries on databases containing very large numbers of trajectories. The efficiency of such queries depends crucially upon finding an appropriate data structure for trajectories of dynamical systems. Suppose that a large number of parameterized trajectories gamma of a dynamical system evolving in R sup N are stored in a database. Let Eta is contained in set R sup N denote a parameterized path in Euclidean Space, and let the Euclidean Norm denote a norm on the space of paths. A data structure is defined to represent trajectories of dynamical systems, and an algorithm is sketched which answers queries.

Structure and dynamics of water inside hydrophobic and hydrophilic nanotubes

NASA Astrophysics Data System (ADS)

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.

Dynamic analysis of the deployment for mesh reflector deployable antennas with the cable-net structure

NASA Astrophysics Data System (ADS)

Zhang, Yiqun; Li, Na; Yang, Guigeng; Ru, Wenrui

2017-02-01

This paper presents a dynamic analysis approach for the composite structure of a deployable truss and cable-net system. An Elastic Catenary Element is adopted to model the slack/tensioned cables. Then, from the energy standpoint, the kinetic energy, elasticity-potential energy and geopotential energy of the cable-net structure and deployable truss are derived. Thus, the flexible multi-body dynamic model of the deployable antenna is built based on the Lagrange equation. The effect of the cable-net tension on the antenna truss is discussed and compared with previous publications and a dynamic deployment analysis is performed. Both the simulation and experimental results verify the validity of the method presented.

Deployable robotic woven wire structures and joints for space applications

NASA Technical Reports Server (NTRS)

Shahinpoor, MO; Smith, Bradford

1991-01-01

Deployable robotic structures are basically expandable and contractable structures that may be transported or launched to space in a compact form. These structures may then be intelligently deployed by suitable actuators. The deployment may also be done by means of either airbag or spring-loaded typed mechanisms. The actuators may be pneumatic, hydraulic, ball-screw type, or electromagnetic. The means to trigger actuation may be on-board EPROMS, programmable logic controllers (PLCs) that trigger actuation based on some input caused by the placement of the structure in the space environment. The actuation may also be performed remotely by suitable remote triggering devices. Several deployable woven wire structures are examined. These woven wire structures possess a unique form of joint, the woven wire joint, which is capable of moving and changing its position and orientation with respect to the structure itself. Due to the highly dynamic and articulate nature of these joints the 3-D structures built using them are uniquely and highly expandable, deployable, and dynamic. The 3-D structure naturally gives rise to a new generation of deployable three-dimensional spatial structures.

Structure-driven turbulence in ``No man's Land''

NASA Astrophysics Data System (ADS)

Kosuga, Yusuke; Diamond, Patrick

2012-10-01

Structures are often observed in many physical systems. In tokamaks, for example, such structures are observed as density blobs and holes. Such density blobs and holes are generated at the tokamak edge, where strong gradient perturbations generate an outgoing blob and an incoming hole. Since density holes can propagate from the edge to the core, such structures may play an important role in understanding the phenomenology of the edge-core coupling region, so-called ``No Man's Land.'' In this work, we discuss the dynamics of such structures in real space. In particular, we consider the dynamics of density blobs and holes in the Hasegawa-Wakatani system. Specific questions addressed here include: i) how these structures extract free energy and enhance transport? how different is the relaxation driven by such structures from that driven by linear drift waves? ii) how these structures interact with shear flows? In particular, how these structures interact with a shear layer, which can absorb structures resonantly? iii) how can we calculate the coupled evolution of structures and shear flows? Implications for edge-core coupling problem are discussed as well.

Structures and Dynamics Division research and technology plans, fiscal year, 1981

NASA Technical Reports Server (NTRS)

Bales, K. S.

1981-01-01

The objectives, expected results, approach, and FY 81 milestones for the Structures and Dynamics Division's research program are presented. This information will be useful in program coordination with other government organizations in areas of mutual interest.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cang, Zixuan; Mu, Lin; Wu, Kedi

Here, protein function and dynamics are closely related to its sequence and structure. However, prediction of protein function and dynamics from its sequence and structure is still a fundamental challenge in molecular biology. Protein classification, which is typically done through measuring the similarity between proteins based on protein sequence or physical information, serves as a crucial step toward the understanding of protein function and dynamics.

Course Modules on Structural Health Monitoring with Smart Materials

ERIC Educational Resources Information Center

Shih, Hui-Ru; Walters, Wilbur L.; Zheng, Wei; Everett, Jessica

2009-01-01

Structural Health Monitoring (SHM) is an emerging technology that has multiple applications. SHM emerged from the wide field of smart structures, and it also encompasses disciplines such as structural dynamics, materials and structures, nondestructive testing, sensors and actuators, data acquisition, signal processing, and possibly much more. To…

Predicting full-field dynamic strain on a three-bladed wind turbine using three dimensional point tracking and expansion techniques

NASA Astrophysics Data System (ADS)

Baqersad, Javad; Niezrecki, Christopher; Avitabile, Peter

2014-03-01

As part of a project to predict the full-field dynamic strain in rotating structures (e.g. wind turbines and helicopter blades), an experimental measurement was performed on a wind turbine attached to a 500-lb steel block and excited using a mechanical shaker. In this paper, the dynamic displacement of several optical targets mounted to a turbine placed in a semi-built-in configuration was measured by using three-dimensional point tracking. Using an expansion algorithm in conjunction with a finite element model of the blades, the measured displacements were expanded to all finite element degrees of freedom. The calculated displacements were applied to the finite element model to extract dynamic strain on the surface as well as within the interior points of the structure. To validate the technique for dynamic strain prediction, the physical strain at eight locations on the blades was measured during excitation using strain-gages. The expansion was performed by using both structural modes of an individual cantilevered blade and using modes of the entire structure (three-bladed wind turbine and the fixture) and the predicted strain was compared to the physical strain-gage measurements. The results demonstrate the ability of the technique to predict full-field dynamic strain from limited sets of measurements and can be used as a condition based monitoring tool to help provide damage prognosis of structures during operation.

Model structure identification for wastewater treatment simulation based on computational fluid dynamics.

PubMed

Alex, J; Kolisch, G; Krause, K

2002-01-01

The objective of this presented project is to use the results of an CFD simulation to automatically, systematically and reliably generate an appropriate model structure for simulation of the biological processes using CSTR activated sludge compartments. Models and dynamic simulation have become important tools for research but also increasingly for the design and optimisation of wastewater treatment plants. Besides the biological models several cases are reported about the application of computational fluid dynamics ICFD) to wastewater treatment plants. One aim of the presented method to derive model structures from CFD results is to exclude the influence of empirical structure selection to the result of dynamic simulations studies of WWTPs. The second application of the approach developed is the analysis of badly performing treatment plants where the suspicion arises that bad flow behaviour such as short cut flows is part of the problem. The method suggested requires as the first step the calculation of fluid dynamics of the biological treatment step at different loading situations by use of 3-dimensional CFD simulation. The result of this information is used to generate a suitable model structure for conventional dynamic simulation of the treatment plant by use of a number of CSTR modules with a pattern of exchange flows between the tanks automatically. The method is explained in detail and the application to the WWTP Wuppertal Buchenhofen is presented.

Focus: Structure and dynamics of the interfacial layer in polymer nanocomposites with attractive interactions

DOE PAGES

Cheng, Shiwang; Carroll, Bobby; Bocharova, Vera; ...

2017-03-30

In recent years it has become clear that the interfacial layer formed around nanoparticles in polymer nanocomposites (PNCs) is critical for controlling their macroscopic properties. The interfacial layer occupies a significant volume fraction of the polymer matrix in PNCs and creates strong intrinsic heterogeneity in their structure and dynamics. In this paper, we focus on analysis of the structure and dynamics of the interfacial region in model PNCs with well-dispersed, spherical nanoparticles with attractive interactions. First, we discuss several experimental techniques that provide structural and dynamic information on the interfacial region in PNCs. Then, we discuss the role of variousmore » microscopic parameters in controlling structure and dynamics of the interfacial layer. The analysis presented emphasizes the importance of the polymer-nanoparticle interactions for the slowing down dynamics in the interfacial region, while the thickness of the interfacial layer appears to be dependent on chain rigidity, and has been shown to increase with cooling upon approaching the glass transition. Aside from chain rigidity and polymer-nanoparticle interactions, the interfacial layer properties are also affected by the molecular weight of the polymer and the size of the nanoparticles. Finally, in the last part of this focus article, we emphasize the important challenges in the field of polymer nanocomposites and a potential analogy with the behavior observed in thin films.« less

Molecular dynamics simulations of viral RNA polymerases link conserved and correlated motions of functional elements to fidelity

PubMed Central

Moustafa, Ibrahim M.; Shen, Hujun; Morton, Brandon; Colina, Coray M.; Cameron, Craig E.

2011-01-01

The viral RNA-dependent RNA polymerase (RdRp) is essential for multiplication of all RNA viruses. The sequence diversity of an RNA virus population contributes to its ability to infect the host. This diversity emanates from errors made by the RdRp during RNA synthesis. The physical basis for RdRp fidelity is unclear but is linked to conformational changes occurring during the nucleotide-addition cycle. To understand RdRp dynamics that might influence RdRp function, we have analyzed all-atom molecular dynamics (MD) simulations on the nanosecond timescale of four RdRps from the picornavirus family that exhibit 30–74% sequence identity. Principal component analysis showed that the major motions observed during the simulations derived from conserved structural motifs and regions of known function. Dynamics of residues participating in the same biochemical property, for example RNA binding, nucleotide binding or catalysis, were correlated even when spatially distant on the RdRp structure. The conserved and correlated dynamics of functional, structural elements suggest co-evolution of dynamics with structure and function of the RdRp. Crystal structures of all picornavirus RdRps exhibit a template-nascent RNA duplex channel too small to fully accommodate duplex RNA. Simulations revealed opening and closing motions of the RNA and NTP channels, which might be relevant to NTP entry, PPi exit and translocation. A role for nanosecond timescale dynamics in RdRp fidelity is supported by altered dynamics of the high-fidelity G64S derivative of PV RdRp relative to wild-type enzyme. PMID:21575642

High-speed atomic force microscopy for observing protein molecules in dynamic action

NASA Astrophysics Data System (ADS)

Ando, T.

2017-02-01

Directly observing protein molecules in dynamic action at high spatiotemporal resolution has long been a holy grail for biological science. To materialize this long quested dream, I have been developing high-speed atomic force microscopy (HS-AFM) since 1993. Tremendous strides were recently accomplished in its high-speed and low-invasive performances. Consequently, various dynamic molecular actions, including bipedal walking of myosin V and rotary propagation of structural changes in F1-ATPase, were successfully captured on video. The visualized dynamic images not only provided irrefutable evidence for speculated actions of the protein molecules but also brought new discoveries inaccessible with other approaches, thus giving great mechanistic insights into how the molecules function. HS-AFM is now transforming "static" structural biology into dynamic structural bioscience.

Cations Modulate Actin Bundle Mechanics, Assembly Dynamics, and Structure.

PubMed

Castaneda, Nicholas; Zheng, Tianyu; Rivera-Jacquez, Hector J; Lee, Hyun-Ju; Hyun, Jaekyung; Balaeff, Alexander; Huo, Qun; Kang, Hyeran

2018-04-12

Actin bundles are key factors in the mechanical support and dynamic reorganization of the cytoskeleton. High concentrations of multivalent counterions promote bundle formation through electrostatic attraction between actin filaments that are negatively charged polyelectrolytes. In this study, we evaluate how physiologically relevant divalent cations affect the mechanical, dynamic, and structural properties of actin bundles. Using a combination of total internal reflection fluorescence microscopy, transmission electron microscopy, and dynamic light scattering, we demonstrate that divalent cations modulate bundle stiffness, length distribution, and lateral growth. Molecular dynamics simulations of an all-atom model of the actin bundle reveal specific actin residues coordinate cation-binding sites that promote the bundle formation. Our work suggests that specific cation interactions may play a fundamental role in the assembly, structure, and mechanical properties of actin bundles.

Network cosmology.

PubMed

Krioukov, Dmitri; Kitsak, Maksim; Sinkovits, Robert S; Rideout, David; Meyer, David; Boguñá, Marián

2012-01-01

Prediction and control of the dynamics of complex networks is a central problem in network science. Structural and dynamical similarities of different real networks suggest that some universal laws might accurately describe the dynamics of these networks, albeit the nature and common origin of such laws remain elusive. Here we show that the causal network representing the large-scale structure of spacetime in our accelerating universe is a power-law graph with strong clustering, similar to many complex networks such as the Internet, social, or biological networks. We prove that this structural similarity is a consequence of the asymptotic equivalence between the large-scale growth dynamics of complex networks and causal networks. This equivalence suggests that unexpectedly similar laws govern the dynamics of complex networks and spacetime in the universe, with implications to network science and cosmology.

Network Cosmology

PubMed Central

Krioukov, Dmitri; Kitsak, Maksim; Sinkovits, Robert S.; Rideout, David; Meyer, David; Boguñá, Marián

2012-01-01

Prediction and control of the dynamics of complex networks is a central problem in network science. Structural and dynamical similarities of different real networks suggest that some universal laws might accurately describe the dynamics of these networks, albeit the nature and common origin of such laws remain elusive. Here we show that the causal network representing the large-scale structure of spacetime in our accelerating universe is a power-law graph with strong clustering, similar to many complex networks such as the Internet, social, or biological networks. We prove that this structural similarity is a consequence of the asymptotic equivalence between the large-scale growth dynamics of complex networks and causal networks. This equivalence suggests that unexpectedly similar laws govern the dynamics of complex networks and spacetime in the universe, with implications to network science and cosmology. PMID:23162688

An immersed boundary method for fluid-structure interaction with compressible multiphase flows

NASA Astrophysics Data System (ADS)

Wang, Li; Currao, Gaetano M. D.; Han, Feng; Neely, Andrew J.; Young, John; Tian, Fang-Bao

2017-10-01

This paper presents a two-dimensional immersed boundary method for fluid-structure interaction with compressible multiphase flows involving large structure deformations. This method involves three important parts: flow solver, structure solver and fluid-structure interaction coupling. In the flow solver, the compressible multiphase Navier-Stokes equations for ideal gases are solved by a finite difference method based on a staggered Cartesian mesh, where a fifth-order accuracy Weighted Essentially Non-Oscillation (WENO) scheme is used to handle spatial discretization of the convective term, a fourth-order central difference scheme is employed to discretize the viscous term, the third-order TVD Runge-Kutta scheme is used to discretize the temporal term, and the level-set method is adopted to capture the multi-material interface. In this work, the structure considered is a geometrically non-linear beam which is solved by using a finite element method based on the absolute nodal coordinate formulation (ANCF). The fluid dynamics and the structure motion are coupled in a partitioned iterative manner with a feedback penalty immersed boundary method where the flow dynamics is defined on a fixed Lagrangian grid and the structure dynamics is described on a global coordinate. We perform several validation cases (including fluid over a cylinder, structure dynamics, flow induced vibration of a flexible plate, deformation of a flexible panel induced by shock waves in a shock tube, an inclined flexible plate in a hypersonic flow, and shock-induced collapse of a cylindrical helium cavity in the air), and compare the results with experimental and other numerical data. The present results agree well with the published data and the current experiment. Finally, we further demonstrate the versatility of the present method by applying it to a flexible plate interacting with multiphase flows.

The effect of glycosylation on the transferrin structure: A molecular dynamic simulation analysis.

PubMed

Ghanbari, Z; Housaindokht, M R; Bozorgmehr, M R; Izadyar, M

2016-09-07

Transferrins have been defined by the highly cooperative binding of iron and a carbonate anion to form a Fe-CO3-Tf ternary complex. As such, the layout of the binding site residues affects transferrin function significantly; In contrast to N-lobe, C-lobe binding site of the transferrin structure has been less characterized and little research which surveyed the interaction of carbonate with transferrin in the C-lobe binding site has been found. In the present work, molecular dynamic simulation was employed to gain access into the molecular level understanding of carbonate binding site and their interactions in each lobe. Residues responsible for carbonate binding of transferrin structure were pointed out. In addition, native human transferrin is a glycoprotein that two N-linked complex glycan chains located in the C-lobe. Usually, in the molecular dynamic simulation for simplifying, glycan is removed from the protein structure. Here, we explore the effect of glycosylation on the transferrin structure. Glycosylation appears to have an effect on the layout of the binding site residue and transferrin structure. On the other hand, sometimes the entire transferrin formed by separated lobes that it allows the results to be interpreted in a straightforward manner rather than more parameters required for full length protein. But, it should be noted that there are differences between the separated lobe and full length transferrin, hence, a comparative analysis by the molecular dynamic simulation was performed to investigate such structural variations. Results revealed that separation in C-lobe caused a significant structural variation in comparison to N-lobe. Consequently, the separated lobes and the full length one are different, showing the importance of the interlobe communication and the impact of the lobes on each other in the transferrin structure. Copyright © 2016 Elsevier Ltd. All rights reserved.

Dynameomics: data-driven methods and models for utilizing large-scale protein structure repositories for improving fragment-based loop prediction.

PubMed

Rysavy, Steven J; Beck, David A C; Daggett, Valerie

2014-11-01

Protein function is intimately linked to protein structure and dynamics yet experimentally determined structures frequently omit regions within a protein due to indeterminate data, which is often due protein dynamics. We propose that atomistic molecular dynamics simulations provide a diverse sampling of biologically relevant structures for these missing segments (and beyond) to improve structural modeling and structure prediction. Here we make use of the Dynameomics data warehouse, which contains simulations of representatives of essentially all known protein folds. We developed novel computational methods to efficiently identify, rank and retrieve small peptide structures, or fragments, from this database. We also created a novel data model to analyze and compare large repositories of structural data, such as contained within the Protein Data Bank and the Dynameomics data warehouse. Our evaluation compares these structural repositories for improving loop predictions and analyzes the utility of our methods and models. Using a standard set of loop structures, containing 510 loops, 30 for each loop length from 4 to 20 residues, we find that the inclusion of Dynameomics structures in fragment-based methods improves the quality of the loop predictions without being dependent on sequence homology. Depending on loop length, ∼ 25-75% of the best predictions came from the Dynameomics set, resulting in lower main chain root-mean-square deviations for all fragment lengths using the combined fragment library. We also provide specific cases where Dynameomics fragments provide better predictions for NMR loop structures than fragments from crystal structures. Online access to these fragment libraries is available at http://www.dynameomics.org/fragments. © 2014 The Protein Society.

Dynameomics: Data-driven methods and models for utilizing large-scale protein structure repositories for improving fragment-based loop prediction

PubMed Central

Rysavy, Steven J; Beck, David AC; Daggett, Valerie

2014-01-01

Protein function is intimately linked to protein structure and dynamics yet experimentally determined structures frequently omit regions within a protein due to indeterminate data, which is often due protein dynamics. We propose that atomistic molecular dynamics simulations provide a diverse sampling of biologically relevant structures for these missing segments (and beyond) to improve structural modeling and structure prediction. Here we make use of the Dynameomics data warehouse, which contains simulations of representatives of essentially all known protein folds. We developed novel computational methods to efficiently identify, rank and retrieve small peptide structures, or fragments, from this database. We also created a novel data model to analyze and compare large repositories of structural data, such as contained within the Protein Data Bank and the Dynameomics data warehouse. Our evaluation compares these structural repositories for improving loop predictions and analyzes the utility of our methods and models. Using a standard set of loop structures, containing 510 loops, 30 for each loop length from 4 to 20 residues, we find that the inclusion of Dynameomics structures in fragment-based methods improves the quality of the loop predictions without being dependent on sequence homology. Depending on loop length, ∼25–75% of the best predictions came from the Dynameomics set, resulting in lower main chain root-mean-square deviations for all fragment lengths using the combined fragment library. We also provide specific cases where Dynameomics fragments provide better predictions for NMR loop structures than fragments from crystal structures. Online access to these fragment libraries is available at http://www.dynameomics.org/fragments. PMID:25142412

Structural dynamic and aeroelastic considerations for hypersonic vehicles

NASA Technical Reports Server (NTRS)

Cazier, F. W., Jr.; Doggett, Robert V., Jr.; Ricketts, Rodney H.

1991-01-01

The specific geometrical, structural, and operational environment characteristics of hypersonic vehicles are discussed with particular reference to aerospace plane type configurations. A discussion of the structural dynamic and aeroelastic phenomena that must be addressed for this class of vehicles is presented. These phenomena are in the aeroservothermoelasticity technical area. Some illustrative examples of recent experimental and analytical work are given. Some examples of current research are pointed out.

Hamiltonian structures for systems of hyperbolic conservation laws

NASA Astrophysics Data System (ADS)

Olver, Peter J.; Nutku, Yavuz

1988-07-01

The bi-Hamiltonian structure for a large class of one-dimensional hyberbolic systems of conservation laws in two field variables, including the equations of gas dynamics, shallow water waves, one-dimensional elastic media, and the Born-Infeld equation from nonlinear electrodynamics, is exhibited. For polytropic gas dynamics, these results lead to a quadri-Hamiltonian structure. New higher-order entropy-flux pairs (conservation laws) and higher-order symmetries are exhibited.

Process Study of Oceanic Responses to Typhoons Using Arrays of EM-APEX Floats and Moorings

DTIC Science & Technology

2012-09-30

maximum potential intensity, structure , energy, trajectory, and dynamic evolution. The most energetic oceanic responses to tropical cyclone forcing are...during tropical cyclone passage will aid understanding of storm dynamics and structure . The ocean’s recovery after tropical cyclone passage depends...days). The wake was advected hundreds of kilometers from the storm track by a pre- existing mesoscale eddy. Its thermal structure could not be

A space station Structures and Assembly Verification Experiment, SAVE

NASA Technical Reports Server (NTRS)

Russell, R. A.; Raney, J. P.; Deryder, L. J.

1986-01-01

The Space Station structure has been baselined to be a 5 M (16.4 ft) erectable truss. This structure will provide the overall framework to attach laboratory modules and other systems, subsystems and utilities. The assembly of this structure represents a formidable EVA challenge. To validate this capability the Space Station Structures/Dynamics Technical Integration Panel (TIP) met to develop the necessary data for an integrated STS structures flight experiment. As a result of this meeting, the Langley Research Center initiated a joint Langley/Boeing Aerospace Company study which supported the structures/dynamics TIP in developing the preliminary definition and design of a 5 M erectable space station truss and the resources required for a proposed flight experiment. The purpose of the study was to: (1) devise methods of truss assembly by astronauts; (2) define a specific test matrix for dynamic characterization; (3) identify instrumentation and data system requirements; (4) determine the power, propulsion and control requirements for the truss on-orbit for 3 years; (5) study the packaging of the experiment in the orbiter cargo bay; (6) prepare a preliminary cost estimate and schedule for the experiment; and (7) provide a list of potential follow-on experiments using the structure as a free flyer. The results of this three month study are presented.

Structure and dynamics of optically directed self-assembly of nanoparticles

PubMed Central

Roy, Debjit; Mondal, Dipankar; Goswami, Debabrata

2016-01-01

Self-assembly of nanoparticles leading to the formation of colloidal clusters often serves as the representative analogue for understanding molecular assembly. Unravelling the in situ structure and dynamics of such clusters in liquid suspensions is highly challenging. Presently colloidal clusters are first isolated from their generating environment and then their structures are probed by light scattering methods. In order to measure the in situ structure and dynamics of colloidal clusters, we have generated them using the high-repetition-rate femtosecond laser pulse optical tweezer. Since the constituent of our dimer, trimer or tetramer clusters are 250 nm radius two-photon resonant fluorophore coated nanospheres under the optical trap, they inherently produce Two-Photon Fluorescence, which undergo intra-nanosphere Fluorescence Energy Transfer. This unique energy transfer signature, in turn, enables us to visualize structures and orientations of these colloidal clusters during the process of their formation and subsequent dynamics in a liquid suspension. We also show that due to shape-birefringence, orientation and structural control of these colloidal clusters are possible as the polarization of the trapping laser is changed from linear to circular. We thus report important progress in sampling the smallest possible aggregates of nanoparticles, dimers, trimers or tetramers, formed early in the self-assembly process. PMID:27006305

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

PubMed

Rathner, Petr; Rathner, Adriana; Horničáková, Michaela; Wohlschlager, Christian; Chandra, Kousik; Kohoutová, Jaroslava; Ettrich, Rüdiger; Wimmer, Reinhard; Müller, Norbert

2015-09-01

The extrinsic proteins of photosystem II of higher plants and green algae PsbO, PsbP, PsbQ, and PsbR are essential for stable oxygen production in the oxygen evolving center. In the available X-ray crystallographic structure of higher plant PsbQ residues S14-Y33 are missing. Building on the backbone NMR assignment of PsbQ, which includes this "missing link", we report the extended resonance assignment including side chain atoms. Based on nuclear Overhauser effect spectra a high resolution solution structure of PsbQ with a backbone RMSD of 0.81 Å was obtained from torsion angle dynamics. Within the N-terminal residues 1-45 the solution structure deviates significantly from the X-ray crystallographic one, while the four-helix bundle core found previously is confirmed. A short α-helix is observed in the solution structure at the location where a β-strand had been proposed in the earlier crystallographic study. NMR relaxation data and unrestrained molecular dynamics simulations corroborate that the N-terminal region behaves as a flexible tail with a persistent short local helical secondary structure, while no indications of forming a β-strand are found. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

Structural dynamics of free proteins in diffraction.

PubMed

Lin, Milo M; Shorokhov, Dmitry; Zewail, Ahmed H

2011-10-26

Among the macromolecular patterns of biological significance, right-handed α-helices are perhaps the most abundant structural motifs. Here, guided by experimental findings, we discuss both ultrafast initial steps and longer-time-scale structural dynamics of helix-coil transitions induced by a range of temperature jumps in large, isolated macromolecular ensembles of an α-helical protein segment thymosin β(9) (Tβ(9)), and elucidate the comprehensive picture of (un)folding. In continuation of an earlier theoretical work from this laboratory that utilized a simplistic structure-scrambling algorithm combined with a variety of self-avoidance thresholds to approximately model helix-coil transitions in Tβ(9), in the present contribution we focus on the actual dynamics of unfolding as obtained from massively distributed ensemble-convergent MD simulations which provide an unprecedented scope of information on the nature of transient macromolecular structures, and with atomic-scale spatiotemporal resolution. In addition to the use of radial distribution functions of ultrafast electron diffraction (UED) simulations in gaining an insight into the elementary steps of conformational interconversions, we also investigate the structural dynamics of the protein via the native (α-helical) hydrogen bonding contact metric which is an intuitive coarse graining approach. Importantly, the decay of α-helical motifs and the (globular) conformational annealing in Tβ(9) occur consecutively or competitively, depending on the magnitude of temperature jump.

Destabilization of Human Serum Albumin by Ionic Liquids Studied Using Enhanced Molecular Dynamics Simulations.

PubMed

Jaeger, Vance W; Pfaendtner, Jim

2016-12-01

Ionic liquid (IL) containing solvents can change the structure, dynamics, function, and stability of proteins. In order to investigate the mechanisms by which ILs induce structural changes in a large multidomain protein, we study the interactions of human serum albumin (HSA) with two different ILs, 1-butyl-3-methylimidazolium tetrafluoroborate and choline dihydrogen phosphate. Root mean square deviation and fluctuation calculations indicate that high concentrations of ILs in mixtures with water lead to protein structures that remain close to their crystallographic structures on time scales of hundreds of nanoseconds. To overcome potential time scale limitations due to the high viscosity of the solvent, we employed enhanced sampling techniques to estimate the free energy of an experimentally determined important transition within the protein structure. Metadynamics simulations show that the free energy landscape of the unfolding of loop 1 of domain I is different in the presence of ILs than it is in water, consistent with previously published experimental evidence. We then apply essential dynamics coarse graining to systematically predict differences in the dynamics of proteins solvated in IL-water mixtures versus pure water systems. We also demonstrate that the presence of ionic liquids changes the distribution of intermolecular distances among several ligands, indicating that the protein structure swells in the presence of certain ILs, consistent with experimental evidence.

Decipher the dynamic coordination between enzymatic activity and structural modulation at focal adhesions in living cells

NASA Astrophysics Data System (ADS)

Lu, Shaoying; Seong, Jihye; Wang, Yi; Chang, Shiou-Chi; Eichorst, John Paul; Ouyang, Mingxing; Li, Julie Y.-S.; Chien, Shu; Wang, Yingxiao

2014-07-01

Focal adhesions (FAs) are dynamic subcellular structures crucial for cell adhesion, migration and differentiation. It remains an enigma how enzymatic activities in these local complexes regulate their structural remodeling in live cells. Utilizing biosensors based on fluorescence resonance energy transfer (FRET), we developed a correlative FRET imaging microscopy (CFIM) approach to quantitatively analyze the subcellular coordination between the enzymatic Src activation and the structural FA disassembly. CFIM reveals that the Src kinase activity only within the microdomain of lipid rafts at the plasma membrane is coupled with FA dynamics. FA disassembly at cell periphery was linearly dependent on this raft-localized Src activity, although cells displayed heterogeneous levels of response to stimulation. Within lipid rafts, the time delay between Src activation and FA disassembly was 1.2 min in cells seeded on low fibronectin concentration ([FN]) and 4.3 min in cells on high [FN]. CFIM further showed that the level of Src-FA coupling, as well as the time delay, was regulated by cell-matrix interactions, as a tight enzyme-structure coupling occurred in FA populations mediated by integrin αvβ3, but not in those by integrin α5β1. Therefore, different FA subpopulations have distinctive regulation mechanisms between their local kinase activity and structural FA dynamics.

Self-Organization of Microcircuits in Networks of Spiking Neurons with Plastic Synapses.

PubMed

Ocker, Gabriel Koch; Litwin-Kumar, Ashok; Doiron, Brent

2015-08-01

The synaptic connectivity of cortical networks features an overrepresentation of certain wiring motifs compared to simple random-network models. This structure is shaped, in part, by synaptic plasticity that promotes or suppresses connections between neurons depending on their joint spiking activity. Frequently, theoretical studies focus on how feedforward inputs drive plasticity to create this network structure. We study the complementary scenario of self-organized structure in a recurrent network, with spike timing-dependent plasticity driven by spontaneous dynamics. We develop a self-consistent theory for the evolution of network structure by combining fast spiking covariance with a slow evolution of synaptic weights. Through a finite-size expansion of network dynamics we obtain a low-dimensional set of nonlinear differential equations for the evolution of two-synapse connectivity motifs. With this theory in hand, we explore how the form of the plasticity rule drives the evolution of microcircuits in cortical networks. When potentiation and depression are in approximate balance, synaptic dynamics depend on weighted divergent, convergent, and chain motifs. For additive, Hebbian STDP these motif interactions create instabilities in synaptic dynamics that either promote or suppress the initial network structure. Our work provides a consistent theoretical framework for studying how spiking activity in recurrent networks interacts with synaptic plasticity to determine network structure.

Self-Organization of Microcircuits in Networks of Spiking Neurons with Plastic Synapses

PubMed Central

Ocker, Gabriel Koch; Litwin-Kumar, Ashok; Doiron, Brent

2015-01-01

The synaptic connectivity of cortical networks features an overrepresentation of certain wiring motifs compared to simple random-network models. This structure is shaped, in part, by synaptic plasticity that promotes or suppresses connections between neurons depending on their joint spiking activity. Frequently, theoretical studies focus on how feedforward inputs drive plasticity to create this network structure. We study the complementary scenario of self-organized structure in a recurrent network, with spike timing-dependent plasticity driven by spontaneous dynamics. We develop a self-consistent theory for the evolution of network structure by combining fast spiking covariance with a slow evolution of synaptic weights. Through a finite-size expansion of network dynamics we obtain a low-dimensional set of nonlinear differential equations for the evolution of two-synapse connectivity motifs. With this theory in hand, we explore how the form of the plasticity rule drives the evolution of microcircuits in cortical networks. When potentiation and depression are in approximate balance, synaptic dynamics depend on weighted divergent, convergent, and chain motifs. For additive, Hebbian STDP these motif interactions create instabilities in synaptic dynamics that either promote or suppress the initial network structure. Our work provides a consistent theoretical framework for studying how spiking activity in recurrent networks interacts with synaptic plasticity to determine network structure. PMID:26291697

Phytoestrogens and Mycoestrogens Induce Signature Structure Dynamics Changes on Estrogen Receptor α

PubMed Central

Chen, Xueyan; Uzuner, Ugur; Li, Man; Shi, Weibing; Yuan, Joshua S.; Dai, Susie Y.

2016-01-01

Endocrine disrupters include a broad spectrum of chemicals such as industrial chemicals, natural estrogens and androgens, synthetic estrogens and androgens. Phytoestrogens are widely present in diet and food supplements; mycoestrogens are frequently found in grains. As human beings and animals are commonly exposed to phytoestrogens and mycoestrogens in diet and environment, it is important to understand the potential beneficial or hazardous effects of estrogenic compounds. Many bioassays have been established to study the binding of estrogenic compounds with estrogen receptor (ER) and provided rich data in the literature. However, limited assays can offer structure information with regard to the ligand/ER complex. Our current study surveys the global structure dynamics changes for ERα ligand binding domain (LBD) when phytoestrogens and mycoestrogens bind. The assay is based on the structure dynamics information probed by hydrogen deuterium exchange mass spectrometry and offers a unique viewpoint to elucidate the mechanism how phytoestrogens and mycoestrogens interact with estrogen receptor. The cluster analysis based on the hydrogen deuterium exchange (HDX) assay data reveals a unique pattern when phytoestrogens and mycoestrogens bind with ERα LBD compared to that of estradiol and synthetic estrogen modulators. Our study highlights that structure dynamics could play an important role in the structure function relationship when endocrine disrupters interact with estrogen receptors. PMID:27589781

Molecular dynamics approach to water structure of HII mesophase of monoolein

NASA Astrophysics Data System (ADS)

Kolev, Vesselin; Ivanova, Anela; Madjarova, Galia; Aserin, Abraham; Garti, Nissim

2012-02-01

The goal of the present work is to study theoretically the structure of water inside the water cylinder of the inverse hexagonal mesophase (HII) of glyceryl monooleate (monoolein, GMO), using the method of molecular dynamics. To simplify the computational model, a fixed structure of the GMO tube is maintained. The non-standard cylindrical geometry of the system required the development and application of a novel method for obtaining the starting distribution of water molecules. A predictor-corrector schema is employed for generation of the initial density of water. Molecular dynamics calculations are performed at constant volume and temperature (NVT ensemble) with 1D periodic boundary conditions applied. During the simulations the lipid structure is kept fixed, while the dynamics of water is unrestrained. Distribution of hydrogen bonds and density as well as radial distribution of water molecules across the water cylinder show the presence of water structure deep in the cylinder (about 6 Å below the GMO heads). The obtained results may help understanding the role of water structure in the processes of insertion of external molecules inside the GMO/water system. The present work has a semi-quantitative character and it should be considered as the initial stage of more comprehensive future theoretical studies.

Guest-Induced Two-Way Structural Transformation in a Layered Metal-Organic Framework Thin Film.

PubMed

Haraguchi, Tomoyuki; Otsubo, Kazuya; Sakata, Osami; Fujiwara, Akihiko; Kitagawa, Hiroshi

2016-12-28

Fabrication of thin films made of metal-organic frameworks (MOFs) has been intensively pursued for practical applications that use the structural response of MOFs. However, to date, only physisorption-induced structural response has been studied in these films. Chemisorption can be expected to provide a remarkable structural response because of the formation of bonds between guest molecules and reactive metal sites in host MOFs. Here, we report that chemisorption-induced two-way structural transformation in a nanometer-sized MOF thin film. We prepared a two-dimensional layered-type MOF Fe[Pt(CN) 4 ] thin film using a step-by-step approach. Although the as-synthesized film showed poor crystallinity, the dehydrated form of this thin film had a highly oriented crystalline nature (Film-D) as confirmed by synchrotron X-ray diffraction (XRD). Surprisingly, under water and pyridine vapors, Film-D showed chemisorption-induced dynamic structural transformations to Fe(L) 2 [Pt(CN) 4 ] thin films [L = H 2 O (Film-H), pyridine (Film-P)], where water and pyridine coordinated to the open Fe 2+ site. Dynamic structural transformations were also confirmed by in situ XRD, sorption measurement, and infrared reflection absorption spectroscopy. This is the first report of chemisorption-induced dynamic structural response in a MOF thin film, and it provides useful insights, which would lead to future practical applications of MOFs utilizing chemisorption-induced structural responses.

An Atomistic View of Amyloidogenic Self-assembly: Structure and Dynamics of Heterogeneous Conformational States in the Pre-nucleation Phase

PubMed Central

Matthes, Dirk; Gapsys, Vytautas; Brennecke, Julian T.; de Groot, Bert L.

2016-01-01

The formation of well-defined filamentous amyloid structures involves a polydisperse collection of oligomeric states for which relatively little is known in terms of structural organization. Here we use extensive, unbiased explicit solvent molecular dynamics (MD) simulations to investigate the structural and dynamical features of oligomeric aggregates formed by a number of highly amyloidogenic peptides at atomistic resolution on the μs time scale. A consensus approach has been adopted to analyse the simulations in multiple force fields, yielding an in-depth characterization of pre-fibrillar oligomers and their global and local structure properties. A collision cross section analysis revealed structurally heterogeneous aggregate ensembles for the individual oligomeric states that lack a single defined quaternary structure during the pre-nucleation phase. To gain insight into the conformational space sampled in early aggregates, we probed their substructure and found emerging β-sheet subunit layers and a multitude of ordered intermolecular β-structure motifs with growing aggregate size. Among those, anti-parallel out-of-register β-strands compatible with toxic β-barrel oligomers were particularly prevalent already in smaller aggregates and formed prior to ordered fibrillar structure elements. Notably, also distinct fibril-like conformations emerged in the oligomeric state and underscore the notion that pre-nucleated oligomers serve as a critical intermediate step on-pathway to fibrils. PMID:27616019

Wind Turbine Structural Dynamics

NASA Technical Reports Server (NTRS)

Miller, D. R. (Editor)

1978-01-01

A workshop on wind turbine structural dynamics was held to review and document current United States work on the dynamic behavior of large wind turbines, primarily of the horizontal-axis type, and to identify and discuss other wind turbine configurations that may have lower cost and weight. Information was exchanged on the following topics: (1) Methods for calculating dynamic loads; (2) Aeroelasticity stability (3) Wind loads, both steady and transient; (4) Critical design conditions; (5) Drive train dynamics; and (6) Behavior of operating wind turbines.

Evolutionary dynamics of general group interactions in structured populations

NASA Astrophysics Data System (ADS)

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.

UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.

PubMed

Czaplewski, Cezary; Karczynska, Agnieszka; Sieradzan, Adam K; Liwo, Adam

2018-04-30

A server implementation of the UNRES package (http://www.unres.pl) for coarse-grained simulations of protein structures with the physics-based UNRES model, coined a name UNRES server, is presented. In contrast to most of the protein coarse-grained models, owing to its physics-based origin, the UNRES force field can be used in simulations, including those aimed at protein-structure prediction, without ancillary information from structural databases; however, the implementation includes the possibility of using restraints. Local energy minimization, canonical molecular dynamics simulations, replica exchange and multiplexed replica exchange molecular dynamics simulations can be run with the current UNRES server; the latter are suitable for protein-structure prediction. The user-supplied input includes protein sequence and, optionally, restraints from secondary-structure prediction or small x-ray scattering data, and simulation type and parameters which are selected or typed in. Oligomeric proteins, as well as those containing D-amino-acid residues and disulfide links can be treated. The output is displayed graphically (minimized structures, trajectories, final models, analysis of trajectory/ensembles); however, all output files can be downloaded by the user. The UNRES server can be freely accessed at http://unres-server.chem.ug.edu.pl.

De Novo Proteins with Life-Sustaining Functions Are Structurally Dynamic.

PubMed

Murphy, Grant S; Greisman, Jack B; Hecht, Michael H

2016-01-29

Designing and producing novel proteins that fold into stable structures and provide essential biological functions are key goals in synthetic biology. In initial steps toward achieving these goals, we constructed a combinatorial library of de novo proteins designed to fold into 4-helix bundles. As described previously, screening this library for sequences that function in vivo to rescue conditionally lethal mutants of Escherichia coli (auxotrophs) yielded several de novo sequences, termed SynRescue proteins, which rescued four different E. coli auxotrophs. In an effort to understand the structural requirements necessary for auxotroph rescue, we investigated the biophysical properties of the SynRescue proteins, using both computational and experimental approaches. Results from circular dichroism, size-exclusion chromatography, and NMR demonstrate that the SynRescue proteins are α-helical and relatively stable. Surprisingly, however, they do not form well-ordered structures. Instead, they form dynamic structures that fluctuate between monomeric and dimeric states. These findings show that a well-ordered structure is not a prerequisite for life-sustaining functions, and suggests that dynamic structures may have been important in the early evolution of protein function. Copyright © 2015 Elsevier Ltd. All rights reserved.

Structural features that predict real-value fluctuations of globular proteins

PubMed Central

Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke

2012-01-01

It is crucial to consider dynamics for understanding the biological function of proteins. We used a large number of molecular dynamics trajectories of non-homologous proteins as references and examined static structural features of proteins that are most relevant to fluctuations. We examined correlation of individual structural features with fluctuations and further investigated effective combinations of features for predicting the real-value of residue fluctuations using the support vector regression. It was found that some structural features have higher correlation than crystallographic B-factors with fluctuations observed in molecular dynamics trajectories. Moreover, support vector regression that uses combinations of static structural features showed accurate prediction of fluctuations with an average Pearson’s correlation coefficient of 0.669 and a root mean square error of 1.04 Å. This correlation coefficient is higher than the one observed for the prediction by the Gaussian network model. An advantage of the developed method over the Gaussian network models is that the former predicts the real-value of fluctuation. The results help improve our understanding of relationships between protein structure and fluctuation. Furthermore, the developed method provides a convienient practial way to predict fluctuations of proteins using easily computed static structural features of proteins. PMID:22328193

Structural dynamics of supercooled water from quasielastic neutron scattering and molecular simulations.

PubMed

Qvist, Johan; Schober, Helmut; Halle, Bertil

2011-04-14

One of the outstanding challenges presented by liquid water is to understand how molecules can move on a picosecond time scale despite being incorporated in a three-dimensional network of relatively strong H-bonds. This challenge is exacerbated in the supercooled state, where the dramatic slowing down of structural dynamics is reminiscent of the, equally poorly understood, generic behavior of liquids near the glass transition temperature. By probing single-molecule dynamics on a wide range of time and length scales, quasielastic neutron scattering (QENS) can potentially reveal the mechanistic details of water's structural dynamics, but because of interpretational ambiguities this potential has not been fully realized. To resolve these issues, we present here an extensive set of high-quality QENS data from water in the range 253-293 K and a corresponding set of molecular dynamics (MD) simulations to facilitate and validate the interpretation. Using a model-free approach, we analyze the QENS data in terms of two motional components. Based on the dynamical clustering observed in MD trajectories, we identify these components with two distinct types of structural dynamics: picosecond local (L) structural fluctuations within dynamical basins and slower interbasin jumps (J). The Q-dependence of the dominant QENS component, associated with J dynamics, can be quantitatively rationalized with a continuous-time random walk (CTRW) model with an apparent jump length that depends on low-order moments of the jump length and waiting time distributions. Using a simple coarse-graining algorithm to quantitatively identify dynamical basins, we map the newtonian MD trajectory on a CTRW trajectory, from which the jump length and waiting time distributions are computed. The jump length distribution is gaussian and the rms jump length increases from 1.5 to 1.9 Å as the temperature increases from 253 to 293 K. The rms basin radius increases from 0.71 to 0.75 Å over the same range. The waiting time distribution is exponential at all investigated temperatures, ruling out significant dynamical heterogeneity. However, a simulation at 238 K reveals a small but significant dynamical heterogeneity. The macroscopic diffusion coefficient deduced from the QENS data agrees quantitatively with NMR and tracer results. We compare our QENS analysis with existing approaches, arguing that the apparent dynamical heterogeneity implied by stretched exponential fitting functions results from the failure to distinguish intrabasin (L) from interbasin (J) structural dynamics. We propose that the apparent dynamical singularity at ∼220 K corresponds to freezing out of J dynamics, while the calorimetric glass transition corresponds to freezing out of L dynamics.

Structural dynamics of supercooled water from quasielastic neutron scattering and molecular simulations

NASA Astrophysics Data System (ADS)

Qvist, Johan; Schober, Helmut; Halle, Bertil

2011-04-01

One of the outstanding challenges presented by liquid water is to understand how molecules can move on a picosecond time scale despite being incorporated in a three-dimensional network of relatively strong H-bonds. This challenge is exacerbated in the supercooled state, where the dramatic slowing down of structural dynamics is reminiscent of the, equally poorly understood, generic behavior of liquids near the glass transition temperature. By probing single-molecule dynamics on a wide range of time and length scales, quasielastic neutron scattering (QENS) can potentially reveal the mechanistic details of water's structural dynamics, but because of interpretational ambiguities this potential has not been fully realized. To resolve these issues, we present here an extensive set of high-quality QENS data from water in the range 253-293 K and a corresponding set of molecular dynamics (MD) simulations to facilitate and validate the interpretation. Using a model-free approach, we analyze the QENS data in terms of two motional components. Based on the dynamical clustering observed in MD trajectories, we identify these components with two distinct types of structural dynamics: picosecond local (L) structural fluctuations within dynamical basins and slower interbasin jumps (J). The Q-dependence of the dominant QENS component, associated with J dynamics, can be quantitatively rationalized with a continuous-time random walk (CTRW) model with an apparent jump length that depends on low-order moments of the jump length and waiting time distributions. Using a simple coarse-graining algorithm to quantitatively identify dynamical basins, we map the Newtonian MD trajectory on a CTRW trajectory, from which the jump length and waiting time distributions are computed. The jump length distribution is Gaussian and the rms jump length increases from 1.5 to 1.9 Å as the temperature increases from 253 to 293 K. The rms basin radius increases from 0.71 to 0.75 Å over the same range. The waiting time distribution is exponential at all investigated temperatures, ruling out significant dynamical heterogeneity. However, a simulation at 238 K reveals a small but significant dynamical heterogeneity. The macroscopic diffusion coefficient deduced from the QENS data agrees quantitatively with NMR and tracer results. We compare our QENS analysis with existing approaches, arguing that the apparent dynamical heterogeneity implied by stretched exponential fitting functions results from the failure to distinguish intrabasin (L) from interbasin (J) structural dynamics. We propose that the apparent dynamical singularity at ˜220 K corresponds to freezing out of J dynamics, while the calorimetric glass transition corresponds to freezing out of L dynamics.

Computation of structural flexibility for bridge health monitoring using ambient modal data

DOT National Transportation Integrated Search

1996-01-01

The issues surrounding the use of ambient vibration modes for the location of structural damage via dynamically : measured flexibility are examined. Several methods for obtaining the required mass-normalized : dynamic mode shapes from ambient modal d...

Expansion and improvements of the FORMA system for response and load analysis. Volume 1: Programming manual

NASA Technical Reports Server (NTRS)

Wohlen, R. L.

1976-01-01

Techniques are presented for the solution of structural dynamic systems on an electronic digital computer using FORMA (FORTRAN Matrix Analysis). FORMA is a library of subroutines coded in FORTRAN 4 for the efficient solution of structural dynamics problems. These subroutines are in the form of building blocks that can be put together to solve a large variety of structural dynamics problems. The obvious advantage of the building block approach is that programming and checkout time are limited to that required for putting the blocks together in the proper order.