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.

Dynamic structural disorder in supported nanoscale catalysts

NASA Astrophysics Data System (ADS)

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

2014-04-01

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

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.

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.

Flight Dynamics of Flexible Aircraft with Aeroelastic and Inertial Force Interactions

NASA Technical Reports Server (NTRS)

Nguyen, Nhan T.; Tuzcu, Ilhan

2009-01-01

This paper presents an integrated flight dynamic modeling method for flexible aircraft that captures coupled physics effects due to inertial forces, aeroelasticity, and propulsive forces that are normally present in flight. The present approach formulates the coupled flight dynamics using a structural dynamic modeling method that describes the elasticity of a flexible, twisted, swept wing using an equivalent beam-rod model. The structural dynamic model allows for three types of wing elastic motion: flapwise bending, chordwise bending, and torsion. Inertial force coupling with the wing elasticity is formulated to account for aircraft acceleration. The structural deflections create an effective aeroelastic angle of attack that affects the rigid-body motion of flexible aircraft. The aeroelastic effect contributes to aerodynamic damping forces that can influence aerodynamic stability. For wing-mounted engines, wing flexibility can cause the propulsive forces and moments to couple with the wing elastic motion. The integrated flight dynamics for a flexible aircraft are formulated by including generalized coordinate variables associated with the aeroelastic-propulsive forces and moments in the standard state-space form for six degree-of-freedom flight dynamics. A computational structural model for a generic transport aircraft has been created. The eigenvalue analysis is performed to compute aeroelastic frequencies and aerodynamic damping. The results will be used to construct an integrated flight dynamic model of a flexible generic transport aircraft.

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...

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 (...

Effects of substrate network topologies on competition dynamics

NASA Astrophysics Data System (ADS)

Lee, Sang Hoon; Jeong, Hawoong

2006-08-01

We study a competition dynamics, based on the minority game, endowed with various substrate network structures. We observe the effects of the network topologies by investigating the volatility of the system and the structure of follower networks. The topology of substrate structures significantly influences the system efficiency represented by the volatility and such substrate networks are shown to amplify the herding effect and cause inefficiency in most cases. The follower networks emerging from the leadership structure show a power-law incoming degree distribution. This study shows the emergence of scale-free structures of leadership in the minority game and the effects of the interaction among players on the networked version of the game.

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.

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.

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.

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

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

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…

On the apparent insignificance of the randomness of flexible joints on large space truss dynamics

NASA Technical Reports Server (NTRS)

Koch, R. M.; Klosner, J. M.

1993-01-01

Deployable periodic large space structures have been shown to exhibit high dynamic sensitivity to period-breaking imperfections and uncertainties. These can be brought on by manufacturing or assembly errors, structural imperfections, as well as nonlinear and/or nonconservative joint behavior. In addition, the necessity of precise pointing and position capability can require the consideration of these usually negligible and unknown parametric uncertainties and their effect on the overall dynamic response of large space structures. This work describes the use of a new design approach for the global dynamic solution of beam-like periodic space structures possessing parametric uncertainties. Specifically, the effect of random flexible joints on the free vibrations of simply-supported periodic large space trusses is considered. The formulation is a hybrid approach in terms of an extended Timoshenko beam continuum model, Monte Carlo simulation scheme, and first-order perturbation methods. The mean and mean-square response statistics for a variety of free random vibration problems are derived for various input random joint stiffness probability distributions. The results of this effort show that, although joint flexibility has a substantial effect on the modal dynamic response of periodic large space trusses, the effect of any reasonable uncertainty or randomness associated with these joint flexibilities is insignificant.

A mathematical analysis of the effects of Hebbian learning rules on the dynamics and structure of discrete-time random recurrent neural networks.

PubMed

Siri, Benoît; Berry, Hugues; Cessac, Bruno; Delord, Bruno; Quoy, Mathias

2008-12-01

We present a mathematical analysis of the effects of Hebbian learning in random recurrent neural networks, with a generic Hebbian learning rule, including passive forgetting and different timescales, for neuronal activity and learning dynamics. Previous numerical work has reported that Hebbian learning drives the system from chaos to a steady state through a sequence of bifurcations. Here, we interpret these results mathematically and show that these effects, involving a complex coupling between neuronal dynamics and synaptic graph structure, can be analyzed using Jacobian matrices, which introduce both a structural and a dynamical point of view on neural network evolution. Furthermore, we show that sensitivity to a learned pattern is maximal when the largest Lyapunov exponent is close to 0. We discuss how neural networks may take advantage of this regime of high functional interest.

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.

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

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.

Investigation of Structural Dynamics in a 2-Meter Square Solar Sail Model Including Axial Load Effects

NASA Technical Reports Server (NTRS)

Holland, D. B.; Virgin, L. N.; Belvin, W. K.

2003-01-01

This paper presents a parameter study of the effect of boom axial loading on the global dynamics of a 2-meter solar sail scale model. The experimental model used is meant for building expertise in finite element analysis and experimental execution, not as a predecessor to any planned flight mission or particular design concept. The results here are to demonstrate the ability to predict and measure structural dynamics and mode shapes in the presence of axial loading.

Dynamic resource allocation in a hierarchical multiprocessor system: A preliminary study

NASA Technical Reports Server (NTRS)

Ngai, Tin-Fook

1986-01-01

An integrated system approach to dynamic resource allocation is proposed. Some of the problems in dynamic resource allocation and the relationship of these problems to system structures are examined. A general dynamic resource allocation scheme is presented. A hierarchial system architecture which dynamically maps between processor structure and programs at multiple levels of instantiations is described. Simulation experiments were conducted to study dynamic resource allocation on the proposed system. Preliminary evaluation based on simple dynamic resource allocation algorithms indicates that with the proposed system approach, the complexity of dynamic resource management could be significantly reduced while achieving reasonable effective dynamic resource allocation.

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

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.

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.

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

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

Effective Group Dynamics: Theories and Practices.

ERIC Educational Resources Information Center

Murk, Peter J.

Using a brief experiential group activity called "Choosing a Color Exercise" as an introductory measure, this paper explains the basics of group dynamics and reviews the major theoretical relationships between the group's structure, the dynamics of maintenance and task behaviors, and effective individual performances. The types of functional and…

3D Realistic Radiative Hydrodynamic Modeling of a Moderate-Mass Star: Effects of Rotation

NASA Astrophysics Data System (ADS)

Kitiashvili, Irina; Kosovichev, Alexander G.; Mansour, Nagi N.; Wray, Alan A.

2018-01-01

Recent progress in stellar observations opens new perspectives in understanding stellar evolution and structure. However, complex interactions in the turbulent radiating plasma together with effects of magnetic fields and rotation make inferences of stellar properties uncertain. The standard 1D mixing-length-based evolutionary models are not able to capture many physical processes of stellar interior dynamics, but they provide an initial approximation of the stellar structure that can be used to initialize 3D time-dependent radiative hydrodynamics simulations, based on first physical principles, that take into account the effects of turbulence, radiation, and others. In this presentation we will show simulation results from a 3D realistic modeling of an F-type main-sequence star with mass 1.47 Msun, in which the computational domain includes the upper layers of the radiation zone, the entire convection zone, and the photosphere. The simulation results provide new insight into the formation and properties of the convective overshoot region, the dynamics of the near-surface, highly turbulent layer, the structure and dynamics of granulation, and the excitation of acoustic and gravity oscillations. We will discuss the thermodynamic structure, oscillations, and effects of rotation on the dynamics of the star across these layers.

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.

Changes in actin structural transitions associated with oxidative inhibition of muscle contraction.

PubMed

Prochniewicz, Ewa; Spakowicz, Daniel; Thomas, David D

2008-11-11

We have used transient phosphorescence anisotropy (TPA) to detect changes in actin structural dynamics associated with oxidative inhibition of muscle contraction. Contractility of skinned rabbit psoas muscle fibers was inhibited by treatment with 50 mM H 2O 2, which induced oxidative modifications in the myosin head and in actin, as previously reported. Using proteins purified from oxidized and unoxidized muscle, we used TPA to measure the effects of weakly (+ATP) and strongly (no ATP) bound myosin heads (S1) on the microsecond dynamics of actin labeled at Cys374 with erythrosine iodoacetamide. Oxidative modification of S1 had no effect on actin dynamics in the absence of ATP (strong binding complex), but restricted the dynamics in the presence of ATP (weakly bound complex). In contrast, oxidative modification of actin did not have a significant effect on the weak-to-strong transitions. Thus, we concluded that (1) the effects of oxidation on the dynamics of actin in the actomyosin complex are predominantly determined by oxidation-induced changes in S1, and (2) changes in weak-to-strong structural transitions in actin and myosin are coupled to each other and are associated with oxidative inhibition of muscle contractility.

Changes in actin structural transitions associated with oxidative inhibition of muscle contraction

PubMed Central

Prochniewicz, Ewa; Spakowicz, Daniel; Thomas, David D.

2011-01-01

We have used transient phosphorescence anisotropy (TPA) to detect changes in actin structural dynamics associated with oxidative inhibition of muscle contraction. Contractility of skinned rabbit psoas muscle fibers was inhibited by treatment with 50 mM H2O2, which induced oxidative modifications in the myosin head and in actin, as previously reported. Using proteins purified from oxidized and unoxidized muscle, we used TPA to measure the effects of weakly (+ATP) and strongly (no ATP) bound myosin heads (S1) on the microsecond dynamics of actin labeled at Cys374 with erythrosine iodoacetamide. Oxidative modification of S1 had no effect on actin dynamics in the absence of ATP (strong binding complex), but restricted the dynamics in the presence of ATP (weakly bound complex). In contrast, oxidative modification of actin did not have a significant effect on the weak-to-strong transitions. Thus, we concluded that (1) the effects of oxidation on the dynamics of actin in the actomyosin complex are predominantly determined by oxidation-induced changes in S1, and (2) changes in weak-to-strong structural transitions in actin and myosin are coupled to each other and are associated with oxidative inhibition of muscle contractility. PMID:18855423

Dynamic analysis of solid propellant grains subjected to ignition pressurization loading

NASA Astrophysics Data System (ADS)

Chyuan, Shiang-Woei

2003-11-01

Traditionally, the transient analysis of solid propellant grains subjected to ignition pressurization loading was not considered, and quasi-elastic-static analysis was widely adopted for structural integrity because the analytical task gets simplified. But it does not mean that the dynamic effect is not useful and could be neglected arbitrarily, and this effect usually plays a very important role for some critical design. In order to simulate the dynamic response for solid rocket motor, a transient finite element model, accompanied by concepts of time-temperature shift principle, reduced integration and thermorheologically simple material assumption, was used. For studying the dynamic response, diverse ignition pressurization loading cases were used and investigated in the present paper. Results show that the dynamic effect is important for structural integrity of solid propellant grains under ignition pressurization loading. Comparing the effective stress of transient analysis and of quasi-elastic-static analysis, one can see that there is an obvious difference between them because of the dynamic effect. From the work of quasi-elastic-static and transient analyses, the dynamic analysis highlighted several areas of interest and a more accurate and reasonable result could be obtained for the engineer.

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.

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.

Molecular Dynamics Analysis of Lysozyme Protein in Ethanol- Water Mixed Solvent

DTIC Science & Technology

2012-01-01

molecular dynamics simulations of solvent effect on lysozyme protein, using water, ethanol, and different concentrations of water-ethanol mixtures as...understood. This work focuses on detailed molecular dynamics simulations of solvent effect on lysozyme protein, using water, ethanol, and different...using GROMACS molecular dynamics simulation (MD) code. Compared to water environment, the lysozyme structure showed remarkable changes in water

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.

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.

Microscopic analysis of protein oxidative damage: effect of carbonylation on structure, dynamics, and aggregability of villin headpiece.

PubMed

Petrov, Drazen; Zagrovic, Bojan

2011-05-11

One of the most important irreversible oxidative modifications of proteins is carbonylation, the process of introducing a carbonyl group in reaction with reactive oxygen species. Notably, carbonylation increases with the age of cells and is associated with the formation of intracellular protein aggregates and the pathogenesis of age-related disorders such as neurodegenerative diseases and cancer. However, it is still largely unclear how carbonylation affects protein structure, dynamics, and aggregability at the atomic level. Here, we use classical molecular dynamics simulations to study structure and dynamics of the carbonylated headpiece domain of villin, a key actin-organizing protein. We perform an exhaustive set of molecular dynamics simulations of a native villin headpiece together with every possible combination of carbonylated versions of its seven lysine, arginine, and proline residues, quantitatively the most important carbonylable amino acids. Surprisingly, our results suggest that high levels of carbonylation, far above those associated with cell death in vivo, may be required to destabilize and unfold protein structure through the disruption of specific stabilizing elements, such as salt bridges or proline kinks, or tampering with the hydrophobic effect. On the other hand, by using thermodynamic integration and molecular hydrophobicity potential approaches, we quantitatively show that carbonylation of hydrophilic lysine and arginine residues is equivalent to introducing hydrophobic, charge-neutral mutations in their place, and, by comparison with experimental results, we demonstrate that this by itself significantly increases the intrinsic aggregation propensity of both structured, native proteins and their unfolded states. Finally, our results provide a foundation for a novel experimental strategy to study the effects of carbonylation on protein structure, dynamics, and aggregability using site-directed mutagenesis. © 2011 American Chemical Society

Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm.

PubMed

Yu, Isseki; Mori, Takaharu; Ando, Tadashi; Harada, Ryuhei; Jung, Jaewoon; Sugita, Yuji; Feig, Michael

2016-11-01

Biological macromolecules function in highly crowded cellular environments. The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. Protein-protein interactions also resulted in significant variations in reduced macromolecular diffusion under crowded conditions, while metabolites exhibited significant two-dimensional surface diffusion and altered protein-ligand binding that may reduce the effective concentration of metabolites and ligands in vivo. Metabolic enzymes showed weak non-specific association in cellular environments attributed to solvation and entropic effects. These effects are expected to have broad implications for the in vivo functioning of biomolecules. This work is a first step towards physically realistic in silico whole-cell models that connect molecular with cellular biology.

Roles of dynamical symmetry breaking in driving oblate-prolate transitions of atomic clusters

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

Oka, Yurie, E-mail: ok-yu@fuji.waseda.jp; Yanao, Tomohiro, E-mail: yanao@waseda.jp; Koon, Wang Sang, E-mail: koon@cds.caltech.edu

2015-04-07

This paper explores the driving mechanisms for structural transitions of atomic clusters between oblate and prolate isomers. We employ the hyperspherical coordinates to investigate structural dynamics of a seven-atom cluster at a coarse-grained level in terms of the dynamics of three gyration radii and three principal axes, which characterize overall mass distributions of the cluster. Dynamics of gyration radii is governed by two kinds of forces. One is the potential force originating from the interactions between atoms. The other is the dynamical forces called the internal centrifugal forces, which originate from twisting and shearing motions of the system. The internalmore » centrifugal force arising from twisting motions has an effect of breaking the symmetry between two gyration radii. As a result, in an oblate isomer, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two largest gyration radii is crucial in triggering structural transitions into prolate isomers. In a prolate isomer, on the other hand, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two smallest gyration radii is crucial in triggering structural transitions into oblate isomers. Activation of a twisting motion that switches the movement patterns of three principal axes is also important for the onset of structural transitions between oblate and prolate isomers. Based on these trigger mechanisms, we finally show that selective activations of specific gyration radii and twisting motions, depending on the isomer of the cluster, can effectively induce structural transitions of the cluster. The results presented here could provide further insights into the control of molecular reactions.« less

Roles of dynamical symmetry breaking in driving oblate-prolate transitions of atomic clusters

NASA Astrophysics Data System (ADS)

Oka, Yurie; Yanao, Tomohiro; Koon, Wang Sang

2015-04-01

This paper explores the driving mechanisms for structural transitions of atomic clusters between oblate and prolate isomers. We employ the hyperspherical coordinates to investigate structural dynamics of a seven-atom cluster at a coarse-grained level in terms of the dynamics of three gyration radii and three principal axes, which characterize overall mass distributions of the cluster. Dynamics of gyration radii is governed by two kinds of forces. One is the potential force originating from the interactions between atoms. The other is the dynamical forces called the internal centrifugal forces, which originate from twisting and shearing motions of the system. The internal centrifugal force arising from twisting motions has an effect of breaking the symmetry between two gyration radii. As a result, in an oblate isomer, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two largest gyration radii is crucial in triggering structural transitions into prolate isomers. In a prolate isomer, on the other hand, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two smallest gyration radii is crucial in triggering structural transitions into oblate isomers. Activation of a twisting motion that switches the movement patterns of three principal axes is also important for the onset of structural transitions between oblate and prolate isomers. Based on these trigger mechanisms, we finally show that selective activations of specific gyration radii and twisting motions, depending on the isomer of the cluster, can effectively induce structural transitions of the cluster. The results presented here could provide further insights into the control of molecular reactions.

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.

Parallel processing for nonlinear dynamics simulations of structures including rotating bladed-disk assemblies

NASA Technical Reports Server (NTRS)

Hsieh, Shang-Hsien

1993-01-01

The principal objective of this research is to develop, test, and implement coarse-grained, parallel-processing strategies for nonlinear dynamic simulations of practical structural problems. There are contributions to four main areas: finite element modeling and analysis of rotational dynamics, numerical algorithms for parallel nonlinear solutions, automatic partitioning techniques to effect load-balancing among processors, and an integrated parallel analysis system.

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.

A dynamic organic soil biogeochemical model for simulating the effects of wildfire on soil environmental conditions and carbon dynamics of black spruce forests

Treesearch

Shuhua Yi; A. David McGuire; Eric Kasischke; Jennifer Harden; Kristen Manies; Michelle Mack; Merritt Turetsky

2010-01-01

Ecosystem models have not comprehensively considered how interactions among fire disturbance, soil environmental conditions, and biogeochemical processes affect ecosystem dynamics in boreal forest ecosystems. In this study, we implemented a dynamic organic soil structure in the Terrestrial Ecosystem Model (DOS-TEM) to investigate the effects of fire on soil temperature...

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.

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).

Carrier thermalization dynamics in single zincblende and wurtzite InP Nanowires.

PubMed

Wang, Yuda; Jackson, Howard E; Smith, Leigh M; Burgess, Tim; Paiman, Suriati; Gao, Qiang; Tan, Hark Hoe; Jagadish, Chennupati

2014-12-10

Using transient Rayleigh scattering (TRS) measurements, we obtain photoexcited carrier thermalization dynamics for both zincblende (ZB) and wurtzite (WZ) InP single nanowires (NW) with picosecond resolution. A phenomenological fitting model based on direct band-to-band transition theory is developed to extract the electron-hole-plasma density and temperature as a function of time from TRS measurements of single nanowires, which have complex valence band structures. We find that the thermalization dynamics of hot carriers depends strongly on material (GaAs NW vs InP NW) and less strongly on crystal structure (ZB vs WZ). The thermalization dynamics of ZB and WZ InP NWs are similar. But a comparison of the thermalization dynamics in ZB and WZ InP NWs with ZB GaAs NWs reveals more than an order of magnitude slower relaxation for the InP NWs. We interpret these results as reflecting their distinctive phonon band structures that lead to different hot phonon effects. Knowledge of hot carrier thermalization dynamics is an essential component for effective incorporation of nanowire materials into electronic devices.

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

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.

Dynamic analysis of space-related linear and non-linear structures

NASA Technical Reports Server (NTRS)

Bosela, Paul A.; Shaker, Francis J.; Fertis, Demeter G.

1990-01-01

In order to be cost effective, space structures must be extremely light weight, and subsequently, very flexible structures. The power system for Space Station Freedom is such a structure. Each array consists of a deployable truss mast and a split blanket of photo-voltaic solar collectors. The solar arrays are deployed in orbit, and the blanket is stretched into position as the mast is extended. Geometric stiffness due to the preload make this an interesting non-linear problem. The space station will be subjected to various dynamic loads, during shuttle docking, solar tracking, attitude adjustment, etc. Accurate prediction of the natural frequencies and mode shapes of the space station components, including the solar arrays, is critical for determining the structural adequacy of the components, and for designing a dynamic control system. The process used in developing and verifying the finite element dynamic model of the photo-voltaic arrays is documented. Various problems were identified, such as grounding effects due to geometric stiffness, large displacement effects, and pseudo-stiffness (grounding) due to lack of required rigid body modes. Analysis techniques, such as development of rigorous solutions using continuum mechanics, finite element solution sequence altering, equivalent systems using a curvature basis, Craig-Bampton superelement approach, and modal ordering schemes were utilized. The grounding problems associated with the geometric stiffness are emphasized.

Dynamic analysis of space-related linear and non-linear structures

NASA Technical Reports Server (NTRS)

Bosela, Paul A.; Shaker, Francis J.; Fertis, Demeter G.

1990-01-01

In order to be cost effective, space structures must be extremely light weight, and subsequently, very flexible structures. The power system for Space Station Freedom is such a structure. Each array consists of a deployable truss mast and a split blanket of photovoltaic solar collectors. The solar arrays are deployed in orbit, and the blanket is stretched into position as the mast is extended. Geometric stiffness due to the preload make this an interesting non-linear problem. The space station will be subjected to various dynamic loads, during shuttle docking, solar tracking, attitude adjustment, etc. Accurate prediction of the natural frequencies and mode shapes of the space station components, including the solar arrays, is critical for determining the structural adequacy of the components, and for designing a dynamic controls system. The process used in developing and verifying the finite element dynamic model of the photo-voltaic arrays is documented. Various problems were identified, such as grounding effects due to geometric stiffness, large displacement effects, and pseudo-stiffness (grounding) due to lack of required rigid body modes. Analysis techniques, such as development of rigorous solutions using continuum mechanics, finite element solution sequence altering, equivalent systems using a curvature basis, Craig-Bampton superelement approach, and modal ordering schemes were utilized. The grounding problems associated with the geometric stiffness are emphasized.

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.

Parametric Study of the Effect of Membrane Tension on Sunshield Dynamics

NASA Technical Reports Server (NTRS)

Ross, Brian; Johnston, John D.; Smith, James

2002-01-01

The NGST sunshield is a lightweight, flexible structure consisting of pretensioned 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. A 1/10th scale model of the sunshield has been developed for ground testing to provide data to validate modeling techniques for thin film membrane structures. The validated models can then be used to predict the behaviour of the full scale sunshield. This paper summarizes the most recent tests performed on the 1/10th scale sunshield to study the effect of membrane preload on sunshield dynamics. Topics to be covered include the test setup, procedures, and a summary of results.

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.

Age structure is critical to the population dynamics and survival of honeybee colonies.

PubMed

Betti, M I; Wahl, L M; Zamir, M

2016-11-01

Age structure is an important feature of the division of labour within honeybee colonies, but its effects on colony dynamics have rarely been explored. We present a model of a honeybee colony that incorporates this key feature, and use this model to explore the effects of both winter and disease on the fate of the colony. The model offers a novel explanation for the frequently observed phenomenon of 'spring dwindle', which emerges as a natural consequence of the age-structured dynamics. Furthermore, the results indicate that a model taking age structure into account markedly affects the predicted timing and severity of disease within a bee colony. The timing of the onset of disease with respect to the changing seasons may also have a substantial impact on the fate of a honeybee colony. Finally, simulations predict that an infection may persist in a honeybee colony over several years, with effects that compound over time. Thus, the ultimate collapse of the colony may be the result of events several years past.

Tangled nature model of evolutionary dynamics reconsidered: Structural and dynamical effects of trait inheritance

NASA Astrophysics Data System (ADS)

Andersen, Christian Walther; Sibani, Paolo

2016-05-01

Based on the stochastic dynamics of interacting agents which reproduce, mutate, and die, the tangled nature model (TNM) describes key emergent features of biological and cultural ecosystems' evolution. While trait inheritance is not included in many applications, i.e., the interactions of an agent and those of its mutated offspring are taken to be uncorrelated, in the family of TNMs introduced in this work correlations of varying strength are parametrized by a positive integer K . We first show that the interactions generated by our rule are nearly independent of K . Consequently, the structural and dynamical effects of trait inheritance can be studied independently of effects related to the form of the interactions. We then show that changing K strengthens the core structure of the ecology, leads to population abundance distributions better approximated by log-normal probability densities, and increases the probability that a species extant at time tw also survives at t >tw . Finally, survival probabilities of species are shown to decay as powers of the ratio t /tw , a so-called pure aging behavior usually seen in glassy systems of physical origin. We find a quantitative dynamical effect of trait inheritance, namely, that increasing the value of K numerically decreases the decay exponent of the species survival probability.

Tangled nature model of evolutionary dynamics reconsidered: Structural and dynamical effects of trait inheritance.

PubMed

Andersen, Christian Walther; Sibani, Paolo

2016-05-01

Based on the stochastic dynamics of interacting agents which reproduce, mutate, and die, the tangled nature model (TNM) describes key emergent features of biological and cultural ecosystems' evolution. While trait inheritance is not included in many applications, i.e., the interactions of an agent and those of its mutated offspring are taken to be uncorrelated, in the family of TNMs introduced in this work correlations of varying strength are parametrized by a positive integer K. We first show that the interactions generated by our rule are nearly independent of K. Consequently, the structural and dynamical effects of trait inheritance can be studied independently of effects related to the form of the interactions. We then show that changing K strengthens the core structure of the ecology, leads to population abundance distributions better approximated by log-normal probability densities, and increases the probability that a species extant at time t_{w} also survives at t>t_{w}. Finally, survival probabilities of species are shown to decay as powers of the ratio t/t_{w}, a so-called pure aging behavior usually seen in glassy systems of physical origin. We find a quantitative dynamical effect of trait inheritance, namely, that increasing the value of K numerically decreases the decay exponent of the species survival probability.

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".

Effects of Single Nucleotide Polymorphisms on Human N-Acetyltransferase 2 Structure and Dynamics by Molecular Dynamics Simulation

PubMed Central

Rajasekaran, M.; Abirami, Santhanam; Chen, Chinpan

2011-01-01

Background Arylamine N-acetyltransferase 2 (NAT2) is an important catalytic enzyme that metabolizes the carcinogenic arylamines, hydrazine drugs and chemicals. This enzyme is highly polymorphic in different human populations. Several polymorphisms of NAT2, including the single amino acid substitutions R64Q, I114T, D122N, L137F, Q145P, R197Q, and G286E, are classified as slow acetylators, whereas the wild-type NAT2 is classified as a fast acetylator. The slow acetylators are often associated with drug toxicity and efficacy as well as cancer susceptibility. The biological functions of these 7 mutations have previously been characterized, but the structural basis behind the reduced catalytic activity and reduced protein level is not clear. Methodology/Principal Findings We performed multiple molecular dynamics simulations of these mutants as well as NAT2 to investigate the structural and dynamical effects throughout the protein structure, specifically the catalytic triad, cofactor binding site, and the substrate binding pocket. None of these mutations induced unfolding; instead, their effects were confined to the inter-domain, domain 3 and 17-residue insert region, where the flexibility was significantly reduced relative to the wild-type. Structural effects of these mutations propagate through space and cause a change in catalytic triad conformation, cofactor binding site, substrate binding pocket size/shape and electrostatic potential. Conclusions/Significance Our results showed that the dynamical properties of all the mutant structures, especially in inter-domain, domain 3 and 17-residue insert region were affected in the same manner. Similarly, the electrostatic potential of all the mutants were altered and also the functionally important regions such as catalytic triad, cofactor binding site, and substrate binding pocket adopted different orientation and/or conformation relative to the wild-type that may affect the functions of the mutants. Overall, our study may provide the structural basis for reduced catalytic activity and protein level, as was experimentally observed for these polymorphisms. PMID:21980537

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.

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.

Effects of geometry on blast-induced loadings

NASA Astrophysics Data System (ADS)

Moore, Christopher Dyer

Simulations of blasts in an urban environment were performed using Loci/BLAST, a full-featured fluid dynamics simulation code, and analyzed. A two-structure urban environment blast case was used to perform a mesh refinement study. Results show that mesh spacing on and around the structure must be 12.5 cm or less to resolve fluid dynamic features sufficiently to yield accurate results. The effects of confinement were illustrated by analyzing a blast initiated from the same location with and without the presence of a neighboring structure. Analysis of extreme pressures and impulses on structures showed that confinement can increase blast loading by more than 200 percent.

MODELING MICROBUBBLE DYNAMICS IN BIOMEDICAL APPLICATIONS*

PubMed Central

CHAHINE, Georges L.; HSIAO, Chao-Tsung

2012-01-01

Controlling microbubble dynamics to produce desirable biomedical outcomes when and where necessary and avoid deleterious effects requires advanced knowledge, which can be achieved only through a combination of experimental and numerical/analytical techniques. The present communication presents a multi-physics approach to study the dynamics combining viscous- in-viscid effects, liquid and structure dynamics, and multi bubble interaction. While complex numerical tools are developed and used, the study aims at identifying the key parameters influencing the dynamics, which need to be included in simpler models. PMID:22833696

Improved global simulation of groundwater-ecosystem interactions via tight coupling of a dynamic global ecosystem model and a global hydrological model

NASA Astrophysics Data System (ADS)

Braakhekke, Maarten; Rebel, Karin; Dekker, Stefan; Smith, Benjamin; Sutanudjaja, Edwin; van Beek, Rens; van Kampenhout, Leo; Wassen, Martin

2017-04-01

In up to 30% of the global land surface ecosystems are potentially influenced by the presence of a shallow groundwater table. In these regions upward water flux by capillary rise increases soil moisture availability in the root zone, which has a strong effect on evapotranspiration, vegetation dynamics, and fluxes of carbon and nitrogen. Most global hydrological models and several land surface models simulate groundwater table dynamics and their effects on land surface processes. However, these models typically have relatively simplistic representation of vegetation and do not consider changes in vegetation type and structure. Dynamic global vegetation models (DGVMs), describe land surface from an ecological perspective, combining detailed description of vegetation dynamics and structure, and biogeochemical processes and are thus more appropriate to simulate the ecological and biogeochemical effects of groundwater interactions. However, currently virtually all DGVMs ignore these effects, assuming that water tables are too deep to affect soil moisture in the root zone. We have implemented a tight coupling between the dynamic global ecosystem model LPJ-GUESS and the global hydrological model PCR-GLOBWB, which explicitly simulates groundwater dynamics. This coupled model allows us to explicitly account for groundwater effects on terrestrial ecosystem processes at global scale. Results of global simulations indicate that groundwater strongly influences fluxes of water, carbon and nitrogen, in many regions, adding up to a considerable effect at the global scale.

Effect of short-chain branching on interfacial polymer structure and dynamics under shear flow.

PubMed

Jeong, Sohdam; Kim, Jun Mo; Cho, Soowon; Baig, Chunggi

2017-11-22

We present a detailed analysis on the effect of short-chain branches on the structure and dynamics of interfacial chains using atomistic nonequilibrium molecular dynamics simulations of confined polyethylene melts in a wide range of shear rates. The intrinsically fast random motions of the short branches constantly disturb the overall chain conformation, leading to a more compact and less deformed chain structure of the short-chain branched (SCB) polymer against the imposed flow field in comparison with the corresponding linear polymer. Moreover, such highly mobile short branches along the backbone of the SCB polymer lead to relatively weaker out-of-plane wagging dynamics of interfacial chains, with highly curvy backbone structures in the intermediate flow regime. In conjunction with the contribution of short branches (as opposed to that of the backbone) to the total interfacial friction between the chains and the wall, the SCB polymer shows a nearly constant behavior in the degree of slip (d s ) with respect to shear rate in the weak-to-intermediate flow regimes. On the contrary, in the strong flow regime where irregular chain rotation and tumbling dynamics occur via intensive dynamical collisions between interfacial chains and the wall, an enhancement effect on the chain detachment from the wall, caused by short branches, leads to a steeper increase in d s for the SCB polymer than for the linear polymer. Remarkably, the SCB chains at the interface exhibit two distinct types of rolling mechanisms along the backbone, with a half-dumbbell mesoscopic structure at strong flow fields, in addition to the typical hairpin-like tumbling behavior displayed by the linear chains.

Sulfation effect on levan polysaccharide chains structure with molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Coskunkan, Binnaz; Turgut, Deniz; Rende, Deniz; Malta, Seyda; Baysal, Nihat; Ozisik, Rahmi; Toksoy-Oner, Ebru

Diversity in conformations and structural heterogeneity make polysaccharides the most challenging biopolymer type for experimental and theoretical characterization studies. Levan is a biopolymer chain that consists of fructose rings with β(2-6) linkages. It is a glycan that has great potential as a functional biopolymer in foods, feeds, cosmetics, pharmaceutical and chemical industries. Sulfated polysaccharides are group of macromolecules with sulfated groups in their hydroxyl parts with a range of important biological properties. Sulfate groups and their positions have a major effect on anticoagulant activity. It is reported that sulfate modified levan has anticoagulant activity such as heparin. In the current study, the effect of sulfation on the structure and dynamics of unmodified and sulfate modified levan are investigated via fully atomistic Molecular Dynamics simulations in aqueous media and varying salt concentrations at 310 K. This material is based upon work supported by the National Science Foundation under Grant No. CMMI-1538730.

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.

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.

Bi-layer plate-type acoustic metamaterials with Willis coupling

NASA Astrophysics Data System (ADS)

Ma, Fuyin; Huang, Meng; Xu, Yicai; Wu, Jiu Hui

2018-01-01

Dynamic effective negative parameters are principal to the representation of the physical properties of metamaterials. In this paper, a bi-layer plate-type unit was proposed with both a negative mass density and a negative bulk modulus; moreover, through analysis of these bi-layer structures, some important problems about acoustic metamaterials were studied. First, dynamic effective mass densities and the bulk modulus of the bi-layer plate-type acoustic structure were clarified through both the direct and the retrieval methods, and, in addition, the intrinsic relationship between the sound transmission (absorption) characteristics and the effective parameters was analyzed. Furthermore, the properties of dynamic effective parameters for an asymmetric bi-layer acoustic structure were further considered through an analysis of experimental data, and the modified effective parameters were then obtained through consideration of the Willis coupling in the asymmetric passive system. In addition, by taking both the clamped and the periodic boundary conditions into consideration in the bi-layer plate-type acoustic system, new perspectives were presented for study on the effective parameters and sound insulation properties in the range below the cut-off frequency. The special acoustic properties established by these effective parameters could enrich our knowledge and provide guidance for the design and installation of acoustic metamaterial structures in future sound engineering practice.

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.

Computational Methods for Nonlinear Dynamic Problems in Solid and Structural Mechanics: Progress in the Theory and Modeling of Friction and in the Control of Dynamical Systems with Frictional Forces

DTIC Science & Technology

1989-03-31

present several numerical studies designed to reveal the effect that some of the governing parameters have on the behavior of the system and, whenever...Friction and in the Control of Dynamical Systems with Frictional Forces FINAL TECHNICAL REPORT March 31, 1989 _ -- I -.7: .-.- - : AFOSR Contract F49620...SOLID AND STRUCTURAL MECHANICS: Progress in the Theory and Modeling of Friction and in the Control of Dynamical Systems with Frictional Forces I I * FINAL

Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm

PubMed Central

Yu, Isseki; Mori, Takaharu; Ando, Tadashi; Harada, Ryuhei; Jung, Jaewoon; Sugita, Yuji; Feig, Michael

2016-01-01

Biological macromolecules function in highly crowded cellular environments. The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. Protein-protein interactions also resulted in significant variations in reduced macromolecular diffusion under crowded conditions, while metabolites exhibited significant two-dimensional surface diffusion and altered protein-ligand binding that may reduce the effective concentration of metabolites and ligands in vivo. Metabolic enzymes showed weak non-specific association in cellular environments attributed to solvation and entropic effects. These effects are expected to have broad implications for the in vivo functioning of biomolecules. This work is a first step towards physically realistic in silico whole-cell models that connect molecular with cellular biology. DOI: http://dx.doi.org/10.7554/eLife.19274.001 PMID:27801646

Structure and dynamics of a silica melt in neutral confinement

NASA Astrophysics Data System (ADS)

Geske, Julian; Drossel, Barbara; Vogel, Michael

2017-04-01

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

Structure and dynamics of a silica melt in neutral confinement.

PubMed

Geske, Julian; Drossel, Barbara; Vogel, Michael

2017-04-07

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

The effect of intact talin and talin tail fragment on actin filament dynamics and structure depends on pH and ionic strength.

PubMed

Goldmann, W H; Hess, D; Isenberg, G

1999-03-01

We employed quasi-elastic light scattering and electron microscopy to investigate the influence of intact talin and talin tail fragment on actin filament dynamics and network structure. Using these methods, we confirm previous reports that intact talin induces cross-linking as well as filament shortening on actin networks. We now show that the effect of intact talin as well as talin tail fragment on actin networks is controlled by pH and ionic strength. At pH 7.5, actin filament dynamics in the presence of intact talin and talin tail fragment are characterized by a rapid decay of the dynamic structure factor and by a square root power law for the stretched exponential decay which is in contrast with the theory for pure actin solutions. At pH 6 and low ionic strength, intact talin cross-links actin filaments more tightly than talin tail fragment. Talin head fragment showed no effect on actin networks, indicating that the actin binding sites reside probably exclusively within the tail domain.

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.

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.

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.

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.

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

A Dynamic Model of Sustainment Investment

DTIC Science & Technology

2015-02-01

Sustainment System Dynamics Model 11 Figure 7: Core Structure of Sustainment Work 12 Figure 8: Bandwagon Effect Loop 13 Figure 9: Limits to Growth Loop 14...Dynamics Model sustainment capacity sustainment performance gap Bandwagon Effect R1 Limits to Growth B1 S Work Smarter B3 Work Bigger B2 desired...which is of concern primarily when using the model as a vehicle for research. Figure 8 depicts a reinforcing loop called the “ Bandwagon Effect

Effects of the bond polarity on the structural and dynamical properties of silica-like liquids

NASA Astrophysics Data System (ADS)

Pafong Sanjon, E.; Drossel, B.; Vogel, M.

2018-03-01

Silica is a network-forming liquid that shares many properties with water due to its tetrahedral structure. It undergoes a transition from a fragile to a strong liquid as the temperature is decreased, which is accompanied by a structural change to lower density and higher tetrahedral order. In order to disentangle the effects of Coulomb and van der Waals interactions on the structure and dynamics of liquid silica, we modify the bond polarity by changing the partial charges assigned to each atom. Using molecular dynamics simulations, we show that density, tetrahedral order, and structural relaxation times decrease when reducing bond polarity. Moreover, we find that the density maximum and the fragile-to-strong transition move to lower temperatures until they eventually vanish when the partial charges are decreased below approximately 75% of their regular value. Irrespective of whether strong or fragile behavior exists, structural relaxation is governed by hopping motion at sufficiently low temperatures. As long as there is a strong regime, the energy barrier associated with strong dynamics decreases with decreasing partial charges, but the dependence on the bond polarity differs from that of the activation energy in the Arrhenius regime at high temperatures. We show that the fragile-to-strong transition is associated with structural changes occurring between the first and second coordination shells that lead to a decrease in density and an increase in tetrahedral order. In particular, independent of the value of the partial charges, the distribution of the local structures is the same at this dynamic crossover, but we find no evidence that the effect occurs upon crossing the Widom line. In the fragile regime at intermediate temperatures, the relaxation times are well described by a previously proposed model which decomposes the apparent activation energy into a constant single-particle contribution and a temperature-dependent collective contribution. However, our results for silica-like melts do not obey several common relations of the model parameters reported for molecular glass formers.

Exploring GPCR-Lipid Interactions by Molecular Dynamics Simulations: Excitements, Challenges, and the Way Forward.

PubMed

Sengupta, Durba; Prasanna, Xavier; Mohole, Madhura; Chattopadhyay, Amitabha

2018-06-07

Gprotein-coupled receptors (GPCRs) are seven transmembrane receptors that mediate a large number of cellular responses and are important drug targets. One of the current challenges in GPCR biology is to analyze the molecular signatures of receptor-lipid interactions and their subsequent effects on GPCR structure, organization, and function. Molecular dynamics simulation studies have been successful in predicting molecular determinants of receptor-lipid interactions. In particular, predicted cholesterol interaction sites appear to correspond well with experimentally determined binding sites and estimated time scales of association. In spite of several success stories, the methodologies in molecular dynamics simulations are still emerging. In this Feature Article, we provide a comprehensive overview of coarse-grain and atomistic molecular dynamics simulations of GPCR-lipid interaction in the context of experimental observations. In addition, we discuss the effect of secondary and tertiary structural constraints in coarse-grain simulations in the context of functional dynamics and structural plasticity of GPCRs. We envision that this comprehensive overview will help resolve differences in computational studies and provide a way forward.

Polarizability effects on the structure and dynamics of ionic liquids

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

Cavalcante, Ary de Oliveira, E-mail: arycavalcante@ufam.edu.br; Departamento de Química, Universidade Federal do Amazonas, Av. Rodrigo Octávio, 6200, Coroado, Manaus, AM; Ribeiro, Mauro C. C.

2014-04-14

Polarization effects on the structure and dynamics of ionic liquids are investigated using molecular dynamics simulations. Four different ionic liquids were simulated, formed by the anions Cl{sup −} and PF{sub 6}{sup −}, treated as single fixed charge sites, and the 1-n-alkyl-3-methylimidazolium cations (1-ethyl and 1-butyl-), which are polarizable. The partial charge fluctuation of the cations is provided by the electronegativity equalization model (EEM) and a complete parameter set for the cations electronegativity (χ) and hardness (J) is presented. Results obtained from a non-polarizable model for the cations are also reported for comparison. Relative to the fixed charged model, the equilibriummore » structure of the first solvation shell around the imidazolium cations shows that inclusion of EEM polarization forces brings cations closer to each other and that anions are preferentially distributed above and below the plane of the imidazolium ring. The polarizable model yields faster translational and reorientational dynamics than the fixed charges model in the rotational-diffusion regime. In this sense, the polarizable model dynamics is in better agreement with the experimental data.« less

Structural dynamics of surfaces by ultrafast electron crystallography: experimental and multiple scattering theory.

PubMed

Schäfer, Sascha; Liang, Wenxi; Zewail, Ahmed H

2011-12-07

Recent studies in ultrafast electron crystallography (UEC) using a reflection diffraction geometry have enabled the investigation of a wide range of phenomena on the femtosecond and picosecond time scales. In all these studies, the analysis of the diffraction patterns and their temporal change after excitation was performed within the kinematical scattering theory. In this contribution, we address the question, to what extent dynamical scattering effects have to be included in order to obtain quantitative information about structural dynamics. We discuss different scattering regimes and provide diffraction maps that describe all essential features of scatterings and observables. The effects are quantified by dynamical scattering simulations and examined by direct comparison to the results of ultrafast electron diffraction experiments on an in situ prepared Ni(100) surface, for which structural dynamics can be well described by a two-temperature model. We also report calculations for graphite surfaces. The theoretical framework provided here allows for further UEC studies of surfaces especially at larger penetration depths and for those of heavy-atom materials. © 2011 American Institute of Physics

Atomic structure and dynamics properties of Cu50Zr50 films

NASA Astrophysics Data System (ADS)

Chen, Heng; Qu, Bingyan; Li, Dongdong; Zhou, Rulong; Zhang, Bo

2018-01-01

In this paper, the structural and dynamic properties of Cu50Zr50 films are investigated by molecular dynamics simulations. Our results show that the dynamics of the surface atoms are much faster than those of the bulk. Especially, the diffusion coefficient of the surface atoms is about forty times larger than that of the bulk at 600 K, which qualitatively agrees with the experimental results. Meanwhile, we find that the population of the icosahedral (-like) clusters in the surface region is obviously higher than that of the bulk, which prevents the surface from crystallization. A new method to determine the string-like collective atomic motion is introduced in the paper, and it suggests a possible connection between the glass formation ability and collective atomic motion. By using the method, the effects of surface on collective motion are illustrated. Our results show that the string-like collective atomic motion of surface atoms is weakened while that of the interior atoms is strengthened. The studies clearly explain the effects of surface on the structural and dynamic properties of Cu50Zr50 films from the atomic scale.

Analysis of flexible aircraft longitudinal dynamics and handling qualities. Volume 2: Data

NASA Technical Reports Server (NTRS)

Waszak, M. R.; Schmidt, D. K.

1985-01-01

Two analysis methods are applied to a family of flexible aircraft in order to investigate how and when structural (especially dynamic aeroelastic) effects affect the dynamic characteristics of aircraft. The first type of analysis is an open loop modal analysis technique. This method considers the effect of modal residue magnitudes on determining vehicle handling qualities. The second method is a pilot in the loop analysis procedure that considers several closed loop system characteristics. Both analyses indicated that dynamic aeroelastic effects caused a degradation in vehicle tracking performance, based on the evaluation of some simulation results. Volume 2 consists of the presentation of the state variable models of the flexible aircraft configurations used in the analysis applications mode shape plots for the structural modes, numerical results from the modal analysis frequency response plots from the pilot in the loop analysis and a listing of the modal analysis computer program.

A structural and theoretical study of the alkylammonium nitrates forefather: Liquid methylammonium nitrate

NASA Astrophysics Data System (ADS)

Gontrani, Lorenzo; Caminiti, Ruggero; Salma, Umme; Campetella, Marco

2017-09-01

We present here a structural and vibrational analysis of melted methylammonium nitrate, the simplest compound of the family of alkylammonium nitrates. The static and dynamical features calculated were endorsed by comparing the experimental X-ray data with the theoretical ones. A reliable description cannot be obtained with classical molecular dynamics owing to polarization effects. Contrariwise, the structure factor and the vibrational frequencies obtained from ab initio molecular dynamics trajectories are in very good agreement with the experiment. A careful analysis has provided additional information on the complex hydrogen bonding network that exists in this liquid.

Dynamics of climate-based malaria transmission model with age-structured human population

NASA Astrophysics Data System (ADS)

Addawe, Joel; Pajimola, Aprimelle Kris

2016-10-01

In this paper, we proposed to study the dynamics of malaria transmission with periodic birth rate of the vector and an age-structure for the human population. The human population is divided into two compartments: pre-school (0-5 years) and the rest of the human population. We showed the existence of a disease-free equilibrium point. Using published epidemiological parameters, we use numerical simulations to show potential effect of climate change in the dynamics of age-structured malaria transmission. Numerical simulations suggest that there exists an asymptotically attractive solution that is positive and periodic.

Toward calculations of the 129Xe chemical shift in Xe@C60 at experimental conditions: relativity, correlation, and dynamics.

PubMed

Straka, Michal; Lantto, Perttu; Vaara, Juha

2008-03-27

We calculate the 129Xe chemical shift in endohedral Xe@C60 with systematic inclusion of the contributing physical effects to model the real experimental conditions. These are relativistic effects, electron correlation, the temperature-dependent dynamics, and solvent effects. The ultimate task is to obtain the right result for the right reason and to develop a physically justified methodological model for calculations and simulations of endohedral Xe fullerenes and other confined Xe systems. We use the smaller Xe...C6H6 model to calibrate density functional theory approaches against accurate correlated wave function methods. Relativistic effects as well as the coupling of relativity and electron correlation are evaluated using the leading-order Breit-Pauli perturbation theory. The dynamic effects are treated in two ways. In the first approximation, quantum dynamics of the Xe atom in a rigid cage takes advantage of the centrosymmetric potential for Xe within the thermally accessible distance range from the center of the cage. This reduces the problem of obtaining the solution of a diatomic rovibrational problem. In the second approach, first-principles classical molecular dynamics on the density functional potential energy hypersurface is used to produce the dynamical trajectory for the whole system, including the dynamic cage. Snapshots from the trajectory are used for calculations of the dynamic contribution to the absorption 129Xe chemical shift. The calculated nonrelativistic Xe shift is found to be highly sensitive to the optimized molecular structure and to the choice of the exchange-correlation functional. Relativistic and dynamic effects are significant and represent each about 10% of the nonrelativistic static shift at the minimum structure. While the role of the Xe dynamics inside of the rigid cage is negligible, the cage dynamics turns out to be responsible for most of the dynamical correction to the 129Xe shift. Solvent effects evaluated with a polarized continuum model are found to be very small.

Allosteric effects of gold nanoparticles on human serum albumin.

PubMed

Shao, Qing; Hall, Carol K

2017-01-07

The ability of nanoparticles to alter protein structure and dynamics plays an important role in their medical and biological applications. We investigate allosteric effects of gold nanoparticles on human serum albumin protein using molecular simulations. The extent to which bound nanoparticles influence the structure and dynamics of residues distant from the binding site is analyzed. The root mean square deviation, root mean square fluctuation and variation in the secondary structure of individual residues on a human serum albumin protein are calculated for four protein-gold nanoparticle binding complexes. The complexes are identified in a brute-force search process using an implicit-solvent coarse-grained model for proteins and nanoparticles. They are then converted to atomic resolution and their structural and dynamic properties are investigated using explicit-solvent atomistic molecular dynamics simulations. The results show that even though the albumin protein remains in a folded structure, the presence of a gold nanoparticle can cause more than 50% of the residues to decrease their flexibility significantly, and approximately 10% of the residues to change their secondary structure. These affected residues are distributed on the whole protein, even on regions that are distant from the nanoparticle. We analyze the changes in structure and flexibility of amino acid residues on a variety of binding sites on albumin and confirm that nanoparticles could allosterically affect the ability of albumin to bind fatty acids, thyroxin and metals. Our simulations suggest that allosteric effects must be considered when designing and deploying nanoparticles in medical and biological applications that depend on protein-nanoparticle interactions.

Landscape matrix mediates occupancy dynamics of Neotropical avian insectivores

USGS Publications Warehouse

Kennedy, Christina M.; Campbell Grant, Evan H.; Neel, Maile C.; Fagan, William F.; Marpa, Peter P.

2011-01-01

In addition to patch-level attributes (i.e., area and isolation), the nature of land cover between habitat patches (the matrix) may drive colonization and extinction dynamics in fragmented landscapes. Despite a long-standing recognition of matrix effects in fragmented systems, an understanding of the relative impacts of different types of land cover on patterns and dynamics of species occurrence remains limited. We employed multi-season occupancy models to determine the relative influence of patch area, patch isolation, within-patch vegetation structure, and landscape matrix on occupancy dynamics of nine Neotropical nsectivorous birds in 99 forest patches embedded in four matrix types (agriculture, suburban evelopment, bauxite mining, and forest) in central Jamaica. We found that within-patch vegetation structure and the matrix type between patches were more important than patch area and patch isolation in determining local colonization and local extinction probabilities, and that the effects of patch area, isolation, and vegetation structure on occupancy dynamics tended to be matrix and species dependent. Across the avian community, the landscape matrix influenced local extinction more than local colonization, indicating that extinction processes, rather than movement, likely drive interspecific differences in occupancy dynamics. These findings lend crucial empirical support to the hypothesis that species occupancy dynamics in fragmented systems may depend greatly upon the landscape context.

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.

Effect of gold nanoparticles on structure and dynamics of binary Lennard-Jones liquid: Wave-vector space analysis

NASA Astrophysics Data System (ADS)

Separdar, L.; Davatolhagh, S.

2016-12-01

Molecular dynamics simulations at constant (N , V , T) are used to study the mutual effects of gold nanoparticles on the structure and dynamics of Kob-Andersen binary Lennard-Jones (BLJ) liquid within the framework of mode coupling theory of dynamic glass transition in the reciprocal space. The results show the 'softening' effect of the gold nanoparticles on the liquid dynamics in terms of (i) reducing the mode coupling crossover temperature Tc with respect to that of the bulk BLJ (i.e. BLJ without nanoparticles), (ii) decreasing the time interval of β-relaxation, and (iii) decreasing the exponent γ characterizing the power-law behavior of the α-relaxation time. This softening effect is explained in terms of the van der Waals attraction between the gold atoms comprising the nanoparticle and the BLJ host atoms, such that adsorption of host atoms onto the nanoparticle surface creates more space or free-volume for the other atoms to diffuse. By the same token interactions of purely excluded-volume-type are expected to result in the opposite effect. It is also noted that, much unlike BLJ host particles, the dynamics of gold nanoparticles is much less dependent on the wave-vector and that it exhibits a nearly exponential behavior in the α-relaxation regime.

Diagnostic tool for structural health monitoring: effect of material nonlinearity and vibro-impact process

NASA Astrophysics Data System (ADS)

Hiwarkar, V. R.; Babitsky, V. I.; Silberschmidt, V. V.

2013-07-01

Numerous techniques are available for monitoring structural health. Most of these techniques are expensive and time-consuming. In this paper, vibration-based techniques are explored together with their use as diagnostic tools for structural health monitoring. Finite-element simulations are used to study the effect of material nonlinearity on dynamics of a cracked bar. Additionally, several experiments are performed to study the effect of vibro-impact behavior of crack on its dynamics. It was observed that a change in the natural frequency of the cracked bar due to crack-tip plasticity and vibro-impact behavior linked to interaction of crack faces, obtained from experiments, led to generation of higher harmonics; this can be used as a diagnostic tool for structural health monitoring.

Dynamic response analysis of structure under time-variant interval process model

NASA Astrophysics Data System (ADS)

Xia, Baizhan; Qin, Yuan; Yu, Dejie; Jiang, Chao

2016-10-01

Due to the aggressiveness of the environmental factor, the variation of the dynamic load, the degeneration of the material property and the wear of the machine surface, parameters related with the structure are distinctly time-variant. Typical model for time-variant uncertainties is the random process model which is constructed on the basis of a large number of samples. In this work, we propose a time-variant interval process model which can be effectively used to deal with time-variant uncertainties with limit information. And then two methods are presented for the dynamic response analysis of the structure under the time-variant interval process model. The first one is the direct Monte Carlo method (DMCM) whose computational burden is relative high. The second one is the Monte Carlo method based on the Chebyshev polynomial expansion (MCM-CPE) whose computational efficiency is high. In MCM-CPE, the dynamic response of the structure is approximated by the Chebyshev polynomials which can be efficiently calculated, and then the variational range of the dynamic response is estimated according to the samples yielded by the Monte Carlo method. To solve the dependency phenomenon of the interval operation, the affine arithmetic is integrated into the Chebyshev polynomial expansion. The computational effectiveness and efficiency of MCM-CPE is verified by two numerical examples, including a spring-mass-damper system and a shell structure.

Using NMR and molecular dynamics to link structure and dynamics effects of the universal base 8-aza, 7-deaza, N8 linked adenosine analog

PubMed Central

Spring-Connell, Alexander M.; Evich, Marina G.; Debelak, Harald; Seela, Frank; Germann, Markus W.

2016-01-01

A truly universal nucleobase enables a host of novel applications such as simplified templates for PCR primers, randomized sequencing and DNA based devices. A universal base must pair indiscriminately to each of the canonical bases with little or preferably no destabilization of the overall duplex. In reality, many candidates either destabilize the duplex or do not base pair indiscriminatingly. The novel base 8-aza-7-deazaadenine (pyrazolo[3,4-d]pyrimidin- 4-amine) N8-(2′deoxyribonucleoside), a deoxyadenosine analog (UB), pairs with each of the natural DNA bases with little sequence preference. We have utilized NMR complemented with molecular dynamic calculations to characterize the structure and dynamics of a UB incorporated into a DNA duplex. The UB participates in base stacking with little to no perturbation of the local structure yet forms an unusual base pair that samples multiple conformations. These local dynamics result in the complete disappearance of a single UB proton resonance under native conditions. Accommodation of the UB is additionally stabilized via heightened backbone conformational sampling. NMR combined with various computational techniques has allowed for a comprehensive characterization of both structural and dynamic effects of the UB in a DNA duplex and underlines that the UB as a strong candidate for universal base applications. PMID:27566150

Characterization of the hydrogen-bond network of water around sucrose and trehalose: Microwave and terahertz spectroscopic study

NASA Astrophysics Data System (ADS)

Shiraga, Keiichiro; Adachi, Aya; Nakamura, Masahito; Tajima, Takuro; Ajito, Katsuhiro; Ogawa, Yuichi

2017-03-01

Modification of the water hydrogen bond network imposed by disaccharides is known to serve as a bioprotective agent in living organisms, though its comprehensive understanding is still yet to be reached. In this study, aiming to characterize the dynamical slowing down and destructuring effect of disaccharides, we performed broadband dielectric spectroscopy, ranging from 0.5 GHz to 12 THz, of sucrose and trehalose aqueous solutions. The destructuring effect was examined in two ways (the hydrogen bond fragmentation and disordering) and our result showed that both sucrose and trehalose exhibit an obvious destructuring effect with a similar strength, by fragmenting hydrogen bonds and distorting the tetrahedral-like structure of water. This observation strongly supports a chaotropic (structure-breaking) aspect of disaccharides on the water structure. At the same time, hydration water was found to exhibit slower dynamics and a greater reorientational cooperativity than bulk water because of the strengthened hydrogen bonds. These results lead to the conclusion that strong disaccharide-water hydrogen bonds structurally incompatible with native water-water bonds lead to the rigid but destructured hydrogen bond network around disaccharides. Another important finding in this study is that the greater dynamical slowing down of trehalose was found compared with that of sucrose, at variance with the destructuring effect where no solute dependent difference was observed. This discovery suggests that the exceptionally greater bioprotective impact especially of trehalose among disaccharides is mainly associated with the dynamical slowing down (rather than the destructuring effect).

Climate effects and feedback structure determining weed population dynamics in a long-term experiment.

PubMed

Lima, Mauricio; Navarrete, Luis; González-Andujar, José Luis

2012-01-01

Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years) on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors). Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements.

Climate Effects and Feedback Structure Determining Weed Population Dynamics in a Long-Term Experiment

PubMed Central

Lima, Mauricio; Navarrete, Luis; González-Andujar, José Luis

2012-01-01

Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years) on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors). Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements. PMID:22272362

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.

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.

Communication: Influence of external static and alternating electric fields on water from long-time non-equilibrium ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Futera, Zdenek; English, Niall J.

2017-07-01

The response of water to externally applied electric fields is of central relevance in the modern world, where many extraneous electric fields are ubiquitous. Historically, the application of external fields in non-equilibrium molecular dynamics has been restricted, by and large, to relatively inexpensive, more or less sophisticated, empirical models. Here, we report long-time non-equilibrium ab initio molecular dynamics in both static and oscillating (time-dependent) external electric fields, therefore opening up a new vista in rigorous studies of electric-field effects on dynamical systems with the full arsenal of electronic-structure methods. In so doing, we apply this to liquid water with state-of-the-art non-local treatment of dispersion, and we compute a range of field effects on structural and dynamical properties, such as diffusivities and hydrogen-bond kinetics.

A Method to Capture Macroslip at Bolted Interfaces

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

Hopkins, Ronald Neil; Heitman, Lili Anne Akin

2015-10-01

Relative motion at bolted connections can occur for large shock loads as the internal shear force in the bolted connection overcomes the frictional resistive force. This macroslip in a structure dissipates energy and reduces the response of the components above the bolted connection. There is a need to be able to capture macroslip behavior in a structural dynamics model. A linear model and many nonlinear models are not able to predict marcoslip effectively. The proposed method to capture macroslip is to use the multi-body dynamics code ADAMS to model joints with 3-D contact at the bolted interfaces. This model includesmore » both static and dynamic friction. The joints are preloaded and the pinning effect when a bolt shank impacts a through hole inside diameter is captured. Substructure representations of the components are included to account for component flexibility and dynamics. This method was applied to a simplified model of an aerospace structure and validation experiments were performed to test the adequacy of the method.« less

A Method to Capture Macroslip at Bolted Interfaces [PowerPoint

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

Hopkins, Ronald Neil; Heitman, Lili Anne Akin

2016-01-01

Relative motion at bolted connections can occur for large shock loads as the internal shear force in the bolted connection overcomes the frictional resistive force. This macroslip in a structure dissipates energy and reduces the response of the components above the bolted connection. There is a need to be able to capture macroslip behavior in a structural dynamics model. A linear model and many nonlinear models are not able to predict marcoslip effectively. The proposed method to capture macroslip is to use the multi-body dynamics code ADAMS to model joints with 3-D contact at the bolted interfaces. This model includesmore » both static and dynamic friction. The joints are preloaded and the pinning effect when a bolt shank impacts a through hole inside diameter is captured. Substructure representations of the components are included to account for component flexibility and dynamics. This method was applied to a simplified model of an aerospace structure and validation experiments were performed to test the adequacy of the method.« less

Age structure is critical to the population dynamics and survival of honeybee colonies

PubMed Central

Betti, M. I.; Wahl, L. M.

2016-01-01

Age structure is an important feature of the division of labour within honeybee colonies, but its effects on colony dynamics have rarely been explored. We present a model of a honeybee colony that incorporates this key feature, and use this model to explore the effects of both winter and disease on the fate of the colony. The model offers a novel explanation for the frequently observed phenomenon of ‘spring dwindle’, which emerges as a natural consequence of the age-structured dynamics. Furthermore, the results indicate that a model taking age structure into account markedly affects the predicted timing and severity of disease within a bee colony. The timing of the onset of disease with respect to the changing seasons may also have a substantial impact on the fate of a honeybee colony. Finally, simulations predict that an infection may persist in a honeybee colony over several years, with effects that compound over time. Thus, the ultimate collapse of the colony may be the result of events several years past. PMID:28018627

Effects of random initial conditions on the dynamical scaling behaviors of a fixed-energy Manna sandpile model in one dimension

NASA Astrophysics Data System (ADS)

Kwon, Sungchul; Kim, Jin Min

2015-01-01

For a fixed-energy (FE) Manna sandpile model in one dimension, we investigate the effects of random initial conditions on the dynamical scaling behavior of an order parameter. In the FE Manna model, the density ρ of total particles is conserved, and an absorbing phase transition occurs at ρc as ρ varies. In this work, we show that, for a given ρ , random initial distributions of particles lead to the domain structure in which domains with particle densities higher and lower than ρc alternate with each other. In the domain structure, the dominant length scale is the average domain length, which increases via the coalescence of adjacent domains. At ρc, the domain structure slows down the decay of an order parameter and also causes anomalous finite-size effects, i.e., power-law decay followed by an exponential one before the quasisteady state. As a result, the interplay of particle conservation and random initial conditions causes the domain structure, which is the origin of the anomalous dynamical scaling behaviors for random initial conditions.

The Effect of Complex Solvents on the Structure and Dynamics of Protein Solutions: the case of Lysozyme in Trehalose/Water Mixtures

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

Ghattyvenkatakrishna, Pavan K; Carri, Gustavo A.

We present a Molecular Dynamics simulation study of the effect of trehalose concentration on the structure and dynamics of individual proteins immersed in trehalose/water mixtures. Hen Egg White Lysozyme is used in this study and trehalose concentrations of 0%, 10%, 20%, 30% and 100% by weight are explored. Surprisingly, we have found that changes in trehalose concentration do not change the global structural characteristics of the protein as measured by standard quantities like the mean square deviation, radius of gyration, solvent accessible surface area, inertia tensor and asphericity. Only in the limit of pure trehalose these metrics change significantly. Specifically,more » we found that the protein is compressed by 2% when immersed in pure trehalose. At the amino acid level there is noticeable rearrangement of the surface residues due to the change in polarity of the surrounding environment with the addition of trehalose. From a dynamic perspective, our computation of the Incoherent Intermediate Scattering Function shows that the protein slows down with increasing trehalose concentration; however, this slowdown is not monotonic. Finally, we also report in-depth results for the hydration layer around the protein including its structure, hydrogen- bonding characteristics and dynamic behavior at different length scales.« less

Hierarchical Process Composition: Dynamic Maintenance of Structure in a Distributed Environment

DTIC Science & Technology

1988-01-01

One prominent hne of research stresses the independence of address space and thread of control, and the resulting efficiencies due to shared memory...cooperating processes. StarOS focuses on case of use and a general capability mechanism, while Medusa stresses the effect of distributed hardware on system...process structure and the asynchrony among agents and between agents and sources of failure. By stressing dynamic structure, we are led to adopt an

Coherent dynamic structure factors of strongly coupled plasmas: A generalized hydrodynamic approach

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

Luo, Di; Hu, GuangYue; Gong, Tao

2016-05-15

A generalized hydrodynamic fluctuation model is proposed to simplify the calculation of the dynamic structure factor S(ω, k) of non-ideal plasmas using the fluctuation-dissipation theorem. In this model, the kinetic and correlation effects are both included in hydrodynamic coefficients, which are considered as functions of the coupling strength (Γ) and collision parameter (kλ{sub ei}), where λ{sub ei} is the electron-ion mean free path. A particle-particle particle-mesh molecular dynamics simulation code is also developed to simulate the dynamic structure factors, which are used to benchmark the calculation of our model. A good agreement between the two different approaches confirms the reliabilitymore » of our model.« less

Multidecadal stability in tropical rain forest structure and dynamics across an old-growth landscape

PubMed Central

Clark, Deborah A.; Oberbauer, Steven F.; Kellner, James R.

2017-01-01

Have tropical rain forest landscapes changed directionally through recent decades? To answer this question requires tracking forest structure and dynamics through time and across within-forest environmental heterogeneity. While the impacts of major environmental gradients in soil nutrients, climate and topography on lowland tropical rain forest (TRF) structure and function have been extensively analyzed, the effects of the shorter environmental gradients typical of mesoscale TRF landscapes remain poorly understood. To evaluate multi-decadal performance of an old-growth TRF at the La Selva Biological Station, Costa Rica, we established 18 0.5-ha annually-censused forest inventory plots in a stratified-random design across major landscape edaphic gradients. Over the 17-year study period, there were moderate differences in stand dynamics and structure across these gradients but no detectable difference in woody productivity. We found large effects on forest structure and dynamics from the mega-Niño event at the outset of the study, with subdecadal recovery and subsequent stabilization. To extend the timeline to >40 years, we combined our findings with those from earlier studies at this site. While there were annual to multiannual variations in the structure and dynamics, particularly in relation to local disturbances and the mega-Niño event, at the longer temporal scale and broader spatial scale this landscape was remarkably stable. This stability contrasts notably with a current hypothesis of increasing biomass and dynamics of TRF, which we term the Bigger and Faster Hypothesis (B&FHo). We consider possible reasons for the contradiction and conclude that it is currently not possible to independently assess the vast majority of previously published B&FHo evidence due to restricted data access. PMID:28981502

Structure and effect of sarcosine on water and urea by using molecular dynamics simulations: Implications in protein stabilization.

PubMed

Kumar, Narendra; Kishore, Nand

2013-01-01

Sarcosine is one of the most important protecting osmolytes which is also known to counteract the denaturing effect of urea. We used molecular dynamics simulation methods to investigate the mechanism of protein stabilization and counteraction of urea by sarcosine. We found that sarcosine enhanced the tetrahedral structure of water and strengthened its hydrogen bonding network. We also found that sarcosine did not form clusters unlike glycine. Our results show strong interaction between sarcosine and urea molecules. Addition of sarcosine enhanced the urea-water structure and urea-water lifetime indicated an increase in the solvation of urea. These findings suggest that sarcosine indirectly stabilizes protein by enhancing water-water structure thus decreasing the hydrophobic effect and counteracts the effect of urea by increasing the solvation of urea and directly interacting with it leaving urea less available to interact with protein. Copyright © 2012 Elsevier B.V. All rights reserved.

Moored offshore structures - evaluation of forces in elastic mooring lines

NASA Astrophysics Data System (ADS)

Crudu, L.; Obreja, D. C.; Marcu, O.

2016-08-01

In most situations, the high frequency motions of the floating structure induce important effects in the mooring lines which affect also the motions of the structure. The experience accumulated during systematic experimental tests and calculations, carried out for different moored floating structures, showed a complex influence of various parameters on the dynamic effects. Therefore, it was considered that a systematic investigation is necessary. Due to the complexity of hydrodynamics aspects of offshore structures behaviour, experimental tests are practically compulsory in order to be able to properly evaluate and then to validate their behaviour in real sea. Moreover the necessity to carry out hydrodynamic tests is often required by customers, classification societies and other regulatory bodies. Consequently, the correct simulation of physical properties of the complex scaled models becomes a very important issue. The paper is investigating such kind of problems identifying the possible simplification, generating different approaches. One of the bases of the evaluation has been found consideringtheresults of systematic experimental tests on the dynamic behaviour of a mooring chain reproduced at five different scales. Dynamic effects as well as the influences of the elasticity simulation for 5 different scales are evaluated together. The paper presents systematic diagrams and practical results for a typical moored floating structure operating as pipe layer based on motion evaluations and accelerations in waves.

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.

Considering transient population dynamics in the conservation of slow life-history species: An application to the sandhill crane

USGS Publications Warehouse

Gerber, Brian D.; Kendall, William L.

2016-01-01

The importance of transient dynamics of structured populations is increasingly recognized in ecology, yet these implications are not largely considered in conservation practices. We investigate transient and long-term population dynamics to demonstrate the process and utility of incorporating transient dynamics into conservation research and to better understand the population management of slow life-history species; these species can be theoretically highly sensitive to short- and long-term transient effects. We are specifically interested in the effects of anthropogenic removal of individuals from populations, such as caused by harvest, poaching, translocation, or incidental take. We use the sandhill crane (Grus canadensis) as an exemplar species; it is long-lived, has low reproduction, late maturity, and multiple populations are subject to sport harvest. We found sandhill cranes to have extremely high potential, but low likelihood for transient dynamics, even when the population is being harvested. The typically low population growth rate of slow life-history species appears to buffer against many perturbations causing large transient effects. Transient dynamics will dominate population trajectories of these species when stage structures are highly biased towards the younger and non-reproducing individuals, a situation that may be rare in established populations of long-lived animals. However, short-term transient population growth can be highly sensitive to vital rates that are relatively insensitive under equilibrium, suggesting that stage structure should be known if perturbation analysis is used to identify effective conservation strategies. For populations of slow life-history species that are not prone to large perturbations to their most productive individuals, population growth may be approximated by equilibrium dynamics.

Dynamic characterization, monitoring and control of rotating flexible beam-mass structures via piezo-embedded techniques

NASA Technical Reports Server (NTRS)

Lai, Steven H.-Y.

1992-01-01

A variational principle and a finite element discretization technique were used to derive the dynamic equations for a high speed rotating flexible beam-mass system embedded with piezo-electric materials. The dynamic equation thus obtained allows the development of finite element models which accommodate both the original structural element and the piezoelectric element. The solutions of finite element models provide system dynamics needed to design a sensing system. The characterization of gyroscopic effect and damping capacity of smart rotating devices are addressed. Several simulation examples are presented to validate the analytical solution.

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.

Reduced-Order Aerothermoelastic Analysis of Hypersonic Vehicle Structures

NASA Astrophysics Data System (ADS)

Falkiewicz, Nathan J.

Design and simulation of hypersonic vehicles require consideration of a variety of disciplines due to the highly coupled nature of the flight regime. In order to capture all of the potential effects on vehicle dynamics, one must consider the aerodynamics, aerodynamic heating, heat transfer, and structural dynamics as well as the interactions between these disciplines. The problem is further complicated by the large computational expense involved in capturing all of these effects and their interactions in a full-order sense. While high-fidelity modeling techniques exist for each of these disciplines, the use of such techniques is computationally infeasible in a vehicle design and control system simulation setting for such a highly coupled problem. Early in the design stage, many iterations of analyses may need to be carried out as the vehicle design matures, thus requiring quick analysis turnaround time. Additionally, the number of states used in the analyses must be small enough to allow for efficient control simulation and design. As a result, alternatives to full-order models must be considered. This dissertation presents a fully coupled, reduced-order aerothermoelastic framework for the modeling and analysis of hypersonic vehicle structures. The reduced-order transient thermal solution is a modal solution based on the proper orthogonal decomposition. The reduced-order structural dynamic model is based on projection of the equations of motion onto a Ritz modal subspace that is identified a priori. The reduced-order models are assembled into a time-domain aerothermoelastic simulation framework which uses a partitioned time-marching scheme to account for the disparate time scales of the associated physics. The aerothermoelastic modeling framework is outlined and the formulations associated with the unsteady aerodynamics, aerodynamic heating, transient thermal, and structural dynamics are outlined. Results demonstrate the accuracy of the reduced-order transient thermal and structural dynamic models under variation in boundary conditions and flight conditions. The framework is applied to representative hypersonic vehicle control surface structures and a variety of studies are conducted to assess the impact of aerothermoelastic effects on hypersonic vehicle dynamics. The results presented in this dissertation demonstrate the ability of the proposed framework to perform efficient aerothermoelastic analysis.

Ab Initio Path Integral Molecular Dynamics Study of the Nuclear Quantum Effect on Out-of-Plane Ring Deformation of Hydrogen Maleate Anion.

PubMed

Kawashima, Yukio; Tachikawa, Masanori

2014-01-14

Ab initio path integral molecular dynamics (PIMD) simulation was performed to understand the nuclear quantum effect on the out-of-plane ring deformation of hydrogen maleate anion and investigate the existence of a stable structure with ring deformation, which was suggested in experimental observation (Fillaux et al., Chem. Phys. 1999, 120, 387-403). The isotope effect and the temperature effect are studied as well. We first investigated the nuclear quantum effect on the proton transfer. In static calculation and classical ab initio molecular dynamics simulations, the proton in the hydrogen bond is localized to either oxygen atom. On the other hand, the proton is located at the center of two oxygen atoms in quantum ab initio PIMD simulations. The nuclear quantum effect washes out the barrier of proton transfer. We next examined the nuclear quantum effect on the motion of hydrogen maleate anion. Principal component analysis revealed that the out-of-plane ring bending modes have dominant contribution to the entire molecular motion. In quantum ab initio PIMD simulations, structures with ring deformation were the global minimum for the deuterated isotope at 300 K. We analyzed the out-of-plane ring bending mode further and found that there are three minima along a ring distortion mode. We successfully found a stable structure with ring deformation of hydrogen maleate for the first time, to our knowledge, using theoretical calculation. The structures with ring deformation found in quantum simulation of the deuterated isotope allowed the proton transfer to occur more frequently than the planar structure. Static ab initio electronic structure calculation found that the structures with ring deformation have very small proton transfer barrier compared to the planar structure. We suggest that the "proton transfer driven" mechanism is the origin of stabilization for the structure with out-of-plane ring deformation.

Multivariate dynamical modelling of structural change during development.

PubMed

Ziegler, Gabriel; Ridgway, Gerard R; Blakemore, Sarah-Jayne; Ashburner, John; Penny, Will

2017-02-15

Here we introduce a multivariate framework for characterising longitudinal changes in structural MRI using dynamical systems. The general approach enables modelling changes of states in multiple imaging biomarkers typically observed during brain development, plasticity, ageing and degeneration, e.g. regional gray matter volume of multiple regions of interest (ROIs). Structural brain states follow intrinsic dynamics according to a linear system with additional inputs accounting for potential driving forces of brain development. In particular, the inputs to the system are specified to account for known or latent developmental growth/decline factors, e.g. due to effects of growth hormones, puberty, or sudden behavioural changes etc. Because effects of developmental factors might be region-specific, the sensitivity of each ROI to contributions of each factor is explicitly modelled. In addition to the external effects of developmental factors on regional change, the framework enables modelling and inference about directed (potentially reciprocal) interactions between brain regions, due to competition for space, or structural connectivity, and suchlike. This approach accounts for repeated measures in typical MRI studies of development and aging. Model inversion and posterior distributions are obtained using earlier established variational methods enabling Bayesian evidence-based comparisons between various models of structural change. Using this approach we demonstrate dynamic cortical changes during brain maturation between 6 and 22 years of age using a large openly available longitudinal paediatric dataset with 637 scans from 289 individuals. In particular, we model volumetric changes in 26 bilateral ROIs, which cover large portions of cortical and subcortical gray matter. We account for (1) puberty-related effects on gray matter regions; (2) effects of an early transient growth process with additional time-lag parameter; (3) sexual dimorphism by modelling parameter differences between boys and girls. There is evidence that the regional pattern of sensitivity to dynamic hidden growth factors in late childhood is similar across genders and shows a consistent anterior-posterior gradient with strongest impact to prefrontal cortex (PFC) brain changes. Finally, we demonstrate the potential of the framework to explore the coupling of structural changes across a priori defined subnetworks using an example of previously established resting state functional connectivity. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Correlation of ground tests and analyses of a dynamically scaled Space Station model configuration

NASA Technical Reports Server (NTRS)

Javeed, Mehzad; Edighoffer, Harold H.; Mcgowan, Paul E.

1993-01-01

Verification of analytical models through correlation with ground test results of a complex space truss structure is demonstrated. A multi-component, dynamically scaled space station model configuration is the focus structure for this work. Previously established test/analysis correlation procedures are used to develop improved component analytical models. Integrated system analytical models, consisting of updated component analytical models, are compared with modal test results to establish the accuracy of system-level dynamic predictions. Design sensitivity model updating methods are shown to be effective for providing improved component analytical models. Also, the effects of component model accuracy and interface modeling fidelity on the accuracy of integrated model predictions is examined.

Influence of backup bearings and support structure dynamics on the behavior of rotors with active supports

NASA Technical Reports Server (NTRS)

Flowers, George T.

1995-01-01

This semiannual status report lists specific accomplishments made on the research of the influence of backup bearings and support structure dynamics on the behavior of rotors with active supports. Papers have been presented representing work done on the T-501 engine model; an experimental/simulation study of auxiliary bearing rotordynamics; and a description of a rotordynamical model for a magnetic bearing supported rotor system, including auxiliary bearing effects. A finite element model for a foil bearing has been developed. Additional studies of rotor/bearing/housing dynamics are currently being performed as are studies of the effects of sideloading on auxiliary bearing rotordynamics using the magnetic bearing supported rotor model.

An ignition key for atomic-scale engines

NASA Astrophysics Data System (ADS)

Dundas, Daniel; Cunningham, Brian; Buchanan, Claire; Terasawa, Asako; Paxton, Anthony T.; Todorov, Tchavdar N.

2012-10-01

A current-carrying resonant nanoscale device, simulated by non-adiabatic molecular dynamics, exhibits sharp activation of non-conservative current-induced forces with bias. The result, above the critical bias, is generalized rotational atomic motion with a large gain in kinetic energy. The activation exploits sharp features in the electronic structure, and constitutes, in effect, an ignition key for atomic-scale motors. A controlling factor for the effect is the non-equilibrium dynamical response matrix for small-amplitude atomic motion under current. This matrix can be found from the steady-state electronic structure by a simpler static calculation, providing a way to detect the likely appearance, or otherwise, of non-conservative dynamics, in advance of real-time modelling.

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

From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors.

PubMed

Zafra Ruano, Ana; Cilia, Elisa; Couceiro, José R; Ruiz Sanz, Javier; Schymkowitz, Joost; Rousseau, Frederic; Luque, Irene; Lenaerts, Tom

2016-05-01

Src Homology 3 domains are ubiquitous small interaction modules known to act as docking sites and regulatory elements in a wide range of proteins. Prior experimental NMR work on the SH3 domain of Src showed that ligand binding induces long-range dynamic changes consistent with an induced fit mechanism. The identification of the residues that participate in this mechanism produces a chart that allows for the exploration of the regulatory role of such domains in the activity of the encompassing protein. Here we show that a computational approach focusing on the changes in side chain dynamics through ligand binding identifies equivalent long-range effects in the Src SH3 domain. Mutation of a subset of the predicted residues elicits long-range effects on the binding energetics, emphasizing the relevance of these positions in the definition of intramolecular cooperative networks of signal transduction in this domain. We find further support for this mechanism through the analysis of seven other publically available SH3 domain structures of which the sequences represent diverse SH3 classes. By comparing the eight predictions, we find that, in addition to a dynamic pathway that is relatively conserved throughout all SH3 domains, there are dynamic aspects specific to each domain and homologous subgroups. Our work shows for the first time from a structural perspective, which transduction mechanisms are common between a subset of closely related and distal SH3 domains, while at the same time highlighting the differences in signal transduction that make each family member unique. These results resolve the missing link between structural predictions of dynamic changes and the domain sectors recently identified for SH3 domains through sequence analysis.

From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors

PubMed Central

Ruiz Sanz, Javier; Schymkowitz, Joost; Rousseau, Frederic

2016-01-01

Src Homology 3 domains are ubiquitous small interaction modules known to act as docking sites and regulatory elements in a wide range of proteins. Prior experimental NMR work on the SH3 domain of Src showed that ligand binding induces long-range dynamic changes consistent with an induced fit mechanism. The identification of the residues that participate in this mechanism produces a chart that allows for the exploration of the regulatory role of such domains in the activity of the encompassing protein. Here we show that a computational approach focusing on the changes in side chain dynamics through ligand binding identifies equivalent long-range effects in the Src SH3 domain. Mutation of a subset of the predicted residues elicits long-range effects on the binding energetics, emphasizing the relevance of these positions in the definition of intramolecular cooperative networks of signal transduction in this domain. We find further support for this mechanism through the analysis of seven other publically available SH3 domain structures of which the sequences represent diverse SH3 classes. By comparing the eight predictions, we find that, in addition to a dynamic pathway that is relatively conserved throughout all SH3 domains, there are dynamic aspects specific to each domain and homologous subgroups. Our work shows for the first time from a structural perspective, which transduction mechanisms are common between a subset of closely related and distal SH3 domains, while at the same time highlighting the differences in signal transduction that make each family member unique. These results resolve the missing link between structural predictions of dynamic changes and the domain sectors recently identified for SH3 domains through sequence analysis. PMID:27213566

Centrifugal and Numerical Modeling of Buried Structures. Volume 2. Dynamic Soil-Structure Interaction.

DTIC Science & Technology

1987-07-14

RD-RISE 368 CENTRIFUGAL AND NUMERICAL MODELING OF BURIED STRUCTURES 1/3 VOLUME 2 DYNAMIC..(U) COLORADO UNIV AT BOULDER DEPT OF CIVIL ENVIRONMENTAL...20332-6448 ELEMENT NO NO. NO ACCESSION NO 61102F 2302 Cl 11 TITLE (Include Security Classification) (U) Centrifugal and Numerical Modeling of Buried ...were buried in a dry sand and tested in the centrifuge to simulate the effects of gravity-induced overburden stresses which played a major role in

Cosolvent effect on the dynamics of water in aqueous binary mixtures

NASA Astrophysics Data System (ADS)

Zhang, Xia; Zhang, Lu; Jin, Tan; Zhang, Qiang; Zhuang, Wei

2018-04-01

Water rotational dynamics in the mixtures of water and amphiphilic molecules, such as acetone and dimethyl sulfoxide (DMSO), measured by femtosecond infrared, often vary non-monotonically as the amphiphilic molecule's molar fraction changes from 0 to 1. Recent study has attributed the non-ideal water rotation with concentration in DMSO-water mixtures to different microscopic hydrophilic-hydrophobic segregation structure in water-rich and water-poor mixtures. Interestingly, the acetone molecule has very similar molecular structure to DMSO, but the extremum of the water rotational time in the DMSO-water mixtures significantly shifts to lower concentration and the rotation of water is much faster than those in acetone-water mixtures. The simulation results here shows that the non-ideal rotational dynamics of water in both mixtures are due to the frame rotation during the interval of hydrogen bond (HB) switchings. A turnover of the frame rotation with concentration takes place as the structure transition of mixture from the hydrogen bond percolation structure to the hydrophobic percolation structure. The weak acetone-water hydrogen bond strengthens the hydrophobic aggregation and accelerates the relaxation of the hydrogen bond, so that the structure transition takes places at lower concentration and the rotation of water is faster in acetone-water mixture than in DMSO-water mixture. A generally microscopic picture on the mixing effect on the water dynamics in binary aqueous mixtures is presented here.

The Response of Simple Polymer Structures Under Dynamic Loading

NASA Astrophysics Data System (ADS)

Proud, William; Ellison, Kay; Yapp, Su; Cole, Cloe; Galimberti, Stefano; Institute of Shock Physics Team

2017-06-01

The dynamic response of polymeric materials has been widely studied with the effects of degree of crystallinity, strain rate, temperature and sample size being commonly reported. This study uses a simple PMMA structure, a right cylindrical sample, with structural features such as holes. The features are added an varied in a systematic fashion. Samples were dynamically loaded using a Split Hopkinson Pressure Bar up to failure. The resulting stress-strain curves are presented showing the change in sample response. The strain to failure is shown to increase initially with the presence of holes, while failure stress is relatively unaffected. The fracture patterns seen in the failed samples change, with tensile cracks, Hertzian cones, shear effects being dominant for different holes sizes and geometries. The sample were prepared by laser cutting and checked for residual stress before experiment. The data is used to validate predictive model predictions where material, structure and damage are included.. The Institute of Shock Physics acknowledges the support of Imperial College London and the Atomic Weapons Establishment.

Is the Oxygen Atom Static or Dynamic? The Effect of Generating Animations on Students' Mental Models of Atomic Structure

ERIC Educational Resources Information Center

Akaygun, Sevil

2016-01-01

Visualizing the chemical structure and dynamics of particles has been challenging for many students; therefore, various visualizations and tools have been used in chemistry education. For science educators, it has been important to understand how students visualize and represent particular phenomena--i.e., their mental models-- to design more…

Attitude Dynamics, Stability, and Control of a Heliogyro Solar Sail

NASA Astrophysics Data System (ADS)

Pimienta-Penalver, Adonis Reinier

A heliogyro solar sail concept, dubbed `HELIOS', is proposed as an alternative to deep space missions without the need for on-board propellant. Although this type of solar sail has existed in concept for several decades, and some previous studies have investigated certain aspects of its operation, a significant amount of research is still needed to analyze the dynamic and control characteristics of the structure under the projected range of orbital conditions. This work presents an improvement upon the existing discrete-mass models of the heliogyro blade, and the extension of its application from a single membrane blade to a fully-coupled approximation of the dynamics of the HELIOS system with multiple spinning membrane blades around a central hub. The incorporation of structural stiffness and external forcing effects into the model is demonstrated to add a further degree of fidelity in simulating the stability properties of the system. Additionally, the approximated dynamics of multiple-blade heliogyro structures are examined under the effect of solar radiation pressure. Lastly, this study evaluates a control algorithm at each blade root to impose structural integrity and attitude control by coordinating well-known helicopter blade pitching profiles.

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.

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.

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.

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

The effect of seasonal harvesting on stage-structured population models.

PubMed

Tang, Sanyi; Chen, Lansun

2004-04-01

In most models of population dynamics, increases in population due to birth are assumed to be time-independent, but many species reproduce only during a single period of the year. We propose an exploited single-species model with stage structure for the dynamics in a fish population for which births occur in a single pulse once per time period. Since birth pulse populations are often characterized with a discrete time dynamical system determined by its Poincaré map, we explore the consequences of harvest timing to equilibrium population sizes under seasonal dependence and obtain threshold conditions for their stability, and show that the timing of harvesting has a strong impact on the persistence of the fish population, on the volume of mature fish stock and on the maximum annual-sustainable yield. Moreover, our results imply that the population can sustain much higher harvest rates if the mature fish is removed as early in the season (after the birth pulse) as possible. Further, the effects of harvesting effort and harvest timing on the dynamical complexity are also investigated. Bifurcation diagrams are constructed with the birth rate (or harvesting effort or harvest timing) as the bifurcation parameter, and these are observed to display rich structure, including chaotic bands with periodic windows, pitch-fork and tangent bifurcations, non-unique dynamics (meaning that several attractors coexist) and attractor crisis. This suggests that birth pulse, in effect, provides a natural period or cyclicity that makes the dynamical behavior more complex.

State-Resolved Metal Nanoparticle Dynamics Viewed through the Combined Lenses of Ultrafast and Magneto-optical Spectroscopies.

PubMed

Zhao, Tian; Herbert, Patrick J; Zheng, Hongjun; Knappenberger, Kenneth L

2018-06-19

Electronic carrier dynamics play pivotal roles in the functional properties of nanomaterials. For colloidal metals, the mechanisms and influences of these dynamics are structure dependent. The coherent carrier dynamics of collective plasmon modes for nanoparticles (approximately 2 nm and larger) determine optical amplification factors that are important to applied spectroscopy techniques. In the nanocluster domain (sub-2 nm), carrier coupling to vibrational modes affects photoluminescence yields. The performance of photocatalytic materials featuring both nanoparticles and nanoclusters also depends on the relaxation dynamics of nonequilibrium charge carriers. The challenges for developing comprehensive descriptions of carrier dynamics spanning both domains are multifold. Plasmon coherences are short-lived, persisting for only tens of femtoseconds. Nanoclusters exhibit discrete carrier dynamics that can persist for microseconds in some cases. On this time scale, many state-dependent processes, including vibrational relaxation, charge transfer, and spin conversion, affect carrier dynamics in ways that are nonscalable but, rather, structure specific. Hence, state-resolved spectroscopy methods are needed for understanding carrier dynamics in the nanocluster domain. Based on these considerations, a detailed understanding of structure-dependent carrier dynamics across length scales requires an appropriate combination of spectroscopic methods. Plasmon mode-specific dynamics can be obtained through ultrafast correlated light and electron microscopy (UCLEM), which pairs interferometric nonlinear optical (INLO) with electron imaging methods. INLO yields nanostructure spectral resonance responses, which capture the system's homogeneous line width and coherence dynamics. State-resolved nanocluster dynamics can be obtained by pairing ultrafast with magnetic-optical spectroscopy methods. In particular, variable-temperature variable-field (VTVH) spectroscopies allow quantification of transient, excited states, providing quantification of important parameters such as spin and orbital angular momenta as well as the energy gaps that separate electronic fine structure states. Ultrafast two-dimensional electronic spectroscopy (2DES) can be used to understand how these details influence state-to-state carrier dynamics. In combination, VTVH and 2DES methods can provide chemists with detailed information regarding the structure-dependent and state-specific flow of energy through metal nanoclusters. In this Account, we highlight recent advances toward understanding structure-dependent carrier dynamics for metals spanning the sub-nanometer to tens of nanometers length scale. We demonstrate the use of UCLEM methods for arresting interband scattering effects. For sub-nanometer thiol-protected nanoclusters, we discuss the effectiveness of VTVH for distinguishing state-specific radiative recombination originating from a gold core versus organometallic protecting layers. This state specificity is refined further using femtosecond 2DES and two-color methods to isolate so-called superatom state dynamics and vibrationally mediated spin-conversion and emission processes. Finally, we discuss prospects for merging VTVH and 2DES methods into a single platform.

Topological structure dynamics revealing collective evolution in active nematics

PubMed Central

Shi, Xia-qing; Ma, Yu-qiang

2013-01-01

Topological defects frequently emerge in active matter like bacterial colonies, cytoskeleton extracts on substrates, self-propelled granular or colloidal layers and so on, but their dynamical properties and the relations to large-scale organization and fluctuations in these active systems are seldom touched. Here we reveal, through a simple model for active nematics using self-driven hard elliptic rods, that the excitation, annihilation and transportation of topological defects differ markedly from those in non-active media. These dynamical processes exhibit strong irreversibility in active nematics in the absence of detailed balance. Moreover, topological defects are the key factors in organizing large-scale dynamic structures and collective flows, resulting in multi-spatial temporal effects. These findings allow us to control the self-organization of active matter through topological structures. PMID:24346733

Preliminary results on the dynamics of large and flexible space structures in Halo orbits

NASA Astrophysics Data System (ADS)

Colagrossi, Andrea; Lavagna, Michèle

2017-05-01

The global exploration roadmap suggests, among other ambitious future space programmes, a possible manned outpost in lunar vicinity, to support surface operations and further astronaut training for longer and deeper space missions and transfers. In particular, a Lagrangian point orbit location - in the Earth- Moon system - is suggested for a manned cis-lunar infrastructure; proposal which opens an interesting field of study from the astrodynamics perspective. Literature offers a wide set of scientific research done on orbital dynamics under the Three-Body Problem modelling approach, while less of it includes the attitude dynamics modelling as well. However, whenever a large space structure (ISS-like) is considered, not only the coupled orbit-attitude dynamics should be modelled to run more accurate analyses, but the structural flexibility should be included too. The paper, starting from the well-known Circular Restricted Three-Body Problem formulation, presents some preliminary results obtained by adding a coupled orbit-attitude dynamical model and the effects due to the large structure flexibility. In addition, the most relevant perturbing phenomena, such as the Solar Radiation Pressure (SRP) and the fourth-body (Sun) gravity, are included in the model as well. A multi-body approach has been preferred to represent possible configurations of the large cis-lunar infrastructure: interconnected simple structural elements - such as beams, rods or lumped masses linked by springs - build up the space segment. To better investigate the relevance of the flexibility effects, the lumped parameters approach is compared with a distributed parameters semi-analytical technique. A sensitivity analysis of system dynamics, with respect to different configurations and mechanical properties of the extended structure, is also presented, in order to highlight drivers for the lunar outpost design. Furthermore, a case study for a large and flexible space structure in Halo orbits around one of the Earth-Moon collinear Lagrangian points, L1 or L2, is discussed to point out some relevant outcomes for the potential implementation of such a mission.

Solution x-ray scattering and structure formation in protein dynamics

NASA Astrophysics Data System (ADS)

Nasedkin, Alexandr; Davidsson, Jan; Niemi, Antti J.; Peng, Xubiao

2017-12-01

We propose a computationally effective approach that builds on Landau mean-field theory in combination with modern nonequilibrium statistical mechanics to model and interpret protein dynamics and structure formation in small- to wide-angle x-ray scattering (S/WAXS) experiments. We develop the methodology by analyzing experimental data in the case of Engrailed homeodomain protein as an example. We demonstrate how to interpret S/WAXS data qualitatively with a good precision and over an extended temperature range. We explain experimental observations in terms of protein phase structure, and we make predictions for future experiments and for how to analyze data at different ambient temperature values. We conclude that the approach we propose has the potential to become a highly accurate, computationally effective, and predictive tool for analyzing S/WAXS data. For this, we compare our results with those obtained previously in an all-atom molecular dynamics simulation.

Static and Dynamic Behaviour Assessment of the Trajan Arch by Means of New Monitoring Technologies

NASA Astrophysics Data System (ADS)

Petti, L.; Barone, F.; Mammone, A.; Giordano, G.

2017-08-01

An effective assessment of the static and dynamic structural behavior of historical monuments requires the development and validation of suitable adaptive structural models using high-quality experimental data acquired with an effectively continuous and distributed monitoring. Furthermore, the adaptive strategy allows an efficient evaluation of the health status and of the evolution along the time of a historical monument, providing relevant information to plan appropriate actions for its long-term preservation. The Trajan Arch in Benevento chosen as a case of study to develop and apply this new adaptive strategy in cultural heritage conservation. The paper, after a description of the innovative monitoring system, based on state-of-the-art mechanical sensors, presents and discusses the results of two tests, comparing the measurements with the predictions of an adaptive structural FEM model developed for the dynamical simulation of the Trajan Arch.

Ultra-Low Power Dynamic Knob in Adaptive Compressed Sensing Towards Biosignal Dynamics.

PubMed

Wang, Aosen; Lin, Feng; Jin, Zhanpeng; Xu, Wenyao

2016-06-01

Compressed sensing (CS) is an emerging sampling paradigm in data acquisition. Its integrated analog-to-information structure can perform simultaneous data sensing and compression with low-complexity hardware. To date, most of the existing CS implementations have a fixed architectural setup, which lacks flexibility and adaptivity for efficient dynamic data sensing. In this paper, we propose a dynamic knob (DK) design to effectively reconfigure the CS architecture by recognizing the biosignals. Specifically, the dynamic knob design is a template-based structure that comprises a supervised learning module and a look-up table module. We model the DK performance in a closed analytic form and optimize the design via a dynamic programming formulation. We present the design on a 130 nm process, with a 0.058 mm (2) fingerprint and a 187.88 nJ/event energy-consumption. Furthermore, we benchmark the design performance using a publicly available dataset. Given the energy constraint in wireless sensing, the adaptive CS architecture can consistently improve the signal reconstruction quality by more than 70%, compared with the traditional CS. The experimental results indicate that the ultra-low power dynamic knob can provide an effective adaptivity and improve the signal quality in compressed sensing towards biosignal dynamics.

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.

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.

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.

Natural Frequency Testing and Model Correlation of Rocket Engine Structures in Liquid Hydrogen - Phase I, Cantilever Beam

NASA Technical Reports Server (NTRS)

Brown, Andrew M.; DeLessio, Jennifer L.; Jacobs, Preston W.

2018-01-01

Many structures in the launch vehicle industry operate in liquid hydrogen (LH2), from the hydrogen fuel tanks through the ducts and valves and into the pump sides of the turbopumps. Calculating the structural dynamic response of these structures is critical for successful qualification of this hardware, but accurate knowledge of the natural frequencies is based entirely on numerical or analytical predictions of frequency reduction due to the added-fluid-mass effect because testing in LH2 has always been considered too difficult and dangerous. This fluid effect is predicted to be approximately 4-5% using analytical formulations for simple cantilever beams. As part of a comprehensive test/analysis program to more accurately assess pump inducers operating in LH2, a series of frequency tests in LH2 were performed at NASA/Marshall Space Flight Center's unique cryogenic test facility. These frequency tests are coupled with modal tests in air and water to provide critical information not only on the mass effect of LH2, but also the cryogenic temperature effect on Young's Modulus for which the data is not extensive. The authors are unaware of any other reported natural frequency testing in this media. In addition to the inducer, a simple cantilever beam was also tested in the tank to provide a more easily modeled geometry as well as one that has an analytical solution for the mass effect. This data will prove critical for accurate structural dynamic analysis of these structures, which operate in a highly-dynamic environment.

Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations

PubMed Central

Ahlstrom, Logan S.; Vorontsov, Ivan I.; Shi, Jun; Miyashita, Osamu

2017-01-01

Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure. This agreement is most striking for crystal-contacting residues during crystal simulation. Given the high level of correspondence between our simulations and the X-ray data, we compare side-chain ensembles in solution and crystal simulations. We observe large decreases in conformational entropy in the crystal for several long, polar and contacting residues on the protein surface. Such cases agree well with the average loss in conformational entropy per residue upon protein folding and are accompanied by a change in side-chain conformation. This finding supports the application of surface engineering to facilitate crystallization. Our simulation-based approach demonstrated here with Cyanovirin-N establishes a framework for quantitatively comparing side-chain ensembles in solution and in the crystal across a larger set of proteins to elucidate the effect of the crystal environment on protein conformations. PMID:28107510

Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations.

PubMed

Ahlstrom, Logan S; Vorontsov, Ivan I; Shi, Jun; Miyashita, Osamu

2017-01-01

Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure. This agreement is most striking for crystal-contacting residues during crystal simulation. Given the high level of correspondence between our simulations and the X-ray data, we compare side-chain ensembles in solution and crystal simulations. We observe large decreases in conformational entropy in the crystal for several long, polar and contacting residues on the protein surface. Such cases agree well with the average loss in conformational entropy per residue upon protein folding and are accompanied by a change in side-chain conformation. This finding supports the application of surface engineering to facilitate crystallization. Our simulation-based approach demonstrated here with Cyanovirin-N establishes a framework for quantitatively comparing side-chain ensembles in solution and in the crystal across a larger set of proteins to elucidate the effect of the crystal environment on protein conformations.

Evaluation of the effectiveness of elastomeric mount using vibration power flow and transmissibility methods

NASA Astrophysics Data System (ADS)

Arib Rejab, M. N.; Shukor, S. A. Abdul; Sofian, M. R. Mohd; Inayat-Hussain, J. I.; Nazirah, A.; Asyraf, I.

2017-10-01

This paper presents the results of an experimental work to determine the dynamic stiffness and loss factor of elastomeric mounts. It also presents the results of theoretical analysis to determine the transmissibility and vibration power flow of these mounts, which are associated with their contribution to structure-borne noise. Four types of elastomeric mounts were considered, where three of them were made from green natural rubber material (SMR CV60, Ekoprena and Pureprena) and one made from petroleum based synthetic rubber (EPDM). In order to determine the dynamic stiffness and loss factor of these elastomeric mounts, dynamic tests were conducted using MTS 830 Elastomer Test System. Dynamic stiffness and loss factor of these mounts were measured for a range of frequency between 5 Hz and 150 Hz, and with a dynamic amplitude of 0.2 mm (p-p). The transmissibility and vibration power flow were determined based on a simple 2-Degree-of-Freedom model representing a vibration isolation system with a flexible receiver. This model reprsents the three main parts of a vehicle, which are the powertrain and engine mounting, the flexible structure and the floor of the vehicle. The results revealed that synthetic rubber (EPDM) was only effective at high frequency region. Natural rubber (Ekoprena), on the other hand, was found to be effective at both low and high frequency regions due to its low transmissibility at resonant frequency and its ability to damp the resonance. The estimated structure-borne noise emission showed that Ekoprena has a lower contribution to structure-borne noise as compared to the other types of elastomeric mounts.

Structures and Dynamics Division research and technology plans, FY 1982

NASA Technical Reports Server (NTRS)

Bales, K. S.

1982-01-01

Computational devices to improve efficiency for structural calculations are assessed. The potential of large arrays of microprocessors operating in parallel for finite element analysis is defined, and the impact of specialized computer hardware on static, dynamic, thermal analysis in the optimization of structural analysis and design calculations is determined. General aviation aircraft crashworthiness and occupant survivability is also considered. Mechanics technology required for design coefficient, fault tolerant advanced composite aircraft components subject to combined loads, impact, postbuckling effects and local discontinuities are developed.

Effects of mutations on active site conformation and dynamics of RNA-dependent RNA polymerase from Coxsackievirus B3.

PubMed

Shen, Hujun; Deng, Mingsen; Zhang, Yachao

2017-10-01

Recent crystal structures of RNA-dependent RNA polymerase (3D pol ) from Coxsackievirus B3 (CVB3) revealed that a tyrosine mutation at Phe364 (F364Y) resulted in structures with open active site whereas a hydrophobic mutation at Phe364 (F364A) led to conformations with closed active site. Besides, the crystal structures showed that the F364W mutation had no preference between the open and closed active sites, similar to wild-type. In this paper, we present a molecular dynamics (MD) study on CVB3 3D pol in order to address some important questions raised by experiments. First, MD simulations of F364Y and F364A were carried out to explore how these mutations at Phe364 influence active site dynamics and conformations. Second, MD simulations of wild-type and mutants were performed to discover the connection between active site dynamics and polymerase function. MD simulations reveal that the effect of mutations on active site dynamics is associated with the interaction between the structural motifs A and D in CVB3 3D pol . Interestingly, we discover that the active site state is influenced by the formation of a hydrogen bond between backbone atoms of Ala231 (in motif A) and Ala358 (in motif D), which has never been revealed before. Copyright © 2017 Elsevier Inc. All rights reserved.

A graph-based evolutionary algorithm: Genetic Network Programming (GNP) and its extension using reinforcement learning.

PubMed

Mabu, Shingo; Hirasawa, Kotaro; Hu, Jinglu

2007-01-01

This paper proposes a graph-based evolutionary algorithm called Genetic Network Programming (GNP). Our goal is to develop GNP, which can deal with dynamic environments efficiently and effectively, based on the distinguished expression ability of the graph (network) structure. The characteristics of GNP are as follows. 1) GNP programs are composed of a number of nodes which execute simple judgment/processing, and these nodes are connected by directed links to each other. 2) The graph structure enables GNP to re-use nodes, thus the structure can be very compact. 3) The node transition of GNP is executed according to its node connections without any terminal nodes, thus the past history of the node transition affects the current node to be used and this characteristic works as an implicit memory function. These structural characteristics are useful for dealing with dynamic environments. Furthermore, we propose an extended algorithm, "GNP with Reinforcement Learning (GNPRL)" which combines evolution and reinforcement learning in order to create effective graph structures and obtain better results in dynamic environments. In this paper, we applied GNP to the problem of determining agents' behavior to evaluate its effectiveness. Tileworld was used as the simulation environment. The results show some advantages for GNP over conventional methods.

Effect of the three-dimensional structure of laser emission on the dynamics of low-threshold optical breakdown plasmas

NASA Astrophysics Data System (ADS)

Anisimov, V. N.; Arutiunian, R. V.; Bol'Shov, L. A.; Derkach, O. N.; Kanevskii, M. F.

1989-03-01

The effect of the transverse structure of pulsed CO2 laser emission on the dynamics of laser-induced detonation waves propagating from a metal surface and on plasma transparency recovery is investigated theoretically and experimentally. Particular attention is given to breakdown initiation near the surface. It is suggested that the inclusion of refraction in the plasma into a self-consistent numerical mode is essential for the adequate quantitative description of experimental data on the interaction of laser emission with low-threshold optical breakdown plasmas.

Quantum effects in the dynamics of deeply supercooled water

DOE PAGES

Agapov, Alexander L.; Kolesnikov, Alexander I.; Novikov, Vladimir N.; ...

2015-02-26

In spite of its simple chemical structure, water remains one of the most puzzling liquids with many anomalies at low temperatures. Combining neutron scattering and dielectric relaxation spectroscopy, we show that quantum fluctuations are not negligible in deeply supercooled water. Our dielectric measurements reveal the anomalously weak temperature dependence of structural relaxation in vapor-deposited water close to the glass transition temperature T g~136K. We demonstrate that this anomalous behavior can be explained well by quantum effects. In conclusion, these results have significant implications for our understanding of water dynamics.

UHPC and NSFRC in Severe Environmental Conditions

NASA Astrophysics Data System (ADS)

Rehacek, S.; Citek, D.; Kolisko, J.

2017-10-01

Structure and properties of cement composite are time-varying characteristics, depending among others on environmental conditions. The key idea is a struggle for complex research of joint effect of physical, chemical and dynamic loads on the internal structure of cement composite and understanding the correlation between changes in microstructure and macro-scale properties. During the experimental program, specimens will be exposed to combined influence of freeze-thaw cycles, aggressive chemical agents and dynamic loading. The aim is to create a theoretical basis for design of effective cement composites meant to be used in severe environmental conditions.

Nanostructures nucleation in carbon-metal gaseous phase: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Galiullina, G. M.; Orekhov, N. D.; Stegailov, V. V.

2018-01-01

We perform nonequilibrium molecular dynamics simulation of carbon nanoclusters nucleation and early stages of growth from the gaseous phase. We analyze the catalytic effect of iron atoms on the nucleation kinetics and structure of the resultant nanoparticles. Reactive Force Field (ReaxFF) is used in the simulations for the description of bond formation and dissociation during the nucleation process at the nanoscale. The catalytic effect of iron reveals itself even on nanosecond simulation times: iron atoms accelerate the process of clustering but result in less graphitized carbon structures.

Disruption of sheet-like structures in Alfvénic turbulence by magnetic reconnection

NASA Astrophysics Data System (ADS)

Mallet, A.; Schekochihin, A. A.; Chandran, B. D. G.

2017-07-01

We propose a mechanism whereby the intense, sheet-like structures naturally formed by dynamically aligning Alfvénic turbulence are destroyed by magnetic reconnection at a scale \\hat{λ }_D, larger than the dissipation scale predicted by models of intermittent, dynamically aligning turbulence. The reconnection process proceeds in several stages: first, a linear tearing mode with N magnetic islands grows and saturates, and then the X-points between these islands collapse into secondary current sheets, which then reconnect until the original structure is destroyed. This effectively imposes an upper limit on the anisotropy of the structures within the perpendicular plane, which means that at scale \\hat{λ }_D the turbulent dynamics change: at scales larger than \\hat{λ }_D, the turbulence exhibits scale-dependent dynamic alignment and a spectral index approximately equal to -3/2, while at scales smaller than \\hat{λ }_D, the turbulent structures undergo a succession of disruptions due to reconnection, limiting dynamic alignment, steepening the effective spectral index and changing the final dissipation scale. The scaling of \\hat{λ }_D with the Lundquist (magnetic Reynolds) number S_{L_\\perp } depends on the order of the statistics being considered, and on the specific model of intermittency; the transition between the two regimes in the energy spectrum is predicted at approximately \\hat{λ }_D˜ S_{L_\\perp }^{-0.6}. The spectral index below \\hat{λ }_D is bounded between -5/3 and -2.3. The final dissipation scale is at \\hat{λ }_{η ,∞}˜ S_{L_\\perp }^{-3/4}, the same as the Kolmogorov scale arising in theories of turbulence that do not involve scale-dependent dynamic alignment.

Mechanical features of various silkworm crystalline considering hydration effect via molecular dynamics simulations.

PubMed

Kim, Yoonjung; Lee, Myeongsang; Choi, Hyunsung; Baek, Inchul; Kim, Jae In; Na, Sungsoo

2018-04-01

Silk materials are receiving significant attention as base materials for various functional nanomaterials and nanodevices, due to its exceptionally high mechanical properties, biocompatibility, and degradable characteristics. Although crystalline silk regions are composed of various repetitive motifs with differing amino acid sequences, how the effect of humidity works differently on each of the motifs and their structural characteristics remains unclear. We report molecular dynamics (MD) simulations on various silkworm fibroins composed of major motifs (i.e. (GAGAGS) n , (GAGAGA) n , and (GAGAGY) n ) at varying degrees of hydration, and reveal how each major motifs of silk fibroins change at each degrees of hydration using MD simulations and their structural properties in mechanical perspective via steered molecular dynamics simulations. Our results explain what effects humidity can have on nanoscale materials and devices consisting of crystalline silk materials.

Vortex Filaments in Grids for Scalable, Fine Smoke Simulation.

PubMed

Meng, Zhang; Weixin, Si; Yinling, Qian; Hanqiu, Sun; Jing, Qin; Heng, Pheng-Ann

2015-01-01

Vortex modeling can produce attractive visual effects of dynamic fluids, which are widely applicable for dynamic media, computer games, special effects, and virtual reality systems. However, it is challenging to effectively simulate intensive and fine detailed fluids such as smoke with fast increasing vortex filaments and smoke particles. The authors propose a novel vortex filaments in grids scheme in which the uniform grids dynamically bridge the vortex filaments and smoke particles for scalable, fine smoke simulation with macroscopic vortex structures. Using the vortex model, their approach supports the trade-off between simulation speed and scale of details. After computing the whole velocity, external control can be easily exerted on the embedded grid to guide the vortex-based smoke motion. The experimental results demonstrate the efficiency of using the proposed scheme for a visually plausible smoke simulation with macroscopic vortex structures.

Recent advances in integrated multidisciplinary optimization of rotorcraft

NASA Technical Reports Server (NTRS)

Adelman, Howard M.; Walsh, Joanne L.; Pritchard, Jocelyn I.

1992-01-01

A joint activity involving NASA and Army researchers at NASA LaRC to develop optimization procedures to improve the rotor blade design process by integrating appropriate disciplines and accounting for all of the important interactions among the disciplines is described. The disciplines involved include rotor aerodynamics, rotor dynamics, rotor structures, airframe dynamics, and acoustics. The work is focused on combining these five key disciplines in an optimization procedure capable of designing a rotor system to satisfy multidisciplinary design requirements. Fundamental to the plan is a three-phased approach. In phase 1, the disciplines of blade dynamics, blade aerodynamics, and blade structure are closely coupled while acoustics and airframe dynamics are decoupled and are accounted for as effective constraints on the design for the first three disciplines. In phase 2, acoustics is integrated with the first three disciplines. Finally, in phase 3, airframe dynamics is integrated with the other four disciplines. Representative results from work performed to date are described. These include optimal placement of tuning masses for reduction of blade vibratory shear forces, integrated aerodynamic/dynamic optimization, and integrated aerodynamic/dynamic/structural optimization. Examples of validating procedures are described.

Recent advances in multidisciplinary optimization of rotorcraft

NASA Technical Reports Server (NTRS)

Adelman, Howard M.; Walsh, Joanne L.; Pritchard, Jocelyn I.

1992-01-01

A joint activity involving NASA and Army researchers at NASA LaRC to develop optimization procedures to improve the rotor blade design process by integrating appropriate disciplines and accounting for all of the important interactions among the disciplines is described. The disciplines involved include rotor aerodynamics, rotor dynamics, rotor structures, airframe dynamics, and acoustics. The work is focused on combining these five key disciplines in an optimization procedure capable of designing a rotor system to satisfy multidisciplinary design requirements. Fundamental to the plan is a three-phased approach. In phase 1, the disciplines of blade dynamics, blade aerodynamics, and blade structure are closely coupled while acoustics and airframe dynamics are decoupled and are accounted for as effective constraints on the design for the first three disciplines. In phase 2, acoustics is integrated with the first three disciplines. Finally, in phase 3, airframe dynamics is integrated with the other four disciplines. Representative results from work performed to date are described. These include optimal placement of tuning masses for reduction of blade vibratory shear forces, integrated aerodynamic/dynamic optimization, and integrated aerodynamic/dynamic/structural optimization. Examples of validating procedures are described.

Synchronisation and stability in river metapopulation networks.

PubMed

Yeakel, J D; Moore, J W; Guimarães, P R; de Aguiar, M A M

2014-03-01

Spatial structure in landscapes impacts population stability. Two linked components of stability have large consequences for persistence: first, statistical stability as the lack of temporal fluctuations; second, synchronisation as an aspect of dynamic stability, which erodes metapopulation rescue effects. Here, we determine the influence of river network structure on the stability of riverine metapopulations. We introduce an approach that converts river networks to metapopulation networks, and analytically show how fluctuation magnitude is influenced by interaction structure. We show that river metapopulation complexity (in terms of branching prevalence) has nonlinear dampening effects on population fluctuations, and can also buffer against synchronisation. We conclude by showing that river transects generally increase synchronisation, while the spatial scale of interaction has nonlinear effects on synchronised dynamics. Our results indicate that this dual stability - conferred by fluctuation and synchronisation dampening - emerges from interaction structure in rivers, and this may strongly influence the persistence of river metapopulations. © 2013 John Wiley & Sons Ltd/CNRS.

Impact Damage and Strain Rate Effects for Toughened Epoxy Composite Structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.; Minnetyan, Levon

2006-01-01

Structural integrity of composite systems under dynamic impact loading is investigated herein. The GENOA virtual testing software environment is used to implement the effects of dynamic loading on fracture progression and damage tolerance. Combinations of graphite and glass fibers with a toughened epoxy matrix are investigated. The effect of a ceramic coating for the absorption of impact energy is also included. Impact and post impact simulations include verification and prediction of (1) Load and Impact Energy, (2) Impact Damage Size, (3) Maximum Impact Peak Load, (4) Residual Strength, (5) Maximum Displacement, (6) Contribution of Failure Modes to Failure Mechanisms, (7) Prediction of Impact Load Versus Time, and (8) Damage, and Fracture Pattern. A computer model is utilized for the assessment of structural response, progressive fracture, and defect/damage tolerance characteristics. Results show the damage progression sequence and the changes in the structural response characteristics due to dynamic impact. The fundamental premise of computational simulation is that the complete evaluation of composite fracture requires an assessment of ply and subply level damage/fracture processes as the structure is subjected to loads. Simulation results for the graphite/epoxy composite were compared with the impact and tension failure test data, correlation and verification was obtained that included: (1) impact energy, (2) damage size, (3) maximum impact peak load, (4) residual strength, (5) maximum displacement, and (6) failure mechanisms of the composite structure.

High-Resolution Lithosphere Viscosity and Dynamics Revealed by Magnetotelluric Imaging

NASA Astrophysics Data System (ADS)

Liu, L.; Hasterok, D. P.

2016-12-01

An accurate viscosity structure is critical to truthfully modeling continental lithosphere dynamics, especially at spatial scales of <200 km where active tectonic deformation and volcanism occur. However, the effective viscosity structure of the lithosphere remains a key challenge in geodynamics due to the intimate involvement of viscosity with time and its dependence on many factors including strain rate, plastic failure, composition, and grain size. Current efforts on inferring the detailed lithosphere viscosity structure are sparse and large uncertainties and discrepancies still exist. Here we report an attempt to infer the effective lithospheric viscosity from a high-resolution magnetotelluric (MT) survey across the western United States. The high sensitivity of MT fields to the presence of electrically conductive fluids makes it a promising proxy for determining mechanical strength variations throughout the lithosphere. We demonstrate how a viscosity structure, approximated from electrical resistivity, results in a geodynamic model that successfully predicts short-wavelength surface topography, lithospheric deformation, and mantle upwelling beneath recent volcanism. The results indicate that lithosphere viscosity structure rather than the buoyancy structure is the dominant controlling factor for short-wavelength topography and intra-plate deformation in tectonically active regions. We further show that this viscosity is consistent with and more effective than that derived from laboratory-based rheology. We therefore propose that MT imaging provides a practical observational constraint for quantifying the dynamic evolution of the continental lithosphere.

Reaction Dynamics at Liquid Interfaces

NASA Astrophysics Data System (ADS)

Benjamin, Ilan

2015-04-01

The liquid interface is a narrow, highly anisotropic region, characterized by rapidly varying density, polarity, and molecular structure. I review several aspects of interfacial solvation and show how these affect reactivity at liquid/liquid interfaces. I specifically consider ion transfer, electron transfer, and SN2 reactions, showing that solvent effects on these reactions can be understood by examining the unique structure and dynamics of the liquid interface region.

Spatial evolutionary epidemiology of spreading epidemics

PubMed Central

2016-01-01

Most spatial models of host–parasite interactions either neglect the possibility of pathogen evolution or consider that this process is slow enough for epidemiological dynamics to reach an equilibrium on a fast timescale. Here, we propose a novel approach to jointly model the epidemiological and evolutionary dynamics of spatially structured host and pathogen populations. Starting from a multi-strain epidemiological model, we use a combination of spatial moment equations and quantitative genetics to analyse the dynamics of mean transmission and virulence in the population. A key insight of our approach is that, even in the absence of long-term evolutionary consequences, spatial structure can affect the short-term evolution of pathogens because of the build-up of spatial differentiation in mean virulence. We show that spatial differentiation is driven by a balance between epidemiological and genetic effects, and this quantity is related to the effect of kin competition discussed in previous studies of parasite evolution in spatially structured host populations. Our analysis can be used to understand and predict the transient evolutionary dynamics of pathogens and the emergence of spatial patterns of phenotypic variation. PMID:27798295

Spatial evolutionary epidemiology of spreading epidemics.

PubMed

Lion, S; Gandon, S

2016-10-26

Most spatial models of host-parasite interactions either neglect the possibility of pathogen evolution or consider that this process is slow enough for epidemiological dynamics to reach an equilibrium on a fast timescale. Here, we propose a novel approach to jointly model the epidemiological and evolutionary dynamics of spatially structured host and pathogen populations. Starting from a multi-strain epidemiological model, we use a combination of spatial moment equations and quantitative genetics to analyse the dynamics of mean transmission and virulence in the population. A key insight of our approach is that, even in the absence of long-term evolutionary consequences, spatial structure can affect the short-term evolution of pathogens because of the build-up of spatial differentiation in mean virulence. We show that spatial differentiation is driven by a balance between epidemiological and genetic effects, and this quantity is related to the effect of kin competition discussed in previous studies of parasite evolution in spatially structured host populations. Our analysis can be used to understand and predict the transient evolutionary dynamics of pathogens and the emergence of spatial patterns of phenotypic variation. © 2016 The Author(s).

Population dynamics of HIV-1 inferred from gene sequences.

PubMed Central

Grassly, N C; Harvey, P H; Holmes, E C

1999-01-01

A method for the estimation of population dynamic history from sequence data is described and used to investigate the past population dynamics of HIV-1 subtypes A and B. Using both gag and env gene alignments the effective population size of each subtype is estimated and found to be surprisingly small. This may be a result of the selective sweep of mutations through the population, or may indicate an important role of genetic drift in the fixation of mutations. The implications of these results for the spread of drug-resistant mutations and transmission dynamics, and also the roles of selection and recombination in shaping HIV-1 genetic diversity, are discussed. A larger estimated effective population size for subtype A may be the result of differences in time of origin, transmission dynamics, and/or population structure. To investigate the importance of population structure a model of population subdivision was fitted to each subtype, although the improvement in likelihood was found to be nonsignificant. PMID:9927440

The Role of Linkers in the Excited-State Dynamic Planarization Processes of Macrocyclic Oligothiophene 12-Mers.

PubMed

Kim, Woojae; Sung, Jooyoung; Park, Kyu Hyung; Shimizu, Hideyuki; Imamura, Mika; Han, Minwoo; Sim, Eunji; Iyoda, Masahiko; Kim, Dongho

2015-11-05

Linkers adjoining chromophores play an important role in modulating the structure of conjugated systems, which is bound up with their photophysical properties. However, to date, the focus of works dealing with linker effects was limited only to linear π-conjugated materials, and there have been no detailed studies on cyclic counterparts. Herein we report the linker effects on the dynamic planarization processes of π-conjugated macrocyclic oligothiophene 12-mers, where the different ratio between ethynylene and vinylene linkers was chosen to control the backbone rigidity. By analyzing transient fluorescence spectra, we demonstrate that the connecting linkers play a crucial role in the excited-state dynamics of cyclic conjugated systems. Faster dynamic planarization, longer exciton delocalization length, and higher degree of planarity were observed in vinylene inserted cyclic oligothiophenes. Molecular dynamics simulations and density functional theory calculations also stress the importance of the role of linkers in modulating the structure of cyclic oligothiophenes.

Dynamic Probabilistic Instability of Composite Structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

2009-01-01

A computationally effective method is described to evaluate the non-deterministic dynamic instability (probabilistic dynamic buckling) of thin composite shells. The method is a judicious combination of available computer codes for finite element, composite mechanics and probabilistic structural analysis. The solution method is incrementally updated Lagrangian. It is illustrated by applying it to thin composite cylindrical shell subjected to dynamic loads. Both deterministic and probabilistic buckling loads are evaluated to demonstrate the effectiveness of the method. A universal plot is obtained for the specific shell that can be used to approximate buckling loads for different load rates and different probability levels. Results from this plot show that the faster the rate, the higher the buckling load and the shorter the time. The lower the probability, the lower is the buckling load for a specific time. Probabilistic sensitivity results show that the ply thickness, the fiber volume ratio and the fiber longitudinal modulus, dynamic load and loading rate are the dominant uncertainties in that order.

Dynamical thermal effects in InGaAsP microtubes at telecom wavelengths.

PubMed

Tian, Zhaobing; Bianucci, Pablo; Roche, Philip J R; Dastjerdi, M Hadi Tavakoli; Mi, Zetian; Poole, Philip J; Kirk, Andrew G; Plant, David V

2012-07-01

We report on the observation of a dynamical thermal effect in InGaAsP microtubes at telecom wavelengths. The microtubes are fabricated by releasing a strained semiconductor bilayer and are picked up by abruptly tapered optical fibers for subsequent coupling with adiabatically tapered optical fibers. As a result of absorption by InAs quantum dots embedded in the tube structure, these microtubes show dynamical thermal effects at wavelengths around 1525 nm and 1578 nm, while they are passive at longer wavelengths near 1634 nm. The photon absorption induced thermal effect is visualized by generating a pair of microbottles. The dynamical thermal effect can be avoided or exploited for passive or active applications by utilizing appropriate resonance wavelengths.

Nonlinear structural joint model updating based on instantaneous characteristics of dynamic responses

NASA Astrophysics Data System (ADS)

Wang, Zuo-Cai; Xin, Yu; Ren, Wei-Xin

2016-08-01

This paper proposes a new nonlinear joint model updating method for shear type structures based on the instantaneous characteristics of the decomposed structural dynamic responses. To obtain an accurate representation of a nonlinear system's dynamics, the nonlinear joint model is described as the nonlinear spring element with bilinear stiffness. The instantaneous frequencies and amplitudes of the decomposed mono-component are first extracted by the analytical mode decomposition (AMD) method. Then, an objective function based on the residuals of the instantaneous frequencies and amplitudes between the experimental structure and the nonlinear model is created for the nonlinear joint model updating. The optimal values of the nonlinear joint model parameters are obtained by minimizing the objective function using the simulated annealing global optimization method. To validate the effectiveness of the proposed method, a single-story shear type structure subjected to earthquake and harmonic excitations is simulated as a numerical example. Then, a beam structure with multiple local nonlinear elements subjected to earthquake excitation is also simulated. The nonlinear beam structure is updated based on the global and local model using the proposed method. The results show that the proposed local nonlinear model updating method is more effective for structures with multiple local nonlinear elements. Finally, the proposed method is verified by the shake table test of a real high voltage switch structure. The accuracy of the proposed method is quantified both in numerical and experimental applications using the defined error indices. Both the numerical and experimental results have shown that the proposed method can effectively update the nonlinear joint model.

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.

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.

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.

CFA Films in Amorphous Substrate: Structural Phase Induction and Magnetization Dynamics

NASA Astrophysics Data System (ADS)

Correa, M. A.; Bohn, F.; Escobar, V. M.

We report a systematic study of the structural and quasi-static magnetic properties, as well as of the dynamic magnetic response through MI effect, in Co2FeAl and MgO//Co2FeAl single layers and a MgO//Co2FeAl/Ag/Co2FeAl trilayered film, all grown onto an amorphous substrate. We present a new route to induce the crystalline structure in the Co2FeAl alloy and verify that changes in the structural phase of this material leads to remarkable modifications of the magnetic anisotropy and, consequently, dynamic magnetic behavior. Considering the electrical and magnetic properties of the Co2FeAl, our results open new possibilities for technological applications of this full-Heusler alloy in rigid and flexible spintronic devices.

The dynamical conductance of graphene tunnelling structures.

PubMed

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

2011-12-16

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

Stochastic Erosion of Fractal Structure in Nonlinear Dynamical Systems

NASA Astrophysics Data System (ADS)

Agarwal, S.; Wettlaufer, J. S.

2014-12-01

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

Flight-vehicle materials, structures, and dynamics - Assessment and future directions. Vol. 5 - Structural dynamics and aeroelasticity

NASA Technical Reports Server (NTRS)

Noor, Ahmed K. (Editor); Venneri, Samuel L. (Editor)

1993-01-01

Various papers on flight vehicle materials, structures, and dynamics are presented. Individual topics addressed include: general modeling methods, component modeling techniques, time-domain computational techniques, dynamics of articulated structures, structural dynamics in rotating systems, structural dynamics in rotorcraft, damping in structures, structural acoustics, structural design for control, structural modeling for control, control strategies for structures, system identification, overall assessment of needs and benefits in structural dynamics and controlled structures. Also discussed are: experimental aeroelasticity in wind tunnels, aeroservoelasticity, nonlinear aeroelasticity, aeroelasticity problems in turbomachines, rotary-wing aeroelasticity with application to VTOL vehicles, computational aeroelasticity, structural dynamic testing and instrumentation.

Comparative dynamics in a health investment model.

PubMed

Eisenring, C

1999-10-01

The method of comparative dynamics fully exploits the inter-temporal structure of optimal control models. I derive comparative dynamic results in a simplified demand for health model. The effect of a change in the depreciation rate on the optimal paths for health capital and investment in health is studied by use of a phase diagram.

Intra- and intermolecular effects on the Compton profile of the ionic liquid 1,3-dimethylimidazolium chloride

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

Koskelo, J., E-mail: jaakko.koskelo@helsinki.fi; Juurinen, I.; Ruotsalainen, K. O.

2014-12-28

We present a comprehensive simulation study on the solid-liquid phase transition of the ionic liquid 1,3-dimethylimidazolium chloride in terms of the changes in the atomic structure and their effect on the Compton profile. The structures were obtained by using ab initio molecular dynamics simulations. Chosen radial distribution functions of the liquid structure are presented and found generally to be in good agreement with previous ab initio molecular dynamics and neutron scattering studies. The main contributions to the predicted difference Compton profile are found to arise from intermolecular changes in the phase transition. This prediction can be used for interpreting futuremore » experiments.« less

The Lamb wave bandgap variation of a locally resonant phononic crystal subjected to thermal deformation

NASA Astrophysics Data System (ADS)

Zhu, Yun; Li, Zhen; Li, Yue-ming

2018-05-01

A study on dynamical characteristics of a ternary locally resonant phononic crystal (PC) plate (i.e., hard scatterer with soft coating periodically disperse in stiff host matrix) is carried out in this paper. The effect of thermal deformation on the structure stiffness, which plays an important role in the PC's dynamical characteristics, is considered. Results show that both the start and the stop frequency of bandgap shift to higher range with the thermal deformation. In particular, the characteristics of band structure change suddenly at critical buckling temperature. The effect of thermal deformation could be utilized for tuning of phononic band structures, which can promote their design and further applications.

Modelling of piezoelectric actuator dynamics for active structural control

NASA Technical Reports Server (NTRS)

Hagood, Nesbitt W.; Chung, Walter H.; Von Flotow, Andreas

1990-01-01

The paper models the effects of dynamic coupling between a structure and an electrical network through the piezoelectric effect. The coupled equations of motion of an arbitrary elastic structure with piezoelectric elements and passive electronics are derived. State space models are developed for three important cases: direct voltage driven electrodes, direct charge driven electrodes, and an indirect drive case where the piezoelectric electrodes are connected to an arbitrary electrical circuit with embedded voltage and current sources. The equations are applied to the case of a cantilevered beam with surface mounted piezoceramics and indirect voltage and current drive. The theoretical derivations are validated experimentally on an actively controlled cantilevered beam test article with indirect voltage drive.

Changes in the Coherent Dynamics of Nanoconfined Room Temperature Ionic Liquids

NASA Astrophysics Data System (ADS)

Vallejo, Kevin; Cano, Melissa; Li, Song; Rotner, Gernot; Faraone, Antonio; Banuelos, Jose

Confinement and temperature effects on the coherent dynamics of the room temperature ionic liquid (RTIL) [C10MPy+] [Tf2N-] were investigated using neutron spin-echo (NSE) in two silica matrices with different pore size. Several intermolecular forces give rise to the bulk molecular structure between anions and cations. NSE provided dynamics (via the coherent intermediate scattering function) in the time range of 0.004 to 10 ns, and at Q-values corresponding to intermediate range ordering and inter- and intra-molecular length scales of the RTIL. Pore wall effects were delineated by comparing bulk RTIL dynamics with those of the confined fluid in 2.8 nm and 8 nm pores. Analytical models were applied to the experimental data to extract decay times and amplitudes of each component. We find a fast relaxation outside the experiment time window, a primary relaxation, and slow, surface-induced dynamics, which all speed up with increased temperature, however, the temperature dependence differs between bulk and confinement. This study sheds light on the structure and dynamics of RTILs and is relevant to the optimization of RTILs for green technologies and applications.

The effect of medium structure complexity on the growth of Saccharomyces cerevisiae in gelatin-dextran systems.

PubMed

Boons, Kathleen; Noriega, Estefanía; Verherstraeten, Niels; David, Charlotte C; Hofkens, Johan; Van Impe, Jan F

2015-04-16

As most food systems are (semi-)solid, the effect of food structure on bacterial growth has been widely acknowledged. However, studies on the growth dynamics of yeasts have neglected the effect of food structure. In this paper, the growth dynamics of the spoilage yeast Saccharomyces cerevisiae was investigated at 23.5 °C in broth, singular, homogeneous biopolymer systems and binary biopolymer systems with a heterogeneous microstructure. The biopolymers gelatin and dextran were used to introduce the different levels of structure. The metabolizing ability of gelatin and dextran by S. cerevisiae was examined. To study microbial behavior in the binary systems at the micro level, mixtures were imaged with confocal laser scanning microscopy (CLSM). Growth dynamics and microscopic images of S. cerevisiae were compared with those obtained for Escherichia coli in the same model system (Boons et al., 2014). Different phase-separated, heterogeneous microstructures were obtained by changing the amount of added gelatin and dextran. Regardless of the microstructure, S. cerevisiae was preferentially located in the dextran phase. Metabolizing ability-tests indicated that gelatin could be consumed by S. cerevisiae but in the presence of glucose, no change in gelatin concentration was observed. No indication of dextran metabolizing ability was observed. When supplementing broth with gelatin or dextran alone, an enhanced growth rate and maximum cell density were observed. This enhancement was further increased by adding a second biopolymer, introducing a heterogeneous microstructure and hence increasing the medium structure complexity. The results obtained indicate that food structure complexity plays a significant role in the growth dynamics of S. cerevisiae, an important food spoiler. Copyright © 2014. Published by Elsevier B.V.

Impact of an irregular friction formulation on dynamics of a minimal model for brake squeal

NASA Astrophysics Data System (ADS)

Stender, Merten; Tiedemann, Merten; Hoffmann, Norbert; Oberst, Sebastian

2018-07-01

Friction-induced vibrations are of major concern in the design of reliable, efficient and comfortable technical systems. Well-known examples for systems susceptible to self-excitation can be found in fluid structure interaction, disk brake squeal, rotor dynamics, hip implants noise and many more. While damping elements and amplitude reduction are well-understood in linear systems, nonlinear systems and especially self-excited dynamics still constitute a challenge for damping element design. Additionally, complex dynamical systems exhibit deterministic chaotic cores which add severe sensitivity to initial conditions to the system response. Especially the complex friction interface dynamics remain a challenging task for measurements and modeling. Today, mostly simple and regular friction models are investigated in the field of self-excited brake system vibrations. This work aims at investigating the effect of high-frequency irregular interface dynamics on the nonlinear dynamical response of a self-excited structure. Special focus is put on the characterization of the system response time series. A low-dimensional minimal model is studied which features self-excitation, gyroscopic effects and friction-induced damping. Additionally, the employed friction formulation exhibits temperature as inner variable and superposed chaotic fluctuations governed by a Lorenz attractor. The time scale of the irregular fluctuations is chosen one order smaller than the overall system dynamics. The influence of those fluctuations on the structural response is studied in various ways, i.e. in time domain and by means of recurrence analysis. The separate time scales are studied in detail and regimes of dynamic interactions are identified. The results of the irregular friction formulation indicate dynamic interactions on multiple time scales, which trigger larger vibration amplitudes as compared to regular friction formulations conventionally studied in the field of friction-induced vibrations.

Effects of the infectious period distribution on predicted transitions in childhood disease dynamics

PubMed Central

Krylova, Olga; Earn, David J. D.

2013-01-01

The population dynamics of infectious diseases occasionally undergo rapid qualitative changes, such as transitions from annual to biennial cycles or to irregular dynamics. Previous work, based on the standard seasonally forced ‘susceptible–exposed–infectious–removed’ (SEIR) model has found that transitions in the dynamics of many childhood diseases result from bifurcations induced by slow changes in birth and vaccination rates. However, the standard SEIR formulation assumes that the stage durations (latent and infectious periods) are exponentially distributed, whereas real distributions are narrower and centred around the mean. Much recent work has indicated that realistically distributed stage durations strongly affect the dynamical structure of seasonally forced epidemic models. We investigate whether inferences drawn from previous analyses of transitions in patterns of measles dynamics are robust to the shapes of the stage duration distributions. As an illustrative example, we analyse measles dynamics in New York City from 1928 to 1972. We find that with a fixed mean infectious period in the susceptible–infectious–removed (SIR) model, the dynamical structure and predicted transitions vary substantially as a function of the shape of the infectious period distribution. By contrast, with fixed mean latent and infectious periods in the SEIR model, the shapes of the stage duration distributions have a less dramatic effect on model dynamical structure and predicted transitions. All these results can be understood more easily by considering the distribution of the disease generation time as opposed to the distributions of individual disease stages. Numerical bifurcation analysis reveals that for a given mean generation time the dynamics of the SIR and SEIR models for measles are nearly equivalent and are insensitive to the shapes of the disease stage distributions. PMID:23676892

Effects of the infectious period distribution on predicted transitions in childhood disease dynamics.

PubMed

Krylova, Olga; Earn, David J D

2013-07-06

The population dynamics of infectious diseases occasionally undergo rapid qualitative changes, such as transitions from annual to biennial cycles or to irregular dynamics. Previous work, based on the standard seasonally forced 'susceptible-exposed-infectious-removed' (SEIR) model has found that transitions in the dynamics of many childhood diseases result from bifurcations induced by slow changes in birth and vaccination rates. However, the standard SEIR formulation assumes that the stage durations (latent and infectious periods) are exponentially distributed, whereas real distributions are narrower and centred around the mean. Much recent work has indicated that realistically distributed stage durations strongly affect the dynamical structure of seasonally forced epidemic models. We investigate whether inferences drawn from previous analyses of transitions in patterns of measles dynamics are robust to the shapes of the stage duration distributions. As an illustrative example, we analyse measles dynamics in New York City from 1928 to 1972. We find that with a fixed mean infectious period in the susceptible-infectious-removed (SIR) model, the dynamical structure and predicted transitions vary substantially as a function of the shape of the infectious period distribution. By contrast, with fixed mean latent and infectious periods in the SEIR model, the shapes of the stage duration distributions have a less dramatic effect on model dynamical structure and predicted transitions. All these results can be understood more easily by considering the distribution of the disease generation time as opposed to the distributions of individual disease stages. Numerical bifurcation analysis reveals that for a given mean generation time the dynamics of the SIR and SEIR models for measles are nearly equivalent and are insensitive to the shapes of the disease stage distributions.

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.

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.

Temperature-Dependent Conformational Properties of Human Neuronal Calcium Sensor-1 Protein Revealed by All-Atom Simulations.

PubMed

Zhu, Yuzhen; Ma, Buyong; Qi, Ruxi; Nussinov, Ruth; Zhang, Qingwen

2016-04-14

Neuronal calcium sensor-1 (NCS-1) protein has orthologues from Saccharomyces cerevisiae to human with highly conserved amino acid sequences. NCS-1 is an important factor controlling the animal's response to temperature change. This leads us to investigate the temperature effects on the conformational dynamics of human NCS-1 at 310 and 316 K by all-atom molecular dynamics (MD) simulations and dynamic community network analysis. Four independent 500 ns MD simulations show that secondary structure content at 316 K is similar to that at 310 K, whereas the global protein structure is expanded. Loop 3 (L3) adopts an extended state occuping the hydrophobic crevice, and the number of suboptimal communication paths between residue D176 and V190 is reduced at 316 K. The dynamic community network analysis suggests that the interdomain correlation is weakened, and the intradomain coupling is strengthened at 316 K. The elevated temperature reduces the number of the salt bridges, especially in C-domain. This study suggests that the elevated temperature affects the conformational dynamics of human NCS-1 protein. Comparison of the structural dynamics of R102Q mutant and Δ176-190 truncated NCS-1 suggests that the structural and dynamical response of NCS-1 protein to elevated temperature may be one of its intrinsic functional properties.

Role of oxygen functional groups for structure and dynamics of interfacial water on low rank coal surface: a molecular dynamics simulation

NASA Astrophysics Data System (ADS)

You, Xiaofang; Wei, Hengbin; Zhu, Xianchang; Lyu, Xianjun; Li, Lin

2018-07-01

Molecular dynamics simulations were employed to study the effects of oxygen functional groups for structure and dynamics properties of interfacial water molecules on the subbituminous coal surface. Because of complex composition and structure, the graphite surface modified by hydroxyl, carboxyl and carbonyl groups was used to represent the surface model of subbituminous coal according to XPS results, and the composing proportion for hydroxyl, carbonyl and carboxyl is 25:3:5. The hydration energy with -386.28 kJ/mol means that the adsorption process between water and coal surface is spontaneous. Density profiles for oxygen atoms and hydrogen atoms indicate that the coal surface properties affect the structural and dynamic characteristics of the interfacial water molecules. The interfacial water exhibits much more ordering than bulk water. The results of radial distribution functions, mean square displacement and local self-diffusion coefficient for water molecule related to three oxygen moieties confirmed that the water molecules prefer to absorb with carboxylic groups, and adsorption of water molecules at the hydroxyl and carbonyl is similar.

The middeck 0-gravity dynamics experiment

NASA Technical Reports Server (NTRS)

Crawley, Edward F.; Vanschoor, Marthinus C.; Bokhour, Edward B.

1993-01-01

The Middeck 0-Gravity Dynamics Experiment (MODE), flown onboard the Shuttle STS-48 Mission, consists of three major elements: the Experiment Support Module, a dynamics test bed providing computer experiment control, analog signal conditioning, power conditioning, an operator interface consisting of a keypad and display, experiment electrical and thermal control, and archival data storage: the Fluid Test Article assembly, used to investigate the dynamics of fluid-structure interaction in 0-gravity; and the Structural Test Article for investigating the open-loop dynamics of structures in 0-gravity. Deployable, erectable, and rotary modules were assembled to form three one- and two-dimensional structures, in which variations in bracing wire and rotary joint preload could be introduced. Change in linear modal parameters as well as the change in nonlinear nature of the response is examined. Trends in modal parameters are presented as a function of force amplitude, joint preload, and ambient gravity. An experimental study of the lateral slosh behavior of contained fluids is also presented. A comparison of the measured earth and space results identifies and highlights the effects of gravity on the linear and nonlinear slosh behavior of these fluids.

Rotation of Guanine Amino Groups in G-Quadruplexes: A Probe for Local Structure and Ligand Binding.

PubMed

Adrian, Michael; Winnerdy, Fernaldo Richtia; Heddi, Brahim; Phan, Anh Tuân

2017-08-22

Nucleic acids are dynamic molecules whose functions may depend on their conformational fluctuations and local motions. In particular, amino groups are dynamic components of nucleic acids that participate in the formation of various secondary structures such as G-quadruplexes. Here, we present a cost-efficient NMR method to quantify the rotational dynamics of guanine amino groups in G-quadruplex nucleic acids. An isolated spectrum of amino protons from a specific tetrad-bound guanine can be extracted from the nuclear Overhauser effect spectroscopy spectrum based on the close proximity between the intra-residue imino and amino protons. We apply the method in different structural contexts of G-quadruplexes and their complexes. Our results highlight the role of stacking and hydrogen-bond interactions in restraining amino-group rotation. The measurement of the rotation rate of individual amino groups could give insight into the dynamic processes occurring at specific locations within G-quadruplex nucleic acids, providing valuable probes for local structure, dynamics, and ligand binding. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

At the Frontiers of Modeling Intensive Longitudinal Data: Dynamic Structural Equation Models for the Affective Measurements from the COGITO Study.

PubMed

Hamaker, E L; Asparouhov, T; Brose, A; Schmiedek, F; Muthén, B

2018-04-06

With the growing popularity of intensive longitudinal research, the modeling techniques and software options for such data are also expanding rapidly. Here we use dynamic multilevel modeling, as it is incorporated in the new dynamic structural equation modeling (DSEM) toolbox in Mplus, to analyze the affective data from the COGITO study. These data consist of two samples of over 100 individuals each who were measured for about 100 days. We use composite scores of positive and negative affect and apply a multilevel vector autoregressive model to allow for individual differences in means, autoregressions, and cross-lagged effects. Then we extend the model to include random residual variances and covariance, and finally we investigate whether prior depression affects later depression scores through the random effects of the daily diary measures. We end with discussing several urgent-but mostly unresolved-issues in the area of dynamic multilevel modeling.

Time Allocation in Social Networks: Correlation Between Social Structure and Human Communication Dynamics

NASA Astrophysics Data System (ADS)

Miritello, Giovanna; Lara, Rubén; Moro, Esteban

Recent research has shown the deep impact of the dynamics of human interactions (or temporal social networks) on the spreading of information, opinion formation, etc. In general, the bursty nature of human interactions lowers the interaction between people to the extent that both the speed and reach of information diffusion are diminished. Using a large database of 20 million users of mobile phone calls we show evidence this effect is not homogeneous in the social network but in fact, there is a large correlation between this effect and the social topological structure around a given individual. In particular, we show that social relations of hubs in a network are relatively weaker from the dynamical point than those that are poorer connected in the information diffusion process. Our results show the importance of the temporal patterns of communication when analyzing and modeling dynamical process on social networks.

A juvenile-adult population model: climate change, cannibalism, reproductive synchrony, and strong Allee effects.

PubMed

Veprauskas, Amy; Cushing, J M

2017-03-01

We study a discrete time, structured population dynamic model that is motivated by recent field observations concerning certain life history strategies of colonial-nesting gulls, specifically the glaucous-winged gull (Larus glaucescens). The model focuses on mechanisms hypothesized to play key roles in a population's response to degraded environment resources, namely, increased cannibalism and adjustments in reproductive timing. We explore the dynamic consequences of these mechanics using a juvenile-adult structure model. Mathematically, the model is unusual in that it involves a high co-dimension bifurcation at [Formula: see text] which, in turn, leads to a dynamic dichotomy between equilibrium states and synchronized oscillatory states. We give diagnostic criteria that determine which dynamic is stable. We also explore strong Allee effects caused by positive feedback mechanisms in the model and the possible consequence that a cannibalistic population can survive when a non-cannibalistic population cannot.

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.

Quantification of the effects of architectural traits on dry mass production and light interception of tomato canopy under different temperature regimes using a dynamic functional–structural plant model

PubMed Central

Chen, Tsu-Wei; Nguyen, Thi My Nguyet; Kahlen, Katrin; Stützel, Hartmut

2014-01-01

There is increasing interest in evaluating the environmental effects on crop architectural traits and yield improvement. However, crop models describing the dynamic changes in canopy structure with environmental conditions and the complex interactions between canopy structure, light interception, and dry mass production are only gradually emerging. Using tomato (Solanum lycopersicum L.) as a model crop, a dynamic functional–structural plant model (FSPM) was constructed, parameterized, and evaluated to analyse the effects of temperature on architectural traits, which strongly influence canopy light interception and shoot dry mass. The FSPM predicted the organ growth, organ size, and shoot dry mass over time with high accuracy (>85%). Analyses of this FSPM showed that, in comparison with the reference canopy, shoot dry mass may be affected by leaf angle by as much as 20%, leaf curvature by up to 7%, the leaf length:width ratio by up to 5%, internode length by up to 9%, and curvature ratios and leaf arrangement by up to 6%. Tomato canopies at low temperature had higher canopy density and were more clumped due to higher leaf area and shorter internodes. Interestingly, dry mass production and light interception of the clumped canopy were more sensitive to changes in architectural traits. The complex interactions between architectural traits, canopy light interception, dry mass production, and environmental conditions can be studied by the dynamic FSPM, which may serve as a tool for designing a canopy structure which is ‘ideal’ in a given environment. PMID:25183746

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.

Effect of Helicopter Blade Dynamics on Blade Aerodynamic and Structural Loads

NASA Technical Reports Server (NTRS)

Heffernan, Ruth M.

1987-01-01

The effect of rotor blade dynamics on aerodynamic and structural loads is examined for a conventional, main- rotor helicopter using both a comprehensive rotorcraft analysis (CAMRAD) and night test data. The impact of blade dynamics on blade section lift-coefficient time histories is studied by comparing predictions from both a rigid blade analysis and an elastic blade analysis with helicopter flight test data. The elastic blade analysis better predicts high-frequency behavior of section lift. In addition, components of the blade angle of attack, such as elastic blade twist, blade nap rate, blade slope velocity, and inflow, are examined as a function of blade mode. Elastic blade motion affects the blade angle of attack by a few tenths of a degree, and up to the sixth rotor harmonic. A similar study of the influence of blade dynamics on bending and torsion moments was also conducted. The modal analysis of the predicted blade structural loads suggested that five elastic bending deg of freedom (four flap and one lag) and three elastic torsion deg of freedom contributed to calculations of the blade structural loads. However, when structural bending load predictions from several elastic blade analyses were compared with flight test data, an elastic blade model consisting of only three elastic bending modes (first and second flap, and first lag), and two elastic torsion modes was found to be sufficient for maximum correlation.

Seasonal frost effects on the dynamic behavior of a twenty-story office building

USGS Publications Warehouse

Yang, Z.; Dutta, U.; Xiong, F.; Biswas, N.; Benz, H.

2008-01-01

Studies have shown that seasonal frost can significantly affect the seismic behavior of a bridge foundation system in cold regions. However, little information could be found regarding seasonal frost effects on the dynamic behavior of buildings. Based on the analysis of building vibration data recorded by a permanent strong-motion instrumentation system, the objective of this paper is to show that seasonal frost can impact the building dynamic behavior and the magnitude of impact may be different for different structures. Ambient noise and seismic data recorded on a twenty-story steel-frame building have been analyzed to examine the building dynamic characteristics in relationship to the seasonal frost and other variables including ground shaking intensity. Subsequently, Finite Element modeling of the foundation-soil system and the building superstructure was conducted to verify the seasonal frost effects. The Finite Element modeling was later extended to a reinforced-concrete (RC) type building assumed to exist at a similar site as the steel-frame building. Results show that the seasonal frost has great impact on the foundation stiffness in the horizontal direction and a clear influence on the building dynamic behavior. If other conditions remain the same, the effects of seasonal frost on structural dynamic behavior may be much more prominent for RC-type buildings than for steel-frame buildings. ?? 2007 Elsevier B.V. All rights reserved.

Dynamic curvature sensing employing ionic-polymer-metal composite sensors

NASA Astrophysics Data System (ADS)

Bahramzadeh, Yousef; Shahinpoor, Mohsen

2011-09-01

A dynamic curvature sensor is presented based on ionic-polymer-metal composite (IPMC) for curvature monitoring of deployable/inflatable dynamic space structures. Monitoring the curvature variation is of high importance in various engineering structures including shape monitoring of deployable/inflatable space structures in which the structural boundaries undergo a dynamic deployment process. The high sensitivity of IPMCs to the applied deformations as well as its flexibility make IPMCs a promising candidate for sensing of dynamic curvature changes. Herein, we explore the dynamic response of an IPMC sensor strip with respect to controlled curvature deformations subjected to different forms of input functions. Using a specially designed experimental setup, the voltage recovery effect, phase delay, and rate dependency of the output voltage signal of an IPMC curvature sensor are analyzed. Experimental results show that the IPMC sensor maintains the linearity, sensitivity, and repeatability required for curvature sensing. Besides, in order to describe the dynamic phenomena such as the rate dependency of the IPMC sensor, a chemo-electro-mechanical model based on the Poisson-Nernst-Planck (PNP) equation for the kinetics of ion diffusion is presented. By solving the governing partial differential equations the frequency response of the IPMC sensor is derived. The physical model is able to describe the dynamic properties of the IPMC sensor and the dependency of the signal on rate of excitations.

Effect of the lattice dynamics on the electronic structure of paramagnetic NiO within the disordered local moment picture

NASA Astrophysics Data System (ADS)

Mozafari, Elham; Alling, Björn; Belov, Maxim P.; Abrikosov, Igor A.

2018-01-01

Using the disordered local moments approach in combination with the ab initio molecular dynamics method, we simulate the behavior of a paramagnetic phase of NiO at finite temperatures to investigate the effect of magnetic disorder, thermal expansion, and lattice vibrations on its electronic structure. In addition, we study its lattice dynamics. We verify the reliability of our theoretical scheme via comparison of our results with available experiment and earlier theoretical studies carried out within static approximations. We present the phonon dispersion relations for the paramagnetic rock-salt (B1) phase of NiO and demonstrate that it is dynamically stable. We observe that including the magnetic disorder to simulate the paramagnetic phase has a small yet visible effect on the band gap. The amplitude of the local magnetic moment of Ni ions from our calculations for both antiferromagnetic and paramagnetic phases agree well with other theoretical and experimental values. We demonstrate that the increase of temperature up to 1000 K does not affect the electronic structure strongly. Taking into account the lattice vibrations and thermal expansion at higher temperatures have a major impact on the electronic structure, reducing the band gap from ˜3.5 eV at 600 K to ˜2.5 eV at 2000 K. We conclude that static lattice approximations can be safely employed in simulations of the paramagnetic state of NiO up to relatively high temperatures (˜1000 K), but as we get closer to the melting temperature vibrational effects become quite large and therefore should be included in the calculations.

Dynamic characterization of small fibers based on the flexural vibrations of a piezoelectric cantilever probe

NASA Astrophysics Data System (ADS)

Zhang, Xiaofei; Ye, Xuan; Li, Xide

2016-08-01

In this paper, we present a cantilever-probe system excited by a piezoelectric actuator, and use it to measure the dynamic mechanical properties of a micro- and nanoscale fiber. Coupling the fiber to the free end of the cantilever probe, we found the dynamic stiffness and damping coefficient of the fiber from the resonance frequency and the quality factor of the fiber-cantilever-probe system. The properties of Bacillus subtilis fibers measured using our proposed system agreed with tensile measurements, validating our method. Our measurements show that the piezoelectric actuator coupled to cantilever probe can be made equivalent to a clamped cantilever with an effective length, and calculated results show that the errors of measured natural frequency of the system can be ignored if the coupled fiber has an inclination angle of alignment of less than 10°. A sensitivity analysis indicates that the first or second resonant mode is the sensitive mode to test the sample’s dynamic stiffness, while the damping property has different sensitivities for the first four modes. Our theoretical analysis demonstrates that the double-cantilever probe is also an effective sensitive structure that can be used to perform dynamic loading and characterize dynamic response. Our method has the advantage of using amplitude-frequency curves to obtain the dynamic mechanical properties without directly measuring displacements and forces as in tensile tests, and it also avoids the effects of the complex surface structure and deformation presenting in contact resonance method. Our method is effective for measuring the dynamic mechanical properties of fiber-like one-dimensional (1D) materials.

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.

Fluid-structure interaction study of transcatheter aortic valve dynamics using smoothed particle hydrodynamics

PubMed Central

Mao, Wenbin; Li, Kewei; Sun, Wei

2016-01-01

Computational modeling of heart valve dynamics incorporating both fluid dynamics and valve structural responses has been challenging. In this study, we developed a novel fully-coupled fluid-structure interaction (FSI) model using smoothed particle hydrodynamics (SPH). A previously developed nonlinear finite element (FE) model of transcatheter aortic valves (TAV) was utilized to couple with SPH to simulate valve leaflet dynamics throughout the entire cardiac cycle. Comparative simulations were performed to investigate the impact of using FE-only models versus FSI models, as well as an isotropic versus an anisotropic leaflet material model in TAV simulations. From the results, substantial differences in leaflet kinematics between FE-only and FSI models were observed, and the FSI model could capture the realistic leaflet dynamic deformation due to its more accurate spatial and temporal loading conditions imposed on the leaflets. The stress and the strain distributions were similar between the FE and FSI simulations. However, the peak stresses were different due to the water hammer effect induced by the flow inertia in the FSI model during the closing phase, which led to 13%–28% lower peak stresses in the FE-only model compared to that of the FSI model. The simulation results also indicated that tissue anisotropy had a minor impact on hemodynamics of the valve. However, a lower tissue stiffness in the radial direction of the leaflets could reduce the leaflet peak stress caused by the water hammer effect. It is hoped that the developed FSI models can serve as an effective tool to better assess valve dynamics and optimize next generation TAV designs. PMID:27844463

Fluid-Structure Interaction Study of Transcatheter Aortic Valve Dynamics Using Smoothed Particle Hydrodynamics.

PubMed

Mao, Wenbin; Li, Kewei; Sun, Wei

2016-12-01

Computational modeling of heart valve dynamics incorporating both fluid dynamics and valve structural responses has been challenging. In this study, we developed a novel fully-coupled fluid-structure interaction (FSI) model using smoothed particle hydrodynamics (SPH). A previously developed nonlinear finite element (FE) model of transcatheter aortic valves (TAV) was utilized to couple with SPH to simulate valve leaflet dynamics throughout the entire cardiac cycle. Comparative simulations were performed to investigate the impact of using FE-only models vs. FSI models, as well as an isotropic vs. an anisotropic leaflet material model in TAV simulations. From the results, substantial differences in leaflet kinematics between FE-only and FSI models were observed, and the FSI model could capture the realistic leaflet dynamic deformation due to its more accurate spatial and temporal loading conditions imposed on the leaflets. The stress and the strain distributions were similar between the FE and FSI simulations. However, the peak stresses were different due to the water hammer effect induced by the fluid inertia in the FSI model during the closing phase, which led to 13-28% lower peak stresses in the FE-only model compared to that of the FSI model. The simulation results also indicated that tissue anisotropy had a minor impact on hemodynamics of the valve. However, a lower tissue stiffness in the radial direction of the leaflets could reduce the leaflet peak stress caused by the water hammer effect. It is hoped that the developed FSI models can serve as an effective tool to better assess valve dynamics and optimize next generation TAV designs.

Research on hysteresis loop considering the prestress effect and electrical input dynamics for a giant magnetostrictive actuator

NASA Astrophysics Data System (ADS)

Zhu, Yuchuan; Yang, Xulei; Wereley, Norman M.

2016-08-01

In this paper, focusing on the application-oriented giant magnetostrictive material (GMM)-based electro-hydrostatic actuator, which features an applied magnetic field at high frequency and high amplitude, and concentrating on the static and dynamic characteristics of a giant magnetostrictive actuator (GMA) considering the prestress effect on the GMM rod and the electrical input dynamics involving the power amplifier and the inductive coil, a methodology for studying the static and dynamic characteristics of a GMA using the hysteresis loop as a tool is developed. A GMA that can display the preforce on the GMM rod in real-time is designed, and a magnetostrictive model dependent on the prestress on a GMM rod instead of the existing quadratic domain rotation model is proposed. Additionally, an electrical input dynamics model to excite GMA is developed according to the simplified circuit diagram, and the corresponding parameters are identified by the experimental data. A dynamic magnetization model with the eddy current effect is deduced according to the Jiles-Atherton model and the Maxwell equations. Next, all of the parameters, including the electrical input characteristics, the dynamic magnetization and the mechanical structure of GMA, are identified by the experimental data from the current response, magnetization response and displacement response, respectively. Finally, a comprehensive comparison between the model results and experimental data is performed, and the results show that the test data agree well with the presented model results. An analysis on the relation between the GMA displacement response and the parameters from the electrical input dynamics, magnetization dynamics and mechanical structural dynamics is performed.

Seismic design of passive tuned mass damper parameters using active control algorithm

NASA Astrophysics Data System (ADS)

Chang, Chia-Ming; Shia, Syuan; Lai, Yong-An

2018-07-01

Tuned mass dampers are a widely-accepted control method to effectively reduce the vibrations of tall buildings. A tuned mass damper employs a damped harmonic oscillator with specific dynamic characteristics, thus the response of structures can be regulated by the additive dynamics. The additive dynamics are, however, similar to the feedback control system in active control. Therefore, the objective of this study is to develop a new tuned mass damper design procedure based on the active control algorithm, i.e., the H2/LQG control. This design facilitates the similarity of feedback control in the active control algorithm to determine the spring and damper in a tuned mass damper. Given a mass ratio between the damper and structure, the stiffness and damping coefficient of the tuned mass damper are derived by minimizing the response objective function of the primary structure, where the structural properties are known. Varying a single weighting in this objective function yields the optimal TMD design when the minimum peak in the displacement transfer function of the structure with the TMD is met. This study examines various objective functions as well as derives the associated equations to compute the stiffness and damping coefficient. The relationship between the primary structure and optimal tuned mass damper is parametrically studied. Performance is evaluated by exploring the h2-and h∞-norms of displacements and accelerations of the primary structure. In time-domain analysis, the damping effectiveness of the tune mass damper controlled structures is investigated under impulse excitation. Structures with the optimal tuned mass dampers are also assessed under seismic excitation. As a result, the proposed design procedure produces an effective tuned mass damper to be employed in a structure against earthquakes.

Stereochemistry and solvent role in protein folding: nuclear magnetic resonance and molecular dynamics studies of poly-L and alternating-L,D homopolypeptides in dimethyl sulfoxide.

PubMed

Srivastava, Kinshuk Raj; Kumar, Anil; Goyal, Bhupesh; Durani, Susheel

2011-05-26

The competing interactions folding and unfolding protein structure remain obscure. Using homopolypeptides, we ask if poly-L structure may have a role. We mutate the structure to alternating-L,D stereochemistry and substitute water as the fold-promoting solvent with methanol and dimethyl sulfoxide (DMSO) as the fold-denaturing solvents. Circular dichroism and molecular dynamics established previously that, while both isomers were folded in water, the poly-L isomer was unfolded and alternating-L,D isomer folded in methanol. Nuclear magnetic resonance and molecular dynamics establish now that both isomers are unfolded in DMSO. We calculated energetics of folding-unfolding equilibrium with water and methanol as solvents. We have now calculated interactions of unfolded polypeptide structures with DMSO as solvent. Methanol was found to unfold and water fold poly-L structure as a dielectric. DMSO has now been found to unfold both poly-L and alternating-L,D structures by strong solvation of peptides to disrupt their hydrogen bonds. Accordingly, we propose that while linked peptides fold protein structure with hydrogen bonds they unfold the structure electrostatically due to the stereochemical effect of the poly-L structure. Protein folding to ordering of peptide hydrogen bonds with water as canonical solvent may thus involve two specific and independent solvent effects-one, strong screening of electrostatics of poly-L linked peptides, and two, weak dipolar solvation of peptides. Correspondingly, protein denaturation may involve two independent solvent effects-one, weak dielectric to unfold poly-L structure electrostatically, and two, strong polarity to disrupt peptide hydrogen bonds by solvation of peptides.

Planetary Gearbox Fault Diagnosis Using a Single Piezoelectric Strain Sensor

DTIC Science & Technology

2014-12-23

However, the fault detection of planetary gearbox is very complicate since the c omplex nature of dynamic rolling structure of p lanetary gearbox...vibration transfer paths due to the unique dynamic structure of rotating planet gears. Therefore, it is difficult to diagnose PGB faults via vibration...al. 2014). To overcome the above mentioned challenges in developing effective PGB fau lt diagnosis capability , a research investigation on

Preoutbreak dynamics of a recently established invasive herbivore: roles of natural enemies and habitat structure in stage-specific performance of gypsy moth (Lepidoptera: Lymantriidae) populations in northeastern Wisconsin

Treesearch

Rebecca Hoffman Gray; Craig G. Lorimer; Patrick C. Tobin; Kenneth F. Raffa

2008-01-01

A major challenge to addressing biological invasions is that the need for emergency responses often precludes opportunities to analyze the dynamics between initial establishment and population eruption. Thus, a broader understanding of underlying processes and management opportunities is often lacking. We examined the effects of habitat structure and natural enemies on...

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

Kim, Sang Beom; Dsilva, Carmeline J.; Debenedetti, Pablo G., E-mail: pdebene@princeton.edu

Understanding the mechanisms by which proteins fold from disordered amino-acid chains to spatially ordered structures remains an area of active inquiry. Molecular simulations can provide atomistic details of the folding dynamics which complement experimental findings. Conventional order parameters, such as root-mean-square deviation and radius of gyration, provide structural information but fail to capture the underlying dynamics of the protein folding process. It is therefore advantageous to adopt a method that can systematically analyze simulation data to extract relevant structural as well as dynamical information. The nonlinear dimensionality reduction technique known as diffusion maps automatically embeds the high-dimensional folding trajectories inmore » a lower-dimensional space from which one can more easily visualize folding pathways, assuming the data lie approximately on a lower-dimensional manifold. The eigenvectors that parametrize the low-dimensional space, furthermore, are determined systematically, rather than chosen heuristically, as is done with phenomenological order parameters. We demonstrate that diffusion maps can effectively characterize the folding process of a Trp-cage miniprotein. By embedding molecular dynamics simulation trajectories of Trp-cage folding in diffusion maps space, we identify two folding pathways and intermediate structures that are consistent with the previous studies, demonstrating that this technique can be employed as an effective way of analyzing and constructing protein folding pathways from molecular simulations.« less

Enzymatic Transition States, Transition-State Analogs, Dynamics, Thermodynamics, and Lifetimes

PubMed Central

Schramm, Vern L.

2017-01-01

Experimental analysis of enzymatic transition-state structures uses kinetic isotope effects (KIEs) to report on bonding and geometry differences between reactants and the transition state. Computational correlation of experimental values with chemical models permits three-dimensional geometric and electrostatic assignment of transition states formed at enzymatic catalytic sites. The combination of experimental and computational access to transition-state information permits (a) the design of transition-state analogs as powerful enzymatic inhibitors, (b) exploration of protein features linked to transition-state structure, (c) analysis of ensemble atomic motions involved in achieving the transition state, (d) transition-state lifetimes, and (e) separation of ground-state (Michaelis complexes) from transition-state effects. Transition-state analogs with picomolar dissociation constants have been achieved for several enzymatic targets. Transition states of closely related isozymes indicate that the protein’s dynamic architecture is linked to transition-state structure. Fast dynamic motions in catalytic sites are linked to transition-state generation. Enzymatic transition states have lifetimes of femtoseconds, the lifetime of bond vibrations. Binding isotope effects (BIEs) reveal relative reactant and transition-state analog binding distortion for comparison with actual transition states. PMID:21675920

Dislocation pinning effects induced by nano-precipitates during warm laser shock peening: Dislocation dynamic simulation and experiments

NASA Astrophysics Data System (ADS)

Liao, Yiliang; Ye, Chang; Gao, Huang; Kim, Bong-Joong; Suslov, Sergey; Stach, Eric A.; Cheng, Gary J.

2011-07-01

Warm laser shock peening (WLSP) is a new high strain rate surface strengthening process that has been demonstrated to significantly improve the fatigue performance of metallic components. This improvement is mainly due to the interaction of dislocations with highly dense nanoscale precipitates, which are generated by dynamic precipitation during the WLSP process. In this paper, the dislocation pinning effects induced by the nanoscale precipitates during WLSP are systematically studied. Aluminum alloy 6061 and AISI 4140 steel are selected as the materials with which to conduct WLSP experiments. Multiscale discrete dislocation dynamics (MDDD) simulation is conducted in order to investigate the interaction of dislocations and precipitates during the shock wave propagation. The evolution of dislocation structures during the shock wave propagation is studied. The dislocation structures after WLSP are characterized via transmission electron microscopy and are compared with the results of the MDDD simulation. The results show that nano-precipitates facilitate the generation of highly dense and uniformly distributed dislocation structures. The dislocation pinning effect is strongly affected by the density, size, and space distribution of nano-precipitates.

NASA Handbook for Spacecraft Structural Dynamics Testing

NASA Technical Reports Server (NTRS)

Kern, Dennis L.; Scharton, Terry D.

2005-01-01

Recent advances in the area of structural dynamics and vibrations, in both methodology and capability, have the potential to make spacecraft system testing more effective from technical, cost, schedule, and hardware safety points of view. However, application of these advanced test methods varies widely among the NASA Centers and their contractors. Identification and refinement of the best of these test methodologies and implementation approaches has been an objective of efforts by the Jet Propulsion Laboratory on behalf of the NASA Office of the Chief Engineer. But to develop the most appropriate overall test program for a flight project from the selection of advanced methodologies, as well as conventional test methods, spacecraft project managers and their technical staffs will need overall guidance and technical rationale. Thus, the Chief Engineer's Office has recently tasked JPL to prepare a NASA Handbook for Spacecraft Structural Dynamics Testing. An outline of the proposed handbook, with a synopsis of each section, has been developed and is presented herein. Comments on the proposed handbook are solicited from the spacecraft structural dynamics testing community.

NASA Handbook for Spacecraft Structural Dynamics Testing

NASA Technical Reports Server (NTRS)

Kern, Dennis L.; Scharton, Terry D.

2004-01-01

Recent advances in the area of structural dynamics and vibrations, in both methodology and capability, have the potential to make spacecraft system testing more effective from technical, cost, schedule, and hardware safety points of view. However, application of these advanced test methods varies widely among the NASA Centers and their contractors. Identification and refinement of the best of these test methodologies and implementation approaches has been an objective of efforts by the Jet Propulsion Laboratory on behalf of the NASA Office of the Chief Engineer. But to develop the most appropriate overall test program for a flight project from the selection of advanced methodologies, as well as conventional test methods, spacecraft project managers and their technical staffs will need overall guidance and technical rationale. Thus, the Chief Engineer's Office has recently tasked JPL to prepare a NASA Handbook for Spacecraft Structural Dynamics Testing. An outline of the proposed handbook, with a synopsis of each section, has been developed and is presented herein. Comments on the proposed handbook is solicited from the spacecraft structural dynamics testing community.

Exploring Molecular Mechanisms of Paradoxical Activation in the BRAF Kinase Dimers: Atomistic Simulations of Conformational Dynamics and Modeling of Allosteric Communication Networks and Signaling Pathways

PubMed Central

Tse, Amanda; Verkhivker, Gennady M.

2016-01-01

The recent studies have revealed that most BRAF inhibitors can paradoxically induce kinase activation by promoting dimerization and enzyme transactivation. Despite rapidly growing number of structural and functional studies about the BRAF dimer complexes, the molecular basis of paradoxical activation phenomenon is poorly understood and remains largely hypothetical. In this work, we have explored the relationships between inhibitor binding, protein dynamics and allosteric signaling in the BRAF dimers using a network-centric approach. Using this theoretical framework, we have combined molecular dynamics simulations with coevolutionary analysis and modeling of the residue interaction networks to determine molecular determinants of paradoxical activation. We have investigated functional effects produced by paradox inducer inhibitors PLX4720, Dabrafenib, Vemurafenib and a paradox breaker inhibitor PLX7904. Functional dynamics and binding free energy analyses of the BRAF dimer complexes have suggested that negative cooperativity effect and dimer-promoting potential of the inhibitors could be important drivers of paradoxical activation. We have introduced a protein structure network model in which coevolutionary residue dependencies and dynamic maps of residue correlations are integrated in the construction and analysis of the residue interaction networks. The results have shown that coevolutionary residues in the BRAF structures could assemble into independent structural modules and form a global interaction network that may promote dimerization. We have also found that BRAF inhibitors could modulate centrality and communication propensities of global mediating centers in the residue interaction networks. By simulating allosteric communication pathways in the BRAF structures, we have determined that paradox inducer and breaker inhibitors may activate specific signaling routes that correlate with the extent of paradoxical activation. While paradox inducer inhibitors may facilitate a rapid and efficient communication via an optimal single pathway, the paradox breaker may induce a broader ensemble of suboptimal and less efficient communication routes. The central finding of our study is that paradox breaker PLX7904 could mimic structural, dynamic and network features of the inactive BRAF-WT monomer that may be required for evading paradoxical activation. The results of this study rationalize the existing structure-functional experiments by offering a network-centric rationale of the paradoxical activation phenomenon. We argue that BRAF inhibitors that amplify dynamic features of the inactive BRAF-WT monomer and intervene with the allosteric interaction networks may serve as effective paradox breakers in cellular environment. PMID:27861609

Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method.

PubMed

Molloy, Kevin; Shehu, Amarda

2013-01-01

Many proteins tune their biological function by transitioning between different functional states, effectively acting as dynamic molecular machines. Detailed structural characterization of transition trajectories is central to understanding the relationship between protein dynamics and function. Computational approaches that build on the Molecular Dynamics framework are in principle able to model transition trajectories at great detail but also at considerable computational cost. Methods that delay consideration of dynamics and focus instead on elucidating energetically-credible conformational paths connecting two functionally-relevant structures provide a complementary approach. Effective sampling-based path planning methods originating in robotics have been recently proposed to produce conformational paths. These methods largely model short peptides or address large proteins by simplifying conformational space. We propose a robotics-inspired method that connects two given structures of a protein by sampling conformational paths. The method focuses on small- to medium-size proteins, efficiently modeling structural deformations through the use of the molecular fragment replacement technique. In particular, the method grows a tree in conformational space rooted at the start structure, steering the tree to a goal region defined around the goal structure. We investigate various bias schemes over a progress coordinate for balance between coverage of conformational space and progress towards the goal. A geometric projection layer promotes path diversity. A reactive temperature scheme allows sampling of rare paths that cross energy barriers. Experiments are conducted on small- to medium-size proteins of length up to 214 amino acids and with multiple known functionally-relevant states, some of which are more than 13Å apart of each-other. Analysis reveals that the method effectively obtains conformational paths connecting structural states that are significantly different. A detailed analysis on the depth and breadth of the tree suggests that a soft global bias over the progress coordinate enhances sampling and results in higher path diversity. The explicit geometric projection layer that biases the exploration away from over-sampled regions further increases coverage, often improving proximity to the goal by forcing the exploration to find new paths. The reactive temperature scheme is shown effective in increasing path diversity, particularly in difficult structural transitions with known high-energy barriers.

Thermally-Induced Structural Disturbances of Rigid Panel Solar Arrays

NASA Technical Reports Server (NTRS)

Johnston, John D.; Thornton, Earl A.

1997-01-01

The performance of a significant number of spacecraft has been impacted negatively by attitude disturbances resulting from thermally-induced motions of flexible structures. Recent examples of spacecraft affected by these disturbances include the Hubble Space Telescope (HST) and the Upper Atmosphere Research Satellite (UARS). Thermally-induced structural disturbances occur as the result of rapid changes in thermal loading typically initiated as a satellite exits or enters the Earth's shadow. Temperature differences in flexible appendages give rise to structural deformations, which in turn result in disturbance torques reacting back on the spacecraft. Structures which have proven susceptible to these disturbances include deployable booms and solar arrays. This paper investigates disturbances resulting from thermally-induced deformations of rigid panel solar arrays. An analytical model for the thermal-structural response of the solar array and the corresponding disturbance torque are presented. The effect of these disturbances on the attitude dynamics of a simple spacecraft is then investigated using a coupled system of governing equations which includes the effects of thermally-induced deformations. Numerical results demonstrate the effect of varying solar array geometry on the dynamic response of the system.

How Life History Can Sway the Fixation Probability of Mutants

PubMed Central

Li, Xiang-Yi; Kurokawa, Shun; Giaimo, Stefano; Traulsen, Arne

2016-01-01

In this work, we study the effects of demographic structure on evolutionary dynamics when selection acts on reproduction, survival, or both. In contrast to the previously discovered pattern that the fixation probability of a neutral mutant decreases while the population becomes younger, we show that a mutant with a constant selective advantage may have a maximum or a minimum of the fixation probability in populations with an intermediate fraction of young individuals. This highlights the importance of life history and demographic structure in studying evolutionary dynamics. We also illustrate the fundamental differences between selection on reproduction and selection on survival when age structure is present. In addition, we evaluate the relative importance of size and structure of the population in determining the fixation probability of the mutant. Our work lays the foundation for also studying density- and frequency-dependent effects in populations when demographic structures cannot be neglected. PMID:27129737

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

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.

Integrated Aeromechanics with Three-Dimensional Solid-Multibody Structures

NASA Technical Reports Server (NTRS)

Datta, Anubhav; Johnson, Wayne

2014-01-01

A full three-dimensional finite element-multibody structural dynamic solver is coupled to a three-dimensional Reynolds-averaged Navier-Stokes solver for the prediction of integrated aeromechanical stresses and strains on a rotor blade in forward flight. The objective is to lay the foundations of all major pieces of an integrated three-dimensional rotor dynamic analysis - from model construction to aeromechanical solution to stress/strain calculation. The primary focus is on the aeromechanical solution. Two types of three-dimensional CFD/CSD interfaces are constructed for this purpose with an emphasis on resolving errors from geometry mis-match so that initial-stage approximate structural geometries can also be effectively analyzed. A three-dimensional structural model is constructed as an approximation to a UH-60A-like fully articulated rotor. The aerodynamic model is identical to the UH-60A rotor. For preliminary validation measurements from a UH-60A high speed flight is used where CFD coupling is essential to capture the advancing side tip transonic effects. The key conclusion is that an integrated aeromechanical analysis is indeed possible with three-dimensional structural dynamics but requires a careful description of its geometry and discretization of its parts.

Meta-ecosystem dynamics and functioning on finite spatial networks

PubMed Central

Marleau, Justin N.; Guichard, Frédéric; Loreau, Michel

2014-01-01

The addition of spatial structure to ecological concepts and theories has spurred integration between sub-disciplines within ecology, including community and ecosystem ecology. However, the complexity of spatial models limits their implementation to idealized, regular landscapes. We present a model meta-ecosystem with finite and irregular spatial structure consisting of local nutrient–autotrophs–herbivores ecosystems connected through spatial flows of materials and organisms. We study the effect of spatial flows on stability and ecosystem functions, and provide simple metrics of connectivity that can predict these effects. Our results show that high rates of nutrient and herbivore movement can destabilize local ecosystem dynamics, leading to spatially heterogeneous equilibria or oscillations across the meta-ecosystem, with generally increased meta-ecosystem primary and secondary production. However, the onset and the spatial scale of these emergent dynamics depend heavily on the spatial structure of the meta-ecosystem and on the relative movement rate of the autotrophs. We show how this strong dependence on finite spatial structure eludes commonly used metrics of connectivity, but can be predicted by the eigenvalues and eigenvectors of the connectivity matrix that describe the spatial structure and scale. Our study indicates the need to consider finite-size ecosystems in meta-ecosystem theory. PMID:24403323

Effects of creating two forest structures and using prescribed fire on coarse woody debris in northeastern California, USA

Treesearch

Fabian C. C. Uzoh; Carl N. Skinner

2009-01-01

Little is known about the dynamics of coarse woody debris (CWD) in forests that were originally characterized by frequent, low-moderate intensity fires. We investigated effects of prescribed burning at the Blacks Mountain Experimental Forest in northeastern California following creation of two stand structure conditions: 1) high structural diversity (HiD) that included...

The impact of natural transformation on adaptation in spatially structured bacterial populations.

PubMed

Moradigaravand, Danesh; Engelstädter, Jan

2014-06-20

Recent studies have demonstrated that natural transformation and the formation of highly structured populations in bacteria are interconnected. In spite of growing evidence about this connection, little is known about the dynamics of natural transformation in spatially structured bacterial populations. In this work, we model the interdependency between the dynamics of the bacterial gene pool and those of environmental DNA in space to dissect the effect of transformation on adaptation. Our model reveals that even with only a single locus under consideration, transformation with a free DNA fragment pool results in complex adaptation dynamics that do not emerge in previous models focusing only on the gene shuffling effect of transformation at multiple loci. We demonstrate how spatial restriction on population growth and DNA diffusion in the environment affect the impact of transformation on adaptation. We found that in structured bacterial populations intermediate DNA diffusion rates predominantly cause transformation to impede adaptation by spreading deleterious alleles in the population. Overall, our model highlights distinctive evolutionary consequences of bacterial transformation in spatially restricted compared to planktonic bacterial populations.

Nonlinear dynamic analysis of rigid rotor supported by gas foil bearings: Effects of gas film and foil structure on subsynchronous vibrations

NASA Astrophysics Data System (ADS)

Guo, Zhiyang; Feng, Kai; Liu, Tianyu; Lyu, Peng; Zhang, Tao

2018-07-01

Highly nonlinear subsynchronous vibrations are the main causing factors of failure in gas foil bearing (GFB)-rotor systems. Thus, investigating the vibration generation mechanisms and the relationship between subsynchronous vibrations and GFBs is necessary to ensure the healthy operation of rotor systems. In this study, an integrated nonlinear dynamic model with the consideration of shaft motion, unsteady gas film, and deformations of foil structure is established to investigate the effect of gas film and foil structure on system subsynchronous response. One test rig of GFB-rotor system is developed for model comparison. High agreement is shown between the prediction and test data, especially in the frequency domain. The nonlinear dynamic response is analyzed using waterfall plots, operation deflection shapes, journal orbits, Poincaré maps, and fast Fourier transforms. The parameter studies reveal that subsynchronous vibrations are highly related to gas film and foil structure. Subsynchronous vibrations can be adjusted by parameters such as bump stiffness, nominal clearance, and static loads. Therefore, gas foil bearing parameters should be carefully adjusted by system manufacturers to achieve the best rotordynamic performance.

Mesoscale simulation of the formation and dynamics of lipid-structured poly(ethylene oxide)-block-poly(methyl methacrylate) diblock copolymers.

PubMed

Mu, Dan; Li, Jian-Quan; Feng, Sheng-Yu

2015-05-21

Twelve poly(ethylene oxide)-block-poly(methyl methacrylate) (PEO-b-PMMA) copolymers with lipid-like structures were designed and investigated by MesoDyn simulation. Spherical and worm-like micelles as well as bicontinuous, lamellar and defected lamellar phases were obtained. A special structure, designated B2412, with two lipid structures connected by their heads, was found to undergo four stages prior to forming a spherical micelle phase. Two possible assembly mechanisms were found via thermodynamic and dynamic process analyses; namely, the fusion and fission of micelles in dynamic equilibrium during the adjustment stage. Water can be encapsulated into these micelles, which can affect their size, particularly in low concentration aqueous solutions. The assignment of weak negative charges to the hydrophilic EO blocks resulted in a clear effect on micelle size. Surprisingly, the largest effect was observed with EO blocks with -0.5 e, wherein an ordered perfect hexagonal phase was formed. The obtained results can be applied in numerous fields of study, including adsorption, catalysis, controlled release and drug delivery.

The wave attenuation mechanism of the periodic local resonant metamaterial

NASA Astrophysics Data System (ADS)

Chang, I.-Ling; Liang, Zhen-Xian; Kao, Hao-Wei; Chang, Shih-Hsiang; Yang, Chih-Ying

2018-01-01

This research discusses the wave propagation behavior and attenuation mechanism of the elastic metamaterial with locally resonant sub-structure. The dispersion relation of the single resonance system, i.e., periodic spring mass system with sub-structure, could be derived based on lattice dynamics and the band gap could be easily identified. The dynamically equivalent properties, i.e., mass and elastic property, of the single resonance system are derived and found to be frequency dependent. Negative effective properties are found in the vicinity of the local resonance. It is examined whether the band gap always coincides with the frequency range of negative effective properties. The wave attenuation mechanism and the characteristic dynamic behavior of the elastic metamaterial are also studied from the energy point of view. From the analysis, it is clarified that the coupled Bragg-resonance band gap is much wider than the narrow-banded local resonance and the corresponding effective material properties at band gap could be either positive or negative. However, the band gap is totally overlapping with the frequency range of negative effective properties for the metamaterial with band gap purely caused by local resonance. The presented analysis can be extended to other forms of elastic metamaterials involving periodic resonator structures.

Effect of the alien invasive bivalve Corbicula fluminea on the nutrient dynamics under climate change scenarios

NASA Astrophysics Data System (ADS)

Coelho, J. P.; Lillebø, A. I.; Crespo, D.; Leston, S.; Dolbeth, M.

2018-05-01

The main aim of this study was to evaluate the impact of the alien invasive bivalve Corbicula fluminea (Müller, 1774) in the nutrient dynamics of temperate estuarine systems (oligohaline areas) under climate change scenarios. The scenarios simulated shifts in climatic conditions, following salinity (0 or 5) and temperature (24 or 30 °C) changes, usual during drought and heat wave events. The effect of the individual size/age (different size classes with fixed biomass) and density (various densities of <1 cm clams) on the bioturbation-associated nutrient dynamics were also evaluated under an 18-day laboratory experimental setup. Results highlight the significant effect of C. fluminea on the ecosystem nutrient dynamics, enhancing the efflux of both phosphate and dissolved inorganic nitrogen (DIN) from the sediments to the water column. Both drought and heat wave events will have an impact on the DIN dynamics within C. fluminea colonized systems, favouring a higher NH4-N efflux. The population structure of C. fluminea will have a decisive role on the impact of the species, with stronger nutrient effluxes associated with a predominantly juvenile population structure.

A non-asymptotic model of dynamics of honeycomb lattice-type plates

NASA Astrophysics Data System (ADS)

Cielecka, Iwona; Jędrysiak, Jarosław

2006-09-01

Lightweight structures, consisted of special composite material systems like sandwich plates, are often used in aerospace or naval engineering. In composite sandwich plates, the intermediate core is usually made of cellular structures, e.g. honeycomb micro-frames, reinforcing static and dynamic properties of these plates. Here, a new non-asymptotic continuum model of honeycomb lattice-type plates is shown and applied to the analysis of dynamic problems. The general formulation of the model for periodic lattice-type plates of an arbitrary lay-out was presented by Cielecka and Jędrysiak [Journal of Theoretical and Applied Mechanics 40 (2002) 23-46]. This model, partly based on the tolerance averaging method developed for periodic composite solids by Woźniak and Wierzbicki [Averaging techniques in thermomechanics of composite solids, Wydawnictwo Politechniki Częstochowskiej, Częstochowa, 2000], takes into account the effect of the length microstructure size on the dynamic plate behaviour. The shown method leads to the model equations describing the above effect for honeycomb lattice-type plates. These equations have the form similar to equations for isotropic cases. The dynamic analysis of such plates exemplifies this effect, which is significant and cannot be neglected. The physical correctness of the obtained results is also discussed.

The dynamics and control of large flexible space structures. Part A: Discrete model and modal control

NASA Technical Reports Server (NTRS)

Bainum, P. M.; Sellappan, R.

1978-01-01

Attitude control techniques for the pointing and stabilization of very large, inherently flexible spacecraft systems were investigated. The attitude dynamics and control of a long, homogeneous flexible beam whose center of mass is assumed to follow a circular orbit was analyzed. First order effects of gravity gradient were included. A mathematical model which describes the system rotations and deflections within the orbital plane was developed by treating the beam as a number of discretized mass particles connected by massless, elastic structural elements. The uncontrolled dynamics of the system are simulated and, in addition, the effects of the control devices were considered. The concept of distributed modal control, which provides a means for controlling a system mode independently of all other modes, was examined. The effect of varying the number of modes in the model as well as the number and location of the control devices were also considered.

Nonlinear soil parameter effects on dynamic embedment of offshore pipeline on soft clay

NASA Astrophysics Data System (ADS)

Yu, Su Young; Choi, Han Suk; Lee, Seung Keon; Park, Kyu-Sik; Kim, Do Kyun

2015-06-01

In this paper, the effects of nonlinear soft clay on dynamic embedment of offshore pipeline were investigated. Seabed embedment by pipe-soil interactions has impacts on the structural boundary conditions for various subsea structures such as pipeline, riser, pile, and many other systems. A number of studies have been performed to estimate real soil behavior, but their estimation of seabed embedment has not been fully identified and there are still many uncertainties. In this regards, comparison of embedment between field survey and existing empirical models has been performed to identify uncertainties and investigate the effect of nonlinear soil parameter on dynamic embedment. From the comparison, it is found that the dynamic embedment with installation effects based on nonlinear soil model have an influence on seabed embedment. Therefore, the pipe embedment under dynamic condition by nonlinear parameters of soil models was investigated by Dynamic Embedment Factor (DEF) concept, which is defined as the ratio of the dynamic and static embedment of pipeline, in order to overcome the gap between field embedment and currently used empirical and numerical formula. Although DEF through various researches is suggested, its range is too wide and it does not consider dynamic laying effect. It is difficult to find critical parameters that are affecting to the embedment result. Therefore, the study on dynamic embedment factor by soft clay parameters of nonlinear soil model was conducted and the sensitivity analyses about parameters of nonlinear soil model were performed as well. The tendency on dynamic embedment factor was found by conducting numerical analyses using OrcaFlex software. It is found that DEF was influenced by shear strength gradient than other factors. The obtained results will be useful to understand the pipe embedment on soft clay seabed for applying offshore pipeline designs such as on-bottom stability and free span analyses.

Structural analysis of oligomeric and protofibrillar Aβ amyloid pair structures considering F20L mutation effects using molecular dynamics simulations.

PubMed

Lee, Myeongsang; Chang, Hyun Joon; Baek, Inchul; Na, Sungsoo

2017-04-01

Aβ amyloid proteins are involved in neuro-degenerative diseases such as Alzheimer's, Parkinson's, and so forth. Because of its structurally stable feature under physiological conditions, Aβ amyloid protein disrupts the normal cell function. Because of these concerns, understanding the structural feature of Aβ amyloid protein in detail is crucial. There have been some efforts on lowering the structural stabilities of Aβ amyloid fibrils by decreasing the aromatic residues characteristic and hydrophobic effect. Yet, there is a lack of understanding of Aβ amyloid pair structures considering those effects. In this study, we provide the structural characteristics of wildtype (WT) and phenylalanine residue mutation to leucine (F20L) Aβ amyloid pair structures using molecular dynamics simulation in detail. We also considered the polymorphic feature of F20L and WT Aβ pair amyloids based on the facing β-strand directions between the amyloid pairs. As a result, we were able to observe the varying effects of mutation, polymorphism, and protofibril lengths on the structural stability of pair amyloids. Furthermore, we have also found that opposite structural stability exists on a certain polymorphic Aβ pair amyloids depending on its oligomeric or protofibrillar state, which can be helpful for understanding the amyloid growth mechanism via repetitive fragmentation and elongation mechanism. Proteins 2017; 85:580-592. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Seismology in civil engineering

NASA Astrophysics Data System (ADS)

Dvorak, A.

Properties of soils and rocks exposed to vibrations in the practice of civil engineering are examined. Seismic and dynamic field investigations, determination of seismic and dynamic modulus of elasticity, coefficients of damping and absorption are studied. Seismic effects of blasting and of other sources of vibrations on structures and persons, application of rock-noise and dynamic tests of piles are studied.

A Knowledge-Structure-Based Adaptive Dynamic Assessment System for Calculus Learning

ERIC Educational Resources Information Center

Ting, M.-Y.; Kuo, B.-C.

2016-01-01

The purpose of this study was to investigate the effect of a calculus system that was designed using an adaptive dynamic assessment (DA) framework on performance in the "finding an area using an integral". In this study, adaptive testing and dynamic assessment were combined to provide different test items depending on students'…

Parsing in a Dynamical System: An Attractor-Based Account of the Interaction of Lexical and Structural Constraints in Sentence Processing.

ERIC Educational Resources Information Center

Tabor, Whitney; And Others

1997-01-01

Proposes a dynamical systems approach to parsing in which syntactic hypotheses are associated with attractors in a metric space. The experiments discussed documented various contingent frequency effects that cut across traditional linguistic grains, each of which was predicted by the dynamical systems model. (47 references) (Author/CK)

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.

Conformational changes in intact dengue virus reveal serotype-specific expansion

PubMed Central

Lim, Xin-Xiang; Chandramohan, Arun; Lim, Xin Ying Elisa; Bag, Nirmalya; Sharma, Kamal Kant; Wirawan, Melissa; Wohland, Thorsten; Lok, Shee-Mei; Anand, Ganesh S.

2017-01-01

Dengue virus serotype 2 (DENV2) alone undergoes structural expansion at 37 °C (associated with host entry), despite high sequence and structural homology among the four known serotypes. The basis for this differential expansion across strains and serotypes is unknown and necessitates mapping of the dynamics of dengue whole viral particles to describe their coordinated motions and conformational changes when exposed to host-like environments. Here we capture the dynamics of intact viral particles of two serotypes, DENV1 and DENV2, by amide hydrogen/deuterium exchange mass spectrometry (HDXMS) and time resolved Förster Resonance Energy Transfer. Our results show temperature-dependent dynamics hotspots on DENV2 and DENV1 particles with DENV1 showing expansion at 40 °C but not at 37 °C. HDXMS measurement of virion dynamics in solution offers a powerful approach to identify potential epitopes, map virus-antibody complex structure and dynamics, and test effects of multiple host-specific perturbations on viruses and virus-antibody complexes. PMID:28186093

Molecular Dynamics Methodologies for Probing Cannabinoid Ligand/Receptor Interaction

PubMed Central

Lynch, Diane L.; Hurst, Dow P.; Shore, Derek M.; Pitman, Mike C.; Reggio, Patricia H.

2018-01-01

The cannabinoid type 1 and 2 G-protein-coupled receptors are currently important pharmacological targets with significant drug discovery potential. These receptors have been shown to display functional selectivity or biased agonism, a property currently thought to have substantial therapeutic potential. Although recent advances in crystallization techniques have provided a wealth of structural information about this important class of membrane-embedded proteins, these structures lack dynamical information. In order to fully understand the interplay of structure and function for this important class of proteins, complementary techniques that address the dynamical aspects of their function are required such as NMR as well as a variety of other spectroscopies. Complimentary to these experimental approaches is molecular dynamics, which has been effectively used to help unravel, at the atomic level, the dynamics of ligand binding and activation of these membrane-bound receptors. Here, we discuss and present several representative examples of the application of molecular dynamics simulations to the understanding of the signatures of ligand-binding and -biased signaling at the cannabinoid type 1 and 2 receptors. PMID:28750815

Microscopic observation of carrier-transport dynamics in quantum-structure solar cells using a time-of-flight technique

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

Toprasertpong, Kasidit; Fujii, Hiromasa; Sugiyama, Masakazu

2015-07-27

In this study, we propose a carrier time-of-flight technique to evaluate the carrier transport time across a quantum structure in an active region of solar cells. By observing the time-resolved photoluminescence signal with a quantum-well probe inserted under the quantum structure at forward bias, the carrier transport time can be efficiently determined at room temperature. The averaged drift velocity shows linear dependence on the internal field, allowing us to estimate the quantum structure as a quasi-bulk material with low effective mobility containing the information of carrier dynamics. We show that this direct and real-time observation is more sensitive to carriermore » transport than other conventional techniques, providing better insights into microscopic carrier transport dynamics to overcome a device design difficulty.« less

Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI

NASA Astrophysics Data System (ADS)

Alba, Josephine; Marcaida, Maria Jose; Prieto, Jesus; Montoya, Guillermo; Molina, Rafael; D'Abramo, Marco

2017-12-01

I-DmoI, from the hyperthermophilic archaeon Desulfurococcus mobilis, belongs to the LAGLIDADG homing endonuclease protein family. Its members are highly specific enzymes capable of recognizing long DNA target sequences, thus providing potential tools for genome manipulation. Working towards this particular application, many efforts have been made to generate mesophilic variants of I-DmoI that function at lower temperatures than the wild-type. Here, we report a structural and computational analysis of two I-DmoI mesophilic mutants. Despite very limited structural variations between the crystal structures of these variants and the wild-type, a different dynamical behaviour near the cleavage sites is observed. In particular, both the dynamics of the water molecules and the protein perturbation effect on the cleavage site correlate well with the changes observed in the experimental enzymatic activity.

Simulating Food Web Dynamics along a Gradient: Quantifying Human Influence

PubMed Central

Jordán, Ferenc; Gjata, Nerta; Mei, Shu; Yule, Catherine M.

2012-01-01

Realistically parameterized and dynamically simulated food-webs are useful tool to explore the importance of the functional diversity of ecosystems, and in particular relations between the dynamics of species and the whole community. We present a stochastic dynamical food web simulation for the Kelian River (Borneo). The food web was constructed for six different locations, arrayed along a gradient of increasing human perturbation (mostly resulting from gold mining activities) along the river. Along the river, the relative importance of grazers, filterers and shredders decreases with increasing disturbance downstream, while predators become more dominant in governing eco-dynamics. Human activity led to increased turbidity and sedimentation which adversely impacts primary productivity. Since the main difference between the study sites was not the composition of the food webs (structure is quite similar) but the strengths of interactions and the abundance of the trophic groups, a dynamical simulation approach seemed to be useful to better explain human influence. In the pristine river (study site 1), when comparing a structural version of our model with the dynamical model we found that structurally central groups such as omnivores and carnivores were not the most important ones dynamically. Instead, primary consumers such as invertebrate grazers and shredders generated a greater dynamical response. Based on the dynamically most important groups, bottom-up control is replaced by the predominant top-down control regime as distance downstream and human disturbance increased. An important finding, potentially explaining the poor structure to dynamics relationship, is that indirect effects are at least as important as direct ones during the simulations. We suggest that our approach and this simulation framework could serve systems-based conservation efforts. Quantitative indicators on the relative importance of trophic groups and the mechanistic modeling of eco-dynamics could greatly contribute to understanding various aspects of functional diversity. PMID:22768346

14 CFR 25.629 - Aeroelastic stability requirements.

Code of Federal Regulations, 2012 CFR

2012-01-01

... weights are used, their effectiveness and strength, including supporting structure, must be substantiated... of any single element of the structure supporting any engine, independently mounted propeller shaft... dynamic forces, any single failure of the engine structure that would reduce the rigidity of the...

14 CFR 25.629 - Aeroelastic stability requirements.

Code of Federal Regulations, 2014 CFR

2014-01-01

... weights are used, their effectiveness and strength, including supporting structure, must be substantiated... of any single element of the structure supporting any engine, independently mounted propeller shaft... dynamic forces, any single failure of the engine structure that would reduce the rigidity of the...

14 CFR 25.629 - Aeroelastic stability requirements.

Code of Federal Regulations, 2011 CFR

2011-01-01

... weights are used, their effectiveness and strength, including supporting structure, must be substantiated... of any single element of the structure supporting any engine, independently mounted propeller shaft... dynamic forces, any single failure of the engine structure that would reduce the rigidity of the...

14 CFR 25.629 - Aeroelastic stability requirements.

Code of Federal Regulations, 2013 CFR

2013-01-01

... weights are used, their effectiveness and strength, including supporting structure, must be substantiated... of any single element of the structure supporting any engine, independently mounted propeller shaft... dynamic forces, any single failure of the engine structure that would reduce the rigidity of the...

Interpersonal Dynamics and Organizational Change in Religious Communities.

ERIC Educational Resources Information Center

Barber, William H.; Rock, Leo P.

This paper discusses the organizational structure of religious communities and its effect on interpersonal relations. Religious communities tend to be organized structurally according to the traditional bureaucratic model of (1) relatively rigid structure; (2) carefully defined functional specialization; (3) direction and control implemented…

A Procedure for Modeling Structural Component/Attachment Failure Using Transient Finite Element Analysis

NASA Technical Reports Server (NTRS)

Lovejoy, Andrew E.; Jegley, Dawn C. (Technical Monitor)

2007-01-01

Structures often comprise smaller substructures that are connected to each other or attached to the ground by a set of finite connections. Under static loading one or more of these connections may exceed allowable limits and be deemed to fail. Of particular interest is the structural response when a connection is severed (failed) while the structure is under static load. A transient failure analysis procedure was developed by which it is possible to examine the dynamic effects that result from introducing a discrete failure while a structure is under static load. The failure is introduced by replacing a connection load history by a time-dependent load set that removes the connection load at the time of failure. The subsequent transient response is examined to determine the importance of the dynamic effects by comparing the structural response with the appropriate allowables. Additionally, this procedure utilizes a standard finite element transient analysis that is readily available in most commercial software, permitting the study of dynamic failures without the need to purchase software specifically for this purpose. The procedure is developed and explained, demonstrated on a simple cantilever box example, and finally demonstrated on a real-world example, the American Airlines Flight 587 (AA587) vertical tail plane (VTP).

Disease-emergence dynamics and control in a socially-structured wildlife species

NASA Astrophysics Data System (ADS)

Pepin, Kim M.; Vercauteren, Kurt C.

2016-04-01

Once a pathogen is introduced in a population, key factors governing rate of spread include contact structure, supply of susceptible individuals and pathogen life-history. We examined the interplay of these factors on emergence dynamics and efficacy of disease prevention and response. We contrasted transmission dynamics of livestock viruses with different life-histories in hypothetical populations of feral swine with different contact structures (homogenous, metapopulation, spatial and network). Persistence probability was near 0 for the FMDV-like case under a wide range of parameter values and contact structures, while persistence was probable for the CSFV-like case. There were no sets of conditions where the FMDV-like pathogen persisted in every stochastic simulation. Even when population growth rates were up to 300% annually, the FMDV-like pathogen persisted in <25% of simulations regardless of transmission probabilities and contact structure. For networks and spatial contact structure, persistence probability of the FMDV-like pathogen was always <10%. Because of its low persistence probability, even very early response to the FMDV-like pathogen in feral swine was unwarranted while response to the CSFV-like pathogen was generally effective. When pre-emergence culling of feral swine caused population declines, it was effective at decreasing outbreak size of both diseases by ≥80%.

The effects of disulfide bonds on the denatured state of barnase.

PubMed Central

Clarke, J.; Hounslow, A. M.; Bond, C. J.; Fersht, A. R.; Daggett, V.

2000-01-01

The effects of engineered disulfide bonds on protein stability are poorly understood because they can influence the structure, dynamics, and energetics of both the native and denatured states. To explore the effects of two engineered disulfide bonds on the stability of barnase, we have conducted a combined molecular dynamics and NMR study of the denatured state of the two mutants. As expected, the disulfide bonds constrain the denatured state. However, specific extended beta-sheet structure can also be detected in one of the mutant proteins. This mutant is also more stable than would be predicted. Our study suggests a possible cause of the very high stability conferred by this disulfide bond: the wild-type denatured ensemble is stabilized by a nonnative hydrophobic cluster, which is constrained from occurring in the mutant due to the formation of secondary structure. PMID:11206061

Memory Effect Manifested by a Boson Peak in Metallic Glass.

PubMed

Luo, P; Li, Y Z; Bai, H Y; Wen, P; Wang, W H

2016-04-29

We explore the correlation between a boson peak and structural relaxation in a typical metallic glass. Consistent with enthalpy recovery, a boson peak shows a memory effect in an aging-and-scan procedure. Single-step isothermal aging produces a monotonic decrease of enthalpy and boson peak intensity; for double-step isothermal aging, both enthalpy and boson peak intensity experience, coincidently, an incipient increase to a maximum and a subsequent decrease toward the equilibrium state. Our results indicate a direct link between slow structural relaxation and fast boson peak dynamics, which presents a profound understanding of the two dynamic behaviors in glass.

Understanding the structural and dynamic consequences of DNA epigenetic modifications: Computational insights into cytosine methylation and hydroxymethylation

PubMed Central

Carvalho, Alexandra T P; Gouveia, Leonor; Kanna, Charan Raju; Wärmländer, Sebastian K T S; Platts, Jamie A; Kamerlin, Shina Caroline Lynn

2014-01-01

We report a series of molecular dynamics (MD) simulations of up to a microsecond combined simulation time designed to probe epigenetically modified DNA sequences. More specifically, by monitoring the effects of methylation and hydroxymethylation of cytosine in different DNA sequences, we show, for the first time, that DNA epigenetic modifications change the molecule's dynamical landscape, increasing the propensity of DNA toward different values of twist and/or roll/tilt angles (in relation to the unmodified DNA) at the modification sites. Moreover, both the extent and position of different modifications have significant effects on the amount of structural variation observed. We propose that these conformational differences, which are dependent on the sequence environment, can provide specificity for protein binding. PMID:25625845

Tensor of effective susceptibility in random magnetic composites: Application to two-dimensional and three-dimensional cases

NASA Astrophysics Data System (ADS)

Posnansky, Oleg P.

2018-05-01

The measuring of dynamic magnetic susceptibility by nuclear magnetic resonance is used for revealing information about the internal structure of various magnetoactive composites. The response of such material on the applied external static and time-varying magnetic fields encodes intrinsic dynamic correlations and depends on links between macroscopic effective susceptibility and structure on the microscopic scale. In the current work we carried out computational analysis of the frequency dependent dynamic magnetic susceptibility and demonstrated its dependence on the microscopic architectural elements while also considering Euclidean dimensionality. The proposed numerical method is efficient in the simulation of nuclear magnetic resonance experiments in two- and three-dimensional random magnetic media by choosing and modeling the influence of the concentration of components and internal hierarchical characteristics of physical parameters.

Consequences of stage-structured predators: cannibalism, behavioral effects, and trophic cascades.

PubMed

Rudolf, Volker H W

2007-12-01

Cannibalistic and asymmetrical behavioral interactions between stages are common within stage-structured predator populations. Such direct interactions between predator stages can result in density- and trait-mediated indirect interactions between a predator and its prey. A set of structured predator-prey models is used to explore how such indirect interactions affect the dynamics and structure of communities. Analyses of the separate and combined effects of stage-structured cannibalism and behavior-mediated avoidance of cannibals under different ecological scenarios show that both cannibalism and behavioral avoidance of cannibalism can result in short- and long-term positive indirect connections between predator stages and the prey, including "apparent mutualism." These positive interactions alter the strength of trophic cascades such that the system's dynamics are determined by the interaction between bottom-up and top-down effects. Contrary to the expectation of simpler models, enrichment increases both predator and prey abundance in systems with cannibalism or behavioral avoidance of cannibalism. The effect of behavioral avoidance of cannibalism, however, depends on how strongly it affects the maturation rate of the predator. Behavioral interactions between predator stages reduce the short-term positive effect of cannibalism on the prey density, but can enhance its positive long-term effects. Both interaction types reduce the destabilizing effect of enrichment. These results suggest that inconsistencies between data and simple models can be resolved by accounting for stage-structured interactions within and among species.

A displacement-based approach for determining non-linear effects on pre-tensioned-cable cross-braced structures

NASA Astrophysics Data System (ADS)

Giaccu, Gian Felice; Caracoglia, Luca

2017-04-01

Pre-tensioned-cable bracing systems are widely employed in structural engineering to limit lateral deflections and stabilize structures. A suitable configuration of the pre-tensioned-cable bracing systems in a structure is an important issue since the internal force distribution, emerging from the interaction with the existing structure, significantly affects the structural dynamic behavior. The design, however, is often based on the intuition and the previous experience of the engineer. In recent years, the authors have been investigating the non-linear dynamic response of cable systems, installed on cable-stayed bridges, and in particular the so-called "cable-cross-tie systems" forming a cable network. The bracing cables (cross-ties) can exhibit slackening or snapping. Therefore, a non-linear unilateral model, combined with the taut-cable theory, is required to simulate the incipient slackening conditions in the stays. Capitalizing from this work on non-linear cable dynamics, this paper proposes a new approach to analyze, in laterally- braced truss structures, the unilateral effects and dynamic response accounting for the loss in the pre-tensioning force imparted to the bracing cables. This effect leads to non-linear vibration of the structure. In this preliminary study, the free vibrations of the structure are investigated by using the "Equivalent Linearization Method". A performance coefficient, a real positive number between 0.5 and 1.0, is defined and employed to monitor the relative reduction in the apparent stiffness of the braces during structural vibration, "mode by mode". It is shown that the system can exhibit alternate unilateral behavior of the cross-braces. A reduction of the performance coefficient close to fifty percent is observed in the braces when the initial pre-tensioning force is small. On the other hand the performance coefficient tends to one in the case of a high level of pre-stress. It is concluded that the performance coefficient may possibly be used as an indicator for the design of the braces since a suitable selection of the initial pre-tensioning force can avoid slackening in the braces.

Structure and Entanglement Factors on Dynamics of Polymer-Grafted Nanoparticles

DOE PAGES

Liu, Siqi; Senses, Erkan; Jiao, Yang; ...

2016-04-15

Nanoparticles functionalized with long polymer chains at low graft density are interesting systems to study structure–dynamic relationships in polymer nanocomposites since they are shown to aggregate into strings in both solution and melts and also into spheres and branched aggregates in the presence of free polymer chains. Our work investigates structure and entanglement effects in composites of polystyrene-grafted iron oxide nanoparticles by measuring particle relaxations using X-ray photon correlation spectroscopy. And for particles within highly ordered strings and aggregated systems, they experience a dynamically heterogeneous environment displaying hyperdiffusive relaxation commonly observed in jammed soft glassy systems. Furthermore, particle dynamics ismore » diffusive for branched aggregated structures which could be caused by less penetration of long matrix chains into brushes. These results suggest that particle motion is dictated by the strong interactions of chains grafted at low density with the host matrix polymer.« less

A financial network perspective of financial institutions' systemic risk contributions

NASA Astrophysics Data System (ADS)

Huang, Wei-Qiang; Zhuang, Xin-Tian; Yao, Shuang; Uryasev, Stan

2016-08-01

This study considers the effects of the financial institutions' local topology structure in the financial network on their systemic risk contribution using data from the Chinese stock market. We first measure the systemic risk contribution with the Conditional Value-at-Risk (CoVaR) which is estimated by applying dynamic conditional correlation multivariate GARCH model (DCC-MVGARCH). Financial networks are constructed from dynamic conditional correlations (DCC) with graph filtering method of minimum spanning trees (MSTs). Then we investigate dynamics of systemic risk contributions of financial institution. Also we study dynamics of financial institution's local topology structure in the financial network. Finally, we analyze the quantitative relationships between the local topology structure and systemic risk contribution with panel data regression analysis. We find that financial institutions with greater node strength, larger node betweenness centrality, larger node closeness centrality and larger node clustering coefficient tend to be associated with larger systemic risk contributions.

Control-structure interaction study for the Space Station solar dynamic power module

NASA Technical Reports Server (NTRS)

Cheng, J.; Ianculescu, G.; Ly, J.; Kim, M.

1991-01-01

The authors investigate the feasibility of using a conventional PID (proportional plus integral plus derivative) controller design to perform the pointing and tracking functions for the Space Station Freedom solar dynamic power module. Using this simple controller design, the control/structure interaction effects were also studied without assuming frequency bandwidth separation. From the results, the feasibility of a simple solar dynamic control solution with a reduced-order model, which satisfies the basic system pointing and stability requirements, is suggested. However, the conventional control design approach is shown to be very much influenced by the order of reduction of the plant model, i.e., the number of the retained elastic modes from the full-order model. This suggests that, for complex large space structures, such as the Space Station Freedom solar dynamic, the conventional control system design methods may not be adequate.

Molecular Dynamics Studies of Structure and Functions of Water-Membrane Interfaces

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Wilson, Michael A.; DeVincenzi, Donald L. (Technical Monitor)

2001-01-01

A large number of essential cellular processes occur at the interfaces between water and membranes. The selectivity and dynamics of these processes are largely determined by the structural and electrical properties of the water-membrane interface. We investigate these properties by the molecular dynamics method. Over the time scales of the simulations, the membrane undergoes fluctuations described by the capillary wave model. These fluctuations produce occasional thinning defects in the membrane which provide effective pathways for passive transport of ions and small molecules across the membrane. Ions moving through the membrane markedly disrupt its structure and allow for significant water penetration into the membrane interior. Selectivity of transport, with respect to ionic charge, is determined by the interfacial electrostatic potential. Many small molecules. of potential significance in catalysis, bioenergetics and pharmacology, are shown to bind to the interface. The energetics and dynamics of this process will be discussed.

Graph distance for complex networks

NASA Astrophysics Data System (ADS)

Shimada, Yutaka; Hirata, Yoshito; Ikeguchi, Tohru; Aihara, Kazuyuki

2016-10-01

Networks are widely used as a tool for describing diverse real complex systems and have been successfully applied to many fields. The distance between networks is one of the most fundamental concepts for properly classifying real networks, detecting temporal changes in network structures, and effectively predicting their temporal evolution. However, this distance has rarely been discussed in the theory of complex networks. Here, we propose a graph distance between networks based on a Laplacian matrix that reflects the structural and dynamical properties of networked dynamical systems. Our results indicate that the Laplacian-based graph distance effectively quantifies the structural difference between complex networks. We further show that our approach successfully elucidates the temporal properties underlying temporal networks observed in the context of face-to-face human interactions.

Dynamic Magnification Factor in a Box-Shape Steel Girder

NASA Astrophysics Data System (ADS)

Rahbar-Ranji, A.

2014-01-01

The dynamic effect of moving loads on structures is treated as a dynamic magnification factor when resonant is not imminent. Studies have shown that the calculated magnification factors from field measurements could be higher than the values specified in design codes. It is the main aim of present paper to investigate the applicability and accuracy of a rule-based expression for calculation of dynamic magnification factor for lifting appliances used in marine industry. A steel box shape girder of a crane is considered and transient dynamic analysis using computer code ANSYS is implemented. Dynamic magnification factor is calculated for different loading conditions and compared with rule-based equation. The effects of lifting speeds, acceleration, damping ratio and position of cargo are examined. It is found that rule-based expression underestimate dynamic magnification factor.

Untangleing the effects of chain rigidity on the structure and dynamics of strongly adsorbed polymer melts

DOE PAGES

Carrillo, Jan-Michael Y.; Cheng, Shiwang; Kumar, Rajeev; ...

2015-06-11

Here, we present a detailed analysis of coarse-grained molecular dynamics simulations of semiflexible polymer melts in contact with a strongly adsorbing substrate. We have characterized the segments in the interfacial layer by counting the number of trains, loops, tails and unadsorbed segments. For more rigid chains, a tail and an adsorbed segment (a train) dominate while loops are more prevalent in more flexible chains. The tails exhibit a non-uniformly stretched conformation akin to the polydispersed pseudobrush envisioned by Guiselin. To probe the dynamics of the segments we computed the layer z-resolved intermediate coherent collective dynamics structure factor, S(q, t, z),more » mean-square displacement of segments, and the 2nd Legendre polynomial of the time-autocorrelation of unit bond vectors, 2[n i(t,z)•n i(0,z)]>. Our results show that segmental dynamics is slower for stiffer chains and there is a strong correlation between the structure and dynamics in the interfacial layer. There is no glassy layer, and the slowing down in dynamics of stiffer chains in the adsorbed region can be attributed to the densification and the more persistent layering of segments.« less

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.

Ultrafast electronic dynamics in unipolar n-doped indium gallium arsenide/gallium arsenide self-assembled quantum dots

NASA Astrophysics Data System (ADS)

Wu, Zong-Kwei J.

2006-12-01

Photodetectors based on intraband infrared absorption in the quantum dots have demonstrated improved performance over its quantum well counterpart by lower dark current, relative temperature insensitivity, and its ability for normal incidence operation. Various scattering processes, including phonon emission/absorption and carrier-carrier scattering, are critical in understanding device operation on the fundamental level. In previous studies, our group has investigated carrier dynamics in both low- and high-density regime. Ultrafast electron-hole scattering and the predicted phonon bottleneck effect in intrinsic quantum dots have been observed. Further examination on electron dynamics in unipolar structures is presented in this thesis. We used n-doped quantum dot in mid-infrared photodetector device structure to study the electron dynamics in unipolar structure. Differential transmission spectroscopy with mid-infrared intraband pump and optical interband probe was implemented to measure the electron dynamics directly without creating extra electron-hole pair, Electron relaxation after excitation was measured under various density and temperature conditions. Rapid capture into quantum dot within ˜ 10 ps was observed due to Auger-type electron-electron scattering. Intradot relaxation from the quantum dot excited state to the ground state was also observed on the time scale of 100 ps. With highly doped electron density in the structure, the inter-sublevel relaxation is dominated by Auger-type electron-electron scattering and the phonon bottleneck effect is circumvented. Nanosecond-scale recovery in larger-sized quantum dots was observed, not intrinsic to electron dynamics but due to band-bending and built-in voltage drift. An ensemble Monte Carlo simulation was also established to model the dynamics in quantum dots and in goad agreement with the experimental results. We presented a comprehensive picture of electron dynamics in the unipolar quantum dot structure. Although the phonon bottleneck is circumvented with high doped electron density, relaxation processes in unipolar quantum dots have been measured with time scales longer than that of bipolar systems. The results explain the operation principles of the quantum dot infrared photodetector on a microscopic level and provide basic understanding for future applications and designs.

Static Tensile and Transient Dynamic Response of Cracked Aluminum Plate Repaired with Composite Patch - Numerical Study

NASA Astrophysics Data System (ADS)

Khalili, S. M. R.; Shariyat, M.; Mokhtari, M.

2014-06-01

In this study, the central cracked aluminum plates repaired with two sided composite patches are investigated numerically for their response to static tensile and transient dynamic loadings. Contour integral method is used to define and evaluate the stress intensity factors at the crack tips. The reinforcement for the composite patches is carbon fibers. The effect of adhesive thickness and patch thickness and configuration in tensile loading case and pre-tension, pre-compression and crack length effect on the evolution of the mode I stress intensity factor (SIF) (KI) of the repaired structure under transient dynamic loading case are examined. The results indicated that KI of the central cracked plate is reduced by 1/10 to 1/2 as a result of the bonded composite patch repair in tensile loading case. The crack length and the pre-loads are more effective in repaired structure in transient dynamic loading case in which, the 100 N pre-compression reduces the maximum KI for about 40 %, and the 100 N pre-tension reduces the maximum KI after loading period, by about 196 %.

Drug resistance conferred by mutations outside the active site through alterations in the dynamic and structural ensemble of HIV-1 protease.

PubMed

Ragland, Debra A; Nalivaika, Ellen A; Nalam, Madhavi N L; Prachanronarong, Kristina L; Cao, Hong; Bandaranayake, Rajintha M; Cai, Yufeng; Kurt-Yilmaz, Nese; Schiffer, Celia A

2014-08-27

HIV-1 protease inhibitors are part of the highly active antiretroviral therapy effectively used in the treatment of HIV infection and AIDS. Darunavir (DRV) is the most potent of these inhibitors, soliciting drug resistance only when a complex combination of mutations occur both inside and outside the protease active site. With few exceptions, the role of mutations outside the active site in conferring resistance remains largely elusive. Through a series of DRV-protease complex crystal structures, inhibition assays, and molecular dynamics simulations, we find that single and double site mutations outside the active site often associated with DRV resistance alter the structure and dynamic ensemble of HIV-1 protease active site. These alterations correlate with the observed inhibitor binding affinities for the mutants, and suggest a network hypothesis on how the effect of distal mutations are propagated to pivotal residues at the active site and may contribute to conferring drug resistance.

CFD Fuel Slosh Modeling of Fluid-Structure Interaction in Spacecraft Propellant Tanks with Diaphragms

NASA Technical Reports Server (NTRS)

Sances, Dillon J.; Gangadharan, Sathya N.; Sudermann, James E.; Marsell, Brandon

2010-01-01

Liquid sloshing within spacecraft propellant tanks causes rapid energy dissipation at resonant modes, which can result in attitude destabilization of the vehicle. Identifying resonant slosh modes currently requires experimental testing and mechanical pendulum analogs to characterize the slosh dynamics. Computational Fluid Dynamics (CFD) techniques have recently been validated as an effective tool for simulating fuel slosh within free-surface propellant tanks. Propellant tanks often incorporate an internal flexible diaphragm to separate ullage and propellant which increases modeling complexity. A coupled fluid-structure CFD model is required to capture the damping effects of a flexible diaphragm on the propellant. ANSYS multidisciplinary engineering software employs a coupled solver for analyzing two-way Fluid Structure Interaction (FSI) cases such as the diaphragm propellant tank system. Slosh models generated by ANSYS software are validated by experimental lateral slosh test results. Accurate data correlation would produce an innovative technique for modeling fuel slosh within diaphragm tanks and provide an accurate and efficient tool for identifying resonant modes and the slosh dynamic response.

Aspirin locally disrupts the liquid-ordered phase

NASA Astrophysics Data System (ADS)

Alsop, Richard J.; Himbert, Sebastian; Dhaliwal, Alexander; Schmalzl, Karin; Rheinstädter, Maikel C.

2018-02-01

Local structure and dynamics of lipid membranes play an important role in membrane function. The diffusion of small molecules, the curvature of lipids around a protein and the existence of cholesterol-rich lipid domains (rafts) are examples for the membrane to serve as a functional interface. The collective fluctuations of lipid tails, in particular, are relevant for diffusion of membrane constituents and small molecules in and across membranes, and for structure and formation of membrane domains. We studied the effect of aspirin (acetylsalicylic acid, ASA) on local structure and dynamics of membranes composed of dimyristoylphosphocholine (DMPC) and cholesterol. Aspirin is a common analgesic, but is also used in the treatment of cholesterol. Using coherent inelastic neutron scattering experiments and molecular dynamics (MD) simulations, we present evidence that ASA binds to liquid-ordered, raft-like domains and disturbs domain organization and dampens collective fluctuations. By hydrogen-bonding to lipid molecules, ASA forms `superfluid' complexes with lipid molecules that can organize laterally in superlattices and suppress cholesterol's ordering effect.

Molecular dynamics of conformational substates for a simplified protein model

NASA Astrophysics Data System (ADS)

Grubmüller, Helmut; Tavan, Paul

1994-09-01

Extended molecular dynamics simulations covering a total of 0.232 μs have been carried out on a simplified protein model. Despite its simplified structure, that model exhibits properties similar to those of more realistic protein models. In particular, the model was found to undergo transitions between conformational substates at a time scale of several hundred picoseconds. The computed trajectories turned out to be sufficiently long as to permit a statistical analysis of that conformational dynamics. To check whether effective descriptions neglecting memory effects can reproduce the observed conformational dynamics, two stochastic models were studied. A one-dimensional Langevin effective potential model derived by elimination of subpicosecond dynamical processes could not describe the observed conformational transition rates. In contrast, a simple Markov model describing the transitions between but neglecting dynamical processes within conformational substates reproduced the observed distribution of first passage times. These findings suggest, that protein dynamics generally does not exhibit memory effects at time scales above a few hundred picoseconds, but confirms the existence of memory effects at a picosecond time scale.

Linking Structural Equation Modelling with Bayesian Network and Coastal Phytoplankton Dynamics in Bohai Bay

NASA Astrophysics Data System (ADS)

Chu, Jiangtao; Yang, Yue

2018-06-01

Bayesian networks (BN) have many advantages over other methods in ecological modelling and have become an increasingly popular modelling tool. However, BN are flawed in regard to building models based on inadequate existing knowledge. To overcome this limitation, we propose a new method that links BN with structural equation modelling (SEM). In this method, SEM is used to improve the model structure for BN. This method was used to simulate coastal phytoplankton dynamics in Bohai Bay. We demonstrate that this hybrid approach minimizes the need for expert elicitation, generates more reasonable structures for BN models and increases the BN model's accuracy and reliability. These results suggest that the inclusion of SEM for testing and verifying the theoretical structure during the initial construction stage improves the effectiveness of BN models, especially for complex eco-environment systems. The results also demonstrate that in Bohai Bay, while phytoplankton biomass has the greatest influence on phytoplankton dynamics, the impact of nutrients on phytoplankton dynamics is larger than the influence of the physical environment in summer. Furthermore, despite the Redfield ratio indicating that phosphorus should be the primary nutrient limiting factor, our results indicate that silicate plays the most important role in regulating phytoplankton dynamics in Bohai Bay.

Cytoskeletal mechanics: Structure and Dynamics

NASA Astrophysics Data System (ADS)

Bausch, Andreas

2008-03-01

The actin cytoskeleton, a dynamic network of semiflexible filaments and associated regulatory proteins, is responsible for the extraordinary viscoelastic properties of cells. Especially for cellular motility the controlled self assembly to defined structures and the dynamic reorganization on different time scales are of outstanding importance. A prominent example for the controlled self assembly are actin bundles: in many cytoskeletal processes cells rely on the tight control of the structural and mechanical properties of the actin bundles. Using an in vitro model system we show that size control relies on a mismatch between the helical structure of individual actin filaments and the packing symmetry within bundles. While such self assembled structure may evoke the picture of a static network the contrary is the case: the cytoskeleton is highly dynamic and a constant remodeling takes place in vivo. Such dynamic reorganization of the cytoskeleton relies on the non-static nature of single actin/ABP bonds. Here, we study the thermal and forced unbinding events of individual ABP in such in vitro networks. The binding kinetics of the transient crosslinkers determines the mechanical response of such networks -- in the linear as well in the non-linear regime. These effects are important prerequisites for the high adaptability of cells and at the same time might be the molecular mechanism employed by them for mechanosensing.

The Effect of Dynamic Assessment on L2 Grammar Acquisition by Iranian EFL Learners

ERIC Educational Resources Information Center

Kamali, Mojtaba; Abbasi, Mehdi; Sadighi, Firooz

2018-01-01

This study investigated the effect of dynamic Assessment (DA) on the acquisition of L2 grammar by EFL learners. The focus was on teaching Conditional Type II, or Unreal Conditional, which is a difficult structure for language learners to acquire. To this end, two intact classes of intermediate EFL learners, each consisting of 23 male students were…

The effects of wind disturbance on temperate rain forest structure and dynamics of southeast Alaska.

Treesearch

Gregory J. Nowacki; Marc G. Kramer

1998-01-01

Wind disturbance plays a fundamental role in shaping forest dynamics in southeast Alaska. Recent studies have increased our appreciation for the effects of wind at both large and small scales. Current thinking is that wind disturbance characteristics change over a continuum dependent on landscape features (e.g., exposure, landscape position, topography). Data modeling...

An examination of dynamics crosstalk between SH2 and SH3 domains by hydrogen/deuterium exchange and mass spectrometry

PubMed Central

Hochrein, James M.; Lerner, Edwina C.; Schiavone, Anthony P.; Smithgall, Thomas E.; Engen, John R.

2006-01-01

The ability of proteins to regulate their own enzymatic activity can be facilitated by changes in structure or protein dynamics in response to external regulators. Because many proteins contain SH2 and SH3 domains, transmission of information between the domains is a potential method of allosteric regulation. To determine if ligand binding to one modular domain may alter structural dynamics in an adjacent domain, allowing potential transmission of information through the protein, we used hydrogen exchange and mass spectrometry to measure changes in protein dynamics in the SH3 and SH2 domains of hematopoietic cell kinase (Hck). Ligand binding to either domain had little or no effect on hydrogen exchange in the adjacent domain, suggesting that changes in protein structure or dynamics are not a means of SH2/SH3 crosstalk. Furthermore, ligands of varying affinity covalently attached to SH3/SH2 altered dynamics only in the domain to which they bind. Such results demonstrate that ligand binding may not structurally alter adjacent SH3/SH2 domains and implies that other aspects of protein architecture contribute to the multiple levels of regulation in proteins containing SH3 and SH2 domains. PMID:16322569

Optimization of rotor blades for combined structural, dynamic, and aerodynamic properties

NASA Technical Reports Server (NTRS)

He, Cheng-Jian; Peters, David A.

1990-01-01

Optimal helicopter blade design with computer-based mathematical programming has received more and more attention in recent years. Most of the research has focused on optimum dynamic characteristics of rotor blades to reduce vehicle vibration. There is also work on optimization of aerodynamic performance and on composite structural design. This research has greatly increased our understanding of helicopter optimum design in each of these aspects. Helicopter design is an inherently multidisciplinary process involving strong interactions among various disciplines which can appropriately include aerodynamics; dynamics, both flight dynamics and structural dynamics; aeroelasticity: vibrations and stability; and even acoustics. Therefore, the helicopter design process must satisfy manifold requirements related to the aforementioned diverse disciplines. In our present work, we attempt to combine several of these important effects in a unified manner. First, we design a blade with optimum aerodynamic performance by proper layout of blade planform and spanwise twist. Second, the blade is designed to have natural frequencies that are placed away from integer multiples of the rotor speed for a good dynamic characteristics. Third, the structure is made as light as possible with sufficient rotational inertia to allow for autorotational landing, with safe stress margins and flight fatigue life at each cross-section, and with aeroelastical stability and low vibrations. Finally, a unified optimization refines the solution.

Structure and dynamics of single hydrophobic/ionic heteropolymers at the vapor-liquid interface of water.

PubMed

Vembanur, Srivathsan; Venkateshwaran, Vasudevan; Garde, Shekhar

2014-04-29

We focus on the conformational stability, structure, and dynamics of hydrophobic/charged homopolymers and heteropolymers at the vapor-liquid interface of water using extensive molecular dynamics simulations. Hydrophobic polymers collapse into globular structures in bulk water but unfold and sample a broad range of conformations at the vapor-liquid interface of water. We show that adding a pair of charges to a hydrophobic polymer at the interface can dramatically change its conformations, stabilizing hairpinlike structures, with molecular details depending on the location of the charged pair in the sequence. The translational dynamics of homopolymers and heteropolymers are also different, whereas the homopolymers skate on the interface with low drag, the tendency of charged groups to remain hydrated pulls the heteropolymers toward the liquid side of the interface, thus pinning them, increasing drag, and slowing the translational dynamics. The conformational dynamics of heteropolymers are also slower than that of the homopolymer and depend on the location of the charged groups in the sequence. Conformational dynamics are most restricted for the end-charged heteropolymer and speed up as the charge pair is moved toward the center of the sequence. We rationalize these trends using the fundamental understanding of the effects of the interface on primitive pair-level interactions between two hydrophobic groups and between oppositely charged ions in its vicinity.

Lift enhancement by bats' dynamically changing wingspan

PubMed Central

Wang, Shizhao; Zhang, Xing; He, Guowei; Liu, Tianshu

2015-01-01

This paper elucidates the aerodynamic role of the dynamically changing wingspan in bat flight. Based on direct numerical simulations of the flow over a slow-flying bat, it is found that the dynamically changing wingspan can significantly enhance the lift. Further, an analysis of flow structures and lift decomposition reveal that the elevated vortex lift associated with the leading-edge vortices intensified by the dynamically changing wingspan considerably contributed to enhancement of the time-averaged lift. The nonlinear interaction between the dynamically changing wing and the vortical structures plays an important role in the lift enhancement of a flying bat in addition to the geometrical effect of changing the lifting-surface area in a flapping cycle. In addition, the dynamically changing wingspan leads to the higher efficiency in terms of generating lift for a given amount of the mechanical energy consumed in flight. PMID:26701882

Influence of the piezoelectric parameters on the dynamics of an active rotor

NASA Astrophysics Data System (ADS)

Gawryluk, Jarosław; Mitura, Andrzej; Teter, Andrzej

2018-01-01

The main aim of this paper is an experimental and numerical analysis of the dynamic behavior of an active rotor with three composite blades. The study focuses on developing an effective FE modeling technique of a macro fiber composite element (denoted as MFC or active element) for the dynamic tests of active structures. The active rotor under consideration consists of a hub with a drive shaft, three grips and three glass-epoxy laminate blades with embedded active elements. A simplified FE model of the macro fiber composite element exhibiting the d33 piezoelectric effect is developed using the Abaqus software package. The discussed transducer is modeled as quasi-homogeneous piezoelectric material, and voltage is applied to the opposite faces of the element. In this case, the effective (equivalent) piezoelectric constant d33* is specified. Both static and dynamic tests are performed to verify the proposed model. First, static deflections of the active blade caused by the voltage signal are determined by numerical and experimental analyses. Next, a numerical modal analysis of the active rotor is performed. The eigenmodes and corresponding eigenfrequencies are determined by the Lanczos method. The influence of the model parameters (i.e., the effective piezoelectric constant d33 *, voltage signal, angular velocity) on the dynamics of the active rotor is examined. Finally, selected numerical results are validated in experimental tests. The experimental findings demonstrate that the structural stiffening effect caused by the active element strongly depends on the value of the effective piezoelectric constant.

Crystal structure and equation of state of Fe-Si alloys at super-Earth core conditions

PubMed Central

Fratanduono, Dayne E.; Coppari, Federica; Newman, Matthew G.; Duffy, Thomas S.

2018-01-01

The high-pressure behavior of Fe alloys governs the interior structure and dynamics of super-Earths, rocky extrasolar planets that could be as much as 10 times more massive than Earth. In experiments reaching up to 1300 GPa, we combine laser-driven dynamic ramp compression with in situ x-ray diffraction to study the effect of composition on the crystal structure and density of Fe-Si alloys, a potential constituent of super-Earth cores. We find that Fe-Si alloy with 7 weight % (wt %) Si adopts the hexagonal close-packed structure over the measured pressure range, whereas Fe-15wt%Si is observed in a body-centered cubic structure. This study represents the first experimental determination of the density and crystal structure of Fe-Si alloys at pressures corresponding to the center of a ~3–Earth mass terrestrial planet. Our results allow for direct determination of the effects of light elements on core radius, density, and pressures for these planets. PMID:29707632

Crystal structure and equation of state of Fe-Si alloys at super-Earth core conditions

DOE PAGES

Wicks, June K.; Smith, Raymond F.; Fratanduono, Dayne E.; ...

2018-04-25

In this paper, the high-pressure behavior of Fe alloys governs the interior structure and dynamics of super-Earths, rocky extrasolar planets that could be as much as ten times more massive than Earth. In experiments reaching up to 1300 GPa, we combine laser-driven dynamic ramp compression with in situ X-ray diffraction to study the effect of composition on the crystal structure and density of Fe-Si alloys, a potential constituent of super-Earth cores. We find that Fe-7wt.%Si adopts the hexagonal close packed (hcp) structure over the measured pressure range, whereas Fe-15wt.%Si is observed in a body-centered cubic (bcc) structure. This study representsmore » the first experimental determination of the density and crystal structure of Fe-Si alloys at pressures corresponding to the center of a ~3 Earth-mass terrestrial planet. Our results allow for direct determination of the effects of light elements on core radius, density, and pressures for such planets.« less

Crystal structure and equation of state of Fe-Si alloys at super-Earth core conditions

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

Wicks, June K.; Smith, Raymond F.; Fratanduono, Dayne E.

In this paper, the high-pressure behavior of Fe alloys governs the interior structure and dynamics of super-Earths, rocky extrasolar planets that could be as much as ten times more massive than Earth. In experiments reaching up to 1300 GPa, we combine laser-driven dynamic ramp compression with in situ X-ray diffraction to study the effect of composition on the crystal structure and density of Fe-Si alloys, a potential constituent of super-Earth cores. We find that Fe-7wt.%Si adopts the hexagonal close packed (hcp) structure over the measured pressure range, whereas Fe-15wt.%Si is observed in a body-centered cubic (bcc) structure. This study representsmore » the first experimental determination of the density and crystal structure of Fe-Si alloys at pressures corresponding to the center of a ~3 Earth-mass terrestrial planet. Our results allow for direct determination of the effects of light elements on core radius, density, and pressures for such planets.« less

The dynamic programming high-order Dynamic Bayesian Networks learning for identifying effective connectivity in human brain from fMRI.

PubMed

Dang, Shilpa; Chaudhury, Santanu; Lall, Brejesh; Roy, Prasun Kumar

2017-06-15

Determination of effective connectivity (EC) among brain regions using fMRI is helpful in understanding the underlying neural mechanisms. Dynamic Bayesian Networks (DBNs) are an appropriate class of probabilistic graphical temporal-models that have been used in past to model EC from fMRI, specifically order-one. High-order DBNs (HO-DBNs) have still not been explored for fMRI data. A fundamental problem faced in the structure-learning of HO-DBN is high computational-burden and low accuracy by the existing heuristic search techniques used for EC detection from fMRI. In this paper, we propose using dynamic programming (DP) principle along with integration of properties of scoring-function in a way to reduce search space for structure-learning of HO-DBNs and finally, for identifying EC from fMRI which has not been done yet to the best of our knowledge. The proposed exact search-&-score learning approach HO-DBN-DP is an extension of the technique which was originally devised for learning a BN's structure from static data (Singh and Moore, 2005). The effectiveness in structure-learning is shown on synthetic fMRI dataset. The algorithm reaches globally-optimal solution in appreciably reduced time-complexity than the static counterpart due to integration of properties. The proof of optimality is provided. The results demonstrate that HO-DBN-DP is comparably more accurate and faster than currently used structure-learning algorithms used for identifying EC from fMRI. The real data EC from HO-DBN-DP shows consistency with previous literature than the classical Granger Causality method. Hence, the DP algorithm can be employed for reliable EC estimates from experimental fMRI data. Copyright © 2017 Elsevier B.V. All rights reserved.

Structure of a tethered polymer under flow using molecular dynamics and hybrid molecular-continuum simulations

NASA Astrophysics Data System (ADS)

Delgado-Buscalioni, Rafael; Coveney, Peter V.

2006-03-01

We analyse the structure of a single polymer tethered to a solid surface undergoing a Couette flow. We study the problem using molecular dynamics (MD) and hybrid MD-continuum simulations, wherein the polymer and the surrounding solvent are treated via standard MD, and the solvent flow farther away from the polymer is solved by continuum fluid dynamics (CFD). The polymer represents a freely jointed chain (FJC) and is modelled by Lennard-Jones (LJ) beads interacting through the FENE potential. The solvent (modelled as a LJ fluid) and a weakly attractive wall are treated at the molecular level. At large shear rates the polymer becomes more elongated than predicted by existing theoretical scaling laws. Also, along the normal-to-wall direction the structure observed for the FJC is, surprisingly, very similar to that predicted for a semiflexible chain. Comparison with previous Brownian dynamics simulations (which exclude both solvent and wall potential) indicates that these effects are due to the polymer-solvent and polymer-wall interactions. The hybrid simulations are in perfect agreement with the MD simulations, showing no trace of finite size effects. Importantly, the extra cost required to couple the MD and CFD domains is negligible.

Modeling and Analysis of Structural Dynamics for a One-Tenth Scale Model NGST Sunshield

NASA Technical Reports Server (NTRS)

Johnston, John; Lienard, Sebastien; Brodeur, Steve (Technical Monitor)

2001-01-01

New modeling and analysis techniques have been developed for predicting the dynamic behavior of the Next Generation Space Telescope (NGST) sunshield. The sunshield consists of multiple layers of pretensioned, thin-film membranes supported by deployable booms. Modeling the structural dynamic behavior of the sunshield is a challenging aspect of the problem due to the effects of membrane wrinkling. A finite element model of the sunshield was developed using an approximate engineering approach, the cable network method, to account for membrane wrinkling effects. Ground testing of a one-tenth scale model of the NGST sunshield were carried out to provide data for validating the analytical model. A series of analyses were performed to predict the behavior of the sunshield under the ground test conditions. Modal analyses were performed to predict the frequencies and mode shapes of the test article and transient response analyses were completed to simulate impulse excitation tests. Comparison was made between analytical predictions and test measurements for the dynamic behavior of the sunshield. In general, the results show good agreement with the analytical model correctly predicting the approximate frequency and mode shapes for the significant structural modes.

Gyration-radius dynamics in structural transitions of atomic clusters.

PubMed

Yanao, Tomohiro; Koon, Wang S; Marsden, Jerrold E; Kevrekidis, Ioannis G

2007-03-28

This paper is concerned with the structural transition dynamics of the six-atom Morse cluster with zero total angular momentum, which serves as an illustrative example of the general reaction dynamics of isolated polyatomic molecules. It develops a methodology that highlights the interplay between the effects of the potential energy topography and those of the intrinsic geometry of the molecular internal space. The method focuses on the dynamics of three coarse variables, the molecular gyration radii. By using the framework of geometric mechanics and hyperspherical coordinates, the internal motions of a molecule are described in terms of these three gyration radii and hyperangular modes. The gyration radii serve as slow collective variables, while the remaining hyperangular modes serve as rapidly oscillating "bath" modes. Internal equations of motion reveal that the gyration radii are subject to two different kinds of forces: One is the ordinary force that originates from the potential energy function of the system, while the other is an internal centrifugal force. The latter originates from the dynamical coupling of the gyration radii with the hyperangular modes. The effects of these two forces often counteract each other: The potential force generally works to keep the internal mass distribution of the system compact and symmetric, while the internal centrifugal force works to inflate and elongate it. Averaged fields of these two forces are calculated numerically along a reaction path for the structural transition of the molecule in the three-dimensional space of gyration radii. By integrating the sum of these two force fields along the reaction path, an effective energy curve is deduced, which quantifies the gross work necessary for the system to change its mass distribution along the reaction path. This effective energy curve elucidates the energy-dependent switching of the structural preference between symmetric and asymmetric conformations. The present methodology should be of wide use for the systematic reduction of dimensionality as well as for the identification of kinematic barriers associated with the rearrangement of mass distribution in a variety of molecular reaction dynamics in vacuum.

Gyration-radius dynamics in structural transitions of atomic clusters

NASA Astrophysics Data System (ADS)

Yanao, Tomohiro; Koon, Wang S.; Marsden, Jerrold E.; Kevrekidis, Ioannis G.

2007-03-01

This paper is concerned with the structural transition dynamics of the six-atom Morse cluster with zero total angular momentum, which serves as an illustrative example of the general reaction dynamics of isolated polyatomic molecules. It develops a methodology that highlights the interplay between the effects of the potential energy topography and those of the intrinsic geometry of the molecular internal space. The method focuses on the dynamics of three coarse variables, the molecular gyration radii. By using the framework of geometric mechanics and hyperspherical coordinates, the internal motions of a molecule are described in terms of these three gyration radii and hyperangular modes. The gyration radii serve as slow collective variables, while the remaining hyperangular modes serve as rapidly oscillating "bath" modes. Internal equations of motion reveal that the gyration radii are subject to two different kinds of forces: One is the ordinary force that originates from the potential energy function of the system, while the other is an internal centrifugal force. The latter originates from the dynamical coupling of the gyration radii with the hyperangular modes. The effects of these two forces often counteract each other: The potential force generally works to keep the internal mass distribution of the system compact and symmetric, while the internal centrifugal force works to inflate and elongate it. Averaged fields of these two forces are calculated numerically along a reaction path for the structural transition of the molecule in the three-dimensional space of gyration radii. By integrating the sum of these two force fields along the reaction path, an effective energy curve is deduced, which quantifies the gross work necessary for the system to change its mass distribution along the reaction path. This effective energy curve elucidates the energy-dependent switching of the structural preference between symmetric and asymmetric conformations. The present methodology should be of wide use for the systematic reduction of dimensionality as well as for the identification of kinematic barriers associated with the rearrangement of mass distribution in a variety of molecular reaction dynamics in vacuum.

Visualizing Structure and Dynamics of Disaccharide Simulations

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

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

2012-01-01

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

Dynamical Coordination of Hand Intrinsic Muscles for Precision Grip in Diabetes Mellitus.

PubMed

Li, Ke; Wei, Na; Cheng, Mei; Hou, Xingguo; Song, Jun

2018-03-12

This study investigated the effects of diabetes mellitus (DM) on dynamical coordination of hand intrinsic muscles during precision grip. Precision grip was tested using a custom designed apparatus with stable and unstable loads, during which the surface electromyographic (sEMG) signals of the abductor pollicis brevis (APB) and first dorsal interosseous (FDI) were recorded simultaneously. Recurrence quantification analysis (RQA) was applied to quantify the dynamical structure of sEMG signals of the APB and FDI; and cross recurrence quantification analysis (CRQA) was used to assess the intermuscular coupling between the two intrinsic muscles. This study revealed that the DM altered the dynamical structure of muscle activation for the FDI and the dynamical intermuscular coordination between the APB and FDI during precision grip. A reinforced feedforward mechanism that compensates the loss of sensory feedbacks in DM may be responsible for the stronger intermuscular coupling between the APB and FDI muscles. Sensory deficits in DM remarkably decreased the capacity of online motor adjustment based on sensory feedback, rendering a lower adaptability to the uncertainty of environment. This study shed light on inherent dynamical properties underlying the intrinsic muscle activation and intermuscular coordination for precision grip and the effects of DM on hand sensorimotor function.

Structure and dynamics of the conserved protein GPI anchor core inserted into detergent micelles.

PubMed

Chevalier, Franck; Lopez-Prados, Javier; Groves, Patrick; Perez, Serge; Martín-Lomas, Manuel; Nieto, Pedro M

2006-10-01

A suitable approach which combines nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations have been used to study the structure and the dynamics of the glycosylphosphatidylinositol (GPI) anchor Manalphal-2Manalpha1-6Manalphal -4GlcNalpha1-6myo-inositol-1-OPO(3)-sn-1,2-dimyristoylglycerol (1) incorporated into dodecylphosphatidylcholine (DPC) micelles. The results have been compared to those previously obtained for the products obtainable from (1) after phospholipase cleavage, in aqueous solution. Relaxation and diffusion NMR experiments were used to establish the formation of stable aggregates and the insertion of (1) into the micelles. MD calculations were performed including explicit water, sodium and chloride ions and using the Particle Mesh Ewald approach for the evaluation of the electrostatic energy term. The MD predicted three dimensional structure and dynamics were substantiated by nuclear overhauser effect (NOE) measurements and relaxation data. The pseudopentasaccharide structure, which was not affected by incorporation of (1) into the micelle, showed a complex dynamic behaviour with a faster relative motion at the terminal mannopyranose unit and decreased mobility close to the micelle. This motion may be better described as an oscillation relative to the membrane rather than a folding event.

Flight dynamics simulation modeling and control of a large flexible tiltrotor aircraft

NASA Astrophysics Data System (ADS)

Juhasz, Ondrej

A high order rotorcraft mathematical model is developed and validated against the XV-15 and a Large Civil Tiltrotor (LCTR) concept. The mathematical model is generic and allows for any rotorcraft configuration, from single main rotor helicopters to coaxial and tiltrotor aircraft. Rigid-body and inflow states, as well as flexible wing and blade states are used in the analysis. The separate modeling of each rotorcraft component allows for structural flexibility to be included, which is important when modeling large aircraft where structural modes affect the flight dynamics frequency ranges of interest, generally 1 to 20 rad/sec. Details of the formulation of the mathematical model are given, including derivations of structural, aerodynamic, and inertial loads. The linking of the components of the aircraft is developed using an approach similar to multibody analyses by exploiting a tree topology, but without equations of constraints. Assessments of the effects of wing flexibility are given. Flexibility effects are evaluated by looking at the nature of the couplings between rigid-body modes and wing structural modes and vice versa. The effects of various different forms of structural feedback on aircraft dynamics are analyzed. A proportional-integral feedback on the structural acceleration is deemed to be most effective at both improving the damping and reducing the overall excitation of a structural mode. A model following control architecture is then implemented on full order flexible LCTR models. For this aircraft, the four lowest frequency structural modes are below 20 rad/sec, and are thus needed for control law development and analysis. The impact of structural feedback on both Attitude-Command, Attitude-Hold (ACAH) and Translational Rate Command (TRC) response types are investigated. A rigid aircraft model has optimistic performance characteristics, and a control system designed for a rigid aircraft could potentially destabilize a flexible one. The various control systems are flown in a fixed-base simulator. Pilot inputs and aircraft performance are recorded and analyzed.

Short-Range Order and Collective Dynamics of DMPC Bilayers: A Comparison between Molecular Dynamics Simulations, X-Ray, and Neutron Scattering Experiments

PubMed Central

Hub, Jochen S.; Salditt, Tim; Rheinstädter, Maikel C.; de Groot, Bert L.

2007-01-01

We present an extensive comparison of short-range order and short wavelength dynamics of a hydrated phospholipid bilayer derived by molecular dynamics simulations, elastic x-ray, and inelastic neutron scattering experiments. The quantities that are compared between simulation and experiment include static and dynamic structure factors, reciprocal space mappings, and electron density profiles. We show that the simultaneous use of molecular dynamics and diffraction data can help to extract real space properties like the area per lipid and the lipid chain ordering from experimental data. In addition, we assert that the interchain distance can be computed to high accuracy from the interchain correlation peak of the structure factor. Moreover, it is found that the position of the interchain correlation peak is not affected by the area per lipid, while its correlation length decreases linearly with the area per lipid. This finding allows us to relate a property of the structure factor quantitatively to the area per lipid. Finally, the short wavelength dynamics obtained from the simulations and from inelastic neutron scattering are analyzed and compared. The conventional interpretation in terms of the three-effective-eigenmode model is found to be only partly suitable to describe the complex fluid dynamics of lipid chains. PMID:17631531

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.

Evaluation of vibration limits and mitigation techniques for urban construction : [summary].

DOT National Transportation Integrated Search

2013-10-01

Construction activities such as pile driving and : dynamic compaction of loose soils induce ground : and structure vibrations. Their effects may annoy : local populations, disturb sensitive equipment, or : reduce structures serviceability and dura...

Comparative analysis of on-orbit dynamic performance of several large antenna concepts

NASA Technical Reports Server (NTRS)

Andersen, G. C.; Garrett, L. B.; Calleson, R. E.

1985-01-01

A comparative analysis of the on-orbit dynamic performance of four large anetanna concepts is presented. Among the antenna concepts evaluated are: the box truss; tetrahedral truss; warp-radial rib; and the hoop and column antenna designs. The characteristics and magnitudes of the antennas' dynamic response were evaluated in terms of structural displacements and member loads incurred during various slew-rate maneuvers. The results of the dynamic response analysis are compared to the design requirements of the Land Mobile Satellite System (LMSS) with respect to surface accuracy, decenter, defocus, and angular rocking. Comments are made on the effectiveness of structural damping and the application of active controls for vibrational response reduction. Schematic illustrations of the antenna design concepts are provided.

Effect of fullerenol surface chemistry on nanoparticle binding-induced protein misfolding

NASA Astrophysics Data System (ADS)

Radic, Slaven; Nedumpully-Govindan, Praveen; Chen, Ran; Salonen, Emppu; Brown, Jared M.; Ke, Pu Chun; Ding, Feng

2014-06-01

Fullerene and its derivatives with different surface chemistry have great potential in biomedical applications. Accordingly, it is important to delineate the impact of these carbon-based nanoparticles on protein structure, dynamics, and subsequently function. Here, we focused on the effect of hydroxylation -- a common strategy for solubilizing and functionalizing fullerene -- on protein-nanoparticle interactions using a model protein, ubiquitin. We applied a set of complementary computational modeling methods, including docking and molecular dynamics simulations with both explicit and implicit solvent, to illustrate the impact of hydroxylated fullerenes on the structure and dynamics of ubiquitin. We found that all derivatives bound to the model protein. Specifically, the more hydrophilic nanoparticles with a higher number of hydroxyl groups bound to the surface of the protein via hydrogen bonds, which stabilized the protein without inducing large conformational changes in the protein structure. In contrast, fullerene derivatives with a smaller number of hydroxyl groups buried their hydrophobic surface inside the protein, thereby causing protein denaturation. Overall, our results revealed a distinct role of surface chemistry on nanoparticle-protein binding and binding-induced protein misfolding.Fullerene and its derivatives with different surface chemistry have great potential in biomedical applications. Accordingly, it is important to delineate the impact of these carbon-based nanoparticles on protein structure, dynamics, and subsequently function. Here, we focused on the effect of hydroxylation -- a common strategy for solubilizing and functionalizing fullerene -- on protein-nanoparticle interactions using a model protein, ubiquitin. We applied a set of complementary computational modeling methods, including docking and molecular dynamics simulations with both explicit and implicit solvent, to illustrate the impact of hydroxylated fullerenes on the structure and dynamics of ubiquitin. We found that all derivatives bound to the model protein. Specifically, the more hydrophilic nanoparticles with a higher number of hydroxyl groups bound to the surface of the protein via hydrogen bonds, which stabilized the protein without inducing large conformational changes in the protein structure. In contrast, fullerene derivatives with a smaller number of hydroxyl groups buried their hydrophobic surface inside the protein, thereby causing protein denaturation. Overall, our results revealed a distinct role of surface chemistry on nanoparticle-protein binding and binding-induced protein misfolding. Electronic supplementary information (ESI) is available: Fluorescence spectra, ITC, CD spectra and other data as described in the text. See DOI: 10.1039/c4nr01544d

Characterization, Modeling, and Failure Analysis of Composite Structure Materials under Static and Dynamic Loading

NASA Astrophysics Data System (ADS)

Werner, Brian Thomas

Composite structures have long been used in many industries where it is advantageous to reduce weight while maintaining high stiffness and strength. Composites can now be found in an ever broadening range of applications: sporting equipment, automobiles, marine and aerospace structures, and energy production. These structures are typically sandwich panels composed of fiber reinforced polymer composite (FRPC) facesheets which provide the stiffness and the strength and a low density polymeric foam core that adds bending rigidity with little additional weight. The expanding use of composite structures exposes them to high energy, high velocity dynamic loadings which produce multi-axial dynamic states of stress. This circumstance can present quite a challenge to designers, as composite structures are highly anisotropic and display properties that are sensitive to loading rates. Computer codes are continually in development to assist designers in the creation of safe, efficient structures. While the design of an optimal composite structure is more complex, engineers can take advantage of the effect of enhanced energy dissipation displayed by a composite when loaded at high strain rates. In order to build and verify effective computer codes, the underlying assumptions must be verified by laboratory experiments. Many of these codes look to use a micromechanical approach to determine the response of the structure. For this, the material properties of the constituent materials must be verified, three-dimensional constitutive laws must be developed, and failure of these materials must be investigated under static and dynamic loading conditions. In this study, simple models are sought not only to ease their implementation into such codes, but to allow for efficient characterization of new materials that may be developed. Characterization of composite materials and sandwich structures is a costly, time intensive process. A constituent based design approach evaluates potential combinations of materials in a much faster and more efficient manner.

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.

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

PubMed

Neuwirth, C; Peck, A; Simonović, S P

2015-03-01

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

EFFECTS OF LASER RADIATION ON MATTER: Growth of periodic structures on the surface of germanium subjected to pulsed laser radiation

NASA Astrophysics Data System (ADS)

Barsukov, D. O.; Gusakov, G. M.; Frolov, A. I.

1991-12-01

An experimental investigation was made of the dynamics of growth of periodic surface structures due to the interaction with pulsed laser radiation. Samples of Ge were subjected to laser pulses (λ = 1.06 μm, τ = 70 ns) with energy densities in the range 0.5-5.5 J/cm2. An investigation was made of the dynamics of the first-order diffraction of probe (λ = 0.53 μm) laser pulses with a time resolution 4 ns when p- and s-polarized laser radiation was incident at angles close to normal. A strong nonlinearity of the growth of such periodic surface structures was observed. The energy density from which such growth began depended on the quality of the polished Ge surface. The parameters of the dynamics of the growth of these structures were estimated.

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.

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.

Dynamic Effects of Biochar on the Bacterial Community Structure in Soil Contaminated with Polycyclic Aromatic Hydrocarbons.

PubMed

Song, Yang; Bian, Yongrong; Wang, Fang; Xu, Min; Ni, Ni; Yang, Xinglun; Gu, Chenggang; Jiang, Xin

2017-08-16

Amending soil with biochar is an effective soil remediation strategy for organic contaminants. This study investigated the dynamic effects of wheat straw biochar on the bacterial community structure during remediation by high-throughput sequencing. The wheat straw biochar amended into the soil significantly reduced the bioavailability and toxicity of polycyclic aromatic hydrocarbons (PAHs). Biochar amendment helped to maintain the bacterial diversity in the PAH-contaminated soil. The relationship between the immobilization of PAHs and the soil bacterial diversity fit a quadratic model. Before week 12 of the incubation, the incubation time was the main factor contributing to the changes in the soil bacterial community structure. However, biochar greatly affected the bacterial community structure after 12 weeks of amendment, and the effects were dependent upon the biochar type. Amendment with biochar mainly facilitated the growth of rare bacterial genera (relative abundance of 0.01-1%) in the studied soil. Therefore, the application of wheat straw biochar into PAH-contaminated soil can reduce the environmental risks of PAHs and benefit the soil microbial ecology.

Current Scientific Issues in Large Scale Atmospheric Dynamics

NASA Technical Reports Server (NTRS)

Miller, T. L. (Compiler)

1986-01-01

Topics in large scale atmospheric dynamics are discussed. Aspects of atmospheric blocking, the influence of transient baroclinic eddies on planetary-scale waves, cyclogenesis, the effects of orography on planetary scale flow, small scale frontal structure, and simulations of gravity waves in frontal zones are discussed.

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations.

PubMed

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y; Schwegler, Eric

2016-10-21

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. Such simulations are often performed at elevated temperatures to artificially "correct" for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. To address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na + , K + , and Cl - ions. We show that simulations at 390-400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. Our results suggest that an elevated temperature around 390-400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.

Complex networks under dynamic repair model

NASA Astrophysics Data System (ADS)

Chaoqi, Fu; Ying, Wang; Kun, Zhao; Yangjun, Gao

2018-01-01

Invulnerability is not the only factor of importance when considering complex networks' security. It is also critical to have an effective and reasonable repair strategy. Existing research on network repair is confined to the static model. The dynamic model makes better use of the redundant capacity of repaired nodes and repairs the damaged network more efficiently than the static model; however, the dynamic repair model is complex and polytropic. In this paper, we construct a dynamic repair model and systematically describe the energy-transfer relationships between nodes in the repair process of the failure network. Nodes are divided into three types, corresponding to three structures. We find that the strong coupling structure is responsible for secondary failure of the repaired nodes and propose an algorithm that can select the most suitable targets (nodes or links) to repair the failure network with minimal cost. Two types of repair strategies are identified, with different effects under the two energy-transfer rules. The research results enable a more flexible approach to network repair.

Water Dynamics in Egg White Peptide, Asp-His-Thr-Lys-Glu, Powder Monitored by Dynamic Vapor Sorption and LF-NMR.

PubMed

Yang, Shuailing; Liu, Xuye; Jin, Yan; Li, Xingfang; Chen, Feng; Zhang, Mingdi; Lin, Songyi

2016-03-16

Water absorbed into the bulk amorphous structure of peptides can have profound effects on their properties. Here, we elucidated water dynamics in Asp-His-Thr-Lys-Glu (DHTKE), an antioxidant peptide derived from egg white ovalbumin, using water dynamic vapor sorption (DVS) and low-field nuclear magnetic resonance (LF-NMR). The DVS results indicated that parallel exponential kinetics model fitted well to the data of sorption kinetics behavior of DHTKE. Four different proton fractions with different mobilities were identified based on the degree of interaction between peptide and water. The water could significantly change the proton distribution and structure of the sample. The different phases of moisture absorption were reflected in the T2 parameters. In addition, the combined water content was dominant in the hygroscopicity of DHTKE. This study provides an effective real-time monitoring method for water mobility and distribution in synthetic peptides, and this method may have applications in promoting peptide quality assurance.

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.

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.

Effect of Structure and Disorder on the Charge Transport in Defined Self-Assembled Monolayers of Organic Semiconductors.

PubMed

Schmaltz, Thomas; Gothe, Bastian; Krause, Andreas; Leitherer, Susanne; Steinrück, Hans-Georg; Thoss, Michael; Clark, Timothy; Halik, Marcus

2017-09-26

Self-assembled monolayer field-effect transistors (SAMFETs) are not only a promising type of organic electronic device but also allow detailed analyses of structure-property correlations. The influence of the morphology on the charge transport is particularly pronounced, due to the confined monolayer of 2D-π-stacked organic semiconductor molecules. The morphology, in turn, is governed by relatively weak van-der-Waals interactions and is thus prone to dynamic structural fluctuations. Accordingly, combining electronic and physical characterization and time-averaged X-ray analyses with the dynamic information available at atomic resolution from simulations allows us to characterize self-assembled monolayer (SAM) based devices in great detail. For this purpose, we have constructed transistors based on SAMs of two molecules that consist of the organic p-type semiconductor benzothieno[3,2-b][1]benzothiophene (BTBT), linked to a C 11 or C 12 alkylphosphonic acid. Both molecules form ordered SAMs; however, our experiments show that the size of the crystalline domains and the charge-transport properties vary considerably in the two systems. These findings were confirmed by molecular dynamics (MD) simulations and semiempirical molecular-orbital electronic-structure calculations, performed on snapshots from the MD simulations at different times, revealing, in atomistic detail, how the charge transport in organic semiconductors is influenced and limited by dynamic disorder.

The interaction of cannibalism and omnivory: consequences for community dynamics.

PubMed

Rudolf, Volker H W

2007-11-01

Although cannibalism is ubiquitous in food webs and frequent in systems where a predator and its prey also share a common resource (intraguild predation, IGP), its impacts on species interactions and the dynamics and structure of communities are still poorly understood. In addition, the few existing studies on cannibalism have generally focused on cannibalism in the top-predator, ignoring that it is frequent at intermediate trophic levels. A set of structured models shows that cannibalism can completely alter the dynamics and structure of three-species IGP systems depending on the trophic position where cannibalism occurs. Contrary to the expectations of simple models, the IG predator can exploit the resources more efficiently when it is cannibalistic, enabling the predator to persist at lower resource densities than the IG prey. Cannibalism in the IG predator can also alter the effect of enrichment, preventing predator-mediated extinction of the IG prey at high productivities predicted by simple models. Cannibalism in the IG prey can reverse the effect of top-down cascades, leading to an increase in the resource with decreasing IG predator density. These predictions are consistent with current data. Overall, cannibalism promotes the coexistence of the IG predator and IG prey. These results indicate that including cannibalism in current models can overcome the discrepancy between theory and empirical data. Thus, we need to measure and account for cannibalistic interactions to reliably predict the structure and dynamics of communities.

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.

The matrix exponential in transient structural analysis

NASA Technical Reports Server (NTRS)

Minnetyan, Levon

1987-01-01

The primary usefulness of the presented theory is in the ability to represent the effects of high frequency linear response with accuracy, without requiring very small time steps in the analysis of dynamic response. The matrix exponential contains a series approximation to the dynamic model. However, unlike the usual analysis procedure which truncates the high frequency response, the approximation in the exponential matrix solution is in the time domain. By truncating the series solution to the matrix exponential short, the solution is made inaccurate after a certain time. Yet, up to that time the solution is extremely accurate, including all high frequency effects. By taking finite time increments, the exponential matrix solution can compute the response very accurately. Use of the exponential matrix in structural dynamics is demonstrated by simulating the free vibration response of multi degree of freedom models of cantilever beams.

Interplay of stereoelectronic and enviromental effects in tuning the structural and magnetic properties of a prototypical spin probe: further insights from a first principle dynamical approach.

PubMed

Pavone, Michele; Cimino, Paola; De Angelis, Filippo; Barone, Vincenzo

2006-04-05

The nitrogen isotropic hyperfine coupling constant (hcc) and the g tensor of a prototypical spin probe (di-tert-butyl nitroxide, DTBN) in aqueous solution have been investigated by means of an integrated computational approach including Car-Parrinello molecular dynamics and quantum mechanical calculations involving a discrete-continuum embedding. The quantitative agreement between computed and experimental parameters fully validates our integrated approach. Decoupling of the structural, dynamical, and environmental contributions acting onto the spectral observables allows an unbiased judgment of the role played by different effects in determining the overall experimental observables and highlights the importance of finite-temperature vibrational averaging. Together with their intrinsic interest, our results pave the route toward more reliable interpretations of EPR parameters of complex systems of biological and technological relevance.

Classification of octet AB-type binary compounds using dynamical charges: A materials informatics perspective

DOE PAGES

Pilania, G.; Gubernatis, J. E.; Lookman, T.

2015-12-03

The role of dynamical (or Born effective) charges in classification of octet AB-type binary compounds between four-fold (zincblende/wurtzite crystal structures) and six-fold (rocksalt crystal structure) coordinated systems is discussed. We show that the difference in the dynamical charges of the fourfold and sixfold coordinated structures, in combination with Harrison’s polarity, serves as an excellent feature to classify the coordination of 82 sp–bonded binary octet compounds. We use a support vector machine classifier to estimate the average classification accuracy and the associated variance in our model where a decision boundary is learned in a supervised manner. Lastly, we compare the out-of-samplemore » classification accuracy achieved by our feature pair with those reported previously.« less

Fluid-Structure Interaction in Composite Structures

DTIC Science & Technology

2014-03-01

polymer composite structures. Some previous experimental observations were confirmed using the results from the computer simulations , which also...computer simulations , which also enhanced understanding the effect of FSI on dynamic responses of composite structures. vi THIS PAGE INTENTIONALLY...forces) are applied. A great amount of research has been made using the FEM to study and simulate the cases when the structures are surrounded by

Effective model hierarchies for dynamic and static classical density functional theories

NASA Astrophysics Data System (ADS)

Majaniemi, S.; Provatas, N.; Nonomura, M.

2010-09-01

The origin and methodology of deriving effective model hierarchies are presented with applications to solidification of crystalline solids. In particular, it is discussed how the form of the equations of motion and the effective parameters on larger scales can be obtained from the more microscopic models. It will be shown that tying together the dynamic structure of the projection operator formalism with static classical density functional theories can lead to incomplete (mass) transport properties even though the linearized hydrodynamics on large scales is correctly reproduced. To facilitate a more natural way of binding together the dynamics of the macrovariables and classical density functional theory, a dynamic generalization of density functional theory based on the nonequilibrium generating functional is suggested.

Effects of planning strategies on writing dynamics and final texts.

PubMed

Limpo, Teresa; Alves, Rui A

2018-06-12

Expert writing involves the interaction among three cognitively demanding processes: planning, translating, and revising. To manage the cognitive load brought on by these processes, writers frequently use strategies. Here, we examined the effects of planning strategies on writing dynamics and final texts. Before writing an argumentative text with the triple-task technique, 63 undergraduates were asked either to elaborate an outline with the argumentative structure embedded (structure-based planning condition), to provide a written list of ideas for the text (list-based planning condition), or to do a non-writing-related filler task (no planning condition). Planning showed no effects on the length of the pre-writing pause and cognitive effort, but influenced writing processes occurrences. Compared to participants in the no-planning condition, those in the planning conditions showed a later activation of revising. Moreover, participants in the structure-based condition were mainly focused on translating in the beginning and middle of composition, whereas their peers tended to distribute their attention among all processes. Planning ahead of writing also resulted in texts with longer words, produced at a higher rate. Only the structure-based planning strategy led to an increase in the number of argumentation elements as well as in essays' persuasiveness and overall quality. There was, however, no indication that these improvements in final texts were associated with changes in the dynamics of writing. Overall, the use of structure-based plans seems to be an effective and efficient way of improving undergraduates' argumentative writing. Copyright © 2018 Elsevier B.V. All rights reserved.

Quantitative Analysis of the Effective Functional Structure in Yeast Glycolysis

PubMed Central

De la Fuente, Ildefonso M.; Cortes, Jesus M.

2012-01-01

The understanding of the effective functionality that governs the enzymatic self-organized processes in cellular conditions is a crucial topic in the post-genomic era. In recent studies, Transfer Entropy has been proposed as a rigorous, robust and self-consistent method for the causal quantification of the functional information flow among nonlinear processes. Here, in order to quantify the functional connectivity for the glycolytic enzymes in dissipative conditions we have analyzed different catalytic patterns using the technique of Transfer Entropy. The data were obtained by means of a yeast glycolytic model formed by three delay differential equations where the enzymatic rate equations of the irreversible stages have been explicitly considered. These enzymatic activity functions were previously modeled and tested experimentally by other different groups. The results show the emergence of a new kind of dynamical functional structure, characterized by changing connectivity flows and a metabolic invariant that constrains the activity of the irreversible enzymes. In addition to the classical topological structure characterized by the specific location of enzymes, substrates, products and feedback-regulatory metabolites, an effective functional structure emerges in the modeled glycolytic system, which is dynamical and characterized by notable variations of the functional interactions. The dynamical structure also exhibits a metabolic invariant which constrains the functional attributes of the enzymes. Finally, in accordance with the classical biochemical studies, our numerical analysis reveals in a quantitative manner that the enzyme phosphofructokinase is the key-core of the metabolic system, behaving for all conditions as the main source of the effective causal flows in yeast glycolysis. PMID:22393350

Effects of climate change and shifts in forest composition on forest net primary production

Treesearch

Jyh-Min Chiang; Louts [Louis] R. Iverson; Anantha Prasad; Kim J. Brown

2008-01-01

Forests are dynamic in both structure and species composition, and these dynamics are strongly influenced by climate. However, the net effects of future tree species composition on net primary production (NPP) are not well understood. The objective of this work was to model the potential range shifts of tree species (DISTRIB Model) and predict their impacts on NPP (...

Picosecond to nanosecond reorganization of water in AOT/lecithin mixed reverse micelles of different morphology

NASA Astrophysics Data System (ADS)

Narayanan, S. Shankara; Sinha, Sudarson Sekhar; Sarkar, Rupa; Pal, Samir Kumar

2008-02-01

We report the effect of different geometrical restrictions on the dynamical properties of water using dynamic light scattering (DLS), Fourier transform infrared (FTIR) and picosecond-resolved fluorescence studies. By preparing AOT/lecithin mixed reverse micelles (RMs) of different morphologies (spherical and ellipsoidal), we have investigated the effect of the degree of confinement on the mobility of water in the mixed RMs of similar degree of hydration. The FTIR studies along with solvation dynamics of two fluorescent probes, ANS and coumarin 500 in the RMs reveal structural and dynamical information about the micellar water, which varies with the morphology of the mixed RMs.

[Effects of dynamic high-pressure microfluidization on the structure of waxy rice starch].

PubMed

Tu, Zong-Cai; Zhu, Xiu-Mei; Chen, Gang; Wang, Hui; Zhang, Bo; Huang, Xiao-Qin; Li, Zhi

2010-03-01

The effects of dynamic ultra high-pressure microfluidization on the structure of waxy rice starch solutions (6%) were analyzed using SEM, UV-Vis spectra, polarized light microscopy, and X-ray diffraction spectra. The results showed that: SEM graphs demonstrated that the crystal structure of waxy rice starch under different pressure treatment was destroyed with different degrees and impacted into flake up to 160 MPa; from the ultraviolet-visible spectrum we know the reduction in the blue iodine value and the decrease in the amylopectin content, which illustrated that the structure of waxy rice starch was fractured; polarized microscopic images showed that the polarization crosses of starch molecules became misty with the pressure increasing, and most of starch molecules lost polarization cross when the pressure reached 160 MPa; X-ray diffraction spectra indicated that relative crystallinity began to decline at 120 MPa with pressure treatment, and the decreased amplitude was slightly lower.

Quantum-chemical investigation of the structures and electronic spectra of the nucleic acid bases at the coupled cluster CC2 level.

PubMed

Fleig, Timo; Knecht, Stefan; Hättig, Christof

2007-06-28

We study the ground-state structures and singlet- and triplet-excited states of the nucleic acid bases by applying the coupled cluster model CC2 in combination with a resolution-of-the-identity approximation for electron interaction integrals. Both basis set effects and the influence of dynamic electron correlation on the molecular structures are elucidated; the latter by comparing CC2 with Hartree-Fock and Møller-Plesset perturbation theory to second order. Furthermore, we investigate basis set and electron correlation effects on the vertical excitation energies and compare our highest-level results with experiment and other theoretical approaches. It is shown that small basis sets are insufficient for obtaining accurate results for excited states of these molecules and that the CC2 approach to dynamic electron correlation is a reliable and efficient tool for electronic structure calculations on medium-sized molecules.

Subtle balance of tropoelastin molecular shape and flexibility regulates dynamics and hierarchical assembly.

PubMed

Yeo, Giselle C; Tarakanova, Anna; Baldock, Clair; Wise, Steven G; Buehler, Markus J; Weiss, Anthony S

2016-02-01

The assembly of the tropoelastin monomer into elastin is vital for conferring elasticity on blood vessels, skin, and lungs. Tropoelastin has dual needs for flexibility and structure in self-assembly. We explore the structure-dynamics-function interplay, consider the duality of molecular order and disorder, and identify equally significant functional contributions by local and global structures. To study these organizational stratifications, we perturb a key hinge region by expressing an exon that is universally spliced out in human tropoelastins. We find a herniated nanostructure with a displaced C terminus and explain by molecular modeling that flexible helices are replaced with substantial β sheets. We see atypical higher-order cross-linking and inefficient assembly into discontinuous, thick elastic fibers. We explain this dysfunction by correlating local and global structural effects with changes in the molecule's assembly dynamics. This work has general implications for our understanding of elastomeric proteins, which balance disordered regions with defined structural modules at multiple scales for functional assembly.

Reconstruction of dynamic structures of experimental setups based on measurable experimental data only

NASA Astrophysics Data System (ADS)

Chen, Tian-Yu; Chen, Yang; Yang, Hu-Jiang; Xiao, Jing-Hua; Hu, Gang

2018-03-01

Nowadays, massive amounts of data have been accumulated in various and wide fields, it has become today one of the central issues in interdisciplinary fields to analyze existing data and extract as much useful information as possible from data. It is often that the output data of systems are measurable while dynamic structures producing these data are hidden, and thus studies to reveal system structures by analyzing available data, i.e., reconstructions of systems become one of the most important tasks of information extractions. In the past, most of the works in this respect were based on theoretical analyses and numerical verifications. Direct analyses of experimental data are very rare. In physical science, most of the analyses of experimental setups were based on the first principles of physics laws, i.e., so-called top-down analyses. In this paper, we conducted an experiment of “Boer resonant instrument for forced vibration” (BRIFV) and inferred the dynamic structure of the experimental set purely from the analysis of the measurable experimental data, i.e., by applying the bottom-up strategy. Dynamics of the experimental set is strongly nonlinear and chaotic, and itʼs subjects to inevitable noises. We proposed to use high-order correlation computations to treat nonlinear dynamics; use two-time correlations to treat noise effects. By applying these approaches, we have successfully reconstructed the structure of the experimental setup, and the dynamic system reconstructed with the measured data reproduces good experimental results in a wide range of parameters.

Many-body quantum dynamics in the decay of bent dark solitons of Bose-Einstein condensates

NASA Astrophysics Data System (ADS)

Katsimiga, G. C.; Mistakidis, S. I.; Koutentakis, G. M.; Kevrekidis, P. G.; Schmelcher, P.

2017-12-01

The beyond mean-field (MF) dynamics of a bent dark soliton (BDS) embedded in a two-dimensional repulsively interacting Bose-Einstein condensate is explored. We examine the case of a single BDS comparing the MF dynamics to a correlated approach, the multi-configuration time-dependent Hartree method for bosons. Dynamical snaking of this bent structure is observed, signaling the onset of fragmentation which becomes significant during the vortex nucleation. In contrast to the MF approximation ‘filling’ of the vortex core is observed, leading in turn to the formation of filled-core vortices, instead of the MF vortex-antivortex pairs. The resulting smearing effect in the density is a rather generic feature, occurring when solitonic structures are exposed to quantum fluctuations. Here, we show that this filling owes its existence to the dynamical building of an antidark structure developed in the next-to-leading order orbital. We further demonstrate that the aforementioned beyond MF dynamics can be experimentally detected using the variance of single shot measurements. Additionally, a variety of excitations including vortices, oblique dark solitons, and open ring dark soliton-like structures building upon higher-lying orbitals is observed. We demonstrate that signatures of the higher-lying orbital excitations emerge in the total density, and can be clearly captured by inspecting the one-body coherence. In the latter context, the localization of one-body correlations exposes the existence of the multi-orbital vortex-antidark structure.

Dynamic response mitigation of floating wind turbine platforms using tuned liquid column dampers.

PubMed

Jaksic, V; Wright, C S; Murphy, J; Afeef, C; Ali, S F; Mandic, D P; Pakrashi, V

2015-02-28

In this paper, we experimentally study and compare the effects of three combinations of multiple tuned liquid column dampers (MTLCDs) on the dynamic performance of a model floating tension-leg platform (TLP) structure in a wave basin. The structural stability and safety of the floating structure during operation and maintenance is of concern for the performance of a renewable energy device that it might be supporting. The dynamic responses of the structure should thus be limited for these renewable energy devices to perform as intended. This issue is particularly important during the operation of a TLP in extreme weather conditions. Tuned liquid column dampers (TLCDs) can use the power of sloshing water to reduce surge motions of a floating TLP exposed to wind and waves. This paper demonstrates the potential of MTLCDs in reducing dynamic responses of a scaled TLP model through an experimental study. The potential of using output-only statistical markers for monitoring changes in structural conditions is also investigated through the application of a delay vector variance (DVV) marker for different conditions of control for the experiments. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Finite element modeling of temperature load effects on the vibration of local modes in multi-cable structures

NASA Astrophysics Data System (ADS)

Treyssède, Fabien

2018-01-01

Understanding thermal effects on the vibration of local (cable-dominant) modes in multi-cable structures is a complicated task. The main difficulty lies in the modification by temperature change of cable tensions, which are then undetermined. This paper applies a finite element procedure to investigate the effects of thermal loads on the linear dynamics of prestressed self-weighted multi-cable structures. Provided that boundary conditions are carefully handled, the discretization of cables with nonlinear curved beam elements can properly represent the thermoelastic behavior of cables as well as their linearized dynamics. A three-step procedure that aims to replace applied pretension forces with displacement continuity conditions is used. Despite an increase in the computational cost related to beam rotational degrees of freedom, such an approach has several advantages. Nonlinear beam finite elements are usually available in commercial codes. The overall method follows a thermoelastic geometrically non-linear analysis and hereby includes the main sources of non-linearities in multi-cable structures. The effects of cable bending stiffness, which can be significant, are also naturally accounted for. The accuracy of the numerical approach is assessed thanks to an analytical model for the vibration of a single inclined cable under temperature change. Then, the effects of thermal loads are investigated for two cable bridges, highlighting how natural frequencies can be affected by temperature. Although counterintuitive, a reverse relative change of natural frequency may occur for certain local modes. This phenomenon can be explained by two distinct mechanisms, one related to the physics intrinsic to cables and the other related to the thermal deflection of the superstructure. Numerical results show that cables cannot be isolated from the rest of the structure and the importance of modeling the whole structure for a quantitative analysis of temperature effects on the dynamics of cable bridges.

Structures and Dynamics Division: Research and technology plans for FY 1983 and accomplishments for FY 1982

NASA Technical Reports Server (NTRS)

Bales, K. S.

1983-01-01

The objectives, expected results, approach, and milestones for research projects of the IPAD Project Office and the impact dynamics, structural mechanics, and structural dynamics branches of the Structures and Dynamics Division are presented. Research facilities are described. Topics covered include computer aided design; general aviation/transport crash dynamics; aircraft ground performance; composite structures; failure analysis, space vehicle dynamics; and large space structures.

An experimental and theoretical study of structural damping in compliant foil bearings

NASA Technical Reports Server (NTRS)

Ku, C.-P. Roger

1994-01-01

This paper describes an experimental investigation into the dynamic characteristics of corrugated foil (bump foil) strips used in compliant surface foil bearings. This study provided and opportunity to quantify the structural damping of bump foil strips. The experimental data were compared to results obtained by a theoretical model developed earlier. The effects of bearing design parameters, such as static loads, dynamic displacement amplitudes, bump configurations, pivot locations, surface coatings, and lubricant were also evaluated. An understanding of the dynamic characteristics of bump foil strips resulting from this work offers designers a means for enhancing the design of high-performance compliant foil bearings.

Ab initio study of collective excitations in a disparate mass molten salt.

PubMed

Bryk, Taras; Klevets, Ivan

2012-12-14

Ab initio molecular dynamics simulations and the approach of generalized collective modes are applied for calculations of spectra of longitudinal and transverse collective excitations in molten LiBr. Dispersion and damping of low- and high-frequency branches of collective excitations as well as wave-number dependent relaxing modes were calculated. The main mode contributions to partial, total, and concentration dynamic structure factors were estimated in a wide region of wave numbers. A role of polarization effects is discussed from comparison of mode contributions to concentration dynamic structure factors calculated for molten LiBr from ab initio and classical rigid ion simulations.

A model for a spatially structured metapopulation accounting for within patch dynamics.

PubMed

Smith, Andrew G; McVinish, Ross; Pollett, Philip K

2014-01-01

We develop a stochastic metapopulation model that accounts for spatial structure as well as within patch dynamics. Using a deterministic approximation derived from a functional law of large numbers, we develop conditions for extinction and persistence of the metapopulation in terms of the birth, death and migration parameters. Interestingly, we observe the Allee effect in a metapopulation comprising two patches of greatly different sizes, despite there being decreasing patch specific per-capita birth rates. We show that the Allee effect is due to the way the migration rates depend on the population density of the patches. Copyright © 2013 Elsevier Inc. All rights reserved.

Experimental Analysis of Dynamic Effects of FRP Reinforced Masonry Vaults.

PubMed

Corradi, Marco; Borri, Antonio; Castori, Giulio; Coventry, Kathryn

2015-11-27

An increasing interest in the preservation of historic structures has produced a need for new methods for reinforcing curved masonry structures, such as arches and vaults. These structures are generally very ancient, have geometries and materials which are poorly defined and have been exposed to long-term historical movements and actions. Consequently, they are often in need of repair or reinforcement. This article presents the results of an experimental study carried out in the laboratory and during on-site testing to investigate the behaviour of brick masonry vaults under dynamic loading strengthened with FRPs (Fiber Reinforced Polymers). For the laboratory tests, the brick vaults were built with solid sanded clay bricks and weak mortar and were tested under dynamic loading. The experimental tests were designed to facilitate analysis of the dynamic behaviour of undamaged, damaged and reinforced vaulted structures. On-site tests were carried out on an earthquake-damaged thin brick vault of an 18th century aristocratic residence in the city of L'Aquila, Italy. The provision of FRP reinforcement is shown to re-establish elastic behavior previously compromised by time induced damage in the vaults.

Experimental Analysis of Dynamic Effects of FRP Reinforced Masonry Vaults

PubMed Central

Corradi, Marco; Borri, Antonio; Castori, Giulio; Coventry, Kathryn

2015-01-01

An increasing interest in the preservation of historic structures has produced a need for new methods for reinforcing curved masonry structures, such as arches and vaults. These structures are generally very ancient, have geometries and materials which are poorly defined and have been exposed to long-term historical movements and actions. Consequently, they are often in need of repair or reinforcement. This article presents the results of an experimental study carried out in the laboratory and during on-site testing to investigate the behaviour of brick masonry vaults under dynamic loading strengthened with FRPs (Fiber Reinforced Polymers). For the laboratory tests, the brick vaults were built with solid sanded clay bricks and weak mortar and were tested under dynamic loading. The experimental tests were designed to facilitate analysis of the dynamic behaviour of undamaged, damaged and reinforced vaulted structures. On-site tests were carried out on an earthquake-damaged thin brick vault of an 18th century aristocratic residence in the city of L’Aquila, Italy. The provision of FRP reinforcement is shown to re-establish elastic behavior previously compromised by time induced damage in the vaults. PMID:28793697

Structure and lattice dynamics of the wide band gap semiconductors MgSiN2 and MgGeN2

NASA Astrophysics Data System (ADS)

Râsander, M.; Quirk, J. B.; Wang, T.; Mathew, S.; Davies, R.; Palgrave, R. G.; Moram, M. A.

2017-08-01

We have determined the structural and lattice dynamical properties of the orthorhombic, wide band gap semiconductors MgSiN2 and MgGeN2 using density functional theory. In addition, we present the structural properties and Raman spectra of MgSiN2 powder. The structural properties and lattice dynamics of the orthorhombic systems are compared to those of wurtzite AlN. We find clear differences in the lattice dynamics between MgSiN2, MgGeN2 and AlN, for example, we find that the highest phonon frequency in MgSiN2 is about 100 cm-1 higher than the highest frequency in AlN, and that MgGeN2 is much softer. We also provide the Born effective charge tensors and dielectric tensors of MgSiN2, MgGeN2 and AlN. Phonon related thermodynamic properties, such as the heat capacity and the entropy, have also been evaluated and are found to be in very good agreement with available experimental results.

Impact of constrained rewiring on network structure and node dynamics

NASA Astrophysics Data System (ADS)

Rattana, P.; Berthouze, L.; Kiss, I. Z.

2014-11-01

In this paper, we study an adaptive spatial network. We consider a susceptible-infected-susceptible (SIS) epidemic on the network, with a link or contact rewiring process constrained by spatial proximity. In particular, we assume that susceptible nodes break links with infected nodes independently of distance and reconnect at random to susceptible nodes available within a given radius. By systematically manipulating this radius we investigate the impact of rewiring on the structure of the network and characteristics of the epidemic. We adopt a step-by-step approach whereby we first study the impact of rewiring on the network structure in the absence of an epidemic, then with nodes assigned a disease status but without disease dynamics, and finally running network and epidemic dynamics simultaneously. In the case of no labeling and no epidemic dynamics, we provide both analytic and semianalytic formulas for the value of clustering achieved in the network. Our results also show that the rewiring radius and the network's initial structure have a pronounced effect on the endemic equilibrium, with increasingly large rewiring radiuses yielding smaller disease prevalence.

Dynamic and Progressive Control of DNA Origami Conformation by Modulating DNA Helicity with Chemical Adducts.

PubMed

Chen, Haorong; Zhang, Hanyu; Pan, Jing; Cha, Tae-Gon; Li, Shiming; Andréasson, Joakim; Choi, Jong Hyun

2016-05-24

DNA origami has received enormous attention for its ability to program complex nanostructures with a few nanometer precision. Dynamic origami structures that change conformation in response to environmental cues or external signals hold great promises in sensing and actuation at the nanoscale. The reconfiguration mechanism of existing dynamic origami structures is mostly limited to single-stranded hinges and relies almost exclusively on DNA hybridization or strand displacement. Here, we show an alternative approach by demonstrating on-demand conformation changes with DNA-binding molecules, which intercalate between base pairs and unwind DNA double helices. The unwinding effect modulates the helicity mismatch in DNA origami, which significantly influences the internal stress and the global conformation of the origami structure. We demonstrate the switching of a polymerized origami nanoribbon between different twisting states and a well-constrained torsional deformation in a monomeric origami shaft. The structural transformation is shown to be reversible, and binding isotherms confirm the reconfiguration mechanism. This approach provides a rapid and reversible means to change DNA origami conformation, which can be used for dynamic and progressive control at the nanoscale.

Effect of component substitution on the atomic dynamics in glass-forming binary metallic melts

NASA Astrophysics Data System (ADS)

Nowak, B.; Holland-Moritz, D.; Yang, F.; Voigtmann, Th.; Evenson, Z.; Hansen, T. C.; Meyer, A.

2017-08-01

We investigate the substitution of early transition metals (Zr, Hf, and Nb) in Ni-based binary glass-forming metallic melts and the impact on structural and dynamical properties by using a combination of neutron scattering, electrostatic levitation (ESL), and isotopic substitution. The self-diffusion coefficients measured by quasielastic neutron scattering (QENS) identify a sluggish diffusion as well as an increased activation energy by almost a factor of 2 for Hf35Ni65 compared to Zr36Ni64 . This finding can be explained by the locally higher packing density of Hf atoms in Hf35Ni65 compared to Zr atoms in Zr36Ni64 , which has been derived from interatomic distances by analyzing the measured partial structure factors. Furthermore, QENS measurements of liquid Hf35Ni65 prepared with 60Ni , which has a vanishing incoherent scattering cross section, have demonstrated that self-diffusion of Hf is slowed down compared to the concentration weighted self-diffusion of Hf and Ni. This implies a dynamical decoupling between larger Hf and smaller Ni atoms, which can be related to a saturation effect of unequal atomic nearest-neighbor pairs, that was observed recently for Ni-rich compositions in Zr-Ni metallic melts. In order to establish a structure-dynamics relation, measured partial structure factors have been used as an input for mode-coupling theory (MCT) of the glass transition to calculate self-diffusion coefficients for the different atomic components. Remarkably, MCT can reproduce the increased activation energy for Hf35Ni65 as well as the dynamical decoupling between Hf and Ni atoms.

Dynamic Analyses Including Joints Of Truss Structures

NASA Technical Reports Server (NTRS)

Belvin, W. Keith

1991-01-01

Method for mathematically modeling joints to assess influences of joints on dynamic response of truss structures developed in study. Only structures with low-frequency oscillations considered; only Coulomb friction and viscous damping included in analysis. Focus of effort to obtain finite-element mathematical models of joints exhibiting load-vs.-deflection behavior similar to measured load-vs.-deflection behavior of real joints. Experiments performed to determine stiffness and damping nonlinearities typical of joint hardware. Algorithm for computing coefficients of analytical joint models based on test data developed to enable study of linear and nonlinear effects of joints on global structural response. Besides intended application to large space structures, applications in nonaerospace community include ground-based antennas and earthquake-resistant steel-framed buildings.

Anomalously large isotope effect in the glass transition of water

DOE PAGES

Gainaru, Catalin; Agapov, Alexander L.; Fuentes-Landete, Violeta; ...

2014-11-24

Here we present the discovery of an unusually large isotope effect in the structural relaxation and the glass transition temperature T g of water. Dielectric relaxation spectroscopy of low-density as well as of vapor deposited amorphous water reveal T g differences of 10±2K between H 2O and D 2O, sharply contrasting with other hydrogen bonded liquids for which H/D exchange increases T g by typically less than 1K. We show that the large isotope effect and the unusual variation of relaxation times in water at low temperatures can be explained in terms of quantum effects. Thus, our findings shed newmore » light on water's peculiar low-temperature dynamics and the possible role of quantum effects in its structural relaxation, and possibly in dynamics of other low molecular weight liquids.« less

A finite element model of rigid body structures actuated by dielectric elastomer actuators

NASA Astrophysics Data System (ADS)

Simone, F.; Linnebach, P.; Rizzello, G.; Seelecke, S.

2018-06-01

This paper presents on finite element (FE) modeling and simulation of dielectric elastomer actuators (DEAs) coupled with articulated structures. DEAs have proven to represent an effective transduction technology for the realization of large deformation, low-power consuming, and fast mechatronic actuators. However, the complex dynamic behavior of the material, characterized by nonlinearities and rate-dependent phenomena, makes it difficult to accurately model and design DEA systems. The problem is further complicated in case the DEA is used to activate articulated structures, which increase both system complexity and implementation effort of numerical simulation models. In this paper, we present a model based tool which allows to effectively implement and simulate complex articulated systems actuated by DEAs. A first prototype of a compact switch actuated by DEA membranes is chosen as reference study to introduce the methodology. The commercially available FE software COMSOL is used for implementing and coupling a physics-based dynamic model of the DEA with the external structure, i.e., the switch. The model is then experimentally calibrated and validated in both quasi-static and dynamic loading conditions. Finally, preliminary results on how to use the simulation tool to optimize the design are presented.

Low-energy Structural Dynamics of Multiferroic Domain Walls in Hexagonal Rare-earth Manganites

NASA Astrophysics Data System (ADS)

Wu, Xiaoyu; Petralanda, Urko; Zheng, Lu; Ren, Yuan; Hu, Rongwei; Cheong, Sang-Wook; Artyukhin, Sergey; Lai, Keji

Multiferroic domain walls (DWs), the natural interfaces between domains with different order parameters, usually exhibit unconventional functionalities. For instance, recent discovery of the ferroelectric DW conduction highlights its extraordinary electronic structure that is absent in bulk domains. The structural dynamics of individual DWs in the microwave regime, however, have not been fully explored due to the lack of spatially resolved studies. Here, we report the broadband (106-1010 Hz) scanning impedance microscopy results on the interlocked anti-phase boundaries and ferroelectric DWs in hexagonal rare-earth manganites. Surprisingly, the effective conductivity of the (001) DWs displays a 106-fold increase from dc to GHz frequencies, while the effect is absent on surfaces with in-plane polarized domains. First-principles and model calculations indicate that the frequency range and selection rules are consistent with the periodic sliding of the DW around its equilibrium position. This DW acoustic-wave-like mode, which is associated with the synchronized oscillation of local polarization and apical oxygen atoms, is localized perpendicular to the DW but free to propagate along the DW plane. Our results break the ground to understand structural DW dynamics and exploit new interfacial phenomena for novel devices.

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.

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

THR ROLE OF SEABED DYNAMICS IN STRUCTURING A MESOHALINE MACROBENTIC INFAUNAL COMMUNITY

EPA Science Inventory

Estuaries are dynamic physical environments. The stability of the sediment-water interface is influenced by sources and rates of sediment delivery and reworking of sediments by currents, tides, waves and biology, but effects of disruption of this interface on benthic biology are...

A Hybrid Approach to Data Assimilation for Reconstructing the Evolution of Mantle Dynamics

NASA Astrophysics Data System (ADS)

Zhou, Quan; Liu, Lijun

2017-11-01

Quantifying past mantle dynamic processes represents a major challenge in understanding the temporal evolution of the solid earth. Mantle convection modeling with data assimilation is one of the most powerful tools to investigate the dynamics of plate subduction and mantle convection. Although various data assimilation methods, both forward and inverse, have been created, these methods all have limitations in their capabilities to represent the real earth. Pure forward models tend to miss important mantle structures due to the incorrect initial condition and thus may lead to incorrect mantle evolution. In contrast, pure tomography-based models cannot effectively resolve the fine slab structure and would fail to predict important subduction-zone dynamic processes. Here we propose a hybrid data assimilation approach that combines the unique power of the sequential and adjoint algorithms, which can properly capture the detailed evolution of the downgoing slab and the tomographically constrained mantle structures, respectively. We apply this new method to reconstructing mantle dynamics below the western U.S. while considering large lateral viscosity variations. By comparing this result with those from several existing data assimilation methods, we demonstrate that the hybrid modeling approach recovers the realistic 4-D mantle dynamics the best.

A Hybrid Forward-Adjoint Data Assimilation Method for Reconstructing the Temporal Evolution of Mantle Dynamics

NASA Astrophysics Data System (ADS)

Zhou, Q.; Liu, L.

2017-12-01

Quantifying past mantle dynamic processes represents a major challenge in understanding the temporal evolution of the solid earth. Mantle convection modeling with data assimilation is one of the most powerful tools to investigate the dynamics of plate subduction and mantle convection. Although various data assimilation methods, both forward and inverse, have been created, these methods all have limitations in their capabilities to represent the real earth. Pure forward models tend to miss important mantle structures due to the incorrect initial condition and thus may lead to incorrect mantle evolution. In contrast, pure tomography-based models cannot effectively resolve the fine slab structure and would fail to predict important subduction-zone dynamic processes. Here we propose a hybrid data assimilation method that combines the unique power of the sequential and adjoint algorithms, which can properly capture the detailed evolution of the downgoing slab and the tomographically constrained mantle structures, respectively. We apply this new method to reconstructing mantle dynamics below the western U.S. while considering large lateral viscosity variations. By comparing this result with those from several existing data assimilation methods, we demonstrate that the hybrid modeling approach recovers the realistic 4-D mantle dynamics to the best.

Structural predictions for Correlated Electron Materials Using the Functional Dynamical Mean Field Theory Approach

NASA Astrophysics Data System (ADS)

Haule, Kristjan

2018-04-01

The Dynamical Mean Field Theory (DMFT) in combination with the band structure methods has been able to address reach physics of correlated materials, such as the fluctuating local moments, spin and orbital fluctuations, atomic multiplet physics and band formation on equal footing. Recently it is getting increasingly recognized that more predictive ab-initio theory of correlated systems needs to also address the feedback effect of the correlated electronic structure on the ionic positions, as the metal-insulator transition is almost always accompanied with considerable structural distortions. We will review recently developed extension of merger between the Density Functional Theory (DFT) and DMFT method, dubbed DFT+ embedded DMFT (DFT+eDMFT), whichsuccessfully addresses this challenge. It is based on the stationary Luttinger-Ward functional to minimize the numerical error, it subtracts the exact double-counting of DFT and DMFT, and implements self-consistent forces on all atoms in the unit cell. In a few examples, we will also show how the method elucidated the important feedback effect of correlations on crystal structure in rare earth nickelates to explain the mechanism of the metal-insulator transition. The method showed that such feedback effect is also essential to understand the dynamic stability of the high-temperature body-centered cubic phase of elemental iron, and in particular it predicted strong enhancement of the electron-phonon coupling over DFT values in FeSe, which was very recently verified by pioneering time-domain experiment.

Measuring and modeling stemflow by two xerophytic shrubs in the Loess Plateau: The role of dynamic canopy structure

NASA Astrophysics Data System (ADS)

Zhang, Y.; Li, X.; Li, W.; Shi, F.; Wu, H.; WU, X.; Pei, T.

2016-12-01

Stemflow plays an important role in hydrological processes in dryland shrubs, but it still remains poorly understood, especially regarding the effects of dynamic canopy structure on stemflow. This study aimed to measure and model the stemflow of two dominant xerophytic shrub (Hippophae rhamnoides and Spiraea pubescens) communities and to identify the key controlling factors of stemflow yield. We quantified and scaled-up stemflow from branches and leaves to stand levels. Correlations and stepwise regression analysis between stemflow and meteorological and biological factors indicated that at branch level, the rainfall amount and the branch diameter were the best variables for modelling and predicting stemflow for Hippophae rhamnoides, while the rainfall amount and the aboveground biomass were the best variables for modelling and predicting stemflow for Spiraea pubescens. At stand level, the stemflow yield is mostly affected by rainfall amount and leaf area index for both shrubs. The stemflow fluxes account for 3.5±0.9% of incident rainfall for H. rhamnoides community and 9.4±2.1% for S. pubescens community, respectively. The differences in percentages of stemflow between the two shrub communities was attributed to differences in canopy structures and water storage capacities. This evaluation of the effects of canopy structure dynamics on stemflow, and of the developed model, provided a better understanding of the effect of the canopy structure on the water cycles in dryland shrub ecosystems.

Future Carbon Dynamics of the Northern Rockies Ecoregion due to Climate Impacts and Fire Effects

NASA Astrophysics Data System (ADS)

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

2016-12-01

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.

Team dynamics in isolated, confined environments - Saturation divers and high altitude climbers

NASA Technical Reports Server (NTRS)

Kanki, Barbara G.; Gregorich, Steven E.

1992-01-01

The effects of leadership dynamics and social organization factors on team performance under conditions of high altitude climbing and deep sea diving are studied. Teams of two to four members that know each other well and have a relaxed informal team structure with much sharing of responsibilities are found to do better than military teams with more than four members who do not know each other well and have a formal team structure with highly specialized rules. Professionally guided teams with more than four members, a formally defined team structure, and clearly designated role assignments did better than 'club' teams of more than four members with a fairly informal team structure and little role specialization.

Eco-evolutionary spatial dynamics in the Glanville fritillary butterfly.

PubMed

Hanski, Ilkka A

2011-08-30

Demographic population dynamics, gene flow, and local adaptation may influence each other and lead to coupling of ecological and evolutionary dynamics, especially in species inhabiting fragmented heterogeneous environments. Here, I review long-term research on eco-evolutionary spatial dynamics in the Glanville fritillary butterfly inhabiting a large network of approximately 4,000 meadows in Finland. The metapopulation persists in a balance between frequent local extinctions and recolonizations. The genetic spatial structure as defined by neutral markers is much more coarse-grained than the demographic spatial structure determined by the fragmented habitat, yet small-scale spatial structure has important consequences for the dynamics. I discuss three examples of eco-evolutionary spatial dynamics. (i) Extinction-colonization metapopulation dynamics influence allele frequency changes in the phosphoglucose isomerase (Pgi) gene, which leads to strong associations between genetic variation in Pgi and dispersal, recolonization, and local population dynamics. (ii) Inbreeding in local populations increases their risk for extinction, whereas reciprocal effects between inbreeding, population size, and emigration represent likely eco-evolutionary feedbacks. (iii) Genetically determined female oviposition preference for two host plant species exhibits a cline paralleling a gradient in host plant relative abundances, and host plant preference of dispersing females in relation to the host plant composition of habitat patches influences immigration (gene flow) and recolonization (founder events). Eco-evolutionary spatial dynamics in heterogeneous environments may not lead to directional evolutionary changes unless the environment itself changes, but eco-evolutionary dynamics may contribute to the maintenance of genetic variation attributable to fluctuating selection in space and time.

Loop-loop interactions govern multiple steps in indole-3-glycerol phosphate synthase catalysis

PubMed Central

Zaccardi, Margot J; O'Rourke, Kathleen F; Yezdimer, Eric M; Loggia, Laura J; Woldt, Svenja; Boehr, David D

2014-01-01

Substrate binding, product release, and likely chemical catalysis in the tryptophan biosynthetic enzyme indole-3-glycerol phosphate synthase (IGPS) are dependent on the structural dynamics of the β1α1 active-site loop. Statistical coupling analysis and molecular dynamic simulations had previously indicated that covarying residues in the β1α1 and β2α2 loops, corresponding to Arg54 and Asn90, respectively, in the Sulfolobus sulfataricus enzyme (ssIGPS), are likely important for coordinating functional motions of these loops. To test this hypothesis, we characterized site mutants at these positions for changes in catalytic function, protein stability and structural dynamics for the thermophilic ssIGPS enzyme. Although there were only modest changes in the overall steady-state kinetic parameters, solvent viscosity and solvent deuterium kinetic isotope effects indicated that these amino acid substitutions change the identity of the rate-determining step across multiple temperatures. Surprisingly, the N90A substitution had a dramatic effect on the general acid/base catalysis of the dehydration step, as indicated by the loss of the descending limb in the pH rate profile, which we had previously assigned to Lys53 on the β1α1 loop. These changes in enzyme function are accompanied with a quenching of ps-ns and µs-ms timescale motions in the β1α1 loop as measured by nuclear magnetic resonance studies. Altogether, our studies provide structural, dynamic and functional rationales for the coevolution of residues on the β1α1 and β2α2 loops, and highlight the multiple roles that the β1α1 loop plays in IGPS catalysis. Thus, substitution of covarying residues in the active-site β1α1 and β2α2 loops of indole-3-glycerol phosphate synthase results in functional, structural, and dynamic changes, highlighting the multiple roles that the β1α1 loop plays in enzyme catalysis and the importance of regulating the structural dynamics of this loop through noncovalent interactions with nearby structural elements. PMID:24403092

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.

Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method

PubMed Central

2013-01-01

Background Many proteins tune their biological function by transitioning between different functional states, effectively acting as dynamic molecular machines. Detailed structural characterization of transition trajectories is central to understanding the relationship between protein dynamics and function. Computational approaches that build on the Molecular Dynamics framework are in principle able to model transition trajectories at great detail but also at considerable computational cost. Methods that delay consideration of dynamics and focus instead on elucidating energetically-credible conformational paths connecting two functionally-relevant structures provide a complementary approach. Effective sampling-based path planning methods originating in robotics have been recently proposed to produce conformational paths. These methods largely model short peptides or address large proteins by simplifying conformational space. Methods We propose a robotics-inspired method that connects two given structures of a protein by sampling conformational paths. The method focuses on small- to medium-size proteins, efficiently modeling structural deformations through the use of the molecular fragment replacement technique. In particular, the method grows a tree in conformational space rooted at the start structure, steering the tree to a goal region defined around the goal structure. We investigate various bias schemes over a progress coordinate for balance between coverage of conformational space and progress towards the goal. A geometric projection layer promotes path diversity. A reactive temperature scheme allows sampling of rare paths that cross energy barriers. Results and conclusions Experiments are conducted on small- to medium-size proteins of length up to 214 amino acids and with multiple known functionally-relevant states, some of which are more than 13Å apart of each-other. Analysis reveals that the method effectively obtains conformational paths connecting structural states that are significantly different. A detailed analysis on the depth and breadth of the tree suggests that a soft global bias over the progress coordinate enhances sampling and results in higher path diversity. The explicit geometric projection layer that biases the exploration away from over-sampled regions further increases coverage, often improving proximity to the goal by forcing the exploration to find new paths. The reactive temperature scheme is shown effective in increasing path diversity, particularly in difficult structural transitions with known high-energy barriers. PMID:24565158

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.

System-spanning dynamically jammed region in response to impact of cornstarch and water suspensions

NASA Astrophysics Data System (ADS)

Allen, Benjamin; Sokol, Benjamin; Mukhopadhyay, Shomeek; Maharjan, Rijan; Brown, Eric

2018-05-01

We experimentally characterize the structure of concentrated suspensions of cornstarch and water in response to impact. Using surface imaging and particle tracking at the boundary opposite the impactor, we observed that a visible structure and particle flow at the boundary occur with a delay after impact. We show the delay time is about the same time as the strong stress response, confirming that the strong stress response results from deformation of the dynamically jammed structure once it spans between the impactor and a solid boundary. A characterization of this strong stress response is reported in a companion paper [Maharjan, Mukhopadhyay, Allen, Storz, and Brown, Phys. Rev. E 97, 052602 (2018), 10.1103/PhysRevE.97.052602]. We observed particle flow in the outer part of the dynamically jammed region at the bottom boundary, with a net transverse displacement of up to about 5% of the impactor displacement, indicating shear at the boundary. Direct imaging of the surface of the outer part of the dynamically jammed region reveals a change in surface structure that appears the same as the result of dilation in other cornstarch suspensions. Imaging also reveals cracks, like a brittle solid. These observations suggest the dynamically jammed structure can temporarily support stress according to an effective modulus, like a soil or dense granular material, along a network of frictional contacts between the impactor and solid boundary.

Comparison of Three Ionic Liquid-Tolerant Cellulases by Molecular Dynamics

PubMed Central

Jaeger, Vance; Burney, Patrick; Pfaendtner, Jim

2015-01-01

We have employed molecular dynamics to investigate the differences in ionic liquid tolerance among three distinct family 5 cellulases from Trichoderma viride, Thermogata maritima, and Pyrococcus horikoshii. Simulations of the three cellulases were conducted at a range of temperatures in various binary mixtures of the ionic liquid 1-ethyl-3-methyl-imidazolium acetate with water. Our analysis demonstrates that the effects of ionic liquids on the enzymes vary in each individual case from local structural disturbances to loss of much of one of the enzyme’s secondary structure. Enzymes with more negatively charged surfaces tend to resist destabilization by ionic liquids. Specific and unique structural changes in the enzymes are induced by the presence of ionic liquids. Disruption of the secondary structure, changes in dynamical motion, and local changes in the binding pocket are observed in less tolerant enzymes. Ionic-liquid-induced denaturation of one of the enzymes is indicated over the 500 ns timescale. In contrast, the most tolerant cellulase behaves similarly in water and in ionic-liquid-containing mixtures. Unlike the heuristic approaches that attempt to predict enzyme stability using macroscopic properties, molecular dynamics allows us to predict specific atomic-level structural and dynamical changes in an enzyme’s behavior induced by ionic liquids and other mixed solvents. Using these insights, we propose specific experimentally testable hypotheses regarding the origin of activity loss for each of the systems investigated in this study. PMID:25692593

Measurements and analyses of principal dynamic parameters of building structures as a function of type of vibration excitation

NASA Astrophysics Data System (ADS)

Bartmański, Cezary; Bochenek, Wojciech; Passia, Henryk; Szade, Adam

2006-06-01

The methods of direct measurement and analysis of the dynamic response of a building structure through real-time recording of the amplitude of low-frequency vibration (tilt) have been presented. Subject to analyses was the reaction induced either by kinematic excitation (road traffic and mining-induced vibration) or controlled action of solid-fuel rocket micro-engines installed on the building. The forces were analysed by means of a set of transducers installed both in the ground and on the structure. After the action of excitation forces has been stopped, the system (structure) makes damped vibration around the static equilibrium position. It has been shown that the type of excitation affects the accuracy of evaluation of principal dynamic parameters of the structure. In the authors opinion these are the decrement of damping and natural vibration frequency. Positive results of tests with the use of excitation by means of short-action (0.6 second) rocket micro-engines give a chance to develop a reliable method for periodical assessment of acceptable loss of usability characteristics of building structures heavily influenced by environmental effects.

Finite Element Analysis of Wrinkled Membrane Structures for Sunshield Applications

NASA Technical Reports Server (NTRS)

Johnston, John D.; Brodeur, Stephen J. (Technical Monitor)

2002-01-01

The deployable sunshield is an example of a gossamer structure envisioned for use on future space telescopes. The basic structure consists of multiple layers of pretensioned, thin-film membranes supported by deployable booms. The prediction and verification of sunshield dynamics has been identified as an area in need of technology development due to the difficulties inherent in predicting nonlinear structural behavior of the membranes and because of the challenges involved. in ground testing of the full-scale structure. This paper describes a finite element analysis of a subscale sunshield that has been subjected to ground testing in support of the Next Generation Space Telescope (NGST) program. The analysis utilizes a nonlinear material model that accounts for wrinkling of the membranes. Results are presented from a nonlinear static preloading analysis and subsequent dynamics analyses to illustrate baseline sunshield structural characteristics. Studies are then described which provide further insight into the effect of membrane. preload on sunshield dynamics and the performance of different membrane modeling techniques. Lastly, a comparison of analytical predictions and ground test results is presented.

Dynamics of a passive micro-vibration isolator based on a pretensioned plane cable net structure and fluid damper

NASA Astrophysics Data System (ADS)

Chen, Yanhao; Lu, Qi; Jing, Bo; Zhang, Zhiyi

2016-09-01

This paper addresses dynamic modelling and experiments on a passive vibration isolator for application in the space environment. The isolator is composed of a pretensioned plane cable net structure and a fluid damper in parallel. Firstly, the frequency response function (FRF) of a single cable is analysed according to the string theory, and the FRF synthesis method is adopted to establish a dynamic model of the plane cable net structure. Secondly, the equivalent damping coefficient of the fluid damper is analysed. Thirdly, experiments are carried out to compare the plane cable net structure, the fluid damper and the vibration isolator formed by the net and the damper, respectively. It is shown that the plane cable net structure can achieve substantial vibration attenuation but has a great amplification at its resonance frequency due to the light damping of cables. The damping effect of fluid damper is acceptable without taking the poor carrying capacity into consideration. Compared to the plane cable net structure and the fluid damper, the isolator has an acceptable resonance amplification as well as vibration attenuation.

Numerical Study of Effects of Fluid-Structure Interaction on Dynamic Responses of Composite Plates

DTIC Science & Technology

2009-09-01

FORCE LOAD AND CLAMPED BOUNDARY.................73 APPENDIX F: ADDITIONAL FIGURES FOR COMPOSITE DE NSITY EFFECTS WITH CONCE NTRATED FORCE LOAD AND...Structure Strain and Kine tic Energy Comparison for Elastic Modulus Variations with Concentrated Force and Clamped Boundary .........................31...48 Figure 49. Experiment Strain Gage La yout on Underside of Composite Plate

Dynamical multiferroicity

NASA Astrophysics Data System (ADS)

Juraschek, Dominik M.; Fechner, Michael; Balatsky, Alexander V.; Spaldin, Nicola A.

2017-06-01

An appealing mechanism for inducing multiferroicity in materials is the generation of electric polarization by a spatially varying magnetization that is coupled to the lattice through the spin-orbit interaction. Here we describe the reciprocal effect, in which a time-dependent electric polarization induces magnetization even in materials with no existing spin structure. We develop a formalism for this dynamical multiferroic effect in the case for which the polarization derives from optical phonons, and compute the strength of the phonon Zeeman effect, which is the solid-state equivalent of the well-established vibrational Zeeman effect in molecules, using density functional theory. We further show that a recently observed behavior—the resonant excitation of a magnon by optically driven phonons—is described by the formalism. Finally, we discuss examples of scenarios that are not driven by lattice dynamics and interpret the excitation of Dzyaloshinskii-Moriya-type electromagnons and the inverse Faraday effect from the viewpoint of dynamical multiferroicity.

Vorticity Dynamics in Single and Multiple Swirling Reacting Jets

NASA Astrophysics Data System (ADS)

Smith, Travis; Aguilar, Michael; Emerson, Benjamin; Noble, David; Lieuwen, Tim

2015-11-01

This presentation describes an analysis of the unsteady flow structures in two multinozzle swirling jet configurations. This work is motivated by the problem of combustion instabilities in premixed flames, a major concern in the development of modern low NOx combustors. The objective is to compare the unsteady flow structures in these two configurations for two separate geometries and determine how certain parameters, primarily distance between jets, influence the flow dynamics. The analysis aims to differentiate between the flow dynamics of single nozzle and triple nozzle configurations. This study looks at how the vorticity in the shear layers of one reacting swirling jet can affect the dynamics of a nearby similar jet. The distance between the swirling jets is found to have an effect on the flow field in determining where swirling jets merge and on the dynamics upstream of the merging location. Graduate Student, School of Aerospace Engineering, Georgia Institute of Technology, Atlanta, GA.

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.

Forest dynamics following eastern hemlock mortality in the southern Appalachians

Treesearch

Chelcy R. Ford; Katherine J. Elliott; Barton D. Clinton; Brian D. Kloeppel; James M. Vose

2011-01-01

Understanding changes in community composition caused by invasive species is critical for predicting effects on ecosystem function, particularly when the invasive threatens a foundation species. Here we focus on dynamics of forest structure, composition and microclimate, and how these interact in southern Appalachian riparian forests following invasion by hemlock...

Density matrix renormalization group with efficient dynamical electron correlation through range separation

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

Hedegård, Erik Donovan, E-mail: erik.hedegard@phys.chem.ethz.ch; Knecht, Stefan; Reiher, Markus, E-mail: markus.reiher@phys.chem.ethz.ch

2015-06-14

We present a new hybrid multiconfigurational method based on the concept of range-separation that combines the density matrix renormalization group approach with density functional theory. This new method is designed for the simultaneous description of dynamical and static electron-correlation effects in multiconfigurational electronic structure problems.

The influence of historical climate on the population dynamics of three dominant sagebrush steppe plants.

USDA-ARS?s Scientific Manuscript database

Climate change could alter the population growth of dominant species, leading to profound effects on community structure and ecosystem dynamics. Understanding the links between historical variation in climate and population vital rates (survival, growth, recruitment) is one way to predict the impact...

Dynamic Systems Modeling in Educational System Design & Policy

ERIC Educational Resources Information Center

Groff, Jennifer Sterling

2013-01-01

Over the last several hundred years, local and national educational systems have evolved from relatively simple systems to incredibly complex, interdependent, policy-laden structures, to which many question their value, effectiveness, and direction they are headed. System Dynamics is a field of analysis used to guide policy and system design in…

Molecular dynamics simulation of Bu4N+ in dimethylformamide: Solvation-induced volume changes

NASA Astrophysics Data System (ADS)

Kiselev, M. G.; Safonova, L. P.

2011-06-01

The structure of the Bu4N+-dimethylformamide system in the condensed and gas phases was studied by molecular dynamics simulation and quantum-chemical calculations. The calculation results were used to reveal the role played by steric effects in the volumetric characteristics of ion solvation.

Teacher Behavior and Student Outcomes: Results of a European Study

ERIC Educational Resources Information Center

Panayiotou, Anastasia; Kyriakides, Leonidas; Creemers, Bert P. M.; McMahon, Léan; Vanlaar, Gudrun; Pfeifer, Michael; Rekalidou, Galini; Bren, Matevž

2014-01-01

This study investigates the extent to which the factors included in the dynamic model of educational effectiveness are associated with student achievement gains in six different European countries. At classroom level, the dynamic model refers to eight factors relating to teacher behavior in the classroom: orientation, structuring, questioning,…

Shock Response and Dynamic Failure of Spatially Tailored Aero-Thermal Structures

DTIC Science & Technology

2012-09-15

Deformation Behavior of Nanolaminated Titanium Aluminum Carbide. 36th International Conference and Exposition on Advanced Ceramics and Composites ...Deformation Behavior of Nanolaminated Titanium Aluminum Carbide. Effect of Strain-rate and Temperature on Dynamic Deformation of Nanolaminated...conditions, we are unaware of any studies published in the open literature on the effect of high strain rate deformation behavior of Ti2AlC at room or

Electromagnetic-field effects on structure and dynamics of amyloidogenic peptides

NASA Astrophysics Data System (ADS)

Todorova, Nevena; Bentvelzen, Alan; English, Niall J.; Yarovsky, Irene

2016-02-01

Electromagnetic fields (EMFs) are ever-present, and so is the need to better understand their influence on human health and biological matter in general. The interaction between a molecular system and external EMF can alter the structure, and dynamical behaviour, and, hence, biological function of proteins with uncertain health consequences. This urges a detailed investigation of EMF-induced effects on basic protein biophysics. Here, we used all-atom non-equilibrium molecular dynamics simulations to understand and quantify the response mechanisms of the amyloidogenic apoC-II(60-70) peptides to non-ionising radiation by modelling their behaviour under external electromagnetic and electric fields of different strengths. Our simulations show high strength fields (>0.04 V/nm) cause structural changes in apoC-II(60-70) due to the peptide dipole alignment along the applied field direction, which disrupts the inherent β-hairpin conformation known to be the intermediate state for fibril formation. The intermediate field-strength range (0.04-0.004 V/nm) causes a significant acceleration in peptide dynamics, which leads to the increased population of structures with fibril-inhibiting characteristics, such as the separated N- and C-termini and colocation of the aromatic residues at the same peptide face. In contrast, lower field strengths (<0.004 V/nm) promote the formation of the amyloid-prone hairpin structures relative to the ambient conditions. These findings suggest that intermediate-strength electromagnetic fields could be considered for designing alternative treatments of amyloid diseases, while the very high and low field strengths could be employed for engineering well-ordered fibrillar aggregates for non-medicinal applications.

Competing nucleation pathways in a mixture of oppositely charged colloids: out-of-equilibrium nucleation revisited.

PubMed

Peters, Baron

2009-12-28

Recent simulations of crystal nucleation from a compressed liquid of oppositely charged colloids show that the natural Brownian dynamics results in nuclei of a charge-disordered FCC (DFCC) solid whereas artificially accelerated dynamics with charge swap moves result in charge-ordered nuclei of a CsCl phase. These results were interpreted as a breakdown of the quasiequilibrium assumption for precritical nuclei. We use structure-specific nucleus size coordinates for the CsCl and DFCC structures and equilibrium based sampling methods to understand the dynamical effects on structure selectivity in this system. Nonequilibrium effects observed in previous simulations emerge from a diffusion tensor that dramatically changes when charge swap moves are used. Without the charge swap moves diffusion is strongly anisotropic with very slow motion along the charge-ordered CsCl axis and faster motion along the DFCC axis. Kramers-Langer-Berezhkovskii-Szabo theory predicts that under the realistic dynamics, the diffusion anisotropy shifts the current toward the DFCC axis. The diffusion tensor also varies with location on the free energy landscape. A numerical calculation of the current field with a diffusion tensor that depends on the location in the free energy landscape exacerbates the extent to which the current is skewed toward DFCC structures. Our analysis confirms that quasiequilibrium theories based on equilibrium properties can explain the nonequilibrium behavior of this system. Our analysis also shows that using a structure-specific nucleus size coordinate for each possible nucleation product can provide mechanistic insight on selectivity and competition between nucleation pathways.

Competing nucleation pathways in a mixture of oppositely charged colloids: Out-of-equilibrium nucleation revisited

NASA Astrophysics Data System (ADS)

Peters, Baron

2009-12-01

Recent simulations of crystal nucleation from a compressed liquid of oppositely charged colloids show that the natural Brownian dynamics results in nuclei of a charge-disordered FCC (DFCC) solid whereas artificially accelerated dynamics with charge swap moves result in charge-ordered nuclei of a CsCl phase. These results were interpreted as a breakdown of the quasiequilibrium assumption for precritical nuclei. We use structure-specific nucleus size coordinates for the CsCl and DFCC structures and equilibrium based sampling methods to understand the dynamical effects on structure selectivity in this system. Nonequilibrium effects observed in previous simulations emerge from a diffusion tensor that dramatically changes when charge swap moves are used. Without the charge swap moves diffusion is strongly anisotropic with very slow motion along the charge-ordered CsCl axis and faster motion along the DFCC axis. Kramers-Langer-Berezhkovskii-Szabo theory predicts that under the realistic dynamics, the diffusion anisotropy shifts the current toward the DFCC axis. The diffusion tensor also varies with location on the free energy landscape. A numerical calculation of the current field with a diffusion tensor that depends on the location in the free energy landscape exacerbates the extent to which the current is skewed toward DFCC structures. Our analysis confirms that quasiequilibrium theories based on equilibrium properties can explain the nonequilibrium behavior of this system. Our analysis also shows that using a structure-specific nucleus size coordinate for each possible nucleation product can provide mechanistic insight on selectivity and competition between nucleation pathways.

Self-similarity in nature

NASA Astrophysics Data System (ADS)

Timashev, S. F.

2000-02-01

A general phenomenological approach to the analysis of experimental temporal, spatial and energetic series for extracting truly physical non-model parameters ("passport data") is presented, which may be used to characterize and distinguish the evolution as well as the spatial and energetic structure of any open nonlinear dissipative system. This methodology is based on a postulate concerning the crucial information contained in the sequences of non-regularities of the measured dynamic variable (temporal, spatial, energetic). In accordance with this approach, multi-parametric formulas for dynamic variable power spectra as well as for structural functions of different orders are identical for every spatial-temporal-energetic level of the system under consideration. In effect, this entails the introduction of a new kind of self-similarity in Nature. An algorithm has been developed for obtaining as many "passport data" as are necessary for the characterization of a dynamic system. Applications of this approach in the analysis of various experimental series (temporal, spatial, energetic) demonstrate its potential for defining adequate phenomenological parameters of different dynamic processes and structures.

Estimation of the full-field dynamic response of a floating bridge using Kalman-type filtering algorithms

NASA Astrophysics Data System (ADS)

Petersen, Ø. W.; Øiseth, O.; Nord, T. S.; Lourens, E.

2018-07-01

Numerical predictions of the dynamic response of complex structures are often uncertain due to uncertainties inherited from the assumed load effects. Inverse methods can estimate the true dynamic response of a structure through system inversion, combining measured acceleration data with a system model. This article presents a case study of full-field dynamic response estimation of a long-span floating bridge: the Bergøysund Bridge in Norway. This bridge is instrumented with a network of 14 triaxial accelerometers. The system model consists of 27 vibration modes with natural frequencies below 2 Hz, obtained from a tuned finite element model that takes the fluid-structure interaction with the surrounding water into account. Two methods, a joint input-state estimation algorithm and a dual Kalman filter, are applied to estimate the full-field response of the bridge. The results demonstrate that the displacements and the accelerations can be estimated at unmeasured locations with reasonable accuracy when the wave loads are the dominant source of excitation.

DNA packaging in viral capsids with peptide arms.

PubMed

Cao, Qianqian; Bachmann, Michael

2017-01-18

Strong chain rigidity and electrostatic self-repulsion of packed double-stranded DNA in viruses require a molecular motor to pull the DNA into the capsid. However, what is the role of electrostatic interactions between different charged components in the packaging process? Though various theories and computer simulation models were developed for the understanding of viral assembly and packaging dynamics of the genome, long-range electrostatic interactions and capsid structure have typically been neglected or oversimplified. By means of molecular dynamics simulations, we explore the effects of electrostatic interactions on the packaging dynamics of DNA based on a coarse-grained DNA and capsid model by explicitly including peptide arms (PAs), linked to the inner surface of the capsid, and counterions. Our results indicate that the electrostatic interactions between PAs, DNA, and counterions have a significant influence on the packaging dynamics. We also find that the packed DNA conformations are largely affected by the structure of the PA layer, but the packaging rate is insensitive to the layer structure.

Ultrafast structural dynamics of boron nitride nanotubes studied using transmitted electrons.

PubMed

Li, Zhongwen; Sun, Shuaishuai; Li, Zi-An; Zhang, Ming; Cao, Gaolong; Tian, Huanfang; Yang, Huaixin; Li, Jianqi

2017-09-14

We investigate the ultrafast structural dynamics of multi-walled boron nitride nanotubes (BNNTs) upon femtosecond optical excitation using ultrafast electron diffraction in a transmission electron microscope. Analysis of the time-resolved (100) and (002) diffraction profiles reveals highly anisotropic lattice dynamics of BNNTs, which can be attributed to the distinct nature of the chemical bonds in the tubular structure. Moreover, the changes in (002) diffraction positions and intensities suggest that the lattice response of BNNTs to the femtosecond laser excitation involves a fast and a slow lattice dynamic process. The fast process with a time constant of about 8 picoseconds can be understood to be a result of electron-phonon coupling, while the slow process with a time constant of about 100 to 300 picoseconds depending on pump laser fluence is tentatively associated with an Auger recombination effect. In addition, we discuss the power-law relationship of a three-photon absorption process in the BNNT nanoscale system.

Charge modeling of ionic polymer-metal composites for dynamic curvature sensing

NASA Astrophysics Data System (ADS)

Bahramzadeh, Yousef; Shahinpoor, Mohsen

2011-04-01

A curvature sensor based on Ionic Polymer-Metal Composite (IPMC) is proposed and characterized for sensing of curvature variation in structures such as inflatable space structures in which using low power and flexible curvature sensor is of high importance for dynamic monitoring of shape at desired points. The linearity of output signal of sensor for calibration, effect of deflection rate at low frequencies and the phase delay between the output signal and the input deformation of IPMC curvature sensor is investigated. An analytical chemo-electro-mechanical model for charge dynamic of IPMC sensor is presented based on Nernst-Planck partial differential equation which can be used to explain the phenomena observed in experiments. The rate dependency of output signal and phase delay between the applied deformation and sensor signal is studied using the proposed model. The model provides a background for predicting the general characteristics of IPMC sensor. It is shown that IPMC sensor exhibits good linearity, sensitivity, and repeatability for dynamic curvature sensing of inflatable structures.

Macroscopic damping model for structural dynamics with random polycrystalline configurations

NASA Astrophysics Data System (ADS)

Yang, Yantao; Cui, Junzhi; Yu, Yifan; Xiang, Meizhen

2018-06-01

In this paper the macroscopic damping model for dynamical behavior of the structures with random polycrystalline configurations at micro-nano scales is established. First, the global motion equation of a crystal is decomposed into a set of motion equations with independent single degree of freedom (SDOF) along normal discrete modes, and then damping behavior is introduced into each SDOF motion. Through the interpolation of discrete modes, the continuous representation of damping effects for the crystal is obtained. Second, from energy conservation law the expression of the damping coefficient is derived, and the approximate formula of damping coefficient is given. Next, the continuous damping coefficient for polycrystalline cluster is expressed, the continuous dynamical equation with damping term is obtained, and then the concrete damping coefficients for a polycrystalline Cu sample are shown. Finally, by using statistical two-scale homogenization method, the macroscopic homogenized dynamical equation containing damping term for the structures with random polycrystalline configurations at micro-nano scales is set up.

Dynamical correlation effects in a weakly correlated material: Inelastic x-ray scattering and photoemission spectra of beryllium

NASA Astrophysics Data System (ADS)

Seidu, Azimatu; Marini, Andrea; Gatti, Matteo

2018-03-01

Beryllium is a weakly correlated simple metal. Still we find that dynamical correlation effects, beyond the independent-particle picture, are necessary to successfully interpret the electronic spectra measured by inelastic x-ray scattering (IXS) and photoemission spectroscopies (PES). By combining ab initio time-dependent density-functional theory (TDDFT) and many-body Green's function theory in the G W approximation (G W A ), we calculate the dynamic structure factor, the quasiparticle (QP) properties and PES spectra of bulk Be. We show that band-structure effects (i.e., due to interaction with the crystal potential) and QP lifetimes (LT) are both needed in order to explain the origin of the measured double-peak features in the IXS spectra. A quantitative agreement with experiment is obtained only when LT are supplemented to the adiabatic local-density approximation (ALDA) of TDDFT. Besides the valence band, PES spectra display a satellite, a signature of dynamical correlation due to the coupling of QPs and plasmons, which we are able to reproduce thanks to the combination of the G W A for the self-energy with the cumulant expansion of the Green's function.

Cation solvation with quantum chemical effects modeled by a size-consistent multi-partitioning quantum mechanics/molecular mechanics method.

PubMed

Watanabe, Hiroshi C; Kubillus, Maximilian; Kubař, Tomáš; Stach, Robert; Mizaikoff, Boris; Ishikita, Hiroshi

2017-07-21

In the condensed phase, quantum chemical properties such as many-body effects and intermolecular charge fluctuations are critical determinants of the solvation structure and dynamics. Thus, a quantum mechanical (QM) molecular description is required for both solute and solvent to incorporate these properties. However, it is challenging to conduct molecular dynamics (MD) simulations for condensed systems of sufficient scale when adapting QM potentials. To overcome this problem, we recently developed the size-consistent multi-partitioning (SCMP) quantum mechanics/molecular mechanics (QM/MM) method and realized stable and accurate MD simulations, using the QM potential to a benchmark system. In the present study, as the first application of the SCMP method, we have investigated the structures and dynamics of Na + , K + , and Ca 2+ solutions based on nanosecond-scale sampling, a sampling 100-times longer than that of conventional QM-based samplings. Furthermore, we have evaluated two dynamic properties, the diffusion coefficient and difference spectra, with high statistical certainty. Furthermore the calculation of these properties has not previously been possible within the conventional QM/MM framework. Based on our analysis, we have quantitatively evaluated the quantum chemical solvation effects, which show distinct differences between the cations.

Impact of hydration and temperature history on the structure and dynamics of lignin

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

Vural, Derya; Gainaru, C.; O'Neill, Hugh Michael

The full utilization of plant biomass for the production of energy and novel materials often involves high temperature treatment. Examples include melt spinning of lignin for manufacturing low-cost carbon fiber and the relocalization of lignin to increase the accessibility of cellulose for production of biofuels. These temperature-induced effects arise from poorly understood changes in lignin flexibility. Here, we combine molecular dynamics simulations with neutron scattering and dielectric spectroscopy experiments to probe the dependence of lignin dynamics on hydration and thermal history. We find a dynamical and structural hysteresis: at a given temperature, the lignin molecules are more expanded and theirmore » dynamics faster when the lignin is cooled than when heated. The structural hysteresis is more pronounced for dry lignin. The difference in dynamics, however, follows a different trend, it is found to be more significant at high temperatures and high hydration levels. The simulations also reveal syringyl units to be more dynamic than guiacyl. The results provide an atomic-detailed description of lignin dynamics, important for understanding lignin role in plant cell wall mechanics and for rationally improving lignin processing. The lignin glass transition, at which the polymer softens, is lower when lignin is cooled than when heated, therefore extending the cooling phase of processing and shortening the heating phase may offer ways to lower processing costs.« less

Impact of hydration and temperature history on the structure and dynamics of lignin

DOE PAGES

Vural, Derya; Gainaru, C.; O'Neill, Hugh Michael; ...

2018-03-16

The full utilization of plant biomass for the production of energy and novel materials often involves high temperature treatment. Examples include melt spinning of lignin for manufacturing low-cost carbon fiber and the relocalization of lignin to increase the accessibility of cellulose for production of biofuels. These temperature-induced effects arise from poorly understood changes in lignin flexibility. Here, we combine molecular dynamics simulations with neutron scattering and dielectric spectroscopy experiments to probe the dependence of lignin dynamics on hydration and thermal history. We find a dynamical and structural hysteresis: at a given temperature, the lignin molecules are more expanded and theirmore » dynamics faster when the lignin is cooled than when heated. The structural hysteresis is more pronounced for dry lignin. The difference in dynamics, however, follows a different trend, it is found to be more significant at high temperatures and high hydration levels. The simulations also reveal syringyl units to be more dynamic than guiacyl. The results provide an atomic-detailed description of lignin dynamics, important for understanding lignin role in plant cell wall mechanics and for rationally improving lignin processing. The lignin glass transition, at which the polymer softens, is lower when lignin is cooled than when heated, therefore extending the cooling phase of processing and shortening the heating phase may offer ways to lower processing costs.« less

Constraining hot Jupiter’s atmospheric structure and dynamics through Doppler shifted emission spectra

NASA Astrophysics Data System (ADS)

Zhang, Jisheng; Kempton, Eliza; Rauscher, Emily

2017-01-01

In recent years, astronomers have begun successfully observing the atmospheres of extrasolar planets using ground-based telescopes equipped with spectrographs capable of observing at high spectral resolution (R~105). Such studies are capable of diagnosing the atmospheric structure, composition, and dynamics (winds and rotation) of both transiting and non-transiting exoplanets. However, few studies have examined how the 3-D atmospheric dynamics could alter the emitted light of hot Jupiters at such high spectral resolution. Here, we present a model to explore such influence on the hot Jupiters’ thermal emission spectra. Our aim is to investigate the extent to which the effects of 3-D atmospheric dynamics are imprinted on planet-averaged thermal emission spectra. We couple together a 3-D general circulation model of hot Jupiter atmospheric dynamics (Rauscher & Menou, 2012) with a radiative transfer solver to predict the planet’s disk-integrated emission spectrum as a function of its orbital phase. For the first time, we self-consistently include the effects of the line-of-sight atmospheric motions (resulting from winds and rotation) in the calculation to produce Doppler-shifted spectral line profiles that result from the atmospheric dynamics. We focus our study on three benchmark hot Jupiters, HD 189733b, HD 209458b, and WASP-43b which have been the focus of previous detailed observational studies. We find that the high-resolution Doppler shifted thermal emission spectra can be used to diagnose key properties of the dynamical atmosphere - the planet’s longitudinal temperature and wind structure, and its rotation rate.

Imaging Magnetization Structure and Dynamics in Ultrathin Y3Fe5O12/Pt Bilayers with High Sensitivity Using the Time-Resolved Longitudinal Spin Seebeck Effect

NASA Astrophysics Data System (ADS)

Bartell, Jason M.; Jermain, Colin L.; Aradhya, Sriharsha V.; Brangham, Jack T.; Yang, Fengyuan; Ralph, Daniel C.; Fuchs, Gregory D.

2017-04-01

We demonstrate an instrument for time-resolved magnetic imaging that is highly sensitive to the in-plane magnetization state and dynamics of thin-film bilayers of yttrium iron garnet [Y3Fe5O12(YIG )]/Pt : the time-resolved longitudinal spin Seebeck (TRLSSE) effect microscope. We detect the local in-plane magnetic orientation within the YIG by focusing a picosecond laser to generate thermally driven spin current from the YIG into the Pt by the spin Seebeck effect and then use the inverse spin Hall effect in the Pt to transduce this spin current to an output voltage. To establish the time resolution of TRLSSE, we show that pulsed optical heating of patterned YIG (20 nm )/Pt (6 nm )/Ru (2 nm ) wires generates a magnetization-dependent voltage pulse of less than 100 ps. We demonstrate TRLSSE microscopy to image both static magnetic structure and gigahertz-frequency magnetic resonance dynamics with submicron spatial resolution and a sensitivity to magnetic orientation below 0.3 °/√{H z } in ultrathin YIG.

The effect of host cluster gravitational tidal forces on the internal dynamics of spiral galaxies

NASA Astrophysics Data System (ADS)

Mayer, Alexander

2013-04-01

New empirical observation by Bidin, Carraro, Mendez & Smith finds ``a lack of dark matter in the Solar neighborhood" (2012 ApJ 751, 30). This, and the discovery of a vast polar structure of Milky Way satellites by Pawlowski, Pflamm-Altenburg & Kroupa (2012 MNRAS 423, 1109), conflict with the prevailing interpretation of the measured Galactic rotation curve. Simulating the dynamical effects of host cluster tidal forces on galaxy disks reveals radial migration in a spiral structure and an orbital velocity that accelerates with increasing galactocentric radial coordinate. A virtual ``toy model,'' which is based on an Earth-orbiting system of particles and is physically realizable in principle, is available at GravitySim.net. Given the perturbing gravitational effect of the host cluster on a spiral galaxy disk and that a similar effect does not exist for the Solar System, the two systems represent distinct classes of gravitational dynamical systems. The observed `flat' and accelerating rotation curves of spiral galaxies can be attributed to gravitational interaction with the host cluster; no `dark matter halo' is required to explain the observable.

Von Bertalanffy's dynamics under a polynomial correction: Allee effect and big bang bifurcation

NASA Astrophysics Data System (ADS)

Leonel Rocha, J.; Taha, A. K.; Fournier-Prunaret, D.

2016-02-01

In this work we consider new one-dimensional populational discrete dynamical systems in which the growth of the population is described by a family of von Bertalanffy's functions, as a dynamical approach to von Bertalanffy's growth equation. The purpose of introducing Allee effect in those models is satisfied under a correction factor of polynomial type. We study classes of von Bertalanffy's functions with different types of Allee effect: strong and weak Allee's functions. Dependent on the variation of four parameters, von Bertalanffy's functions also includes another class of important functions: functions with no Allee effect. The complex bifurcation structures of these von Bertalanffy's functions is investigated in detail. We verified that this family of functions has particular bifurcation structures: the big bang bifurcation of the so-called “box-within-a-box” type. The big bang bifurcation is associated to the asymptotic weight or carrying capacity. This work is a contribution to the study of the big bang bifurcation analysis for continuous maps and their relationship with explosion birth and extinction phenomena.

Scaling effects in the static and dynamic response of graphite-epoxy beam-columns. Ph.D. Thesis - Virginia Polytechnic Inst. and State Univ.

NASA Technical Reports Server (NTRS)

Jackson, Karen E.

1990-01-01

Scale model technology represents one method of investigating the behavior of advanced, weight-efficient composite structures under a variety of loading conditions. It is necessary, however, to understand the limitations involved in testing scale model structures before the technique can be fully utilized. These limitations, or scaling effects, are characterized. in the large deflection response and failure of composite beams. Scale model beams were loaded with an eccentric axial compressive load designed to produce large bending deflections and global failure. A dimensional analysis was performed on the composite beam-column loading configuration to determine a model law governing the system response. An experimental program was developed to validate the model law under both static and dynamic loading conditions. Laminate stacking sequences including unidirectional, angle ply, cross ply, and quasi-isotropic were tested to examine a diversity of composite response and failure modes. The model beams were loaded under scaled test conditions until catastrophic failure. A large deflection beam solution was developed to compare with the static experimental results and to analyze beam failure. Also, the finite element code DYCAST (DYnamic Crash Analysis of STructure) was used to model both the static and impulsive beam response. Static test results indicate that the unidirectional and cross ply beam responses scale as predicted by the model law, even under severe deformations. In general, failure modes were consistent between scale models within a laminate family; however, a significant scale effect was observed in strength. The scale effect in strength which was evident in the static tests was also observed in the dynamic tests. Scaling of load and strain time histories between the scale model beams and the prototypes was excellent for the unidirectional beams, but inconsistent results were obtained for the angle ply, cross ply, and quasi-isotropic beams. Results show that valuable information can be obtained from testing on scale model composite structures, especially in the linear elastic response region. However, due to scaling effects in the strength behavior of composite laminates, caution must be used in extrapolating data taken from a scale model test when that test involves failure of the structure.

The Social Origins of Networks and Diffusion.

PubMed

Centola, Damon

2015-03-01

Recent research on social contagion has demonstrated significant effects of network topology on the dynamics of diffusion. However, network topologies are not given a priori. Rather, they are patterns of relations that emerge from individual and structural features of society, such as population composition, group heterogeneity, homophily, and social consolidation. Following Blau and Schwartz, the author develops a model of social network formation that explores how social and structural constraints on tie formation generate emergent social topologies and then explores the effectiveness of these social networks for the dynamics of social diffusion. Results show that, at one extreme, high levels of consolidation can create highly balkanized communities with poor integration of shared norms and practices. As suggested by Blau and Schwartz, reducing consolidation creates more crosscutting circles and significantly improves the dynamics of social diffusion across the population. However, the author finds that further reducing consolidation creates highly intersecting social networks that fail to support the widespread diffusion of norms and practices, indicating that successful social diffusion can depend on moderate to high levels of structural consolidation.

Isotopic differentiation and sublattice melting in dense dynamic ice

NASA Astrophysics Data System (ADS)

Hermann, Andreas; Ashcroft, N. W.; Hoffmann, Roald

2013-12-01

The isotopes of hydrogen provide a unique exploratory laboratory for examining the role of zero point energy (ZPE) in determining the structural and dynamic features of the crystalline ices of water. There are two critical regions of high pressure: (i) near 1 TPa and (ii) near the predicted onset of metallization at around 5 TPa. At the lower pressure of the two, we see the expected small isotopic effects on phase transitions. Near metallization, however, the effects are much greater, leading to a situation where tritiated ice could skip almost entirely a phase available to the other isotopomers. For the higher pressure ices, we investigate in some detail the enthalpics of a dynamic proton sublattice, with the corresponding structures being quite ionic. The resistance toward diffusion of single protons in the ground state structures of high-pressure H2O is found to be large, in fact to the point that the ZPE reservoir cannot overcome these. However, the barriers toward a three-dimensional coherent or concerted motion of protons can be much lower, and the ensuing consequences are explored.

Effects of Ohmic Resistance on Dynamic Characteristics and Impedance of Micro/Nano Cantilever Beam resonators

NASA Astrophysics Data System (ADS)

Rezazadeh, Ghader; Keyvani, Aliasghar; Sadeghi, Morteza H.; Bahrami, Manouchehr

2013-06-01

Effects of Ohmic resistance on MEMS/NEMS vibrating structures that have always been dismissed in some situations may cause important changes in resonance properties and impedance parameters of the MEMS/NEMS based circuits. In this paper it is aimed to present a theoretical model to precisely investigate the problem on a simple cantilever-substrate resonator. In this favor the Ohm's current law and charge conservation law have been merged to find a differential Equation for voltage propagation on the beam and because mostly nano structures are expected as the scope of the problem, modified couple stress theory is used to formulate the dynamic motion of the beam. The two governing equations were coupled and both nonlinear that have been solved simultaneously using a Galerkin based state space formulation. The obtained results that are in exact agreement with previous works show that dynamic pull-in voltage, switching time, and impedance of structure as a MEMS capacitor especially in frequencies higher than natural resonance frequency strongly relay on electrical resistance of the beam and substrate material.

Using the prisms of gender and rank to interpret research collaboration power dynamics.

PubMed

Gaughan, Monica; Bozeman, Barry

2016-08-01

Collaboration is central to modern scientific inquiry, and increasingly important to the professional experiences of academic scientists. While the effects of collaboration have been widely studied, much less is understood about the motivations to collaborate and collaboration dynamics that generate scientific outcomes. A particular interest of this study is to understand how collaboration experiences differ between women and men, and the attributions used to explain these differences. We use a multi-method study of university Science, Technology, Engineering, and Mathematics faculty research collaborators. We employ 177 anonymous open-ended responses to a web-based survey, and 60 semi-structured interviews of academic scientists in US research universities. We find similarities and differences in collaborative activity between men and women. Open-ended qualitative textual analysis suggests that some of these differences are attributed to power dynamics - both general ones related to differences in organizational status, and in power dynamics related specifically to gender. In analysis of semi-structured interviews, we find that both status and gender were used as interpretive frames for collaborative behavior, with more emphasis placed on status than gender differences. Overall, the findings support that gender structures some part of the collaborative experience, but that status hierarchy exerts more clear effects.

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations

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

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. In such simulations we often perform them at elevated temperaturesmore » to artificially “correct” for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. In order to address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na +, K +, and Cl - ions. We show that simulations at 390–400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. These results suggest that an elevated temperature around 390–400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.« less

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations

DOE PAGES

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.; ...

2016-10-17

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. In such simulations we often perform them at elevated temperaturesmore » to artificially “correct” for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. In order to address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na +, K +, and Cl - ions. We show that simulations at 390–400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. These results suggest that an elevated temperature around 390–400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.« less

Decomposition of Proteins into Dynamic Units from Atomic Cross-Correlation Functions.

PubMed

Calligari, Paolo; Gerolin, Marco; Abergel, Daniel; Polimeno, Antonino

2017-01-10

In this article, we present a clustering method of atoms in proteins based on the analysis of the correlation times of interatomic distance correlation functions computed from MD simulations. The goal is to provide a coarse-grained description of the protein in terms of fewer elements that can be treated as dynamically independent subunits. Importantly, this domain decomposition method does not take into account structural properties of the protein. Instead, the clustering of protein residues in terms of networks of dynamically correlated domains is defined on the basis of the effective correlation times of the pair distance correlation functions. For these properties, our method stands as a complementary analysis to the customary protein decomposition in terms of quasi-rigid, structure-based domains. Results obtained for a prototypal protein structure illustrate the approach proposed.

Exploring the formation pathways of donor-acceptor catenanes in aqueous dynamic combinatorial libraries.

PubMed

Cougnon, Fabien B L; Au-Yeung, Ho Yu; Pantoş, G Dan; Sanders, Jeremy K M

2011-03-09

The discovery through dynamic combinatorial chemistry (DCC) of a new generation of donor-acceptor [2]catenanes highlights the power of DCC to access unprecedented structures. While conventional thinking has limited the scope of donor-acceptor catenanes to strictly alternating stacks of donor (D) and acceptor (A) aromatic units, DCC is demonstrated in this paper to give access to unusual DAAD, DADD, and ADAA stacks. Each of these catenanes has specific structural requirements, allowing control of their formation. On the basis of these results, and on the observation that the catenanes represent kinetic bottlenecks in the reaction pathway, we propose a mechanism that explains and predicts the structures formed. Furthermore, the spontaneous assembly of catenanes in aqueous dynamic systems gives a fundamental insight into the role played by hydrophobic effect and donor-acceptor interactions when building such complex architectures.

Effects of fir sawyer beetle on spatial structure of Siberian fir stands

Treesearch

Vladimir L. Gavrikov; Valentina P. Vetrova

1991-01-01

Insects not only use plants for food and habitat; they also change plant populations by influencing their structure and dynamics. This influence is evidenced in the alteration of the spatial structure of a stand. The fir sawyer, Monochamus urussovi Fisch. (Coleoptera: Cerambycidae), is the most abundant xylophagous insect injuring siberian fir,...

Effect of particle-size dynamics on properties of dense spongy-particle systems: Approach towards equilibrium.

PubMed

Zakhari, Monica E A; Anderson, Patrick D; Hütter, Markus

2017-07-01

Open-porous deformable particles, often envisaged as sponges, are ubiquitous in biological and industrial systems (e.g., casein micelles in dairy products and microgels in cosmetics). The rich behavior of these suspensions is owing to the elasticity of the supporting network of the particle, and the viscosity of permeating solvent. Therefore, the rate-dependent size change of these particles depends on their structure, i.e., the permeability. This work aims at investigating the effect of the particle-size dynamics and the underlying particle structure, i.e., the particle permeability, on the transient and long-time behavior of suspensions of spongy particles in the absence of applied deformation, using the dynamic two-scale model developed by Hütter et al. [Farad. Discuss. 158, 407 (2012)1359-664010.1039/c2fd20025b]. In the high-density limit, the transient behavior is found to be accelerated by the particle-size dynamics, even at average size changes as small as 1%. The accelerated dynamics is evidenced by (i) the higher short-time diffusion coefficient as compared to elastic-particle systems and (ii) the accelerated formation of the stable fcc crystal structure. Furthermore, after long times, the particle-size dynamics of spongy particles is shown to result in lower stationary values of the energy and normal stresses as compared to elastic-particle systems. This dependence of the long-time behavior of these systems on the permeability, that essentially is a transport coefficient and hence must not affect the equilibrium properties, confirms that full equilibration has not been reached.

Effect of particle-size dynamics on properties of dense spongy-particle systems: Approach towards equilibrium

NASA Astrophysics Data System (ADS)

Zakhari, Monica E. A.; Anderson, Patrick D.; Hütter, Markus

2017-07-01

Open-porous deformable particles, often envisaged as sponges, are ubiquitous in biological and industrial systems (e.g., casein micelles in dairy products and microgels in cosmetics). The rich behavior of these suspensions is owing to the elasticity of the supporting network of the particle, and the viscosity of permeating solvent. Therefore, the rate-dependent size change of these particles depends on their structure, i.e., the permeability. This work aims at investigating the effect of the particle-size dynamics and the underlying particle structure, i.e., the particle permeability, on the transient and long-time behavior of suspensions of spongy particles in the absence of applied deformation, using the dynamic two-scale model developed by Hütter et al. [Farad. Discuss. 158, 407 (2012), 10.1039/c2fd20025b]. In the high-density limit, the transient behavior is found to be accelerated by the particle-size dynamics, even at average size changes as small as 1 % . The accelerated dynamics is evidenced by (i) the higher short-time diffusion coefficient as compared to elastic-particle systems and (ii) the accelerated formation of the stable fcc crystal structure. Furthermore, after long times, the particle-size dynamics of spongy particles is shown to result in lower stationary values of the energy and normal stresses as compared to elastic-particle systems. This dependence of the long-time behavior of these systems on the permeability, that essentially is a transport coefficient and hence must not affect the equilibrium properties, confirms that full equilibration has not been reached.

Independent Metrics for Protein Backbone and Side-Chain Flexibility: Time Scales and Effects of Ligand Binding.

PubMed

Fuchs, Julian E; Waldner, Birgit J; Huber, Roland G; von Grafenstein, Susanne; Kramer, Christian; Liedl, Klaus R

2015-03-10

Conformational dynamics are central for understanding biomolecular structure and function, since biological macromolecules are inherently flexible at room temperature and in solution. Computational methods are nowadays capable of providing valuable information on the conformational ensembles of biomolecules. However, analysis tools and intuitive metrics that capture dynamic information from in silico generated structural ensembles are limited. In standard work-flows, flexibility in a conformational ensemble is represented through residue-wise root-mean-square fluctuations or B-factors following a global alignment. Consequently, these approaches relying on global alignments discard valuable information on local dynamics. Results inherently depend on global flexibility, residue size, and connectivity. In this study we present a novel approach for capturing positional fluctuations based on multiple local alignments instead of one single global alignment. The method captures local dynamics within a structural ensemble independent of residue type by splitting individual local and global degrees of freedom of protein backbone and side-chains. Dependence on residue type and size in the side-chains is removed via normalization with the B-factors of the isolated residue. As a test case, we demonstrate its application to a molecular dynamics simulation of bovine pancreatic trypsin inhibitor (BPTI) on the millisecond time scale. This allows for illustrating different time scales of backbone and side-chain flexibility. Additionally, we demonstrate the effects of ligand binding on side-chain flexibility of three serine proteases. We expect our new methodology for quantifying local flexibility to be helpful in unraveling local changes in biomolecular dynamics.

Vibrational Properties of Hydrogen-Bonded Systems Using the Multireference Generalization to the "On-the-Fly" Electronic Structure within Quantum Wavepacket ab Initio Molecular Dynamics (QWAIMD).

PubMed

Li, Junjie; Li, Xiaohu; Iyengar, Srinivasan S

2014-06-10

We discuss a multiconfigurational treatment of the "on-the-fly" electronic structure within the quantum wavepacket ab initio molecular dynamics (QWAIMD) method for coupled treatment of quantum nuclear effects with electronic structural effects. Here, multiple single-particle electronic density matrices are simultaneously propagated with a quantum nuclear wavepacket and other classical nuclear degrees of freedom. The multiple density matrices are coupled through a nonorthogonal configuration interaction (NOCI) procedure to construct the instantaneous potential surface. An adaptive-mesh-guided set of basis functions composed of Gaussian primitives are used to simplify the electronic structure calculations. Specifically, with the replacement of the atom-centered basis functions positioned on the centers of the quantum-mechanically treated nuclei by a mesh-guided band of basis functions, the two-electron integrals used to compute the electronic structure potential surface become independent of the quantum nuclear variable and hence reusable along the entire Cartesian grid representing the quantum nuclear coordinates. This reduces the computational complexity involved in obtaining a potential surface and facilitates the interpretation of the individual density matrices as representative diabatic states. The parametric nuclear position dependence of the diabatic states is evaluated at the initial time-step using a Shannon-entropy-based sampling function that depends on an approximation to the quantum nuclear wavepacket and the potential surface. This development is meant as a precursor to an on-the-fly fully multireference electronic structure procedure embedded, on-the-fly, within a quantum nuclear dynamics formalism. We benchmark the current development by computing structural, dynamic, and spectroscopic features for a series of bihalide hydrogen-bonded systems: FHF(-), ClHCl(-), BrHBr(-), and BrHCl(-). We find that the donor-acceptor structural features are in good agreement with experiments. Spectroscopic features are computed using a unified velocity/flux autocorrelation function and include vibrational fundamentals and combination bands. These agree well with experiments and other theories.

Effects of nonadditive interactions on ion solvation at the water/vapor interface: a molecular dynamics study.

PubMed

Yagasaki, Takuma; Saito, Shinji; Ohmine, Iwao

2010-12-09

The solvation of halide ions at the water/vapor interface is investigated by using molecular dynamics simulations with nonpolarizable molecular mechanical (MM), polarizable MM, and quantum mechanical (QM)/MM methods. The free energy profile of the ion solvation is decomposed into the energy and the entropic contributions along the ion displacement from inside to the surface of water. It is found that the surface affinity of the ion, relative to the bulk value, is determined by a subtle balance between the energetic destabilization and the entropic stabilization with the ion displacement. The amount of energetic destabilization is found to be reduced when nonadditive interactions are included, as in the polarizable MM and QM/MM models. The structure of water around the ion at the interface is also largely modified when the higher order effects are considered. For example, the induced dipole effect enhances the solvation structure around the ion at the interface significantly and thus reduces the amount of entropic stabilization at the interface, relative to in the bulk. It is found that this induced dipole effect causes the slowing in the ion-water hydrogen bond dynamics at the interface. On the other hand, the higher order induced multipole effects in the QM/MM method suppress both the excessive enhancement of the solvation structure and the slowing of the ion-water hydrogen bond dynamics at the interface. The present study demonstrates that not only the induced dipole moment but also the higher order induced multipole moments, which are neglected in standard empirical models, are essential for the correct description of the ion solvation at the water/vapor interface.

Investigating the effect of key mutations on the conformational dynamics of toll-like receptor dimers through molecular dynamics simulations and protein structure networks.

PubMed

Mahita, Jarjapu; Sowdhamini, Ramanathan

2018-04-01

The Toll-like receptors (TLRs) are critical components of the innate immune system due to their ability to detect conserved pathogen-associated molecular patterns, present in bacteria, viruses, and other microorganisms. Ligand detection by TLRs leads to a signaling cascade, mediated by interactions among TIR domains present in the receptors, the bridging adaptors and sorting adaptors. The BB loop is a highly conserved region present in the TIR domain and is crucial for mediating interactions among TIR domain-containing proteins. Mutations in the BB loop of the Toll-like receptors, such as the A795P mutation in TLR3 and the P712H mutation (Lps d mutation) in TLR4, have been reported to disrupt or alter downstream signaling. While the phenotypic effect of these mutations is known, the underlying effect of these mutations on the structure, dynamics and interactions with other TIR domain-containing proteins is not well understood. Here, we have attempted to investigate the effect of the BB loop mutations on the dimer form of TLRs, using TLR2 and TLR3 as case studies. Our results based on molecular dynamics simulations, protein-protein interaction analyses and protein structure network analyses highlight significant differences between the dimer interfaces of the wild-type and mutant forms and provide a logical reasoning for the effect of these mutations on adaptor binding to TLRs. Furthermore, it also leads us to propose a hypothesis for the differential requirement of signaling and bridging adaptors by TLRs. This could aid in further understanding of the mechanisms governing such signaling pathways. © 2018 Wiley Periodicals, Inc.

Dynamic contrast-enhanced diffuse optical tomography (DCE-DOT): experimental validation with a dynamic phantom

NASA Astrophysics Data System (ADS)

Burcin Unlu, Mehmet; Lin, Yuting; Gulsen, Gultekin

2009-11-01

Dynamic contrast-enhanced diffuse optical tomography (DCE-DOT) can provide spatially resolved enhancement kinetics of an optical contrast agent. We undertook a systematic phantom study to evaluate the effects of the geometrical parameters such as the depth and size of the inclusion as well as the optical parameters of the background on the recovered enhancement kinetics of the most commonly used optical contrast agent, indocyanine green (ICG). For this purpose a computer-controlled dynamic phantom was constructed. An ICG-intralipid-water mixture was circulated through the inclusions while the DCE-DOT measurements were acquired with a temporal resolution of 16 s. The same dynamic study was repeated using inclusions of different sizes located at different depths. In addition to this, the effect of non-scattering regions was investigated by placing a second inclusion filled with water in the background. The phantom studies confirmed that although the peak enhancement varied substantially for each case, the recovered injection and dilution rates obtained from the percentage enhancement maps agreed within 15% independent of not only the depth and the size of the inclusion but also the presence of a non-scattering region in the background. Although no internal structural information was used in these phantom studies, it may be necessary to use it for small objects buried deep in tissue. However, the different contrast mechanisms of optical and other imaging modalities as well as imperfect co-registration between both modalities may lead to potential errors in the structural a priori. Therefore, the effect of erroneous selection of structural priors was investigated as the final step. Again, the injection and dilution rates obtained from the percentage enhancement maps were also immune to the systematic errors introduced by erroneous selection of the structural priors, e.g. choosing the diameter of the inclusion 20% smaller increased the peak enhancement 60% but changed the injection and dilution rates only less than 10%.

Highly dynamic animal contact network and implications on disease transmission

PubMed Central

Chen, Shi; White, Brad J.; Sanderson, Michael W.; Amrine, David E.; Ilany, Amiyaal; Lanzas, Cristina

2014-01-01

Contact patterns among hosts are considered as one of the most critical factors contributing to unequal pathogen transmission. Consequently, networks have been widely applied in infectious disease modeling. However most studies assume static network structure due to lack of accurate observation and appropriate analytic tools. In this study we used high temporal and spatial resolution animal position data to construct a high-resolution contact network relevant to infectious disease transmission. The animal contact network aggregated at hourly level was highly variable and dynamic within and between days, for both network structure (network degree distribution) and individual rank of degree distribution in the network (degree order). We integrated network degree distribution and degree order heterogeneities with a commonly used contact-based, directly transmitted disease model to quantify the effect of these two sources of heterogeneity on the infectious disease dynamics. Four conditions were simulated based on the combination of these two heterogeneities. Simulation results indicated that disease dynamics and individual contribution to new infections varied substantially among these four conditions under both parameter settings. Changes in the contact network had a greater effect on disease dynamics for pathogens with smaller basic reproduction number (i.e. R0 < 2). PMID:24667241

Active Polar Two-Fluid Macroscopic Dynamics

NASA Astrophysics Data System (ADS)

Pleiner, Harald; Svensek, Daniel; Brand, Helmut R.

2014-03-01

We study the dynamics of systems with a polar dynamic preferred direction. Examples include the pattern-forming growth of bacteria (in a solvent, shoals of fish (moving in water currents), flocks of birds and migrating insects (flying in windy air). Because the preferred direction only exists dynamically, but not statically, the macroscopic variable of choice is the macroscopic velocity associated with the motion of the active units. We derive the macroscopic equations for such a system and discuss novel static, reversible and irreversible cross-couplings connected to this second velocity. We find a normal mode structure quite different compared to the static descriptions, as well as linear couplings between (active) flow and e.g. densities and concentrations due to the genuine two-fluid transport derivatives. On the other hand, we get, quite similar to the static case, a direct linear relation between the stress tensor and the structure tensor. This prominent ``active'' term is responsible for many active effects, meaning that our approach can describe those effects as well. In addition, we also deal with explicitly chiral systems, which are important for many active systems. In particular, we find an active flow-induced heat current specific for the dynamic chiral polar order.

Size effects on the structural, electronic, and optical properties of (5,0) finite-length carbon nanotube: An ab-initio electronic structure study

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

Tarighi Ahmadpour, Mahdi; Rostamnejadi, Ali; Hashemifar, S. Javad

2016-07-07

We use density functional computations to study the zero temperature structural, electronic, magnetic, and optical properties of (5,0) finite carbon nanotubes (FCNT), with length in the range of 4–44 Å. It is found that the structural and electronic properties of (5,0) FCNTs, in the ground state, converge at a length of about 30 Å, while the excited state properties exhibit long-range edge effects. We discuss that curvature effects enhance energy gap of FCNTs, in contrast to the known trend in the periodic limit. It is seen that compensation of curvature effects in two special small sizes may give rise to spontaneous magnetization.more » The obtained cohesive energies provide some insights into the effects of environment on the growth of FCNTs. The second-order difference of the total energies reveals an important magic size of about 15 Å. The optical and dynamical magnetic responses of the FCNTs to polarized electromagnetic pulses are studied by time dependent density functional theory. The results show that the static and dynamic magnetic properties mainly come from the edge carbon atoms. The optical absorption properties are described in terms of local field effects and characterized by Casida linear response method.« less

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

Identification of Rotorcraft Structural Dynamics from Flight and Wind Tunnel Data

NASA Technical Reports Server (NTRS)

McKillip, Robert M., Jr.

1997-01-01

Excessive vibration remains one one of the most difficult problems that faces the helicopter industry today, affecting all production helicopters at some phase of their development. Vibrations in rotating structures may arise from external periodic dynamic airloads whose frequencies are are close to the natural frequencies of the rotating system itself. The goal for the structures engineer would thus be to design a structure as free from resonance effects as possible. In the case of a helicopter rotor blade these dynamic loads are a consequence of asymmetric airload distribution on the rotor blade in forward flight, leading to a rich collection of higher harmonic airloads that force rotor and airframe response. Accurate prediction of the dynamic characteristics of a helicopter rotor blade will provide the opportunity to affect in a positive manner noise intensity, vibration level, durability, reliability and operating costs by reducing objectionable frequencies or moving them to a different frequency range and thus providing us with a lower vibration rotor. In fact, the dynamic characteristics tend to define the operating limits of a rotorcraft. As computing power has increased greatly over the last decade, researchers and engineers have turned to analyzing the vibrational characteristics of aerospace structures at the design and development stage of the production of an aircraft. Modern rotor blade construction methods lead to products with low mass and low inherent damping so careful design and analysis is required to avoid resonance and an undesirable dynamic performance. In addition, accurate modal analysis is necessary for several current approaches in elastic system identification and active control.

Ice Load Project Final Technical Report

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

McCoy, Timothy J.; Brown, Thomas; Byrne, Alex

As interest and investment in offshore wind projects increase worldwide, some turbines will be installed in locations where ice of significant thickness forms on the water surface. This ice moves under the driving forces of wind, current, and thermal effects and may result in substantial forces on bottom-fixed support structures. The North and Baltic Seas in Europe have begun to see significant wind energy development and the Great Lakes of the United States and Canada may host wind energy development in the near future. Design of the support structures for these projects is best performed through the use of anmore » integrated tool that can calculate the cumulative effects of forces due to turbine operations, wind, waves, and floating ice. The dynamic nature of ice forces requires that these forces be included in the design simulations, rather than added as static forces to simulation results. The International Electrotechnical Commission (IEC) standard[2] for offshore wind turbine design and the International Organization for Standardization (ISO) standard[3] for offshore structures provide requirements and algorithms for the calculation of forces induced by surface ice; however, currently none of the major wind turbine dynamic simulation codes provides the ability to model ice loads. The scope of work of the project described in this report includes the development of a suite of subroutines, collectively named IceFloe, that meet the requirements of the IEC and ISO standards and couples with four of the major wind turbine dynamic simulation codes. The mechanisms by which ice forces impinge on offshore structures generally include the forces required for crushing of the ice against vertical-sided structures and the forces required to fracture the ice as it rides up on conical-sided structures. Within these two broad categories, the dynamic character of the forces with respect to time is also dependent on other factors such as the velocity and thickness of the moving ice and the response of the structure. In some cases, the dynamic effects are random and in other cases they are deterministic, such as the effect of structural resonance and coupling of the ice forces with the defection of the support structure. The initial versions of the IceFloe routines incorporate modules that address these varied force and dynamic phenomena with seven alternative algorithms that can be specified by the user. The IceFloe routines have been linked and tested with four major wind turbine aeroelastic simulation codes: FAST, a tool developed under the management of the National Renewable Energy Laboratory (NREL) and available free of charge from its web site; Bladed[4], a widely-used commercial package available from DNV GL; ADAMS[5], a general purpose multi-body simulation code used in the wind industry and available from MSC Software; and HAWC2[6], a code developed by and available for purchase from Danmarks Tekniske Universitet (DTU). Interface routines have been developed and tested with full wind turbine simulations for each of these codes and the source code and example inputs and outputs are available from the NREL website.« less

Temperature and pressure effects on GFP mutants: explaining spectral changes by molecular dynamics simulations and TD-DFT calculations.

PubMed

Jacchetti, Emanuela; Gabellieri, Edi; Cioni, Patrizia; Bizzarri, Ranieri; Nifosì, Riccardo

2016-05-14

By combining spectroscopic measurements under high pressure with molecular dynamics simulations and quantum mechanics calculations we investigate how sub-angstrom structural perturbations are able to tune protein function. We monitored the variations in fluorescence output of two green fluorescent protein mutants (termed Mut2 and Mut2Y, the latter containing the key T203Y mutation) subjected to pressures up to 600 MPa, at various temperatures in the 280-320 K range. By performing 150 ns molecular dynamics simulations of the protein structures at various pressures, we evidenced subtle changes in conformation and dynamics around the light-absorbing chromophore. Such changes explain the measured spectral tuning in the case of the sizable 120 cm(-1) red-shift observed for pressurized Mut2Y, but absent in Mut2. Previous work [Barstow et al., Proc. Natl. Acad. Sci. U. S. A., 2008, 105, 13362] on pressure effects on GFP also involved a T203Y mutant. On the basis of cryocooling X-ray crystallography, the pressure-induced fluorescence blue shift at low temperature (77 K) was attributed to key changes in relative conformation of the chromophore and Tyr203 phenol ring. At room temperature, however, a red shift was observed at high pressure, analogous to the one we observe in Mut2Y. Our investigation of structural variations in compressed Mut2Y also explains their result, bridging the gap between low-temperature and room-temperature high-pressure effects.

Pilot-Induced Oscillations and Human Dynamic Behavior

NASA Technical Reports Server (NTRS)

McRuer, Duane T.

1995-01-01

This is an in-depth survey and study of pilot-induced oscillations (PIO's) as interactions between human pilot and vehicle dynamics; it includes a broad and comprehensive theory of PIO's. A historical perspective provides examples of the diversity of PIO's in terms of control axes and oscillation frequencies. The constituents involved in PIO phenomena, including effective aircraft dynamics, human pilot dynamic behavior patterns, and triggering precursor events, are examined in detail as the structural elements interacting to produce severe pilot-induced oscillations. The great diversity of human pilot response patterns, excessive lags and/or inappropriate gain in effective aircraft dynamics, and transitions in either the human or effective aircraft dynamics are among the key sources implicated as factors in severe PIO's. The great variety of interactions which may result in severe PIO's is illustrated by examples drawn from famous PIO's. These are generalized under a pilot-behavior-theory-based set of categories proposed as a classification scheme pertinent to a theory of PIO's. Finally, a series of interim prescriptions to avoid PIO is provided.

First principles investigation of structural, mechanical, dynamical and thermodynamic properties of AgMg under pressure

NASA Astrophysics Data System (ADS)

Cui, Rong Hua; Chao Dong, Zheng; Gui Zhong, Chong

2017-12-01

The effects of pressure on the structural, mechanical, dynamical and thermodynamic properties of AgMg have been investigated using first principles based on density functional theory. The optimized lattice constants agree well with previous experimental and theoretical results. The bulk modulus, shear modulus, Young’s modulus, Poisson’s ratio and Debye temperature under pressures were calculated. The calculated results of Cauchy pressure and B/G ratio indicate that AgMg shows ductile nature. Phonon dispersion curves suggest the dynamical stability of AgMg. The pressure dependent behavior of thermodynamic properties are calculated, the Helmholtz free energy and internal energy increase with increase of pressure, while entropy and heat capacity decrease.

Competition-Driven Network Dynamics: Emergence of a Scale-Free Leadership Structure and Collective Efficiency

NASA Astrophysics Data System (ADS)

Anghel, M.; Toroczkai, Zoltán; Bassler, Kevin E.; Korniss, G.

2004-02-01

Using the minority game as a model for competition dynamics, we investigate the effects of interagent communications across a network on the global evolution of the game. Agent communication across this network leads to the formation of an influence network, which is dynamically coupled to the evolution of the game, and it is responsible for the information flow driving the agents' actions. We show that the influence network spontaneously develops hubs with a broad distribution of in-degrees, defining a scale-free robust leadership structure. Furthermore, in realistic parameter ranges, facilitated by information exchange on the network, agents can generate a high degree of cooperation making the collective almost maximally efficient.

Ares I Flight Control System Overview

NASA Technical Reports Server (NTRS)

Hall, Charles; Lee, Chong; Jackson, Mark; Whorton, Mark; West, mark; Brandon, Jay; Hall, Rob A.; Jang, Jimmy; Bedrossian, Naz; Compton, Jimmy;

Wave propagation in equivalent continuums representing truss lattice materials

DOE PAGES

Messner, Mark C.; Barham, Matthew I.; Kumar, Mukul; ...

2015-07-29

Stiffness scales linearly with density in stretch-dominated lattice meta-materials offering the possibility of very light yet very stiff structures. Current additive manufacturing techniques can assemble structures from lattice materials, but the design of such structures will require accurate, efficient simulation methods. Equivalent continuum models have several advantages over discrete truss models of stretch dominated lattices, including computational efficiency and ease of model construction. However, the development an equivalent model suitable for representing the dynamic response of a periodic truss in the small deformation regime is complicated by microinertial effects. This study derives a dynamic equivalent continuum model for periodic trussmore » structures suitable for representing long-wavelength wave propagation and verifies it against the full Bloch wave theory and detailed finite element simulations. The model must incorporate microinertial effects to accurately reproduce long wavelength characteristics of the response such as anisotropic elastic soundspeeds. Finally, the formulation presented here also improves upon previous work by preserving equilibrium at truss joints for simple lattices and by improving numerical stability by eliminating vertices in the effective yield surface.« less

Role of quantum fluctuations in structural dynamics of liquids of light molecules

DOE PAGES

Agapov, A.; Novikov, V. N.; Kisliuk, A.; ...

2016-12-16

A possible role of quantum effects, such as tunneling and zero-point energy, in the structural dynamics of supercooled liquids is studied by dielectric spectroscopy. Our results demonstrate that the liquids, bulk 3-methyl pentane and confined normal and deuterated water, have low glass transition temperature and unusually low for their class of materials steepness of the temperature dependence of structural relaxation (fragility). Although we do not find any signs of tunneling in the structural relaxation of these liquids, their unusually low fragility can be well described by the influence of the quantum fluctuations. Confined water presents an especially interesting case inmore » comparison to the earlier data on bulk low-density amorphous and vapor deposited water. Confined water exhibits a much weaker isotope effect than bulk water, although the effect is still significant. Here, we show that it can be ascribed to the change of the energy barrier for relaxation due to a decrease in the zeropoint energy upon D/H substitution. We observed a difference in the behavior of confined and bulk water demonstrates high sensitivity of quantum effects to the barrier heights and structure of water. Moreover, these results demonstrate that extrapolation of confined water properties to the bulk water behavior is questionable.« less

Bioinspired Photonic Pigments from Colloidal Self-Assembly.

PubMed

Goerlitzer, Eric S A; Klupp Taylor, Robin N; Vogel, Nicolas

2018-05-07

The natural world is a colorful environment. Stunning displays of coloration have evolved throughout nature to optimize camouflage, warning, and communication. The resulting flamboyant visual effects and remarkable dynamic properties, often caused by an intricate structural design at the nano- and microscale, continue to inspire scientists to unravel the underlying physics and to recreate the observed effects. Here, the methodologies to create bioinspired photonic pigments using colloidal self-assembly approaches are considered. The physics governing the interaction of light with structural features and natural examples of structural coloration are briefly introduced. It is then outlined how the self-assembly of colloidal particles, acting as wavelength-scale building blocks, can be particularly useful to replicate coloration from nature. Different coloration effects that result from the defined structure of the self-assembled colloids are introduced and it is highlighted how these optical properties can be translated into photonic pigments by modifications of the assembly processes. The importance of absorbing elements, as well as the role of surface chemistry and wettability to control structural coloration is discussed. Finally, approaches to integrate dynamic control of coloration into such self-assembled photonic pigments are outlined. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dissipative particle dynamics (DPD) simulations with fragment molecular orbital (FMO) based effective parameters for 1-Palmitoyl-2-oleoyl phosphatidyl choline (POPC) membrane

NASA Astrophysics Data System (ADS)

Doi, Hideo; Okuwaki, Koji; Mochizuki, Yuji; Ozawa, Taku; Yasuoka, Kenji

2017-09-01

In dissipative particle dynamics (DPD) simulations, it is necessary to use the so-called χ parameter set that express the effective interactions between particles. Recently, we have developed a new scheme to evaluate the χ parameters in a non-empirical way through a series of fragment molecular orbital (FMO) calculations. As a challenging test, we have performed the DPD simulations using the FMO-based χ parameters for a mixture of 1-Palmitoyl-2-oleoyl phosphatidyl choline (POPC) and water. The structures of both membrane and vesicle were formed successfully. The calculated structural parameters of membrane were in good agreement with experimental results.

Tests of general relativity using Starprobe radio metric tracking data

NASA Technical Reports Server (NTRS)

Mease, K. D.; Anderson, J. D.; Wood, L. J.; White, L. K.

1982-01-01

The potential of a proposed spacecraft mission, called Starprobe, for testing general relativity and providing information on the interior structure and dynamics of the sun is investigated. Parametric, gravitational perturbation terms are derived which represent relativistic effects and effects due to spatial and temporal variations in the solar potential at a given radial distance. A covariance analysis based on Kalman filtering theory predicts the accuracies with which the free parameters in the perturbation terms can be estimated with radio metric tracking data through the process of trajectory reconstruction. It is concluded that Starprobe can contribute significant information on both the nature of gravitation and the structure and dynamics of the solar interior.

Team structure and regulatory focus: the impact of regulatory fit on team dynamic.

PubMed

Dimotakis, Nikolaos; Davison, Robert B; Hollenbeck, John R

2012-03-01

We report a within-teams experiment testing the effects of fit between team structure and regulatory task demands on task performance and satisfaction through average team member positive affect and helping behaviors. We used a completely crossed repeated-observations design in which 21 teams enacted 2 tasks with different regulatory focus characteristics (prevention and promotion) in 2 organizational structures (functional and divisional), resulting in 84 observations. Results suggested that salient regulatory demands inherent in the task interacted with structure to determine objective and subjective team-level outcomes, such that functional structures were best suited to (i.e., had best fit with) tasks with a prevention regulatory focus and divisional structures were best suited to tasks with a promotion regulatory focus. This contingency finding integrates regulatory focus and structural contingency theories, and extends them to the team level with implications for models of performance, satisfaction, and team dynamics.

Luminescent tunable polydots: Charge effects in confined geometry

DOE PAGES

Wijesinghe, Sidath; Maskey, Sabina; Perahia, Dvora; ...

2017-06-28

Long-lived soft nanoparticles, formed by conjugated polymers, constitute a new class of far-from-equilibrium responsive structures for nano-medicine. Tethering ionizable groups to the polymers enables functionality. However concurrently, the ionic groups perturb the delicate balance of interactions that governs these particles. Using fully atomistic molecular dynamics simulations, this study probed the effects of charged groups tethered to poly para phenylene ethynylene substituted by alkyl groups on the polymer conformation and dynamics in confined geometry. As a result, we find that the ionizable groups affect the entire shape of the polydots and impact the conformation and dynamics of the polymer.

Effect of molecular shape on rotation under severe confinement

DOE PAGES

Dhiman, Indu; Bhowmik, Debsindhu; Shrestha, Utsab R.; ...

2018-01-31

Orientational structure and dynamics of molecules is known to be affected by confinement in space comparable in size to the molecule itself. ZSM-5 with porous channels of ≈0.55 nm is such a porous medium, which offers a strict spatial confinement on low molecular weight hydrocarbons. An important factor that determines these properties is the shape of the confined molecules. In this work, we employed molecular dynamics simulation to study the orientational structure and dynamics of four molecules that differ in shape but have similar kinetic diameters and moments of inertia, confined in ZSM-5. The effect of molecular shape on themore » orientational structure and dynamics of propane, acetonitrile, acetaldehyde and acetone in ZSM-5 is studied by means of probing the differences in the orientational distribution of molecules in the ZSM-5 channels, and extracting time scales of the decay of correlation functions related to rotational motion. Orientational correlation functions of all the four molecules exhibit two regimes of rotational motion. While the short time regime represents free rotation of the molecules before they collide with the pore walls, the long time orientational jumps driven by inter-channel migrations give rise to a very slow varying second regime. Of the molecules studied, orientational structure and dynamics of propane is found to be least affected by confinement under ZSM-5, whereas charge and shape asymmetry of other molecules makes their interchannel migration-driven rotation slow. The time scales involved in the rotational motion for the molecules studied are compared with similar studies reported in literature. Lastly, this study reveals the important role that molecular shape plays in the behavior of confined molecules.« less

Effect of molecular shape on rotation under severe confinement

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

Dhiman, Indu; Bhowmik, Debsindhu; Shrestha, Utsab R.

Orientational structure and dynamics of molecules is known to be affected by confinement in space comparable in size to the molecule itself. ZSM-5 with porous channels of ≈0.55 nm is such a porous medium, which offers a strict spatial confinement on low molecular weight hydrocarbons. An important factor that determines these properties is the shape of the confined molecules. In this work, we employed molecular dynamics simulation to study the orientational structure and dynamics of four molecules that differ in shape but have similar kinetic diameters and moments of inertia, confined in ZSM-5. The effect of molecular shape on themore » orientational structure and dynamics of propane, acetonitrile, acetaldehyde and acetone in ZSM-5 is studied by means of probing the differences in the orientational distribution of molecules in the ZSM-5 channels, and extracting time scales of the decay of correlation functions related to rotational motion. Orientational correlation functions of all the four molecules exhibit two regimes of rotational motion. While the short time regime represents free rotation of the molecules before they collide with the pore walls, the long time orientational jumps driven by inter-channel migrations give rise to a very slow varying second regime. Of the molecules studied, orientational structure and dynamics of propane is found to be least affected by confinement under ZSM-5, whereas charge and shape asymmetry of other molecules makes their interchannel migration-driven rotation slow. The time scales involved in the rotational motion for the molecules studied are compared with similar studies reported in literature. Lastly, this study reveals the important role that molecular shape plays in the behavior of confined molecules.« less

Effect of crown class and habitat type on climate-growth relationships of ponderosa pine and Douglas-fir

Treesearch

Gunnar C. Carnwath; David W. Peterson; Cara R. Nelson

2012-01-01

There is increasing interest in actively managing forests to increase their resilience to climate-related changes. Although forest managers rely heavily on the use of silvicultural treatments that manipulate stand structure and stand dynamics to modify responses to climate change, few studies have directly assessed the effects of stand structure or canopy position on...

Effects of fire frequency on long-term development of an oak-hickory forest in Missouri, U.S.A.

Treesearch

Benjamin O. Knapp; Michael A. Hullinger; John M. Kabrick

2017-01-01

Repeated prescribed burning over long timescales has some predictable effects on forest structure and composition, but multi-decadal patterns of stand dynamics and successional change with different fire frequencies have rarely been described. We used longitudinal data from a prescribed burning study conducted over a 63-year period to quantify stand structure (stem...

Effects of structural error on the estimates of parameters of dynamical systems

NASA Technical Reports Server (NTRS)

Hadaegh, F. Y.; Bekey, G. A.

1986-01-01

In this paper, the notion of 'near-equivalence in probability' is introduced for identifying a system in the presence of several error sources. Following some basic definitions, necessary and sufficient conditions for the identifiability of parameters are given. The effects of structural error on the parameter estimates for both the deterministic and stochastic cases are considered.

Active site CP-loop dynamics modulate substrate binding, catalysis, oligomerization, stability, over-oxidation and recycling of 2-Cys Peroxiredoxins.

PubMed

Kamariah, Neelagandan; Eisenhaber, Birgit; Eisenhaber, Frank; Grüber, Gerhard

2018-04-01

Peroxiredoxins (Prxs) catalyse the rapid reduction of hydrogen peroxide, organic hydroperoxide and peroxynitrite, using a fully conserved peroxidatic cysteine (C P ) located in a conserved sequence Pxxx(T/S)xxC P motif known as C P -loop. In addition, Prxs are involved in cellular signaling pathways and regulate several redox-dependent process related disease. The effective catalysis of Prxs is associated with alterations in the C P -loop between reduced, Fully Folded (FF), and oxidized, Locally Unfolded (LU) conformations, which are linked to dramatic changes in the oligomeric structure. Despite many studies, little is known about the precise structural and dynamic roles of the C P -loop on Prxs functions. Herein, the comprehensive biochemical and biophysical studies on Escherichia coli alkyl hydroperoxide reductase subunit C (EcAhpC) and the C P -loop mutants, EcAhpC-F45A and EcAhpC-F45P reveal that the reduced form of the C P -loop adopts conformational dynamics, which is essential for effective peroxide reduction. Furthermore, the point mutants alter the structure and dynamics of the reduced form of the C P -loop and, thereby, affect substrate binding, catalysis, oligomerization, stability and overoxidiation. In the oxidized form, due to restricted C P -loop dynamics, the EcAhpC-F45P mutant favours a decamer formation, which enhances the effective recycling by physiological reductases compared to wild-type EcAhpC. In addition, the study reveals that residue F45 increases the specificity of Prxs-reductase interactions. Based on these studies, we propose an evolution of the C P -loop with confined sequence conservation within Prxs subfamilies that might optimize the functional adaptation of Prxs into various physiological roles. Copyright © 2018 Elsevier Inc. All rights reserved.

Simulation of nanopowder compaction in terms of granular dynamics

NASA Astrophysics Data System (ADS)

Boltachev, G. Sh.; Volkov, N. B.

2011-07-01

The uniaxial compaction of nanopowders is simulated using the granular dynamics in the 2D geometry. The initial arrangement of particles is represented by (i) a layer of particles executing Brownian motion (isotropic structures) and (ii) particles falling in the gravity field (anisotropic structures). The influence of size effects and the size of a model cell on the properties of the structures are studied. The compaction of the model cell is simulated with regard to Hertz elastic forces between particles, Cattaneo-Mindlin-Deresiewicz shear friction forces, and van der Waals-Hamaker dispersion forces of attraction. Computation is performed for monodisperse powders with particle sizes ranging from 10 to 400 nm and for "cohesionless" powder, in which attractive forces are absent. It is shown that taking into account dispersion forces makes it possible to simulate the size effect in the nanopowder compaction: the compressibility of the nanopowder drops as the particles get finer. The mean coordination number and the axial and lateral pressures in the powder systems are found, and the effect of the density and isotropy of the initial structure on the compressibility is analyzed. The applicability of well-known Rumpf's formula for the size effect is discussed.

Controlling the influence of elastic eigenmodes on nanomagnet dynamics through pattern geometry

NASA Astrophysics Data System (ADS)

Berk, C.; Yahagi, Y.; Dhuey, S.; Cabrini, S.; Schmidt, H.

2017-03-01

The effect of the nanoscale array geometry on the interaction between optically generated surface acoustic waves (SAWs) and nanomagnet dynamics is investigated using Time-Resolved Magneto-Optical Kerr Effect Microscopy (TR-MOKE). It is demonstrated that altering the nanomagnet geometry from a periodic to a randomized aperiodic pattern effectively removes the magneto-elastic effect of SAWs on the magnetization dynamics. The efficiency of this method depends on the extent of any residual spatial correlations and is quantified by spatial Fourier analysis of the two structures. Randomization allows observation and extraction of intrinsic magnetic parameters such as spin wave frequencies and damping to be resolvable using all-optical methods, enabling the conclusion that the fabrication process does not affect the damping.

Deployment Simulation of Ultra-Lightweight Inflatable Structures

NASA Technical Reports Server (NTRS)

Wang, John T.; Johnson, Arthur R.

2002-01-01

Dynamic deployment analyses of folded inflatable tubes are conducted to investigate modeling issues related to the deployment of solar sail booms. The analyses are necessary because ground tests include gravity effects and may poorly represent deployment in space. A control volume approach, available in the LS-DYNA nonlinear dynamic finite element code, and the ideal gas law are used to simulate the dynamic inflation deployment process. Three deployment issues are investigated for a tube packaged in a Z-fold configuration. The issues are the effect of the rate of inflation, the effect of residual air, and the effect of gravity. The results of the deployment analyses reveal that the time and amount of inflation gas required to achieve a full deployment are related to these issues.

The Mechanism of Covalent Bonding: Analysis within the Huckel Model of Electronic Structure

ERIC Educational Resources Information Center

Nordholm, Sture; Back, Andreas; Backsay, George B.

2007-01-01

The commonly used Huckel model of electronic structure is employed to study the mechanisms of covalent bonding, a quantum effect related to electron dynamics. The model also explains the conjugation and aromaticity of planar hydrocarbon molecules completely.

The atypical Rho GTPase RhoD is a regulator of actin cytoskeleton dynamics and directed cell migration

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

Blom, Magdalena; Reis, Katarina; Heldin, Johan

RhoD belongs to the Rho GTPases, a protein family responsible for the regulation and organization of the actin cytoskeleton, and, consequently, many cellular processes like cell migration, cell division and vesicle trafficking. Here, we demonstrate that the actin cytoskeleton is dynamically regulated by increased or decreased protein levels of RhoD. Ectopic expression of RhoD has previously been shown to give an intertwined weave of actin filaments. We show that this RhoD-dependent effect is detected in several cell types and results in a less dynamic actin filament system. In contrast, RhoD depletion leads to increased actin filament-containing structures, such as corticalmore » actin, stress fibers and edge ruffles. Moreover, vital cellular functions such as cell migration and proliferation are defective when RhoD is silenced. Taken together, we present data suggesting that RhoD is an important component in the control of actin dynamics and directed cell migration. - Highlights: • Increased RhoD expression leads to loss of actin structures, e.g. stress fibers and gives rise to decreased actin dynamics. • RhoD knockdown induces various actin-containing structures such as edge ruffles, stress fibers and cortical actin, in a cell-type specific manner. • RhoD induces specific actin rearrangements depending on its subcellular localization. • RhoD knockdown has effects on cellular processes, such as directed cell migration and proliferation.« less

Deformation effect simulation and optimization for double front axle steering mechanism

NASA Astrophysics Data System (ADS)

Wu, Jungang; Zhang, Siqin; Yang, Qinglong

2013-03-01

This paper research on tire wear problem of heavy vehicles with Double Front Axle Steering Mechanism from the flexible effect of Steering Mechanism, and proposes a structural optimization method which use both traditional static structural theory and dynamic structure theory - Equivalent Static Load (ESL) method to optimize key parts. The good simulated and test results show this method has high engineering practice and reference value for tire wear problem of Double Front Axle Steering Mechanism design.

Effect of group walking traffic on dynamic properties of pedestrian structures

NASA Astrophysics Data System (ADS)

Shahabpoor, E.; Pavic, A.; Racic, V.; Zivanovic, S.

2017-01-01

The increasing number of reported vibration serviceability problems in newly built pedestrian structures, such as footbridges and floors, under walking load has attracted considerable attention in the civil engineering community over the past two decades. The key design challenges are: the inter- and intra-subject variability of walking people, the unknown mechanisms of their interaction with the vibrating walking surfaces and the synchronisation between individuals in a group. Ignoring all or some of these factors makes the current design methods an inconsistent approximation of reality. This often leads to considerable over- or under-estimation of the structural response, yielding an unreliable assessment of vibration performance. Changes to the dynamic properties of an empty structure due to the presence of stationary people have been studied extensively over the past two decades. The understanding of the similar effect of walking people on laterally swaying bridges has improved tremendously in the past decade, due to considerable research prompted by the Millennium Bridge problem. However, there is currently a gap in knowledge about how moving pedestrians affect the dynamic properties of vertically vibrating structures. The key reason for this gap is the scarcity of credible experimental data pertinent to moving pedestrians on vertically vibrating structures, especially for multi-pedestrian traffic. This paper addresses this problem by studying the dynamic properties of the combined human-structure system, i.e. occupied structure damping ratio, natural frequency and modal mass. This was achieved using a comprehensive set of frequency response function records, measured on a full-scale test structure, which was occupied by various numbers of moving pedestrians under different walking scenarios. Contrary to expectations, it was found that the natural frequency of the joint moving human-structure system was higher than that of the empty structure, while it was lower when the same people were standing still. The damping ratio of the joint human-structure system was considerably higher than that of the empty structure for both the walking and standing people - in agreement with previous reports for stationary people - and was more prominent for larger groups. Interestingly, it was found that the walking human-structure system has more damping compared with the equivalent standing human-structure system. The properties of a single degree of freedom mass-spring-damper system representing a moving crowd needed to replicate these observations have been identified.

Size effect on atomic structure in low-dimensional Cu-Zr amorphous systems.

PubMed

Zhang, W B; Liu, J; Lu, S H; Zhang, H; Wang, H; Wang, X D; Cao, Q P; Zhang, D X; Jiang, J Z

2017-08-04

The size effect on atomic structure of a Cu 64 Zr 36 amorphous system, including zero-dimensional small-size amorphous particles (SSAPs) and two-dimensional small-size amorphous films (SSAFs) together with bulk sample was investigated by molecular dynamics simulations. We revealed that sample size strongly affects local atomic structure in both Cu 64 Zr 36 SSAPs and SSAFs, which are composed of core and shell (surface) components. Compared with core component, the shell component of SSAPs has lower average coordination number and average bond length, higher degree of ordering, and lower packing density due to the segregation of Cu atoms on the shell of Cu 64 Zr 36 SSAPs. These atomic structure differences in SSAPs with various sizes result in different glass transition temperatures, in which the glass transition temperature for the shell component is found to be 577 K, which is much lower than 910 K for the core component. We further extended the size effect on the structure and glasses transition temperature to Cu 64 Zr 36 SSAFs, and revealed that the T g decreases when SSAFs becomes thinner due to the following factors: different dynamic motion (mean square displacement), different density of core and surface and Cu segregation on the surface of SSAFs. The obtained results here are different from the results for the size effect on atomic structure of nanometer-sized crystalline metallic alloys.

Dynamic response for structural health monitoring of the Penang (I) cable-stayed bridge

NASA Astrophysics Data System (ADS)

Mohammed, M. I.; Sulaeman, E.; Mustapha, F.

2017-03-01

The paper discusses the dynamic response of the Penang (I) cable stayed bridge structure under various moving load representing typical traffic load of the bridge. The bridge has a total span of 440 m excluding the transition bridge that assumed to be not connected structurally to the main bridge structure. The bridge that links the fast growing Pinang Island and the Malaysian Mainland Peninsula has been known to be fully utilized which leads to the construction of Penang (II) bridge and now the third one. Due to highly traffic use of the bridge that may lead to reduction of the bridge design life, the dynamic response of the bridge becomes important to predict critical part of the bridge structure elements including the main girder and the 144 stay cables. The present study reveals that, due to flexible nature of the cable stayed bridge, the moving load that interacts with the natural dynamic characteristics of the bridge, gives significant stress increment compare to proportional static load especially when the moving load is un-symmetric. For this reason, several classes of typical vehicle passing the bridge with various vehicle speeds are investigated to demonstrate their effect on the bridge displacement, internal forces and stresses. The results can be used for further fatigue assessment of the bridge.

Fluid and particle transport of a hairy structure

NASA Astrophysics Data System (ADS)

Lee, Hongki; Lahooti, Mohsen; Kim, Daegyoum; Jung, Seyeong

2017-11-01

Hairy appendages of animals are used to capture particles, sense surrounding flow, and generate propulsive force. Due to the small size of the hairy structures, their hydrodynamics have been studied mostly in very low Reynolds number. In this work, in a broad range of Reynolds number, O(1) - O(100), flow structure and inertial particle dynamics around an array of two-dimensional cylinders are investigated numerically by using an immersed boundary method. Given flow fields, Maxey-Riley equation is adopted to examine particle dynamics. Here, we discuss the effects of Reynolds number, density ratio of inertial particles and fluid, and distance between cylinders on particle behaviors around a moving structure. In addition, drift volume of inertial particles is correlated with the model parameters.

Study of iron structure stability in high temperature molten lead-bismuth eutectic with oxygen injection using molecular dynamics simulation

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

Arkundato, Artoto; Su'ud, Zaki; Sudarko

2014-09-30

Corrosion of structural materials in high temperature molten lead-bismuth eutectic is a major problem for design of PbBi cooled reactor. One technique to inhibit corrosion process is to inject oxygen into coolant. In this paper we study and focus on a way of inhibiting the corrosion of iron using molecular dynamics method. For the simulation results we concluded that effective corrosion inhibition of iron may be achieved by injection 0.0532 wt% to 0.1156 wt% oxygen into liquid lead-bismuth. At this oxygen concentration the structure of iron material will be maintained at about 70% in bcc crystal structure during interaction withmore » liquid metal.« less

The Differential Response of Proteins to Macromolecular Crowding

PubMed Central

Candotti, Michela; Orozco, Modesto

2016-01-01

The habitat in which proteins exert their function contains up to 400 g/L of macromolecules, most of which are proteins. The repercussions of this dense environment on protein behavior are often overlooked or addressed using synthetic agents such as poly(ethylene glycol), whose ability to mimic protein crowders has not been demonstrated. Here we performed a comprehensive atomistic molecular dynamic analysis of the effect of protein crowders on the structure and dynamics of three proteins, namely an intrinsically disordered protein (ACTR), a molten globule conformation (NCBD), and a one-fold structure (IRF-3) protein. We found that crowding does not stabilize the native compact structure, and, in fact, often prevents structural collapse. Poly(ethylene glycol) PEG500 failed to reproduce many aspects of the physiologically-relevant protein crowders, thus indicating its unsuitability to mimic the cell interior. Instead, the impact of protein crowding on the structure and dynamics of a protein depends on its degree of disorder and results from two competing effects: the excluded volume, which favors compact states, and quinary interactions, which favor extended conformers. Such a viscous environment slows down protein flexibility and restricts the conformational landscape, often biasing it towards bioactive conformations but hindering biologically relevant protein-protein contacts. Overall, the protein crowders used here act as unspecific chaperons that modulate the protein conformational space, thus having relevant consequences for disordered proteins. PMID:27471851

The analysis of the influence of fractal structure of stimuli on fractal dynamics in fixational eye movements and EEG signal

NASA Astrophysics Data System (ADS)

Namazi, Hamidreza; Kulish, Vladimir V.; Akrami, Amin

2016-05-01

One of the major challenges in vision research is to analyze the effect of visual stimuli on human vision. However, no relationship has been yet discovered between the structure of the visual stimulus, and the structure of fixational eye movements. This study reveals the plasticity of human fixational eye movements in relation to the ‘complex’ visual stimulus. We demonstrated that the fractal temporal structure of visual dynamics shifts towards the fractal dynamics of the visual stimulus (image). The results showed that images with higher complexity (higher fractality) cause fixational eye movements with lower fractality. Considering the brain, as the main part of nervous system that is engaged in eye movements, we analyzed the governed Electroencephalogram (EEG) signal during fixation. We have found out that there is a coupling between fractality of image, EEG and fixational eye movements. The capability observed in this research can be further investigated and applied for treatment of different vision disorders.

Influence of wing tip morphology on vortex dynamics of flapping flight

NASA Astrophysics Data System (ADS)

Krishna, Swathi; Mulleners, Karen

2013-11-01

The mechanism of flapping wing flight provides insects with extraordinary flight capabilities. The uniquely shaped wing tips give insects an edge in flight performance and the interaction between the leading edge vortices and wing tip vortices enhance their propelling efficiencies and manoeuvrability. These are qualities that are sought after in current-day Micro Air Vehicles. A detailed understanding of the vortex dynamics of flapping flight and the influence of the wing tip planform is imperative for technical application. An experimental study is conducted to investigate the effects of different wing tip planforms on the formation, evolution and interaction of vortical structures. We thereby focus on the interaction between the coherent structures evolving from the leading edge and the wing tip during pitching and flapping motions.The spatial and temporal evolution of the three-dimensional flow structures are determined using Scanning (Stereo) Particle Image Velocimetry and an in-depth coherent structure analysis. By comparing the vortex dynamics, the aerodynamic performance of various wing tip planforms are evaluated.

Stand dynamics in 60-year-old Allegheny hardwoods after thinning

Treesearch

Gary W. Miller

1997-01-01

Stand dynamics and tree growth in even-aged hardwood stands can be influenced by manipulating relative stand density, species composition, and stand structure. Land managers need quantitative information on the effect of vegetation manipulation to prescribe stand treatments that are appropriate for specific management objectives. Sixty-year-old stands composed of black...

Beam Dynamics Simulation Platform and Studies of Beam Breakup in Dielectric Wakefield Structures

NASA Astrophysics Data System (ADS)

Schoessow, P.; Kanareykin, A.; Jing, C.; Kustov, A.; Altmark, A.; Gai, W.

2010-11-01

A particle-Green's function beam dynamics code (BBU-3000) to study beam breakup effects is incorporated into a parallel computing framework based on the Boinc software environment, and supports both task farming on a heterogeneous cluster and local grid computing. User access to the platform is through a web browser.

Dynamic Creative Interaction Networks and Team Creativity Evolution: A Longitudinal Study

ERIC Educational Resources Information Center

Jiang, Hui; Zhang, Qing-Pu; Zhou, Yang

2018-01-01

To assess the dynamical effects of creative interaction networks on team creativity evolution, this paper elaborates a theoretical framework that links the key elements of creative interaction networks, including node, edge and network structure, to creativity in teams. The process of team creativity evolution is divided into four phases,…

Dynamic equilibrium strategy for drought emergency temporary water transfer and allocation management

NASA Astrophysics Data System (ADS)

Xu, Jiuping; Ma, Ning; Lv, Chengwei

2016-08-01

Efficient water transfer and allocation are critical for disaster mitigation in drought emergencies. This is especially important when the different interests of the multiple decision makers and the fluctuating water resource supply and demand simultaneously cause space and time conflicts. To achieve more effective and efficient water transfers and allocations, this paper proposes a novel optimization method with an integrated bi-level structure and a dynamic strategy, in which the bi-level structure works to deal with space dimension conflicts in drought emergencies, and the dynamic strategy is used to deal with time dimension conflicts. Combining these two optimization methods, however, makes calculation complex, so an integrated interactive fuzzy program and a PSO-POA are combined to develop a hybrid-heuristic algorithm. The successful application of the proposed model in a real world case region demonstrates its practicality and efficiency. Dynamic cooperation between multiple reservoirs under the coordination of a global regulator reflects the model's efficiency and effectiveness in drought emergency water transfer and allocation, especially in a fluctuating environment. On this basis, some corresponding management recommendations are proposed to improve practical operations.

Effect of helicopter blade dynamics on blade aerodynamic and structural loads

NASA Technical Reports Server (NTRS)

Heffernan, Ruth M.

1987-01-01

The effect of rotor blade dynamics on aerodynamic and structural loads is examined for a conventional, main-rotor helicopter using a comprehensive rotorcraft analysis (CAMRAD) and flight-test data. The impact of blade dynamics on blade section lift-coefficient time histories is studied by comparing predictions from a rigid-blade analysis and an elastic-blade analysis with helicopter flight test data. The elastic blade analysis better predicts high-frequency behavior of section lift. In addition, components of the blade angle of attack such as elastic blade twist, blade flap rate, blade slope velocity, and inflow are examined as a function of blade mode. Elastic blade motion changed blade angle of attack by a few tenths of a degree, and up to the sixth rotor harmonic. A similar study of the influence of blade dynamics on bending and torsion moments was also conducted. A correlation study comparing predictions from several elastic-blade analyses with flight-test data revealed that an elastic-blade model consisting of only three elastic bending modes (first and second flap and first lag), and two elastic torsion modes was sufficient for good correlation.

The effect of various quantum mechanically derived partial atomic charges on the bulk properties of chloride-based ionic liquids

NASA Astrophysics Data System (ADS)

Zolghadr, Amin Reza; Ghatee, Mohammad Hadi; Moosavi, Fatemeh

2016-08-01

Partial atomic charges using various quantum mechanical calculations for [Cnmim]Cl (n = 1, 4) ionic liquids (ILs) are obtained and used for development of molecular dynamics simulation (MD) force fields. The isolated ion pairs are optimized using HF, B3LYP, and MP2 methods for electronic structure with 6-311++G(d,p) basis set. Partial atomic charges are assigned to the atomic center with CHELPG and NBO methods. The effect of these sets of partial charges on the static and dynamic properties of ILs is evaluated by performing a series of MD simulations and comparing the essential thermodynamic properties with the available experimental data and available molecular dynamics simulation results. In contrast to the general trends reported for ionic liquids with BF4, PF6, and iodide anions (in which restrained electrostatic potential (RESP) charges are preferred), partial charges derived by B3LYP-NBO method are relatively good in prediction of the structural, dynamical, and thermodynamic energetic properties of the chloride based ILs.

Eco-evolutionary spatial dynamics in the Glanville fritillary butterfly

PubMed Central

Hanski, Ilkka A.

2011-01-01

Demographic population dynamics, gene flow, and local adaptation may influence each other and lead to coupling of ecological and evolutionary dynamics, especially in species inhabiting fragmented heterogeneous environments. Here, I review long-term research on eco-evolutionary spatial dynamics in the Glanville fritillary butterfly inhabiting a large network of approximately 4,000 meadows in Finland. The metapopulation persists in a balance between frequent local extinctions and recolonizations. The genetic spatial structure as defined by neutral markers is much more coarse-grained than the demographic spatial structure determined by the fragmented habitat, yet small-scale spatial structure has important consequences for the dynamics. I discuss three examples of eco-evolutionary spatial dynamics. (i) Extinction-colonization metapopulation dynamics influence allele frequency changes in the phosphoglucose isomerase (Pgi) gene, which leads to strong associations between genetic variation in Pgi and dispersal, recolonization, and local population dynamics. (ii) Inbreeding in local populations increases their risk for extinction, whereas reciprocal effects between inbreeding, population size, and emigration represent likely eco-evolutionary feedbacks. (iii) Genetically determined female oviposition preference for two host plant species exhibits a cline paralleling a gradient in host plant relative abundances, and host plant preference of dispersing females in relation to the host plant composition of habitat patches influences immigration (gene flow) and recolonization (founder events). Eco-evolutionary spatial dynamics in heterogeneous environments may not lead to directional evolutionary changes unless the environment itself changes, but eco-evolutionary dynamics may contribute to the maintenance of genetic variation attributable to fluctuating selection in space and time. PMID:21788506

Dynamic Topography at Earth's Surface: Fact or Fiction? (Invited)

NASA Astrophysics Data System (ADS)

Lithgow-Bertelloni, C. R.; Silver, P. G.

2009-12-01

Contributions to Earth’s surface topography range from short-wavelength uncompensated features due to tectonic activity, to variations in crustal structure and long-wavelength deflections of the lithosphere caused by mantle dynamics. The latter we call dynamic topography. Dynamic topography elevates or depresses the surface even if the density anomaly giving rise to flow is deep in the mantle. Dynamic topography is also a major contributor to Earth’s gravitational potential and to surface deformation. However, direct observations of dynamic topography are elusive, because signals are obscured by the isostatic contribution due to crustal and lithospheric structure. The only seemingly unequivocal signals of dynamically supported topography have been found over mantle upwellings on both continents (Africa [Lithgow-Bertelloni and Silver, 1998] and Arabia [Daradich et al., 2004]) and oceanic basins (North-Atlantic [Conrad et al., 2004]). Recent work on Africa’s geomorphic history [Moore et al., 2009] and North Atlantic gravity and topography have called even these results into questions. In downwelling regions (near slabs) no clear signals have been found. I will explore why this dichotomy may exist and relate it to the need for dynamic topography in mantle flow models, with an eye towards the effects of phase transitions, lateral variations in viscosity and layered convection. I will also present recent results on dynamic topography over flat slab segments that overturn the conventional wisdom and explain basin topography in the Andean foreland. Along with the new models I will discuss a recent global lithospheric structure model with which to compute the residual topography, i.e. the “observed” dynamic topography.

Flexibility damps macromolecular crowding effects on protein folding dynamics: Application to the murine prion protein (121-231)

NASA Astrophysics Data System (ADS)

Bergasa-Caceres, Fernando; Rabitz, Herschel A.

2014-01-01

A model of protein folding kinetics is applied to study the combined effects of protein flexibility and macromolecular crowding on protein folding rate and stability. It is found that the increase in stability and folding rate promoted by macromolecular crowding is damped for proteins with highly flexible native structures. The model is applied to the folding dynamics of the murine prion protein (121-231). It is found that the high flexibility of the native isoform of the murine prion protein (121-231) reduces the effects of macromolecular crowding on its folding dynamics. The relevance of these findings for the pathogenic mechanism are discussed.

Neighborhood Age Structure and its Implications for Health

PubMed Central

2006-01-01

Age structure at the neighborhood level is rarely considered in contextual studies of health. However, age structure can play a critical role in shaping community life, the availability of resources, and the opportunities for social engagement—all factors that, research suggests, have direct and indirect effects on health. Age structure can be theorized as a compositional effect and as a contextual effect. In addition, the dynamic nature of age structure and the utility of a life course perspective as applied to neighborhood effects research merits attention. Four Chicago neighborhoods are summarized to illustrate how age structure varies across small space, suggesting that neighborhood age structure should be considered a key structural covariate in contextual research on health. Considering age structure implies incorporating not only meaningful cut points for important age groups (e.g., proportion 65 years and over) but attention to the shape of the distribution as well. PMID:16865558

Dynamical Casimir effect in a Josephson metamaterial

PubMed Central

Lähteenmäki, Pasi; Paraoanu, G. S.; Hassel, Juha; Hakonen, Pertti J.

2013-01-01

The zero-point energy stored in the modes of an electromagnetic cavity has experimentally detectable effects, giving rise to an attractive interaction between the opposite walls, the static Casimir effect. A dynamical version of this effect was predicted to occur when the vacuum energy is changed either by moving the walls of the cavity or by changing the index of refraction, resulting in the conversion of vacuum fluctuations into real photons. Here, we demonstrate the dynamical Casimir effect using a Josephson metamaterial embedded in a microwave cavity at 5.4 GHz. We modulate the effective length of the cavity by flux-biasing the metamaterial based on superconducting quantum interference devices (SQUIDs), which results in variation of a few percentage points in the speed of light. We extract the full 4 × 4 covariance matrix of the emitted microwave radiation, demonstrating that photons at frequencies symmetrical with respect to half of the modulation frequency are generated in pairs. At large detunings of the cavity from half of the modulation frequency, we find power spectra that clearly show the theoretically predicted hallmark of the Casimir effect: a bimodal, “sparrow-tail” structure. The observed substantial photon flux cannot be assigned to parametric amplification of thermal fluctuations; its creation is a direct consequence of the noncommutativity structure of quantum field theory.

Allee’s dynamics and bifurcation structures in von Bertalanffy’s population size functions

NASA Astrophysics Data System (ADS)

Leonel Rocha, J.; Taha, Abdel-Kaddous; Fournier-Prunaret, D.

2018-03-01

The interest and the relevance of the study of the population dynamics and the extinction phenomenon are our main motivation to investigate the induction of Allee Effect in von Bertalanffy’s population size functions. The adjustment or correction factor of rational type introduced allows us to analyze simultaneously strong and weak Allee’s functions and functions with no Allee effect, whose classification is dependent on the stability of the fixed point x = 0. This classification is founded on the concepts of strong and weak Allee’s effects to the population growth rates associated. The transition from strong Allee effect to no Allee effect, passing through the weak Allee effect, is verified with the evolution of the rarefaction critical density or Allee’s limit. The existence of cusp points on a fold bifurcation curve is related to this phenomenon of transition on Allee’s dynamics. Moreover, the “foliated” structure of the parameter plane considered is also explained, with respect to the evolution of the Allee limit. The bifurcation analysis is based on the configurations of fold and flip bifurcation curves. The chaotic semistability and the nonadmissibility bifurcation curves are proposed to this family of 1D maps, which allow us to define and characterize the corresponding Allee effect region.

Equation of state and some structural and dynamical properties of the confined Lennard-Jones fluid into carbon nanotube: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Abbaspour, Mohsen; Akbarzadeh, Hamed; Salemi, Sirous; Abroodi, Mousarreza

2016-11-01

By considering the anisotropic pressure tensor, two separate equations of state (EoS) as functions of the density, temperature, and carbon nanotube (CNT) diameter have been proposed for the radial and axial directions for the confined Lennard-Jones (LJ) fluid into (11,11), (12,10), and (19,0) CNTs from 120 to 600 K using molecular dynamics (MD) simulations. We have also investigated the effects of the pore size, pore loading, chirality, and temperature on some of the structural and dynamical properties of the confined LJ fluid into (11,11), (12,10), (19,0), and (19,19) CNTs such as the radial density profile and self-diffusion coefficient. We have also determined the EoS for the confined LJ fluid into double and triple walled CNTs.

Ultrafast X-Ray Spectroscopy of Conical Intersections

NASA Astrophysics Data System (ADS)

Neville, Simon P.; Chergui, Majed; Stolow, Albert; Schuurman, Michael S.

2018-06-01

Ongoing developments in ultrafast x-ray sources offer powerful new means of probing the complex nonadiabatically coupled structural and electronic dynamics of photoexcited molecules. These non-Born-Oppenheimer effects are governed by general electronic degeneracies termed conical intersections, which play a key role, analogous to that of a transition state, in the electronic-nuclear dynamics of excited molecules. Using high-level ab initio quantum dynamics simulations, we studied time-resolved x-ray absorption (TRXAS) and photoelectron spectroscopy (TRXPS) of the prototypical unsaturated organic chromophore, ethylene, following excitation to its S2(π π*) state. The TRXAS, in particular, is highly sensitive to all aspects of the ensuing dynamics. These x-ray spectroscopies provide a clear signature of the wave packet dynamics near conical intersections, related to charge localization effects driven by the nuclear dynamics. Given the ubiquity of charge localization in excited state dynamics, we believe that ultrafast x-ray spectroscopies offer a unique and powerful route to the direct observation of dynamics around conical intersections.

CFD Investigation of Effect of Depth to Diameter Ratio on Dimple Flow Dynamics

DTIC Science & Technology

2007-06-01

contained dynamic vortical flow structures with behavior varying between each dimple studied. This dynamic vortex activity was observed to be linked... 1 1.1 Research Goals . . . . . . . . . . . . . . . . . . . . . . . 1 1.2 Motivation for Research . . . . . . . . . . . . . . . . . . 1 1.3...59 F. 1 . Pressure tap for ReD 20500 Rex 5000 0.05 h/D dimple . . . . . 66 F.2. Pressure tap for ReD 20500 Rex 77000 0.05 h/D dimple

DARPA Helicopter Quieting Program W911NF0410424

DTIC Science & Technology

2009-05-01

Leishman , J. G. and Beddoes , T. S., “A Semi-Empirical Model for Dynamic Stall ,” Journal of the American Heli- copter Society, Vol. 34, No. 3, July 1989...of physical phenomena that include transonic and compressibility effects on the advancing blade, dynamic stall on the retreating blades and the...research approach is that even the most advanced models of a given discipline, e.g., comprehensive structural or flight dynamics codes , concentrate on a very

Dynamic Restarting Schemes for Eigenvalue Problems

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

Wu, Kesheng; Simon, Horst D.

1999-03-10

In studies of restarted Davidson method, a dynamic thick-restart scheme was found to be excellent in improving the overall effectiveness of the eigen value method. This paper extends the study of the dynamic thick-restart scheme to the Lanczos method for symmetric eigen value problems and systematically explore a range of heuristics and strategies. We conduct a series of numerical tests to determine their relative strength and weakness on a class of electronic structure calculation problems.

Virtual sensors for active noise control in acoustic-structural coupled enclosures using structural sensing: robust virtual sensor design.

PubMed

Halim, Dunant; Cheng, Li; Su, Zhongqing

2011-03-01

The work was aimed to develop a robust virtual sensing design methodology for sensing and active control applications of vibro-acoustic systems. The proposed virtual sensor was designed to estimate a broadband acoustic interior sound pressure using structural sensors, with robustness against certain dynamic uncertainties occurring in an acoustic-structural coupled enclosure. A convex combination of Kalman sub-filters was used during the design, accommodating different sets of perturbed dynamic model of the vibro-acoustic enclosure. A minimax optimization problem was set up to determine an optimal convex combination of Kalman sub-filters, ensuring an optimal worst-case virtual sensing performance. The virtual sensing and active noise control performance was numerically investigated on a rectangular panel-cavity system. It was demonstrated that the proposed virtual sensor could accurately estimate the interior sound pressure, particularly the one dominated by cavity-controlled modes, by using a structural sensor. With such a virtual sensing technique, effective active noise control performance was also obtained even for the worst-case dynamics. © 2011 Acoustical Society of America

Single walled boron nitride nanotube-based biosensor: an atomistic finite element modelling approach.

PubMed

Panchal, Mitesh B; Upadhyay, Sanjay H

2014-09-01

The unprecedented dynamic characteristics of nanoelectromechanical systems make them suitable for nanoscale mass sensing applications. Owing to superior biocompatibility, boron nitride nanotubes (BNNTs) are being increasingly used for such applications. In this study, the feasibility of single walled BNNT (SWBNNT)-based bio-sensor has been explored. Molecular structural mechanics-based finite element (FE) modelling approach has been used to analyse the dynamic behaviour of SWBNNT-based biosensors. The application of an SWBNNT-based mass sensing for zeptogram level of mass has been reported. Also, the effect of size of the nanotube in terms of length as well as different chiral atomic structures of SWBNNT has been analysed for their sensitivity analysis. The vibrational behaviour of SWBNNT has been analysed for higher-order modes of vibrations to identify the intermediate landing position of biological object of zeptogram scale. The present molecular structural mechanics-based FE modelling approach is found to be very effectual to incorporate different chiralities of the atomic structures. Also, different boundary conditions can be effectively simulated using the present approach to analyse the dynamic behaviour of the SWBNNT-based mass sensor. The presented study has explored the potential of SWBNNT, as a nanobiosensor having the capability of zeptogram level mass sensing.

Atomistic modeling of La3+ doping segregation effect on nanocrystalline yttria-stabilized zirconia.

PubMed

Zhang, Shenli; Sha, Haoyan; Castro, Ricardo H R; Faller, Roland

2018-05-16

The effect of La3+ doping on the structure and ionic conductivity change in nanocrystalline yttria-stabilized zirconia (YSZ) was studied using a combination of Monte Carlo and molecular dynamics simulations. The simulation revealed the segregation of La3+ at eight tilt grain boundary (GB) structures and predicted an average grain boundary (GB) energy decrease of 0.25 J m-2, which is close to the experimental values reported in the literature. Cation stabilization was found to be the main reason for the GB energy decrease, and energy fluctuations near the grain boundary are smoothed out with La3+ segregation. Both dynamic and energetic analysis on the Σ13(510)/[001] GB structure revealed La3+ doping hinders O2- diffusion in the GB region, where the diffusion coefficient monotonically decreases with increasing La3+ doping concentration. The effect was attributed to the increase in the site-dependent migration barriers for O2- hopping caused by segregated La3+, which also leads to anisotropic diffusion at the GB.

Influence of oak woodland composition and structure on infection by Phytophthora ramorum

Treesearch

Nathan Rank; Hall Cushman; Brian Anacker; David Rizzo; Ross Meentemeyer

2008-01-01

Introduced plant pathogens have major ecological impacts in many parts of the world. While the spread of pathogens can be strongly mediated by the composition and structure of local host plant communities, little is known about effects of plant community structure on invasion dynamics of introduced pathogens. The progress of infection by the invasive pathogen ...

Flexible Animation Computer Program

NASA Technical Reports Server (NTRS)

Stallcup, Scott S.

1990-01-01

FLEXAN (Flexible Animation), computer program animating structural dynamics on Evans and Sutherland PS300-series graphics workstation with VAX/VMS host computer. Typical application is animation of spacecraft undergoing structural stresses caused by thermal and vibrational effects. Displays distortions in shape of spacecraft. Program displays single natural mode of vibration, mode history, or any general deformation of flexible structure. Written in FORTRAN 77.

Adaptive Sliding Mode Control of Dynamic Systems Using Double Loop Recurrent Neural Network Structure.

PubMed

Fei, Juntao; Lu, Cheng

2018-04-01

In this paper, an adaptive sliding mode control system using a double loop recurrent neural network (DLRNN) structure is proposed for a class of nonlinear dynamic systems. A new three-layer RNN is proposed to approximate unknown dynamics with two different kinds of feedback loops where the firing weights and output signal calculated in the last step are stored and used as the feedback signals in each feedback loop. Since the new structure has combined the advantages of internal feedback NN and external feedback NN, it can acquire the internal state information while the output signal is also captured, thus the new designed DLRNN can achieve better approximation performance compared with the regular NNs without feedback loops or the regular RNNs with a single feedback loop. The new proposed DLRNN structure is employed in an equivalent controller to approximate the unknown nonlinear system dynamics, and the parameters of the DLRNN are updated online by adaptive laws to get favorable approximation performance. To investigate the effectiveness of the proposed controller, the designed adaptive sliding mode controller with the DLRNN is applied to a -axis microelectromechanical system gyroscope to control the vibrating dynamics of the proof mass. Simulation results demonstrate that the proposed methodology can achieve good tracking property, and the comparisons of the approximation performance between radial basis function NN, RNN, and DLRNN show that the DLRNN can accurately estimate the unknown dynamics with a fast speed while the internal states of DLRNN are more stable.

Formation and field-driven dynamics of nematic spheroids.

PubMed

Fu, Fred; Abukhdeir, Nasser Mohieddin

2017-07-19

Unlike the canonical application of liquid crystals (LCs), LC displays, emerging technologies based on LC materials are increasingly leveraging the presence of nanoscale defects. The inherent nanoscale characteristics of LC defects present both significant opportunities as well as barriers for the application of this fascinating class of materials. Simulation-based approaches to the study of the effects of confinement and interface anchoring conditions on LC domains has resulted in significant progress over the past decade, where simulations are now able to access experimentally-relevant length scales while simultaneously capturing nanoscale defect structures. In this work, continuum simulations were performed in order to study the dynamics of micron-scale nematic LC spheroids of varying shape. Nematic spheroids are one of the simplest inherently defect-containing LC structures and are relevant to polymer-dispersed LC-based "smart" window technology. Simulation results include nematic phase formation and external field-switching dynamics of nematic spheroids ranging in shape from oblate to prolate. Results include both qualitative and quantitative insight into the complex coupling of nanoscale defect dynamics and structure transitions to micron-scale reorientation. Dynamic mechanisms are presented and related to structural transitions in LC defects present in the nematic domain. Domain-averaged metrics including order parameters and response times are determined for a range of experimentally-accessible electric field strengths. These results have both fundamental and technological relevance, in that increased understanding of LC dynamics in the presence of defects is a key barrier to continued advancement in the field.

Comparing the dynamics of skyrmions and superconducting vortices

NASA Astrophysics Data System (ADS)

Olson Reichhardt, C. J.; Lin, S. Z.; Ray, D.; Reichhardt, C.

2014-08-01

Vortices in type-II superconductors have attracted enormous attention as ideal systems in which to study nonequilibrium collective phenomena, since the self-ordering of the vortices competes with quenched disorder and thermal effects. Dynamic effects found in vortex systems include depinning, nonequilibrium phase transitions, creep, structural order-disorder transitions, and melting. Understanding vortex dynamics is also important for applications of superconductors which require the vortices either to remain pinned or to move in a controlled fashion. Recently, topological defects called skyrmions have been realized experimentally in chiral magnets. Here we highlight similarities and differences between skyrmion dynamics and vortex dynamics. Many of the previous ideas and experimental setups that have been applied to superconducting vortices can also be used to study skyrmions. We also discuss some of the differences between the two systems, such as the potentially large contribution of the Magnus force in the skyrmion system that can dramatically alter the dynamics and transport properties.

Emergent explosive synchronization in adaptive complex networks

NASA Astrophysics Data System (ADS)

Avalos-Gaytán, Vanesa; Almendral, Juan A.; Leyva, I.; Battiston, F.; Nicosia, V.; Latora, V.; Boccaletti, S.

2018-04-01

Adaptation plays a fundamental role in shaping the structure of a complex network and improving its functional fitting. Even when increasing the level of synchronization in a biological system is considered as the main driving force for adaptation, there is evidence of negative effects induced by excessive synchronization. This indicates that coherence alone cannot be enough to explain all the structural features observed in many real-world networks. In this work, we propose an adaptive network model where the dynamical evolution of the node states toward synchronization is coupled with an evolution of the link weights based on an anti-Hebbian adaptive rule, which accounts for the presence of inhibitory effects in the system. We found that the emergent networks spontaneously develop the structural conditions to sustain explosive synchronization. Our results can enlighten the shaping mechanisms at the heart of the structural and dynamical organization of some relevant biological systems, namely, brain networks, for which the emergence of explosive synchronization has been observed.

Emergent explosive synchronization in adaptive complex networks.

PubMed

Avalos-Gaytán, Vanesa; Almendral, Juan A; Leyva, I; Battiston, F; Nicosia, V; Latora, V; Boccaletti, S

2018-04-01

Adaptation plays a fundamental role in shaping the structure of a complex network and improving its functional fitting. Even when increasing the level of synchronization in a biological system is considered as the main driving force for adaptation, there is evidence of negative effects induced by excessive synchronization. This indicates that coherence alone cannot be enough to explain all the structural features observed in many real-world networks. In this work, we propose an adaptive network model where the dynamical evolution of the node states toward synchronization is coupled with an evolution of the link weights based on an anti-Hebbian adaptive rule, which accounts for the presence of inhibitory effects in the system. We found that the emergent networks spontaneously develop the structural conditions to sustain explosive synchronization. Our results can enlighten the shaping mechanisms at the heart of the structural and dynamical organization of some relevant biological systems, namely, brain networks, for which the emergence of explosive synchronization has been observed.

The effect of high pressure on the lattice structure and dynamics of phenacenes

NASA Astrophysics Data System (ADS)

Capitani, F.; Höppner, M.; Malavasi, L.; Marini, C.; Dore, P.; Boeri, L.; Postorino, Paolo

2017-10-01

We studied the effect of high pressure on three phenacenes, aromatic molecules with a zig-zag configuration of the benzene rings. The lattice structure and vibrational dynamics of crystalline phenanthrene (C14H10, three benzene rings), chrysene (C18H12, four), and picene (C22H14, five) were investigated by means of X-ray diffraction and Raman measurements. Raman spectra were compared with theoretical ones obtained from ab-initio Density Functional Theory calculations. Experimental and theoretical results allowed to identify the onset of a structural transition in phenanthrene at 7.8 GPa under hydrostatic conditions and at 5.7 GPa under non-hydrostatic conditions. We found that this transition is related to a reorientantion of the molecules in the ab plane. On the contrary, chrysene and picene do not undergo any phase transition in the investigated pressure range, thus suggesting that molecular size plays an important role in the occurence of pressure induced structural modifications in aromatic compounds.