Clustering of short and long-term co-movements in international financial and commodity markets in wavelet domain

NASA Astrophysics Data System (ADS)

Lahmiri, Salim; Uddin, Gazi Salah; Bekiros, Stelios

2017-11-01

We propose a general framework for measuring short and long term dynamics in asset classes based on the wavelet presentation of clustering analysis. The empirical results show strong evidence of instability of the financial system aftermath of the global financial crisis. Indeed, both short and long-term dynamics have significantly changed after the global financial crisis. This study provides an interesting insights complex structure of global financial and economic system.

Research and development activities in unified control-structure modeling and design

NASA Technical Reports Server (NTRS)

Nayak, A. P.

1985-01-01

Results of work sponsored by JPL and other organizations to develop a unified control/structures modeling and design capability for large space structures is presented. Recent analytical results are presented to demonstrate the significant interdependence between structural and control properties. A new design methodology is suggested in which the structure, material properties, dynamic model and control design are all optimized simultaneously. The development of a methodology for global design optimization is recommended as a long term goal. It is suggested that this methodology should be incorporated into computer aided engineering programs, which eventually will be supplemented by an expert system to aid design optimization. Recommendations are also presented for near term research activities at JPL. The key recommendation is to continue the development of integrated dynamic modeling/control design techniques, with special attention given to the development of structural models specially tailored to support design.

Structural dynamics division research and technology accomplishments for fiscal year 1990 and plans for fiscal year 1991

NASA Technical Reports Server (NTRS)

Wynne, Eleanor C.

1991-01-01

The research accomplishments of the Structural Dynamics Division for F.Y. 1991 are presented. The work is discussed in terms of highlights of accomplishments during the past year and plans for the current year as they relate to 5-year plans and the objectives of each technical area. Included is research on unsteady aerodynamics, helicopter rotors, computational fluid dynamics, oscillations of leading edge flaps of a delta wing, and aircraft wing loads.

Calculation of structural dynamic forces and stresses using mode acceleration

NASA Technical Reports Server (NTRS)

Blelloch, Paul

1989-01-01

While the standard mode acceleration formulation in structural dynamics has often been interpreted to suggest that the reason for improved convergence obtainable is that the dynamic correction factor is divided by the modal frequencies-squared, an alternative formulation is presented which clearly indicates that the only difference between mode acceleration and mode displacement data recovery is the addition of a static correction term. Attention is given to the advantages in numerical implementation associated with this alternative, as well as to an illustrative example.

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.

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).

Microgravity Foam Structure and Rheology

NASA Technical Reports Server (NTRS)

Durian, Douglas J.

1997-01-01

To exploit rheological and multiple-light scattering techniques, and ultimately microgravity conditions, in order to quantify and elucidate the unusual elastic character of foams in terms of their underlying microscopic structure and dynamics. Special interest is in determining how this elastic character vanishes, i.e. how the foam melts into a simple viscous liquid, as a function of both increasing liquid content and shear strain rate. The unusual elastic character of foams will be quantified macroscopically by measurement of the shear stress as a function of static shear strain, shear strain rate, and time following a step strain; such data will be analyzed in terms of a yield stress, a static shear modulus, and dynamical time scales. Microscopic information about bubble packing and rearrangement dynamics, from which these macroscopic non-Newtonian properties presumably arise, will be obtained non-invasively by novel multiple-light scattering diagnostics such as Diffusing-Wave Spectroscopy (DWS). Quantitative trends with materials parameters, such as average bubble size, and liquid content, will be sought in order to elucidate the fundamental connection between the microscopic structure and dynamics and the macroscopic rheology.

Non-destructive testing on aramid fibres for the long-term assessment of interventions on heritage structures

NASA Astrophysics Data System (ADS)

Ceravolo, R.; De Marchi, A.; Pinotti, E.; Surace, C.; Zanotti Fragonara, L.

2015-07-01

High strength fibre reinforced polymers (FRPs) are composite materials made of fibres such as carbon, aramid and/or glass, and a resin matrix. FRPs are commonly used for structural repair and strengthening interventions and exhibit high potential for applications to existing constructions, including heritage buildings. In regard to aramid fibres, uncertainties about the long-term behaviour of these materials have often made the designers reluctant to use them in structural engineering. The present study describes simple and non-destructive nonlinearity tests for assessing damage or degradation of structural properties in Kevlar fibres. This was obtained by using high precision measurements to detect small deviations in the dynamic response measured on fibres and ropes. The change in dynamic properties was then related to a damage produced by exposure of the sample to UV rays for a defined time period, which simulated long-term sun exposure. In order to investigate the sensitivity of such an approach to damage detection, non-linearity characterisation tests were conducted on aramid fibres in both damaged and undamaged states. With the purpose of carrying out dynamic tests on small fibre specimens, a dedicated instrumentation was designed and built in cooperation with the Metrology Laboratory of the Department of Electronics at the Politecnico di Torino.

An improved wavelet-Galerkin method for dynamic response reconstruction and parameter identification of shear-type frames

NASA Astrophysics Data System (ADS)

Bu, Haifeng; Wang, Dansheng; Zhou, Pin; Zhu, Hongping

2018-04-01

An improved wavelet-Galerkin (IWG) method based on the Daubechies wavelet is proposed for reconstructing the dynamic responses of shear structures. The proposed method flexibly manages wavelet resolution level according to excitation, thereby avoiding the weakness of the wavelet-Galerkin multiresolution analysis (WGMA) method in terms of resolution and the requirement of external excitation. IWG is implemented by this work in certain case studies, involving single- and n-degree-of-freedom frame structures subjected to a determined discrete excitation. Results demonstrate that IWG performs better than WGMA in terms of accuracy and computation efficiency. Furthermore, a new method for parameter identification based on IWG and an optimization algorithm are also developed for shear frame structures, and a simultaneous identification of structural parameters and excitation is implemented. Numerical results demonstrate that the proposed identification method is effective for shear frame structures.

Information Dynamics and Aspects of Musical Perception

NASA Astrophysics Data System (ADS)

Dubnov, Shlomo

Musical experience has been often suggested to be related to forming of expectations, their fulfillment or denial. In terms of information theory, expectancies and predictions serve to reduce uncertainty about the future and might be used to efficiently represent and "compress" data. In this chapter we present an information theoretic model of musical listening based on the idea that expectations that arise from past musical material are framing our appraisal of what comes next, and that this process eventually results in creation of emotions or feelings. Using a notion of "information rate" we can measure the amount of information between past and present in the musical signal on different time scales using statistics of sound spectral features. Several musical pieces are analyzed in terms of short and long term information rate dynamics and are compared to analysis of musical form and its structural functions. The findings suggest that a relation exists between information dynamics and musical structure that eventually leads to creation of human listening experience and feelings such as "wow" and "aha".

Transient Dynamic Response and Failure of Composite Structure Under Cyclic Loading with Fluid Structure Interaction

DTIC Science & Technology

2014-09-01

TERMS fluid structure interaction, composite structures shipbuilding, fatigue loading 15. NUMBER OF PAGES 85 16. PRICE CODE 17. SECURITY...under the three point bending test. All the composites exhibit an initial nonlinear and inelastic deformation trend and end with a catastrophic abrupt

Some aspects of control of a large-scale dynamic system

NASA Technical Reports Server (NTRS)

Aoki, M.

1975-01-01

Techniques of predicting and/or controlling the dynamic behavior of large scale systems are discussed in terms of decentralized decision making. Topics discussed include: (1) control of large scale systems by dynamic team with delayed information sharing; (2) dynamic resource allocation problems by a team (hierarchical structure with a coordinator); and (3) some problems related to the construction of a model of reduced dimension.

Coherent structures and dynamical systems

NASA Technical Reports Server (NTRS)

Jimenez, Javier

1987-01-01

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

Three decades of recurrent declines and recoveries in corals belie ongoing change in fish assemblages

NASA Astrophysics Data System (ADS)

Lamy, T.; Galzin, R.; Kulbicki, M.; Lison de Loma, T.; Claudet, J.

2016-03-01

Coral reefs are increasingly being altered by a myriad of anthropogenic activities and natural disturbances. Long-term studies offer unique opportunities to understand how multiple and recurrent disturbances can influence coral reef resilience and long-term dynamics. While the long-term dynamics of coral assemblages have been extensively documented, the long-term dynamics of coral reef fish assemblages have received less attention. Here, we describe the changes in fish assemblages on Tiahura reef, Moorea, from 1979 to 2011. During this 33-yr period, Tiahura was exposed to multiple disturbances (crown-of-thorns seastar outbreaks and cyclones) that caused recurrent declines and recoveries of coral cover and changes in the dominant coral genera. These shifts in coral composition were associated with long-term cascading effects on fish assemblages. The composition and trophic structure of fish assemblages continuously shifted without returning to their initial composition, whereas fish species richness remained stable, albeit with a small increase over time. We detected nonlinear responses of fish density when corals were most degraded. When coral cover dropped below 10 % following a severe crown-of-thorns sea star outbreak, the density of most fish trophic groups sharply decreased. Our study shows that historical contingency may potentially be an important but largely underestimated factor explaining the contemporary structure of reef fish assemblages and suggests that temporal stability in their structure and function should not necessarily be the target of management strategies that aim at increasing or maintaining coral reef resilience.

Dynamic behavior of solar wind as revealed by a correlation study of magnetic fields observed at the Venus and Earth orbits

NASA Technical Reports Server (NTRS)

Marubashi, K.

1995-01-01

Correlations between interplanetary magnetic fields (IMFs) at 0.72 AU and 1.0 AU have been examined using data sets obtained from the Pioneer Venus orbiter and Earth-orbiting spacecraft. While the two-sector structures are evident in long-term variations at these two heliocentric distances, the corresponding auto-correlation coefficients are consistently smaller at 1.0 AU than at 0.72 AU. This suggests that the IMF structures become less persistent at 1.0 AU due to the effects of changing solar wind dynamics between the Venus and Earth orbits. Short-term variations exhibit generally poor correlations between IMFs near Venus and those near Earth, though good correlations are sometimes obtained for well-defined structures when the Sun, Venus, and Earth are closely aligned. The rather poor correlations in the background streams indicate that the IMFs are still changing between the Venus and Earth orbits under the strong influence of solar wind dynamics.

A Data-Driven Diagnostic Framework for Wind Turbine Structures: A Holistic Approach

PubMed Central

Bogoevska, Simona; Spiridonakos, Minas; Chatzi, Eleni; Dumova-Jovanoska, Elena; Höffer, Rudiger

2017-01-01

The complex dynamics of operational wind turbine (WT) structures challenges the applicability of existing structural health monitoring (SHM) strategies for condition assessment. At the center of Europe’s renewable energy strategic planning, WT systems call for implementation of strategies that may describe the WT behavior in its complete operational spectrum. The framework proposed in this paper relies on the symbiotic treatment of acting environmental/operational variables and the monitored vibration response of the structure. The approach aims at accurate simulation of the temporal variability characterizing the WT dynamics, and subsequently at the tracking of the evolution of this variability in a longer-term horizon. The bi-component analysis tool is applied on long-term data, collected as part of continuous monitoring campaigns on two actual operating WT structures located in different sites in Germany. The obtained data-driven structural models verify the potential of the proposed strategy for development of an automated SHM diagnostic tool. PMID:28358346

Structure-based control of complex networks with nonlinear dynamics.

PubMed

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

2017-07-11

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

Vortex rings

NASA Technical Reports Server (NTRS)

Shariff, Karim; Leonard, Anthony

1992-01-01

The vortex-ring problem in fluid mechanics is examined generally in terms of formation, the steady state, the duration of the rings, and vortex interactions. The formation is studied by examining the generation of laminar and turbulent vortex rings and their resulting structures with attention given to the three stages of laminar ring development. Inviscid dynamics is addressed to show how core dynamics affects overall ring motion, and laminar vortex structures are described in two dimensions. Viscous and inviscid structures are related in terms of 'leapfrogging', head-on collisions, and collisions with a no-slip wall. Linear instability theory is shown to successfully describe observational data, although late stages in the breakdown are not completely understood. This study of vortex rings has important implications for key aerodynamic issues including sound generation, transport and mixing, and vortex interactions.

Long-term impacts of recurrent logging and fire in Amazon forests: a modeling study using the Ecosystem Demography Model (ED2)

NASA Astrophysics Data System (ADS)

Longo, M.; Keller, M.; Scaranello, M. A., Sr.; dos-Santos, M. N.; Xu, Y.; Huang, M.; Morton, D. C.

2017-12-01

Logging and understory fires are major drivers of tropical forest degradation, reducing carbon stocks and changing forest structure, composition, and dynamics. In contrast to deforested areas, sites that are disturbed by logging and fires retain some, albeit severely altered, forest structure and function. In this study we simulated selective logging using the Ecosystem Demography Model (ED-2) to investigate the impact of a broad range of logging techniques, harvest intensities, and recurrence cycles on the long-term dynamics of Amazon forests, including the magnitude and duration of changes in forest flammability following timber extraction. Model results were evaluated using eddy covariance towers at logged sites at the Tapajos National Forest in Brazil and data on long-term dynamics reported in the literature. ED-2 is able to reproduce both the fast (< 5yr) recovery of water, energy fluxes compared to flux tower, and the typical, field-observed, decadal time scales for biomass recovery when no additional logging occurs. Preliminary results using the original ED-2 fire model show that canopy cover loss of forests under high-intensity, conventional logging cause sufficient drying to support more intense fires. These results indicate that under intense degradation, forests may shift to novel disturbance regimes, severely reducing carbon stocks, and inducing long-term changes in forest structure and composition from recurrent fires.

Structural Mechanics and Dynamics Branch

NASA Technical Reports Server (NTRS)

Stefko, George

2003-01-01

The 2002 annual report of the Structural Mechanics and Dynamics Branch reflects the majority of the work performed by the branch staff during the 2002 calendar year. Its purpose is to give a brief review of the branch s technical accomplishments. The Structural Mechanics and Dynamics Branch develops innovative computational tools, benchmark experimental data, and solutions to long-term barrier problems in the areas of propulsion aeroelasticity, active and passive damping, engine vibration control, rotor dynamics, magnetic suspension, structural mechanics, probabilistics, smart structures, engine system dynamics, and engine containment. Furthermore, the branch is developing a compact, nonpolluting, bearingless electric machine with electric power supplied by fuel cells for future "more electric" aircraft. An ultra-high-power-density machine that can generate projected power densities of 50 hp/lb or more, in comparison to conventional electric machines, which generate usually 0.2 hp/lb, is under development for application to electric drives for propulsive fans or propellers. In the future, propulsion and power systems will need to be lighter, to operate at higher temperatures, and to be more reliable in order to achieve higher performance and economic viability. The Structural Mechanics and Dynamics Branch is working to achieve these complex, challenging goals.

Structural aspects of Hamilton-Jacobi theory

NASA Astrophysics Data System (ADS)

Cariñena, J. F.; Gràcia, X.; Marmo, G.; Martínez, E.; Muñoz-Lecanda, M. C.; Román-Roy, N.

2016-12-01

In our previous papers [J. F. Cariñena, X. Gràcia, G. Marmo, E. Martínez, M. C. Muñoz-Lecanda and N. Román-Roy, Geometric Hamilton-Jacobi theory, Int. J. Geom. Meth. Mod. Phys. 3 (2006) 1417-1458; Geometric Hamilton-Jacobi theory for nonholonomic dynamical systems, Int. J. Geom. Meth. Mod. Phys. 7 (2010) 431-454] we showed that the Hamilton-Jacobi problem can be regarded as a way to describe a given dynamics on a phase space manifold in terms of a family of dynamics on a lower-dimensional manifold. We also showed how constants of the motion help to solve the Hamilton-Jacobi equation. Here we want to delve into this interpretation by considering the most general case: a dynamical system on a manifold that is described in terms of a family of dynamics (slicing vector fields) on lower-dimensional manifolds. We identify the relevant geometric structures that lead from this decomposition of the dynamics to the classical Hamilton-Jacobi theory, by considering special cases like fibered manifolds and Hamiltonian dynamics, in the symplectic framework and the Poisson one. We also show how a set of functions on a tangent bundle can determine a second-order dynamics for which they are constants of the motion.

Disturbance dynamics of forested ecosystems

Treesearch

John A. Stanturf

2004-01-01

Forested ecosystems are dynamic, subject to natural developmental processes as well as natural and anthropogenic stresses and disturbances. Degradation is a related term. for lowered productive capacity from changes to forest structure of function (FAO. 2001). Degradation is not synonymous with disturbance, however; disturbance becomes degradation when natural...

Minimal complexity control law synthesis

NASA Technical Reports Server (NTRS)

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

1989-01-01

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

Low-dose dynamic myocardial perfusion CT image reconstruction using pre-contrast normal-dose CT scan induced structure tensor total variation regularization

NASA Astrophysics Data System (ADS)

Gong, Changfei; Han, Ce; Gan, Guanghui; Deng, Zhenxiang; Zhou, Yongqiang; Yi, Jinling; Zheng, Xiaomin; Xie, Congying; Jin, Xiance

2017-04-01

Dynamic myocardial perfusion CT (DMP-CT) imaging provides quantitative functional information for diagnosis and risk stratification of coronary artery disease by calculating myocardial perfusion hemodynamic parameter (MPHP) maps. However, the level of radiation delivered by dynamic sequential scan protocol can be potentially high. The purpose of this work is to develop a pre-contrast normal-dose scan induced structure tensor total variation regularization based on the penalized weighted least-squares (PWLS) criteria to improve the image quality of DMP-CT with a low-mAs CT acquisition. For simplicity, the present approach was termed as ‘PWLS-ndiSTV’. Specifically, the ndiSTV regularization takes into account the spatial-temporal structure information of DMP-CT data and further exploits the higher order derivatives of the objective images to enhance denoising performance. Subsequently, an effective optimization algorithm based on the split-Bregman approach was adopted to minimize the associative objective function. Evaluations with modified dynamic XCAT phantom and preclinical porcine datasets have demonstrated that the proposed PWLS-ndiSTV approach can achieve promising gains over other existing approaches in terms of noise-induced artifacts mitigation, edge details preservation, and accurate MPHP maps calculation.

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.

Fluctuating Nonlinear Spring Model of Mechanical Deformation of Biological Particles

PubMed Central

Kononova, Olga; Snijder, Joost; Kholodov, Yaroslav; Marx, Kenneth A.; Wuite, Gijs J. L.; Roos, Wouter H.; Barsegov, Valeri

2016-01-01

The mechanical properties of virus capsids correlate with local conformational dynamics in the capsid structure. They also reflect the required stability needed to withstand high internal pressures generated upon genome loading and contribute to the success of important events in viral infectivity, such as capsid maturation, genome uncoating and receptor binding. The mechanical properties of biological nanoparticles are often determined from monitoring their dynamic deformations in Atomic Force Microscopy nanoindentation experiments; but a comprehensive theory describing the full range of observed deformation behaviors has not previously been described. We present a new theory for modeling dynamic deformations of biological nanoparticles, which considers the non-linear Hertzian deformation, resulting from an indenter-particle physical contact, and the bending of curved elements (beams) modeling the particle structure. The beams’ deformation beyond the critical point triggers a dynamic transition of the particle to the collapsed state. This extreme event is accompanied by a catastrophic force drop as observed in the experimental or simulated force (F)-deformation (X) spectra. The theory interprets fine features of the spectra, including the nonlinear components of the FX-curves, in terms of the Young’s moduli for Hertzian and bending deformations, and the structural damage dependent beams’ survival probability, in terms of the maximum strength and the cooperativity parameter. The theory is exemplified by successfully describing the deformation dynamics of natural nanoparticles through comparing theoretical curves with experimental force-deformation spectra for several virus particles. This approach provides a comprehensive description of the dynamic structural transitions in biological and artificial nanoparticles, which is essential for their optimal use in nanotechnology and nanomedicine applications. PMID:26821264

Dynamics of Opinion Forming in Structurally Balanced Social Networks

PubMed Central

Altafini, Claudio

2012-01-01

A structurally balanced social network is a social community that splits into two antagonistic factions (typical example being a two-party political system). The process of opinion forming on such a community is most often highly predictable, with polarized opinions reflecting the bipartition of the network. The aim of this paper is to suggest a class of dynamical systems, called monotone systems, as natural models for the dynamics of opinion forming on structurally balanced social networks. The high predictability of the outcome of a decision process is explained in terms of the order-preserving character of the solutions of this class of dynamical systems. If we represent a social network as a signed graph in which individuals are the nodes and the signs of the edges represent friendly or hostile relationships, then the property of structural balance corresponds to the social community being splittable into two antagonistic factions, each containing only friends. PMID:22761667

Intergenerational Long-Term Effects of Preschool - Structural Estimates from a Discrete Dynamic Programming Model*

PubMed Central

Heckman, James J.; Raut, Lakshmi K.

2015-01-01

This paper formulates a structural dynamic programming model of preschool investment choices of altruistic parents and then empirically estimates the structural parameters of the model using the NLSY79 data. The paper finds that preschool investment significantly boosts cognitive and non-cognitive skills, which enhance earnings and school outcomes. It also finds that a standard Mincer earnings function, by omitting measures of non-cognitive skills on the right-hand side, overestimates the rate of return to schooling. From the estimated equilibrium Markov process, the paper studies the nature of within generation earnings distribution, intergenerational earnings mobility, and schooling mobility. The paper finds that a tax-financed free preschool program for the children of poor socioeconomic status generates positive net gains to the society in terms of average earnings, higher intergenerational earnings mobility, and schooling mobility. PMID:26709326

Signs of universality in the structure of culture

NASA Astrophysics Data System (ADS)

Băbeanu, Alexandru-Ionuţ; Talman, Leandros; Garlaschelli, Diego

2017-11-01

Understanding the dynamics of opinions, preferences and of culture as whole requires more use of empirical data than has been done so far. It is clear that an important role in driving this dynamics is played by social influence, which is the essential ingredient of many quantitative models. Such models require that all traits are fixed when specifying the "initial cultural state". Typically, this initial state is randomly generated, from a uniform distribution over the set of possible combinations of traits. However, recent work has shown that the outcome of social influence dynamics strongly depends on the nature of the initial state. If the latter is sampled from empirical data instead of being generated in a uniformly random way, a higher level of cultural diversity is found after long-term dynamics, for the same level of propensity towards collective behavior in the short-term. Moreover, if the initial state is randomized by shuffling the empirical traits among people, the level of long-term cultural diversity is in-between those obtained for the empirical and uniformly random counterparts. The current study repeats the analysis for multiple empirical data sets, showing that the results are remarkably similar, although the matrix of correlations between cultural variables clearly differs across data sets. This points towards robust structural properties inherent in empirical cultural states, possibly due to universal laws governing the dynamics of culture in the real world. The results also suggest that this dynamics might be characterized by criticality and involve mechanisms beyond social influence.

Time Scale Hierarchies in the Functional Organization of Complex Behaviors

PubMed Central

Perdikis, Dionysios; Huys, Raoul; Jirsa, Viktor K.

2011-01-01

Traditional approaches to cognitive modelling generally portray cognitive events in terms of ‘discrete’ states (point attractor dynamics) rather than in terms of processes, thereby neglecting the time structure of cognition. In contrast, more recent approaches explicitly address this temporal dimension, but typically provide no entry points into cognitive categorization of events and experiences. With the aim to incorporate both these aspects, we propose a framework for functional architectures. Our approach is grounded in the notion that arbitrary complex (human) behaviour is decomposable into functional modes (elementary units), which we conceptualize as low-dimensional dynamical objects (structured flows on manifolds). The ensemble of modes at an agent’s disposal constitutes his/her functional repertoire. The modes may be subjected to additional dynamics (termed operational signals), in particular, instantaneous inputs, and a mechanism that sequentially selects a mode so that it temporarily dominates the functional dynamics. The inputs and selection mechanisms act on faster and slower time scales then that inherent to the modes, respectively. The dynamics across the three time scales are coupled via feedback, rendering the entire architecture autonomous. We illustrate the functional architecture in the context of serial behaviour, namely cursive handwriting. Subsequently, we investigate the possibility of recovering the contributions of functional modes and operational signals from the output, which appears to be possible only when examining the output phase flow (i.e., not from trajectories in phase space or time). PMID:21980278

Long-Term Dynamic Monitoring of the Historical Masonry FAÇADE: the Case of Palazzo Ducale in Venice, Italy

NASA Astrophysics Data System (ADS)

Noh, J.; Russo, S.

2017-08-01

Long-term dynamic monitoring of the masonry façade of Palazzo Ducale known as Doge's palace in Venice, Italy was performed from September 2010 to October 2012. This article demonstrates the results of preliminary analysis on the data set of the first 12-month long monitoring campaign for out-of-plumb dynamic responses of the medieval façade of the monument. The aim of the analysis of the dynamic signals is to validate the data set and investigate dynamic characteristics of the vibration signature of the historical masonry wall in the long-term. Palazzo Ducale is a heavily visited heritage due to its high cultural importance and architectural value. Nevertheless, little is known about the dynamic behaviour of the double-leaf masonry façade. In this study, the dynamic properties of the structure are presented by dynamic identification carried out with the effect of the ambient vibration measured at four different locations on the façade and portico level. The trend and intensity of the vibration at each measurement locations are identified over the year. In addition, the issue on eliminating the noise blended in the signals for reliable analysis are also discussed.

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.

Electrical resistivity and thermal conductivity of liquid aluminum in the two-temperature state

NASA Astrophysics Data System (ADS)

Petrov, Yu V.; Inogamov, N. A.; Mokshin, A. V.; Galimzyanov, B. N.

2018-01-01

The electrical resistivity and thermal conductivity of liquid aluminum in the two-temperature state is calculated by using the relaxation time approach and structural factor of ions obtained by molecular dynamics simulation. Resistivity witin the Ziman-Evans approach is also considered to be higher than in the approach with previously calculated conductivity via the relaxation time. Calculations based on the construction of the ion structural factor through the classical molecular dynamics and kinetic equation for electrons are more economical in terms of computing resources and give results close to the Kubo-Greenwood with the quantum molecular dynamics calculations.

Discrete piezoelectric sensors and actuators for active control of two-dimensional spacecraft components

NASA Technical Reports Server (NTRS)

Bayer, Janice I.; Varadan, V. V.; Varadan, V. K.

1991-01-01

This paper describes research into the use of discrete piezoelectric sensors and actuators for active modal control of flexible two-dimensional structures such as might be used as components for spacecraft. A dynamic coupling term is defined between the sensor/actuator and the structure in terms of structural model shapes, location and piezoelectric behavior. The relative size of the coupling term determines sensor/actuator placement. Results are shown for a clamped square plate and for a large antenna. An experiment was performed on a thin foot-square plate clamped on all sides. Sizable vibration control was achieved for first, second/third (degenerate) and fourth modes.

Structure-based control of complex networks with nonlinear dynamics

NASA Astrophysics Data System (ADS)

Zanudo, Jorge G. T.; Yang, Gang; Albert, Reka

What can we learn about controlling a system solely from its underlying network structure? Here we use a framework for control of networks governed by a broad class of nonlinear dynamics that includes the major dynamic models of biological, technological, and social processes. This feedback-based framework provides realizable node overrides that steer a system towards any of its natural long term dynamic behaviors, regardless of the dynamic details and system parameters. We use this framework on several real networks, identify the topological characteristics that underlie the predicted node overrides, and compare its predictions to those of classical structural control theory. Finally, we demonstrate this framework's applicability in dynamic models of gene regulatory networks and identify nodes whose override is necessary for control in the general case, but not in specific model instances. This work was supported by NSF Grants PHY 1205840 and IIS 1160995. JGTZ is a recipient of a Stand Up To Cancer - The V Foundation Convergence Scholar Award.

High frequency, multi-axis dynamic stiffness analysis of a fractionally damped elastomeric isolator using continuous system theory

NASA Astrophysics Data System (ADS)

Fredette, Luke; Singh, Rajendra

2017-02-01

A spectral element approach is proposed to determine the multi-axis dynamic stiffness terms of elastomeric isolators with fractional damping over a broad range of frequencies. The dynamic properties of a class of cylindrical isolators are modeled by using the continuous system theory in terms of homogeneous rods or Timoshenko beams. The transfer matrix type dynamic stiffness expressions are developed from exact harmonic solutions given translational or rotational displacement excitations. Broadband dynamic stiffness magnitudes (say up to 5 kHz) are computationally verified for axial, torsional, shear, flexural, and coupled stiffness terms using a finite element model. Some discrepancies are found between finite element and spectral element models for the axial and flexural motions, illustrating certain limitations of each method. Experimental validation is provided for an isolator with two cylindrical elements (that work primarily in the shear mode) using dynamic measurements, as reported in the prior literature, up to 600 Hz. Superiority of the fractional damping formulation over structural or viscous damping models is illustrated via experimental validation. Finally, the strengths and limitations of the spectral element approach are briefly discussed.

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

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

NASA Astrophysics Data System (ADS)

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

2016-11-01

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

Division H Commission 33: Structure & Dynamics of the Galactic System

NASA Astrophysics Data System (ADS)

Nordström, Birgitta; Bland-Hawthorn, Joss; Wyse, Rosemary; Athanassoula, Lia; Feltzing, Sofia; Jog, Chanda; Lockman, Jay; Minniti, Dante; Robin, Annie

2016-04-01

Research on the structure and dynamics of the Galactic System covers a large field of research, from formation scenarios to long-term evolution and secular processes. Today we speak of near-field cosmology where the oldest parts of the Galaxy are used to probe back to early times, e.g. studying the chemical signatures of the oldest star clusters and dwarf galaxies to learn about the byproducts of the first stars. Some of the most detailed work relates to the structure of the dark matter and baryons in order to compare with expectation from N-body models. Secular processes have been identified (e.g. stellar migration) where material within the Galaxy is being reorganized by dynamical resonances and feedback processes.

Analysis of the structure and dynamics of human serum albumin.

PubMed

Guizado, T R Cuya

2014-10-01

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

Exploration of the folding dynamics of human telomeric G-quadruplex with a hybrid atomistic structure-based model

NASA Astrophysics Data System (ADS)

Bian, Yunqiang; Ren, Weitong; Song, Feng; Yu, Jiafeng; Wang, Jihua

2018-05-01

Structure-based models or Gō-like models, which are built from one or multiple particular experimental structures, have been successfully applied to the folding of proteins and RNAs. Recently, a variant termed the hybrid atomistic model advances the description of backbone and side chain interactions of traditional structure-based models, by borrowing the description of local interactions from classical force fields. In this study, we assessed the validity of this model in the folding problem of human telomeric DNA G-quadruplex, where local dihedral terms play important roles. A two-state model was developed and a set of molecular dynamics simulations was conducted to study the folding dynamics of sequence Htel24, which was experimentally validated to adopt two different (3 + 1) hybrid G-quadruplex topologies in K+ solution. Consistent with the experimental observations, the hybrid-1 conformation was found to be more stable and the hybrid-2 conformation was kinetically more favored. The simulations revealed that the hybrid-2 conformation folded in a higher cooperative manner, which may be the reason why it was kinetically more accessible. Moreover, by building a Markov state model, a two-quartet G-quadruplex state and a misfolded state were identified as competing states to complicate the folding process of Htel24. Besides, the simulations also showed that the transition between hybrid-1 and hybrid-2 conformations may proceed an ensemble of hairpin structures. The hybrid atomistic structure-based model reproduced the kinetic partitioning folding dynamics of Htel24 between two different folds, and thus can be used to study the complex folding processes of other G-quadruplex structures.

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

NASA Astrophysics Data System (ADS)

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

2015-03-01

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

Multiscale molecular dynamics simulations of rotary motor proteins.

PubMed

Ekimoto, Toru; Ikeguchi, Mitsunori

2018-04-01

Protein functions require specific structures frequently coupled with conformational changes. The scale of the structural dynamics of proteins spans from the atomic to the molecular level. Theoretically, all-atom molecular dynamics (MD) simulation is a powerful tool to investigate protein dynamics because the MD simulation is capable of capturing conformational changes obeying the intrinsically structural features. However, to study long-timescale dynamics, efficient sampling techniques and coarse-grained (CG) approaches coupled with all-atom MD simulations, termed multiscale MD simulations, are required to overcome the timescale limitation in all-atom MD simulations. Here, we review two examples of rotary motor proteins examined using free energy landscape (FEL) analysis and CG-MD simulations. In the FEL analysis, FEL is calculated as a function of reaction coordinates, and the long-timescale dynamics corresponding to conformational changes is described as transitions on the FEL surface. Another approach is the utilization of the CG model, in which the CG parameters are tuned using the fluctuation matching methodology with all-atom MD simulations. The long-timespan dynamics is then elucidated straightforwardly by using CG-MD simulations.

Study on dynamic response measurement of the submarine pipeline by full-term FBG sensors.

PubMed

Zhou, Jinghai; Sun, Li; Li, Hongnan

2014-01-01

The field of structural health monitoring is concerned with accurately and reliably assessing the integrity of a given structure to reduce ownership costs, increase operational lifetime, and improve safety. In structural health monitoring systems, fiber Bragg grating (FBG) is a promising measurement technology for its superior ability of explosion proof, immunity to electromagnetic interference, and high accuracy. This paper is a study on the dynamic characteristics of fiber Bragg grating (FBG) sensors applied to a submarine pipeline, as well as an experimental investigation on a laboratory model of the pipeline. The dynamic response of a submarine pipeline under seismic excitation is a coupled vibration of liquid and solid interaction. FBG sensors and strain gauges are used to monitor the dynamic response of a submarine pipeline model under a variety of dynamic loading conditions and the maximum working frequency of an FBG strain sensor is calculated according to its dynamic strain responses. Based on the theoretical and experimental results, it can be concluded that FBG sensor is superior to strain gauge and satisfies the demand of dynamic strain measurement.

Study on Dynamic Response Measurement of the Submarine Pipeline by Full-Term FBG Sensors

PubMed Central

Zhou, Jinghai; Sun, Li; Li, Hongnan

2014-01-01

The field of structural health monitoring is concerned with accurately and reliably assessing the integrity of a given structure to reduce ownership costs, increase operational lifetime, and improve safety. In structural health monitoring systems, fiber Bragg grating (FBG) is a promising measurement technology for its superior ability of explosion proof, immunity to electromagnetic interference, and high accuracy. This paper is a study on the dynamic characteristics of fiber Bragg grating (FBG) sensors applied to a submarine pipeline, as well as an experimental investigation on a laboratory model of the pipeline. The dynamic response of a submarine pipeline under seismic excitation is a coupled vibration of liquid and solid interaction. FBG sensors and strain gauges are used to monitor the dynamic response of a submarine pipeline model under a variety of dynamic loading conditions and the maximum working frequency of an FBG strain sensor is calculated according to its dynamic strain responses. Based on the theoretical and experimental results, it can be concluded that FBG sensor is superior to strain gauge and satisfies the demand of dynamic strain measurement. PMID:24971391

Canonical Structure and Orthogonality of Forces and Currents in Irreversible Markov Chains

NASA Astrophysics Data System (ADS)

Kaiser, Marcus; Jack, Robert L.; Zimmer, Johannes

2018-03-01

We discuss a canonical structure that provides a unifying description of dynamical large deviations for irreversible finite state Markov chains (continuous time), Onsager theory, and Macroscopic Fluctuation Theory (MFT). For Markov chains, this theory involves a non-linear relation between probability currents and their conjugate forces. Within this framework, we show how the forces can be split into two components, which are orthogonal to each other, in a generalised sense. This splitting allows a decomposition of the pathwise rate function into three terms, which have physical interpretations in terms of dissipation and convergence to equilibrium. Similar decompositions hold for rate functions at level 2 and level 2.5. These results clarify how bounds on entropy production and fluctuation theorems emerge from the underlying dynamical rules. We discuss how these results for Markov chains are related to similar structures within MFT, which describes hydrodynamic limits of such microscopic models.

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.

Space station rotational equations of motion

NASA Technical Reports Server (NTRS)

Rheinfurth, M. H.; Carroll, S. N.

1985-01-01

Dynamic equations of motion are developed which describe the rotational motion for a large space structure having rotating appendages. The presence of the appendages produce torque coupling terms which are dependent on the inertia properties of the appendages and the rotational rates for both the space structure and the appendages. These equations were formulated to incorporate into the Space Station Attitude Control and Stabilization Test Bed to accurately describe the influence rotating solar arrays and thermal radiators have on the dynamic behavior of the Space Station.

Structural dynamics division research and technology accomplishments for FY 1993 and plans for FY 1994

NASA Technical Reports Server (NTRS)

Wynne, Eleanor C.

1994-01-01

The purpose is to present the Structural Dynamics Division's research accomplishments for F.Y. 1993 and research plans for F.Y. 1994. The work under each Branch (technical area) is described in terms of highlights of accomplishments during the past year and highlights of plans for the current year as they relate to 5-year plans for each technical area. This information will be useful in program coordination with other government organizations and industry in areas of mutual interest.

Structural dynamics division research and technology accomplishments for FY 1989 and plans for FY 1990

NASA Technical Reports Server (NTRS)

Smith, Jacqueline G.; Gardner, James E.

1990-01-01

The purpose is to present the Structural Dynamics Division's research accomplishments for FY 1989 and research plans for FY 1990. The work under each Branch (technical area) is described in terms of highlights of accomplishments during the past year and highlights of plans for the current year as they relate to five year plans for each technical area. This information will be useful in program coordination with other government organizations and industry in areas of mutual interest.

Logic Dynamics for Deductive Inference -- Its Stability and Neural Basis

NASA Astrophysics Data System (ADS)

Tsuda, Ichiro

2014-12-01

We propose a dynamical model that represents a process of deductive inference. We discuss the stability of logic dynamics and a neural basis for the dynamics. We propose a new concept of descriptive stability, thereby enabling a structure of stable descriptions of mathematical models concerning dynamic phenomena to be clarified. The present theory is based on the wider and deeper thoughts of John S. Nicolis. In particular, it is based on our joint paper on the chaos theory of human short-term memories with a magic number of seven plus or minus two.

Structure and development of old-growth, unmanaged second-growth, and extended rotation Pinus resinosa forests in Minnesota, USA

Treesearch

Emily J. Silver; Anthony W. D' Amato; Shawn Fraver; Brian J. Palik; John B. Bradford

2013-01-01

The structure and developmental dynamics of old-growth forests often serve as important baselines for restoration prescriptions aimed at promoting more complex structural conditions in managed forest landscapes. Nonetheless, long-term information on natural patterns of development is rare for many commercially important and ecologically widespread forest types....

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.

Using simulation to interpret experimental data in terms of protein conformational ensembles.

PubMed

Allison, Jane R

2017-04-01

In their biological environment, proteins are dynamic molecules, necessitating an ensemble structural description. Molecular dynamics simulations and solution-state experiments provide complimentary information in the form of atomically detailed coordinates and averaged or distributions of structural properties or related quantities. Recently, increases in the temporal and spatial scale of conformational sampling and comparison of the more diverse conformational ensembles thus generated have revealed the importance of sampling rare events. Excitingly, new methods based on maximum entropy and Bayesian inference are promising to provide a statistically sound mechanism for combining experimental data with molecular dynamics simulations. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

Coherent organization in gene regulation: a study on six networks

NASA Astrophysics Data System (ADS)

Aral, Neşe; Kabakçıoğlu, Alkan

2016-04-01

Structural and dynamical fingerprints of evolutionary optimization in biological networks are still unclear. Here we analyze the dynamics of genetic regulatory networks responsible for the regulation of cell cycle and cell differentiation in three organisms or cell types each, and show that they follow a version of Hebb's rule which we have termed coherence. More precisely, we find that simultaneously expressed genes with a common target are less likely to act antagonistically at the attractors of the regulatory dynamics. We then investigate the dependence of coherence on structural parameters, such as the mean number of inputs per node and the activatory/repressory interaction ratio, as well as on dynamically determined quantities, such as the basin size and the number of expressed genes.

Assessment of dynamic and long-term performance of an innovative multi-story timber building via structural monitoring and dynamic testing

NASA Astrophysics Data System (ADS)

Omenzetter, Piotr; Morris, Hugh; Worth, Margaret; Gaul, Andrew; Jager, Simon; Desgeorges, Yohann

2012-04-01

An innovative three-story timber building, using self-centering, post-tensioned timber shear walls as the main horizontal load resisting system and lightweight non-composite timber-concrete floors, has recently been completed in Nelson, New Zealand. It is expected to be the trailblazer for similar but taller structures to be more widely adopted. Performance based standards require an advanced understanding of building responses and in order to meet the need for in-situ performance data the building has been subjected to forced vibration testing and instrumented for continuous monitoring using a total of approximately 90 data channels to capture its dynamic and long-term responses. The first part of the paper presents a brief discussion of the existing research on the seismic performance of timber frame buildings and footfall induced floor vibrations. An outline of the building structural system, focusing on the novel design solutions, is then discussed. This is followed by the description of the monitoring system. The analysis of monitoring results starts with a discussion of the monitoring of long-term deformations. Next, the assessment of the floor vibration serviceability performance is outlined. Then, the forced vibration tests conducted on the whole building at different construction stages are reviewed. The system identification results from seismic shaking records are also discussed. Finally, updating of a finite element model of the building is conducted.

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

PubMed

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

2015-09-21

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

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

NASA Astrophysics Data System (ADS)

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

2015-09-01

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

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

Using Dynamic Risk and Protective Factors to Predict Inpatient Aggression: Reliability and Validity of START Assessments

PubMed Central

Desmarais, Sarah L.; Nicholls, Tonia L.; Wilson, Catherine M.; Brink, Johann

2012-01-01

The Short-Term Assessment of Risk and Treatability (START) is a relatively new structured professional judgment guide for the assessment and management of short-term risks associated with mental, substance use, and personality disorders. The scheme may be distinguished from other violence risk instruments because of its inclusion of 20 dynamic factors that are rated in terms of both vulnerability and strength. This study examined the reliability and validity of START assessments in predicting inpatient aggression. Research assistants completed START assessments for 120 male forensic psychiatric patients through review of hospital files. They additionally completed Historical-Clinical-Risk Management – 20 (HCR-20) and the Hare Psychopathy Checklist: Screening Version (PCL:SV) assessments. Outcome data was coded from hospital files for a 12-month follow-up period using the Overt Aggression Scale (OAS). START assessments evidenced excellent interrater reliability and demonstrated both predictive and incremental validity over the HCR-20 Historical subscale scores and PCL:SV total scores. Overall, results support the reliability and validity of START assessments, and use of the structured professional judgment approach more broadly, as well as the value of using dynamic risk and protective factors to assess violence risk. PMID:22250595

Dynamic Structure Factor: An Introduction

NASA Astrophysics Data System (ADS)

Sturm, K.

1993-02-01

The doubly differential cross-section for weak inelastic scattering of waves or particles by manybody systems is derived in Born approximation and expressed in terms of the dynamic structure factor according to van Hove. The application of this very general scheme to scattering of neutrons, x-rays and high-energy electrons is discussed briefly. The dynamic structure factor, which is the space and time Fourier transform of the density-density correlation function, is a property of the many-body system independent of the external probe and carries information on the excitation spectrum of the system. The relation of the electronic structure factor to the density-density response function defined in linear-response theory is shown using the fluctuation-dissipation theorem. This is important for calculations, since the response function can be calculated approximately from the independent-particle response function in self-consistent field approximations, such as the random-phase approximation or the local-density approximation of the density functional theory. Since the density-density response function also determines the dielectric function, the dynamic structure can be expressed by the dielectric function.

Nickel-aluminum alloy clusters -- structural and dynamical properties

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

Jellinek, J.; Krissinel, E.B.

1997-08-01

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

Multiscale structure in eco-evolutionary dynamics

NASA Astrophysics Data System (ADS)

Stacey, Blake C.

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

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

NASA Astrophysics Data System (ADS)

Wu, Qiong; Li, Dapeng

2015-03-01

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

Construction of the Free Energy Landscape of Peptide Aggregation from Molecular Dynamics Simulations.

PubMed

Riccardi, Laura; Nguyen, Phuong H; Stock, Gerhard

2012-04-10

To describe the structure and dynamics of oligomers during peptide aggregation, a method is proposed that considers both the intramolecular and intermolecular structures of the multimolecule system and correctly accounts for its degeneracy. The approach is based on the "by-parts" strategy, which partitions a complex molecular system into parts, determines the metastable conformational states of each part, and describes the overall conformational state of the system in terms of a product basis of the states of the parts. Starting from a molecular dynamics simulation of n molecules, the method consists of three steps: (i) characterization of the intramolecular structure, that is, of the conformational states of a single molecule in the presence of the other molecules (e.g., β-strand or random coil); (ii) characterization of the intermolecular structure through the identification of all occurring aggregate states of the peptides (dimers, trimers, etc.); and (iii) construction of the overall conformational states of the system in terms of a product basis of the n "single-molecule" states and the aggregate states. Considering the Alzheimer β-amyloid peptide fragment Aβ16-22 as a first application, about 700 overall conformational states of the trimer (Aβ16-22)3 were constructed from all-atom molecular dynamics simulation in explicit water. Based on these states, a transition network reflecting the free energy landscape of the aggregation process can be constructed that facilitates the identification of the aggregation pathways.

Microscopic and histochemical manifestations of hyaline cartilage dynamics.

PubMed

Malinin, G I; Malinin, T I

1999-01-01

Structure and function of hyaline cartilages has been the focus of many correlative studies for over a hundred years. Much of what is known regarding dynamics and function of cartilage constituents has been derived or inferred from biochemical and electron microscopic investigations. Here we show that in conjunction with ultrastructural, and high-magnification transmission light and polarization microscopy, the well-developed histochemical methods are indispensable for the analysis of cartilage dynamics. Microscopically demonstrable aspects of cartilage dynamics include, but are not limited to, formation of the intracellular liquid crystals, phase transitions of the extracellular matrix and tubular connections between chondrocytes. The role of the interchondrocytic liquid crystals is considered in terms of the tensegrity hypothesis and non-apoptotic cell death. Phase transitions of the extracellular matrix are discussed in terms of self-alignment of chondrons, matrix guidance pathways and cartilage growth in the absence of mitosis. The possible role of nonenzymatic glycation reactions in cartilage dynamics is also reviewed.

Long-term fragmentation effects on the distribution and dynamics of canopy gaps in a tropical montane forest

Treesearch

Nicholas R. Vaughn; Gregory P. Asner; Christian P. Giardina

2015-01-01

Fragmentation alters forest canopy structure through various mechanisms, which in turn drive subsequent changes to biogeochemical processes and biological diversity. Using repeated airborne LiDAR (Light Detection and Ranging) mappings, we investigated the size distribution and dynamics of forest canopy gaps across a topical montane forest landscape in Hawaii naturally...

Mass and nutrient dynamics of decaying litter from Passiflora mollissima and selected native species in a Hawaiian montane rain forest

Treesearch

Paul G. Scowcroft

1997-01-01

The structure and functioning of Acacia koa-Metrosideros polymorpha forests between 1200 and 1800 m elevation on the island of Hawaii are being threatened by Passiflora mollissima, an aggressive introduced liana from South America. This study was done to evaluate the short-term decomposition dynamics of...

Linking dynamics of the inhibitory network to the input structure

PubMed Central

Komarov, Maxim

2017-01-01

Networks of inhibitory interneurons are found in many distinct classes of biological systems. Inhibitory interneurons govern the dynamics of principal cells and are likely to be critically involved in the coding of information. In this theoretical study, we describe the dynamics of a generic inhibitory network in terms of low-dimensional, simplified rate models. We study the relationship between the structure of external input applied to the network and the patterns of activity arising in response to that stimulation. We found that even a minimal inhibitory network can generate a great diversity of spatio-temporal patterning including complex bursting regimes with non-trivial ratios of burst firing. Despite the complexity of these dynamics, the network’s response patterns can be predicted from the rankings of the magnitudes of external inputs to the inhibitory neurons. This type of invariant dynamics is robust to noise and stable in densely connected networks with strong inhibitory coupling. Our study predicts that the response dynamics generated by an inhibitory network may provide critical insights about the temporal structure of the sensory input it receives. PMID:27650865

Black liquor and the hangover effect: fish assemblage recovery dynamics following a pulse disturbance

PubMed Central

Piller, Kyle R; Geheber, Aaron D

2015-01-01

Anthropogenic perturbations impact aquatic systems causing wide-ranging responses, from assemblage restructuring to assemblage recovery. Previous studies indicate the duration and intensity of disturbances play a role in the dynamics of assemblage recovery. In August 2011, the Pearl River, United States, was subjected to a weak black liquor spill from a paper mill which resulted in substantial loss of fish in a large stretch of the main channel. We quantified resilience and recovery of fish assemblage structure in the impacted area following the event. We compared downstream (impacted) assemblages to upstream (unimpacted) assemblages to determine initial impacts on structure. Additionally, we incorporated historic fish collections (1988–2011) to examine impacts on assemblage structure across broad temporal scales. Based on NMDS, upstream and downstream sites generally showed similar assemblage structure across sample periods with the exception of the 2 months postdischarge, where upstream and downstream sites visually differed. Multivariate analysis of variance (PERMANOVA) indicated significant seasonal variation among samples, but found no significant interaction between impacted and unimpacted assemblages following the discharge event. However, multivariate dispersion (MVDISP) showed greater variance among assemblage structure following the discharge event. These results suggest that 2 months following the disturbance represent a time period of stochasticity in regard to assemblage structure dynamics, and this was followed by rapid recovery. We term this dynamic the “hangover effect” as it represents the time frame from the cessation of the perturbation to the assemblage's return to predisturbance conditions. The availability and proximity of tributaries and upstream refugia, which were not affected by the disturbance, as well as the rapid recovery of abiotic parameters likely played a substantial role in assemblage recovery. This study not only demonstrates rapid recovery in an aquatic system, but further demonstrates the value of continuous, long-term, data collections which enhance our understanding of assemblage dynamics. PMID:26120432

Predicting the Development of Analytical and Creative Abilities in Upper Elementary Grades

ERIC Educational Resources Information Center

Gubbels, Joyce; Segers, Eliane; Verhoeven, Ludo

2017-01-01

In some models, intelligence has been described as a multidimensional construct comprising both analytical and creative abilities. In addition, intelligence is considered to be dynamic rather than static. A structural equation model was used to examine the predictive role of cognitive (visual short-term memory, verbal short-term memory, selective…

Microbial community structure is affected by cropping sequences and poultry litter under long-term no-tillage

USDA-ARS?s Scientific Manuscript database

Soil microorganisms play essential roles in soil organic matter dynamics and nutrient cycling in agroecosystems and have been used as soil quality indicators. The response of soil microbial communities to land management is complex and the long-term impacts of cropping systems on soil microbes is l...

Integrated modeling of long-term vegetation and hydrologic dynamics in Rocky Mountain watersheds

Treesearch

Robert Steven Ahl

2007-01-01

Changes in forest structure resulting from natural disturbances, or managed treatments, can have negative and long lasting impacts on water resources. To facilitate integrated management of forest and water resources, a System for Long-Term Integrated Management Modeling (SLIMM) was developed. By combining two spatially explicit, continuous time models, vegetation...

Exotic dark spinor fields

NASA Astrophysics Data System (ADS)

Da Rocha, Roldão; Bernardini, Alex E.; da Silva, J. M. Hoff

2011-04-01

Exotic dark spinor fields are introduced and investigated in the context of inequivalent spin structures on arbitrary curved spacetimes, which induces an additional term on the associated Dirac operator, related to a Čech cohomology class. For the most kinds of spinor fields, any exotic term in the Dirac operator can be absorbed and encoded as a shift of the electromagnetic vector potential representing an element of the cohomology group {H^1}( {M,{{Z}_2}} ) . The possibility of concealing such an exotic term does not exist in case of dark (ELKO) spinor fields, as they cannot carry electromagnetic charge, so that the full topological analysis must be evaluated. Since exotic dark spinor fields also satisfy Klein-Gordon propagators, the dynamical constraints related to the exotic term in the Dirac equation can be explicitly calculated. It forthwith implies that the non-trivial topology associated to the spacetime can drastically engender — from the dynamics of dark spinor fields — constraints in the spacetime metric structure. Meanwhile, such constraints may be alleviated, at the cost of constraining the exotic spacetime topology. Besides being prime candidates to the dark matter problem, dark spinor fields are shown to be potential candidates to probe non-trivial topologies in spacetime, as well as probe the spacetime metric structure.

Correlation structures in short-term variabilities of stock indices and exchange rates

NASA Astrophysics Data System (ADS)

Nakamura, Tomomichi; Small, Michael

2007-09-01

Financial data usually show irregular fluctuations and some trends. We investigate whether there are correlation structures in short-term variabilities (irregular fluctuations) among financial data from the viewpoint of deterministic dynamical systems. Our method is based on the small-shuffle surrogate method. The data we use are daily closing price of Standard & Poor's 500 and the volume, and daily foreign exchange rates, Euro/US Dollar (USD), British Pound/USD and Japanese Yen/USD. We found that these data are not independent.

Relative role of different radii in the dynamics of 8B+58Ni reaction

NASA Astrophysics Data System (ADS)

Kaur, Amandeep; Sandhu, Kirandeep; Sharma, Manoj K.

2018-05-01

In the present work, we intend to analyze the significance of three different radius terms in the framework of dynamical cluster-decay model (DCM) based calculations. In the majority of DCM based calculations the impact of mass- dependent radius R(A) is extensively analyzed. The other two factors on which the radius term may depend are, the neutron- proton asymmetry and the charge of the decaying fragments. Hence, the asymmetry dependent radius term R(I) and charge dependent radius term R(Z) are incorporated in DCM based calculations to investigate their effect on the reaction dynamics involved. Here, we present an extension of an earlier work based on the decay of 66As* compound nucleus by including R(I) and R(Z) radii in addition to the R(A) term. The effect of replacement of R(A) with R(I) and R(Z) is analyzed via fragmentation structure, tunneling probabilities (P) and other barrier characteristics like barrier height (VB), barrier position (RB), barrier turning point Ra etc. The role of temperature, deformations and angular momentum is duly incorporated in the present calculations.

Impact of Hydrologic Variability on Ecosystem Dynamics and the Sustainable Use of Soil and Water Resources

NASA Astrophysics Data System (ADS)

Porporato, A. M.

2013-05-01

We discuss the key processes by which hydrologic variability affects the probabilistic structure of soil moisture dynamics in water-controlled ecosystems. These in turn impact biogeochemical cycling and ecosystem structure through plant productivity and biodiversity as well as nitrogen availability and soil conditions. Once the long-term probabilistic structure of these processes is quantified, the results become useful to understand the impact of climatic changes and human activities on ecosystem services, and can be used to find optimal strategies of water and soil resources management under unpredictable hydro-climatic fluctuations. Particular applications regard soil salinization, phytoremediation and optimal stochastic irrigation.

A new sensitivity analysis for structural optimization of composite rotor blades

NASA Technical Reports Server (NTRS)

Venkatesan, C.; Friedmann, P. P.; Yuan, Kuo-An

1993-01-01

This paper presents a detailed mathematical derivation of the sensitivity derivatives for the structural dynamic, aeroelastic stability and response characteristics of a rotor blade in hover and forward flight. The formulation is denoted by the term semianalytical approach, because certain derivatives have to be evaluated by a finite difference scheme. Using the present formulation, sensitivity derivatives for the structural dynamic and aeroelastic stability characteristics, were evaluated for both isotropic and composite rotor blades. Based on the results, useful conclusions are obtained regarding the relative merits of the semi-analytical approach, for calculating sensitivity derivatives, when compared to a pure finite difference approach.

Thin tailored composite wing for civil tiltrotor

NASA Technical Reports Server (NTRS)

Rais-Rohani, Masoud

1994-01-01

The tiltrotor aircraft is a flight vehicle which combines the efficient low speed (i.e., take-off, landing, and hover) characteristics of a helicopter with the efficient cruise speed of a turboprop airplane. A well-known example of such vehicle is the Bell-Boeing V-22 Osprey. The high cruise speed and range constraints placed on the civil tiltrotor require a relatively thin wing to increase the drag-divergence Mach number which translates into lower compressibility drag. It is required to reduce the wing maximum thickness-to-chord ratio t/c from 23% (i.e., V-22 wing) to 18%. While a reduction in wing thickness results in improved aerodynamic efficiency, it has an adverse effect on the wing structure and it tends to reduce structural stiffness. If ignored, the reduction in wing stiffness leads to susceptibility to aeroelastic and dynamic instabilities which may consequently cause a catastrophic failure. By taking advantage of the directional stiffness characteristics of composite materials the wing structure may be tailored to have the necessary stiffness, at a lower thickness, while keeping the weight low. The goal of this study is to design a wing structure for minimum weight subject to structural, dynamic and aeroelastic constraints. The structural constraints are in terms of strength and buckling allowables. The dynamic constraints are in terms of wing natural frequencies in vertical and horizontal bending and torsion. The aeroelastic constraints are in terms of frequency placement of the wing structure relative to those of the rotor system. The wing-rotor-pylon aeroelastic and dynamic interactions are limited in this design study by holding the cruise speed, rotor-pylon system, and wing geometric attributes fixed. To assure that the wing-rotor stability margins are maintained a more rigorous analysis based on a detailed model of the rotor system will need to ensue following the design study. The skin-stringer-rib type architecture is used for the wing-box structure. The design variables include upper and lower skin ply thicknesses and orientation angles, spar and rib web thicknesses and cap areas, and stringer cross-sectional areas. These design variables will allow the maximum tailoring of the structure to meet the design requirements most efficiently. Initial dynamic analysis has been conducted using MSC/NASTRAN to determine the baseline wing's frequencies and mode shapes. For the design study we intend to use the finite-element based code called WIDOWAC (Wing Design Optimization With Aeroeastic Constraints) that was developed at NASA Langley in early 1970's for airplane wing structural analysis and preliminary design. Currently, the focus is on modification and validation of this code which will be used for the civil tiltrotor design efforts.

Collaborative Research. Damage and Burst Dynamics in Failure of Complex Geomaterials. A Statistical Physics Approach to Understanding the Complex Emergent Dynamics in Near Mean-Field Geological Materials

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

Rundle, John B.; Klein, William

We have carried out research to determine the dynamics of failure in complex geomaterials, specifically focusing on the role of defects, damage and asperities in the catastrophic failure processes (now popularly termed “Black Swan events”). We have examined fracture branching and flow processes using models for invasion percolation, focusing particularly on the dynamics of bursts in the branching process. We have achieved a fundamental understanding of the dynamics of nucleation in complex geomaterials, specifically in the presence of inhomogeneous structures.

Gyrodampers for large space structures

NASA Technical Reports Server (NTRS)

Aubrun, J. N.; Margulies, G.

1979-01-01

The problem of controlling the vibrations of a large space structures by the use of actively augmented damping devices distributed throughout the structure is addressed. The gyrodamper which consists of a set of single gimbal control moment gyros which are actively controlled to extract the structural vibratory energy through the local rotational deformations of the structure, is described and analyzed. Various linear and nonlinear dynamic simulations of gyrodamped beams are shown, including results on self-induced vibrations due to sensor noise and rotor imbalance. The complete nonlinear dynamic equations are included. The problem of designing and sizing a system of gyrodampers for a given structure, or extrapolating results for one gyrodamped structure to another is solved in terms of scaling laws. Novel scaling laws for gyro systems are derived, based upon fundamental physical principles, and various examples are given.

Dynamic mechanical analysis and organization/storage of data for polymetric materials

NASA Technical Reports Server (NTRS)

Rosenberg, M.; Buckley, W.

1982-01-01

Dynamic mechanical analysis was performed on a variety of temperature resistant polymers and composite resin matrices. Data on glass transition temperatures and degree of cure attained were derived. In addition a laboratory based computer system was installed and data base set up to allow entry of composite data. The laboratory CPU termed TYCHO is based on a DEC PDP 11/44 CPU with a Datatrieve relational data base. The function of TYCHO is integration of chemical laboratory analytical instrumentation and storage of chemical structures for modeling of new polymeric structures and compounds

Mathematical model of the loan portfolio dynamics in the form of Markov chain considering the process of new customers attraction

NASA Astrophysics Data System (ADS)

Bozhalkina, Yana

2017-12-01

Mathematical model of the loan portfolio structure change in the form of Markov chain is explored. This model considers in one scheme both the process of customers attraction, their selection based on the credit score, and loans repayment. The model describes the structure and volume of the loan portfolio dynamics, which allows to make medium-term forecasts of profitability and risk. Within the model corrective actions of bank management in order to increase lending volumes or to reduce the risk are formalized.

Dynamic characteristics of specialty composite structures with embedded damping layers

NASA Technical Reports Server (NTRS)

Saravanos, D. A.; Chamis, C. C.

1993-01-01

Damping mechanics for simulating the damped dynamic characteristics in specialty composite structures with compliant interlaminar damping layers are presented. Finite-element based mechanics incorporating a discrete layer (or layer-wise) laminate damping theory are utilized to represent general laminate configurations in terms of lay-up and fiber orientation angles, cross-sectional thickness, shape, and boundary conditions. Evaluations of the method with exact solutions and experimental data illustrate the accuracy of the method. Additional applications investigate the potential for significant damping enhancement in angle-ply composite laminates with cocured interlaminar damping layers.

Structural dynamics division research and technology accomplishments for FY 1992 and plans for FY 1993

NASA Technical Reports Server (NTRS)

Wynne, Eleanor C.

1993-01-01

The purpose of this paper is to present the Structural Dynamics Division's research accomplishments for F.Y. 1992 and research plans for F.Y. 1993. The work under each Branch (technical area) is described in terms of highlights of accomplishments during the past year and highlights of plans for the current year as they relate to 5-year plans for each technical area. This information will be useful in program coordination with other government organizations and industry in areas of mutual interest.

The temporal representation of the delay of dynamic iterated rippled noise with positive and negative gain by single units in the ventral cochlear nucleus.

PubMed

Sayles, Mark; Winter, Ian Michael

2007-09-26

Spike trains were recorded from single units in the ventral cochlear nucleus of the anaesthetised guinea-pig in response to dynamic iterated rippled noise with positive and negative gain. The short-term running waveform autocorrelation functions of these stimuli show peaks at integer multiples of the time-varying delay when the gain is +1, and troughs at odd-integer multiples and peaks at even-integer multiples of the time-varying delay when the gain is -1. In contrast, the short-term autocorrelation of the Hilbert envelope shows peaks at integer multiples of the time-varying delay for both positive and negative gain stimuli. A running short-term all-order interspike interval analysis demonstrates the ability of single units to represent the modulated pitch contour in their short-term interval statistics. For units with low best frequency (approximate < or = 1.1 kHz) the temporal discharge pattern reflected the waveform fine structure regardless of unit classification (Primary-like, Chopper). For higher best frequency units the pattern of response varied according to unit type. Chopper units with best frequency approximate > or = 1.1 kHz responded to envelope modulation; showing no difference between their response to stimuli with positive and negative gain. Primary-like units with best frequencies in the range 1-3 kHz were still able to represent the difference in the temporal fine structure between dynamic rippled noise with positive and negative gain. No unit with a best frequency above 3 kHz showed a response to the temporal fine structure. Chopper units in this high frequency group showed significantly greater representation of envelope modulation relative to primary-like units with the same range of best frequencies. These results show that at the level of the cochlear nucleus there exists sufficient information in the time domain to represent the time-varying pitch associated with dynamic iterated rippled noise.

Radiation from quantum weakly dynamical horizons in loop quantum gravity.

PubMed

Pranzetti, Daniele

2012-07-06

We provide a statistical mechanical analysis of quantum horizons near equilibrium in the grand canonical ensemble. By matching the description of the nonequilibrium phase in terms of weakly dynamical horizons with a local statistical framework, we implement loop quantum gravity dynamics near the boundary. The resulting radiation process provides a quantum gravity description of the horizon evaporation. For large black holes, the spectrum we derive presents a discrete structure which could be potentially observable.

First order coupled dynamic model of flexible space structures with time-varying configurations

NASA Astrophysics Data System (ADS)

Wang, Jie; Li, Dongxu; Jiang, Jianping

2017-03-01

This paper proposes a first order coupled dynamic modeling method for flexible space structures with time-varying configurations for the purpose of deriving the characteristics of the system. The model considers the first time derivative of the coordinate transformation matrix between the platform's body frame and the appendage's floating frame. As a result it can accurately predict characteristics of the system even if flexible appendages rotate with complex trajectory relative to the rigid part. In general, flexible appendages are fixed on the rigid platform or forced to rotate with a slow angular velocity. So only the zero order of the transformation matrix is considered in conventional models. However, due to neglecting of time-varying terms of the transformation matrix, these models introduce severe error when appendages, like antennas, for example, rotate with a fast speed relative to the platform. The first order coupled dynamic model for flexible space structures proposed in this paper resolve this problem by introducing the first time derivative of the transformation matrix. As a numerical example, a central core with a rotating solar panel is considered and the results are compared with those given by the conventional model. It has been shown that the first order terms are of great importance on the attitude of the rigid body and dynamic response of the flexible appendage.

Electronic Excitation in Molecular Collisions: Structural, Dynamic and Kinetic Considerations.

DTIC Science & Technology

1981-08-01

electronically excited species are examined. The problem is studied both in general terms (i.e., the development of the required theoretical framework ) and in application to specific systems. (Author)

Electronic Excitation in Molecular Collisions: Structural, Dynamic and Kinetic Considerations.

DTIC Science & Technology

1980-09-01

electronically excited species are examined. The problem is studied both in general terms (i.e., the development of the required theoretical framework ) and in application to specific systems. (Author)

Electronic Excitation in Molecular Collisions: Structural, Dynamic and Kinetic Considerations.

DTIC Science & Technology

1979-09-01

electronically excited species are examined. The problem is studied both in general terms (i.e., the development of the required theoretical framework ) and in application to specific systems. (Author)

Electronic Excitation in Molecular Collisions: Structural, Dynamic and Kinetic Considerations.

DTIC Science & Technology

electronically excited specied are examined. The problem is studied both in general terms (i.e., the development of the required theoretical framework ) and in application to specific systems. (Author)

Time series analysis of forest carbon dynamics: recovery of Pinus palustris physiology following a prescribed fire

Treesearch

G. Starr; C. L. Staudhammer; H. W. Loescher; R. Mitchell; A. Whelan; J. K. Hiers; J. J. O’Brien

2015-01-01

Frequency and intensity of fire determines the structure and regulates the function of savanna ecosystems worldwide, yet our understanding of prescribed fire impacts on carbon in these systems is rudimentary. We combined eddy covariance (EC) techniques and fuel consumption plots to examine the short-term response of longleaf pine forest carbon dynamics to one...

Foam Optics and Mechanics

NASA Technical Reports Server (NTRS)

Durian, Douglas J.; Zimmerli, Gregory A.

2002-01-01

The Foam Optics and Mechanics (FOAM) project will exploit the microgravity environment to more accurately measure the rheological and optical characteristics of wet aqueous foams. Using both rheology and laser light scattering diagnostics, the goal is to quantify the unusual elastic character of foams in terms of their underlying microscopic structure and dynamics. Of particular interest is determining how the elastic character vanishes, i.e., how the foam 'melts' into a simple viscous liquid, as a function of both increasing liquid content and increasing shear strain rate. The unusual elastic character of foams will be quantified macroscopically by measurement of the shear stress as a function of shear strain rate and of time following a step strain. Such data will be analyzed in terms of a yield stress, shear moduli, and dynamical time scales. Microscopic information about bubble packing and rearrangement dynamics, from which the macroscopic non-Newtonian properties ultimately arise, will be obtained non-invasively by multiple-light scattering: diffuse transmission spectroscopy (DTS) and diffusing wave spectroscopy (DWS). Quantitative trends with materials parameters, most importantly average bubble size and liquid content, will be sought in order to elucidate the fundamental connection between the microscopic structure and dynamics and the macroscopic rheology.

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.

Dyonic Flux Tube Structure of Nonperturbative QCD Vacuum

NASA Astrophysics Data System (ADS)

Chandola, H. C.; Pandey, H. C.

We study the flux tube structure of the nonperturbative QCD vacuum in terms of its dyonic excitations by using an infrared effective Lagrangian and show that the dyonic condensation of QCD vacuum has a close connection with the process of color confinement. Using the fiber bundle formulation of QCD, the magnetic symmetry condition is presented in a gauge covariant form and the gauge potential has been constructed in terms of the magnetic vectors on global sections. The dynamical breaking of the magnetic symmetry has been shown to lead the dyonic condensation of QCD vacuum in the infrared energy sector. Deriving the asymptotic solutions of the field equations in the dynamically broken phase, the dyonic flux tube structure of QCD vacuum is explored which has been shown to lead the confinement parameters in terms of the vector and scalar mass modes of the condensed vacuum. Evaluating the charge quantum numbers and energy associated with the dyonic flux tube solutions, the effect of electric excitation of monopole is analyzed using the Regge slope parameter (as an input parameter) and an enhancement in the dyonic pair correlations and the confining properties of QCD vacuum in its dyonically condensed mode has been demonstrated.

The cultural implications of growth: Modeling nonlinear interaction of trait selection and population dynamics

NASA Astrophysics Data System (ADS)

Antoci, Angelo; Galeotti, Marcello; Russu, Paolo; Luigi Sacco, Pier

2018-05-01

In this paper, we study a nonlinear model of the interaction between trait selection and population dynamics, building on previous work of Ghirlanda et al. [Theor. Popul. Biol. 77, 181-188 (2010)] and Antoci et al. [Commun. Nonlinear Sci. Numer. Simul. 58, 92-106 (2018)]. We establish some basic properties of the model dynamics and present some simulations of the fine-grained structure of alternative dynamic regimes for chosen combinations of parameters. The role of the parameters that govern the reinforcement/corruption of maladaptive vs. adaptive traits is of special importance in determining the model's dynamic evolution. The main implication of this result is the need to pay special attention to the structural forces that may favor the emergence and consolidation of maladaptive traits in contemporary socio-economies, as it is the case, for example, for the stimulation of dysfunctional consumption habits and lifestyles in the pursuit of short-term profits.

The cultural implications of growth: Modeling nonlinear interaction of trait selection and population dynamics.

PubMed

Antoci, Angelo; Galeotti, Marcello; Russu, Paolo; Luigi Sacco, Pier

2018-05-01

In this paper, we study a nonlinear model of the interaction between trait selection and population dynamics, building on previous work of Ghirlanda et al. [Theor. Popul. Biol. 77, 181-188 (2010)] and Antoci et al. [Commun. Nonlinear Sci. Numer. Simul. 58, 92-106 (2018)]. We establish some basic properties of the model dynamics and present some simulations of the fine-grained structure of alternative dynamic regimes for chosen combinations of parameters. The role of the parameters that govern the reinforcement/corruption of maladaptive vs. adaptive traits is of special importance in determining the model's dynamic evolution. The main implication of this result is the need to pay special attention to the structural forces that may favor the emergence and consolidation of maladaptive traits in contemporary socio-economies, as it is the case, for example, for the stimulation of dysfunctional consumption habits and lifestyles in the pursuit of short-term profits.

The Dynamics and Inequality of Italian Men's Earnings: Long-Term Changes or Transitory Fluctuations?

ERIC Educational Resources Information Center

Cappellari, Lorenzo

2004-01-01

This paper provides a longitudinal perspective on changes in Italian men's earnings inequality since the late 1970s by decomposing the earnings autocovariance structure into its long-term and transitory parts. Cross-sectional earnings differentials grew over the period and the longitudinal analysis shows that such growth was determined by the…

Lipopolysaccharide Membrane Building and Simulation

PubMed Central

Jo, Sunhwan; Wu, Emilia L.; Stuhlsatz, Danielle; Klauda, Jeffery B.; Widmalm, Göran; Im, Wonpil

2015-01-01

Summary While membrane simulations are widely employed to study the structure and dynamics of various lipid bilayers and membrane proteins in the bilayers, simulations of lipopolysaccharides (LPS) in membrane environments have been limited due to its structural complexity, difficulties in building LPS-membrane systems, and lack of appropriate molecular force field. In this work, as a first step to extend CHARMM-GUI Membrane Builder to incorporate LPS molecules and to explore their structures and dynamics in membrane environments using molecular dynamics simulations, we describe step-by-step procedures to build LPS bilayer systems using CHARMM and the recently developed CHARMM carbohydrate and lipid force fields. Such procedures are illustrated by building various bilayers of Escherichia coli O6 LPS and their preliminary simulation results are given in terms of per-LPS area and density distributions of various components along the membrane normal. PMID:25753722

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

DOE PAGES

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

2016-12-27

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

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

PubMed

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

2017-01-10

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

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

PubMed

Hati, Sanchita; Bhattacharyya, Sudeep

2016-01-01

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

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

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

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

2015-09-21

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

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

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

Dynamic Load Predictions for Launchers Using Extra-Large Eddy Simulations X-Les

NASA Astrophysics Data System (ADS)

Maseland, J. E. J.; Soemarwoto, B. I.; Kok, J. C.

2005-02-01

Flow-induced unsteady loads can have a strong impact on performance and flight characteristics of aerospace vehicles and therefore play a crucial role in their design and operation. Complementary to costly flight tests and delicate wind-tunnel experiments, unsteady loads can be calculated using time-accurate Computational Fluid Dynamics. A capability to accurately predict the dynamic loads on aerospace structures at flight Reynolds numbers can be of great value for the design and analysis of aerospace vehicles. Advanced space launchers are subject to dynamic loads in the base region during the ascent to space. In particular the engine and nozzle experience aerodynamic pressure fluctuations resulting from massive flow separations. Understanding these phenomena is essential for performance enhancements for future launchers which operate a larger nozzle. A new hybrid RANS-LES turbulence modelling approach termed eXtra-Large Eddy Simulations (X-LES) holds the promise to capture the flow structures associated with massive separations and enables the prediction of the broad-band spectrum of dynamic loads. This type of method has become a focal point, reducing the cost of full LES, driven by the demand for their applicability in an industrial environment. The industrial feasibility of X-LES simulations is demonstrated by computing the unsteady aerodynamic loads on the main-engine nozzle of a generic space launcher configuration. The potential to calculate the dynamic loads is qualitatively assessed for transonic flow conditions in a comparison to wind-tunnel experiments. In terms of turn-around-times, X-LES computations are already feasible within the time-frames of the development process to support the structural design. Key words: massive separated flows; buffet loads; nozzle vibrations; space launchers; time-accurate CFD; composite RANS-LES formulation.

Long-term dynamics emerging in floodplains and deltas from the interactions between hydrology and society in a changing climate

NASA Astrophysics Data System (ADS)

Di Baldassarre, Giuliano; Viglione, Alberto; Yan, Kun; Brandimarte, Luigia; Blöschl, Günter

2014-05-01

Economic losses and fatalities associated to flood events have increased dramatically over the past decades. This situation might worsen in the near future because of rapid urbanization of many floodplains and deltas, along with enhancement of flood water levels as a result of human interventions, climate variability or sea level rise. To explore future dynamics, we developed a novel approach, which takes into account the dynamic nature of flood risk by an explicit treatment of the interactions and feedbacks between the hydrological and social components of flood risk (i.e. probability of flooding, and potential adverse consequences). In particular, we developed a socio-hydrological model that allows considering how the frequency and magnitude of flooding shapes the evolution of societies, while, at the same time, dynamic societies shape the frequency and magnitude of flooding. We then use this model to simulate long-term dynamics of different types of societies under hydrological change, e.g. increasing flood frequency. Based on the study of long-term dynamics of different floodplains and deltas around the world (e.g. Netherlands, Bangladesh), we identify two main typologies of flood-shaped societies: i) techno-societies, which "fight floods", and typically deal with risk by building and strengthening flood protection structures, such as levees or dikes; and ii) green-societies, which "lives with floods", and mainly cope with risk via adaptation measures, such as resettling out of flood prone areas. The outcomes of this study are relevant for the management of deltas and floodplains as they allow a comparison of long-term dynamics between diverse types of societies in terms of robustness to hydrological change.

Elements of the cellular metabolic structure

PubMed Central

De la Fuente, Ildefonso M.

2015-01-01

A large number of studies have demonstrated the existence of metabolic covalent modifications in different molecular structures, which are able to store biochemical information that is not encoded by DNA. Some of these covalent mark patterns can be transmitted across generations (epigenetic changes). Recently, the emergence of Hopfield-like attractor dynamics has been observed in self-organized enzymatic networks, which have the capacity to store functional catalytic patterns that can be correctly recovered by specific input stimuli. Hopfield-like metabolic dynamics are stable and can be maintained as a long-term biochemical memory. In addition, specific molecular information can be transferred from the functional dynamics of the metabolic networks to the enzymatic activity involved in covalent post-translational modulation, so that determined functional memory can be embedded in multiple stable molecular marks. The metabolic dynamics governed by Hopfield-type attractors (functional processes), as well as the enzymatic covalent modifications of specific molecules (structural dynamic processes) seem to represent the two stages of the dynamical memory of cellular metabolism (metabolic memory). Epigenetic processes appear to be the structural manifestation of this cellular metabolic memory. Here, a new framework for molecular information storage in the cell is presented, which is characterized by two functionally and molecularly interrelated systems: a dynamic, flexible and adaptive system (metabolic memory) and an essentially conservative system (genetic memory). The molecular information of both systems seems to coordinate the physiological development of the whole cell. PMID:25988183

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

PubMed

Wikan, Arild

2012-06-01

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

Structure and dynamics of the CrIII ion in aqueous solution: Ab initio QM/MM molecular dynamics simulation.

PubMed

Kritayakornupong, Chinapong; Plankensteiner, Kristof; Rode, Bernd M

2004-10-01

Structural and dynamical properties of the Cr(III) ion in aqueous solution have been investigated using a combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation. The hydration structure of Cr(III) was determined in terms of radial distribution functions, coordination numbers, and angular distributions. The QM/MM simulation gives coordination numbers of 6 and 15.4 for the first and second hydration shell, respectively. The first hydration shell is kinetically very inert but by no means rigid and variations of the first hydration shell geometry lead to distinct splitting in the vibrational spectra of Cr(H(2)O)(6) (3+). A mean residence time of 22 ps was obtained for water ligands residing in the second hydration shell, which is remarkably shorter than the experimentally estimated value. The hydration energy of -1108 +/- 7 kcal/mol, obtained from the QM/MM simulation, corresponds well to the experimental hydration enthalpy value. Copyright 2004 Wiley Periodicals, Inc.

Fokker-Planck description for the queue dynamics of large tick stocks.

PubMed

Garèche, A; Disdier, G; Kockelkoren, J; Bouchaud, J-P

2013-09-01

Motivated by empirical data, we develop a statistical description of the queue dynamics for large tick assets based on a two-dimensional Fokker-Planck (diffusion) equation. Our description explicitly includes state dependence, i.e., the fact that the drift and diffusion depend on the volume present on both sides of the spread. "Jump" events, corresponding to sudden changes of the best limit price, must also be included as birth-death terms in the Fokker-Planck equation. All quantities involved in the equation can be calibrated using high-frequency data on the best quotes. One of our central findings is that the dynamical process is approximately scale invariant, i.e., the only relevant variable is the ratio of the current volume in the queue to its average value. While the latter shows intraday seasonalities and strong variability across stocks and time periods, the dynamics of the rescaled volumes is universal. In terms of rescaled volumes, we found that the drift has a complex two-dimensional structure, which is a sum of a gradient contribution and a rotational contribution, both stable across stocks and time. This drift term is entirely responsible for the dynamical correlations between the ask queue and the bid queue.

Fokker-Planck description for the queue dynamics of large tick stocks

NASA Astrophysics Data System (ADS)

Garèche, A.; Disdier, G.; Kockelkoren, J.; Bouchaud, J.-P.

2013-09-01

Motivated by empirical data, we develop a statistical description of the queue dynamics for large tick assets based on a two-dimensional Fokker-Planck (diffusion) equation. Our description explicitly includes state dependence, i.e., the fact that the drift and diffusion depend on the volume present on both sides of the spread. “Jump” events, corresponding to sudden changes of the best limit price, must also be included as birth-death terms in the Fokker-Planck equation. All quantities involved in the equation can be calibrated using high-frequency data on the best quotes. One of our central findings is that the dynamical process is approximately scale invariant, i.e., the only relevant variable is the ratio of the current volume in the queue to its average value. While the latter shows intraday seasonalities and strong variability across stocks and time periods, the dynamics of the rescaled volumes is universal. In terms of rescaled volumes, we found that the drift has a complex two-dimensional structure, which is a sum of a gradient contribution and a rotational contribution, both stable across stocks and time. This drift term is entirely responsible for the dynamical correlations between the ask queue and the bid queue.

Optimal orbit transfer suitable for large flexible structures

NASA Technical Reports Server (NTRS)

Chatterjee, Alok K.

1989-01-01

The problem of continuous low-thrust planar orbit transfer of large flexible structures is formulated as an optimal control problem with terminal state constraints. The dynamics of the spacecraft motion are treated as a point-mass central force field problem; the thrust-acceleration magnitude is treated as an additional state variable; and the rate of change of thrust-acceleration is treated as a control variable. To ensure smooth transfer, essential for flexible structures, an additional quadratic term is appended to the time cost functional. This term penalizes any abrupt change in acceleration. Numerical results are presented for the special case of a planar transfer.

Resolving dispersion and induction components for polarisable molecular simulations of ionic liquids

NASA Astrophysics Data System (ADS)

Pádua, Agílio A. H.

2017-05-01

One important development in interaction potential models, or atomistic force fields, for molecular simulation is the inclusion of explicit polarisation, which represents the induction effects of charged or polar molecules on polarisable electron clouds. Polarisation can be included through fluctuating charges, induced multipoles, or Drude dipoles. This work uses Drude dipoles and is focused on room-temperature ionic liquids, for which fixed-charge models predict too slow dynamics. The aim of this study is to devise a strategy to adapt existing non-polarisable force fields upon addition of polarisation, because induction was already contained to an extent, implicitly, due to parametrisation against empirical data. Therefore, a fraction of the van der Waals interaction energy should be subtracted so that the Lennard-Jones terms only account for dispersion and the Drude dipoles for induction. Symmetry-adapted perturbation theory is used to resolve the dispersion and induction terms in dimers and to calculate scaling factors to reduce the Lennard-Jones terms from the non-polarisable model. Simply adding Drude dipoles to an existing fixed-charge model already improves the prediction of transport properties, increasing diffusion coefficients, and lowering the viscosity. Scaling down the Lennard-Jones terms leads to still faster dynamics and densities that match experiment extremely well. The concept developed here improves the overall prediction of density and transport properties and can be adapted to other models and systems. In terms of microscopic structure of the ionic liquids, the inclusion of polarisation and the down-scaling of Lennard-Jones terms affect only slightly the ordering of the first shell of counterions, leading to small decreases in coordination numbers. Remarkably, the effect of polarisation is major beyond first neighbours, significantly weakening spatial correlations, a structural effect that is certainly related to the faster dynamics of polarisable models.

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

Short-term effects of reduced-impact logging on Copaifera spp. (Fabaceae) regeneration in eastern Amazon

Treesearch

Carine Klauberg; Edson Vidal; Carlos Alberto Silva; Andrew Thomas Hudak; Manuela Oliveira; Pedro Higuchi

2017-01-01

Timber management directly influences the population dynamics of tree species, like Copaifera spp. (copaíba), which provide oil-resin with ecological and economic importance. The aim of this study was to evaluate the structure and population dynamics of Copaifera in unmanaged and managed stands by reduced-impact logging (RIL) in eastern Amazon in Pará state, Brazil....

Hurricane impacts on a pair of coastal forested watersheds: implications of selective hurricane damage to forest structure and streamflow dynamics

Treesearch

A.D. Jayakaran; T.M. Williams; H. Ssegane; D.M. Amatya; B. Song; C.C. Trettin

2014-01-01

Hurricanes are infrequent but influential disruptors of ecosystem processes in the southeastern Atlantic and Gulf coasts. Every southeastern forested wetland has the potential to be struck by a tropical cyclone. We examined the impact of Hurricane Hugo on two paired coastal South Carolina watersheds in terms of streamflow and vegetation dynamics, both before and after...

Structure and development of old-growth, unmanaged second-growth, and extended rotation Pinus resinosa forests in Minnesota, USA

USGS Publications Warehouse

Silver, Emily J.; D'Amato, Anthony W.; Fraver, Shawn; Palik, Brian J.; Bradford, John B.

2013-01-01

The structure and developmental dynamics of old-growth forests often serve as important baselines for restoration prescriptions aimed at promoting more complex structural conditions in managed forest landscapes. Nonetheless, long-term information on natural patterns of development is rare for many commercially important and ecologically widespread forest types. Moreover, the effectiveness of approaches recommended for restoring old-growth structural conditions to managed forests, such as the application of extended rotation forestry, has been little studied. This study uses several long-term datasets from old growth, extended rotation, and unmanaged second growth Pinus resinosa (red pine) forests in northern Minnesota, USA, to quantify the range of variation in structural conditions for this forest type and to evaluate the effectiveness of extended rotation forestry at promoting the development of late-successional structural conditions. Long-term tree population data from permanent plots for one of the old-growth stands and the extended rotation stands (87 and 61 years, respectively) also allowed for an examination of the long-term structural dynamics of these systems. Old-growth forests were more structurally complex than unmanaged second-growth and extended rotation red pine stands, due in large part to the significantly higher volumes of coarse woody debris (70.7 vs. 11.5 and 4.7 m3/ha, respectively) and higher snag basal area (6.9 vs. 2.9 and 0.5 m2/ha, respectively). In addition, old-growth forests, although red pine-dominated, contained a greater abundance of other species, including Pinus strobus, Abies balsamea, and Picea glauca relative to the other stand types examined. These differences between stand types largely reflect historic gap-scale disturbances within the old-growth systems and their corresponding structural and compositional legacies. Nonetheless, extended rotation thinning treatments, by accelerating advancement to larger tree diameter classes, generated diameter distributions more closely approximating those found in old growth within a shorter time frame than depicted in long-term examinations of old-growth structural development. These results suggest that extended rotation treatments may accelerate the development of old-growth structural characteristics, provided that coarse woody debris and snags are deliberately retained and created on site. These and other developmental characteristics of old-growth systems can inform forest management when objectives include the restoration of structural conditions found in late-successional forests.

Dynamics of American Universities. Research & Occasional Paper Series: CSHE.1.12

ERIC Educational Resources Information Center

Smelser, Neil J.

2012-01-01

The history of higher education has revealed all the forms of structural change associated with growth. The following focuses on a special form that involves growth, specialization, and proliferation, and applies mainly but not exclusively to universities. In search for a descriptive term, I have settled on the concept of "structural accretion," a…

Insights on Forest Structure and Composition from Long-Term Research in the Luquillo Mountains

Treesearch

Tamara Heartsill Scalley

2017-01-01

The science of ecology fundamentally aims to understand species and their relation to the environment. At sites where hurricane disturbance is part of the environmental context, permanent forest plots are critical to understand ecological vegetation dynamics through time. An overview of forest structure and species composition from two of the longest continuously...

A network of discrete events for the representation and analysis of diffusion dynamics.

PubMed

Pintus, Alberto M; Pazzona, Federico G; Demontis, Pierfranco; Suffritti, Giuseppe B

2015-11-14

We developed a coarse-grained description of the phenomenology of diffusive processes, in terms of a space of discrete events and its representation as a network. Once a proper classification of the discrete events underlying the diffusive process is carried out, their transition matrix is calculated on the basis of molecular dynamics data. This matrix can be represented as a directed, weighted network where nodes represent discrete events, and the weight of edges is given by the probability that one follows the other. The structure of this network reflects dynamical properties of the process of interest in such features as its modularity and the entropy rate of nodes. As an example of the applicability of this conceptual framework, we discuss here the physics of diffusion of small non-polar molecules in a microporous material, in terms of the structure of the corresponding network of events, and explain on this basis the diffusivity trends observed. A quantitative account of these trends is obtained by considering the contribution of the various events to the displacement autocorrelation function.

New Perspectives: Wave Mechanical Interpretations of Dark Matter, Baryon and Dark Energy

NASA Astrophysics Data System (ADS)

Russell, Esra

We model the cosmic components: dark matter, dark energy and baryon distributions in the Cosmic Web by means of highly nonlinear Schrodinger type and reaction diffusion type wave mechanical descriptions. The construction of these wave mechanical models of the structure formation is achieved by introducing the Fisher information measure and its comparison with highly nonlinear term which has dynamical analogy to infamous quantum potential in the wave equations. Strikingly, the comparison of this nonlinear term and the Fisher information measure provides a dynamical distinction between lack of self-organization and self-organization in the dynamical evolution of the cosmic components. Mathematically equivalent to the standard cosmic fluid equations, these approaches make it possible to follow the evolution of the matter distribution even into the highly nonlinear regime by circumventing singularities. Also, numerical realizations of the emerging web-like patterns are presented from the nonlinear dynamics of the baryon component while dark energy component shows Gaussian type dynamics corresponding to soliton-like solutions.

Determinants of Market Structure and the Airline Industry

NASA Technical Reports Server (NTRS)

Raduchel, W.

1972-01-01

The general economic determinants of market structure are outlined with special reference to the airline industry. Included are the following facets: absolute size of firms; distributions of firms by size; concentration; entry barriers; product and service differentiation; diversification; degrees of competition; vertical integration; market boundaries; and economies of scale. Also examined are the static and dynamic properties of market structure in terms of mergers, government policies, and economic growth conditions.

Simulation of Aircraft Engine Blade-Out Structural Dynamics

NASA Technical Reports Server (NTRS)

Lawrence, Charles; Carney, Kelly; Gallardo, Vicente

2001-01-01

A primary concern of aircraft structure designers is the accurate simulation of the blade-out event and the subsequent windmilling of the engine. Reliable simulations of the blade-out event are required to insure structural integrity during flight as well as to guarantee successful blade-out certification testing. The system simulation includes the lost blade loadings and the interactions between the rotating turbomachinery and the remaining aircraft structural components. General-purpose finite element structural analysis codes such as MSC NASTRAN are typically used and special provisions are made to include transient effects from the blade loss and rotational effects resulting from the engine's turbomachinery. The present study provides the equations of motion for rotordynamic response including the effect of spooldown speed and rotor unbalance and examines the effects of these terms on a cantilevered rotor. The effect of spooldown speed is found to be greater with increasing spooldown rate. The parametric term resulting from the mass unbalance has a more significant effect on the rotordynamic response than does the spooldown term. The parametric term affects both the peak amplitudes as well as the resonant frequencies of the rotor.

Simulation of Aircraft Engine Blade-Out Structural Dynamics. Revised

NASA Technical Reports Server (NTRS)

Lawrence, Charles; Carney, Kelly; Gallardo, Vicente

2001-01-01

A primary concern of aircraft structure designers is the accurate simulation of the blade-out event and the subsequent windmilling of the engine. Reliable simulations of the blade-out event are required to insure structural integrity during flight as well as to guarantee successful blade-out certification testing. The system simulation includes the lost blade loadings and the interactions between the rotating turbomachinery and the remaining aircraft structural components. General-purpose finite element structural analysis codes such as MSC NASTRAN are typically used and special provisions are made to include transient effects from the blade loss and rotational effects resulting from the engine's turbomachinery. The present study provides the equations of motion for rotordynamic response including the effect of spooldown speed and rotor unbalance and examines the effects of these terms on a cantilevered rotor. The effect of spooldown speed is found to be greater with increasing spooldown rate. The parametric term resulting from the mass unbalance has a more significant effect on the rotordynamic response than does the spooldown term. The parametric term affects both the peak amplitudes as well as the resonant frequencies of the rotor.

Fixed order dynamic compensation for multivariable linear systems

NASA Technical Reports Server (NTRS)

Kramer, F. S.; Calise, A. J.

1986-01-01

This paper considers the design of fixed order dynamic compensators for multivariable time invariant linear systems, minimizing a linear quadratic performance cost functional. Attention is given to robustness issues in terms of multivariable frequency domain specifications. An output feedback formulation is adopted by suitably augmenting the system description to include the compensator states. Either a controller or observer canonical form is imposed on the compensator description to reduce the number of free parameters to its minimal number. The internal structure of the compensator is prespecified by assigning a set of ascending feedback invariant indices, thus forming a Brunovsky structure for the nominal compensator.

The free and forced vibrations of structures using the finite dynamic element method. Ph.D. Thesis, Aug. 1991 Final Report

NASA Technical Reports Server (NTRS)

Fergusson, Neil J.

1992-01-01

In addition to an extensive review of the literature on exact and corrective displacement based methods of vibration analysis, a few theorems are proven concerning the various structural matrices involved in such analyses. In particular, the consistent mass matrix and the quasi-static mass matrix are shown to be equivalent, in the sense that the terms in their respective Taylor expansions are proportional to one another, and that they both lead to the same dynamic stiffness matrix when used with the appropriate stiffness matrix.

Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes.

PubMed

Lin, Milo M; Meinhold, Lars; Shorokhov, Dmitry; Zewail, Ahmed H

2008-08-07

A 2D free-energy landscape model is presented to describe the (un)folding transition of DNA/RNA hairpins, together with molecular dynamics simulations and experimental findings. The dependence of the (un)folding transition on the stem sequence and the loop length is shown in the enthalpic and entropic contributions to the free energy. Intermediate structures are well defined by the two coordinates of the landscape during (un)zipping. Both the free-energy landscape model and the extensive molecular dynamics simulations totaling over 10 mus predict the existence of temperature-dependent kinetic intermediate states during hairpin (un)zipping and provide the theoretical description of recent ultrafast temperature-jump studies which indicate that hairpin (un)zipping is, in general, not a two-state process. The model allows for lucid prediction of the collapsed state(s) in simple 2D space and we term it the kinetic intermediate structure (KIS) model.

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.

A Coupled Approach for Structural Damage Detection with Incomplete Measurements

NASA Technical Reports Server (NTRS)

James, George; Cao, Timothy; Kaouk, Mo; Zimmerman, David

2013-01-01

This historical work couples model order reduction, damage detection, dynamic residual/mode shape expansion, and damage extent estimation to overcome the incomplete measurements problem by using an appropriate undamaged structural model. A contribution of this work is the development of a process to estimate the full dynamic residuals using the columns of a spring connectivity matrix obtained by disassembling the structural stiffness matrix. Another contribution is the extension of an eigenvector filtering procedure to produce full-order mode shapes that more closely match the measured active partition of the mode shapes using a set of modified Ritz vectors. The full dynamic residuals and full mode shapes are used as inputs to the minimum rank perturbation theory to provide an estimate of damage location and extent. The issues associated with this process are also discussed as drivers of near-term development activities to understand and improve this approach.

On Cognition, Structured Sequence Processing, and Adaptive Dynamical Systems

NASA Astrophysics Data System (ADS)

Petersson, Karl Magnus

2008-11-01

Cognitive neuroscience approaches the brain as a cognitive system: a system that functionally is conceptualized in terms of information processing. We outline some aspects of this concept and consider a physical system to be an information processing device when a subclass of its physical states can be viewed as representational/cognitive and transitions between these can be conceptualized as a process operating on these states by implementing operations on the corresponding representational structures. We identify a generic and fundamental problem in cognition: sequentially organized structured processing. Structured sequence processing provides the brain, in an essential sense, with its processing logic. In an approach addressing this problem, we illustrate how to integrate levels of analysis within a framework of adaptive dynamical systems. We note that the dynamical system framework lends itself to a description of asynchronous event-driven devices, which is likely to be important in cognition because the brain appears to be an asynchronous processing system. We use the human language faculty and natural language processing as a concrete example through out.

Theoretical study of the Hoogsteen-Watson-Crick junctions in DNA.

PubMed

Cubero, Elena; Luque, F Javier; Orozco, Modesto

2006-02-01

A series of d (AT)(n) oligonucleotides containing mixtures of normal B-type Watson-Crick and antiparallel Hoogsteen helices have been studied using molecular dynamics simulation techniques to analyze the structural and thermodynamic impact of the junction between Watson-Crick and antiparallel Hoogsteen structures. Analysis of molecular dynamics simulations strongly suggests that for all oligonucleotides studied the antiparallel Hoogsteen appears as a reasonable conformation, only slightly less stable than the canonical B-type Watson-Crick one. The junctions between the Watson-Crick and Hoogsteen structures introduces a priori a sharp discontinuity in the helix, because the properties of each type of conformation are very well preserved in the corresponding fragments. However, and quite counterintuitively, junctions do not largely distort the duplex in structural, dynamics or energetic terms. Our results strongly support the possibility that small fragments of antiparallel Hoogsteen duplex might be embedded into large fragments of B-type Watson-Crick helices, making possible protein-DNA interactions that are specific of the antiparallel Hoogsteen conformation.

Theoretical Study of the Hoogsteen–Watson-Crick Junctions in DNA

PubMed Central

Cubero, Elena; Luque, F. Javier; Orozco, Modesto

2006-01-01

A series of d (AT)n oligonucleotides containing mixtures of normal B-type Watson-Crick and antiparallel Hoogsteen helices have been studied using molecular dynamics simulation techniques to analyze the structural and thermodynamic impact of the junction between Watson-Crick and antiparallel Hoogsteen structures. Analysis of molecular dynamics simulations strongly suggests that for all oligonucleotides studied the antiparallel Hoogsteen appears as a reasonable conformation, only slightly less stable than the canonical B-type Watson-Crick one. The junctions between the Watson-Crick and Hoogsteen structures introduces a priori a sharp discontinuity in the helix, because the properties of each type of conformation are very well preserved in the corresponding fragments. However, and quite counterintuitively, junctions do not largely distort the duplex in structural, dynamics or energetic terms. Our results strongly support the possibility that small fragments of antiparallel Hoogsteen duplex might be embedded into large fragments of B-type Watson-Crick helices, making possible protein-DNA interactions that are specific of the antiparallel Hoogsteen conformation. PMID:16287814

Scoring of Side-Chain Packings: An Analysis of Weight Factors and Molecular Dynamics Structures.

PubMed

Colbes, Jose; Aguila, Sergio A; Brizuela, Carlos A

2018-02-26

The protein side-chain packing problem (PSCPP) is a central task in computational protein design. The problem is usually modeled as a combinatorial optimization problem, which consists of searching for a set of rotamers, from a given rotamer library, that minimizes a scoring function (SF). The SF is a weighted sum of terms, that can be decomposed in physics-based and knowledge-based terms. Although there are many methods to obtain approximate solutions for this problem, all of them have similar performances and there has not been a significant improvement in recent years. Studies on protein structure prediction and protein design revealed the limitations of current SFs to achieve further improvements for these two problems. In the same line, a recent work reported a similar result for the PSCPP. In this work, we ask whether or not this negative result regarding further improvements in performance is due to (i) an incorrect weighting of the SFs terms or (ii) the constrained conformation resulting from the protein crystallization process. To analyze these questions, we (i) model the PSCPP as a bi-objective combinatorial optimization problem, optimizing, at the same time, the two most important terms of two SFs of state-of-the-art algorithms and (ii) performed a preprocessing relaxation of the crystal structure through molecular dynamics to simulate the protein in the solvent and evaluated the performance of these two state-of-the-art SFs under these conditions. Our results indicate that (i) no matter what combination of weight factors we use the current SFs will not lead to better performances and (ii) the evaluated SFs will not be able to improve performance on relaxed structures. Furthermore, the experiments revealed that the SFs and the methods are biased toward crystallized structures.

Form and function in gene regulatory networks: the structure of network motifs determines fundamental properties of their dynamical state space.

PubMed

Ahnert, S E; Fink, T M A

2016-07-01

Network motifs have been studied extensively over the past decade, and certain motifs, such as the feed-forward loop, play an important role in regulatory networks. Recent studies have used Boolean network motifs to explore the link between form and function in gene regulatory networks and have found that the structure of a motif does not strongly determine its function, if this is defined in terms of the gene expression patterns the motif can produce. Here, we offer a different, higher-level definition of the 'function' of a motif, in terms of two fundamental properties of its dynamical state space as a Boolean network. One is the basin entropy, which is a complexity measure of the dynamics of Boolean networks. The other is the diversity of cyclic attractor lengths that a given motif can produce. Using these two measures, we examine all 104 topologically distinct three-node motifs and show that the structural properties of a motif, such as the presence of feedback loops and feed-forward loops, predict fundamental characteristics of its dynamical state space, which in turn determine aspects of its functional versatility. We also show that these higher-level properties have a direct bearing on real regulatory networks, as both basin entropy and cycle length diversity show a close correspondence with the prevalence, in neural and genetic regulatory networks, of the 13 connected motifs without self-interactions that have been studied extensively in the literature. © 2016 The Authors.

Surface structure determines dynamic wetting.

PubMed

Wang, Jiayu; Do-Quang, Minh; Cannon, James J; Yue, Feng; Suzuki, Yuji; Amberg, Gustav; Shiomi, Junichiro

2015-02-16

Liquid wetting of a surface is omnipresent in nature and the advance of micro-fabrication and assembly techniques in recent years offers increasing ability to control this phenomenon. Here, we identify how surface roughness influences the initial dynamic spreading of a partially wetting droplet by studying the spreading on a solid substrate patterned with microstructures just a few micrometers in size. We reveal that the roughness influence can be quantified in terms of a line friction coefficient for the energy dissipation rate at the contact line, and that this can be described in a simple formula in terms of the geometrical parameters of the roughness and the line-friction coefficient of the planar surface. We further identify a criterion to predict if the spreading will be controlled by this surface roughness or by liquid inertia. Our results point to the possibility of selectively controlling the wetting behavior by engineering the surface structure.

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

NASA Astrophysics Data System (ADS)

Gao, Zilin; Wang, Yinhe; Zhang, Lili

2018-02-01

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

Low Dynamics, High Longevity and Persistence of Sessile Structural Species Dwelling on Mediterranean Coralligenous Outcrops

PubMed Central

Teixidó, Núria; Garrabou, Joaquim; Harmelin, Jean-George

2011-01-01

There is still limited understanding of the processes underlying benthic species dynamics in marine coastal habitats, which are of disproportionate importance in terms of productivity and biodiversity. The life-history traits of long-lived benthic species in these habitats are particularly poorly documented. In this study, we assessed decadal patterns of population dynamics for ten sponge and anthozoan species that play key structural roles in coralligenous outcrops (∼25 m depth) in two areas of the NW Mediterranean Sea. This study was based on examination of a unique long-term photographic series, which allowed analysis of population dynamics over extensive spatial and time spans for the very first time. Specifically, 671 individuals were censused annually over periods of 25-, 15-, and 5-years. This long-term study quantitatively revealed a common life-history pattern among the ten studied species, despite the fact they present different growth forms. Low mortality rates (3.4% yr−1 for all species combined) and infrequent recruitment events (mean value of 3.1±0.5 SE recruits yr−1) provided only a very small fraction of the new colonies required to maintain population sizes. Overall, annual mortality and recruitment rates did not differ significantly among years; however, some species displayed important mortality events and recruitment pulses, indicating variability among species. Based on the growth rates of these 10 species, we projected their longevity and, obtained a mean estimated age of 25–200 years. Finally, the low to moderate turnover rates (mean value 0.80% yr−1) observed among the coralligenous species were in agreement with their low dynamics and persistence. These results offer solid baseline data and reveal that these habitats are among the most vulnerable to the current increases of anthropogenic disturbances. PMID:21887308

Molecular dynamics study of thermodynamic scaling of the glass-transition dynamics in ionic liquids over wide temperature and pressure ranges.

PubMed

Habasaki, J; Casalini, R; Ngai, K L

2010-03-25

Experimentally, superpositioning of dynamic properties such as viscosity, relaxation times, or diffusion coefficients under different conditions of temperature T, pressure P, and volume V by the scaling variable TV(gamma) (where gamma is a material constant) has been reported as a general feature of many kinds of glass-forming materials. In the present work, molecular dynamics (MD) simulations have been performed to study the scaling of dynamics near the glass-transition regime of ionic liquids. Scaling in the simulated 1-ethyl-3-methylimidazolium nitrate (EMIM-NO(3)) system has been tested over wide ranges of temperatures and pressures. TV(gamma) scaling of the dynamics is well described by master curves with gamma = 4.0 +/- 0.2 and 3.8 +/- 0.2 for cation and anion, respectively. Structures and Coulombic terms of the corresponding states are found to be quite similar. The temperature and pressure dependence of the pair correlation function show similar trends and therefore can be superpositioned onto the master curve. Although the behaviors with gamma = 4 might be expected from the relation, gamma = n/3, for the dynamics with the soft-core-type potential U = epsilon(sigma/r)(n), with n = 12, pair potentials used in the MD simulation have a more complex form, and not all the repulsive terms can play their roles in the heterogeneous structures determined by ion-ion interactions. Scaling is related to the common part of effective potentials related to the pair correlation functions, including the many-body effect in real space.

Dielectric Properties of Poly(ethylene oxide) from Molecular Dynamics Simulations

NASA Technical Reports Server (NTRS)

Smith, Grant D.

1994-01-01

The order, conformations and dynamics of poly(oxyethylene) (POE) melts have been investigated through molecular dynamics simulations. The potential energy functions were determined from detailed ab initio electronic structure calculations of the conformational energies of the model molecules 1,2-dimethoxyethane (DME) and diethylether. The x-ray structure factor for POE from simulation will be compared to experiment. In terms of conformation, simulations reveal that chains are extended in the melt relative to isolated chains due to the presence of strong intermolecular O...H interactions, which occur at the expense of intramolecular O...H interactions. Conformational dynamics about the C-C bond were found to be significantly faster than in polymethylene, while conformational dynamics about the C-O bond even faster than the C-C dynamics. The faster local dynamics in POE relative to polymethylene is consistent with C-13 NMR spin-lattice relaxation experiments. Conformational transitions showed significant second-neighbor correlation, as was found for polymethylene. This correlation of transitions with C-C neighbors was found to be reduced relative to C-O neighbors. Dielectric relaxation from simulation will also be compared with experiment.

De Novo Proteins with Life-Sustaining Functions Are Structurally Dynamic.

PubMed

Murphy, Grant S; Greisman, Jack B; Hecht, Michael H

2016-01-29

Designing and producing novel proteins that fold into stable structures and provide essential biological functions are key goals in synthetic biology. In initial steps toward achieving these goals, we constructed a combinatorial library of de novo proteins designed to fold into 4-helix bundles. As described previously, screening this library for sequences that function in vivo to rescue conditionally lethal mutants of Escherichia coli (auxotrophs) yielded several de novo sequences, termed SynRescue proteins, which rescued four different E. coli auxotrophs. In an effort to understand the structural requirements necessary for auxotroph rescue, we investigated the biophysical properties of the SynRescue proteins, using both computational and experimental approaches. Results from circular dichroism, size-exclusion chromatography, and NMR demonstrate that the SynRescue proteins are α-helical and relatively stable. Surprisingly, however, they do not form well-ordered structures. Instead, they form dynamic structures that fluctuate between monomeric and dimeric states. These findings show that a well-ordered structure is not a prerequisite for life-sustaining functions, and suggests that dynamic structures may have been important in the early evolution of protein function. Copyright © 2015 Elsevier Ltd. All rights reserved.

Large space erectable structures - building block structures study

NASA Technical Reports Server (NTRS)

Armstrong, W. H.; Skoumal, D. E.; Straayer, J. W.

1977-01-01

A modular planar truss structure and a long slender boom concept identified as building block approaches to construction of large spacecraft configurations are described. The concepts are compatible in weight and volume goals with the Space Transportation System, use standard structural units, and represent high on-orbit productivity in terms of structural area or beam length. Results of structural trade studies involving static and dynamic analyses of a single module and rigid body deployment analyses to assess kinetics and kinematics of automatic deployment of the building block modules are presented.

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.

Estimation of beam material random field properties via sensitivity-based model updating using experimental frequency response functions

NASA Astrophysics Data System (ADS)

Machado, M. R.; Adhikari, S.; Dos Santos, J. M. C.; Arruda, J. R. F.

2018-03-01

Structural parameter estimation is affected not only by measurement noise but also by unknown uncertainties which are present in the system. Deterministic structural model updating methods minimise the difference between experimentally measured data and computational prediction. Sensitivity-based methods are very efficient in solving structural model updating problems. Material and geometrical parameters of the structure such as Poisson's ratio, Young's modulus, mass density, modal damping, etc. are usually considered deterministic and homogeneous. In this paper, the distributed and non-homogeneous characteristics of these parameters are considered in the model updating. The parameters are taken as spatially correlated random fields and are expanded in a spectral Karhunen-Loève (KL) decomposition. Using the KL expansion, the spectral dynamic stiffness matrix of the beam is expanded as a series in terms of discretized parameters, which can be estimated using sensitivity-based model updating techniques. Numerical and experimental tests involving a beam with distributed bending rigidity and mass density are used to verify the proposed method. This extension of standard model updating procedures can enhance the dynamic description of structural dynamic models.

Initial observations on tree mortality following a severe drought in 2012 in two Indiana state forests and implications for long-term compositional dynamics

Treesearch

Andrew R. Meier; Mike R. Saunders

2014-01-01

Compositional and structural changes in response to silvicultural treatments in forest stands are well documented (e.g., Saunders and Wagner 2008), but the stochastic nature of natural disturbance events often precludes direct observation of their impacts on stand dynamics. Though the current dominance of oak-hickory forest types in the Central Hardwoods Forest region...

Workshop on Closed System Ecology

NASA Technical Reports Server (NTRS)

1982-01-01

Self maintaining laboratory scale ecological systems completely isolated from exchanges of matter with external systems were demonstrated. These research tools are discussed in terms of their anticipated value in understanding (1) global ecological material and energy balances, (2) the dynamics of stability and instability in ecosystems, (3) the effects of man-made substances and structures on ecosystems, and (4) the precise requirements for dynamic control of controlled ecology life support systems (CELSS).

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.

Long-term spatiotemporal stability and dynamic changes in helminth infracommunities of bank voles (Myodes glareolus) in NE Poland.

PubMed

Grzybek, Maciej; Bajer, Anna; Bednarska, Małgorzata; Al-Sarraf, Mohammed; Behnke-Borowczyk, Jolanta; Harris, Philip D; Price, Stephen J; Brown, Gabrielle S; Osborne, Sarah-Jane; Siński, Edward; Behnke, Jerzy M

2015-12-01

Parasites are considered to be an important selective force in host evolution but ecological studies of host-parasite systems are usually short-term providing only snap-shots of what may be dynamic systems. We have conducted four surveys of helminths of bank voles at three ecologically similar woodland sites in NE Poland, spaced over a period of 11 years, to assess the relative importance of temporal and spatial effects on helminth infracommunities. Some measures of infracommunity structure maintained relative stability: the rank order of prevalence and abundance of Heligmosomum mixtum, Heligmosomoides glareoli and Mastophorus muris changed little between the four surveys. Other measures changed markedly: dynamic changes were evident in Syphacia petrusewiczi which declined to local extinction, while the capillariid Aonchotheca annulosa first appeared in 2002 and then increased in prevalence and abundance over the remaining three surveys. Some species are therefore dynamic and both introductions and extinctions can be expected in ecological time. At higher taxonomic levels and for derived measures, year and host-age effects and their interactions with site are important. Our surveys emphasize that the site of capture is the major determinant of the species contributing to helminth community structure, providing some predictability in these systems.

Towards the prediction of multiple necking during dynamic extension of round bar : linear stability approach versus finite element calculations

NASA Astrophysics Data System (ADS)

El Maï, S.; Mercier, S.; Petit, J.; Molinari, A.

2014-05-01

The fragmentation of structures subject to dynamic conditions is a matter of interest for civil industries as well as for Defence institutions. Dynamic expansions of structures, such as cylinders or rings, have been performed to obtain crucial information on fragment distributions. Many authors have proposed to capture by FEA the experimental distribution of fragment size by introducing in the FE model a perturbation. Stability and bifurcation analyses have also been proposed to describe the evolution of the perturbation growth rate. In the proposed contribution, the multiple necking of a round bar in dynamic tensile loading is analysed by the FE method. A perturbation on the initial flow stress is introduced in the numerical model to trigger instabilities. The onset time and the dominant mode of necking have been characterized precisely and showed power law evolutions, with the loading velocities and moderately with the amplitudes and the cell sizes of the perturbations. In the second part of the paper, the development of linear stability analysis and the use of salient criteria in terms of the growth rate of perturbations enabled comparisons with the numerical results. A good correlation in terms of onset time of instabilities and of number of necks is shown.

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.

Host Resistance, Population Structure and the Long-Term Persistence of Bubonic Plague: Contributions of a Modelling Approach in the Malagasy Focus

PubMed Central

Gascuel, Fanny; Choisy, Marc; Duplantier, Jean-Marc; Débarre, Florence; Brouat, Carine

2013-01-01

Although bubonic plague is an endemic zoonosis in many countries around the world, the factors responsible for the persistence of this highly virulent disease remain poorly known. Classically, the endemic persistence of plague is suspected to be due to the coexistence of plague resistant and plague susceptible rodents in natural foci, and/or to a metapopulation structure of reservoirs. Here, we test separately the effect of each of these factors on the long-term persistence of plague. We analyse the dynamics and equilibria of a model of plague propagation, consistent with plague ecology in Madagascar, a major focus where this disease is endemic since the 1920s in central highlands. By combining deterministic and stochastic analyses of this model, and including sensitivity analyses, we show that (i) endemicity is favoured by intermediate host population sizes, (ii) in large host populations, the presence of resistant rats is sufficient to explain long-term persistence of plague, and (iii) the metapopulation structure of susceptible host populations alone can also account for plague endemicity, thanks to both subdivision and the subsequent reduction in the size of subpopulations, and extinction-recolonization dynamics of the disease. In the light of these results, we suggest scenarios to explain the localized presence of plague in Madagascar. PMID:23675291

Host resistance, population structure and the long-term persistence of bubonic plague: contributions of a modelling approach in the Malagasy focus.

PubMed

Gascuel, Fanny; Choisy, Marc; Duplantier, Jean-Marc; Débarre, Florence; Brouat, Carine

2013-01-01

Although bubonic plague is an endemic zoonosis in many countries around the world, the factors responsible for the persistence of this highly virulent disease remain poorly known. Classically, the endemic persistence of plague is suspected to be due to the coexistence of plague resistant and plague susceptible rodents in natural foci, and/or to a metapopulation structure of reservoirs. Here, we test separately the effect of each of these factors on the long-term persistence of plague. We analyse the dynamics and equilibria of a model of plague propagation, consistent with plague ecology in Madagascar, a major focus where this disease is endemic since the 1920s in central highlands. By combining deterministic and stochastic analyses of this model, and including sensitivity analyses, we show that (i) endemicity is favoured by intermediate host population sizes, (ii) in large host populations, the presence of resistant rats is sufficient to explain long-term persistence of plague, and (iii) the metapopulation structure of susceptible host populations alone can also account for plague endemicity, thanks to both subdivision and the subsequent reduction in the size of subpopulations, and extinction-recolonization dynamics of the disease. In the light of these results, we suggest scenarios to explain the localized presence of plague in Madagascar.

Through-Space Ultrafast Photoinduced Electron Transfer Dynamics of a C 70 -Encapsulated Bisporphyrin Covalent Organic Polyhedron in a Low-Dielectric Medium

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

Ortiz, Michael; Cho, Sung; Niklas, Jens

Ultrafast photoinduced electron transfer (PIET) dynamics of a C 70-encapsulated bisporphyrin covalent organic polyhedron hybrid (C 70@COP-5) is studied in a nonpolar toluene medium with fluorescence and transient absorption spectroscopies. This structurally rigid donor (D)-acceptor (A) molecular hybrid offers a new platform featuring conformationally predetermined cofacial D-A orientation with a fixed edge-to-edge separation, R EE (2.8 Å), without the aid of covalent bonds. Sub-picosecond PIET (T ET ≤ 0.4 ps) and very slow charge recombination (T CR ≈ 600 ps) dynamics are observed. The origin of these dynamics is discussed in terms of enhanced D-A coupling (V = 675 cmmore » -1) and extremely small reorganization energy (λ ≈ 0.18 eV), induced by the intrinsic structural rigidity of the C 70@COP-5 complex.« less

Structural, dynamic and photophysical properties of a fluorescent dye incorporated in an amorphous hydrophobic polymer bundle.

PubMed

De Mitri, N; Prampolini, G; Monti, S; Barone, V

2014-08-21

The properties of a low molecular weight organic dye, namely 4-naphthyloxy-1-methoxy-2,2,6,6-tetramethylpiperidine, covalently bound to an apolar polyolefin were investigated by means of a multi-level approach, combining classical molecular dynamics simulations, based on purposely parameterized force fields, and quantum mechanical calculations based on density functional theory (DFT) and its time-dependent extension (TD-DFT). The structure and dynamics of the dye in its embedding medium were analyzed and discussed taking the entangling effect of the surrounding polymer into account, and also by comparing the results to those obtained for a different environment, i.e. toluene solution. Finally, the influence was investigated of long lived cages found in the polymeric embedding on photophysical properties, in terms of the slow and fast dye's internal dynamics, by comparing computed IR and UV spectra with their experimental counterparts.

Through-Space Ultrafast Photoinduced Electron Transfer Dynamics of a C 70 -Encapsulated Bisporphyrin Covalent Organic Polyhedron in a Low-Dielectric Medium

DOE PAGES

Ortiz, Michael; Cho, Sung; Niklas, Jens; ...

2017-03-13

Ultrafast photoinduced electron transfer (PIET) dynamics of a C 70-encapsulated bisporphyrin covalent organic polyhedron hybrid (C 70@COP-5) is studied in a nonpolar toluene medium with fluorescence and transient absorption spectroscopies. This structurally rigid donor (D)-acceptor (A) molecular hybrid offers a new platform featuring conformationally predetermined cofacial D-A orientation with a fixed edge-to-edge separation, R EE (2.8 Å), without the aid of covalent bonds. Sub-picosecond PIET (T ET ≤ 0.4 ps) and very slow charge recombination (T CR ≈ 600 ps) dynamics are observed. The origin of these dynamics is discussed in terms of enhanced D-A coupling (V = 675 cmmore » -1) and extremely small reorganization energy (λ ≈ 0.18 eV), induced by the intrinsic structural rigidity of the C 70@COP-5 complex.« less

Through-Space Ultrafast Photoinduced Electron Transfer Dynamics of a C70-Encapsulated Bisporphyrin Covalent Organic Polyhedron in a Low-Dielectric Medium.

PubMed

Ortiz, Michael; Cho, Sung; Niklas, Jens; Kim, Seonah; Poluektov, Oleg G; Zhang, Wei; Rumbles, Garry; Park, Jaehong

2017-03-29

Ultrafast photoinduced electron transfer (PIET) dynamics of a C 70 -encapsulated bisporphyrin covalent organic polyhedron hybrid (C 70 @COP-5) is studied in a nonpolar toluene medium with fluorescence and transient absorption spectroscopies. This structurally rigid donor (D)-acceptor (A) molecular hybrid offers a new platform featuring conformationally predetermined cofacial D-A orientation with a fixed edge-to-edge separation, R EE (2.8 Å), without the aid of covalent bonds. Sub-picosecond PIET (τ ET ≤ 0.4 ps) and very slow charge recombination (τ CR ≈ 600 ps) dynamics are observed. The origin of these dynamics is discussed in terms of enhanced D-A coupling (V = 675 cm -1 ) and extremely small reorganization energy (λ ≈ 0.18 eV), induced by the intrinsic structural rigidity of the C 70 @COP-5 complex.

Birefringence imaging directly reveals architectural dynamics of filamentous actin in living growth cones.

PubMed

Katoh, K; Hammar, K; Smith, P J; Oldenbourg, R

1999-01-01

We have investigated the dynamic behavior of cytoskeletal fine structure in the lamellipodium of nerve growth cones using a new type of polarized light microscope (the Pol-Scope). Pol-Scope images display with exquisite resolution and definition birefringent fine structures, such as filaments and membranes, without having to treat the cell with exogenous dyes or fluorescent labels. Furthermore, the measured birefringence of protein fibers in the thin lamellipodial region can be interpreted in terms of the number of filaments in the bundles. We confirmed that birefringent fibers are actin-based using conventional fluorescence-labeling methods. By recording movies of time-lapsed Pol-Scope images, we analyzed the creation and dynamic composition of radial fibers, filopodia, and intrapodia in advancing growth cones. The strictly quantitative information available in time-lapsed Pol-Scope images confirms previously deduced behavior and provides new insight into the architectural dynamics of filamentous actin.

Using Dynamic Risk and Protective Factors to Predict Inpatient Aggression: Reliability and Validity of START Assessments

ERIC Educational Resources Information Center

Desmarais, Sarah L.; Nicholls, Tonia L.; Wilson, Catherine M.; Brink, Johann

2012-01-01

The Short-Term Assessment of Risk and Treatability (START; C. D. Webster, M. L. Martin, J. Brink, T. L. Nicholls, & S. L. Desmarais, 2009; C. D. Webster, M. L. Martin, J. Brink, T. L. Nicholls, & C. Middleton, 2004) is a relatively new structured professional judgment guide for the assessment and management of short-term risks associated…

Saying Good-by: An Example of Using a Good-by Technique and Concomitant Psychodrama in the Resolving of Family Grief.

ERIC Educational Resources Information Center

Kaminski, Robert C.

A structured technique for saying "good-bye," or terminating a relationship, an important aspect of the therapeutic relationship, is presented. It consists of three distinct phases that are all dynamically interrelated, and can also be structured into separation caused by death. The technique is described in terms of three specific areas…

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...

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

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

Leoni, Fabio; Franzese, Giancarlo

2014-11-07

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

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

PubMed

Leoni, Fabio; Franzese, Giancarlo

2014-11-07

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

Local structural mechanism for frozen-in dynamics in metallic glasses

NASA Astrophysics Data System (ADS)

Liu, X. J.; Wang, S. D.; Wang, H.; Wu, Y.; Liu, C. T.; Li, M.; Lu, Z. P.

2018-04-01

The nature of the glass transition is a fundamental and long-standing intriguing issue in the condensed-matter physics and materials science community. In particular, the structural response by which a liquid is arrested dynamically to form a glass or amorphous solid upon approaching its freezing temperature [the glass transition temperature (Tg)] remains unclear. Various structural scenarios in terms of the percolation theory have been proposed recently to understand such a phenomenon; however, there is still no consensus on what the general percolation entity is and how the entity responds to the sudden slowdown dynamics during the glass transition. In this paper, we demonstrate that one-dimensional local linear ordering (LLO) is a universal structural motif associated with the glass transition for various metallic glasses. The quantitative evolution of LLO with temperature indicates that a percolating LLO network forms to serve as the backbone of the rigid glass solid when the temperature approaches the freezing point, resulting in the frozen-in dynamics accompanying the glass transition. The percolation transition occurs by pinning different LLO networks together, which only needs the introduction of a small number of "joint" atoms between them, and therefore the energy expenditure is very low.

Precision pointing and control of flexible spacecraft

NASA Technical Reports Server (NTRS)

Bantell, M. H., Jr.

1987-01-01

The problem and long term objectives for the precision pointing and control of flexible spacecraft are given. The four basic objectives are stated in terms of two principle tasks. Under Task 1, robust low order controllers, improved structural modeling methods for control applications and identification methods for structural dynamics are being developed. Under Task 2, a lab test experiment for verification of control laws and system identification algorithms is being developed. For Task 1, work has focused on robust low order controller design and some initial considerations for structural modeling in control applications. For Task 2, work has focused on experiment design and fabrication, along with sensor selection and initial digital controller implementation. Conclusions are given.

Long-Term Plasticity of Neurotransmitter Release: Emerging Mechanisms and Contributions to Brain Function and Disease.

PubMed

Monday, Hannah R; Younts, Thomas J; Castillo, Pablo E

2018-04-25

Long-lasting changes of brain function in response to experience rely on diverse forms of activity-dependent synaptic plasticity. Chief among them are long-term potentiation and long-term depression of neurotransmitter release, which are widely expressed by excitatory and inhibitory synapses throughout the central nervous system and can dynamically regulate information flow in neural circuits. This review article explores recent advances in presynaptic long-term plasticity mechanisms and contributions to circuit function. Growing evidence indicates that presynaptic plasticity may involve structural changes, presynaptic protein synthesis, and transsynaptic signaling. Presynaptic long-term plasticity can alter the short-term dynamics of neurotransmitter release, thereby contributing to circuit computations such as novelty detection, modifications of the excitatory/inhibitory balance, and sensory adaptation. In addition, presynaptic long-term plasticity underlies forms of learning and its dysregulation participates in several neuropsychiatric conditions, including schizophrenia, autism, intellectual disabilities, neurodegenerative diseases, and drug abuse. Expected final online publication date for the Annual Review of Neuroscience Volume 41 is July 8, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Molecular dynamics of individual alpha-helices of bacteriorhodopsin in dimyristol phosphatidylocholine. I. Structure and dynamics.

PubMed

Woolf, T B

1997-11-01

Understanding the role of the lipid bilayer in membrane protein structure and dynamics is needed for tertiary structure determination methods. However, the molecular details are not well understood. Molecular dynamics computer calculations can provide insight into these molecular details of protein:lipid interactions. This paper reports on 10 simulations of individual alpha-helices in explicit lipid bilayers. The 10 helices were selected from the bacteriorhodopsin structure as representative alpha-helical membrane folding components. The bilayer is constructed of dimyristoyl phosphatidylcholine molecules. The only major difference between simulations is the primary sequence of the alpha-helix. The results show dramatic differences in motional behavior between alpha-helices. For example, helix A has much smaller root-mean-squared deviations than does helix D. This can be understood in terms of the presence of aromatic residues at the interface for helix A that are not present in helix D. Additional motions are possible for the helices that contain proline side chains relative to other amino acids. The results thus provide insight into the types of motion and the average structures possible for helices within the bilayer setting and demonstrate the strength of molecular simulations in providing molecular details that are not directly visualized in experiments.

Direct Prediction of EPR Spectra from Lipid Bilayers: Understanding Structure and Dynamics in Biological Membranes.

PubMed

Catte, Andrea; White, Gaye F; Wilson, Mark R; Oganesyan, Vasily S

2018-06-02

Of the many biophysical techniques now being brought to bear on studies of membranes, electron paramagnetic resonance (EPR) of nitroxide spin probes was the first to provide information about both mobility and ordering in lipid membranes. Here, we report the first prediction of variable temperature EPR spectra of model lipid bilayers in the presence and absence of cholesterol from the results of large scale fully atomistic molecular dynamics (MD) simulations. Three types of structurally different spin probes were employed in order to study different parts of the bilayer. Our results demonstrate very good agreement with experiment and thus confirm the accuracy of the latest lipid force fields. The atomic resolution of the simulations allows the interpretation of the molecular motions and interactions in terms of their impact on the sensitive EPR line shapes. Direct versus indirect effects of cholesterol on the dynamics of spin probes are analysed. Given the complexity of structural organisation in lipid bilayers, the advantage of using a combined MD-EPR simulation approach is two-fold. Firstly, prediction of EPR line shapes directly from MD trajectories of actual phospholipid structures allows unambiguous interpretation of EPR spectra of biological membranes in terms of complex motions. Secondly, such an approach provides an ultimate test bed for the up-to-date MD simulation models employed in the studies of biological membranes, an area that currently attracts great attention. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dynamic instabilities in strongly correlated VSe2 monolayers and bilayers

NASA Astrophysics Data System (ADS)

Esters, Marco; Hennig, Richard G.; Johnson, David C.

2017-12-01

With the emergence of graphene and other two-dimensional (2D) materials, transition-metal dichalcogenides have been investigated intensely as potential 2D materials using experimental and theoretical methods. VSe2 is an especially interesting material since its bulk modification exhibits a charge-density wave (CDW), the CDW is retained even for few-layer nanosheets, and monolayers of VSe2 are predicted to be ferromagnetic. In this work, we show that electron correlation has a profound effect on the magnetic properties and dynamic stability of VSe2 monolayers and bilayers. Including a Hubbard-U term in the density-functional-theory calculations strongly affects the magnetocrystalline anisotropy in the 1 T -VSe2 structure while leaving the 2 H -polytype virtually unchanged. This demonstrates the importance of electronic correlations for the electrical and magnetic properties of 1 T -VSe2 . The Hubbard-U term changes the dynamic stability and the presence of imaginary modes of ferromagnetic 1 T -VSe2 while affecting only the amplitudes in the nonmagnetic phase. The Fermi surface of nonmagnetic 1 T -VSe2 allows for nesting along the CDW vector, but it plays no role in ferromagnetic 1 T -VSe2 . Following the eigenvectors of the soft modes in nonmagnetic 1 T -VSe2 monolayers yields a CDW structure with a 4 ×4 supercell and Peierls-type distortion in the atomic positions and electronic structure. The magnetic order indicates the potential for spin-density-wave structures.

Rethinking the logistic approach for population dynamics of mutualistic interactions.

PubMed

García-Algarra, Javier; Galeano, Javier; Pastor, Juan Manuel; Iriondo, José María; Ramasco, José J

2014-12-21

Mutualistic communities have an internal structure that makes them resilient to external perturbations. Late research has focused on their stability and the topology of the relations between the different organisms to explain the reasons of the system robustness. Much less attention has been invested in analyzing the systems dynamics. The main population models in use are modifications of the r-K formulation of logistic equation with additional terms to account for the benefits produced by the interspecific interactions. These models have shortcomings as the so-called r-K formulation diverges under some conditions. In this work, we introduce a model for population dynamics under mutualism that preserves the original logistic formulation. It is mathematically simpler than the widely used type II models, although it shows similar complexity in terms of fixed points and stability of the dynamics. We perform an analytical stability analysis and numerical simulations to study the model behavior in general interaction scenarios including tests of the resilience of its dynamics under external perturbations. Despite its simplicity, our results indicate that the model dynamics shows an important richness that can be used to gain further insights in the dynamics of mutualistic communities. Copyright © 2014 Elsevier Ltd. All rights reserved.

Social structure affects mating competition in a damselfish

NASA Astrophysics Data System (ADS)

Wacker, Sebastian; Ness, Miriam Horstad; Östlund-Nilsson, Sara; Amundsen, Trond

2017-12-01

The strength of mating competition and sexual selection varies over space and time in many animals. Such variation is typically driven by ecological and demographic factors, including adult sex ratio and consequent availability of mates. The spatial scale at which demographic factors affect mating competition and sexual selection may vary but is not often investigated. Here, we analyse variation in size and sex ratio of social groups, and how group structure affects mating competition, in the site-attached damselfish Chrysiptera cyanea. Site-attached reef fishes are known to show extensive intraspecific variation in social structure. Previous work has focused on species for which the size and dynamics of social groups are constrained by habitat, whereas species with group structure unconstrained by habitat have received little attention. Chrysiptera cyanea is such a species, with individuals occurring in spatial clusters that varied widely in size and sex ratio. Typically, only one male defended a nest in multi-male groups. Nest-holding males were frequently visited by mate-searching females, with more visits in groups with more females, suggesting that courtship and mating mostly occur within groups and that male mating success depends on the number of females in the group. Male-male aggression was frequent in multi-male groups but absent in single-male groups. These findings demonstrate that groups are distinct social units. In consequence, the dynamics of mating and reproduction are mainly a result of group structure, largely unaffected short term by overall population demography which would be important in open social systems. Future studies of the C. cyanea model system should analyse longer-term dynamics, including how groups are formed, how they vary in relation to density and time of season and how social structure affects sexual selection.

Structure and property relations of macromolecular self-assemblies at interfaces

NASA Astrophysics Data System (ADS)

Yang, Zhihao

Hydrophilic polymer chains, poly(ethylene glycol) (PEG), are attached to glass surfaces by silylation of the silanol groups on glass surfaces with the omega-(methoxyl terminated PEG) trimethoxysilanes. These tethered polymer chains resemble the self-assembled monolayers (SAMs) of PEG, which exhibit excellent biocompatibility and provide a model system for studying the interactions of proteins with polymer surfaces. The low molecular weight PEGs tend to extend, forming a brush-like monolayer, whereas the longer polymer chains tend to interpenetrate each other, forming a mushroom-like PEG monolayer at the interface. Interactions between a plasma protein, bovine serum albumin, and the PEG-SAMs are investigated in terms of protein adsorption and diffusion on the surfaces by the technique of fluorescence recovery after photobleaching (FRAP). The diffusion and aggregation behaviors of the protein on the two monolayers are found to be quite different despite the similarities in adsorption and desorption behaviors. The results are analyzed with a hypothesis of the hydrated surface dynamics. A method of covalently bonding phospholipid molecules to silica substrates followed by loading with free phospholipids is demonstrated to form well organized and stable phospholipid self-assembled monolayers. Surfaces of such SAMs structurally mimic the aqueous sides of phospholipid bilayer membranes. The dynamics of phospholipids and an adsorbed protein, lipase, in the SAMs are probed with FRAP, in terms of lateral diffusion of both phospholipids and protein molecules. The esterase activity of lipase on the SAM surfaces is confirmed by the hydrolysis reaction of a substrate, umbelliferone stearate, showing such lipid SAMs posess biomembrane functionality in terms of interfacial activation of the membranous enzymes. Dynamics of polyethylene oxide and polypropylene oxide tri-block copolymers, PEO-PPO-PEO and PPO-PEO-PPO, at the air/water interface upon thermal stimulation is studied by surface light scattering, in terms of the dynamic surface tension changes in response to a temperature jump. The characteristic of the surface tension relaxation is found to be highly related to the molecular structure and concentration of the copolymers at the interface.

Nuclear quantum fluctuations in ice I(h).

PubMed

Moreira, Pedro Augusto Franco Pinheiro; de Koning, Maurice

2015-10-14

We discuss the role of nuclear quantum fluctuations in ice Ih, focusing on the hydrogen-bond (HB) structure and the molecular dipole-moment distribution. For this purpose we carry out DFT-based first-principles molecular dynamics and path-integral molecular dynamics simulations at T = 100 K. We analyze the HB structure in terms of a set of parameters previously employed to characterize molecular structures in the liquid phase and compute the molecular dipole moments using the maximally-localized Wannier functions. The results show that the protons experience very large digressions driven by quantum fluctuations, accompanied by major rearrangements in the electronic density. As a result of these protonic quantum fluctuations the molecular dipole-moment distribution is substantially broadened as well as shifted to a larger mean value when compared to the results obtained when such fluctuations are neglected. In terms of dielectric constants, the reconciliation between the greater mean dipole moment and experimental indications that the dielectric constant of H2O ice is lower than that of D2O ice would indicate that the topology of the HB network is sensitive to protonic quantum fluctuations.

The Phase Space Structure Near Neptune Resonances in the Kuiper Belt

NASA Technical Reports Server (NTRS)

Malhotra, Renu

1996-01-01

The Solar system beyond Neptune is believed to house a population of small primordial bodies left over from the planet formation process. The region up to heliocentric distance -50 AU (a.k.a. the Kuiper Belt) may be the source of the observed short-period comets. In this region, the phase space structure near orbital resonances with Neptune is of special interest for the long-term stability of orbits. There is reason to believe that a significant fraction (perhaps most) of the Kuiper Belt objects reside preferentially in these resonance locations. This paper describes the dynamics of small objects near the major orbital resonances with Neptune. Estimates of the widths of stable resonance zones as well as the properties of resonant orbits are obtained from the circular, planar restricted three-body model. Although this model does not contain the full complexity of the long-term orbital dynamics of Kuiper Belt objects subject to the full N-body perturbations of all the planets, it does provide a baseline for the phase space structure and properties of resonant orbits in the trans-Neptunian Solar system.

Structural impact analysis of missense SNPs present in the uroguanylin gene by long-term molecular dynamics simulations.

PubMed

Marcolino, Antonio C S; Porto, William F; Pires, Állan S; Franco, Octavio L; Alencar, Sérgio A

2016-12-07

The guanylate cyclase activator 2B, also known as uroguanylin, is part of the guanylin peptide family, which includes peptides such as guanylin and lymphoguanylin. The guanylin peptides could be related to sodium absorption inhibition and water secretion induction and their dysfunction may be related to various pathologies such as chronic renal failure, congestive heart failure and nephrotic syndrome. Besides, uroguanylin point mutations have been associated with essential hypertension. However, currently there are no studies on the impact of missense SNPs on uroguanylin structure. This study applied in silico SNP impact prediction tools to evaluate the impact of uroguanylin missense SNPs and to filter those considered as convergent deleterious, which were then further analyzed through long-term molecular dynamics simulations of 1μs of duration. The simulations suggested that all missense SNPs considered as convergent deleterious caused some kind of structural change to the uroguanylin peptide. Additionally, four of these SNPs were also shown to cause modifications in peptide flexibility, possibly resulting in functional changes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Singularities of the dynamical structure factors of the spin-1/2 XXX chain at finite magnetic field.

PubMed

Carmelo, J M P; Sacramento, P D; Machado, J D P; Campbell, D K

2015-10-14

We study the longitudinal and transverse spin dynamical structure factors of the spin-1/2 XXX chain at finite magnetic field h, focusing in particular on the singularities at excitation energies in the vicinity of the lower thresholds. While the static properties of the model can be studied within a Fermi-liquid like description in terms of pseudoparticles, our derivation of the dynamical properties relies on the introduction of a form of the 'pseudofermion dynamical theory' (PDT) of the 1D Hubbard model suitably modified for the spin-only XXX chain and other models with two pseudoparticle Fermi points. Specifically, we derive the exact momentum and spin-density dependences of the exponents ζ(τ)(k) controlling the singularities for both the longitudinal (τ = l) and transverse (τ = t) dynamical structure factors for the whole momentum range k ∈ ]0,π[, in the thermodynamic limit. This requires the numerical solution of the integral equations that define the phase shifts in these exponents expressions. We discuss the relation to neutron scattering and suggest new experiments on spin-chain compounds using a carefully oriented crystal to test our predictions.

Singularities of the dynamical structure factors of the spin-1/2 XXX chain at finite magnetic field

NASA Astrophysics Data System (ADS)

Carmelo, J. M. P.; Sacramento, P. D.; Machado, J. D. P.; Campbell, D. K.

2015-10-01

We study the longitudinal and transverse spin dynamical structure factors of the spin-1/2 XXX chain at finite magnetic field h, focusing in particular on the singularities at excitation energies in the vicinity of the lower thresholds. While the static properties of the model can be studied within a Fermi-liquid like description in terms of pseudoparticles, our derivation of the dynamical properties relies on the introduction of a form of the ‘pseudofermion dynamical theory’ (PDT) of the 1D Hubbard model suitably modified for the spin-only XXX chain and other models with two pseudoparticle Fermi points. Specifically, we derive the exact momentum and spin-density dependences of the exponents {{\\zeta}τ}(k) controlling the singularities for both the longitudinal ≤ft(τ =l\\right) and transverse ≤ft(τ =t\\right) dynamical structure factors for the whole momentum range k\\in ]0,π[ , in the thermodynamic limit. This requires the numerical solution of the integral equations that define the phase shifts in these exponents expressions. We discuss the relation to neutron scattering and suggest new experiments on spin-chain compounds using a carefully oriented crystal to test our predictions.

Nonlinear wave propagation in discrete and continuous systems

NASA Astrophysics Data System (ADS)

Rothos, V. M.

2016-09-01

In this review we try to capture some of the recent excitement induced by a large volume of theoretical and computational studies addressing nonlinear Schrödinger models (discrete and continuous) and the localized structures that they support. We focus on some prototypical structures, namely the breather solutions and solitary waves. In particular, we investigate the bifurcation of travelling wave solution in Discrete NLS system applying dynamical systems methods. Next, we examine the combined effects of cubic and quintic terms of the long range type in the dynamics of a double well potential. The relevant bifurcations, the stability of the branches and their dynamical implications are examined both in the reduced (ODE) and in the full (PDE) setting. We also offer an outlook on interesting possibilities for future work on this theme.

Dynamic impact testing with servohydraulic testing machines

NASA Astrophysics Data System (ADS)

Bardenheier, R.; Rogers, G.

2006-08-01

The design concept of “Crashworthiness” requires the information on material behaviour under dynamic impact loading in order to describe and predict the crash behaviour of structures. Especially the transport related industries, like car, railway or aircraft industry, pursue the concept of lightweight design for a while now. The materials' maximum constraint during loading is pushed to permanently increasing figures. This means in terms of crashworthiness that the process of energy absorption in structures and the mechanical behaviour of materials must well understood and can be described appropriately by material models. In close cooperation with experts from various industries and research institutes Instron has developed throughout the past years a new family of servohydraulic testing machines specifically designed to cope with the dynamics of high rate testing. Main development steps are reflected versus their experimental necessities.

Advanced composite structural concepts and materials technologies for primary aircraft structures: Advanced material concepts

NASA Technical Reports Server (NTRS)

Lau, Kreisler S. Y.; Landis, Abraham L.; Chow, Andrea W.; Hamlin, Richard D.

1993-01-01

To achieve acceptable performance and long-term durability at elevated temperatures (350 to 600 F) for high-speed transport systems, further improvements of the high-performance matrix materials will be necessary to achieve very long-term (60,000-120,000 service hours) retention of mechanical properties and damage tolerance. This report emphasizes isoimide modification as a complementary technique to semi-interpenetrating polymer networks (SIPN's) to achieve greater processibility, better curing dynamics, and possibly enhanced thermo-mechanical properties in composites. A key result is the demonstration of enhanced processibility of isoimide-modified linear and thermo-setting polyimide systems.

Friction damping of two-dimensional motion and its application in vibration control

NASA Technical Reports Server (NTRS)

Menq, C.-H.; Chidamparam, P.; Griffin, J. H.

1991-01-01

This paper presents an approximate method for analyzing the two-dimensional friction contact problem so as to compute the dynamic response of a structure constrained by friction interfaces. The friction force at the joint is formulated based on the Coulomb model. The single-term harmonic balance scheme, together with the receptance approach of decoupling the effect of the friction force on the structure from those of the external forces has been utilized to obtain the steady state response. The computational efficiency and accuracy of the method are demonstrated by comparing the results with long-term time solutions.

Nonlinear Dynamical Modes as a Basis for Short-Term Forecast of Climate Variability

NASA Astrophysics Data System (ADS)

Feigin, A. M.; Mukhin, D.; Gavrilov, A.; Seleznev, A.; Loskutov, E.

2017-12-01

We study abilities of data-driven stochastic models constructed by nonlinear dynamical decomposition of spatially distributed data to quantitative (short-term) forecast of climate characteristics. We compare two data processing techniques: (i) widely used empirical orthogonal function approach, and (ii) nonlinear dynamical modes (NDMs) framework [1,2]. We also make comparison of two kinds of the prognostic models: (i) traditional autoregression (linear) model and (ii) model in the form of random ("stochastic") nonlinear dynamical system [3]. We apply all combinations of the above-mentioned data mining techniques and kinds of models to short-term forecasts of climate indices based on sea surface temperature (SST) data. We use NOAA_ERSST_V4 dataset (monthly SST with space resolution 20 × 20) covering the tropical belt and starting from the year 1960. We demonstrate that NDM-based nonlinear model shows better prediction skill versus EOF-based linear and nonlinear models. Finally we discuss capability of NDM-based nonlinear model for long-term (decadal) prediction of climate variability. [1] D. Mukhin, A. Gavrilov, E. Loskutov , A.Feigin, J.Kurths, 2015: Principal nonlinear dynamical modes of climate variability, Scientific Reports, rep. 5, 15510; doi: 10.1038/srep15510. [2] Gavrilov, A., Mukhin, D., Loskutov, E., Volodin, E., Feigin, A., & Kurths, J., 2016: Method for reconstructing nonlinear modes with adaptive structure from multidimensional data. Chaos: An Interdisciplinary Journal of Nonlinear Science, 26(12), 123101. [3] Ya. Molkov, D. Mukhin, E. Loskutov, A. Feigin, 2012: Random dynamical models from time series. Phys. Rev. E, Vol. 85, n.3.

Modeling Cancer Cell Growth Dynamics In vitro in Response to Antimitotic Drug Treatment

PubMed Central

Lorz, Alexander; Botesteanu, Dana-Adriana; Levy, Doron

2017-01-01

Investigating the role of intrinsic cell heterogeneity emerging from variations in cell-cycle parameters and apoptosis is a crucial step toward better informing drug administration. Antimitotic agents, widely used in chemotherapy, target exclusively proliferative cells and commonly induce a prolonged mitotic arrest followed by cell death via apoptosis. In this paper, we developed a physiologically motivated mathematical framework for describing cancer cell growth dynamics that incorporates the intrinsic heterogeneity in the time individual cells spend in the cell-cycle and apoptosis process. More precisely, our model comprises two age-structured partial differential equations for the proliferative and apoptotic cell compartments and one ordinary differential equation for the quiescent compartment. To reflect the intrinsic cell heterogeneity that governs the growth dynamics, proliferative and apoptotic cells are structured in “age,” i.e., the amount of time remaining to be spent in each respective compartment. In our model, we considered an antimitotic drug whose effect on the cellular dynamics is to induce mitotic arrest, extending the average cell-cycle length. The prolonged mitotic arrest induced by the drug can trigger apoptosis if the time a cell will spend in the cell cycle is greater than the mitotic arrest threshold. We studied the drug’s effect on the long-term cancer cell growth dynamics using different durations of prolonged mitotic arrest induced by the drug. Our numerical simulations suggest that at confluence and in the absence of the drug, quiescence is the long-term asymptotic behavior emerging from the cancer cell growth dynamics. This pattern is maintained in the presence of small increases in the average cell-cycle length. However, intermediate increases in cell-cycle length markedly decrease the total number of cells and can drive the cancer population to extinction. Intriguingly, a large “switch-on/switch-off” increase in the average cell-cycle length maintains an active cell population in the long term, with oscillating numbers of proliferative cells and a relatively constant quiescent cell number. PMID:28913178

Theoretical prediction and direct observation of the 9R structure in Ag

NASA Astrophysics Data System (ADS)

Ernst, F.; Finnis, M. W.; Hofmann, D.; Muschik, T.; Schönberger, U.; Wolf, U.; Methfessel, M.

1992-07-01

Molecular-dynamics simulations of the Σ3<110>(211) twin boundary in Ag predict a thin (1 nm) boundary phase of the 9R (α-Sm) structure. High-resolution electron microscopy shows the presence of the predicted structure. We also calculate the energy ab initio for several hypothetical structures of Cu and Ag. Low energies of the 9R structure and other polytypes, low experimental stacking-fault energies, and the hcp-fcc energy difference are correlated and explained in terms of an effective nearest-neighbor Ising interaction.

Modeling the structural, dynamical, and magnetic properties of liquid Al1-xMnx ( x=0.14 , 0.2, and 0.4): A first-principles investigation

NASA Astrophysics Data System (ADS)

Jakse, N.; Pasturel, A.

2007-07-01

We report the results of first-principles molecular dynamics simulations of liquid Al1-xMnx alloys at three different compositions. The local structure as defined by the Bhatia-Thornton partial structure factors is found to display significant changes at x=0.4 . In addition, a structural analysis using three-dimensional pair-analysis techniques evidences a fivefold symmetry around x=0.14 , in agreement with the experimental quasicrystal-forming range, and an increasing complexity of the Frank-Kasper polytetrahedral symmetry around Mn atoms at x=0.4 . We also examine the time evolution of the configurations at the three compositions in terms of the mean-square displacements and self-diffusion coefficients. Finally, we show a strong interplay between the structural changes and the evolution of the magnetic properties of the Mn atoms as a function of composition.

Ion acoustic shock wave in collisional equal mass plasma

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

Adak, Ashish, E-mail: ashish-adak@yahoo.com; Ghosh, Samiran, E-mail: sran-g@yahoo.com; Chakrabarti, Nikhil, E-mail: nikhil.chakrabarti@saha.ac.in

The effect of ion-ion collision on the dynamics of nonlinear ion acoustic wave in an unmagnetized pair-ion plasma has been investigated. The two-fluid model has been used to describe the dynamics of both positive and negative ions with equal masses. It is well known that in the dynamics of the weakly nonlinear wave, the viscosity mediates wave dissipation in presence of weak nonlinearity and dispersion. This dissipation is responsible for the shock structures in pair-ion plasma. Here, it has been shown that the ion-ion collision in presence of collective phenomena mediated by the plasma current is the source of dissipationmore » that causes the Burgers' term which is responsible for the shock structures in equal mass pair-ion plasma. The dynamics of the weakly nonlinear wave is governed by the Korteweg-de Vries Burgers equation. The analytical and numerical investigations revealed that the ion acoustic wave exhibits both oscillatory and monotonic shock structures depending on the frequency of ion-ion collision parameter. The results have been discussed in the context of the fullerene pair-ion plasma experiments.« less

Creating a Test Validated Structural Dynamic Finite Element Model of the X-56A Aircraft

NASA Technical Reports Server (NTRS)

Pak, Chan-Gi; Truong, Samson

2014-01-01

Small modeling errors in the finite element model will eventually induce errors in the structural flexibility and mass, thus propagating into unpredictable errors in the unsteady aerodynamics and the control law design. One of the primary objectives of the Multi Utility Technology Test-bed, X-56A aircraft, is the flight demonstration of active flutter suppression, and therefore in this study, the identification of the primary and secondary modes for the structural model tuning based on the flutter analysis of the X-56A aircraft. The ground vibration test-validated structural dynamic finite element model of the X-56A aircraft is created in this study. The structural dynamic finite element model of the X-56A aircraft is improved using a model tuning tool. In this study, two different weight configurations of the X-56A aircraft have been improved in a single optimization run. Frequency and the cross-orthogonality (mode shape) matrix were the primary focus for improvement, while other properties such as center of gravity location, total weight, and offdiagonal terms of the mass orthogonality matrix were used as constraints. The end result was a more improved and desirable structural dynamic finite element model configuration for the X-56A aircraft. Improved frequencies and mode shapes in this study increased average flutter speeds of the X-56A aircraft by 7.6% compared to the baseline model.

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.

Structure of a viscoplastic theory

NASA Technical Reports Server (NTRS)

Freed, Alan D.

1988-01-01

The general structure of a viscoplastic theory is developed from physical and thermodynamical considerations. The flow equation is of classical form. The dynamic recovery approach is shown to be superior to the hardening function approach for incorporating nonlinear strain hardening into the material response through the evolutionary equation for back stress. A novel approach for introducing isotropic strain hardening into the theory is presented, which results in a useful simplification. In particular, the limiting stress for the kinematic saturation of state (not the drag stress) is the chosen scalar-valued state variable. The resulting simplification is that there is no coupling between dynamic and thermal recovery terms in each evolutionary equation. The derived theory of viscoplasticity has the structure of a two-surface plasticity theory when the response is plasticlike, and the structure of a Bailey-Orowan creep theory when the response is creeplike.

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

Key Process Uncertainties in Soil Carbon Dynamics: Comparing Multiple Model Structures and Observational Meta-analysis

NASA Astrophysics Data System (ADS)

Sulman, B. N.; Moore, J.; Averill, C.; Abramoff, R. Z.; Bradford, M.; Classen, A. T.; Hartman, M. D.; Kivlin, S. N.; Luo, Y.; Mayes, M. A.; Morrison, E. W.; Riley, W. J.; Salazar, A.; Schimel, J.; Sridhar, B.; Tang, J.; Wang, G.; Wieder, W. R.

2016-12-01

Soil carbon (C) dynamics are crucial to understanding and predicting C cycle responses to global change and soil C modeling is a key tool for understanding these dynamics. While first order model structures have historically dominated this area, a recent proliferation of alternative model structures representing different assumptions about microbial activity and mineral protection is providing new opportunities to explore process uncertainties related to soil C dynamics. We conducted idealized simulations of soil C responses to warming and litter addition using models from five research groups that incorporated different sets of assumptions about processes governing soil C decomposition and stabilization. We conducted a meta-analysis of published warming and C addition experiments for comparison with simulations. Assumptions related to mineral protection and microbial dynamics drove strong differences among models. In response to C additions, some models predicted long-term C accumulation while others predicted transient increases that were counteracted by accelerating decomposition. In experimental manipulations, doubling litter addition did not change soil C stocks in studies spanning as long as two decades. This result agreed with simulations from models with strong microbial growth responses and limited mineral sorption capacity. In observations, warming initially drove soil C loss via increased CO2 production, but in some studies soil C rebounded and increased over decadal time scales. In contrast, all models predicted sustained C losses under warming. The disagreement with experimental results could be explained by physiological or community-level acclimation, or by warming-related changes in plant growth. In addition to the role of microbial activity, assumptions related to mineral sorption and protected C played a key role in driving long-term model responses. In general, simulations were similar in their initial responses to perturbations but diverged over decadal time scales. This suggests that more long-term soil experiments may be necessary to resolve important process uncertainties related to soil C storage. We also suggest future experiments examine how microbial activity responds to warming under a range of soil clay contents and in concert with changes in litter inputs.

Litter and dead wood dynamics in ponderosa pine forests along a 160-year chronosequence.

PubMed

Hall, S A; Burke, I C; Hobbs, N T

2006-12-01

Disturbances such as fire play a key role in controlling ecosystem structure. In fire-prone forests, organic detritus comprises a large pool of carbon and can control the frequency and intensity of fire. The ponderosa pine forests of the Colorado Front Range, USA, where fire has been suppressed for a century, provide an ideal system for studying the long-term dynamics of detrital pools. Our objectives were (1) to quantify the long-term temporal dynamics of detrital pools; and (2) to determine to what extent present stand structure, topography, and soils constrain these dynamics. We collected data on downed dead wood, litter, duff (partially decomposed litter on the forest floor), stand structure, topographic position, and soils for 31 sites along a 160-year chronosequence. We developed a compartment model and parameterized it to describe the temporal trends in the detrital pools. We then developed four sets of statistical models, quantifying the hypothesized relationship between pool size and (1) stand structure, (2) topography, (3) soils variables, and (4) time since fire. We contrasted how much support each hypothesis had in the data using Akaike's Information Criterion (AIC). Time since fire explained 39-80% of the variability in dead wood of different size classes. Pool size increased to a peak as material killed by the fire fell, then decomposed rapidly to a minimum (61-85 years after fire for the different pools). It then increased, presumably as new detritus was produced by the regenerating stand. Litter was most strongly related to canopy cover (r2 = 77%), suggesting that litter fall, rather than decomposition, controls its dynamics. The temporal dynamics of duff were the hardest to predict. Detrital pool sizes were more strongly related to time since fire than to environmental variables. Woody debris peak-to-minimum time was 46-67 years, overlapping the range of historical fire return intervals (1 to > 100 years). Fires may therefore have burned under a wide range of fuel conditions, supporting the hypothesis that this region's fire regime was mixed severity.

Relaxation processes of the liquid crystal ME6N in the isotropic phase studied by Raman scattering experiments

NASA Astrophysics Data System (ADS)

Giorgini, Maria Grazia; Arcioni, Alberto; Polizzi, Ciro; Musso, Maurizio; Ottaviani, Paolo

2004-03-01

We have investigated the Raman profiles of the ν(C≡N) and ν(C=O) vibrational modes of the nematic liquid crystal ME6N (4-cyanophenyl-4'-hexylbenzoate) in the isotropic phase at different temperatures and used them as probes of the dynamics and structural organization of this liquid. The vibrational time correlation functions of the ν(C≡N) mode, rather adequately interpreted within the assumption of exponential modulation function (the Kubo-Rothschild theory), indicate that the system experiences an intermediate dynamical regime that gets only slightly faster with increasing temperature. However, this theory fails in predicting the non-exponential behavior that the time correlation functions manifest in the long time range (t>3 ps). For this reason we have additionally approached the interpretation of vibrational correlation functions in terms of the theory formulated by Rothschild and co-workers for locally structured liquids. The application of this theory reveals that the molecular dynamics in this liquid crystal in the isotropic phase is that deriving from a distribution of differently sized clusters, which narrows as the temperature increases. Even at the highest temperature reached in this study (87 °C above the nematic-isotropic transition), the liquid has not yet achieved the structure of the simple liquid and the dynamics has not reached the limit of the single channel process. The vibrational and orientational relaxations occur in very different time scales. The temperature independence of the orientational dynamics in the whole range from 55 °C to 135 °C has been referred to the nonhydrodynamic behavior of the system, arising when local pseudonematic structures persist for times longer than the orientational relaxation. The occurrence of the process of resonant vibrational energy transfer between the C=O groups of adjacent molecules has been revealed in the isotropic phase by a slightly positive Raman noncoincidence effect in the band associated with the ν(C=O) mode. A qualitative interpretation is tentatively given in terms of partial cancellation of contributions deriving from structures having opposite orientations of their C=O groups.

Long-term changes in structure and composition following hurricanes in a primary lower montane rain forest in Puerto Rico

Treesearch

P.L. Weaver

2013-01-01

Ridges within the lower montane rain forests (sensu Beard) of the Caribbean Basin are dominated by Dacryodes excelsa, a tree species known as tabonuco in Puerto Rico and gommier in the Lesser Antilles. Periodially, hurricanes traverse the islands causing changes in structure, species composition, and dynamics of forests. The chronology of post-hurricane vegetation...

Protein structure modeling for CASP10 by multiple layers of global optimization.

PubMed

Joo, Keehyoung; Lee, Juyong; Sim, Sangjin; Lee, Sun Young; Lee, Kiho; Heo, Seungryong; Lee, In-Ho; Lee, Sung Jong; Lee, Jooyoung

2014-02-01

In the template-based modeling (TBM) category of CASP10 experiment, we introduced a new protocol called protein modeling system (PMS) to generate accurate protein structures in terms of side-chains as well as backbone trace. In the new protocol, a global optimization algorithm, called conformational space annealing (CSA), is applied to the three layers of TBM procedure: multiple sequence-structure alignment, 3D chain building, and side-chain re-modeling. For 3D chain building, we developed a new energy function which includes new distance restraint terms of Lorentzian type (derived from multiple templates), and new energy terms that combine (physical) energy terms such as dynamic fragment assembly (DFA) energy, DFIRE statistical potential energy, hydrogen bonding term, etc. These physical energy terms are expected to guide the structure modeling especially for loop regions where no template structures are available. In addition, we developed a new quality assessment method based on random forest machine learning algorithm to screen templates, multiple alignments, and final models. For TBM targets of CASP10, we find that, due to the combination of three stages of CSA global optimizations and quality assessment, the modeling accuracy of PMS improves at each additional stage of the protocol. It is especially noteworthy that the side-chains of the final PMS models are far more accurate than the models in the intermediate steps. Copyright © 2013 Wiley Periodicals, Inc.

The architecture of dynamic reservoir in the echo state network

NASA Astrophysics Data System (ADS)

Cui, Hongyan; Liu, Xiang; Li, Lixiang

2012-09-01

Echo state network (ESN) has recently attracted increasing interests because of its superior capability in modeling nonlinear dynamic systems. In the conventional echo state network model, its dynamic reservoir (DR) has a random and sparse topology, which is far from the real biological neural networks from both structural and functional perspectives. We hereby propose three novel types of echo state networks with new dynamic reservoir topologies based on complex network theory, i.e., with a small-world topology, a scale-free topology, and a mixture of small-world and scale-free topologies, respectively. We then analyze the relationship between the dynamic reservoir structure and its prediction capability. We utilize two commonly used time series to evaluate the prediction performance of the three proposed echo state networks and compare them to the conventional model. We also use independent and identically distributed time series to analyze the short-term memory and prediction precision of these echo state networks. Furthermore, we study the ratio of scale-free topology and the small-world topology in the mixed-topology network, and examine its influence on the performance of the echo state networks. Our simulation results show that the proposed echo state network models have better prediction capabilities, a wider spectral radius, but retain almost the same short-term memory capacity as compared to the conventional echo state network model. We also find that the smaller the ratio of the scale-free topology over the small-world topology, the better the memory capacities.

Lagrangian transport in a class of three-dimensional buoyancy-driven flows

NASA Astrophysics Data System (ADS)

Contreras, Sebastian; Speetjens, Michel; Clercx, Herman

2017-11-01

The study concerns the Lagrangian dynamics of three-dimensional (3D) buoyancy-driven cavity flows under steady and laminar conditions due to a global temperature gradient imposed via an opposite hot and cold sidewall. This serves as archetypal configuration for natural-convection flows in which gravity is perpendicular to the global temperature gradient. Limited insight into the Lagrangian properties of this class of flows motivates this study. The 3D Lagrangian dynamics are investigated in terms of the generic structure of the Lagrangian flow topology that is described in terms of the Grashof number (Gr) and the Prandtl number (Pr). Gr is the principal control parameter for the flow topology: vanishing Gr yields a state of closed streamlines (integrable state); increasing Gr causes the formation of toroidal coherent structures embedded in chaotic streamlines governed by Hamiltonian mechanisms. Fluid inertia prevails for ``smaller'' Gr. A buoyancy-induced bifurcation of the flow topology occurs for ``larger'' Gr and underlies the emergence of ``secondary rolls'' and secondary tori for ``larger'' Pr. Stagnation points and corresponding manifold interactions are key to the dynamics. S.C. acknowledges financial support from Consejo Nacional de Ciencia y Tecnología (CONACYT).

A Scalable Multicore Architecture With Heterogeneous Memory Structures for Dynamic Neuromorphic Asynchronous Processors (DYNAPs).

PubMed

Moradi, Saber; Qiao, Ning; Stefanini, Fabio; Indiveri, Giacomo

2018-02-01

Neuromorphic computing systems comprise networks of neurons that use asynchronous events for both computation and communication. This type of representation offers several advantages in terms of bandwidth and power consumption in neuromorphic electronic systems. However, managing the traffic of asynchronous events in large scale systems is a daunting task, both in terms of circuit complexity and memory requirements. Here, we present a novel routing methodology that employs both hierarchical and mesh routing strategies and combines heterogeneous memory structures for minimizing both memory requirements and latency, while maximizing programming flexibility to support a wide range of event-based neural network architectures, through parameter configuration. We validated the proposed scheme in a prototype multicore neuromorphic processor chip that employs hybrid analog/digital circuits for emulating synapse and neuron dynamics together with asynchronous digital circuits for managing the address-event traffic. We present a theoretical analysis of the proposed connectivity scheme, describe the methods and circuits used to implement such scheme, and characterize the prototype chip. Finally, we demonstrate the use of the neuromorphic processor with a convolutional neural network for the real-time classification of visual symbols being flashed to a dynamic vision sensor (DVS) at high speed.

Comparative static curing versus dynamic curing on tablet coating structures.

PubMed

Gendre, Claire; Genty, Muriel; Fayard, Barbara; Tfayli, Ali; Boiret, Mathieu; Lecoq, Olivier; Baron, Michel; Chaminade, Pierre; Péan, Jean Manuel

2013-09-10

Curing is generally required to stabilize film coating from aqueous polymer dispersion. This post-coating drying step is traditionally carried out in static conditions, requiring the transfer of solid dosage forms to an oven. But, curing operation performed directly inside the coating equipment stands for an attractive industrial application. Recently, the use of various advanced physico-chemical characterization techniques i.e., X-ray micro-computed tomography, vibrational spectroscopies (near infrared and Raman) and X-ray microdiffraction, allowed new insights into the film-coating structures of dynamically cured tablets. Dynamic curing end-point was efficiently determined after 4h. The aim of the present work was to elucidate the influence of curing conditions on film-coating structures. Results demonstrated that 24h of static curing and 4h of dynamic curing, both performed at 60°C and ambient relative humidity, led to similar coating layers in terms of drug release properties, porosity, water content, structural rearrangement of polymer chains and crystalline distribution. Furthermore, X-ray microdiffraction measurements pointed out different crystalline coating compositions depending on sample storage time. An aging mechanism might have occur during storage, resulting in the crystallization and the upward migration of cetyl alcohol, coupled to the downward migration of crystalline sodium lauryl sulfate within the coating layer. Interestingly, this new study clearly provided further knowledge into film-coating structures after a curing step and confirmed that curing operation could be performed in dynamic conditions. Copyright © 2013 Elsevier B.V. All rights reserved.

Evolutionary dynamics of social dilemmas in structured heterogeneous populations.

PubMed

Santos, F C; Pacheco, J M; Lenaerts, Tom

2006-02-28

Real populations have been shown to be heterogeneous, in which some individuals have many more contacts than others. This fact contrasts with the traditional homogeneous setting used in studies of evolutionary game dynamics. We incorporate heterogeneity in the population by studying games on graphs, in which the variability in connectivity ranges from single-scale graphs, for which heterogeneity is small and associated degree distributions exhibit a Gaussian tale, to scale-free graphs, for which heterogeneity is large with degree distributions exhibiting a power-law behavior. We study the evolution of cooperation, modeled in terms of the most popular dilemmas of cooperation. We show that, for all dilemmas, increasing heterogeneity favors the emergence of cooperation, such that long-term cooperative behavior easily resists short-term noncooperative behavior. Moreover, we show how cooperation depends on the intricate ties between individuals in scale-free populations.

The Dynamic Structure of Everyday Life

DTIC Science & Technology

1988-10-12

Computational theories of action have generally understood the organized nature of human activity in terms of the construction and execution of...led to grossly impractical technical proposals. I would like to propose an alternative view of human activity . According to this view, contingency is

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

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.

Discrete Molecular Dynamics Can Predict Helical Prestructured Motifs in Disordered Proteins

PubMed Central

Han, Kyou-Hoon; Dokholyan, Nikolay V.; Tompa, Péter; Kalmár, Lajos; Hegedűs, Tamás

2014-01-01

Intrinsically disordered proteins (IDPs) lack a stable tertiary structure, but their short binding regions termed Pre-Structured Motifs (PreSMo) can form transient secondary structure elements in solution. Although disordered proteins are crucial in many biological processes and designing strategies to modulate their function is highly important, both experimental and computational tools to describe their conformational ensembles and the initial steps of folding are sparse. Here we report that discrete molecular dynamics (DMD) simulations combined with replica exchange (RX) method efficiently samples the conformational space and detects regions populating α-helical conformational states in disordered protein regions. While the available computational methods predict secondary structural propensities in IDPs based on the observation of protein-protein interactions, our ab initio method rests on physical principles of protein folding and dynamics. We show that RX-DMD predicts α-PreSMos with high confidence confirmed by comparison to experimental NMR data. Moreover, the method also can dissect α-PreSMos in close vicinity to each other and indicate helix stability. Importantly, simulations with disordered regions forming helices in X-ray structures of complexes indicate that a preformed helix is frequently the binding element itself, while in other cases it may have a role in initiating the binding process. Our results indicate that RX-DMD provides a breakthrough in the structural and dynamical characterization of disordered proteins by generating the structural ensembles of IDPs even when experimental data are not available. PMID:24763499

Poisson structure of dynamical systems with three degrees of freedom

NASA Astrophysics Data System (ADS)

Gümral, Hasan; Nutku, Yavuz

1993-12-01

It is shown that the Poisson structure of dynamical systems with three degrees of freedom can be defined in terms of an integrable one-form in three dimensions. Advantage is taken of this fact and the theory of foliations is used in discussing the geometrical structure underlying complete and partial integrability. Techniques for finding Poisson structures are presented and applied to various examples such as the Halphen system which has been studied as the two-monopole problem by Atiyah and Hitchin. It is shown that the Halphen system can be formulated in terms of a flat SL(2,R)-valued connection and belongs to a nontrivial Godbillon-Vey class. On the other hand, for the Euler top and a special case of three-species Lotka-Volterra equations which are contained in the Halphen system as limiting cases, this structure degenerates into the form of globally integrable bi-Hamiltonian structures. The globally integrable bi-Hamiltonian case is a linear and the SL(2,R) structure is a quadratic unfolding of an integrable one-form in 3+1 dimensions. It is shown that the existence of a vector field compatible with the flow is a powerful tool in the investigation of Poisson structure and some new techniques for incorporating arbitrary constants into the Poisson one-form are presented herein. This leads to some extensions, analogous to q extensions, of Poisson structure. The Kermack-McKendrick model and some of its generalizations describing the spread of epidemics, as well as the integrable cases of the Lorenz, Lotka-Volterra, May-Leonard, and Maxwell-Bloch systems admit globally integrable bi-Hamiltonian structure.

Motional timescale predictions by molecular dynamics simulations: case study using proline and hydroxyproline sidechain dynamics.

PubMed

Aliev, Abil E; Kulke, Martin; Khaneja, Harmeet S; Chudasama, Vijay; Sheppard, Tom D; Lanigan, Rachel M

2014-02-01

We propose a new approach for force field optimizations which aims at reproducing dynamics characteristics using biomolecular MD simulations, in addition to improved prediction of motionally averaged structural properties available from experiment. As the source of experimental data for dynamics fittings, we use (13) C NMR spin-lattice relaxation times T1 of backbone and sidechain carbons, which allow to determine correlation times of both overall molecular and intramolecular motions. For structural fittings, we use motionally averaged experimental values of NMR J couplings. The proline residue and its derivative 4-hydroxyproline with relatively simple cyclic structure and sidechain dynamics were chosen for the assessment of the new approach in this work. Initially, grid search and simplexed MD simulations identified large number of parameter sets which fit equally well experimental J couplings. Using the Arrhenius-type relationship between the force constant and the correlation time, the available MD data for a series of parameter sets were analyzed to predict the value of the force constant that best reproduces experimental timescale of the sidechain dynamics. Verification of the new force-field (termed as AMBER99SB-ILDNP) against NMR J couplings and correlation times showed consistent and significant improvements compared to the original force field in reproducing both structural and dynamics properties. The results suggest that matching experimental timescales of motions together with motionally averaged characteristics is the valid approach for force field parameter optimization. Such a comprehensive approach is not restricted to cyclic residues and can be extended to other amino acid residues, as well as to the backbone. Copyright © 2013 Wiley Periodicals, Inc.

Structural dynamics of supercooled water from quasielastic neutron scattering and molecular simulations.

PubMed

Qvist, Johan; Schober, Helmut; Halle, Bertil

2011-04-14

One of the outstanding challenges presented by liquid water is to understand how molecules can move on a picosecond time scale despite being incorporated in a three-dimensional network of relatively strong H-bonds. This challenge is exacerbated in the supercooled state, where the dramatic slowing down of structural dynamics is reminiscent of the, equally poorly understood, generic behavior of liquids near the glass transition temperature. By probing single-molecule dynamics on a wide range of time and length scales, quasielastic neutron scattering (QENS) can potentially reveal the mechanistic details of water's structural dynamics, but because of interpretational ambiguities this potential has not been fully realized. To resolve these issues, we present here an extensive set of high-quality QENS data from water in the range 253-293 K and a corresponding set of molecular dynamics (MD) simulations to facilitate and validate the interpretation. Using a model-free approach, we analyze the QENS data in terms of two motional components. Based on the dynamical clustering observed in MD trajectories, we identify these components with two distinct types of structural dynamics: picosecond local (L) structural fluctuations within dynamical basins and slower interbasin jumps (J). The Q-dependence of the dominant QENS component, associated with J dynamics, can be quantitatively rationalized with a continuous-time random walk (CTRW) model with an apparent jump length that depends on low-order moments of the jump length and waiting time distributions. Using a simple coarse-graining algorithm to quantitatively identify dynamical basins, we map the newtonian MD trajectory on a CTRW trajectory, from which the jump length and waiting time distributions are computed. The jump length distribution is gaussian and the rms jump length increases from 1.5 to 1.9 Å as the temperature increases from 253 to 293 K. The rms basin radius increases from 0.71 to 0.75 Å over the same range. The waiting time distribution is exponential at all investigated temperatures, ruling out significant dynamical heterogeneity. However, a simulation at 238 K reveals a small but significant dynamical heterogeneity. The macroscopic diffusion coefficient deduced from the QENS data agrees quantitatively with NMR and tracer results. We compare our QENS analysis with existing approaches, arguing that the apparent dynamical heterogeneity implied by stretched exponential fitting functions results from the failure to distinguish intrabasin (L) from interbasin (J) structural dynamics. We propose that the apparent dynamical singularity at ∼220 K corresponds to freezing out of J dynamics, while the calorimetric glass transition corresponds to freezing out of L dynamics.

Structural dynamics of supercooled water from quasielastic neutron scattering and molecular simulations

NASA Astrophysics Data System (ADS)

Qvist, Johan; Schober, Helmut; Halle, Bertil

2011-04-01

One of the outstanding challenges presented by liquid water is to understand how molecules can move on a picosecond time scale despite being incorporated in a three-dimensional network of relatively strong H-bonds. This challenge is exacerbated in the supercooled state, where the dramatic slowing down of structural dynamics is reminiscent of the, equally poorly understood, generic behavior of liquids near the glass transition temperature. By probing single-molecule dynamics on a wide range of time and length scales, quasielastic neutron scattering (QENS) can potentially reveal the mechanistic details of water's structural dynamics, but because of interpretational ambiguities this potential has not been fully realized. To resolve these issues, we present here an extensive set of high-quality QENS data from water in the range 253-293 K and a corresponding set of molecular dynamics (MD) simulations to facilitate and validate the interpretation. Using a model-free approach, we analyze the QENS data in terms of two motional components. Based on the dynamical clustering observed in MD trajectories, we identify these components with two distinct types of structural dynamics: picosecond local (L) structural fluctuations within dynamical basins and slower interbasin jumps (J). The Q-dependence of the dominant QENS component, associated with J dynamics, can be quantitatively rationalized with a continuous-time random walk (CTRW) model with an apparent jump length that depends on low-order moments of the jump length and waiting time distributions. Using a simple coarse-graining algorithm to quantitatively identify dynamical basins, we map the Newtonian MD trajectory on a CTRW trajectory, from which the jump length and waiting time distributions are computed. The jump length distribution is Gaussian and the rms jump length increases from 1.5 to 1.9 Å as the temperature increases from 253 to 293 K. The rms basin radius increases from 0.71 to 0.75 Å over the same range. The waiting time distribution is exponential at all investigated temperatures, ruling out significant dynamical heterogeneity. However, a simulation at 238 K reveals a small but significant dynamical heterogeneity. The macroscopic diffusion coefficient deduced from the QENS data agrees quantitatively with NMR and tracer results. We compare our QENS analysis with existing approaches, arguing that the apparent dynamical heterogeneity implied by stretched exponential fitting functions results from the failure to distinguish intrabasin (L) from interbasin (J) structural dynamics. We propose that the apparent dynamical singularity at ˜220 K corresponds to freezing out of J dynamics, while the calorimetric glass transition corresponds to freezing out of L dynamics.

Seeing with the nano-eye: accessing structure, function, and dynamics of matter on its natural length and time scales

NASA Astrophysics Data System (ADS)

Raschke, Markus

2015-03-01

To understand and ultimately control the properties of most functional materials, from molecular soft-matter to quantum materials, requires access to the structure, coupling, and dynamics on the elementary time and length scales that define the microscopic interactions in these materials. To gain the desired nanometer spatial resolution with simultaneous spectroscopic specificity we combine scanning probe microscopy with different optical, including coherent, nonlinear, and ultrafast spectroscopies. The underlying near-field interaction mediated by the atomic-force or scanning tunneling microscope tip provides the desired deep-sub wavelength nano-focusing enabling few-nm spatial resolution. I will introduce our generalization of the approach in terms of the near-field impedance matching to a quantum system based on special optical antenna-tip designs. The resulting enhanced and qualitatively new forms of light-matter interaction enable measurements of quantum dynamics in an interacting environment or to image the electromagnetic local density of states of thermal radiation. Other applications include the inter-molecular coupling and dynamics in soft-matter hetero-structures, surface plasmon interferometry as a probe of electronic structure and dynamics in graphene, and quantum phase transitions in correlated electron materials. These examples highlight the general applicability of the new near-field microscopy approach, complementing emergent X-ray and electron imaging tools, aiming towards the ultimate goal of probing matter on its most elementary spatio-temporal level.

An NMR database for simulations of membrane dynamics.

PubMed

Leftin, Avigdor; Brown, Michael F

2011-03-01

Computational methods are powerful in capturing the results of experimental studies in terms of force fields that both explain and predict biological structures. Validation of molecular simulations requires comparison with experimental data to test and confirm computational predictions. Here we report a comprehensive database of NMR results for membrane phospholipids with interpretations intended to be accessible by non-NMR specialists. Experimental ¹³C-¹H and ²H NMR segmental order parameters (S(CH) or S(CD)) and spin-lattice (Zeeman) relaxation times (T(1Z)) are summarized in convenient tabular form for various saturated, unsaturated, and biological membrane phospholipids. Segmental order parameters give direct information about bilayer structural properties, including the area per lipid and volumetric hydrocarbon thickness. In addition, relaxation rates provide complementary information about molecular dynamics. Particular attention is paid to the magnetic field dependence (frequency dispersion) of the NMR relaxation rates in terms of various simplified power laws. Model-free reduction of the T(1Z) studies in terms of a power-law formalism shows that the relaxation rates for saturated phosphatidylcholines follow a single frequency-dispersive trend within the MHz regime. We show how analytical models can guide the continued development of atomistic and coarse-grained force fields. Our interpretation suggests that lipid diffusion and collective order fluctuations are implicitly governed by the viscoelastic nature of the liquid-crystalline ensemble. Collective bilayer excitations are emergent over mesoscopic length scales that fall between the molecular and bilayer dimensions, and are important for lipid organization and lipid-protein interactions. Future conceptual advances and theoretical reductions will foster understanding of biomembrane structural dynamics through a synergy of NMR measurements and molecular simulations. Copyright © 2010 Elsevier B.V. All rights reserved.

Carbon fluxes in tropical forest ecosystems: the value of Eddy-covariance data for individual-based dynamic forest gap models

NASA Astrophysics Data System (ADS)

Roedig, Edna; Cuntz, Matthias; Huth, Andreas

2015-04-01

The effects of climatic inter-annual fluctuations and human activities on the global carbon cycle are uncertain and currently a major issue in global vegetation models. Individual-based forest gap models, on the other hand, model vegetation structure and dynamics on a small spatial (<100 ha) and large temporal scale (>1000 years). They are well-established tools to reproduce successions of highly-diverse forest ecosystems and investigate disturbances as logging or fire events. However, the parameterizations of the relationships between short-term climate variability and forest model processes are often uncertain in these models (e.g. daily variable temperature and gross primary production (GPP)) and cannot be constrained from forest inventories. We addressed this uncertainty and linked high-resolution Eddy-covariance (EC) data with an individual-based forest gap model. The forest model FORMIND was applied to three diverse tropical forest sites in the Amazonian rainforest. Species diversity was categorized into three plant functional types. The parametrizations for the steady-state of biomass and forest structure were calibrated and validated with different forest inventories. The parameterizations of relationships between short-term climate variability and forest model processes were evaluated with EC-data on a daily time step. The validations of the steady-state showed that the forest model could reproduce biomass and forest structures from forest inventories. The daily estimations of carbon fluxes showed that the forest model reproduces GPP as observed by the EC-method. Daily fluctuations of GPP were clearly reflected as a response to daily climate variability. Ecosystem respiration remains a challenge on a daily time step due to a simplified soil respiration approach. In the long-term, however, the dynamic forest model is expected to estimate carbon budgets for highly-diverse tropical forests where EC-measurements are rare.

Structure and collective dynamics of hydrated anti-freeze protein type III from 180 K to 298 K by X-ray diffraction and inelastic X-ray scattering

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

Yoshida, Koji; Baron, Alfred Q. R.; Uchiyama, Hiroshi

We investigated hydrated antifreeze protein type III (AFP III) powder with a hydration level h (=mass of water/mass of protein) of 0.4 in the temperature range between 180 K and 298 K using X-ray diffraction and inelastic X-ray scattering (IXS). The X-ray diffraction data showed smooth, largely monotonic changes between 180 K and 298 K without freezing water. Meanwhile, the collective dynamics observed by IXS showed a strong change in the sound velocity at 180 K, after being largely temperature independent at higher temperatures (298–220 K). We interpret this change in terms of the dynamic transition previously discussed using othermore » probes including THz IR absorption spectroscopy and incoherent elastic and quasi-elastic neutron scattering. This finding suggests that the dynamic transition of hydrated proteins is observable on the subpicosecond time scale as well as nano- and pico-second scales, both in collective dynamics from IXS and single particle dynamics from neutron scattering. Moreover, it is most likely that the dynamic transition of hydrated AFP III is not directly correlated with its hydration structure.« less

Structure and collective dynamics of hydrated anti-freeze protein type III from 180 K to 298 K by X-ray diffraction and inelastic X-ray scattering

NASA Astrophysics Data System (ADS)

Yoshida, Koji; Baron, Alfred Q. R.; Uchiyama, Hiroshi; Tsutsui, Satoshi; Yamaguchi, Toshio

2016-04-01

We investigated hydrated antifreeze protein type III (AFP III) powder with a hydration level h (=mass of water/mass of protein) of 0.4 in the temperature range between 180 K and 298 K using X-ray diffraction and inelastic X-ray scattering (IXS). The X-ray diffraction data showed smooth, largely monotonic changes between 180 K and 298 K without freezing water. Meanwhile, the collective dynamics observed by IXS showed a strong change in the sound velocity at 180 K, after being largely temperature independent at higher temperatures (298-220 K). We interpret this change in terms of the dynamic transition previously discussed using other probes including THz IR absorption spectroscopy and incoherent elastic and quasi-elastic neutron scattering. This finding suggests that the dynamic transition of hydrated proteins is observable on the subpicosecond time scale as well as nano- and pico-second scales, both in collective dynamics from IXS and single particle dynamics from neutron scattering. Moreover, it is most likely that the dynamic transition of hydrated AFP III is not directly correlated with its hydration structure.

Structure and collective dynamics of hydrated anti-freeze protein type III from 180 K to 298 K by X-ray diffraction and inelastic X-ray scattering.

PubMed

Yoshida, Koji; Baron, Alfred Q R; Uchiyama, Hiroshi; Tsutsui, Satoshi; Yamaguchi, Toshio

2016-04-07

We investigated hydrated antifreeze protein type III (AFP III) powder with a hydration level h (=mass of water/mass of protein) of 0.4 in the temperature range between 180 K and 298 K using X-ray diffraction and inelastic X-ray scattering (IXS). The X-ray diffraction data showed smooth, largely monotonic changes between 180 K and 298 K without freezing water. Meanwhile, the collective dynamics observed by IXS showed a strong change in the sound velocity at 180 K, after being largely temperature independent at higher temperatures (298-220 K). We interpret this change in terms of the dynamic transition previously discussed using other probes including THz IR absorption spectroscopy and incoherent elastic and quasi-elastic neutron scattering. This finding suggests that the dynamic transition of hydrated proteins is observable on the subpicosecond time scale as well as nano- and pico-second scales, both in collective dynamics from IXS and single particle dynamics from neutron scattering. Moreover, it is most likely that the dynamic transition of hydrated AFP III is not directly correlated with its hydration structure.

Second order nonlinear equations of motion for spinning highly flexible line-elements. [for spacecraft solar sail

NASA Technical Reports Server (NTRS)

Salama, M.; Trubert, M.

1979-01-01

A formulation is given for the second order nonlinear equations of motion for spinning line-elements having little or no intrinsic structural stiffness. Such elements have been employed in recent studies of structural concepts for future large space structures such as the Heliogyro solar sailer. The derivation is based on Hamilton's variational principle and includes the effect of initial geometric imperfections (axial, curvature, and twist) on the line-element dynamics. For comparison with previous work, the nonlinear equations are reduced to a linearized form frequently found in the literature. The comparison has revealed several new spin-stiffening terms that have not been previously identified and/or retained. They combine geometric imperfections, rotary inertia, Coriolis, and gyroscopic terms.

Stochastic Time Models of Syllable Structure

PubMed Central

Shaw, Jason A.; Gafos, Adamantios I.

2015-01-01

Drawing on phonology research within the generative linguistics tradition, stochastic methods, and notions from complex systems, we develop a modelling paradigm linking phonological structure, expressed in terms of syllables, to speech movement data acquired with 3D electromagnetic articulography and X-ray microbeam methods. The essential variable in the models is syllable structure. When mapped to discrete coordination topologies, syllabic organization imposes systematic patterns of variability on the temporal dynamics of speech articulation. We simulated these dynamics under different syllabic parses and evaluated simulations against experimental data from Arabic and English, two languages claimed to parse similar strings of segments into different syllabic structures. Model simulations replicated several key experimental results, including the fallibility of past phonetic heuristics for syllable structure, and exposed the range of conditions under which such heuristics remain valid. More importantly, the modelling approach consistently diagnosed syllable structure proving resilient to multiple sources of variability in experimental data including measurement variability, speaker variability, and contextual variability. Prospects for extensions of our modelling paradigm to acoustic data are also discussed. PMID:25996153

Curing dynamics of photopolymers measured by single-shot heterodyne transient grating method.

PubMed

Arai, Mika; Fujii, Tomomi; Inoue, Hayato; Kuwahara, Shota; Katayama, Kenji

2013-01-01

The heterodyne transient grating (HD-TG) method was first applied to the curing dynamics measurement of photopolymers. The curing dynamics for various monomers including an initiator (2.5 vol%) was monitored optically via the refractive index change after a single UV pulse irradiation. We could obtain the polymerization time and the final change in the refractive index, and the parameters were correlated with the viscosity, molecular structure, and reaction sites. As the polymerization time was longer, the final refractive change was larger, and the polymerization time was explained in terms of the monomer properties.

Unfolding stabilities of two structurally similar proteins as probed by temperature-induced and force-induced molecular dynamics simulations.

PubMed

Gorai, Biswajit; Prabhavadhni, Arasu; Sivaraman, Thirunavukkarasu

2015-09-01

Unfolding stabilities of two homologous proteins, cardiotoxin III and short-neurotoxin (SNTX) belonging to three-finger toxin (TFT) superfamily, have been probed by means of molecular dynamics (MD) simulations. Combined analysis of data obtained from steered MD and all-atom MD simulations at various temperatures in near physiological conditions on the proteins suggested that overall structural stabilities of the two proteins were different from each other and the MD results are consistent with experimental data of the proteins reported in the literature. Rationalization for the differential structural stabilities of the structurally similar proteins has been chiefly attributed to the differences in the structural contacts between C- and N-termini regions in their three-dimensional structures, and the findings endorse the 'CN network' hypothesis proposed to qualitatively analyse the thermodynamic stabilities of proteins belonging to TFT superfamily of snake venoms. Moreover, the 'CN network' hypothesis has been revisited and the present study suggested that 'CN network' should be accounted in terms of 'structural contacts' and 'structural strengths' in order to precisely describe order of structural stabilities of TFTs.

An Atomistic View of Amyloidogenic Self-assembly: Structure and Dynamics of Heterogeneous Conformational States in the Pre-nucleation Phase

PubMed Central

Matthes, Dirk; Gapsys, Vytautas; Brennecke, Julian T.; de Groot, Bert L.

2016-01-01

The formation of well-defined filamentous amyloid structures involves a polydisperse collection of oligomeric states for which relatively little is known in terms of structural organization. Here we use extensive, unbiased explicit solvent molecular dynamics (MD) simulations to investigate the structural and dynamical features of oligomeric aggregates formed by a number of highly amyloidogenic peptides at atomistic resolution on the μs time scale. A consensus approach has been adopted to analyse the simulations in multiple force fields, yielding an in-depth characterization of pre-fibrillar oligomers and their global and local structure properties. A collision cross section analysis revealed structurally heterogeneous aggregate ensembles for the individual oligomeric states that lack a single defined quaternary structure during the pre-nucleation phase. To gain insight into the conformational space sampled in early aggregates, we probed their substructure and found emerging β-sheet subunit layers and a multitude of ordered intermolecular β-structure motifs with growing aggregate size. Among those, anti-parallel out-of-register β-strands compatible with toxic β-barrel oligomers were particularly prevalent already in smaller aggregates and formed prior to ordered fibrillar structure elements. Notably, also distinct fibril-like conformations emerged in the oligomeric state and underscore the notion that pre-nucleated oligomers serve as a critical intermediate step on-pathway to fibrils. PMID:27616019

Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms

PubMed Central

Stone, John E.; Hynninen, Antti-Pekka; Phillips, James C.; Schulten, Klaus

2017-01-01

All-atom molecular dynamics simulations of biomolecules provide a powerful tool for exploring the structure and dynamics of large protein complexes within realistic cellular environments. Unfortunately, such simulations are extremely demanding in terms of their computational requirements, and they present many challenges in terms of preparation, simulation methodology, and analysis and visualization of results. We describe our early experiences porting the popular molecular dynamics simulation program NAMD and the simulation preparation, analysis, and visualization tool VMD to GPU-accelerated OpenPOWER hardware platforms. We report our experiences with compiler-provided autovectorization and compare with hand-coded vector intrinsics for the POWER8 CPU. We explore the performance benefits obtained from unique POWER8 architectural features such as 8-way SMT and its value for particular molecular modeling tasks. Finally, we evaluate the performance of several GPU-accelerated molecular modeling kernels and relate them to other hardware platforms. PMID:29202130

Research Program Overview

Science.gov Websites

coordinates research in support of the PEER mission in performance-based earthquake engineering. The broad system dynamic response; assessment of the performance of the structural and nonstructural systems ; consequences in terms of casualties, capital costs, and post-earthquake functionality; and decision-making to

Psychosynthesis: The Metapsychology of Roberto Assagioli.

ERIC Educational Resources Information Center

Petrie, R. Donna

1983-01-01

Attempts to fill in the gap in the literature regarding Assagioli's theories by: (1) summarizing the assumptions, terms, and concepts of psychosynthesis; (2) presenting the structure and dynamics of the personality theory; and (3) providing illustrations of the theory's application. Discusses the implications of these points. (JAC)

Decorrelation dynamics and spectra in drift-Alfven turbulence

NASA Astrophysics Data System (ADS)

Fernandez Garcia, Eduardo

Motivated by the inability of one-fluid magnetohydrodynamics (MHD) to explain key turbulence characteristics in systems ranging from the solar wind and interstellar medium to fusion devices like the reversed field pinch, this thesis studies magnetic turbulence using a drift-Alfven model that extends MHD by including electron density dynamics. Electron effects play a significant role in the dynamics by changing the structure of turbulent decorrelation in the Alfvenic regime (where fast Alfvenic propagation provides the fastest decorrelation of the system): besides the familiar counter-propagating Alfvenic branches of MHD, an additional branch tied to the diamagnetic and eddy-turn- over rates enters in the turbulent response. This kinematic branch gives hydrodynamic features to turbulence that is otherwise strongly magnetic. Magnetic features are observed in the RMS frequency, energy partitions, cross-field energy transfer and in the turbulent response, whereas hydrodynamic features appear in the average frequency, self-field transfer, turbulent response and finally the wavenumber spectrum. These features are studied via renormalized closure theory and numerical simulation. The closure calculation naturally incorporates the eigenmode structure of the turbulent response in specifying spectral energy balance equations for the magnetic, kinetic and internal (density) energies. Alfvenic terms proportional to cross correlations and involved in cross field transfer compete with eddy-turn-over, self transfer, auto-correlation terms. In the steady state, the kinematic terms dominate the energy balances and yield a 5/3 Kolmogorov spectrum (as observed in the interstellar medium) for the three field energies in the strong turbulence, long wavelength limit. Alfvenic terms establish equipartition of kinetic and magnetic energies. In the limit where wavelengths are short compared to the gyroradius, the Alfvenic terms equipartition the internal and magnetic energies resulting in a steep (-2) spectrum fall-off for those energies while the largely uncoupled kinetic modes still obey a 5/3 law. From the numerical simulations, the response function of drift-Alfven turbulence is measured. Here, a statistical ensemble is constructed from small perturbations of the turbulent amplitudes at fixed wavenumber. The decorrelation structure born out of the eigenmode calculation is verified in the numerical measurement.

Translation invariant time-dependent massive gravity: Hamiltonian analysis

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

Mourad, Jihad; Steer, Danièle A.; Noui, Karim, E-mail: mourad@apc.univ-paris7.fr, E-mail: karim.noui@lmpt.univ-tours.fr, E-mail: steer@apc.univ-paris7.fr

2014-09-01

The canonical structure of the massive gravity in the first order moving frame formalism is studied. We work in the simplified context of translation invariant fields, with mass terms given by general non-derivative interactions, invariant under the diagonal Lorentz group, depending on the moving frame as well as a fixed reference frame. We prove that the only mass terms which give 5 propagating degrees of freedom are the dRGT mass terms, namely those which are linear in the lapse. We also complete the Hamiltonian analysis with the dynamical evolution of the system.

Recursive thoughts on the simulation of the flexible multibody dynamics of slender offshore structures

NASA Astrophysics Data System (ADS)

Schilder, J.; Ellenbroek, M.; de Boer, A.

2017-12-01

In this work, the floating frame of reference formulation is used to create a flexible multibody model of slender offshore structures such as pipelines and risers. It is shown that due to the chain-like topology of the considered structures, the equation of motion can be expressed in terms of absolute interface coordinates. In the presented form, kinematic constraint equations are satisfied explicitly and the Lagrange multipliers are eliminated from the equations. Hence, the structures can be conveniently coupled to finite element or multibody models of for example seabed and vessel. The chain-like topology enables the efficient use of recursive solution procedures for both transient dynamic analysis and equilibrium analysis. For this, the transfer matrix method is used. In order to improve the convergence of the equilibrium analysis, the analytical solution of an ideal catenary is used as an initial configuration, reducing the number of required iterations.

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.

Moral motivation based on multiple developmental structures: an exploration of cognitive and emotional dynamics.

PubMed

Kaplan, Ulas; Tivnan, Terrence

2014-01-01

Intrapersonal variability and multiplicity in the complexity of moral motivation were examined from Dynamic Systems and Self-Determination Theory perspectives. L. Kohlberg's (1969) stages of moral development are reconceptualized as soft-assembled and dynamically transformable process structures of motivation that may operate simultaneously within person in different degrees. Moral motivation is conceptualized as the real-time process of self-organization of cognitive and emotional dynamics out of which moral judgment and action emerge. A detailed inquiry into intrapersonal variation in moral motivation is carried out based on the differential operation of multiple motivational structures. A total of 74 high school students and 97 college students participated in the study by completing a new questionnaire, involving 3 different hypothetical moral judgments. As hypothesized, findings revealed significant multiplicity in the within-person operation of developmental stage structures, and intrapersonal variability in the degrees to which stages were used. Developmental patterns were found in terms of different distributions of multiple stages between high school and college samples, as well as the association between age and overall motivation scores. Differential relations of specific emotions to moral motivation revealed and confirmed the value of differentiating multiple emotions. Implications of the present theoretical perspective and the findings for understanding the complexity of moral judgment and motivation are discussed.

Generalised teleparallel quintom dark energy non-minimally coupled with the scalar torsion and a boundary term

NASA Astrophysics Data System (ADS)

Bahamonde, Sebastian; Marciu, Mihai; Rudra, Prabir

2018-04-01

Within this work, we propose a new generalised quintom dark energy model in the teleparallel alternative of general relativity theory, by considering a non-minimal coupling between the scalar fields of a quintom model with the scalar torsion component T and the boundary term B. In the teleparallel alternative of general relativity theory, the boundary term represents the divergence of the torsion vector, B=2∇μTμ, and is related to the Ricci scalar R and the torsion scalar T, by the fundamental relation: R=‑T+B. We have investigated the dynamical properties of the present quintom scenario in the teleparallel alternative of general relativity theory by performing a dynamical system analysis in the case of decomposable exponential potentials. The study analysed the structure of the phase space, revealing the fundamental dynamical effects of the scalar torsion and boundary couplings in the case of a more general quintom scenario. Additionally, a numerical approach to the model is presented to analyse the cosmological evolution of the system.

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids.

PubMed

Aradi, Bálint; Niklasson, Anders M N; Frauenheim, Thomas

2015-07-14

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. For systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can be applied to a broad range of problems in materials science, chemistry, and biology.

Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations.

PubMed

Takada, Shoji; Kanada, Ryo; Tan, Cheng; Terakawa, Tsuyoshi; Li, Wenfei; Kenzaki, Hiroo

2015-12-15

Due to hierarchic nature of biomolecular systems, their computational modeling calls for multiscale approaches, in which coarse-grained (CG) simulations are used to address long-time dynamics of large systems. Here, we review recent developments and applications of CG modeling methods, focusing on our methods primarily for proteins, DNA, and their complexes. These methods have been implemented in the CG biomolecular simulator, CafeMol. Our CG model has resolution such that ∼10 non-hydrogen atoms are grouped into one CG particle on average. For proteins, each amino acid is represented by one CG particle. For DNA, one nucleotide is simplified by three CG particles, representing sugar, phosphate, and base. The protein modeling is based on the idea that proteins have a globally funnel-like energy landscape, which is encoded in the structure-based potential energy function. We first describe two representative minimal models of proteins, called the elastic network model and the classic Go̅ model. We then present a more elaborate protein model, which extends the minimal model to incorporate sequence and context dependent local flexibility and nonlocal contacts. For DNA, we describe a model developed by de Pablo's group that was tuned to well reproduce sequence-dependent structural and thermodynamic experimental data for single- and double-stranded DNAs. Protein-DNA interactions are modeled either by the structure-based term for specific cases or by electrostatic and excluded volume terms for nonspecific cases. We also discuss the time scale mapping in CG molecular dynamics simulations. While the apparent single time step of our CGMD is about 10 times larger than that in the fully atomistic molecular dynamics for small-scale dynamics, large-scale motions can be further accelerated by two-orders of magnitude with the use of CG model and a low friction constant in Langevin dynamics. Next, we present four examples of applications. First, the classic Go̅ model was used to emulate one ATP cycle of a molecular motor, kinesin. Second, nonspecific protein-DNA binding was studied by a combination of elaborate protein and DNA models. Third, a transcription factor, p53, that contains highly fluctuating regions was simulated on two perpendicularly arranged DNA segments, addressing intersegmental transfer of p53. Fourth, we simulated structural dynamics of dinucleosomes connected by a linker DNA finding distinct types of internucleosome docking and salt-concentration-dependent compaction. Finally, we discuss many of limitations in the current approaches and future directions. Especially, more accurate electrostatic treatment and a phospholipid model that matches our CG resolutions are of immediate importance.

Microgravity Foam Structure and Rheology

NASA Technical Reports Server (NTRS)

Durian, Douglas J.

1996-01-01

The objective of this research was to exploit rheological and multiple-light scattering techniques, and ultimately microgravity conditions, in order to quantify and elucidate the unusual elastic character of foams in terms of their underlying microscopic structure and dynamics. Special interest was in determining how this elastic character vanishes, i.e. how the foam melts into a simple viscous liquid, as a function of both increasing liquid content and shear strain rate.

The Zel'dovich approximation: key to understanding cosmic web complexity

NASA Astrophysics Data System (ADS)

Hidding, Johan; Shandarin, Sergei F.; van de Weygaert, Rien

2014-02-01

We describe how the dynamics of cosmic structure formation defines the intricate geometric structure of the spine of the cosmic web. The Zel'dovich approximation is used to model the backbone of the cosmic web in terms of its singularity structure. The description by Arnold et al. in terms of catastrophe theory forms the basis of our analysis. This two-dimensional analysis involves a profound assessment of the Lagrangian and Eulerian projections of the gravitationally evolving four-dimensional phase-space manifold. It involves the identification of the complete family of singularity classes, and the corresponding caustics that we see emerging as structure in Eulerian space evolves. In particular, as it is instrumental in outlining the spatial network of the cosmic web, we investigate the nature of spatial connections between these singularities. The major finding of our study is that all singularities are located on a set of lines in Lagrangian space. All dynamical processes related to the caustics are concentrated near these lines. We demonstrate and discuss extensively how all 2D singularities are to be found on these lines. When mapping this spatial pattern of lines to Eulerian space, we find a growing connectedness between initially disjoint lines, resulting in a percolating network. In other words, the lines form the blueprint for the global geometric evolution of the cosmic web.

Dancing to the rhythms of the Pleistocene? Early Middle Paleolithic population dynamics in NW Iberia (Duero Basin and Cantabrian Region)

NASA Astrophysics Data System (ADS)

Sánchez Yustos, Policarpo; Diez Martín, Fernando

2015-08-01

The Northwest of Iberia has yielded one of the most complete European Middle Paleolithic records. Despite this wealth of information, very little is known about population dynamics during this period. For that reason, the main concern of this paper is to provide socio-environmental models that may help explain Early Middle Paleolithic (EMP) population dynamics in NW Iberia, assessing to what extent they were shaped by climate forces. The archaeological record is analyzed on the basis of the heuristics of ecological models, already employed in the European Pleistocene record but never at a regional scale, in order to detect long-term changes in the composition of EMP populations, and the environmental, biological and sociocultural process influencing those changes. According to the models proposed, we have detected a long-term population dynamic between MIS 11 and MIS 6, characterized by low environmental stress, high biological productivity, interaction among populations and sociocultural complexity. Eventually, this population dynamic was broken due to an extreme climate phase in late MIS 6 that had a profound impact on populations and sociocultural structures. As a result, the Upper Pleistocene population of NW Iberia was concentrated in the Cantabrian region. This area became an isolated Neanderthal glacial refugium that hosted a population with different origins and fragile long-term demographic stability.

Dynamic Scaling of Colloidal Gel Formation at Intermediate Concentrations

DOE PAGES

Zhang, Qingteng; Bahadur, Divya; Dufresne, Eric M.; ...

2017-10-25

Here, we have examined the formation and dissolution of gels composed of intermediate volume-fraction nanoparticles with temperature-dependent short-range attractions using small-angle x-ray scatter- ing (SAXS), x-ray photon correlation spectroscopy (XPCS), and rheology to obtain nanoscale and macroscale sensitivity to structure and dynamics. Gel formation after temperature quenches to the vicinity of the rheologically-determined gel temperature, T gel, was characterized via the slow-down of dynamics and changes in microstructure observed in the intensity autocorrelation functions and structure factor, respectively, as a function of quench depth (ΔT = T quench - T gel), wave vector, and formation time (t f). We findmore » similar patterns in the slow-down of dynamics that maps the wave-vector-dependent dynamics at a particular ΔT and t f to that at other ΔTs and t fs via an effective scaling temperature, Ts. A single Ts applies to a broad range of ΔT and tf but does depend on the particle size. The rate of formation implied by the scaling is a far stronger function of ΔT than that of the attraction strength between colloids. Finally, we interpret this strong temperature de- pendence in terms of changes in cooperative bonding required to form stable, energetically favored, local structures.« less

Dynamic Scaling of Colloidal Gel Formation at Intermediate Concentrations

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

Zhang, Qingteng; Bahadur, Divya; Dufresne, Eric M.

Here, we have examined the formation and dissolution of gels composed of intermediate volume-fraction nanoparticles with temperature-dependent short-range attractions using small-angle x-ray scatter- ing (SAXS), x-ray photon correlation spectroscopy (XPCS), and rheology to obtain nanoscale and macroscale sensitivity to structure and dynamics. Gel formation after temperature quenches to the vicinity of the rheologically-determined gel temperature, T gel, was characterized via the slow-down of dynamics and changes in microstructure observed in the intensity autocorrelation functions and structure factor, respectively, as a function of quench depth (ΔT = T quench - T gel), wave vector, and formation time (t f). We findmore » similar patterns in the slow-down of dynamics that maps the wave-vector-dependent dynamics at a particular ΔT and t f to that at other ΔTs and t fs via an effective scaling temperature, Ts. A single Ts applies to a broad range of ΔT and tf but does depend on the particle size. The rate of formation implied by the scaling is a far stronger function of ΔT than that of the attraction strength between colloids. Finally, we interpret this strong temperature de- pendence in terms of changes in cooperative bonding required to form stable, energetically favored, local structures.« less

Structural analysis of eyespots: dynamics of morphogenic signals that govern elemental positions in butterfly wings

PubMed Central

2012-01-01

Background To explain eyespot colour-pattern determination in butterfly wings, the induction model has been discussed based on colour-pattern analyses of various butterfly eyespots. However, a detailed structural analysis of eyespots that can serve as a foundation for future studies is still lacking. In this study, fundamental structural rules related to butterfly eyespots are proposed, and the induction model is elaborated in terms of the possible dynamics of morphogenic signals involved in the development of eyespots and parafocal elements (PFEs) based on colour-pattern analysis of the nymphalid butterfly Junonia almana. Results In a well-developed eyespot, the inner black core ring is much wider than the outer black ring; this is termed the inside-wide rule. It appears that signals are wider near the focus of the eyespot and become narrower as they expand. Although fundamental signal dynamics are likely to be based on a reaction-diffusion mechanism, they were described well mathematically as a type of simple uniformly decelerated motion in which signals associated with the outer and inner black rings of eyespots and PFEs are released at different time points, durations, intervals, and initial velocities into a two-dimensional field of fundamentally uniform or graded resistance; this produces eyespots and PFEs that are diverse in size and structure. The inside-wide rule, eyespot distortion, structural differences between small and large eyespots, and structural changes in eyespots and PFEs in response to physiological treatments were explained well using mathematical simulations. Natural colour patterns and previous experimental findings that are not easily explained by the conventional gradient model were also explained reasonably well by the formal mathematical simulations performed in this study. Conclusions In a mode free from speculative molecular interactions, the present study clarifies fundamental structural rules related to butterfly eyespots, delineates a theoretical basis for the induction model, and proposes a mathematically simple mode of long-range signalling that may reflect developmental mechanisms associated with butterfly eyespots. PMID:22409965

Structural analysis of eyespots: dynamics of morphogenic signals that govern elemental positions in butterfly wings.

PubMed

Otaki, Joji M

2012-03-13

To explain eyespot colour-pattern determination in butterfly wings, the induction model has been discussed based on colour-pattern analyses of various butterfly eyespots. However, a detailed structural analysis of eyespots that can serve as a foundation for future studies is still lacking. In this study, fundamental structural rules related to butterfly eyespots are proposed, and the induction model is elaborated in terms of the possible dynamics of morphogenic signals involved in the development of eyespots and parafocal elements (PFEs) based on colour-pattern analysis of the nymphalid butterfly Junonia almana. In a well-developed eyespot, the inner black core ring is much wider than the outer black ring; this is termed the inside-wide rule. It appears that signals are wider near the focus of the eyespot and become narrower as they expand. Although fundamental signal dynamics are likely to be based on a reaction-diffusion mechanism, they were described well mathematically as a type of simple uniformly decelerated motion in which signals associated with the outer and inner black rings of eyespots and PFEs are released at different time points, durations, intervals, and initial velocities into a two-dimensional field of fundamentally uniform or graded resistance; this produces eyespots and PFEs that are diverse in size and structure. The inside-wide rule, eyespot distortion, structural differences between small and large eyespots, and structural changes in eyespots and PFEs in response to physiological treatments were explained well using mathematical simulations. Natural colour patterns and previous experimental findings that are not easily explained by the conventional gradient model were also explained reasonably well by the formal mathematical simulations performed in this study. In a mode free from speculative molecular interactions, the present study clarifies fundamental structural rules related to butterfly eyespots, delineates a theoretical basis for the induction model, and proposes a mathematically simple mode of long-range signalling that may reflect developmental mechanisms associated with butterfly eyespots.

Critical neural networks with short- and long-term plasticity.

PubMed

Michiels van Kessenich, L; Luković, M; de Arcangelis, L; Herrmann, H J

2018-03-01

In recent years self organized critical neuronal models have provided insights regarding the origin of the experimentally observed avalanching behavior of neuronal systems. It has been shown that dynamical synapses, as a form of short-term plasticity, can cause critical neuronal dynamics. Whereas long-term plasticity, such as Hebbian or activity dependent plasticity, have a crucial role in shaping the network structure and endowing neural systems with learning abilities. In this work we provide a model which combines both plasticity mechanisms, acting on two different time scales. The measured avalanche statistics are compatible with experimental results for both the avalanche size and duration distribution with biologically observed percentages of inhibitory neurons. The time series of neuronal activity exhibits temporal bursts leading to 1/f decay in the power spectrum. The presence of long-term plasticity gives the system the ability to learn binary rules such as xor, providing the foundation of future research on more complicated tasks such as pattern recognition.

Critical neural networks with short- and long-term plasticity

NASA Astrophysics Data System (ADS)

Michiels van Kessenich, L.; Luković, M.; de Arcangelis, L.; Herrmann, H. J.

2018-03-01

In recent years self organized critical neuronal models have provided insights regarding the origin of the experimentally observed avalanching behavior of neuronal systems. It has been shown that dynamical synapses, as a form of short-term plasticity, can cause critical neuronal dynamics. Whereas long-term plasticity, such as Hebbian or activity dependent plasticity, have a crucial role in shaping the network structure and endowing neural systems with learning abilities. In this work we provide a model which combines both plasticity mechanisms, acting on two different time scales. The measured avalanche statistics are compatible with experimental results for both the avalanche size and duration distribution with biologically observed percentages of inhibitory neurons. The time series of neuronal activity exhibits temporal bursts leading to 1 /f decay in the power spectrum. The presence of long-term plasticity gives the system the ability to learn binary rules such as xor, providing the foundation of future research on more complicated tasks such as pattern recognition.

Earth Structure, Ice Mass Changes, and the Local Dynamic Geoid

NASA Astrophysics Data System (ADS)

Harig, C.; Simons, F. J.

2014-12-01

Spherical Slepian localization functions are a useful method for studying regional mass changes observed by satellite gravimetry. By projecting data onto a sparse basis set, the local field can be estimated more easily than with the full spherical harmonic basis. We have used this method previously to estimate the ice mass change in Greenland from GRACE data, and it can also be applied to other planetary problems such as global magnetic fields. Earth's static geoid, in contrast to the time-variable field, is in large part related to the internal density and rheological structure of the Earth. Past studies have used dynamic geoid kernels to relate this density structure and the internal deformation it induces to the surface geopotential at large scales. These now classical studies of the eighties and nineties were able to estimate the mantle's radial rheological profile, placing constraints on the ratio between upper and lower mantle viscosity. By combining these two methods, spherical Slepian localization and dynamic geoid kernels, we have created local dynamic geoid kernels which are sensitive only to density variations within an area of interest. With these kernels we can estimate the approximate local radial rheological structure that best explains the locally observed geoid on a regional basis. First-order differences of the regional mantle viscosity structure are accessible to this technique. In this contribution we present our latest, as yet unpublished results on the geographical and temporal pattern of ice mass changes in Antarctica over the past decade, and we introduce a new approach to extract regional information about the internal structure of the Earth from the static global gravity field. Both sets of results are linked in terms of the relevant physics, but also in being developed from the marriage of Slepian functions and geoid kernels. We make predictions on the utility of our approach to derive fully three-dimensional rheological Earth models, to be used for corrections for glacio-isostatic adjustment, as necessary for the interpretation of time-variable gravity observations in terms of ice sheet mass-balance studies.

Mode decomposition and Lagrangian structures of the flow dynamics in orbitally shaken bioreactors

NASA Astrophysics Data System (ADS)

Weheliye, Weheliye Hashi; Cagney, Neil; Rodriguez, Gregorio; Micheletti, Martina; Ducci, Andrea

2018-03-01

In this study, two mode decomposition techniques were applied and compared to assess the flow dynamics in an orbital shaken bioreactor (OSB) of cylindrical geometry and flat bottom: proper orthogonal decomposition and dynamic mode decomposition. Particle Image Velocimetry (PIV) experiments were carried out for different operating conditions including fluid height, h, and shaker rotational speed, N. A detailed flow analysis is provided for conditions when the fluid and vessel motions are in-phase (Fr = 0.23) and out-of-phase (Fr = 0.47). PIV measurements in vertical and horizontal planes were combined to reconstruct low order models of the full 3D flow and to determine its Finite-Time Lyapunov Exponent (FTLE) within OSBs. The combined results from the mode decomposition and the FTLE fields provide a useful insight into the flow dynamics and Lagrangian coherent structures in OSBs and offer a valuable tool to optimise bioprocess design in terms of mixing and cell suspension.

Young's moduli of carbon materials investigated by various classical molecular dynamics schemes

NASA Astrophysics Data System (ADS)

Gayk, Florian; Ehrens, Julian; Heitmann, Tjark; Vorndamme, Patrick; Mrugalla, Andreas; Schnack, Jürgen

2018-05-01

For many applications classical carbon potentials together with classical molecular dynamics are employed to calculate structures and physical properties of such carbon-based materials where quantum mechanical methods fail either due to the excessive size, irregular structure or long-time dynamics. Although such potentials, as for instance implemented in LAMMPS, yield reasonably accurate bond lengths and angles for several carbon materials such as graphene, it is not clear how accurate they are in terms of mechanical properties such as for instance Young's moduli. We performed large-scale classical molecular dynamics investigations of three carbon-based materials using the various potentials implemented in LAMMPS as well as the EDIP potential of Marks. We show how the Young's moduli vary with classical potentials and compare to experimental results. Since classical descriptions of carbon are bound to be approximations it is not astonishing that different realizations yield differing results. One should therefore carefully check for which observables a certain potential is suited. Our aim is to contribute to such a clarification.

Dynamic Analysis and Control of Lightweight Manipulators with Flexible Parallel Link Mechanisms. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Lee, Jeh Won

1990-01-01

The objective is the theoretical analysis and the experimental verification of dynamics and control of a two link flexible manipulator with a flexible parallel link mechanism. Nonlinear equations of motion of the lightweight manipulator are derived by the Lagrangian method in symbolic form to better understand the structure of the dynamic model. The resulting equation of motion have a structure which is useful to reduce the number of terms calculated, to check correctness, or to extend the model to higher order. A manipulator with a flexible parallel link mechanism is a constrained dynamic system whose equations are sensitive to numerical integration error. This constrained system is solved using singular value decomposition of the constraint Jacobian matrix. Elastic motion is expressed by the assumed mode method. Mode shape functions of each link are chosen using the load interfaced component mode synthesis. The discrepancies between the analytical model and the experiment are explained using a simplified and a detailed finite element model.

Detecting Molecular Rotational Dynamics Complementing the Low-Frequency Terahertz Vibrations in a Zirconium-Based Metal-Organic Framework

NASA Astrophysics Data System (ADS)

Ryder, Matthew R.; Van de Voorde, Ben; Civalleri, Bartolomeo; Bennett, Thomas D.; Mukhopadhyay, Sanghamitra; Cinque, Gianfelice; Fernandez-Alonso, Felix; De Vos, Dirk; Rudić, Svemir; Tan, Jin-Chong

2017-06-01

We show clear experimental evidence of cooperative terahertz (THz) dynamics observed below 3 THz (˜100 cm-1 ), for a low-symmetry Zr-based metal-organic framework structure, termed MIL-140A [ZrO (O2C-C 6H4-CO2) ]. Utilizing a combination of high-resolution inelastic neutron scattering and synchrotron radiation far-infrared spectroscopy, we measured low-energy vibrations originating from the hindered rotations of organic linkers, whose energy barriers and detailed dynamics have been elucidated via ab initio density functional theory calculations. The complex pore architecture caused by the THz rotations has been characterized. We discovered an array of soft modes with trampolinelike motions, which could potentially be the source of anomalous mechanical phenomena such as negative thermal expansion. Our results demonstrate coordinated shear dynamics (2.47 THz), a mechanism which we have shown to destabilize the framework structure, in the exact crystallographic direction of the minimum shear modulus (Gmin ).

Multi-scale compositionality: identifying the compositional structures of social dynamics using deep learning.

PubMed

Peng, Huan-Kai; Marculescu, Radu

2015-01-01

Social media exhibit rich yet distinct temporal dynamics which cover a wide range of different scales. In order to study this complex dynamics, two fundamental questions revolve around (1) the signatures of social dynamics at different time scales, and (2) the way in which these signatures interact and form higher-level meanings. In this paper, we propose the Recursive Convolutional Bayesian Model (RCBM) to address both of these fundamental questions. The key idea behind our approach consists of constructing a deep-learning framework using specialized convolution operators that are designed to exploit the inherent heterogeneity of social dynamics. RCBM's runtime and convergence properties are guaranteed by formal analyses. Experimental results show that the proposed method outperforms the state-of-the-art approaches both in terms of solution quality and computational efficiency. Indeed, by applying the proposed method on two social network datasets, Twitter and Yelp, we are able to identify the compositional structures that can accurately characterize the complex social dynamics from these two social media. We further show that identifying these patterns can enable new applications such as anomaly detection and improved social dynamics forecasting. Finally, our analysis offers new insights on understanding and engineering social media dynamics, with direct applications to opinion spreading and online content promotion.

Multi-Scale Compositionality: Identifying the Compositional Structures of Social Dynamics Using Deep Learning

PubMed Central

Peng, Huan-Kai; Marculescu, Radu

2015-01-01

Objective Social media exhibit rich yet distinct temporal dynamics which cover a wide range of different scales. In order to study this complex dynamics, two fundamental questions revolve around (1) the signatures of social dynamics at different time scales, and (2) the way in which these signatures interact and form higher-level meanings. Method In this paper, we propose the Recursive Convolutional Bayesian Model (RCBM) to address both of these fundamental questions. The key idea behind our approach consists of constructing a deep-learning framework using specialized convolution operators that are designed to exploit the inherent heterogeneity of social dynamics. RCBM’s runtime and convergence properties are guaranteed by formal analyses. Results Experimental results show that the proposed method outperforms the state-of-the-art approaches both in terms of solution quality and computational efficiency. Indeed, by applying the proposed method on two social network datasets, Twitter and Yelp, we are able to identify the compositional structures that can accurately characterize the complex social dynamics from these two social media. We further show that identifying these patterns can enable new applications such as anomaly detection and improved social dynamics forecasting. Finally, our analysis offers new insights on understanding and engineering social media dynamics, with direct applications to opinion spreading and online content promotion. PMID:25830775

Measuring succession: methods for establishing long term vegetation monitoring sites

USDA-ARS?s Scientific Manuscript database

Successional stages are often characterized by dominant plant species (species with the highest cover) and their effect on the structure and function of an area through time. However, the plant species determining the ecosystem properties and plant community dynamics may not be the dominant, especia...

Population Dynamics of Genetic Regulatory Networks

NASA Astrophysics Data System (ADS)

Braun, Erez

2005-03-01

Unlike common objects in physics, a biological cell processes information. The cell interprets its genome and transforms the genomic information content, through the action of genetic regulatory networks, into proteins which in turn dictate its metabolism, functionality and morphology. Understanding the dynamics of a population of biological cells presents a unique challenge. It requires to link the intracellular dynamics of gene regulation, through the mechanism of cell division, to the level of the population. We present experiments studying adaptive dynamics of populations of genetically homogeneous microorganisms (yeast), grown for long durations under steady conditions. We focus on population dynamics that do not involve random genetic mutations. Our experiments follow the long-term dynamics of the population distributions and allow to quantify the correlations among generations. We focus on three interconnected issues: adaptation of genetically homogeneous populations following environmental changes, selection processes on the population and population variability and expression distributions. We show that while the population exhibits specific short-term responses to environmental inputs, it eventually adapts to a robust steady-state, largely independent of external conditions. Cycles of medium-switch show that the adapted state is imprinted in the population and that this memory is maintained for many generations. To further study population adaptation, we utilize the process of gene recruitment whereby a gene naturally regulated by a specific promoter is placed under a different regulatory system. This naturally occurring process has been recognized as a major driving force in evolution. We have recruited an essential gene to a foreign regulatory network and followed the population long-term dynamics. Rewiring of the regulatory network allows us to expose their complex dynamics and phase space structure.

Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS.

PubMed

Grindon, Christina; Harris, Sarah; Evans, Tom; Novik, Keir; Coveney, Peter; Laughton, Charles

2004-07-15

Molecular modelling played a central role in the discovery of the structure of DNA by Watson and Crick. Today, such modelling is done on computers: the more powerful these computers are, the more detailed and extensive can be the study of the dynamics of such biological macromolecules. To fully harness the power of modern massively parallel computers, however, we need to develop and deploy algorithms which can exploit the structure of such hardware. The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a scalable molecular dynamics code including long-range Coulomb interactions, which has been specifically designed to function efficiently on parallel platforms. Here we describe the implementation of the AMBER98 force field in LAMMPS and its validation for molecular dynamics investigations of DNA structure and flexibility against the benchmark of results obtained with the long-established code AMBER6 (Assisted Model Building with Energy Refinement, version 6). Extended molecular dynamics simulations on the hydrated DNA dodecamer d(CTTTTGCAAAAG)(2), which has previously been the subject of extensive dynamical analysis using AMBER6, show that it is possible to obtain excellent agreement in terms of static, dynamic and thermodynamic parameters between AMBER6 and LAMMPS. In comparison with AMBER6, LAMMPS shows greatly improved scalability in massively parallel environments, opening up the possibility of efficient simulations of order-of-magnitude larger systems and/or for order-of-magnitude greater simulation times.

Development of a cyber physical apparatus for investigating fluid structure interaction on leading edge vortex evolution

NASA Astrophysics Data System (ADS)

Raghu Gowda, Belagumba Venkatachalaiah

This dissertation examines how simple structural compliance impacts a specific transient vortex phenomenon that occurs on high angle of attack lifting surfaces termed dynamic stall. In many Fluid structure interaction (FSI) research efforts, a purely physical or purely computational approach is taken. In this work a low cost cyber-physical (CPFD) system is designed and developed for representing the FSI in the leading edge vortex (LEV) development problem. The leading edge compliance appears to be favorable in a specific spring constant range for a given wing. When the leading edge compliance prescribed via CPFD system is too low compared with the moment due to dynamic pressure or fluid unsteady effect, the LEV behavior is similar to that of a rigid wing system. When the leading edge compliance is too high, excessive compliance is introduced into the wing system and the leading edge vortex evolution is affected by the large change in wing angle. At moderate leading edge compliance, a balance appears to be achieved in which the leading edge vorticity shedding rate supports the long term evolution of the leading edge vortex. Further investigation is required to determine specific parameters governing these leading edge compliance ranges.

Significance of Dynamic Pore Pressure Variations - Comparison of Observations on Mud Volcanoes on the Costa Rica Margin and in the Gulf of Cadiz

NASA Astrophysics Data System (ADS)

Brueckmann, W.; Linke, P.; Pieper, M.; Hensen, C.; Tuerk, M.

2006-12-01

Research in the cooperative research center (SFB) 574 "Volatiles and Fluids in Subduction Zones" at the University Kiel focuses on volatile and fluid exchange processes at subduction zones. These have a significant impact on the long-term geochemical evolution of the hydrosphere and atmosphere. In the SFB 574 working area off Central America more than 120 mud volcanoes, mud diapirs and cold seeps have been identified and sampled. To better understand the internal dynamics of these structures and the temporal variability of fluid expulsion an in-situ tool for monitoring shallow pore pressure variations was devised. The tool (PWPL) monitors pore pressure variations along a 2m profile in the shallow subsurface using a stinger with 4 pressure ports. Positioned with a video-guided lander the stinger is gently pushed into the seafloor where it remains for several weeks or months in autonomous mode before being retrieved. While particular emphasis was placed on the convergent margin of Central America, mud volcanoes in other tectonic settings suitable for long-term observations of fluid flux are used for comparison. Here we will present data and interpretations from two mud volcanoes off Costa Rica and in the Gulf of Cadiz where we have conducted successful tests. Pore pressure data from short-term tests on Mound 11 on the continental slope off Costa Rica are compared with new results from a long-term (3-month) campaign on the Captain Arutjunov deep water mud volcano in the Gulf of Cadiz. Rates of fluid flow at both structures have been thoroughly characterized and quantified with geochemical methods providing a frame of reference for judging the significance of dynamic pore pressure variations.

The Artificial Hamiltonian, First Integrals, and Closed-Form Solutions of Dynamical Systems for Epidemics

NASA Astrophysics Data System (ADS)

Naz, Rehana; Naeem, Imran

2018-03-01

The non-standard Hamiltonian system, also referred to as a partial Hamiltonian system in the literature, of the form {\\dot q^i} = {partial H}/{partial {p_i}},\\dot p^i = - {partial H}/{partial {q_i}} + {Γ ^i}(t,{q^i},{p_i}) appears widely in economics, physics, mechanics, and other fields. The non-standard (partial) Hamiltonian systems arise from physical Hamiltonian structures as well as from artificial Hamiltonian structures. We introduce the term `artificial Hamiltonian' for the Hamiltonian of a model having no physical structure. We provide here explicitly the notion of an artificial Hamiltonian for dynamical systems of ordinary differential equations (ODEs). Also, we show that every system of second-order ODEs can be expressed as a non-standard (partial) Hamiltonian system of first-order ODEs by introducing an artificial Hamiltonian. This notion of an artificial Hamiltonian gives a new way to solve dynamical systems of first-order ODEs and systems of second-order ODEs that can be expressed as a non-standard (partial) Hamiltonian system by using the known techniques applicable to the non-standard Hamiltonian systems. We employ the proposed notion to solve dynamical systems of first-order ODEs arising in epidemics.

Unsteady bio-fluid dynamics in flying and swimming

NASA Astrophysics Data System (ADS)

Liu, Hao; Kolomenskiy, Dmitry; Nakata, Toshiyuki; Li, Gen

2017-08-01

Flying and swimming in nature present sophisticated and exciting ventures in biomimetics, which seeks sustainable solutions and solves practical problems by emulating nature's time-tested patterns, functions, and strategies. Bio-fluids in insect and bird flight, as well as in fish swimming are highly dynamic and unsteady; however, they have been studied mostly with a focus on the phenomena associated with a body or wings moving in a steady flow. Characterized by unsteady wing flapping and body undulation, fluid-structure interactions, flexible wings and bodies, turbulent environments, and complex maneuver, bio-fluid dynamics normally have challenges associated with low Reynolds number regime and high unsteadiness in modeling and analysis of flow physics. In this article, we review and highlight recent advances in unsteady bio-fluid dynamics in terms of leading-edge vortices, passive mechanisms in flexible wings and hinges, flapping flight in unsteady environments, and micro-structured aerodynamics in flapping flight, as well as undulatory swimming, flapping-fin hydrodynamics, body-fin interaction, C-start and maneuvering, swimming in turbulence, collective swimming, and micro-structured hydrodynamics in swimming. We further give a perspective outlook on future challenges and tasks of several key issues of the field.

Crystal water dynamics of guanosine dihydrate: analysis of atomic displacement parameters, time profile of hydrogen-bonding probability, and translocation of water by MD simulation.

PubMed

Yoneda, Shigetaka; Sugawara, Yoko; Urabe, Hisako

2005-01-27

The dynamics of crystal water molecules of guanosine dihydrate are investigated in detail by molecular dynamics (MD) simulation. A 2 ns simulation is performed using a periodic boundary box composed of 4 x 5 x 8 crystallographic unit cells and using the particle-mesh Ewald method for calculation of electrostatic energy. The simulated average atomic positions and atomic displacement parameters are remarkably coincident with the experimental values determined by X-ray analysis, confirming the high accuracy of this simulation. The dynamics of crystal water are analyzed in terms of atomic displacement parameters, orientation vectors, order parameters, self-correlation functions of the orientation vectors, time profiles of hydrogen-bonding probability, and translocations. The simulation clarifies that the average structure is composed of various stable and transient structures of the molecules. The simulated guanosine crystal forms a layered structure, with four water sites per asymmetric unit, classified as either interlayer water or intralayer water. From a detailed analysis of the translocations of water molecules in the simulation, columns of intralayer water molecules along the c axis appear to represent a pathway for hydration and dehydration by a kind of molecular valve mechanism.

Dynamic analysis of an inflatable dam subjected to a flood

NASA Astrophysics Data System (ADS)

Lowery, K.; Liapis, S.

A dynamic simulation of the response of an inflatable dam subjected to a flood is carried out to determine the survivability envelope of the dam where it can operate without rupture, or overflow. The free-surface flow problem is solved in two dimensions using a fully nonlinear mixed Eulerian-Lagrangian formulation. The dam is modeled as an elastic shell inflated with air and simply supported from two points. The finite element method is employed to determine the dynamic response of the structure using ABAQUS with a shell element. The problem is solved in the time domain which allows the prediction of a number of transient phenomena such as the generation of upstream advancing waves, the dynamic structural response and structural failure. Failure takes place when the dam either ruptures or overflows. Stresses in the dam material were monitored to determine when rupture occurs. An iterative study was performed to find the serviceability envelope of the dam in terms of the internal pressure and the flood Froude number for two flood depths. It was found that existing inflatable dams are quite effective in suppressing floods for a relatively wide range of flood velocities.

Dynamic Modeling and Very Short-term Prediction of Wind Power Output Using Box-Cox Transformation

NASA Astrophysics Data System (ADS)

Urata, Kengo; Inoue, Masaki; Murayama, Dai; Adachi, Shuichi

2016-09-01

We propose a statistical modeling method of wind power output for very short-term prediction. The modeling method with a nonlinear model has cascade structure composed of two parts. One is a linear dynamic part that is driven by a Gaussian white noise and described by an autoregressive model. The other is a nonlinear static part that is driven by the output of the linear part. This nonlinear part is designed for output distribution matching: we shape the distribution of the model output to match with that of the wind power output. The constructed model is utilized for one-step ahead prediction of the wind power output. Furthermore, we study the relation between the prediction accuracy and the prediction horizon.

A procedure for damage detection and localization of framed buildings based on curvature variation

NASA Astrophysics Data System (ADS)

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

2014-05-01

Structural Health Monitoring and Damage Detection are topics of current interest in civil, mechanical and aerospace engineering. Damage Detection approach based on dynamic monitoring of structural properties over time has received a considerable attention in recent scientific literature of the last years. The basic idea arises from the observation that spectral properties, described in terms of the so-called modal parameters (eigenfrequencies, mode shapes, and modal damping), are functions of the physical properties of the structure (mass, energy dissipation mechanisms and stiffness). Structural damage exhibits its main effects in terms of stiffness and damping variation. As a consequence, a permanent dynamic monitoring system makes it possible to detect and, if suitably concentrated on the structure, to localize structural and non-structural damage occurred on the structure during a strong earthquake. In the last years many researchers are working to set-up new methodologies for Non-destructive Damage Evaluation (NDE) based on the variation of the dynamic behaviour of structures under seismic loads. Pandey et al. (1991) highlighted on the possibility to use the structural mode shapes to extract useful information for structural damage localization. In this paper a new procedure for damage detection on framed structures based on changes in modal curvature is proposed. The proposed approach is based on the use of Stockwell Transform, a special kind of integral transformation that become a powerful tool for nonlinear signal analysis and then to analyse the nonlinear behaviour of a general structure. Using this kind of approach, it is possible to use a band-variable filter (Ditommaso et al., 2012) to extract from a signal recorded on a structure (excited by an earthquake) the response related to a single mode of vibration for which the related frequency changes over time (if the structure is being damaged). İn general, by acting simultaneously in both frequency and time domain, it is possible to use the band-variable filter to extract the dynamic characteristics of a system that evolves over time. Aim of this paper is to show, through practical examples, how it is possible to identify and to localize damage on a structure comparing mode shapes and the related curvature variations over time. It is possible to demonstrate that mode curvature variation is strongly related with the damage occurred on a structure. This paper resumes the main outcomes retrieved from many numerical non linear dynamic models of reinforced concrete framed structures characterized by different geometric configurations and designed for gravity loads only. The numerical campaign was conducted using both natural and artificial accelerograms compatible with the Italian code. The main results of experimental shaking table tests carried out on a steel framed model are also showed to confirm the effectiveness of the proposed procedure. REFERENCES Ditommaso R., Mucciarelli M., Ponzo F. C. (2012). Analysis of non-stationary structural systems by using a band-variable filter. Bulletin of Earthquake Engineering. Volume 10, Number 3, pp. 895-911. DOI: 10.1007/s10518-012-9338-y. Pandey AK, Biswas M, Samman MM (1991) "Damage detection from changes in curvature mode shapes", Journal of Sound and Vibration, Vol. 145: Issue 2, pp. 321-332.

Statistical analysis of modal properties of a cable-stayed bridge through long-term structural health monitoring with wireless smart sensor networks

NASA Astrophysics Data System (ADS)

Asadollahi, Parisa; Li, Jian

2016-04-01

Understanding the dynamic behavior of complex structures such as long-span bridges requires dense deployment of sensors. Traditional wired sensor systems are generally expensive and time-consuming to install due to cabling. With wireless communication and on-board computation capabilities, wireless smart sensor networks have the advantages of being low cost, easy to deploy and maintain and therefore facilitate dense instrumentation for structural health monitoring. A long-term monitoring project was recently carried out for a cable-stayed bridge in South Korea with a dense array of 113 smart sensors, which feature the world's largest wireless smart sensor network for civil structural monitoring. This paper presents a comprehensive statistical analysis of the modal properties including natural frequencies, damping ratios and mode shapes of the monitored cable-stayed bridge. Data analyzed in this paper is composed of structural vibration signals monitored during a 12-month period under ambient excitations. The correlation between environmental temperature and the modal frequencies is also investigated. The results showed the long-term statistical structural behavior of the bridge, which serves as the basis for Bayesian statistical updating for the numerical model.

Dynamic switching enables efficient bacterial colonization in flow.

PubMed

Kannan, Anerudh; Yang, Zhenbin; Kim, Minyoung Kevin; Stone, Howard A; Siryaporn, Albert

2018-05-22

Bacteria colonize environments that contain networks of moving fluids, including digestive pathways, blood vasculature in animals, and the xylem and phloem networks in plants. In these flow networks, bacteria form distinct biofilm structures that have an important role in pathogenesis. The physical mechanisms that determine the spatial organization of bacteria in flow are not understood. Here, we show that the bacterium P. aeruginosa colonizes flow networks using a cyclical process that consists of surface attachment, upstream movement, detachment, movement with the bulk flow, and surface reattachment. This process, which we have termed dynamic switching, distributes bacterial subpopulations upstream and downstream in flow through two phases: movement on surfaces and cellular movement via the bulk. The model equations that describe dynamic switching are identical to those that describe dynamic instability, a process that enables microtubules in eukaryotic cells to search space efficiently to capture chromosomes. Our results show that dynamic switching enables bacteria to explore flow networks efficiently, which maximizes dispersal and colonization and establishes the organizational structure of biofilms. A number of eukaryotic and mammalian cells also exhibit movement in two phases in flow, which suggests that dynamic switching is a modality that enables efficient dispersal for a broad range of cell types.

Disentangling the effects of feedback structure and climate on Poaceae annual airborne pollen fluctuations and the possible consequences of climate change.

PubMed

García de León, David; García-Mozo, Herminia; Galán, Carmen; Alcázar, Purificación; Lima, Mauricio; González-Andújar, José L

2015-10-15

Pollen allergies are the most common form of respiratory allergic disease in Europe. Most studies have emphasized the role of environmental processes, as the drivers of airborne pollen fluctuations, implicitly considering pollen production as a random walk. This work shows that internal self-regulating processes of the plants (negative feedback) should be included in pollen dynamic systems in order to give a better explanation of the observed pollen temporal patterns. This article proposes a novel methodological approach based on dynamic systems to investigate the interaction between feedback structure of plant populations and climate in shaping long-term airborne Poaceae pollen fluctuations and to quantify the effects of climate change on future airborne pollen concentrations. Long-term historical airborne Poaceae pollen data (30 years) from Cordoba city (Southern Spain) were analyzed. A set of models, combining feedback structure, temperature and actual evapotranspiration effects on airborne Poaceae pollen were built and compared, using a model selection approach. Our results highlight the importance of first-order negative feedback and mean annual maximum temperature in driving airborne Poaceae pollen dynamics. The best model was used to predict the effects of climate change under two standardized scenarios representing contrasting temporal patterns of economic development and CO2 emissions. Our results predict an increase in pollen levels in southern Spain by 2070 ranging from 28.5% to 44.3%. The findings from this study provide a greater understanding of airborne pollen dynamics and how climate change might impact the future evolution of airborne Poaceae pollen concentrations and thus the future evolution of related pollen allergies. Copyright © 2015 Elsevier B.V. All rights reserved.

From seconds to months: an overview of multi-scale dynamics of mobile telephone calls

NASA Astrophysics Data System (ADS)

Saramäki, Jari; Moro, Esteban

2015-06-01

Big Data on electronic records of social interactions allow approaching human behaviour and sociality from a quantitative point of view with unforeseen statistical power. Mobile telephone Call Detail Records (CDRs), automatically collected by telecom operators for billing purposes, have proven especially fruitful for understanding one-to-one communication patterns as well as the dynamics of social networks that are reflected in such patterns. We present an overview of empirical results on the multi-scale dynamics of social dynamics and networks inferred from mobile telephone calls. We begin with the shortest timescales and fastest dynamics, such as burstiness of call sequences between individuals, and "zoom out" towards longer temporal and larger structural scales, from temporal motifs formed by correlated calls between multiple individuals to long-term dynamics of social groups. We conclude this overview with a future outlook.

Motional timescale predictions by molecular dynamics simulations: Case study using proline and hydroxyproline sidechain dynamics

PubMed Central

Aliev, Abil E; Kulke, Martin; Khaneja, Harmeet S; Chudasama, Vijay; Sheppard, Tom D; Lanigan, Rachel M

2014-01-01

We propose a new approach for force field optimizations which aims at reproducing dynamics characteristics using biomolecular MD simulations, in addition to improved prediction of motionally averaged structural properties available from experiment. As the source of experimental data for dynamics fittings, we use 13C NMR spin-lattice relaxation times T1 of backbone and sidechain carbons, which allow to determine correlation times of both overall molecular and intramolecular motions. For structural fittings, we use motionally averaged experimental values of NMR J couplings. The proline residue and its derivative 4-hydroxyproline with relatively simple cyclic structure and sidechain dynamics were chosen for the assessment of the new approach in this work. Initially, grid search and simplexed MD simulations identified large number of parameter sets which fit equally well experimental J couplings. Using the Arrhenius-type relationship between the force constant and the correlation time, the available MD data for a series of parameter sets were analyzed to predict the value of the force constant that best reproduces experimental timescale of the sidechain dynamics. Verification of the new force-field (termed as AMBER99SB-ILDNP) against NMR J couplings and correlation times showed consistent and significant improvements compared to the original force field in reproducing both structural and dynamics properties. The results suggest that matching experimental timescales of motions together with motionally averaged characteristics is the valid approach for force field parameter optimization. Such a comprehensive approach is not restricted to cyclic residues and can be extended to other amino acid residues, as well as to the backbone. Proteins 2014; 82:195–215. © 2013 Wiley Periodicals, Inc. PMID:23818175

Simulations of the Boreal Winter Upper Mesosphere and Lower Thermosphere With Meteorological Specifications in SD-WACCM-X

NASA Astrophysics Data System (ADS)

Sassi, Fabrizio; Siskind, David E.; Tate, Jennifer L.; Liu, Han-Li; Randall, Cora E.

2018-04-01

We investigate the benefit of high-altitude nudging in simulations of the structure and short-term variability of the upper mesosphere and lower thermosphere (UMLT) dynamical meteorology during boreal winter, specifically around the time of the January 2009 sudden stratospheric warming. We compare simulations using the Specified Dynamics, Whole Atmosphere Community Climate Model, extended version, nudged using atmospheric specifications generated by the Navy Operational Global Atmospheric Prediction System, Advanced Level Physics High Altitude. Two sets of simulations are carried out: one uses nudging over a vertical domain from 0 to 90 km; the other uses nudging over a vertical domain from 0 to 50 km. The dynamical behavior is diagnosed from ensemble mean and standard deviation of winds, temperature, and zonal accelerations due to resolved and parameterized waves. We show that the dynamical behavior of the UMLT is quite different in the two experiments, with prominent differences in the structure and variability of constituent transport. We compare the results of our numerical experiments to observations of carbon monoxide by the Atmospheric Chemistry Experiment-Fourier Transform Spectrometer to show that the high-altitude nudging is capable of reproducing with high fidelity the observed variability, and traveling planetary waves are a crucial component of the dynamics. The results of this study indicate that to capture the key physical processes that affect short-term variability (defined as the atmospheric behavior within about 10 days of a stratospheric warming) in the UMLT, specification of the atmospheric state in the stratosphere alone is not sufficient, and upper atmospheric specifications are needed.

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.

Determination of the hydrogen-bond network and the ferrimagnetic structure of a rockbridgeite-type compound, [Formula: see text].

PubMed

Röska, B; Park, S-H; Behal, D; Hess, K-U; Günther, A; Benka, G; Pfleiderer, C; Hoelzel, M; Kimura, T

2018-06-13

Applying neutron powder diffraction, four unique hydrogen positions were determined in a rockbridgeite-type compound, [Formula: see text] [Formula: see text]. Its honeycomb-like H-bond network running without interruption along the crystallographic [Formula: see text] axis resembles those in alkali sulphatic and arsenatic oxyhydroxides. They provide the so-called dynamically disordered H-bond network over which protons are superconducting in a vehicle mechanism. This is indicated by dramatic increases of dielectric constant and loss factor at room temperature. The relevance of static and dynamic disorder of OH and HOH groups are explained in terms of a high number of structural defects at octahedral chains alternatingly half-occupied by [Formula: see text] cations. The structure is built up by unusual octahedral doublet, triplet, and quartet clusters of aliovalent 3d transition metal cations, predicting complicate magnetic ordering and interaction. The ferrimagnetic structure below the Curie temperature [Formula: see text]-83 K could be determined from the structure analysis with neutron diffraction data at 25 K.

[The structure of psychopathology associated with addictive disorders, against alcohol addiction and the possibility of it's neurometabolic correction in the elderly].

PubMed

Belov, V G; Parfenov, Iu A; Zaplutanov, V A; Khaĭrutdinov, D R

2013-01-01

The article presents the analysis of the structure and dynamics of psychopathology associated with addictive disorders in elderly patients with alcohol dependence. In terms of syndromic approach the structure of neurotic disease in elderly patients with a verified diagnosis of mental and behavioral disorders associated with alcohol consumption was evaluated. In the overall structure of neurotic pathology in these patients the analysis of symptoms of neurotic diseases, the research of the structure of syndromes and their dynamics were carried out, as well as the patient's attitude to the disease and to its manifestations was determined. A factor model of the pathogenesis of neurotic pathology connected with mental and behavioral disorders due to alcohol use in elderly patients was developed. The high clinical effectiveness of the drug "Cytoflavin" used in the reduction of psychiatric symptoms in patients aged from 62 to 74 years with a diagnosis of mental and behavioral disorders associated with alcohol consumption has been shown.

Close-packed structure dynamics with finite-range interaction: computational mechanics with individual layer interaction.

PubMed

Rodriguez-Horta, Edwin; Estevez-Rams, Ernesto; Lora-Serrano, Raimundo; Neder, Reinhard

2017-09-01

This is the second contribution in a series of papers dealing with dynamical models in equilibrium theories of polytypism. A Hamiltonian introduced by Ahmad & Khan [Phys. Status Solidi B (2000), 218, 425-430] avoids the unphysical assignment of interaction terms to fictitious entities given by spins in the Hägg coding of the stacking arrangement. In this paper an analysis of polytype generation and disorder in close-packed structures is made for such a Hamiltonian. Results are compared with a previous analysis using the Ising model. Computational mechanics is the framework under which the analysis is performed. The competing effects of disorder and structure, as given by entropy density and excess entropy, respectively, are discussed. It is argued that the Ahmad & Khan model is simpler and predicts a larger set of polytypes than previous treatments.

Branching, Chain Scission, and Solution Stability of Worm-Like Micelles

NASA Astrophysics Data System (ADS)

Beaucage, Greg; Vogtt, Karsten; Jiang, Hanqui

As salt is added to a simple micelle solution such as SDS or SLES, the zero shear rate specific viscosity rises rapidly followed by a maximum and decay. The rapid rise in viscosity is associated with formation of elliptical and extended chain worm-like micelles, WLMs. Entanglement of these long chain micelles leads to the viscoelastic behavior we associate with shampoo and body wash. The plateau and drop in viscosity at high salt concentrations is caused by a special type of topological branching where the branch points have no energy penalty to motion along the chain according to Cates theory. These have some similarity to catenane crosslinks. Predictive dynamic theories for WLMs rely on structural details; the diameter, persistence length, contour length, branch length, segment length between branch points, and mesh size. Further, since the contour length and other large scale features are in kinetic equilibrium, with frequent chain breakage and formation, the thermodynamics of these long chain structures are of interest both in terms of chain scission as well as in terms of the stability of the colloidal solution as a whole. Recent structural studies of WLMs using static neutron scattering based on new scattering models will be presented demonstrating that these input parameters for dynamic models of complex topological systems are quantitatively and directly available. In this context it is important to consider a comparison between dynamic features, for instance entanglement, and their static analogs, chain overlap.

Quantum Bose-Hubbard model with an evolving graph as a toy model for emergent spacetime

NASA Astrophysics Data System (ADS)

Hamma, Alioscia; Markopoulou, Fotini; Lloyd, Seth; Caravelli, Francesco; Severini, Simone; Markström, Klas

2010-05-01

We present a toy model for interacting matter and geometry that explores quantum dynamics in a spin system as a precursor to a quantum theory of gravity. The model has no a priori geometric properties; instead, locality is inferred from the more fundamental notion of interaction between the matter degrees of freedom. The interaction terms are themselves quantum degrees of freedom so that the structure of interactions and hence the resulting local and causal structures are dynamical. The system is a Hubbard model where the graph of the interactions is a set of quantum evolving variables. We show entanglement between spatial and matter degrees of freedom. We study numerically the quantum system and analyze its entanglement dynamics. We analyze the asymptotic behavior of the classical model. Finally, we discuss analogues of trapped surfaces and gravitational attraction in this simple model.

Global patterns of phytoplankton dynamics in coastal ecosystems

USGS Publications Warehouse

Paerl, H.; Yin, Kedong; Cloern, J.

2011-01-01

Scientific Committee on Ocean Research Working Group 137 Meeting; Hangzhou, China, 17-21 October 2010; Phytoplankton biomass and community structure have undergone dramatic changes in coastal ecosystems over the past several decades in response to climate variability and human disturbance. These changes have short- and long-term impacts on global carbon and nutrient cycling, food web structure and productivity, and coastal ecosystem services. There is a need to identify the underlying processes and measure the rates at which they alter coastal ecosystems on a global scale. Hence, the Scientific Committee on Ocean Research (SCOR) formed Working Group 137 (WG 137), "Global Patterns of Phytoplankton Dynamics in Coastal Ecosystems: A Comparative Analysis of Time Series Observations" (http://wg137.net/). This group evolved from a 2007 AGU-sponsored Chapman Conference entitled "Long Time-Series Observations in Coastal Ecosystems: Comparative Analyses of Phytoplankton Dynamics on Regional to Global Scales.".

Turbine blade forced response prediction using FREPS

NASA Technical Reports Server (NTRS)

Murthy, Durbha, V.; Morel, Michael R.

1993-01-01

This paper describes a software system called FREPS (Forced REsponse Prediction System) that integrates structural dynamic, steady and unsteady aerodynamic analyses to efficiently predict the forced response dynamic stresses in axial flow turbomachinery blades due to aerodynamic and mechanical excitations. A flutter analysis capability is also incorporated into the system. The FREPS system performs aeroelastic analysis by modeling the motion of the blade in terms of its normal modes. The structural dynamic analysis is performed by a finite element code such as MSC/NASTRAN. The steady aerodynamic analysis is based on nonlinear potential theory and the unsteady aerodynamic analyses is based on the linearization of the non-uniform potential flow mean. The program description and presentation of the capabilities are reported herein. The effectiveness of the FREPS package is demonstrated on the High Pressure Oxygen Turbopump turbine of the Space Shuttle Main Engine. Both flutter and forced response analyses are performed and typical results are illustrated.

Microgels: Structure, Dynamics, and Possible Applications.

NASA Astrophysics Data System (ADS)

McKenna, John; Streletzky, Kiril

2007-03-01

We cross-linked Hydropxypropylcellulose (HPC) polymer chains to produce microgel nanoparticles and studied their structure and dynamics using Dynamic Light Scattering spectroscopy. The complex nature of the fluid and large size distribution of the particles renders typical characterization algorithm CONTIN ineffective and inconsistent. Instead, the particles spectra have been fit to a sum of stretched exponentials. Each term offers three parameters for analysis and represents a single mode. The results of this analysis show that the microgels undergo a transition to a fewer modes around 41C. The CONTIN size distribution analysis shows similar results, but these come with much less consistency and resolution. Our experiments prove that microgel particles shrink under volume phase transition. The shrinkage is reversible and depends on the amount of cross-linker, salt and polymer concentrations and rate of heating. Reversibility of microgel volume phase transition property might be particularly useful for a controlled drug delivery and release.

Challenging Cognitive Construals: A Dynamic Alternative to Stable Misconceptions

ERIC Educational Resources Information Center

Gouvea, Julia S.; Simon, Matt R.

2018-01-01

In biology education research, it has been common to model cognition in terms of relatively stable knowledge structures (e.g., mental models, alternative frameworks, deeply held misconceptions). For example, John D. Coley and Kimberley D. Tanner recently proposed that many student difficulties in biology stem from underlying cognitive frameworks…

Analysing Structure Dynamics in Arable Soils using X-ray Micro-Tomography

NASA Astrophysics Data System (ADS)

Schlüter, S.; Weller, U.; Vogel, H.-J.

2009-04-01

Structure is a dynamic property of soil. It interacts with many biotic and abiotic features and controls various soil functions. We analyzed soil structure within different plots of the ''Static Fertilisation Experiment'' at the agricultural research station in Bad Lauchstaedt (Germany) using X-ray micro tomography. The aim was to investigate in how far different levels of organic carbon, increased microbial activity and enhanced plant growth affects structural properties of an arable soil. Since 106 years one plot has experienced a constant application of farmyard manure and fertilisers, whereas the other has never been fertilised in this period. Intact soil cores from the chernozem soil at the two plots were taken from a depth of 5 to 15 cm (Ap-horizon) and 35 to 45 cm (Ah-horizon) to analyse structural changes with depth and in two different seasons (spring and summer) to investigate structure dynamics. The pore structure was analysed by quantifying the mean geometrical and topological characteristics of the pore network as a function of pore size. This was done by a combination of Minkowski functionals and morphological size distibution. For small structural features close to the image resolution the results clearly depend on the applied filtering technique and segmentation thresholds. Therefore the application of different image enhancement techniques is discussed. Furthermore, a new method for an automated determination of grey value thesholds for the segmentation of CT-images into pore space and solid is developed and evaluated. We highlight the relevance of image resolution for structure analysis. Results of the structure analysis reveal that the spring samples of the ploughed layer (Ap-horizon) from the fertilised plot have significantly higher macroporosities (P < 0.05) than those from the non-fertilised plot. The internal connectivity of the pore network is better in the fertilised plot and the pore size distribution was found to be different, too. The differences in porosity and pore connectivity increase from spring to summer. Both plots were compacted by a rolling machine in late winter. So the difference in structure dynamics is interpreted as an enhanced structure resiliency in the fertilised and carbon enriched plot after that compaction. A comparison with porosity features of a nearby reference profil under grassland demonstrates that the impact of tillage on pore structure is higher than the different contents in organic carbon. The carbon enriched horizon beneath the ploughed layer (Ah-horizon) shows no differences in pore size distribution and connectivity as a function of fertilisation. Thus, at that soil depth, no long-term effects of fertilization in terms of soil structure are detectable. Obviously, the highly different energy input during 106 years only affects the structure of the top soil.

Adaptive Actor-Critic Design-Based Integral Sliding-Mode Control for Partially Unknown Nonlinear Systems With Input Disturbances.

PubMed

Fan, Quan-Yong; Yang, Guang-Hong

2016-01-01

This paper is concerned with the problem of integral sliding-mode control for a class of nonlinear systems with input disturbances and unknown nonlinear terms through the adaptive actor-critic (AC) control method. The main objective is to design a sliding-mode control methodology based on the adaptive dynamic programming (ADP) method, so that the closed-loop system with time-varying disturbances is stable and the nearly optimal performance of the sliding-mode dynamics can be guaranteed. In the first step, a neural network (NN)-based observer and a disturbance observer are designed to approximate the unknown nonlinear terms and estimate the input disturbances, respectively. Based on the NN approximations and disturbance estimations, the discontinuous part of the sliding-mode control is constructed to eliminate the effect of the disturbances and attain the expected equivalent sliding-mode dynamics. Then, the ADP method with AC structure is presented to learn the optimal control for the sliding-mode dynamics online. Reconstructed tuning laws are developed to guarantee the stability of the sliding-mode dynamics and the convergence of the weights of critic and actor NNs. Finally, the simulation results are presented to illustrate the effectiveness of the proposed method.

Long-term metapopulation study of the Glanville fritillary butterfly (Melitaea cinxia): survey methods, data management, and long-term population trends.

PubMed

Ojanen, Sami P; Nieminen, Marko; Meyke, Evgeniy; Pöyry, Juha; Hanski, Ilkka

2013-10-01

Long-term observational studies conducted at large (regional) spatial scales contribute to better understanding of landscape effects on population and evolutionary dynamics, including the conditions that affect long-term viability of species, but large-scale studies are expensive and logistically challenging to keep running for a long time. Here, we describe the long-term metapopulation study of the Glanville fritillary butterfly (Melitaea cinxia) that has been conducted since 1991 in a large network of 4000 habitat patches (dry meadows) within a study area of 50 by 70 km in the Åland Islands in Finland. We explain how the landscape structure has been described, including definition, delimitation, and mapping of the habitat patches; methods of field survey, including the logistics, cost, and reliability of the survey; and data management using the EarthCape biodiversity platform. We describe the long-term metapopulation dynamics of the Glanville fritillary based on the survey. There has been no long-term change in the overall size of the metapopulation, but the level of spatial synchrony and hence the amplitude of fluctuations in year-to-year metapopulation dynamics have increased over the years, possibly due to increasing frequency of exceptional weather conditions. We discuss the added value of large-scale and long-term population studies, but also emphasize the need to integrate more targeted experimental studies in the context of long-term observational studies. For instance, in the case of the Glanville fritillary project, the long-term study has produced an opportunity to sample individuals for experiments from local populations with a known demographic history. These studies have demonstrated striking differences in dispersal rate and other life-history traits of individuals from newly established local populations (the offspring of colonizers) versus individuals from old, established local populations. The long-term observational study has stimulated the development of metapopulation models and provided an opportunity to test model predictions. This combination of empirical studies and modeling has facilitated the study of key phenomena in spatial dynamics, such as extinction threshold and extinction debt.

Long-term metapopulation study of the Glanville fritillary butterfly (Melitaea cinxia): survey methods, data management, and long-term population trends

PubMed Central

Ojanen, Sami P; Nieminen, Marko; Meyke, Evgeniy; Pöyry, Juha; Hanski, Ilkka

2013-01-01

Long-term observational studies conducted at large (regional) spatial scales contribute to better understanding of landscape effects on population and evolutionary dynamics, including the conditions that affect long-term viability of species, but large-scale studies are expensive and logistically challenging to keep running for a long time. Here, we describe the long-term metapopulation study of the Glanville fritillary butterfly (Melitaea cinxia) that has been conducted since 1991 in a large network of 4000 habitat patches (dry meadows) within a study area of 50 by 70 km in the Åland Islands in Finland. We explain how the landscape structure has been described, including definition, delimitation, and mapping of the habitat patches; methods of field survey, including the logistics, cost, and reliability of the survey; and data management using the EarthCape biodiversity platform. We describe the long-term metapopulation dynamics of the Glanville fritillary based on the survey. There has been no long-term change in the overall size of the metapopulation, but the level of spatial synchrony and hence the amplitude of fluctuations in year-to-year metapopulation dynamics have increased over the years, possibly due to increasing frequency of exceptional weather conditions. We discuss the added value of large-scale and long-term population studies, but also emphasize the need to integrate more targeted experimental studies in the context of long-term observational studies. For instance, in the case of the Glanville fritillary project, the long-term study has produced an opportunity to sample individuals for experiments from local populations with a known demographic history. These studies have demonstrated striking differences in dispersal rate and other life-history traits of individuals from newly established local populations (the offspring of colonizers) versus individuals from old, established local populations. The long-term observational study has stimulated the development of metapopulation models and provided an opportunity to test model predictions. This combination of empirical studies and modeling has facilitated the study of key phenomena in spatial dynamics, such as extinction threshold and extinction debt. PMID:24198935

Stochastic thermodynamics across scales: Emergent inter-attractoral discrete Markov jump process and its underlying continuous diffusion

NASA Astrophysics Data System (ADS)

Santillán, Moisés; Qian, Hong

2013-01-01

We investigate the internal consistency of a recently developed mathematical thermodynamic structure across scales, between a continuous stochastic nonlinear dynamical system, i.e., a diffusion process with Langevin and Fokker-Planck equations, and its emergent discrete, inter-attractoral Markov jump process. We analyze how the system’s thermodynamic state functions, e.g. free energy F, entropy S, entropy production ep, free energy dissipation Ḟ, etc., are related when the continuous system is described with coarse-grained discrete variables. It is shown that the thermodynamics derived from the underlying, detailed continuous dynamics gives rise to exactly the free-energy representation of Gibbs and Helmholtz. That is, the system’s thermodynamic structure is the same as if one only takes a middle road and starts with the natural discrete description, with the corresponding transition rates empirically determined. By natural we mean in the thermodynamic limit of a large system, with an inherent separation of time scales between inter- and intra-attractoral dynamics. This result generalizes a fundamental idea from chemistry, and the theory of Kramers, by incorporating thermodynamics: while a mechanical description of a molecule is in terms of continuous bond lengths and angles, chemical reactions are phenomenologically described by a discrete representation, in terms of exponential rate laws and a stochastic thermodynamics.

Pursuit tracking and higher levels of skill development in the human pilot

NASA Technical Reports Server (NTRS)

Hess, R. A.

1981-01-01

A model of the human pilot is offered for pursuit tracking tasks; the model encompasses an existing model for compensatory tracking. The central hypothesis in the development of this model states that those primary structural elements in the compensatory model responsible for the pilot's equalization capabilities remain intact in the pursuit model. In this latter case, effective low-frequency inversion of the controlled-element dynamics occurs by feeding-forward derived input rate through the equalization dynamics, with low-frequency phase droop minimized. The sharp reduction in low-frequency phase lag beyond that associated with the disappearance of phase droop is seen to accompany relatively low-gain feedback of vehicle output. The results of some recent motion cue research are discussed and interpreted in terms of the compensatory-pursuit display dichotomy. Tracking with input preview is discussed in a qualitative way. In terms of the model, preview is shown to demand no fundamental changes in structure or equalization and to allow the pilot to eliminate the effective time delays that accrue in the inversion of the controlled-element dynamics. Precognitive behavior is discussed, and a model that encompasses all the levels of skill development outlined in the successive organizations of perception theory is finally proposed.

Breakdown of the Simple Arrhenius Law in the Normal Liquid State.

PubMed

Thoms, Erik; Grzybowski, Andrzej; Pawlus, Sebastian; Paluch, Marian

2018-04-05

It is common practice to discuss the temperature effect on molecular dynamics of glass formers above the melting temperature in terms of the Arrhenius law. Using dielectric spectroscopy measurements of dc conductivity and structural relaxation time on the example of the typical glass former propylene carbonate, we provide experimental evidence that this practice is not justified. Our conclusions are supported by employing thermodynamic density scaling and the occurrence of inflection points in isothermal dynamic data measured at elevated pressure. Additionally, we propose a more suitable approach to describe the dynamics both above and below the inflection point based on a modified MYEGA model.

Chiral dynamics with (non)strange quarks

NASA Astrophysics Data System (ADS)

Kubis, Bastian; Meißner, Ulf-G.

2017-01-01

We review the results and achievements of the project B.3. Topics addressed include pion photoproduction off the proton and off deuterium, three-flavor chiral perturbation theory studies, chiral symmetry tests in Goldstone boson decays, the development of unitarized chiral perturbation theory to next-to-leading order, the two-pole structure of the Λ(1405), the dynamical generation of the lowest S11 resonances, the theory of hadronic atoms and its application to various systems, precision studies in light-meson decays based on dispersion theory, the Roy-Steiner analysis of pion-nucleon scattering, a high-precision extraction of the elusive pion-nucleon σ-term, and aspects of chiral dynamics in few-nucleon systems.

Visualizing long-term single-molecule dynamics in vivo by stochastic protein labeling.

PubMed

Liu, Hui; Dong, Peng; Ioannou, Maria S; Li, Li; Shea, Jamien; Pasolli, H Amalia; Grimm, Jonathan B; Rivlin, Patricia K; Lavis, Luke D; Koyama, Minoru; Liu, Zhe

2018-01-09

Our ability to unambiguously image and track individual molecules in live cells is limited by packing of multiple copies of labeled molecules within the resolution limit. Here we devise a universal genetic strategy to precisely control copy number of fluorescently labeled molecules in a cell. This system has a dynamic range of ∼10,000-fold, enabling sparse labeling of proteins expressed at different abundance levels. Combined with photostable labels, this system extends the duration of automated single-molecule tracking by two orders of magnitude. We demonstrate long-term imaging of synaptic vesicle dynamics in cultured neurons as well as in intact zebrafish. We found axon initial segment utilizes a "waterfall" mechanism gating synaptic vesicle transport polarity by promoting anterograde transport processivity. Long-time observation also reveals that transcription factor hops between clustered binding sites in spatially restricted subnuclear regions, suggesting that topological structures in the nucleus shape local gene activities by a sequestering mechanism. This strategy thus greatly expands the spatiotemporal length scales of live-cell single-molecule measurements, enabling new experiments to quantitatively understand complex control of molecular dynamics in vivo.

XVII International Conference on Hadron Spectroscopy and Structure

NASA Astrophysics Data System (ADS)

2017-09-01

The Hadron 2017 Conference is the seventeenth of a series of biennial conferences started in 1985 at Maryland, USA. Its official name, XVII International Conference on Hadron Spectroscopy and Structure, includes for the first time the term structure to emphasize the importance that this issue has acquired in recent editions of the series. The aim of the conference is to provide an overview of the present status and progress in hadron structure and dynamics, as well as a preview of the forthcoming investigations. It will cover lectures on both experimental and theoretical aspects, including in particular the presentation of new results.

Effect of ion-beam treatment on structure and fracture resistance of 12Cr1MoV steel under static, cyclic and dynamic loading

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

Panin, S. V., E-mail: svp@ispms.tsc.ru; Vlasov, I. V., E-mail: good0@yandex.ru; Sergeev, V. P., E-mail: retc@ispms.tsc.ru

2015-10-27

Features of the structure and properties modification of 12Cr1MoV steel subjected to irradiation by zirconium ion beam have been investigated with the use of optical and electron microscopy as well as microhardness measurement. It has been shown that upon treatment the structure modification occurred across the entire cross-section of specimens with the thickness of 1 mm. Changes in the mechanical properties of these specimens under static, cyclic and impact loading are interpreted in terms of identified structure changes.

The role of deep Earth dynamics in driving the flooding and emergence of New Guinea since the Jurassic

NASA Astrophysics Data System (ADS)

Harrington, Lauren; Zahirovic, Sabin; Flament, Nicolas; Müller, R. Dietmar

2017-12-01

The paleogeography of New Guinea indicates fluctuating periods of flooding and emergence since the Jurassic, which are inconsistent with estimates of global sea level change since the Eocene. The role of deep Earth dynamics in explaining these discrepancies has not been explored, despite the strongly time-dependent geodynamic setting within which New Guinea has evolved. We aim to investigate the role of subduction-driven mantle flow in controlling long-wavelength dynamic topography and its manifestation in the regional sedimentary record, within a tectonically complex region leading to orogeny. We couple regionally refined global plate reconstructions with forward geodynamic models to compare trends of dynamic topography with estimates of eustasy and regional paleogeography. Qualitative corroboration of modelled mantle structure with equivalent tomographic profiles allows us to ground-truth the models. We show that predicted dynamic topography correlates with the paleogeographic record of New Guinea from the Jurassic to the present. We find that subduction at the East Gondwana margin locally enhanced the high eustatic sea levels from the Early Cretaceous (∼145 Ma) to generate long-term regional flooding. During the Miocene, however, dynamic subsidence associated with subduction of the Maramuni Arc played a fundamental role in causing long-term inundation of New Guinea during a period of global sea level fall.

Spatio-temporal variation in age structure and abundance of the endangered snail kite: Pooling across regions masks a declining and aging population

USGS Publications Warehouse

Reichert, Brian E.; Kendall, William L.; Fletcher, Robert J.; Kitchens, Wiley M.

2016-01-01

While variation in age structure over time and space has long been considered important for population dynamics and conservation, reliable estimates of such spatio-temporal variation in age structure have been elusive for wild vertebrate populations. This limitation has arisen because of problems of imperfect detection, the potential for temporary emigration impacting assessments of age structure, and limited information on age. However, identifying patterns in age structure is important for making reliable predictions of both short- and long-term dynamics of populations of conservation concern. Using a multistate superpopulation estimator, we estimated region-specific abundance and age structure (the proportion of individuals within each age class) of a highly endangered population of snail kites for two separate regions in Florida over 17 years (1997–2013). We find that in the southern region of the snail kite—a region known to be critical for the long-term persistence of the species—the population has declined significantly since 1997, and during this time, it has increasingly become dominated by older snail kites (> 12 years old). In contrast, in the northern region—a region historically thought to serve primarily as drought refugia—the population has increased significantly since 2007 and age structure is more evenly distributed among age classes. Given that snail kites show senescence at approximately 13 years of age, where individuals suffer higher mortality rates and lower breeding rates, these results reveal an alarming trend for the southern region. Our work illustrates the importance of accounting for spatial structure when assessing changes in abundance and age distribution and the need for monitoring of age structure in imperiled species.

Integrability and Poisson Structures of Three Dimensional Dynamical Systems and Equations of Hydrodynamic Type

NASA Astrophysics Data System (ADS)

Gumral, Hasan

Poisson structure of completely integrable 3 dimensional dynamical systems can be defined in terms of an integrable 1-form. We take advantage of this fact and use the theory of foliations in discussing the geometrical structure underlying complete and partial integrability. We show that the Halphen system can be formulated in terms of a flat SL(2,R)-valued connection and belongs to a non-trivial Godbillon-Vey class. On the other hand, for the Euler top and a special case of 3-species Lotka-Volterra equations which are contained in the Halphen system as limiting cases, this structure degenerates into the form of globally integrable bi-Hamiltonian structures. The globally integrable bi-Hamiltonian case is a linear and the sl_2 structure is a quadratic unfolding of an integrable 1-form in 3 + 1 dimensions. We complete the discussion of the Hamiltonian structure of 2-component equations of hydrodynamic type by presenting the Hamiltonian operators for Euler's equation and a continuum limit of Toda lattice. We present further infinite sequences of conserved quantities for shallow water equations and show that their generalizations by Kodama admit bi-Hamiltonian structure. We present a simple way of constructing the second Hamiltonian operators for N-component equations admitting some scaling properties. The Kodama reduction of the dispersionless-Boussinesq equations and the Lax reduction of the Benney moment equations are shown to be equivalent by a symmetry transformation. They can be cast into the form of a triplet of conservation laws which enable us to recognize a non-trivial scaling symmetry. The resulting bi-Hamiltonian structure generates three infinite sequences of conserved densities.

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

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

Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materialsmore » science, chemistry, and biology.« less

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

DOE PAGES

Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

2015-06-26

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materialsmore » science, chemistry, and biology.« less

Hybrid state vector methods for structural dynamic and aeroelastic boundary value problems

NASA Technical Reports Server (NTRS)

Lehman, L. L.

1982-01-01

A computational technique is developed that is suitable for performing preliminary design aeroelastic and structural dynamic analyses of large aspect ratio lifting surfaces. The method proves to be quite general and can be adapted to solving various two point boundary value problems. The solution method, which is applicable to both fixed and rotating wing configurations, is based upon a formulation of the structural equilibrium equations in terms of a hybrid state vector containing generalized force and displacement variables. A mixed variational formulation is presented that conveniently yields a useful form for these state vector differential equations. Solutions to these equations are obtained by employing an integrating matrix method. The application of an integrating matrix provides a discretization of the differential equations that only requires solutions of standard linear matrix systems. It is demonstrated that matrix partitioning can be used to reduce the order of the required solutions. Results are presented for several example problems in structural dynamics and aeroelasticity to verify the technique and to demonstrate its use. These problems examine various types of loading and boundary conditions and include aeroelastic analyses of lifting surfaces constructed from anisotropic composite materials.

The impact of 850,000 years of climate changes on the structure and dynamics of mammal food webs.

PubMed

Nenzén, Hedvig K; Montoya, Daniel; Varela, Sara

2014-01-01

Most evidence of climate change impacts on food webs comes from modern studies and little is known about how ancient food webs have responded to climate changes in the past. Here, we integrate fossil evidence from 71 fossil sites, body-size relationships and actualism to reconstruct food webs for six large mammal communities that inhabited the Iberian Peninsula at different times during the Quaternary. We quantify the long-term dynamics of these food webs and study how their structure changed across the Quaternary, a period for which fossil data and climate changes are well known. Extinction, immigration and turnover rates were correlated with climate changes in the last 850 kyr. Yet, we find differences in the dynamics and structural properties of Pleistocene versus Holocene mammal communities that are not associated with glacial-interglacial cycles. Although all Quaternary mammal food webs were highly nested and robust to secondary extinctions, general food web properties changed in the Holocene. These results highlight the ability of communities to re-organize with the arrival of phylogenetically similar species without major structural changes, and the impact of climate change and super-generalist species (humans) on Iberian Holocene mammal communities.

The Impact of 850,000 Years of Climate Changes on the Structure and Dynamics of Mammal Food Webs

PubMed Central

Nenzén, Hedvig K.; Montoya, Daniel; Varela, Sara

2014-01-01

Most evidence of climate change impacts on food webs comes from modern studies and little is known about how ancient food webs have responded to climate changes in the past. Here, we integrate fossil evidence from 71 fossil sites, body-size relationships and actualism to reconstruct food webs for six large mammal communities that inhabited the Iberian Peninsula at different times during the Quaternary. We quantify the long-term dynamics of these food webs and study how their structure changed across the Quaternary, a period for which fossil data and climate changes are well known. Extinction, immigration and turnover rates were correlated with climate changes in the last 850 kyr. Yet, we find differences in the dynamics and structural properties of Pleistocene versus Holocene mammal communities that are not associated with glacial-interglacial cycles. Although all Quaternary mammal food webs were highly nested and robust to secondary extinctions, general food web properties changed in the Holocene. These results highlight the ability of communities to re-organize with the arrival of phylogenetically similar species without major structural changes, and the impact of climate change and super-generalist species (humans) on Iberian Holocene mammal communities. PMID:25207754

Kinematics and depth-integrated terms in surf zone waves from laboratory measurement

NASA Astrophysics Data System (ADS)

Stansby, Peter K.; Feng, Tong

2005-04-01

Kinematics of nominally periodic surf zone waves have been measured in the laboratory using LDA (laser Doppler anemometry), above trough level as well as below, for weakly plunging breakers transforming into bores in shallower water. The aim was to determine, through phase- or ensemble-averaging, periodic flow structures in a two-dimensional vertical plane, from large-scale down to small-scale vortical structures. Coherent multiple vortical structures were evident at the initiation of breaking, becoming elongated along the surface during bore propagation. The initial region is likely to become more extensive as waves become more strongly plunging and could explain the difference in turbulence characteristics between plunging and spilling breakers observed elsewhere. Comparison of vorticity magnitudes with hydraulic-jump measurements showed some similarities during the initial stages of breaking, but these quickly grew less as breaking progressed into shallower water. Period-averaged kinematics and vorticity were also obtained showing shoreward mass transport above trough level and undertow below, with a thick layer of vorticity at trough level and a thin layer of vorticity of opposite rotation at the bed. There were also concentrated regions of mean vorticity near the end of the plunging region. Residual turbulence of relatively high frequency was presented as Reynolds stresses, showing marked anisotrophy. Dynamic pressure (pressure minus its hydrostatic component) was determined from the kinematics. The magnitudes of different effects were evaluated through the depth-integrated Reynolds-averaged Navier-Stokes (RANS) equations, which may be reduced to nine terms (the standard inviscid terms of the shallow-water equations conserving mass and momentum with hydrostatic pressure, and six additional terms), assuming that the complex, often aerated, free surface is treated as a simple interface. All terms were evaluated, assuming that a space/time transformation was justified with a slowly varying phase speed, and the net balance was always small in relation to the maxima of the larger terms. Terms due to dynamic pressure and vertical dispersion (due to the vertical variation of velocity) were as significant as the three terms in the inviscid shallow-water equations; terms involving residual turbulence were insignificant. The r.m.s. (root mean square) variation of each along the slope is highly irregular, with the inertia term due to (Eulerian) acceleration always greatest. This is consistent with complex, though repetitive, coherent structures. Modelling the flow with the shallow-water equations, using the surface elevation variation at the break point as input, nevertheless gave a good prediction of the wave height variation up the slope.

Research and development activities in unified control-structure modeling and design

NASA Technical Reports Server (NTRS)

Nayak, A. P.

1985-01-01

Results of work to develop a unified control/structures modeling and design capability for large space structures modeling are presented. Recent analytical results are presented to demonstrate the significant interdependence between structural and control properties. A new design methodology is suggested in which the structure, material properties, dynamic model and control design are all optimized simultaneously. Parallel research done by other researchers is reviewed. The development of a methodology for global design optimization is recommended as a long-term goal. It is suggested that this methodology should be incorporated into computer aided engineering programs, which eventually will be supplemented by an expert system to aid design optimization.

Characterization of a Novel Water Pocket Inside the Human Cx26 Hemichannel Structure

PubMed Central

Araya-Secchi, Raul; Perez-Acle, Tomas; Kang, Seung-gu; Huynh, Tien; Bernardin, Alejandro; Escalona, Yerko; Garate, Jose-Antonio; Martínez, Agustin D.; García, Isaac E.; Sáez, Juan C.; Zhou, Ruhong

2014-01-01

Connexins (Cxs) are a family of vertebrate proteins constituents of gap junction channels (GJCs) that connect the cytoplasm of adjacent cells by the end-to-end docking of two Cx hemichannels. The intercellular transfer through GJCs occurs by passive diffusion allowing the exchange of water, ions, and small molecules. Despite the broad interest to understand, at the molecular level, the functional state of Cx-based channels, there are still many unanswered questions regarding structure-function relationships, perm-selectivity, and gating mechanisms. In particular, the ordering, structure, and dynamics of water inside Cx GJCs and hemichannels remains largely unexplored. In this work, we describe the identification and characterization of a believed novel water pocket—termed the IC pocket—located in-between the four transmembrane helices of each human Cx26 (hCx26) monomer at the intracellular (IC) side. Using molecular dynamics (MD) simulations to characterize hCx26 internal water structure and dynamics, six IC pockets were identified per hemichannel. A detailed characterization of the dynamics and ordering of water including conformational variability of residues forming the IC pockets, together with multiple sequence alignments, allowed us to propose a functional role for this cavity. An in vitro assessment of tracer uptake suggests that the IC pocket residue Arg-143 plays an essential role on the modulation of the hCx26 hemichannel permeability. PMID:25099799

Review of probabilistic analysis of dynamic response of systems with random parameters

NASA Technical Reports Server (NTRS)

Kozin, F.; Klosner, J. M.

1989-01-01

The various methods that have been studied in the past to allow probabilistic analysis of dynamic response for systems with random parameters are reviewed. Dynamic response may have been obtained deterministically if the variations about the nominal values were small; however, for space structures which require precise pointing, the variations about the nominal values of the structural details and of the environmental conditions are too large to be considered as negligible. These uncertainties are accounted for in terms of probability distributions about their nominal values. The quantities of concern for describing the response of the structure includes displacements, velocities, and the distributions of natural frequencies. The exact statistical characterization of the response would yield joint probability distributions for the response variables. Since the random quantities will appear as coefficients, determining the exact distributions will be difficult at best. Thus, certain approximations will have to be made. A number of techniques that are available are discussed, even in the nonlinear case. The methods that are described were: (1) Liouville's equation; (2) perturbation methods; (3) mean square approximate systems; and (4) nonlinear systems with approximation by linear systems.

[What to do to avoid death by starvation? Domestic dynamics and childhood feeding practices in a rural area of extreme poverty in Mexico].

PubMed

Pelcastre-Villafuerte, Blanca; Riquer-Fernández, Florinda; de León-Reyes, Verónica; Reyes-Morales, Hortensia; Gutiérrez-Trujillo, Gonzalo; Bronfman, Mario

2006-01-01

To describe and compare household dynamics in terms of structure, beliefs and nutrition-related behavior in the homes of malnourished and well-nourished children less than five years of age. The authors carried out a qualitative ethnographic study using participant observation, and in depth interviews. Interviews were conducted with the child's caretaker or key informants, prior oral informed consent. Child care and childhood feeding practices at home and in the community were the focus of observations. The study included two periods of field work conducted in 2001, in three rural municipalities from the Río Balsas region, in Guerrero state, Mexico. The study's ethical and methodological aspects were approved by the National Research Commission of the Mexican Institute of Social Security. Households were differentially characterized by number of members, composition, type of relationship, source of income, and interactions among household members and with the community. Monoparental structures, in an early stage of the household cycle, give rise to conditions that render the child prone to malnutrition. Extended family structure represented more favorable household dynamics.

High-rate RTK and PPP multi-GNSS positioning for small-scale dynamic displacements monitoring

NASA Astrophysics Data System (ADS)

Paziewski, Jacek; Sieradzki, Rafał; Baryła, Radosław; Wielgosz, Pawel

2017-04-01

The monitoring of dynamic displacements and deformations of engineering structures such as buildings, towers and bridges is of great interest due to several practical and theoretical reasons. The most important is to provide information required for safe maintenance of the constructions. High temporal resolution and precision of GNSS observations predestine this technology to be applied to most demanding application in terms of accuracy, availability and reliability. GNSS technique supported by appropriate processing methodology may meet the specific demands and requirements of ground and structures monitoring. Thus, high-rate multi-GNSS signals may be used as reliable source of information on dynamic displacements of ground and engineering structures, also in real time applications. In this study we present initial results of application of precise relative GNSS positioning for detection of small scale (cm level) high temporal resolution dynamic displacements. Methodology and algorithms applied in self-developed software allowing for relative positioning using high-rate dual-frequency phase and pseudorange GPS+Galileo observations are also given. Additionally, an approach was also made to use the Precise Point Positioning technique to such application. In the experiment were used the observations obtained from high-rate (20 Hz) geodetic receivers. The dynamic displacements were simulated using specially constructed device moving GNSS antenna with dedicated amplitude and frequency. The obtained results indicate on possibility of detection of dynamic displacements of the GNSS antenna even at the level of few millimetres using both relative and Precise Point Positioning techniques after suitable signals processing.

The Influence of 150-Cavity Binders on the Dynamics of Influenza A Neuraminidases as Revealed by Molecular Dynamics Simulations and Combined Clustering

PubMed Central

Greenway, Kyle T.; LeGresley, Eric B.; Pinto, B. Mario

2013-01-01

Neuraminidase inhibitors are the main pharmaceutical agents employed for treatments of influenza infections. The neuraminidase structures typically exhibit a 150-cavity, an exposed pocket that is adjacent to the catalytic site. This site offers promising additional contact points for improving potency of existing pharmaceuticals, as well as generating entirely new candidate inhibitors. Several inhibitors based on known compounds and designed to interact with 150-cavity residues have been reported. However, the dynamics of any of these inhibitors remains unstudied and their viability remains unknown. This work reports the outcome of long-term, all-atom molecular dynamics simulations of four such inhibitors, along with three standard inhibitors for comparison. Each is studied in complex with four representative neuraminidase structures, which are also simulated in the absence of ligands for comparison, resulting in a total simulation time of 9.6µs. Our results demonstrate that standard inhibitors characteristically reduce the mobility of these dynamic proteins, while the 150-binders do not, instead giving rise to many unique conformations. We further describe an improved RMSD-based clustering technique that isolates these conformations – the structures of which are provided to facilitate future molecular docking studies – and reveals their interdependence. We find that this approach confers many advantages over previously described techniques, and the implications for rational drug design are discussed. PMID:23544106

The influence of 150-cavity binders on the dynamics of influenza A neuraminidases as revealed by molecular dynamics simulations and combined clustering.

PubMed

Greenway, Kyle T; LeGresley, Eric B; Pinto, B Mario

2013-01-01

Neuraminidase inhibitors are the main pharmaceutical agents employed for treatments of influenza infections. The neuraminidase structures typically exhibit a 150-cavity, an exposed pocket that is adjacent to the catalytic site. This site offers promising additional contact points for improving potency of existing pharmaceuticals, as well as generating entirely new candidate inhibitors. Several inhibitors based on known compounds and designed to interact with 150-cavity residues have been reported. However, the dynamics of any of these inhibitors remains unstudied and their viability remains unknown. This work reports the outcome of long-term, all-atom molecular dynamics simulations of four such inhibitors, along with three standard inhibitors for comparison. Each is studied in complex with four representative neuraminidase structures, which are also simulated in the absence of ligands for comparison, resulting in a total simulation time of 9.6 µs. Our results demonstrate that standard inhibitors characteristically reduce the mobility of these dynamic proteins, while the 150-binders do not, instead giving rise to many unique conformations. We further describe an improved RMSD-based clustering technique that isolates these conformations--the structures of which are provided to facilitate future molecular docking studies--and reveals their interdependence. We find that this approach confers many advantages over previously described techniques, and the implications for rational drug design are discussed.

Quantifying long-term evolution of intra-urban spatial interactions

PubMed Central

Sun, Lijun; Jin, Jian Gang; Axhausen, Kay W.; Lee, Der-Horng; Cebrian, Manuel

2015-01-01

Understanding the long-term impact that changes in a city's transportation infrastructure have on its spatial interactions remains a challenge. The difficulty arises from the fact that the real impact may not be revealed in static or aggregated mobility measures, as these are remarkably robust to perturbations. More generally, the lack of longitudinal, cross-sectional data demonstrating the evolution of spatial interactions at a meaningful urban scale also hinders us from evaluating the sensitivity of movement indicators, limiting our capacity to understand the evolution of urban mobility in depth. Using very large mobility records distributed over 3 years, we quantify the impact of the completion of a metro line extension: the Circle Line (CCL) in Singapore. We find that the commonly used movement indicators are almost identical before and after the project was completed. However, in comparing the temporal community structure across years, we do observe significant differences in the spatial reorganization of the affected geographical areas. The completion of CCL enables travellers to re-identify their desired destinations collectively with lower transport cost, making the community structure more consistent. These changes in locality are dynamic and characterized over short timescales, offering us a different approach to identify and analyse the long-term impact of new infrastructures on cities and their evolution dynamics. PMID:25551142

Radionuclide Incorporation and Long Term Performance of Apatite Waste Forms

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

Wang, Jianwei; Lian, Jie; Gao, Fei

2016-01-04

This project aims to combines state-of-the-art experimental and characterization techniques with atomistic simulations based on density functional theory (DFT) and molecular dynamics (MD) simulations. With an initial focus on long-lived I-129 and other radionuclides such as Cs, Sr in apatite structure, specific research objectives include the atomic scale understanding of: (1) incorporation behavior of the radionuclides and their effects on the crystal chemistry and phase stability; (2) stability and microstructure evolution of designed waste forms under coupled temperature and radiation environments; (3) incorporation and migration energetics of radionuclides and release behaviors as probed by DFT and molecular dynamics (MD) simulations;more » and (4) chemical durability as measured in dissolution experiments for long term performance evaluation and model validation.« less

Centrifuge modeling of rocking-isolated inelastic RC bridge piers

PubMed Central

Loli, Marianna; Knappett, Jonathan A; Brown, Michael J; Anastasopoulos, Ioannis; Gazetas, George

2014-01-01

Experimental proof is provided of an unconventional seismic design concept, which is based on deliberately underdesigning shallow foundations to promote intense rocking oscillations and thereby to dramatically improve the seismic resilience of structures. Termed rocking isolation, this new seismic design philosophy is investigated through a series of dynamic centrifuge experiments on properly scaled models of a modern reinforced concrete (RC) bridge pier. The experimental method reproduces the nonlinear and inelastic response of both the soil-footing interface and the structure. To this end, a novel scale model RC (1:50 scale) that simulates reasonably well the elastic response and the failure of prototype RC elements is utilized, along with realistic representation of the soil behavior in a geotechnical centrifuge. A variety of seismic ground motions are considered as excitations. They result in consistent demonstrably beneficial performance of the rocking-isolated pier in comparison with the one designed conventionally. Seismic demand is reduced in terms of both inertial load and deck drift. Furthermore, foundation uplifting has a self-centering potential, whereas soil yielding is shown to provide a particularly effective energy dissipation mechanism, exhibiting significant resistance to cumulative damage. Thanks to such mechanisms, the rocking pier survived, with no signs of structural distress, a deleterious sequence of seismic motions that caused collapse of the conventionally designed pier. © 2014 The Authors Earthquake Engineering & Structural Dynamics Published by John Wiley & Sons Ltd. PMID:26300573

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.

Creating a Test-Validated Finite-Element Model of the X-56A Aircraft Structure

NASA Technical Reports Server (NTRS)

Pak, Chan-Gi; Truong, Samson

2014-01-01

Small modeling errors in a finite-element model will eventually induce errors in the structural flexibility and mass, thus propagating into unpredictable errors in the unsteady aerodynamics and the control law design. One of the primary objectives of the X-56A Multi-Utility Technology Testbed aircraft is the flight demonstration of active flutter suppression and, therefore, in this study, the identification of the primary and secondary modes for the structural model tuning based on the flutter analysis of the X-56A aircraft. The ground-vibration test-validated structural dynamic finite-element model of the X-56A aircraft is created in this study. The structural dynamic finite-element model of the X-56A aircraft is improved using a model-tuning tool. In this study, two different weight configurations of the X-56A aircraft have been improved in a single optimization run. Frequency and the cross-orthogonality (mode shape) matrix were the primary focus for improvement, whereas other properties such as c.g. location, total weight, and off-diagonal terms of the mass orthogonality matrix were used as constraints. The end result was an improved structural dynamic finite-element model configuration for the X-56A aircraft. Improved frequencies and mode shapes in this study increased average flutter speeds of the X-56A aircraft by 7.6% compared to the baseline model.

Sex-related differences in the development of fetal heart rate dynamics.

PubMed

Kim, Kyu Nam; Park, Young-Sun; Hoh, Jeong-Kyu

2016-02-01

Despite previous efforts to explain the general advantages of female fetuses over males regarding health, sex-related differences in the dynamics or complexity of fetal heart rate (FHR) variability and FHR maturation patterns have not yet been identified. To make linear and nonlinear comparisons of antepartum FHR indices, dynamics, complexity, and reactivity to the non-stress test (NST) and vibroacoustic-stimulation test (VAST) in male and female fetuses. A total of 3835 singleton term deliveries without maternal and fetal complications were divided into female (n=1849) and male (n=1986) groups, and subjected to comparison and analyses. Linear FHR indices, approximate entropy (ApEn), sample entropy (SampEn), short-term/long-term exponents (α1/α2), correlation dimension (CD), NST and VAST criteria, and modified nonlinear reactive criteria (MNRC) were used to evaluate outcomes. ApEn was consistently higher in female fetuses than in male ones. ApEn in female fetuses was maximal at 29-30 gestational weeks, while the increase in ApEn was delayed in male fetuses but more rapid, reaching its peak at 31-32 gestational weeks. In both sexes, CD increased up to term, and α2 rapidly decreased up to 31-32weeks in an analogous manner. The two sexes differed significantly in response to VAST at <31 gestational weeks and there was a structural difference in reactive patterns under MNRC. Female fetuses exhibit greater heart rate dynamics in early gestational periods, suggesting that their cardiovascular system matures earlier than that of males. Male fetuses undergo a compensatory period of rapid change to catch up with females at term. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

An adaptively refined XFEM with virtual node polygonal elements for dynamic crack problems

NASA Astrophysics Data System (ADS)

Teng, Z. H.; Sun, F.; Wu, S. C.; Zhang, Z. B.; Chen, T.; Liao, D. M.

2018-02-01

By introducing the shape functions of virtual node polygonal (VP) elements into the standard extended finite element method (XFEM), a conforming elemental mesh can be created for the cracking process. Moreover, an adaptively refined meshing with the quadtree structure only at a growing crack tip is proposed without inserting hanging nodes into the transition region. A novel dynamic crack growth method termed as VP-XFEM is thus formulated in the framework of fracture mechanics. To verify the newly proposed VP-XFEM, both quasi-static and dynamic cracked problems are investigated in terms of computational accuracy, convergence, and efficiency. The research results show that the present VP-XFEM can achieve good agreement in stress intensity factor and crack growth path with the exact solutions or experiments. Furthermore, better accuracy, convergence, and efficiency of different models can be acquired, in contrast to standard XFEM and mesh-free methods. Therefore, VP-XFEM provides a suitable alternative to XFEM for engineering applications.

The Schrödinger-Poisson equations as the large-N limit of the Newtonian N-body system: applications to the large scale dark matter dynamics

NASA Astrophysics Data System (ADS)

Briscese, Fabio

2017-09-01

In this paper it is argued how the dynamics of the classical Newtonian N-body system can be described in terms of the Schrödinger-Poisson equations in the large N limit. This result is based on the stochastic quantization introduced by Nelson, and on the Calogero conjecture. According to the Calogero conjecture, the emerging effective Planck constant is computed in terms of the parameters of the N-body system as \\hbar ˜ M^{5/3} G^{1/2} (N/< ρ > )^{1/6}, where is G the gravitational constant, N and M are the number and the mass of the bodies, and < ρ > is their average density. The relevance of this result in the context of large scale structure formation is discussed. In particular, this finding gives a further argument in support of the validity of the Schrödinger method as numerical double of the N-body simulations of dark matter dynamics at large cosmological scales.

A qualitative analysis of parental decision making for childhood immunisation.

PubMed

Marshall, S; Swerissen, H

1999-10-01

Achieving high rates of childhood immunisation is an important public health aim. Currently, however, immunisation uptake in Australia is disappointing. This qualitative study investigated the factors that influence parental decision making for childhood immunisation, and whether parents' experiences were better conceptualised in terms of static subjective expected utility models or in terms of a more dynamic process. Semi-structured in-depth interviews were conducted with 20 predominantly middle-class mothers--17 immunizers and three non-immunizers, in Melbourne, Victoria, in 1997. The data were then examined using thematic analysis. The results suggested that for these participants the decision regarding childhood immunization was better conceptualized as a dynamic process. The decision required initial consideration, implementation then maintenance. If a better understanding of immunization decision making is to be achieved, future studies must look beyond static frameworks. Clearer insight into the dynamic nature of immunization decision making should assist in the identification of more effective methods of promoting childhood immunization to groups at risk of non-compliance.

Family Structure and Long-Term Care Insurance Purchase

PubMed Central

Van Houtven, Courtney Harold; Coe, Norma B.; Konetzka, R. Tamara

2015-01-01

While it has long been assumed that family structure and potential sources of informal care play a large role in the purchase decisions for long-term care insurance (LTCI), current empirical evidence is inconclusive. Our study examines the relationship between family structure and LTCI purchase and addresses several major limitations of the prior literature by using a long panel of data and considering modern family relationships, such as presence of stepchildren. We find that family structure characteristics from one’s own generation, particularly about one’s spouse, are associated with purchase, but that few family structure attributes from the younger generation have an influence. Family factors that may indicate future caregiver supply are negatively associated with purchase: having a coresidential child, signaling close proximity, and having a currently working spouse, signaling a healthy and able spouse, that LTC planning has not occurred yet, or that there is less need for asset protection afforded by LTCI. Dynamic factors, such as increasing wealth or turning 65, are associated with higher likelihood of LTCI purchase. PMID:25760583

Development and Verification of the Soil-Pile Interaction Extension for SubDyn

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

Damiani, Rick R; Wendt, Fabian F

SubDyn is the substructure structural-dynamics module for the aero-hydro-servo-elastic tool FAST v8. SubDyn uses a finite-element model (FEM) to simulate complex multimember lattice structures connected to conventional turbines and towers, and it can make use of the Craig-Bampton model reduction. Here we describe the newly added capability to handle soil-pile stiffness and compare results for monopile and jacket-based offshore wind turbines as obtained with FAST v8, SACS, and EDP (the latter two are modeling software packages commonly used in the offshore oil and gas industry). The level of agreement in terms of modal properties and loads for the entire offshoremore » wind turbine components is excellent, thus allowing SubDyn and FAST v8 to accurately simulate offshore wind turbines on fixed-bottom structures and accounting for the effect of soil dynamics, thus reducing risk to the project.« less

Dynamics and Emergent Structures in Active Fluids

NASA Astrophysics Data System (ADS)

Baskaran, Aparna

2014-03-01

In this talk, we consider an active fluid of colloidal sized particles, with the primary manifestation of activity being a self-replenishing velocity along one body axis of the particle. This is a minimal model for varied systems such as bacterial colonies, cytoskeletal filament motility assays vibrated granular particles and self propelled diffusophoretic colloids, depending on the nature of interaction among the particles. Using microscopic Brownian dynamics simulations, coarse-graining using the tools of non-equilibrium statistical mechanics and analysis of macroscopic hydrodynamic theories, we characterize emergent structures seen in these systems, which are determined by the symmetry of the interactions among the active units, such as propagating density waves, dense stationary bands, asters and phase separated isotropic clusters. We identify a universal mechanism, termed ``self-regulation,'' as the underlying physics that leads to these structures in diverse systems. Support from NSF through DMR-1149266 and DMR-0820492.

Effects of proton irradiation on luminescence and carrier dynamics of self-assembled III-V quatum dots

NASA Technical Reports Server (NTRS)

Leon, R.; Marcinkevicius, S.; Siegert, J.; Magness, B.; Taylor, W.; Lobo, C.

2002-01-01

The effects of proton irradiation (1.5 MeV) on photoluminescence intensities and carrier dynamics were compared between III-V quantum dots and similar quantum well structures. A significant enhancement in radiation tolerance is seen with three-dimensional quantum confinement. Measurements were carried out in different quantum dot (QD) structures, varying in material (InGaAs/GaAs and InAlAs/AlGaAs), QD surface density (4x10^8 to 3x10'^10 cm^-2), and substrate orientation [(100) and (311) B]. Similar trends were observed for all QD samples. A slight increase in PL emission after low to intermediate proton doses, are also observed in InGaAs/GaAs (100) QD structures. The latter is explained in terms of more efficient carrier transfer from the wetting layer via radiation-induced defects.

Spreading Effect in Industrial Complex Network Based on Revised Structural Holes Theory

PubMed Central

Ye, Qing; Guan, Jun

2016-01-01

This paper analyzed the spreading effect of industrial sectors with complex network model under perspective of econophysics. Input-output analysis, as an important research tool, focuses more on static analysis. However, the fundamental aim of industry analysis is to figure out how interaction between different industries makes impacts on economic development, which turns out to be a dynamic process. Thus, industrial complex network based on input-output tables from WIOD is proposed to be a bridge connecting accurate static quantitative analysis and comparable dynamic one. With application of revised structural holes theory, flow betweenness and random walk centrality were respectively chosen to evaluate industrial sectors’ long-term and short-term spreading effect process in this paper. It shows that industries with higher flow betweenness or random walk centrality would bring about more intensive industrial spreading effect to the industrial chains they stands in, because value stream transmission of industrial sectors depends on how many products or services it can get from the other ones, and they are regarded as brokers with bigger information superiority and more intermediate interests. PMID:27218468

Spreading Effect in Industrial Complex Network Based on Revised Structural Holes Theory.

PubMed

Xing, Lizhi; Ye, Qing; Guan, Jun

2016-01-01

This paper analyzed the spreading effect of industrial sectors with complex network model under perspective of econophysics. Input-output analysis, as an important research tool, focuses more on static analysis. However, the fundamental aim of industry analysis is to figure out how interaction between different industries makes impacts on economic development, which turns out to be a dynamic process. Thus, industrial complex network based on input-output tables from WIOD is proposed to be a bridge connecting accurate static quantitative analysis and comparable dynamic one. With application of revised structural holes theory, flow betweenness and random walk centrality were respectively chosen to evaluate industrial sectors' long-term and short-term spreading effect process in this paper. It shows that industries with higher flow betweenness or random walk centrality would bring about more intensive industrial spreading effect to the industrial chains they stands in, because value stream transmission of industrial sectors depends on how many products or services it can get from the other ones, and they are regarded as brokers with bigger information superiority and more intermediate interests.

Combined aerodynamic and structural dynamic problem emulating routines (CASPER): Theory and implementation

NASA Technical Reports Server (NTRS)

Jones, William H.

1985-01-01

The Combined Aerodynamic and Structural Dynamic Problem Emulating Routines (CASPER) is a collection of data-base modification computer routines that can be used to simulate Navier-Stokes flow through realistic, time-varying internal flow fields. The Navier-Stokes equation used involves calculations in all three dimensions and retains all viscous terms. The only term neglected in the current implementation is gravitation. The solution approach is of an interative, time-marching nature. Calculations are based on Lagrangian aerodynamic elements (aeroelements). It is assumed that the relationships between a particular aeroelement and its five nearest neighbor aeroelements are sufficient to make a valid simulation of Navier-Stokes flow on a small scale and that the collection of all small-scale simulations makes a valid simulation of a large-scale flow. In keeping with these assumptions, it must be noted that CASPER produces an imitation or simulation of Navier-Stokes flow rather than a strict numerical solution of the Navier-Stokes equation. CASPER is written to operate under the Parallel, Asynchronous Executive (PAX), which is described in a separate report.

Continuous and discrete extreme climatic events affecting the dynamics of a high-arctic reindeer population.

PubMed

Chan, Kung-Sik; Mysterud, Atle; Øritsland, Nils Are; Severinsen, Torbjørn; Stenseth, Nils Chr

2005-10-01

Climate at northern latitudes are currently changing both with regard to the mean and the temporal variability at any given site, increasing the frequency of extreme events such as cold and warm spells. Here we use a conceptually new modelling approach with two different dynamic terms of the climatic effects on a Svalbard reindeer population (the Brøggerhalvøya population) which underwent an extreme icing event ("locked pastures") with 80% reduction in population size during one winter (1993/94). One term captures the continuous and linear effect depending upon the Arctic Oscillation and another the discrete (rare) "event" process. The introduction of an "event" parameter describing the discrete extreme winter resulted in a more parsimonious model. Such an approach may be useful in strongly age-structured ungulate populations, with young and very old individuals being particularly prone to mortality factors during adverse conditions (resulting in a population structure that differs before and after extreme climatic events). A simulation study demonstrates that our approach is able to properly detect the ecological effects of such extreme climate events.

Solution structures, dynamics, and ice growth inhibitory activity of peptide fragments derived from an antarctic yeast protein.

PubMed

Shah, Syed Hussinien H; Kar, Rajiv K; Asmawi, Azren A; Rahman, Mohd Basyaruddin A; Murad, Abdul Munir A; Mahadi, Nor M; Basri, Mahiran; Rahman, Raja Noor Zaliha A; Salleh, Abu B; Chatterjee, Subhrangsu; Tejo, Bimo A; Bhunia, Anirban

2012-01-01

Exotic functions of antifreeze proteins (AFP) and antifreeze glycopeptides (AFGP) have recently been attracted with much interest to develop them as commercial products. AFPs and AFGPs inhibit ice crystal growth by lowering the water freezing point without changing the water melting point. Our group isolated the Antarctic yeast Glaciozyma antarctica that expresses antifreeze protein to assist it in its survival mechanism at sub-zero temperatures. The protein is unique and novel, indicated by its low sequence homology compared to those of other AFPs. We explore the structure-function relationship of G. antarctica AFP using various approaches ranging from protein structure prediction, peptide design and antifreeze activity assays, nuclear magnetic resonance (NMR) studies and molecular dynamics simulation. The predicted secondary structure of G. antarctica AFP shows several α-helices, assumed to be responsible for its antifreeze activity. We designed several peptide fragments derived from the amino acid sequences of α-helical regions of the parent AFP and they also showed substantial antifreeze activities, below that of the original AFP. The relationship between peptide structure and activity was explored by NMR spectroscopy and molecular dynamics simulation. NMR results show that the antifreeze activity of the peptides correlates with their helicity and geometrical straightforwardness. Furthermore, molecular dynamics simulation also suggests that the activity of the designed peptides can be explained in terms of the structural rigidity/flexibility, i.e., the most active peptide demonstrates higher structural stability, lower flexibility than that of the other peptides with lower activities, and of lower rigidity. This report represents the first detailed report of downsizing a yeast AFP into its peptide fragments with measurable antifreeze activities.

Solution Structures, Dynamics, and Ice Growth Inhibitory Activity of Peptide Fragments Derived from an Antarctic Yeast Protein

PubMed Central

Asmawi, Azren A.; Rahman, Mohd Basyaruddin A.; Murad, Abdul Munir A.; Mahadi, Nor M.; Basri, Mahiran; Rahman, Raja Noor Zaliha A.; Salleh, Abu B.; Chatterjee, Subhrangsu; Tejo, Bimo A.; Bhunia, Anirban

2012-01-01

Exotic functions of antifreeze proteins (AFP) and antifreeze glycopeptides (AFGP) have recently been attracted with much interest to develop them as commercial products. AFPs and AFGPs inhibit ice crystal growth by lowering the water freezing point without changing the water melting point. Our group isolated the Antarctic yeast Glaciozyma antarctica that expresses antifreeze protein to assist it in its survival mechanism at sub-zero temperatures. The protein is unique and novel, indicated by its low sequence homology compared to those of other AFPs. We explore the structure-function relationship of G. antarctica AFP using various approaches ranging from protein structure prediction, peptide design and antifreeze activity assays, nuclear magnetic resonance (NMR) studies and molecular dynamics simulation. The predicted secondary structure of G. antarctica AFP shows several α-helices, assumed to be responsible for its antifreeze activity. We designed several peptide fragments derived from the amino acid sequences of α-helical regions of the parent AFP and they also showed substantial antifreeze activities, below that of the original AFP. The relationship between peptide structure and activity was explored by NMR spectroscopy and molecular dynamics simulation. NMR results show that the antifreeze activity of the peptides correlates with their helicity and geometrical straightforwardness. Furthermore, molecular dynamics simulation also suggests that the activity of the designed peptides can be explained in terms of the structural rigidity/flexibility, i.e., the most active peptide demonstrates higher structural stability, lower flexibility than that of the other peptides with lower activities, and of lower rigidity. This report represents the first detailed report of downsizing a yeast AFP into its peptide fragments with measurable antifreeze activities. PMID:23209600

Estimating Rheological Parameters of Anhydrite from Folded Evaporite sequences: Implications for Internal Dynamics of Salt Structure

NASA Astrophysics Data System (ADS)

Adamuszek, Marta; Dabrowski, Marcin; Schmalholz, Stefan M.; Urai, Janos L.; Raith, Alexander

2015-04-01

Salt structures have been identified as a potential target for hydrocarbon, CO2, or radioactive waste storage. The most suitable locations for magazines are considered in the thick and relatively homogeneous rock salt layers. However, salt structures often consist of the evaporite sequence including rock salt intercalated with other rock types e.g.: anhydrite, gypsum, potassium and magnesium salt, calcite, dolomite, or shale. The presence of such heterogeneities causes a serious disturbance in the structure management. Detailed analysis of the internal architecture and internal dynamics of the salt structure are crucial for evaluating them as suitable repositories and also their long-term stability. The goal of this study is to analyse the influence of the presence of anhydrite layers on the internal dynamics of salt structures. Anhydrite is a common rock in evaporite sequences. Its physical and mechanical properties strongly differ from the properties of rock salt. The density of anhydrite is much higher than the density of salt, thus anhydrite is likely to sink in salt causing the disturbance of the surrounding structures. This suggestion was the starting point to the discussion about the long-term stability of the magazines in salt structures [1]. However, the other important parameter that has to be taken into account is the viscosity of anhydrite. The high viscosity ratio between salt and anhydrite can restrain the layer from sinking. The rheological behaviour of anhydrite has been studied in laboratory experiments [2], but the results only provide information about the short-term behaviour. The long-term behaviour can be best predicted using indirect methods e.g. based on the analysis of natural structures that developed over geological time scale. One of the most promising are fold structures, the shape of which is very sensitive to the rheological parameters of the deforming materials. Folds can develop in mechanically stratified materials during layer parallel shortening. Mechanical model have been developed to rigorously correlate rheological properties of rock to the fold shape. A quantitative fold shape analysis combined with the folding theory allows deciphering the rock rheology. In this study, we analyse anhydrite layers embedded in the rock salt from the Upper Permian Zechstein salt formation from Dutch offshore. The anhydrite layers are common intercalation in the sequence. Their thickness varies between few millimetres up to hundred meters. The layers are strongly deformed often forming fold structures, which can be observed on a wide range of scales: in core samples, mine galleries, and also in the seismic sections. For our analysis, we select single layer fold trains. Quantitative fold shape analysis is carried out using Fold Geometry Toolbox [3], which allows deciphering the viscosity ratio between anhydrite and salt. The results indicate that anhydrite layer is ca. 10 to 30 times more viscous than the embedding salt. Further, we use the estimated rheological parameters of anhydrite in the numerical analysis of the internal salt dynamics. We solve an incompressible Stokes equation in the presence of the gravity using the finite element method solver MILAMIN [4]. We show that the presence of denser and more viscous anhydrite layers in the tectonically stable regime is insignificant for the internal stability of the salt structures. [1] Chemia, Z., Koyi, H., Schmeling, H. 2008. Numerical modelling of rise and fall of a dense layer in salt diapirs. Geophysical Journal International, 172: 798-816. [2] Muller, W.H., Briegel, U. 1978. The rheological behaviour of polycrystalline Anhydrite. Eclogae Geol. Helv, 71(2): 397-407 [3] Adamuszek M., Schmid D.W., Dabrowski M. 2011. Fold geometry toolbox - Automated determination of fold shape, shortening, and material properties, Journal of Structural Geology, 33: 1406-1416. [4] Dabrowski, M., Krotkiewski, M., and Schmid, D. W. 2008. MILAMIN: MATLAB-based finite element method solver for large problems. Geochemistry Geophysics Geosystems, 9: Q04030.

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.

Structural model for fluctuations in financial markets

NASA Astrophysics Data System (ADS)

Anand, Kartik; Khedair, Jonathan; Kühn, Reimer

2018-05-01

In this paper we provide a comprehensive analysis of a structural model for the dynamics of prices of assets traded in a market which takes the form of an interacting generalization of the geometric Brownian motion model. It is formally equivalent to a model describing the stochastic dynamics of a system of analog neurons, which is expected to exhibit glassy properties and thus many metastable states in a large portion of its parameter space. We perform a generating functional analysis, introducing a slow driving of the dynamics to mimic the effect of slowly varying macroeconomic conditions. Distributions of asset returns over various time separations are evaluated analytically and are found to be fat-tailed in a manner broadly in line with empirical observations. Our model also allows us to identify collective, interaction-mediated properties of pricing distributions and it predicts pricing distributions which are significantly broader than their noninteracting counterparts, if interactions between prices in the model contain a ferromagnetic bias. Using simulations, we are able to substantiate one of the main hypotheses underlying the original modeling, viz., that the phenomenon of volatility clustering can be rationalized in terms of an interplay between the dynamics within metastable states and the dynamics of occasional transitions between them.

Functional liposomes and supported lipid bilayers: towards the complexity of biological archetypes.

PubMed

Berti, Debora; Caminati, Gabriella; Baglioni, Piero

2011-05-21

This perspective paper provides some illustrative examples on the interplay between information gathered on planar supported lipid bilayers (SLB) and unilamellar lipid vesicles (ULV) to get an integrated description of phenomena occurring at the nanoscale that involve locally bilayered structures. Similarities and differences are underlined and critically compared in terms of biomimetic fidelity and instrumental accessibility to structural and dynamical parameters, focusing on some recent reports that either explicitly address this comparison or introducing some studies that separately investigate the same process in SLB and lipid vesicles. Despite the structural similarity on the nanoscale, the different topology implies radically different characterization techniques that have evolved in sectorial and separated approaches. The quest for increasing levels of compositional complexity for bilayered systems should not result in a loss of structural and dynamical control: this is the central challenge of future research in this area, where the integrated approach highlighted in this contribution would enable improved levels of understanding. © The Owner Societies 2011

Magnetic structure and excitation spectrum of the hyperhoneycomb Kitaev magnet β -Li2IrO3

NASA Astrophysics Data System (ADS)

Ducatman, Samuel; Rousochatzakis, Ioannis; Perkins, Natalia B.

2018-03-01

We present a theoretical study of the static and dynamical properties of the three-dimensional, hyperhoneycomb Kitaev magnet β -Li2IrO3 . We argue that the observed incommensurate order can be understood in terms of a long-wavelength twisting of a nearby commensurate period-3 state, with the same key qualitatively features. The period-3 state shows very different structure when either the Kitaev interaction K or the off-diagonal exchange anisotropy Γ is dominant. A comparison of the associated static spin structure factors with reported scattering experiments in zero and finite fields gives strong evidence that β -Li2IrO3 lies in the regime of dominant Kitaev coupling, and that the Heisenberg exchange J is much weaker than both K and Γ . Our predictions for the magnon excitation spectra, the dynamical spin structure factors, and their polarization dependence provide additional distinctive fingerprints that can be checked experimentally.

Dynamic environmental control mechanisms for pneumatic foil constructions

NASA Astrophysics Data System (ADS)

Flor, Jan-Frederik; Wu, Yupeng; Beccarelli, Paolo; Chilton, John

2017-11-01

Membrane and foil structures have become over the last decades an attractive alternative to conventional materials and building systems with increasing implementation in different typologies and scale. The development of transparent, light, flexible and resistant materials like Ethylene Tetrafluoroethylene (ETFE) has triggered a rethinking of the building envelope in the building industry towards lightweight systems. ETFE foil cushions have proven to fulfil the design requirements in terms of structural efficiency and aesthetic values. But the strategies to satisfy increasing demands of energy efficiency and comfort conditions are still under development. The prediction and manipulation of the thermo-optical behaviour of ETFE foil cushion structures currently remain as one of the main challenges for designers and manufacturers. This paper reviews ongoing research regarding the control of the thermo-optical performance of ETFE cushion structures and highlights challenges and possible improvements. An overview of different dynamic and responsive environmental control mechanisms for multilayer foil constructions is provided and the state of the art in building application outlined by the discussion of case studies.

Impacts of exotic mangrove forests and mangrove deforestation on carbon remineralization and ecosystem functioning in marine sediments

USGS Publications Warehouse

Sweetman, A.K.; Middelburg, J.J.; Berle, A.M.; Bernardino, A.F.; Schander, C.; Demopoulos, A.W.J.; Smith, C.R.

2010-01-01

To evaluate how mangrove invasion and removal can modify benthic carbon cycling processes and ecosystem functioning, we used stable-isotopically labelled algae as a deliberate tracer to quantify benthic respiration and C-flow through macrofauna and bacteria in sediments collected from (1) an invasive mangrove forest, (2) deforested mangrove sites 2 and 6 years after removal of above-sediment mangrove biomass, and (3) two mangrove-free, control sites in the Hawaiian coastal zone. Sediment oxygen consumption (SOC) rates were significantly greater in the mangrove and mangrove removal site experiments than in controls and were significantly correlated with total benthic (macrofauna and bacteria) biomass and sedimentary mangrove biomass (SMB). Bacteria dominated short-term C-processing of added microalgal-C and benthic biomass in sediments from the invasive mangrove forest habitat. In contrast, macrofauna were the most important agents in the short-term processing of microalgal-C in sediments from the mangrove removal and control sites. Mean faunal abundance and short term C-uptake rates in sediments from both removal sites were significantly higher than in control cores, which collectively suggest that community structure and short-term C-cycling dynamics in habitats where mangroves have been cleared can remain fundamentally different from un-invaded mudflat sediments for at least 6-yrs following above-sediment mangrove removal. In summary, invasion by mangroves can lead to large shifts in benthic ecosystem function, with sediment metabolism, benthic community structure and short-term C-remineralization dynamics being affected for years following invader removal. ?? 2010 Author(s).

Phase diagram and quench dynamics of the cluster-XY spin chain

NASA Astrophysics Data System (ADS)

Montes, Sebastián; Hamma, Alioscia

2012-08-01

We study the complete phase space and the quench dynamics of an exactly solvable spin chain, the cluster-XY model. In this chain, the cluster term and the XY couplings compete to give a rich phase diagram. The phase diagram is studied by means of the quantum geometric tensor. We study the time evolution of the system after a critical quantum quench using the Loschmidt echo. The structure of the revivals after critical quantum quenches presents a nontrivial behavior depending on the phase of the initial state and the critical point.

The mu-derivative and its applications to finding exact solutions of the Cahn-Hilliard, Korteveg-de Vries, and Burgers equations.

PubMed

Mitlin, Vlad

2005-10-15

A new transformation termed the mu-derivative is introduced. Applying it to the Cahn-Hilliard equation yields dynamical exact solutions. It is shown that the mu-transformed Cahn-Hilliard equation can be presented in a separable form. This transformation also yields dynamical exact solutions and separable forms for other nonlinear models such as the modified Korteveg-de Vries and the Burgers equations. The general structure of a nonlinear partial differential equation that becomes separable upon applying the mu-derivative is described.

Engineering model of the electric drives of separation device for simulation of automatic control systems of reactive power compensation by means of serially connected capacitors

NASA Astrophysics Data System (ADS)

Juromskiy, V. M.

2016-09-01

It is developed a mathematical model for an electric drive of high-speed separation device in terms of the modeling dynamic systems Simulink, MATLAB. The model is focused on the study of the automatic control systems of the power factor (Cosφ) of an actuator by compensating the reactive component of the total power by switching a capacitor bank in series with the actuator. The model is based on the methodology of the structural modeling of dynamic processes.

Phase diagram and quench dynamics of the cluster-XY spin chain.

PubMed

Montes, Sebastián; Hamma, Alioscia

2012-08-01

We study the complete phase space and the quench dynamics of an exactly solvable spin chain, the cluster-XY model. In this chain, the cluster term and the XY couplings compete to give a rich phase diagram. The phase diagram is studied by means of the quantum geometric tensor. We study the time evolution of the system after a critical quantum quench using the Loschmidt echo. The structure of the revivals after critical quantum quenches presents a nontrivial behavior depending on the phase of the initial state and the critical point.

Static Stability in the Global Upper Troposphere and Lower Stratosphere: Observations of Long-term Mean Structure and Variability using GPS Radio Occultation Data

NASA Astrophysics Data System (ADS)

Grise, K. M.; Thompson, D. W.; Birner, T.

2009-12-01

Static stability is a fundamental dynamical quantity that measures the vertical temperature stratification of the atmosphere. The long-term mean static stability field is characterized by the well-known transition from low values in the troposphere to high values in the stratosphere. However, the magnitude and structure of fine-scale static stability features near the tropopause are difficult to discern in temperature data with low vertical resolution. In this study, the authors apply over six years of high vertical resolution Global Positioning System radio occultation temperature profiles to document the long-term mean structure and variability of static stability in the global upper troposphere and lower stratosphere (UTLS). The results of this study demonstrate that a shallow but pronounced maximum in static stability exists just above the tropopause at all latitudes (i.e., the “tropopause inversion layer,” or TIL). This study also uncovers two novel aspects of static stability in the global UTLS. In the tropical lower stratosphere, the results reveal a unique vertically and horizontally varying static stability structure, with maxima located at ~17 km and ~19 km. The upper feature peaks during the NH cold season and has its largest magnitude between 10 and 15 degrees latitude in both hemispheres; the lower feature exhibits a weaker seasonal cycle and is centered at the Equator. The results also demonstrate that the strength of the TIL is closely tied to stratospheric dynamic variability. The magnitude of the TIL is enhanced following sudden stratospheric warmings in the polar regions and the easterly phase of the quasi-biennial oscillation in the tropics.

Static Stability in the Global Upper Troposphere and Lower Stratosphere: Observations of Long-term Mean Structure and Variability using GPS Radio Occultation Data

NASA Astrophysics Data System (ADS)

Grise, Kevin M.; Thompson, David W. J.; Birner, Thomas

2010-05-01

Static stability is a fundamental dynamical quantity that measures the vertical temperature stratification of the atmosphere. The long-term mean static stability field is characterized by the well-known transition from low values in the troposphere to high values in the stratosphere. However, the magnitude and structure of fine-scale static stability features near the tropopause are difficult to discern in temperature data with low vertical resolution. In this study, the authors apply over six years of high vertical resolution Global Positioning System radio occultation temperature profiles to document the long-term mean structure and variability of static stability in the global upper troposphere and lower stratosphere (UTLS). The results of this study demonstrate that a shallow but pronounced maximum in static stability exists just above the tropopause at all latitudes (i.e., the "tropopause inversion layer," or TIL). This study also uncovers two novel aspects of static stability in the global UTLS. In the tropical lower stratosphere, the results reveal a unique vertically and horizontally varying static stability structure, with maxima located at ~17 km and ~19 km. The upper feature peaks during the NH cold season and has its largest magnitude between 10 and 15 degrees latitude in both hemispheres; the lower feature exhibits a weaker seasonal cycle and is centered at the Equator. The results also demonstrate that the strength of the TIL is closely tied to stratospheric dynamic variability. The magnitude of the TIL is enhanced following sudden stratospheric warmings in the polar regions and the easterly phase of the quasi-biennial oscillation in the tropics.

Nonequilibrium dynamics of probe filaments in actin-myosin networks

NASA Astrophysics Data System (ADS)

Gladrow, J.; Broedersz, C. P.; Schmidt, C. F.

2017-08-01

Active dynamic processes of cells are largely driven by the cytoskeleton, a complex and adaptable semiflexible polymer network, motorized by mechanoenzymes. Small dimensions, confined geometries, and hierarchical structures make it challenging to probe dynamics and mechanical response of such networks. Embedded semiflexible probe polymers can serve as nonperturbing multiscale probes to detect force distributions in active polymer networks. We show here that motor-induced forces transmitted to the probe polymers are reflected in nonequilibrium bending dynamics, which we analyze in terms of spatial eigenmodes of an elastic beam under steady-state conditions. We demonstrate how these active forces induce correlations among the mode amplitudes, which furthermore break time-reversal symmetry. This leads to a breaking of detailed balance in this mode space. We derive analytical predictions for the magnitude of resulting probability currents in mode space in the white-noise limit of motor activity. We relate the structure of these currents to the spatial profile of motor-induced forces along the probe polymers and provide a general relation for observable currents on two-dimensional hyperplanes.

Electrostatic cloaking of surface structure for dynamic wetting

NASA Astrophysics Data System (ADS)

Shiomi, Junichiro; Nita, Satoshi; Do-Quang, Minh; Wang, Jiayu; Chen, Yu-Chung; Suzuki, Yuji; Amberg, Gustav

2017-11-01

Dynamic wetting problems are fundamental to the understanding of the interaction between liquids and solids. Even in a superficially simple experimental situation, such as a droplet spreading over a dry surface, the result may depend not only on the liquid properties but also strongly on the substrate-surface properties; even for macroscopically smooth surfaces, the microscopic geometrical roughness can be important. In addition, as surfaces may often be naturally charged, or electric fields are used to manipulate fluids, electric effects are crucial components that influence wetting phenomena. Here we investigate the interplay between electric forces and surface structures in dynamic wetting. While surface microstructures can significantly hinder the spreading, we find that the electrostatics can ``cloak'' the microstructures, i.e. deactivate the hindering. We identify the physics in terms of reduction in contact-line friction, which makes the dynamic wetting inertial force dominant and insensitive to the substrate properties. This work was financially supported in part by, the Japan Society for the Promotion of Science, Swedish Governmental Agency for Innovation Systems, and the Japan Science and Technology Agency.

Robust Structural Analysis and Design of Distributed Control Systems to Prevent Zero Dynamics Attacks

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

Weerakkody, Sean; Liu, Xiaofei; Sinopoli, Bruno

We consider the design and analysis of robust distributed control systems (DCSs) to ensure the detection of integrity attacks. DCSs are often managed by independent agents and are implemented using a diverse set of sensors and controllers. However, the heterogeneous nature of DCSs along with their scale leave such systems vulnerable to adversarial behavior. To mitigate this reality, we provide tools that allow operators to prevent zero dynamics attacks when as many as p agents and sensors are corrupted. Such a design ensures attack detectability in deterministic systems while removing the threat of a class of stealthy attacks in stochasticmore » systems. To achieve this goal, we use graph theory to obtain necessary and sufficient conditions for the presence of zero dynamics attacks in terms of the structural interactions between agents and sensors. We then formulate and solve optimization problems which minimize communication networks while also ensuring a resource limited adversary cannot perform a zero dynamics attacks. Polynomial time algorithms for design and analysis are provided.« less

Dynamico-FE: A Structure-Preserving Hydrostatic Dynamical Core

NASA Astrophysics Data System (ADS)

Eldred, Christopher; Dubos, Thomas; Kritsikis, Evaggelos

2017-04-01

It is well known that the inviscid, adiabatic equations of atmospheric motion constitute a non-canonical Hamiltonian system, and therefore posses many important conserved quantities such as as mass, potential vorticity and total energy. In addition, there are also key mimetic properties (such as curl grad = 0) of the underlying continuous vector calculus. Ideally, a dynamical core should have similar properties. A general approach to deriving such structure-preserving numerical schemes has been developed under the frameworks of Hamiltonian methods and mimetic discretizations, and over the past decade, there has been a great deal of work on the development of atmospheric dynamical cores using these techniques. An important example is Dynamico, which conserves mass, potential vorticity and total energy; and possesses additional mimetic properties such as a curl-free pressure gradient. Unfortunately, the underlying finite-difference discretization scheme used in Dynamico has been shown to be inconsistent on general grids. To resolve these accuracy issues, a scheme based on mimetic Galerkin discretizations has been developed that achieves higher-order accuracy while retaining the structure-preserving properties of the existing discretization. This presentation will discuss the new dynamical core, termed Dynamico-FE, and show results from a standard set of test cases on both the plane and the sphere.

Impact of Ionic Liquids on the Structure and Dynamics of Collagen.

PubMed

Tarannum, Aafiya; Adams, Alina; Blümich, Bernhard; Fathima, Nishter Nishad

2018-01-25

The changes in the structure and dynamics of collagen treated with two different classes of ionic liquids, bis-choline sulfate (CS) and 1-butyl-3-methyl imidazolium dimethyl phosphate (IDP), have been studied at the molecular and fibrillar levels. At the molecular level, circular dichroic studies revealed an increase in molar ellipticity values for CS when compared with native collagen, indicating cross-linking, albeit pronounced conformational changes for IDP were witnessed indicating denaturation. The impedance was analyzed to correlate the conformational changes with the hydration dynamics of protein. Changes in the dielectric properties of collagen observed upon treatment with CS and IDP reported molecular reorientation in the surrounding water milieu, suggesting compactness or destabilization of the collagen. This was further confirmed by proton transverse NMR relaxation time measurements, which demonstrated that the water mobility changes in the presence of the ILs. At the fibrillar level, differential scanning calorimetry thermograms for rat tail tendon collagen fibers treated with CS show a 5 °C increase in denaturation temperature, suggesting imparted stability. On the contrary, a significant temperature decrease was noticed for IDP, indicating the destabilization of collagen fibers. The obtained results clearly indicate that the changes in the secondary structure of protein are due to the changes in the hydration dynamics of collagen upon interaction with ILs. Thus, this study on the interaction of collagen with ionic liquids unfolds the propensity of ILs to stabilize or destabilize collagen depending on the changes invoked at the molecular level in terms of structure and dynamics of protein, which also got manifested at the fibrillar level.

Aerodynamic performance of a hovering hawkmoth with flexible wings: a computational approach

PubMed Central

Nakata, Toshiyuki; Liu, Hao

2012-01-01

Insect wings are deformable structures that change shape passively and dynamically owing to inertial and aerodynamic forces during flight. It is still unclear how the three-dimensional and passive change of wing kinematics owing to inherent wing flexibility contributes to unsteady aerodynamics and energetics in insect flapping flight. Here, we perform a systematic fluid-structure interaction based analysis on the aerodynamic performance of a hovering hawkmoth, Manduca, with an integrated computational model of a hovering insect with rigid and flexible wings. Aerodynamic performance of flapping wings with passive deformation or prescribed deformation is evaluated in terms of aerodynamic force, power and efficiency. Our results reveal that wing flexibility can increase downwash in wake and hence aerodynamic force: first, a dynamic wing bending is observed, which delays the breakdown of leading edge vortex near the wing tip, responsible for augmenting the aerodynamic force-production; second, a combination of the dynamic change of wing bending and twist favourably modifies the wing kinematics in the distal area, which leads to the aerodynamic force enhancement immediately before stroke reversal. Moreover, an increase in hovering efficiency of the flexible wing is achieved as a result of the wing twist. An extensive study of wing stiffness effect on aerodynamic performance is further conducted through a tuning of Young's modulus and thickness, indicating that insect wing structures may be optimized not only in terms of aerodynamic performance but also dependent on many factors, such as the wing strength, the circulation capability of wing veins and the control of wing movements. PMID:21831896

Passivity of Directed and Undirected Complex Dynamical Networks With Adaptive Coupling Weights.

PubMed

Wang, Jin-Liang; Wu, Huai-Ning; Huang, Tingwen; Ren, Shun-Yan; Wu, Jigang

2017-08-01

A complex dynamical network consisting of N identical neural networks with reaction-diffusion terms is considered in this paper. First, several passivity definitions for the systems with different dimensions of input and output are given. By utilizing some inequality techniques, several criteria are presented, ensuring the passivity of the complex dynamical network under the designed adaptive law. Then, we discuss the relationship between the synchronization and output strict passivity of the proposed network model. Furthermore, these results are extended to the case when the topological structure of the network is undirected. Finally, two examples with numerical simulations are provided to illustrate the correctness and effectiveness of the proposed results.

Structural self-assembly and avalanchelike dynamics in locally adaptive networks

NASA Astrophysics Data System (ADS)

Gräwer, Johannes; Modes, Carl D.; Magnasco, Marcelo O.; Katifori, Eleni

2015-07-01

Transport networks play a key role across four realms of eukaryotic life: slime molds, fungi, plants, and animals. In addition to the developmental algorithms that build them, many also employ adaptive strategies to respond to stimuli, damage, and other environmental changes. We model these adapting network architectures using a generic dynamical system on weighted graphs and find in simulation that these networks ultimately develop a hierarchical organization of the final weighted architecture accompanied by the formation of a system-spanning backbone. In addition, we find that the long term equilibration dynamics exhibit behavior reminiscent of glassy systems characterized by long periods of slow changes punctuated by bursts of reorganization events.

Dynamics of a minimal consumer network with bi-directional influence

NASA Astrophysics Data System (ADS)

Ekaterinchuk, Ekaterina; Jungeilges, Jochen; Ryazanova, Tatyana; Sushko, Iryna

2018-05-01

We study the dynamics of a model of interdependent consumer behavior defined by a family of two-dimensional noninvertible maps. This family belongs to a class of coupled logistic maps with different nonlinearity parameters and coupling terms that depend on one variable only. In our companion paper we considered the case of independent consumers as well as the case of uni-directionally connected consumers. The present paper aims at describing the dynamics in the case of a bi-directional connection. In particular, we investigate the bifurcation structure of the parameter plane associated with the strength of coupling between the consumers, focusing on the mechanisms of qualitative transformations of coexisting attractors and their basins of attraction.

On Discerning Critical Elements, Relationships and Shifts in Attaining Scientific Terms: The Challenge of Polysemy/Homonymy and Reference

NASA Astrophysics Data System (ADS)

Strömdahl, Helge R.

2012-01-01

Words with well-known meaning in colloquial language often make up an educational challenge when introduced as terms with formal scientific meaning. New connections must be established between the word, already constrained by existing meaning and reference, and the intended formal scientific meaning and reference. A two-dimensional semantic/semiotic analysing schema (acronym 2-D SAS) has been developed to clarify a given word/term in a structured mode both according to non-formal senses and referents and formal scientific meaning and referents. The schema is constructed on ideas from semantics, semiotics and history and philosophy of science. The approach is supposed to be a contribution to make a fine-gained analysis of the structure and dynamics of conceptual change. The role of referents and referent change in conceptual change is highlighted by analysing the character of the recurrent mix-up of the terms heat and temperature among students at different educational levels.

Native fishes in the Truckee River: Are in-stream structures and patterns of population genetic structure related?

PubMed

Peacock, Mary M; Gustin, Mae S; Kirchoff, Veronica S; Robinson, Morgan L; Hekkala, Evon; Pizzarro-Barraza, Claudia; Loux, Tim

2016-09-01

In-stream structures are recognized as significant impediments to movement for freshwater fishes. Apex predators such as salmonids have been the focus of much research on the impacts of such barriers to population dynamics and population viability however much less research has focused on native fishes, where in-stream structures may have a greater impact on long term population viability of these smaller, less mobile species. Patterns of genetic structure on a riverscape can provide information on which structures represent real barriers to movement for fish species and under what specific flow conditions. Here we characterize the impact of 41 dam and diversion structures on movement dynamics under varying flow conditions for a suite of six native fishes found in the Truckee River of California and Nevada. Microsatellite loci were used to estimate total allelic diversity, effective population size and assess genetic population structure. Although there is spatial overlap among species within the river there are clear differences in species distributions within the watershed. Observed population genetic structure was associated with in-stream structures, but only under low flow conditions. High total discharge in 2006 allowed fish to move over potential barriers resulting in no observed population genetic structure for any species in 2007. The efficacy of in-stream structures to impede movement and isolate fish emerged only after multiple years of low flow conditions. Our results suggest that restricted movement of fish species, as a result of in-stream barriers, can be mitigated by flow management. However, as flow dynamics are likely to be altered under global climate change, fragmentation due to barriers could isolate stream fishes into small subpopulations susceptible to both demographic losses and losses of genetic variation. Copyright © 2016 Elsevier B.V. All rights reserved.

Interplay between Shear Loading and Structural Aging in a Physical Gelatin Gel

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

Ronsin, O.; Caroli, C.; Baumberger, T.

2009-09-25

We show that the aging of the mechanical relaxation of a gelatin gel exhibits the same scaling phenomenology as polymer and colloidal glasses. In addition, gelatin is known to exhibit logarithmic structural aging (stiffening). We find that stress accelerates this process. However, this effect is definitely irreducible to a mere age shift with respect to natural aging. We suggest that it is interpretable in terms of elastically aided elementary (coil->helix) local events whose dynamics gradually slows down as aging increases geometric frustration.

Projections of limiting states for load-bearing structures of reflectors made of polymer composites

NASA Astrophysics Data System (ADS)

Doronin, S. V.

2017-12-01

This paper deals with limiting states typical for reflector antennas for terrestrial satellite communication systems. Reflectors made of polymer composites are studied. These limiting states are projected by results of the numerical analysis of the stress and strain states. The analysis is executed for reflectors under conditions of static and dynamic loading. It takes into account both overshoot of the state variables of allowed level and the processes of long-term structural material degradation.

Akhmediev Breather dynamics and the nonlinear modulation instability spectrum

NASA Astrophysics Data System (ADS)

Genty, Go"ry; Dias, Frederic; Kibler, Bertrand; Akhmediev, Nail; Dudley, John M.

2010-06-01

We consider various aspects of supercontinuum generation in the quasi-CW regime through analysis, numerical simulations and experiments. A new interpretation of certain features of the developing spectrum in terms of localized periodic structures known as "Akhmediev Breathers" is proposed. We also briefly consider the role of breather collisions and turbulence in the presence of higher order dispersion and show that they lead to the formation of very large amplitude localized structures that may be analogous to the infamous oceanic rogue waves.

Effect of small perturbations on the evolution of polycrystalline structure during plastic deformation

NASA Astrophysics Data System (ADS)

Korznikova, E. A.; Baimova, Yu. A.; Kistanov, A. A.; Dmitriev, S. V.; Korznikov, A. V.

2014-09-01

The method of molecular dynamics has been used to study the influence of initial perturbations on the evolution of grain boundaries during the shear plastic deformation of a two-dimensional polycrystalline material with nanoscale grains. It has been shown that short-term thermalization-induced small perturbations result in noticeable differences in grain boundaries configurations at the deformation of 0.05 and the polycrystal completely loses its initial grain boundary structure at the deformation of 0.4.

From kinetic-structure analysis to engineering crystalline fiber networks in soft materials.

PubMed

Wang, Rong-Yao; Wang, Peng; Li, Jing-Liang; Yuan, Bing; Liu, Yu; Li, Li; Liu, Xiang-Yang

2013-03-07

Understanding the role of kinetics in fiber network microstructure formation is of considerable importance in engineering gel materials to achieve their optimized performances/functionalities. In this work, we present a new approach for kinetic-structure analysis for fibrous gel materials. In this method, kinetic data is acquired using a rheology technique and is analyzed in terms of an extended Dickinson model in which the scaling behaviors of dynamic rheological properties in the gelation process are taken into account. It enables us to extract the structural parameter, i.e. the fractal dimension, of a fibrous gel from the dynamic rheological measurement of the gelation process, and to establish the kinetic-structure relationship suitable for both dilute and concentrated gelling systems. In comparison to the fractal analysis method reported in a previous study, our method is advantageous due to its general validity for a wide range of fractal structures of fibrous gels, from a highly compact network of the spherulitic domains to an open fibrous network structure. With such a kinetic-structure analysis, we can gain a quantitative understanding of the role of kinetic control in engineering the microstructure of the fiber network in gel materials.

De novo protein structure prediction by dynamic fragment assembly and conformational space annealing.

PubMed

Lee, Juyong; Lee, Jinhyuk; Sasaki, Takeshi N; Sasai, Masaki; Seok, Chaok; Lee, Jooyoung

2011-08-01

Ab initio protein structure prediction is a challenging problem that requires both an accurate energetic representation of a protein structure and an efficient conformational sampling method for successful protein modeling. In this article, we present an ab initio structure prediction method which combines a recently suggested novel way of fragment assembly, dynamic fragment assembly (DFA) and conformational space annealing (CSA) algorithm. In DFA, model structures are scored by continuous functions constructed based on short- and long-range structural restraint information from a fragment library. Here, DFA is represented by the full-atom model by CHARMM with the addition of the empirical potential of DFIRE. The relative contributions between various energy terms are optimized using linear programming. The conformational sampling was carried out with CSA algorithm, which can find low energy conformations more efficiently than simulated annealing used in the existing DFA study. The newly introduced DFA energy function and CSA sampling algorithm are implemented into CHARMM. Test results on 30 small single-domain proteins and 13 template-free modeling targets of the 8th Critical Assessment of protein Structure Prediction show that the current method provides comparable and complementary prediction results to existing top methods. Copyright © 2011 Wiley-Liss, Inc.

Corrections to the Eckhaus' stability criterion for one-dimensional stationary structures

NASA Astrophysics Data System (ADS)

Malomed, B. A.; Staroselsky, I. E.; Konstantinov, A. B.

1989-01-01

Two amendments to the well-known Eckhaus' stability criterion for small-amplitude non-linear structures generated by weak instability of a spatially uniform state of a non-equilibrium one-dimensional system against small perturbations with finite wavelengths are obtained. Firstly, we evaluate small corrections to the main Eckhaus' term which, on the contrary so that term, do not have a universal form. Comparison of those non-universal corrections with experimental or numerical results gives a possibility to select a more relevant form of an effective nonlinear evolution equation. In particular, the comparison with such results for convective rolls and Taylor vortices gives arguments in favor of the Swift-Hohenberg equation. Secondly, we derive an analog of the Eckhaus criterion for systems degenerate in the sense that in an expansion of their non-linear parts in powers of dynamical variables, the second and third degree terms are absent.

Determination of the hydrogen-bond network and the ferrimagnetic structure of a rockbridgeite-type compound, {Fe^{2+Fe^{3+}_{3.2}(Mn^{2+}, Zn)_{0.8}(PO_{4})_{3}(OH)_{4.2}(HOH)_{0.8}}}

NASA Astrophysics Data System (ADS)

Röska, B.; Park, S.-H.; Behal, D.; Hess, K.-U.; Günther, A.; Benka, G.; Pfleiderer, C.; Hoelzel, M.; Kimura, T.

2018-06-01

Applying neutron powder diffraction, four unique hydrogen positions were determined in a rockbridgeite-type compound, . Its honeycomb-like H-bond network running without interruption along the crystallographic axis resembles those in alkali sulphatic and arsenatic oxyhydroxides. They provide the so-called dynamically disordered H-bond network over which protons are superconducting in a vehicle mechanism. This is indicated by dramatic increases of dielectric constant and loss factor at room temperature. The relevance of static and dynamic disorder of OH and HOH groups are explained in terms of a high number of structural defects at octahedral chains alternatingly half-occupied by cations. The structure is built up by unusual octahedral doublet, triplet, and quartet clusters of aliovalent 3d transition metal cations, predicting complicate magnetic ordering and interaction. The ferrimagnetic structure below the Curie temperature –83 K could be determined from the structure analysis with neutron diffraction data at 25 K.

Using Decision Structures for Policy Analysis in Software Product-line Evolution - A Case Study

NASA Astrophysics Data System (ADS)

Sarang, Nita; Sanglikar, Mukund A.

Project management decisions are the primary basis for project success (or failure). Mostly, such decisions are based on an intuitive understanding of the underlying software engineering and management process and have a likelihood of being misjudged. Our problem domain is product-line evolution. We model the dynamics of the process by incorporating feedback loops appropriate to two decision structures: staffing policy, and the forces of growth associated with long-term software evolution. The model is executable and supports project managers to assess the long-term effects of possible actions. Our work also corroborates results from earlier studies of E-type systems, in particular the FEAST project and the rules for software evolution, planning and management.

Scale-freeness or partial synchronization in neural mass phase oscillator networks: Pick one of two?

PubMed

Daffertshofer, Andreas; Ton, Robert; Pietras, Bastian; Kringelbach, Morten L; Deco, Gustavo

2018-04-04

Modeling and interpreting (partial) synchronous neural activity can be a challenge. We illustrate this by deriving the phase dynamics of two seminal neural mass models: the Wilson-Cowan firing rate model and the voltage-based Freeman model. We established that the phase dynamics of these models differed qualitatively due to an attractive coupling in the first and a repulsive coupling in the latter. Using empirical structural connectivity matrices, we determined that the two dynamics cover the functional connectivity observed in resting state activity. We further searched for two pivotal dynamical features that have been reported in many experimental studies: (1) a partial phase synchrony with a possibility of a transition towards either a desynchronized or a (fully) synchronized state; (2) long-term autocorrelations indicative of a scale-free temporal dynamics of phase synchronization. Only the Freeman phase model exhibited scale-free behavior. Its repulsive coupling, however, let the individual phases disperse and did not allow for a transition into a synchronized state. The Wilson-Cowan phase model, by contrast, could switch into a (partially) synchronized state, but it did not generate long-term correlations although being located close to the onset of synchronization, i.e. in its critical regime. That is, the phase-reduced models can display one of the two dynamical features, but not both. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Structure and Dynamics of Solvent Landscapes in Charge-Transfer Reactions

NASA Astrophysics Data System (ADS)

Leite, Vitor B. Pereira

The dynamics of solvent polarization plays a major role in the control of charge transfer reactions. The success of Marcus theory describing the solvent influence via a single collective quadratic polarization coordinate has been remarkable. Onuchic and Wolynes have recently proposed (J. Chem Phys 98 (3) 2218, 1993) a simple model demonstrating how a many-dimensional-complex model composed by several dipole moments (representing solvent molecules or polar groups in proteins) can be reduced under the appropriate limits into the Marcus Model. This work presents a dynamical study of the same model, which is characterized by two parameters, an average dipole-dipole interaction as a term associated with the potential energy landscape roughness. It is shown why the effective potential, obtained using a thermodynamic approach, is appropriate for the dynamics of the system. At high temperatures, the system exhibits effective diffusive one-dimensional dynamics, where the Born-Marcus limit is recovered. At low temperatures, a glassy phase appears with a slow non-self-averaging dynamics. At intermediate temperatures, the concept of equivalent diffusion paths and polarization dependence effects are discussed. This approach is extended to treat more realistic solvent models. Real solvents are discussed in terms of simple parameters described above, and an analysis of how different regimes affect the rate of charge transfer is presented. Finally, these ideas are correlated to analogous problems in other areas.

Dynamic primitives in the control of locomotion.

PubMed

Hogan, Neville; Sternad, Dagmar

2013-01-01

Humans achieve locomotor dexterity that far exceeds the capability of modern robots, yet this is achieved despite slower actuators, imprecise sensors, and vastly slower communication. We propose that this spectacular performance arises from encoding motor commands in terms of dynamic primitives. We propose three primitives as a foundation for a comprehensive theoretical framework that can embrace a wide range of upper- and lower-limb behaviors. Building on previous work that suggested discrete and rhythmic movements as elementary dynamic behaviors, we define submovements and oscillations: as discrete movements cannot be combined with sufficient flexibility, we argue that suitably-defined submovements are primitives. As the term "rhythmic" may be ambiguous, we define oscillations as the corresponding class of primitives. We further propose mechanical impedances as a third class of dynamic primitives, necessary for interaction with the physical environment. Combination of these three classes of primitive requires care. One approach is through a generalized equivalent network: a virtual trajectory composed of simultaneous and/or sequential submovements and/or oscillations that interacts with mechanical impedances to produce observable forces and motions. Reliable experimental identification of these dynamic primitives presents challenges: identification of mechanical impedances is exquisitely sensitive to assumptions about their dynamic structure; identification of submovements and oscillations is sensitive to their assumed form and to details of the algorithm used to extract them. Some methods to address these challenges are presented. Some implications of this theoretical framework for locomotor rehabilitation are considered.

Characterization of structural connections using free and forced response test data

NASA Technical Reports Server (NTRS)

Lawrence, Charles; Huckelbridge, Arthur A.

1989-01-01

The accurate prediction of system dynamic response often has been limited by deficiencies in existing capabilities to characterize connections adequately. Connections between structural components often are complex mechanically, and difficult to accurately model analytically. Improved analytical models for connections are needed to improve system dynamic preditions. A procedure for identifying physical connection properties from free and forced response test data is developed, then verified utilizing a system having both a linear and nonlinear connection. Connection properties are computed in terms of physical parameters so that the physical characteristics of the connections can better be understood, in addition to providing improved input for the system model. The identification procedure is applicable to multi-degree of freedom systems, and does not require that the test data be measured directly at the connection locations.

Dynamic evolution of recurrent mass ejections observed in H-alpha and C IV lines

NASA Technical Reports Server (NTRS)

Schmieder, B.; Mein, P.; Martres, M. J.; Tandberg-Hanssen, E.

1984-01-01

The mass ejections of 1 September, 1980 are studied from observations obtained with the MSDP spectrograph and with the Ultraviolet Spectrometer and Polarimeter aboard the Solar Maximum Mission satellite. The analysis is focused on observations in the chromospheric H-alpha line and the transition region C IV 1548 A line. It is noted that cold and hot material had the same projection, although the upward C IV velocity structure was more extended than the H-alpha one. It is shown that the observed contrast of the H-alpha absorbing structure can be interpreted in terms of a dynamic cloud model overlying the chromosphere. Radial velocities of 25-30 km/s and -40 km/s are estimated for the first and second phases of ejection, respectively.

Route to non-Abelian quantum turbulence in spinor Bose-Einstein condensates

NASA Astrophysics Data System (ADS)

Mawson, Thomas; Ruben, Gary; Simula, Tapio

2015-06-01

We have studied computationally the collision dynamics of spin-2 Bose-Einstein condensates initially confined in a triple-well trap. Depending on the phase structure of the initial-state spinor wave function, the collision of the three condensate fragments produces one of many possible vortex-antivortex lattices, after which the system transitions to quantum turbulence. We find that the emerging vortex lattice structures can be described in terms of multiwave interference. We show that the three-fragment collisions can be used to systematically produce staggered vortex-antivortex honeycomb lattices of fractional-charge vortices, whose collision dynamics are known to be non-Abelian. Such condensate collider experiments could potentially be used as a controllable pathway to generating non-Abelian superfluid turbulence with networks of vortex rungs.

Structure of hydrated gibbsite and brucite edge surfaces: DFT results and further development of the ClayFF classical force field with metal–O–H angle bending terms

DOE PAGES

Pouvreau, Maxime; Greathouse, Jeffery A.; Cygan, Randall T.; ...

2017-06-28

Molecular scale understanding of the structure and properties of aqueous interfaces with clays, metal (oxy-) hydroxides, layered double hydroxides, and other inorganic phases is strongly affected by significant degrees of structural and compositional disorder of the interfaces. ClayFF was originally developed as a robust and flexible force field for classical molecular simulations of such systems. However, despite its success, multiple limitations have also become evident with its use. One of the most important limitations is the difficulty to accurately model the edges of finite size nanoparticles or pores rather than infinitely layered periodic structures. Here we propose a systematic approachmore » to solve this problem by developing specific metal–O–H (M–O–H) bending terms for ClayFF, E bend = k (θ – θ 0) 2 to better describe the structure and dynamics of singly protonated hydroxyl groups at mineral surfaces, particularly edge surfaces. On the basis of a series of DFT calculations, the optimal values of the Al–O–H and Mg–O–H parameters for Al and Mg in octahedral coordination are determined to be θ 0,AlOH = θ 0,MgOH = 110°, k AlOH = 15 kcal mol –1 rad –2 and k MgOH = 6 kcal mol –1 rad –2. Molecular dynamics simulations were performed for fully hydrated models of the basal and edge surfaces of gibbsite, Al(OH) 3, and brucite, Mg(OH) 2, at the DFT level of theory and at the classical level, using ClayFF with and without the M–O–H term. The addition of the new bending term leads to a much more accurate representation of the orientation of O–H groups at the basal and edge surfaces. Finally, the previously observed unrealistic desorption of OH 2 groups from the particle edges within the original ClayFF model is also strongly constrained by the new modification.« less

Capacity Fading Mechanism of the Commercial 18650 LiFePO4-Based Lithium-Ion Batteries: An in Situ Time-Resolved High-Energy Synchrotron XRD Study.

PubMed

Liu, Qi; Liu, Yadong; Yang, Fan; He, Hao; Xiao, Xianghui; Ren, Yang; Lu, Wenquan; Stach, Eric; Xie, Jian

2018-02-07

In situ high-energy synchrotron XRD studies were carried out on commercial 18650 LiFePO 4 cells at different cycles to track and investigate the dynamic, chemical, and structural changes in the course of long-term cycling to elucidate the capacity fading mechanism. The results indicate that the crystalline structural deterioration of the LiFePO 4 cathode and the graphite anode is unlikely to happen before capacity fades below 80% of the initial capacity. Rather, the loss of the active lithium source is the primary cause for the capacity fade, which leads to the appearance of inactive FePO 4 that is proportional to the absence of the lithium source. Our in situ HESXRD studies further show that the lithium-ion insertion and deinsertion behavior of LiFePO 4 continuously changed with cycling. For a fresh cell, the LiFePO 4 experienced a dual-phase solid-solution behavior, whereas with increasing cycle numbers, the dynamic change, which is characteristic of the continuous decay of solid solution behavior, is obvious. The unpredicted dynamic change may result from the morphology evolution of LiFePO 4 particles and the loss of the lithium source, which may be the cause of the decreased rate capability of LiFePO 4 cells after long-term cycling.

Onset of jamming for gas-fluidized grains

NASA Astrophysics Data System (ADS)

Abate, Adam

2006-03-01

Upon approach to jamming, whether for molecular liquids or colloidal particles or grains of sand, the microscopic dynamics can develop dramatic long-ranged correlations while the microscopic structure remains relatively unchanged. Experimentally, it has been difficult to study such phenomena in full detail due to the range of temporal and spatial scales involved. Here we introduce a new model system that is both easier to image and to manipulate at the microscale: a bidisperse system of steel beads rolling stochastically due to a nearly-levitating upflow of air. At fixed air flow, we demonstrate that this system exhibits all the hallmarks of a jamming transition as spheres are added and the area fraction increases toward close-packing. In terms of structure, the pair correlation function and the Voronoi cell shape distribution functions exhibit peak splitting. In terms of dynamics, the mean-squared displacement develops a plateau separating the short-time ballistic from the long-time diffusive motions; in this plateau the displacement distribution is non-Gaussian, due to spatial heterogeneities. While this phenomenology is familiar, one feature observed previously only in simulation is the presence of string-like swirls of rearranging grains. We highlight these by movies of an appropriately time-averaged velocity field. We hope to connect such dynamics both to a microscopic measure of effective temperature and to the macroscopic viscosity of the system.

Inferring microbial interaction networks from metagenomic data using SgLV-EKF algorithm.

PubMed

Alshawaqfeh, Mustafa; Serpedin, Erchin; Younes, Ahmad Bani

2017-03-27

Inferring the microbial interaction networks (MINs) and modeling their dynamics are critical in understanding the mechanisms of the bacterial ecosystem and designing antibiotic and/or probiotic therapies. Recently, several approaches were proposed to infer MINs using the generalized Lotka-Volterra (gLV) model. Main drawbacks of these models include the fact that these models only consider the measurement noise without taking into consideration the uncertainties in the underlying dynamics. Furthermore, inferring the MIN is characterized by the limited number of observations and nonlinearity in the regulatory mechanisms. Therefore, novel estimation techniques are needed to address these challenges. This work proposes SgLV-EKF: a stochastic gLV model that adopts the extended Kalman filter (EKF) algorithm to model the MIN dynamics. In particular, SgLV-EKF employs a stochastic modeling of the MIN by adding a noise term to the dynamical model to compensate for modeling uncertainties. This stochastic modeling is more realistic than the conventional gLV model which assumes that the MIN dynamics are perfectly governed by the gLV equations. After specifying the stochastic model structure, we propose the EKF to estimate the MIN. SgLV-EKF was compared with two similarity-based algorithms, one algorithm from the integral-based family and two regression-based algorithms, in terms of the achieved performance on two synthetic data-sets and two real data-sets. The first data-set models the randomness in measurement data, whereas, the second data-set incorporates uncertainties in the underlying dynamics. The real data-sets are provided by a recent study pertaining to an antibiotic-mediated Clostridium difficile infection. The experimental results demonstrate that SgLV-EKF outperforms the alternative methods in terms of robustness to measurement noise, modeling errors, and tracking the dynamics of the MIN. Performance analysis demonstrates that the proposed SgLV-EKF algorithm represents a powerful and reliable tool to infer MINs and track their dynamics.

Specifying structural constraints of architectural patterns in the ARCHERY language

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

Sanchez, Alejandro; HASLab INESC TEC and Universidade do Minho, Campus de Gualtar, 4710-057 Braga; Barbosa, Luis S.

ARCHERY is an architectural description language for modelling and reasoning about distributed, heterogeneous and dynamically reconfigurable systems in terms of architectural patterns. The language supports the specification of architectures and their reconfiguration. This paper introduces a language extension for precisely describing the structural design decisions that pattern instances must respect in their (re)configurations. The extension is a propositional modal logic with recursion and nominals referencing components, i.e., a hybrid µ-calculus. Its expressiveness allows specifying safety and liveness constraints, as well as paths and cycles over structures. Refinements of classic architectural patterns are specified.

Characterizing heterogeneous dynamics at hydrated electrode surfaces.

PubMed

Willard, Adam P; Limmer, David T; Madden, Paul A; Chandler, David

2013-05-14

In models of Pt 111 and Pt 100 surfaces in water, motions of molecules in the first hydration layer are spatially and temporally correlated. To interpret these collective motions, we apply quantitative measures of dynamic heterogeneity that are standard tools for considering glassy systems. Specifically, we carry out an analysis in terms of mobility fields and distributions of persistence times and exchange times. In so doing, we show that dynamics in these systems is facilitated by transient disorder in frustrated two-dimensional hydrogen bonding networks. The frustration is the result of unfavorable geometry imposed by strong metal-water bonding. The geometry depends upon the structure of the underlying metal surface. Dynamic heterogeneity of water on the Pt 111 surface is therefore qualitatively different than that for water on the Pt 100 surface. In both cases, statistics of this ad-layer dynamic heterogeneity responds asymmetrically to applied voltage.

Characterizing heterogeneous dynamics at hydrated electrode surfaces

NASA Astrophysics Data System (ADS)

Willard, Adam P.; Limmer, David T.; Madden, Paul A.; Chandler, David

2013-05-01

In models of Pt 111 and Pt 100 surfaces in water, motions of molecules in the first hydration layer are spatially and temporally correlated. To interpret these collective motions, we apply quantitative measures of dynamic heterogeneity that are standard tools for considering glassy systems. Specifically, we carry out an analysis in terms of mobility fields and distributions of persistence times and exchange times. In so doing, we show that dynamics in these systems is facilitated by transient disorder in frustrated two-dimensional hydrogen bonding networks. The frustration is the result of unfavorable geometry imposed by strong metal-water bonding. The geometry depends upon the structure of the underlying metal surface. Dynamic heterogeneity of water on the Pt 111 surface is therefore qualitatively different than that for water on the Pt 100 surface. In both cases, statistics of this ad-layer dynamic heterogeneity responds asymmetrically to applied voltage.

Seventy years of forest growth and community dynamics in an undisturbed northern hardwood forest

Treesearch

Jennifer Pontius; Joshua M. Halman; Paul G. Schaberg

2016-01-01

Long-term forest inventories provide a unique opportunity to quantify changes in forest structure and evaluate how changes compare with current stand development models. An examination of a 70 year record at the Bartlett Experimental Forest, New Hampshire, indicated that although species abundances have primarily changed as expected under natural succession, some...

Five Residents Speak: The Meaning of Living with Dying in a Long-Term Care Home

ERIC Educational Resources Information Center

Djivre, Sandra E.; Levin, Elizabeth; Schinke, Robert J.; Porter, Elaine

2012-01-01

Personal meanings given to the experience of living with nursing home death were shared by 5 nursing home residents. Data were collected using semi-structured interviews. Using M. van Manen's (1990) hermeneutic phenomenology, the lived experience of residents emerged as a compilation of 5 dynamically occurring themes, including (a) mapping…

Institutional Approaches to Innovation and Change: A Review of the Esman Model of Institution Building.

ERIC Educational Resources Information Center

Bhola, H. S.

The definitional and conceptual structure of the Esman model of institution building is described in great detail, emphasizing its philosophic and process assumptions and its latent dynamics. The author systematically critiques the Esman model in terms of its (1) specificity to the universe of institution building, (2) generalizability across…

The Trend of "Quasi-Religiosity" among Krasnoiarsk College Students

ERIC Educational Resources Information Center

Nemirovskii, V. G.; Starikov, P. A.

2005-01-01

This article is devoted to a study of the structure and dynamics of "quasi-religious" ideas in the everyday consciousness of Russian college students. What is meant by the term quasi-religiosity is a whole set of unsystematized ideas, the respondents' belief in idealistic concepts that are popular on the level of mass consciousness. The study's…

Long-term dynamics of organic matter and elements exported as coarse particulates from two Caribbean montane watersheds

Treesearch

T. Heartsill Scalley; F.N. Scatena; S. Moya; A.E. Lugo

2012-01-01

In heterotrophic streams the retention and export of coarse particulate organic matter and associated elements are fundamental biogeochemical processes that influence water quality, food webs and the structural complexity of forested headwater streams. Nevertheless, few studies have documented the quantity and quality of exported organic matter over multiple years and...

Exploring the Micro-Social Geography of Children's Interactions in Preschool: A Long-Term Observational Study and Analysis Using Geographic Information Technologies

ERIC Educational Resources Information Center

Torrens, Paul M.; Griffin, William A.

2013-01-01

The authors describe an observational and analytic methodology for recording and interpreting dynamic microprocesses that occur during social interaction, making use of space--time data collection techniques, spatial-statistical analysis, and visualization. The scheme has three investigative foci: Structure, Activity Composition, and Clustering.…

Literature Review on Achievement Goals and Classroom Goal Structure: Implications for Future Research

ERIC Educational Resources Information Center

Alkharusi, Hussain

2010-01-01

Since its origin in the late 1970s and early 1980s, achievement goal theory has provided significant contributions to the research and practice in education and psychology. The theory has been considered to be an influential framework for conceptualizing student motivation. The term motivation refers to the interaction dynamics of many factors in…

Determinants of Multiple Semantic Priming: A Meta-Analysis and Spike Frequency Adaptive Model of a Cortical Network

ERIC Educational Resources Information Center

Lavigne, Frederic; Dumercy, Laurent; Darmon, Nelly

2011-01-01

Recall and language comprehension while processing sequences of words involves multiple semantic priming between several related and/or unrelated words. Accounting for multiple and interacting priming effects in terms of underlying neuronal structure and dynamics is a challenge for current models of semantic priming. Further elaboration of current…

Molecular dynamics simulations of theoretical cellulose nanotube models.

PubMed

Uto, Takuya; Kodama, Yuta; Miyata, Tatsuhiko; Yui, Toshifumi

2018-06-15

Nanotubes are remarkable nanoscale architectures for a wide range of potential applications. In the present paper, we report a molecular dynamics (MD) study of the theoretical cellulose nanotube (CelNT) models to evaluate their dynamic behavior in solution (either chloroform or benzene). Based on the one-quarter chain staggering relationship, we constructed six CelNT models by combining the two chain polarities (parallel (P) and antiparallel (AP)) and three symmetry operations (helical right (H R ), helical left (H L ), and rotation (R)) to generate a circular arrangement of molecular chains. Among the four models that retained the tubular form (P-H R , P-H L , P-R, and AP-R), the P-R and AP-R models have the lowest steric energies in benzene and chloroform, respectively. The structural features of the CelNT models were characterized in terms of the hydroxymethyl group conformation and intermolecular hydrogen bonds. Solvent structuring more clearly occurred with benzene than chloroform, suggesting that the CelNT models may disperse in benzene. Copyright © 2018 Elsevier Ltd. All rights reserved.

Lunar and planetary studies

NASA Technical Reports Server (NTRS)

Muhleman, Duane O.; Goldreich, P.; Ingersoll, A. P.; Westphal, J. A.

1988-01-01

This grant supports the core program in planetary astronomy at Caltech. The research includes observations in the IR, sub-mm, mm and cm wavelengths at national and Caltech observatories with a strong emphasis on integrating the observations with spacecraft data and with models of atmospheric structure, dynamics and chemistry. Muhleman's group made extensive observations of Saturn, Uranus and Neptune which are being interpreted in terms of deep atmospheric structures which are obvious in the 2 and 6 cm maps of Saturn and Uranus. The microwave measurements are one of the few sources of information below the 2 bar level. Goldreich is investigating the dynamics of narrow rings with postdoctoral fellow, Pierre-Yves Longaretti. Their work has focused on the role of collisional stresses on the precession of the rings, since the Voyager radio science results imply that the previous model based on the ring's self-gravity is not the entire story. In addition Borderies, Goldreich and Tremaine have completed an investigation of the dynamics of the Encke division in Saturn's A ring.

Stream dynamics between 1 AU and 2 AU: A detailed comparison of observations and theory

NASA Technical Reports Server (NTRS)

Burlaga, L. F.; Pizzo, V.; Lazarus, A.; Gazis, P. R.

1984-01-01

A radial alignment of three solar wind stream structures observed by IMP-7 and -8 (at 1.0 AU) and Voyager 1 and 2 (in the range 1.4 to 1.8 AU) in late 1977 is presented. It is demonstrated that several important aspects of the observed dynamical evolution can be both qualitatively and quantitatively described with a single-fluid 2-D MHD numerical model of quasi-steady corotating flow, including accurate prediction of: (1) the formation of a corotating shock pair at 1.75 AU in the case of a simple, quasi-steady stream; (2) the coalescence of the thermodynamic and magnetic structures associated with the compression regions of two neighboring, interacting, corotating streams; and (3) the dynamical destruction of a small (i.e., low velocity-amplitude, short spatial-scale) stream by its overtaking of a slower moving, high-density region associated with a preceding transient flow. The evolution of these flow systems is discussed in terms of the concepts of filtering and entrainment.

Changes in the electronic structure and spin dynamics across the metal-insulator transition in LaLa 1-xSr xCoO 3

DOE PAGES

Smith, R. X.; Hoch, M. J. R.; Moulton, W. G.; ...

2016-01-25

The magnetoelectronic properties of La 1-xSr xCoO 3, which include giant magnetoresistance, are strongly dependent on the level of hole doping. The system evolves, with increasing x, from a spin glass insulator to a metallic ferromagnet with a metal-insulator (MI) transition at x C ~ 0.18. Nanoscale phase separation occurs in the insulating phase and persists, to some extent, into the just-metallic phase. The present experiments at 4.2 K have used 139La NMR to investigate the transition from hopping dynamics for x < x C to Korringa-like ferromagnetic metal behavior for x > x C. A marked decrease in themore » spin-lattice relaxation rate is found in the vicinity of x C as the MI transition is crossed. Lastly, this behavior is accounted for in terms of the evolution of the electronic structure and dynamics with cluster size.« less

X-Ray Thomson Scattering Without the Chihara Decomposition

NASA Astrophysics Data System (ADS)

Magyar, Rudolph; Baczewski, Andrew; Shulenburger, Luke; Hansen, Stephanie B.; Desjarlais, Michael P.; Sandia National Laboratories Collaboration

X-Ray Thomson Scattering is an important experimental technique used in dynamic compression experiments to measure the properties of warm dense matter. The fundamental property probed in these experiments is the electronic dynamic structure factor that is typically modeled using an empirical three-term decomposition (Chihara, J. Phys. F, 1987). One of the crucial assumptions of this decomposition is that the system's electrons can be either classified as bound to ions or free. This decomposition may not be accurate for materials in the warm dense regime. We present unambiguous first principles calculations of the dynamic structure factor independent of the Chihara decomposition that can be used to benchmark these assumptions. Results are generated using a finite-temperature real-time time-dependent density functional theory applied for the first time in these conditions. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Security Administration under contract DE-AC04-94AL85000.

Information diffusion in structured online social networks

NASA Astrophysics Data System (ADS)

Li, Pei; Zhang, Yini; Qiao, Fengcai; Wang, Hui

2015-05-01

Nowadays, due to the word-of-mouth effect, online social networks have been considered to be efficient approaches to conduct viral marketing, which makes it of great importance to understand the diffusion dynamics in online social networks. However, most research on diffusion dynamics in epidemiology and existing social networks cannot be applied directly to characterize online social networks. In this paper, we propose models to characterize the information diffusion in structured online social networks with push-based forwarding mechanism. We introduce the term user influence to characterize the average number of times that messages are browsed which is incurred by a given type user generating a message, and study the diffusion threshold, above which the user influence of generating a message will approach infinity. We conduct simulations and provide the simulation results, which are consistent with the theoretical analysis results perfectly. These results are of use in understanding the diffusion dynamics in online social networks and also critical for advertisers in viral marketing who want to estimate the user influence before posting an advertisement.

Molecular dynamics simulations of lysozyme-lipid systems: probing the early steps of protein aggregation.

PubMed

Trusova, Valeriya M; Gorbenko, Galyna P

2017-07-10

Using the molecular dynamics simulation, the role of lipids in the lysozyme transition into the aggregation-competent conformation has been clarified. Analysis of the changes of lysozyme secondary structure upon its interactions with the model bilayer membranes composed of phosphatidylcholine and its mixtures with phosphatidylglycerol (10, 40, and 80 mol%) within the time interval of 100 ns showed that lipid-bound protein is characterized by the increased content of β-structures. Along with this, the formation of protein-lipid complexes was accompanied by the increase in the gyration radius and the decrease in RMSD of polypeptide chain. The results obtained were interpreted in terms of the partial unfolding of lysozyme molecule on the lipid matrix, with the magnitude of this effect being increased with increasing the fraction of anionic lipids. Based on the results of molecular dynamics simulation, a hypothetical model of the nucleation of lysozyme amyloid fibrils in a membrane environment was suggested.

Spontaneous oscillation and fluid-structure interaction of cilia.

PubMed

Han, Jihun; Peskin, Charles S

2018-04-24

The exact mechanism to orchestrate the action of hundreds of dynein motor proteins to generate wave-like ciliary beating remains puzzling and has fascinated many scientists. We present a 3D model of a cilium and the simulation of its beating in a fluid environment. The model cilium obeys a simple geometric constraint that arises naturally from the microscopic structure of a real cilium. This constraint allows us to determine the whole 3D structure at any instant in terms of the configuration of a single space curve. The tensions of active links, which model the dynein motor proteins, follow a postulated dynamical law, and together with the passive elasticity of microtubules, this dynamical law is responsible for the ciliary motions. In particular, our postulated tension dynamics lead to the instability of a symmetrical steady state, in which the cilium is straight and its active links are under equal tensions. The result of this instability is a stable, wave-like, limit cycle oscillation. We have also investigated the fluid-structure interaction of cilia using the immersed boundary (IB) method. In this setting, we see not only coordination within a single cilium but also, coordinated motion, in which multiple cilia in an array organize their beating to pump fluid, in particular by breaking phase synchronization.

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.

Bacterial dynamics in steady-state biofilters: beyond functional stability.

PubMed

Cabrol, Léa; Malhautier, Luc; Poly, Franck; Lepeuple, Anne-Sophie; Fanlo, Jean-Louis

2012-01-01

The spatial and temporal dynamics of microbial community structure and function were surveyed in duplicated woodchip-biofilters operated under constant conditions for 231 days. The contaminated gaseous stream for treatment was representative of composting emissions, included ammonia, dimethyl disulfide and a mixture of five oxygenated volatile organic compounds. The community structure and diversity were investigated by denaturing gradient gel electrophoresis on 16S rRNA gene fragments. During the first 42 days, microbial acclimatization revealed the influence of operating conditions and contaminant loading on the biofiltration community structure and diversity, as well as the limited impact of inoculum compared to the greater persistence of the endogenous woodchip community. During long-term operation, a high and stable removal efficiency was maintained despite a highly dynamic microbial community, suggesting the probable functional redundancy of the community. Most of the contaminant removal occurred in the first compartment, near the gas inlet, where the microbial diversity was the highest. The stratification of the microbial structures along the filter bed was statistically correlated to the longitudinal distribution of environmental conditions (selective pressure imposed by contaminant concentrations) and function (contaminant elimination capacity), highlighting the central role of the bacterial community. The reproducibility of microbial succession in replicates suggests that the community changes were presumably driven by a deterministic process.

Microphysics of liquid complex plasmas in equilibrium and non-equilibrium systems

NASA Astrophysics Data System (ADS)

Piel, Alexander; Block, Dietmar; Melzer, André; Mulsow, Matthias; Schablinski, Jan; Schella, André; Wieben, Frank; Wilms, Jochen

2018-05-01

The dynamic evolution of the microscopic structure of solid and liquid phases of complex plasmas is studied experimentally and by means of molecular dynamics (MD) simulations. In small finite systems, the cooperative motion can be described in terms of discrete modes. These modes are studied with different experimental approaches. Using diffuse scattered laser light, applying laser tweezer forces to individual particles, and periodic laser pulses, the excitation of modes is investigated. The instantaneous normal mode analysis of experimental data from two-dimensional liquid clusters gives access to the local dynamics of the liquid phase. Our investigations shed light on the role of compressional and shear modes as well as the determination of diffusion constants and melting temperatures in finite systems. Special attention is paid to hydrodynamic situations with a stationary inhomogeneous dust flow. MD simulations allow to study the collective motion in the shell of nearest neighbors, which can be linked to smooth and sudden changes of the macroscopic flow. Finally, the observed micro-motion in all situations above allows to shed light on the preference of shear-like over compressional motion in terms of a minimized potential energy and a dynamic incompressibility.

Short and long term evolution of deep giant submarine dunes in continental shelf environment: the example of the 'Banc du Four' (Western Brittany, France)

NASA Astrophysics Data System (ADS)

Franzetti, M.; Le Roy, P.; Garlan, T.; Delacourt, C.; Thibaud, R.; Cancouet, R.; Graindorge, D.; Prunier, C.; Sukhovich, A.; Deschamps, A.

2013-12-01

The deep sandwave dynamics is still in debate. Understanding the migration processes and the resulting evolution of their 3D internal architecture are scientifically challenging. To address these questions we realized two swath bathymetry surveys complemented with seismic reflection across the large sandwaves field named 'Banc du Four'. It is located offshore the Western Brittany and is composed of more 500 dunes. Some of the dunes' wavelengths and heights exceed 1000m and 30m respectively placing them among the largest dunes ever described. Equilibrium laws obtained from our morphological analysis are not completely in agreement with those described in previous studies of similar structures in shallow waters. Relatively high migration velocities on deep continental shelves (from 3 to 20m.yr-1) attest of their still present dynamical equilibrium. Internal-external morphological and kinematical analyses show the existence of two different dynamic regimes. Interpretation of the seismic reflection data allowed reconstructing long-term evolution of the sandbank and the establishment of progressive connections between stepped submarine channels and tidal dynamics during the last sea-level rise.

Initial value formulation of dynamical Chern-Simons gravity

NASA Astrophysics Data System (ADS)

Delsate, Térence; Hilditch, David; Witek, Helvi

2015-01-01

We derive an initial value formulation for dynamical Chern-Simons gravity, a modification of general relativity involving parity-violating higher derivative terms. We investigate the structure of the resulting system of partial differential equations thinking about linearization around arbitrary backgrounds. This type of consideration is necessary if we are to establish well-posedness of the Cauchy problem. Treating the field equations as an effective field theory we find that weak necessary conditions for hyperbolicity are satisfied. For the full field equations we find that there are states from which subsequent evolution is not determined. Generically the evolution system closes, but is not hyperbolic in any sense that requires a first order pseudodifferential reduction. In a cursory mode analysis we find that the equations of motion contain terms that may cause ill-posedness of the initial value problem.

Pollinator specialization: from the individual to the community.

PubMed

Brosi, Berry J

2016-06-01

1190 I. 1190 II. 1191 III. 1191 IV. 1193 V. 1193 1194 References 1194 SUMMARY: Most spermatophytes need conspecific pollen in order to produce seed. This need for specialization seems to conflict with the generalized nature of most plant-pollinator interactions. Specialization and generalization are dynamic - not fixed - and exist simultaneously in multiple states at different levels of biological hierarchy. Over the short term, specialization ensures conspecific pollen transfer, whereas over the long term, generalization improves system-level robustness. The balance between specialization and generalization at different scales is critical for different kinds of ecological functioning and is an important factor in plant speciation and the evolution of plant mating systems. Community context, including diversity and interaction network structure at different levels of aggregation, is a key driver of specialization dynamics. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Catastrophe theory—one of the basic components in the analysis of the seismic response of rock mass to explosions

NASA Astrophysics Data System (ADS)

Khachay, OA; Khachay, OYu

2018-03-01

It is shown that the dynamic process of mining can be controlled using the catastrophe theory. The control parameters can be values of blasting energy and locations of explosions relative to an area under study or operation. The kinematic and dynamic parameters of the deformation waves, as well as the structural features of rock mass through which these waves pass act as internal parameters. The use of the analysis methods for short-term and medium-term forecast of rock mass condition with the control parameters only is insufficient in the presence of sharp heterogeneity. However, the joint use of qualitative recommendations of the catastrophe theory and spatial–temporal data of changes in the internal parameters of rock mass will allow accident prevention in the course of mining.

Confronting dynamics and uncertainty in optimal decision making for conservation

USGS Publications Warehouse

Williams, Byron K.; Johnson, Fred A.

2013-01-01

The effectiveness of conservation efforts ultimately depends on the recognition that decision making, and the systems that it is designed to affect, are inherently dynamic and characterized by multiple sources of uncertainty. To cope with these challenges, conservation planners are increasingly turning to the tools of decision analysis, especially dynamic optimization methods. Here we provide a general framework for optimal, dynamic conservation and then explore its capacity for coping with various sources and degrees of uncertainty. In broadest terms, the dynamic optimization problem in conservation is choosing among a set of decision options at periodic intervals so as to maximize some conservation objective over the planning horizon. Planners must account for immediate objective returns, as well as the effect of current decisions on future resource conditions and, thus, on future decisions. Undermining the effectiveness of such a planning process are uncertainties concerning extant resource conditions (partial observability), the immediate consequences of decision choices (partial controllability), the outcomes of uncontrolled, environmental drivers (environmental variation), and the processes structuring resource dynamics (structural uncertainty). Where outcomes from these sources of uncertainty can be described in terms of probability distributions, a focus on maximizing the expected objective return, while taking state-specific actions, is an effective mechanism for coping with uncertainty. When such probability distributions are unavailable or deemed unreliable, a focus on maximizing robustness is likely to be the preferred approach. Here the idea is to choose an action (or state-dependent policy) that achieves at least some minimum level of performance regardless of the (uncertain) outcomes. We provide some examples of how the dynamic optimization problem can be framed for problems involving management of habitat for an imperiled species, conservation of a critically endangered population through captive breeding, control of invasive species, construction of biodiversity reserves, design of landscapes to increase habitat connectivity, and resource exploitation. Although these decision making problems and their solutions present significant challenges, we suggest that a systematic and effective approach to dynamic decision making in conservation need not be an onerous undertaking. The requirements are shared with any systematic approach to decision making--a careful consideration of values, actions, and outcomes.

Shading responses of carbon allocation dynamics in mountain grassland

NASA Astrophysics Data System (ADS)

Bahn, M.; Lattanzi, F. A.; Brueggemann, N.; Siegwolf, R. T.; Richter, A.

2012-12-01

Carbon (C) allocation strongly influences plant and soil processes. Global environmental changes can alter source - sink relations of plants with potential implications for C allocation. Short-term C allocation dynamics in ecosystems and their responses to environmental changes are still poorly understood. To analyze effects of assimilate supply (i.e. C source strength) on ecosystem C allocation dynamics and the role of non-structural carbohydrates, canopy sections of a mountain meadow were pulse labeled with 13CO2 and subsequently shaded for a week or left unshaded (control). Tracer dynamics in above- and belowground sucrose and starch pools were analysed and coupled using compartmental modelling. The hypothesis was tested that shading affects tracer dynamics in non-structural carbohydrates and diminishes the transfer of recently assimilated C to roots and their storage pools. In unshaded plots up to 40% of assimilated C was routed through short-term storage in shoot starch and sucrose to buffer day / night cycles in photosynthesis. Shoot- and root sucrose and shoot starch were kinetically closely related pools. The tracer dynamics of the modelled root sucrose pool corresponded well with those in soil CO2 efflux. Root starch played no role in buffering day / night cycles and likely acted as a seasonal store. Shading strongly reduced sucrose and starch concentrations in shoots but not roots and resulted in a massive reduction of leaf respiration, while root respiration was much less diminished. Shading affected tracer dynamics in sucrose and starch of shoots: shoot starch rapidly lost tracer, while sucrose transiently increased its tracer content. Surprisingly, shading did not alter the dynamics of root carbohydrates. Even under severe C limitation after one week of shading, tracer C continued to be incorporated in root starch. Also the amount of 13C incorporated in phospholipid fatty acids of soil microbial communities was not reduced by shading, though its residence time followed a changed pattern, suggesting an influence of C source strength on the utilization and turnover of recent plant-derived C. These findings will be discussed in the broader context of plant and ecosystem carbon allocation, with particular reference to the concepts of 'source versus sink strength' and 'passive versus active C storage'.

Confronting dynamics and uncertainty in optimal decision making for conservation

NASA Astrophysics Data System (ADS)

Williams, Byron K.; Johnson, Fred A.

2013-06-01

The effectiveness of conservation efforts ultimately depends on the recognition that decision making, and the systems that it is designed to affect, are inherently dynamic and characterized by multiple sources of uncertainty. To cope with these challenges, conservation planners are increasingly turning to the tools of decision analysis, especially dynamic optimization methods. Here we provide a general framework for optimal, dynamic conservation and then explore its capacity for coping with various sources and degrees of uncertainty. In broadest terms, the dynamic optimization problem in conservation is choosing among a set of decision options at periodic intervals so as to maximize some conservation objective over the planning horizon. Planners must account for immediate objective returns, as well as the effect of current decisions on future resource conditions and, thus, on future decisions. Undermining the effectiveness of such a planning process are uncertainties concerning extant resource conditions (partial observability), the immediate consequences of decision choices (partial controllability), the outcomes of uncontrolled, environmental drivers (environmental variation), and the processes structuring resource dynamics (structural uncertainty). Where outcomes from these sources of uncertainty can be described in terms of probability distributions, a focus on maximizing the expected objective return, while taking state-specific actions, is an effective mechanism for coping with uncertainty. When such probability distributions are unavailable or deemed unreliable, a focus on maximizing robustness is likely to be the preferred approach. Here the idea is to choose an action (or state-dependent policy) that achieves at least some minimum level of performance regardless of the (uncertain) outcomes. We provide some examples of how the dynamic optimization problem can be framed for problems involving management of habitat for an imperiled species, conservation of a critically endangered population through captive breeding, control of invasive species, construction of biodiversity reserves, design of landscapes to increase habitat connectivity, and resource exploitation. Although these decision making problems and their solutions present significant challenges, we suggest that a systematic and effective approach to dynamic decision making in conservation need not be an onerous undertaking. The requirements are shared with any systematic approach to decision making—a careful consideration of values, actions, and outcomes.

Solvation dynamics of tryptophan in water-dimethyl sulfoxide binary mixture: in search of molecular origin of composition dependent multiple anomalies.

PubMed

Roy, Susmita; Bagchi, Biman

2013-07-21

Experimental and simulation studies have uncovered at least two anomalous concentration regimes in water-dimethyl sulfoxide (DMSO) binary mixture whose precise origin has remained a subject of debate. In order to facilitate time domain experimental investigation of the dynamics of such binary mixtures, we explore strength or extent of influence of these anomalies in dipolar solvation dynamics by carrying out long molecular dynamics simulations over a wide range of DMSO concentration. The solvation time correlation function so calculated indeed displays strong composition dependent anomalies, reflected in pronounced non-exponential kinetics and non-monotonous composition dependence of the average solvation time constant. In particular, we find remarkable slow-down in the solvation dynamics around 10%-20% and 35%-50% mole percentage. We investigate microscopic origin of these two anomalies. The population distribution analyses of different structural morphology elucidate that these two slowing down are reflections of intriguing structural transformations in water-DMSO mixture. The structural transformations themselves can be explained in terms of a change in the relative coordination number of DMSO and water molecules, from 1DMSO:2H2O to 1H2O:1DMSO and 1H2O:2DMSO complex formation. Thus, while the emergence of first slow down (at 15% DMSO mole percentage) is due to the percolation among DMSO molecules supported by the water molecules (whose percolating network remains largely unaffected), the 2nd anomaly (centered on 40%-50%) is due to the formation of the network structure where the unit of 1DMSO:1H2O and 2DMSO:1H2O dominates to give rise to rich dynamical features. Through an analysis of partial solvation dynamics an interesting negative cross-correlation between water and DMSO is observed that makes an important contribution to relaxation at intermediate to longer times.

Coarse-Grained Descriptions of Dynamics for Networks with Both Intrinsic and Structural Heterogeneities

PubMed Central

Bertalan, Tom; Wu, Yan; Laing, Carlo; Gear, C. William; Kevrekidis, Ioannis G.

2017-01-01

Finding accurate reduced descriptions for large, complex, dynamically evolving networks is a crucial enabler to their simulation, analysis, and ultimately design. Here, we propose and illustrate a systematic and powerful approach to obtaining good collective coarse-grained observables—variables successfully summarizing the detailed state of such networks. Finding such variables can naturally lead to successful reduced dynamic models for the networks. The main premise enabling our approach is the assumption that the behavior of a node in the network depends (after a short initial transient) on the node identity: a set of descriptors that quantify the node properties, whether intrinsic (e.g., parameters in the node evolution equations) or structural (imparted to the node by its connectivity in the particular network structure). The approach creates a natural link with modeling and “computational enabling technology” developed in the context of Uncertainty Quantification. In our case, however, we will not focus on ensembles of different realizations of a problem, each with parameters randomly selected from a distribution. We will instead study many coupled heterogeneous units, each characterized by randomly assigned (heterogeneous) parameter value(s). One could then coin the term Heterogeneity Quantification for this approach, which we illustrate through a model dynamic network consisting of coupled oscillators with one intrinsic heterogeneity (oscillator individual frequency) and one structural heterogeneity (oscillator degree in the undirected network). The computational implementation of the approach, its shortcomings and possible extensions are also discussed. PMID:28659781

Methods for evaluating the predictive accuracy of structural dynamic models

NASA Technical Reports Server (NTRS)

Hasselman, Timothy K.; Chrostowski, Jon D.

1991-01-01

Modeling uncertainty is defined in terms of the difference between predicted and measured eigenvalues and eigenvectors. Data compiled from 22 sets of analysis/test results was used to create statistical databases for large truss-type space structures and both pretest and posttest models of conventional satellite-type space structures. Modeling uncertainty is propagated through the model to produce intervals of uncertainty on frequency response functions, both amplitude and phase. This methodology was used successfully to evaluate the predictive accuracy of several structures, including the NASA CSI Evolutionary Structure tested at Langley Research Center. Test measurements for this structure were within + one-sigma intervals of predicted accuracy for the most part, demonstrating the validity of the methodology and computer code.

Direct comparison of elastic incoherent neutron scattering experiments with molecular dynamics simulations of DMPC phase transitions.

PubMed

Aoun, Bachir; Pellegrini, Eric; Trapp, Marcus; Natali, Francesca; Cantù, Laura; Brocca, Paola; Gerelli, Yuri; Demé, Bruno; Marek Koza, Michael; Johnson, Mark; Peters, Judith

2016-04-01

Neutron scattering techniques have been employed to investigate 1,2-dimyristoyl-sn -glycero-3-phosphocholine (DMPC) membranes in the form of multilamellar vesicles (MLVs) and deposited, stacked multilamellar-bilayers (MLBs), covering transitions from the gel to the liquid phase. Neutron diffraction was used to characterise the samples in terms of transition temperatures, whereas elastic incoherent neutron scattering (EINS) demonstrates that the dynamics on the sub-macromolecular length-scale and pico- to nano-second time-scale are correlated with the structural transitions through a discontinuity in the observed elastic intensities and the derived mean square displacements. Molecular dynamics simulations have been performed in parallel focussing on the length-, time- and temperature-scales of the neutron experiments. They correctly reproduce the structural features of the main gel-liquid phase transition. Particular emphasis is placed on the dynamical amplitudes derived from experiment and simulations. Two methods are used to analyse the experimental data and mean square displacements. They agree within a factor of 2 irrespective of the probed time-scale, i.e. the instrument utilized. Mean square displacements computed from simulations show a comparable level of agreement with the experimental values, albeit, the best match with the two methods varies for the two instruments. Consequently, experiments and simulations together give a consistent picture of the structural and dynamical aspects of the main lipid transition and provide a basis for future, theoretical modelling of dynamics and phase behaviour in membranes. The need for more detailed analytical models is pointed out by the remaining variation of the dynamical amplitudes derived in two different ways from experiments on the one hand and simulations on the other.

New lumped-mass-stick model based on modal characteristics of structures: development and application to a nuclear containment building

NASA Astrophysics Data System (ADS)

Roh, Hwasung; Lee, Huseok; Lee, Jong Seh

2013-06-01

In this study, a new lumped-mass-stick model (LMSM) is developed based on the modal characteristics of a structure such as eigenvalues and eigenvectors. The simplified model, named the "frequency adaptive lumped-massstick model," hasonly a small number of stick elements and nodes to provide the same natural frequencies of the structure and is applied to a nuclear containment building. To investigate the numerical performance of the LMSM, a time history analysis is carried out on both the LMSM and the finite element model (FEM) for a nuclear containment building. A comparison of the results shows that the dynamic responses of the LMSM in terms of displacement and acceleration are almost identical to those of the FEM. In addition, the results in terms of fl oor response spectra at certain elevations are also in good agreement.

Surface structural changes of naturally aged silicone and EPDM composite insulators

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

Vlastos, A.E.; Gubanski, S.M.

1991-04-01

In a long-term outdoor test with high direct and alternating voltages, silicone and EPDM rubber composite insulators have, at the beginning, shown a superior performance to that of glass and porcelain insulators. In the long-term test, however, the silicone rubber composite insulator has, in spite of the ageing of both insulator types, kept its good performance, while the performance of the EPDM rubber composite insulator was drastically deteriorated. In order to get a better insight into results obtained, the wettability and the surface structural changes of the insulators were studied by the drop deposition method (using a goniometer) and bymore » advanced techniques such as SEM, ESCA, FTIR and SIMS respectively. The results show that the differences in performance have to be found in the differences in the surface structural changes and in the dynamic ability of the surface to compensate the ageing.« less

Selective logging: do rates of forest turnover in stems, species composition and functional traits decrease with time since disturbance? – A 45 year perspective

PubMed Central

Osazuwa-Peters, Oyomoare L.; Jiménez, Iván; Oberle, Brad; Chapman, Colin A.; Zanne, Amy E.

2015-01-01

Selective logging, the targeted harvesting of timber trees in a single cutting cycle, is globally rising in extent and intensity. Short-term impacts of selective logging on tropical forests have been widely investigated, but long-term effects on temporal dynamics of forest structure and composition are largely unknown. Understanding these long-term dynamics will help determine whether tropical forests are resilient to selective logging and inform choices between competing demands of anthropogenic use versus conservation of tropical forests. Forest dynamics can be studied within the framework of succession theory, which predicts that temporal turnover rates should decline with time since disturbance. Here, we investigated the temporal dynamics of a tropical forest in Kibale National Park, Uganda over 45 years following selective logging. We estimated turnover rates in stems, species composition, and functional traits (wood density and diameter at breast height), using observations from four censuses in 1989, 1999, 2006, and 2013, of stems ≥ 10 cm diameter within 17 unlogged and 9 logged 200 × 10 m vegetation plots. We used null models to account for interdependencies among turnover rates in stems, species composition, and functional traits. We tested predictions that turnover rates should be higher and decrease with increasing time since the selective logging event in logged forest, but should be less temporally variable in unlogged forest. Overall, we found higher turnover rates in logged forest for all three attributes, but turnover rates did not decline through time in logged forest and was not less temporally variable in unlogged forest. These results indicate that successional models that assume recovery to pre-disturbance conditions are inadequate for predicting the effects of selective logging on the dynamics of the tropical forest in Kibale. Selective logging resulted in persistently higher turnover rates, which may compromise the carbon storage capacity of Kibale’s forest. Selective logging effects may also interact with effects from other global trends, potentially causing major long-term shifts in the dynamics of tropical forests. Similar studies in tropical forests elsewhere will help determine the generality of these conclusions. Ultimately, the view that selective logging is a benign approach to the management of tropical forests should be reconsidered in the light of studies of the effects of this practice on long-term forest dynamics. PMID:26339115

Selective logging: do rates of forest turnover in stems, species composition and functional traits decrease with time since disturbance? - A 45 year perspective.

PubMed

Osazuwa-Peters, Oyomoare L; Jiménez, Iván; Oberle, Brad; Chapman, Colin A; Zanne, Amy E

2015-12-01

Selective logging, the targeted harvesting of timber trees in a single cutting cycle, is globally rising in extent and intensity. Short-term impacts of selective logging on tropical forests have been widely investigated, but long-term effects on temporal dynamics of forest structure and composition are largely unknown. Understanding these long-term dynamics will help determine whether tropical forests are resilient to selective logging and inform choices between competing demands of anthropogenic use versus conservation of tropical forests. Forest dynamics can be studied within the framework of succession theory, which predicts that temporal turnover rates should decline with time since disturbance. Here, we investigated the temporal dynamics of a tropical forest in Kibale National Park, Uganda over 45 years following selective logging. We estimated turnover rates in stems, species composition, and functional traits (wood density and diameter at breast height), using observations from four censuses in 1989, 1999, 2006, and 2013, of stems ≥ 10 cm diameter within 17 unlogged and 9 logged 200 × 10 m vegetation plots. We used null models to account for interdependencies among turnover rates in stems, species composition, and functional traits. We tested predictions that turnover rates should be higher and decrease with increasing time since the selective logging event in logged forest, but should be less temporally variable in unlogged forest. Overall, we found higher turnover rates in logged forest for all three attributes, but turnover rates did not decline through time in logged forest and was not less temporally variable in unlogged forest. These results indicate that successional models that assume recovery to pre-disturbance conditions are inadequate for predicting the effects of selective logging on the dynamics of the tropical forest in Kibale. Selective logging resulted in persistently higher turnover rates, which may compromise the carbon storage capacity of Kibale's forest. Selective logging effects may also interact with effects from other global trends, potentially causing major long-term shifts in the dynamics of tropical forests. Similar studies in tropical forests elsewhere will help determine the generality of these conclusions. Ultimately, the view that selective logging is a benign approach to the management of tropical forests should be reconsidered in the light of studies of the effects of this practice on long-term forest dynamics.

Differential Dynamic Engagement within 24 SH3 Domain: Peptide Complexes Revealed by Co-Linear Chemical Shift Perturbation Analysis

PubMed Central

Stollar, Elliott J.; Lin, Hong; Davidson, Alan R.; Forman-Kay, Julie D.

2012-01-01

There is increasing evidence for the functional importance of multiple dynamically populated states within single proteins. However, peptide binding by protein-protein interaction domains, such as the SH3 domain, has generally been considered to involve the full engagement of peptide to the binding surface with minimal dynamics and simple methods to determine dynamics at the binding surface for multiple related complexes have not been described. We have used NMR spectroscopy combined with isothermal titration calorimetry to comprehensively examine the extent of engagement to the yeast Abp1p SH3 domain for 24 different peptides. Over one quarter of the domain residues display co-linear chemical shift perturbation (CCSP) behavior, in which the position of a given chemical shift in a complex is co-linear with the same chemical shift in the other complexes, providing evidence that each complex exists as a unique dynamic rapidly inter-converting ensemble. The extent the specificity determining sub-surface of AbpSH3 is engaged as judged by CCSP analysis correlates with structural and thermodynamic measurements as well as with functional data, revealing the basis for significant structural and functional diversity amongst the related complexes. Thus, CCSP analysis can distinguish peptide complexes that may appear identical in terms of general structure and percent peptide occupancy but have significant local binding differences across the interface, affecting their ability to transmit conformational change across the domain and resulting in functional differences. PMID:23251481

Using structure to explore the sequence alignment space of remote homologs.

PubMed

Kuziemko, Andrew; Honig, Barry; Petrey, Donald

2011-10-01

Protein structure modeling by homology requires an accurate sequence alignment between the query protein and its structural template. However, sequence alignment methods based on dynamic programming (DP) are typically unable to generate accurate alignments for remote sequence homologs, thus limiting the applicability of modeling methods. A central problem is that the alignment that is "optimal" in terms of the DP score does not necessarily correspond to the alignment that produces the most accurate structural model. That is, the correct alignment based on structural superposition will generally have a lower score than the optimal alignment obtained from sequence. Variations of the DP algorithm have been developed that generate alternative alignments that are "suboptimal" in terms of the DP score, but these still encounter difficulties in detecting the correct structural alignment. We present here a new alternative sequence alignment method that relies heavily on the structure of the template. By initially aligning the query sequence to individual fragments in secondary structure elements and combining high-scoring fragments that pass basic tests for "modelability", we can generate accurate alignments within a small ensemble. Our results suggest that the set of sequences that can currently be modeled by homology can be greatly extended.

The Spatiotemporal Structure of 20th Century Climate Variations in Observations and Reanalyses. Part 1; Long-term Trend

NASA Technical Reports Server (NTRS)

Chen, Junye; DelGenio, Anthony D.; Carlson, Barbara e.; Bosilovich, Michael G.

2007-01-01

The dominant interannual El Nino-Southern Oscillation phenomenon (ENSO) and the short length of climate observation records make it difficult to study long-term climate variations in the spatiotemporal domain. Based on the fact that the ENS0 signal spreads to remote regions and induces delayed climate variation through atmospheric teleconnections, we develop an ENSO-removal method through which the ENS0 signal can be approximately removed at the grid box level from the spatiotemporal field of a climate parameter. After this signal is removed, long-term climate variations, namely, the global warming trend (GW) and the Pacific pan-decadal variability (PDV), are isolated at middle and low latitudes in the climate parameter fields from observed and reanalyses datasets. Except for known GW characteristics, the warming that occurs in the Pacific basin (approximately 0.4K in the 2oth century) is much weaker than in surrounding regions and the other two ocean basins (approximately 0.8K). The modest warming in the Pacific basin is likely due to its dynamic nature on the interannual and decadal time scales and/or the leakage of upper ocean water through the Indonesian Throughflow. Based on NCEP/NCAR and ERA-40 reanalyses, a comprehensive atmospheric structure associated with GW is given. Significant discrepancies exist between the two datasets, especially in the tightly coupled dynamic and water vapor fields. The dynamic field based on NCEP/NCAR reanalysis, which shows a change in the Walker Circulation, is consistent with the GW change in the surface temperature field. However, intensification in the Hadley Circulation is associated with GW trend in the ERA-40 reanalysis.

Genetic connectivity among swarming sites in the wide ranging and recently declining little brown bat (Myotis lucifugus)

PubMed Central

Burns, Lynne E; Frasier, Timothy R; Broders, Hugh G

2014-01-01

Characterizing movement dynamics and spatial aspects of gene flow within a species permits inference on population structuring. As patterns of structuring are products of historical and current demographics and gene flow, assessment of structure through time can yield an understanding of evolutionary dynamics acting on populations that are necessary to inform management. Recent dramatic population declines in hibernating bats in eastern North America from white-nose syndrome have prompted the need for information on movement dynamics for multiple bat species. We characterized population genetic structure of the little brown bat, Myotis lucifugus, at swarming sites in southeastern Canada using 9 nuclear microsatellites and a 292-bp region of the mitochondrial genome. Analyses of FST, ΦST, and Bayesian clustering (STRUCTURE) found weak levels of genetic structure among swarming sites for the nuclear and mitochondrial genome (Global FST = 0.001, P < 0.05, Global ΦST = 0.045, P < 0.01, STRUCTURE K = 1) suggesting high contemporary gene flow. Hierarchical AMOVA also suggests little structuring at a regional (provincial) level. Metrics of nuclear genetic structure were not found to differ between males and females suggesting weak asymmetries in gene flow between the sexes. However, a greater degree of mitochondrial structuring does support male-biased dispersal long term. Demographic analyses were consistent with past population growth and suggest a population expansion occurred from approximately 1250 to 12,500 BP, following Pleistocene deglaciation in the region. Our study suggests high gene flow and thus a high degree of connectivity among bats that visit swarming sites whereby mainland areas of the region may be best considered as one large gene pool for management and conservation. PMID:25505539

Estimating network parameters from combined dynamics of firing rate and irregularity of single neurons.

PubMed

Hamaguchi, Kosuke; Riehle, Alexa; Brunel, Nicolas

2011-01-01

High firing irregularity is a hallmark of cortical neurons in vivo, and modeling studies suggest a balance of excitation and inhibition is necessary to explain this high irregularity. Such a balance must be generated, at least partly, from local interconnected networks of excitatory and inhibitory neurons, but the details of the local network structure are largely unknown. The dynamics of the neural activity depends on the local network structure; this in turn suggests the possibility of estimating network structure from the dynamics of the firing statistics. Here we report a new method to estimate properties of the local cortical network from the instantaneous firing rate and irregularity (CV(2)) under the assumption that recorded neurons are a part of a randomly connected sparse network. The firing irregularity, measured in monkey motor cortex, exhibits two features; many neurons show relatively stable firing irregularity in time and across different task conditions; the time-averaged CV(2) is widely distributed from quasi-regular to irregular (CV(2) = 0.3-1.0). For each recorded neuron, we estimate the three parameters of a local network [balance of local excitation-inhibition, number of recurrent connections per neuron, and excitatory postsynaptic potential (EPSP) size] that best describe the dynamics of the measured firing rates and irregularities. Our analysis shows that optimal parameter sets form a two-dimensional manifold in the three-dimensional parameter space that is confined for most of the neurons to the inhibition-dominated region. High irregularity neurons tend to be more strongly connected to the local network, either in terms of larger EPSP and inhibitory PSP size or larger number of recurrent connections, compared with the low irregularity neurons, for a given excitatory/inhibitory balance. Incorporating either synaptic short-term depression or conductance-based synapses leads many low CV(2) neurons to move to the excitation-dominated region as well as to an increase of EPSP size.

A Coupled Fluid-Structure Interaction Analysis of Solid Rocket Motor with Flexible Inhibitors

NASA Technical Reports Server (NTRS)

Yang, H. Q.; West, Jeff

2014-01-01

A capability to couple NASA production CFD code, Loci/CHEM, with CFDRC's structural finite element code, CoBi, has been developed. This paper summarizes the efforts in applying the installed coupling software to demonstrate/investigate fluid-structure interaction (FSI) between pressure wave and flexible inhibitor inside reusable solid rocket motor (RSRM). First a unified governing equation for both fluid and structure is presented, then an Eulerian-Lagrangian framework is described to satisfy the interfacial continuity requirements. The features of fluid solver, Loci/CHEM and structural solver, CoBi, are discussed before the coupling methodology of the solvers is described. The simulation uses production level CFD LES turbulence model with a grid resolution of 80 million cells. The flexible inhibitor is modeled with full 3D shell elements. Verifications against analytical solutions of structural model under steady uniform pressure condition and under dynamic condition of modal analysis show excellent agreements in terms of displacement distribution and eigen modal frequencies. The preliminary coupled result shows that due to acoustic coupling, the dynamics of one of the more flexible inhibitors shift from its first modal frequency to the first acoustic frequency of the solid rocket motor.

Protein structure modeling and refinement by global optimization in CASP12.

PubMed

Hong, Seung Hwan; Joung, InSuk; Flores-Canales, Jose C; Manavalan, Balachandran; Cheng, Qianyi; Heo, Seungryong; Kim, Jong Yun; Lee, Sun Young; Nam, Mikyung; Joo, Keehyoung; Lee, In-Ho; Lee, Sung Jong; Lee, Jooyoung

2018-03-01

For protein structure modeling in the CASP12 experiment, we have developed a new protocol based on our previous CASP11 approach. The global optimization method of conformational space annealing (CSA) was applied to 3 stages of modeling: multiple sequence-structure alignment, three-dimensional (3D) chain building, and side-chain re-modeling. For better template selection and model selection, we updated our model quality assessment (QA) method with the newly developed SVMQA (support vector machine for quality assessment). For 3D chain building, we updated our energy function by including restraints generated from predicted residue-residue contacts. New energy terms for the predicted secondary structure and predicted solvent accessible surface area were also introduced. For difficult targets, we proposed a new method, LEEab, where the template term played a less significant role than it did in LEE, complemented by increased contributions from other terms such as the predicted contact term. For TBM (template-based modeling) targets, LEE performed better than LEEab, but for FM targets, LEEab was better. For model refinement, we modified our CASP11 molecular dynamics (MD) based protocol by using explicit solvents and tuning down restraint weights. Refinement results from MD simulations that used a new augmented statistical energy term in the force field were quite promising. Finally, when using inaccurate information (such as the predicted contacts), it was important to use the Lorentzian function for which the maximal penalty arising from wrong information is always bounded. © 2017 Wiley Periodicals, Inc.

Density-dependent microbial turnover improves soil carbon model predictions of long-term litter manipulations

NASA Astrophysics Data System (ADS)

Georgiou, Katerina; Abramoff, Rose; Harte, John; Riley, William; Torn, Margaret

2017-04-01

Climatic, atmospheric, and land-use changes all have the potential to alter soil microbial activity via abiotic effects on soil or mediated by changes in plant inputs. Recently, many promising microbial models of soil organic carbon (SOC) decomposition have been proposed to advance understanding and prediction of climate and carbon (C) feedbacks. Most of these models, however, exhibit unrealistic oscillatory behavior and SOC insensitivity to long-term changes in C inputs. Here we diagnose the sources of instability in four models that span the range of complexity of these recent microbial models, by sequentially adding complexity to a simple model to include microbial physiology, a mineral sorption isotherm, and enzyme dynamics. We propose a formulation that introduces density-dependence of microbial turnover, which acts to limit population sizes and reduce oscillations. We compare these models to results from 24 long-term C-input field manipulations, including the Detritus Input and Removal Treatment (DIRT) experiments, to show that there are clear metrics that can be used to distinguish and validate the inherent dynamics of each model structure. We find that widely used first-order models and microbial models without density-dependence cannot readily capture the range of long-term responses observed across the DIRT experiments as a direct consequence of their model structures. The proposed formulation improves predictions of long-term C-input changes, and implies greater SOC storage associated with CO2-fertilization-driven increases in C inputs over the coming century compared to common microbial models. Finally, we discuss our findings in the context of improving microbial model behavior for inclusion in Earth System Models.

Reversible and dissipative macroscopic contributions to the stress tensor: active or passive?

PubMed

Brand, H R; Pleiner, H; Svenšek, D

2014-09-01

The issue of dynamic contributions to the macroscopic stress tensor has been of high interest in the field of bio-inspired active systems over the last few years. Of particular interest is a direct coupling ("active term") of the stress tensor with the order parameter, the latter describing orientational order induced by active processes. Here we analyze more generally possible reversible and irreversible dynamic contributions to the stress tensor for various passive and active macroscopic systems. This includes systems with tetrahedral/octupolar order, polar and non-polar (chiral) nematic and smectic liquid crystals, as well as active fluids with a dynamic preferred (polar or non-polar) direction. We show that it cannot a priori be seen, neither from the symmetry properties of the macroscopic variables involved, nor from the structure of the cross-coupling contributions to the stress tensor, whether the system studied is active or passive. Rather, that depends on whether the variables that give rise to those cross-couplings in the stress tensor are driven or not. We demonstrate that several simplified descriptions of active systems in the literature that neglect the necessary counter term to the active term violate linear irreversible thermodynamics and lead to an unphysical contribution to the entropy production.

Relative phase asynchrony and long-range correlation of long-term solar magnetic activity

NASA Astrophysics Data System (ADS)

Deng, Linhua

2017-07-01

Statistical signal processing is one of the most important tasks in a large amount of areas of scientific studies, such as astrophysics, geophysics, and space physics. Phase recurrence analysis and long-range persistence are the two dynamical structures of the underlying processes for the given natural phenomenon. Linear and nonlinear time series analysis approaches (cross-correlation analysis, cross-recurrence plot, wavelet coherent transform, and Hurst analysis) are combined to investigate the relative phase interconnection and long-range correlation between solar activity and geomagnetic activity for the time interval from 1932 January to 2017 January. The following prominent results are found: (1) geomagnetic activity lags behind sunspot numbers with a phase shift of 21 months, and they have a high level of asynchronous behavior; (2) their relative phase interconnections are in phase for the periodic scales during 8-16 years, but have a mixing behavior for the periodic belts below 8 years; (3) both sunspot numbers and geomagnetic activity can not be regarded as a stochastic phenomenon because their dynamical behaviors display a long-term correlation and a fractal nature. We believe that the presented conclusions could provide further information on understanding the dynamical coupling of solar dynamo process with geomagnetic activity variation, and the crucial role of solar and geomagnetic activity in the long-term climate change.

Insights into the Structural Dynamics of Nucleocytoplasmic Transport of tRNA by Exportin-t

PubMed Central

Gupta, Asmita; Kailasam, Senthilkumar; Bansal, Manju

2016-01-01

Exportin-t (Xpot) transports mature 5′- and 3′-end processed tRNA from the nucleus to the cytoplasm by associating with a small G-protein Ran (RAs-related nuclear protein), in the nucleus. The release of tRNA in cytoplasm involves RanGTP hydrolysis. Despite the availability of crystal structures of nuclear and cytosolic forms of Xpot, the molecular details regarding the sequential events leading to tRNA release and subsequent conformational changes occurring in Xpot remain unknown. We have performed a combination of classical all-atom and accelerated molecular dynamics simulations on a set of complexes involving Xpot to study a range of features including conformational flexibility of free and cargo-bound Xpot and functionally critical contacts between Xpot and its cargo. The systems investigated include free Xpot and its different complexes, bound either to Ran (GTP/GDP) or tRNA or both. This approach provided a statistically reliable estimate of structural dynamics of Xpot after cargo release. The mechanistic basis for Xpot opening after cargo release has been explained in terms of dynamic structural hinges, about which neighboring region could be displaced to facilitate the nuclear to cytosolic state transition. Post-RanGTP hydrolysis, a cascade of events including local conformational change in RanGTP and loss of critical contacts at Xpot/tRNA interface suggest factors responsible for eventual release of tRNA. The level of flexibility in different Xpot complexes varied depending on the arrangement of individual HEAT repeats. Current study provides one of the most comprehensive and robust analysis carried out on this protein using molecular dynamics schemes. PMID:27028637

A classical molecular dynamics investigation of the free energy and structure of short polyproline conformers

NASA Astrophysics Data System (ADS)

Moradi, Mahmoud; Babin, Volodymyr; Roland, Christopher; Sagui, Celeste

2010-09-01

Folded polyproline peptides can exist as either left-(PPII) or right-handed (PPI) helices, depending on their environment. In this work, we have characterized the conformations and the free energy landscapes of Ace-(Pro)n-Nme, n =2,3,…,9, and 13 peptides both in vacuo and in an implicit solvent environment. In order to enhance the sampling provided by regular molecular dynamics simulations, we have used the recently developed adaptively biased molecular dynamics method—which provides an accurate description of the free energy landscapes in terms of a set of relevant collective variables—combined with Hamiltonian and temperature replica exchange molecular dynamics methods. The collective variables, which are chosen so as to reflect the stable structures and the "slow modes" of the polyproline system, were based primarily on properties of length and of the cis/trans isomerization associated with the prolyl bonds. Results indicate that the space of peptide structures is characterized not just by pure PPII and PPI structures, but rather by a broad distribution of stable minima with similar free energies. These results are in agreement with recent experimental work. In addition, we have used steered molecular dynamics methods in order to quantitatively estimate the free energy difference of PPI and PPII for peptides of the length n =2,…,5 in vacuo and implicit water and qualitatively investigate transition pathways and mechanisms for the PPII to PPI transitions. A zipper-like mechanism, starting from either the center of the peptide or the amidated end, appear to be the most likely mechanisms for the PPII→PPI transition for the longer peptides.

Filamentation of ultrashort light pulses in a liquid scattering medium

NASA Astrophysics Data System (ADS)

Jukna, V.; Tamošauskas, G.; Valiulis, G.; Aputis, M.; Puida, M.; Ivanauskas, F.; Dubietis, A.

2009-01-01

We have studied filamentation of 1-ps laser pulses in a scattering medium (aqueous suspension of 2-μm polystyrene microspheres) and compared filamentation dynamics to that in pure water. Our results indicate that light scattering does not alter filamentation dynamics in general, but rather results in farther position of the nonlinear focus, shorter filament length, and the development of speckle structure in the peripheral part of the beam. The experimental observations are qualitatively reproduced by the numerical model which accounts for diffraction, self-focusing, multiphoton absorption, and light scattering introduced through a stochastic diffusion and diffraction term.

Integrated multidisciplinary design optimization of rotorcraft

NASA Technical Reports Server (NTRS)

Adelman, Howard M.; Mantay, Wayne R.

1989-01-01

The NASA/Army research plan for developing the logic elements for helicopter rotor design optimization by integrating appropriate disciplines and accounting for important interactions among the disciplines is discussed. The paper describes the optimization formulation in terms of the objective function, design variables, and constraints. The analysis aspects are discussed, and an initial effort at defining the interdisciplinary coupling is summarized. Results are presented on the achievements made in the rotor aerodynamic performance optimization for minimum hover horsepower, rotor dynamic optimization for vibration reduction, rotor structural optimization for minimum weight, and integrated aerodynamic load/dynamics optimization for minimum vibration and weight.

Mars

NASA Technical Reports Server (NTRS)

Kieffer, Hugh H. (Editor); Jakosky, Bruce M. (Editor); Snyder, Conway W. (Editor); Matthews, Mildred S. (Editor)

1992-01-01

The present volume on Mars discusses visual, photographic and polarimetric telescopic observations, spacecraft exploration of Mars, the origin and thermal evolution of Mars, and the bulk composition, mineralogy, and internal structure of the planet. Attention is given to Martian gravity and topography, stress and tectonics on Mars, long-term orbital and spin dynamics of Mars, and Martian geodesy and cartography. Topics addressed include the physical volcanology of Mars, the canyon system on planet, Martian channels and valley networks, and ice in the Martian regolith. Also discussed are Martian aeolian processes, sediments, and features, polar deposits of Mars, dynamics of the Martian atmosphere, and the seasonal behavior of water on Mars.

Using Lidar and Radar measurements to constrain predictions of forest ecosystem structure and function.

PubMed

Antonarakis, Alexander S; Saatchi, Sassan S; Chazdon, Robin L; Moorcroft, Paul R

2011-06-01

Insights into vegetation and aboveground biomass dynamics within terrestrial ecosystems have come almost exclusively from ground-based forest inventories that are limited in their spatial extent. Lidar and synthetic-aperture Radar are promising remote-sensing-based techniques for obtaining comprehensive measurements of forest structure at regional to global scales. In this study we investigate how Lidar-derived forest heights and Radar-derived aboveground biomass can be used to constrain the dynamics of the ED2 terrestrial biosphere model. Four-year simulations initialized with Lidar and Radar structure variables were compared against simulations initialized from forest-inventory data and output from a long-term potential-vegtation simulation. Both height and biomass initializations from Lidar and Radar measurements significantly improved the representation of forest structure within the model, eliminating the bias of too many large trees that arose in the potential-vegtation-initialized simulation. The Lidar and Radar initializations decreased the proportion of larger trees estimated by the potential vegetation by approximately 20-30%, matching the forest inventory. This resulted in improved predictions of ecosystem-scale carbon fluxes and structural dynamics compared to predictions from the potential-vegtation simulation. The Radar initialization produced biomass values that were 75% closer to the forest inventory, with Lidar initializations producing canopy height values closest to the forest inventory. Net primary production values for the Radar and Lidar initializations were around 6-8% closer to the forest inventory. Correcting the Lidar and Radar initializations for forest composition resulted in improved biomass and basal-area dynamics as well as leaf-area index. Correcting the Lidar and Radar initializations for forest composition and fine-scale structure by combining the remote-sensing measurements with ground-based inventory data further improved predictions, suggesting that further improvements of structural and carbon-flux metrics will also depend on obtaining reliable estimates of forest composition and accurate representation of the fine-scale vertical and horizontal structure of plant canopies.

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.

Enhanced Molecular Dynamics Methods Applied to Drug Design Projects.

PubMed

Ziada, Sonia; Braka, Abdennour; Diharce, Julien; Aci-Sèche, Samia; Bonnet, Pascal

2018-01-01

Nobel Laureate Richard P. Feynman stated: "[…] everything that living things do can be understood in terms of jiggling and wiggling of atoms […]." The importance of computer simulations of macromolecules, which use classical mechanics principles to describe atom behavior, is widely acknowledged and nowadays, they are applied in many fields such as material sciences and drug discovery. With the increase of computing power, molecular dynamics simulations can be applied to understand biological mechanisms at realistic timescales. In this chapter, we share our computational experience providing a global view of two of the widely used enhanced molecular dynamics methods to study protein structure and dynamics through the description of their characteristics, limits and we provide some examples of their applications in drug design. We also discuss the appropriate choice of software and hardware. In a detailed practical procedure, we describe how to set up, run, and analyze two main molecular dynamics methods, the umbrella sampling (US) and the accelerated molecular dynamics (aMD) methods.

Finite element normal mode analysis of resistance welding jointed of dissimilar plate hat structure

NASA Astrophysics Data System (ADS)

Nazri, N. A.; Sani, M. S. M.

2017-10-01

Structural joints offer connection between structural element (beam, plate, solid etc.) in order to build a whole assembled structure. The complex behaviour of connecting elements plays a valuable role in characteristics of dynamic such as natural frequencies and mode shapes. In automotive structures, the trustworthiness arrangement of the structure extremely depends on joints. In this paper, top hat structure is modelled and designed with spot welding joint using dissimilar materials which is mild steel 1010 and stainless steel 304, using finite element software. Different types of connector elements such as rigid body element (RBE2), welding joint element (CWELD), and bar element (CBAR) are applied to represent real connection between two dissimilar plates. Normal mode analysis is simulated with different types of joining element in order to determine modal properties. Natural frequencies using RBE2, CBAR and CWELD are compared to equivalent rigid body method. Connection that gives the lowest percentage error among these three will be selected as the most reliable joining for resistance spot weld. From the analysis, it is shown that CWELD is better compared to others in term of weld joining among dissimilar plate materials. It is expected that joint modelling of finite element plays significant role in structural dynamics.

Homology Modeling of Dopamine D2 and D3 Receptors: Molecular Dynamics Refinement and Docking Evaluation

PubMed Central

Platania, Chiara Bianca Maria; Salomone, Salvatore; Leggio, Gian Marco; Drago, Filippo; Bucolo, Claudio

2012-01-01

Dopamine (DA) receptors, a class of G-protein coupled receptors (GPCRs), have been targeted for drug development for the treatment of neurological, psychiatric and ocular disorders. The lack of structural information about GPCRs and their ligand complexes has prompted the development of homology models of these proteins aimed at structure-based drug design. Crystal structure of human dopamine D3 (hD3) receptor has been recently solved. Based on the hD3 receptor crystal structure we generated dopamine D2 and D3 receptor models and refined them with molecular dynamics (MD) protocol. Refined structures, obtained from the MD simulations in membrane environment, were subsequently used in molecular docking studies in order to investigate potential sites of interaction. The structure of hD3 and hD2L receptors was differentiated by means of MD simulations and D3 selective ligands were discriminated, in terms of binding energy, by docking calculation. Robust correlation of computed and experimental Ki was obtained for hD3 and hD2L receptor ligands. In conclusion, the present computational approach seems suitable to build and refine structure models of homologous dopamine receptors that may be of value for structure-based drug discovery of selective dopaminergic ligands. PMID:22970199

The Resolvent Algebra of Non-relativistic Bose Fields: Observables, Dynamics and States

NASA Astrophysics Data System (ADS)

Buchholz, Detlev

2018-05-01

The structure of the gauge invariant (particle number preserving) C*-algebra generated by the resolvents of a non-relativistic Bose field is analyzed. It is shown to form a dense subalgebra of the bounded inverse limit of a directed system of approximately finite dimensional C*-algebras. Based on this observation, it is proven that the closure of the gauge invariant algebra is stable under the dynamics induced by Hamiltonians involving pair potentials. These facts allow to proceed to a description of interacting Bosons in terms of C*-dynamical systems. It is outlined how the present approach leads to simplifications in the construction of infinite bosonic states and sheds new light on topics in many body theory.

Carbon monoxide recombination dynamics in truncated hemoglobins studied with visible-pump midIR-probe spectroscopy.

PubMed

Lapini, Andrea; Di Donato, Mariangela; Patrizi, Barbara; Marcelli, Agnese; Lima, Manuela; Righini, Roberto; Foggi, Paolo; Sciamanna, Natascia; Boffi, Alberto

2012-08-02

Carbon monoxide recombination dynamics upon photodissociation with visible light has been characterized by means of ultrafast visible-pump/MidIR probe spectroscopy for the truncated hemoglobins from Thermobifida fusca and Bacillus subtilis. Photodissociation has been induced by exciting the sample at two different wavelengths: 400 nm, corresponding to the heme absorption in the B-band, and 550 nm, in the Q-bands. The bleached iron-CO coordination band located at 1850-1950 cm(-1) and the free CO absorption band in the region 2050-2200 cm(-1) have been observed by probe pulses tuned in the appropriate infrared region. The kinetic traces measured at 1850-1950 cm(-1) reveal multiexponential subnanosecond dynamics that have been interpreted as arising from fast geminate recombination of the photolyzed CO. A compared analysis of the crystal structure of the two proteins reveals a similar structure of their distal heme pocket, which contains conserved polar and aromatic amino acid residues closely interacting with the iron ligand. Although fast geminate recombination is observed in both proteins, several kinetic differences can be evidenced, which can be interpreted in terms of a different structural flexibility of the corresponding heme distal pockets. The analysis of the free CO band-shape and of its dynamic evolution brings out novel features about the nature of the docking site inside the protein cavity.

Behavior control in the sensorimotor loop with short-term synaptic dynamics induced by self-regulating neurons.

PubMed

Toutounji, Hazem; Pasemann, Frank

2014-01-01

The behavior and skills of living systems depend on the distributed control provided by specialized and highly recurrent neural networks. Learning and memory in these systems is mediated by a set of adaptation mechanisms, known collectively as neuronal plasticity. Translating principles of recurrent neural control and plasticity to artificial agents has seen major strides, but is usually hampered by the complex interactions between the agent's body and its environment. One of the important standing issues is for the agent to support multiple stable states of behavior, so that its behavioral repertoire matches the requirements imposed by these interactions. The agent also must have the capacity to switch between these states in time scales that are comparable to those by which sensory stimulation varies. Achieving this requires a mechanism of short-term memory that allows the neurocontroller to keep track of the recent history of its input, which finds its biological counterpart in short-term synaptic plasticity. This issue is approached here by deriving synaptic dynamics in recurrent neural networks. Neurons are introduced as self-regulating units with a rich repertoire of dynamics. They exhibit homeostatic properties for certain parameter domains, which result in a set of stable states and the required short-term memory. They can also operate as oscillators, which allow them to surpass the level of activity imposed by their homeostatic operation conditions. Neural systems endowed with the derived synaptic dynamics can be utilized for the neural behavior control of autonomous mobile agents. The resulting behavior depends also on the underlying network structure, which is either engineered or developed by evolutionary techniques. The effectiveness of these self-regulating units is demonstrated by controlling locomotion of a hexapod with 18 degrees of freedom, and obstacle-avoidance of a wheel-driven robot.

Behavior control in the sensorimotor loop with short-term synaptic dynamics induced by self-regulating neurons

PubMed Central

Toutounji, Hazem; Pasemann, Frank

2014-01-01

The behavior and skills of living systems depend on the distributed control provided by specialized and highly recurrent neural networks. Learning and memory in these systems is mediated by a set of adaptation mechanisms, known collectively as neuronal plasticity. Translating principles of recurrent neural control and plasticity to artificial agents has seen major strides, but is usually hampered by the complex interactions between the agent's body and its environment. One of the important standing issues is for the agent to support multiple stable states of behavior, so that its behavioral repertoire matches the requirements imposed by these interactions. The agent also must have the capacity to switch between these states in time scales that are comparable to those by which sensory stimulation varies. Achieving this requires a mechanism of short-term memory that allows the neurocontroller to keep track of the recent history of its input, which finds its biological counterpart in short-term synaptic plasticity. This issue is approached here by deriving synaptic dynamics in recurrent neural networks. Neurons are introduced as self-regulating units with a rich repertoire of dynamics. They exhibit homeostatic properties for certain parameter domains, which result in a set of stable states and the required short-term memory. They can also operate as oscillators, which allow them to surpass the level of activity imposed by their homeostatic operation conditions. Neural systems endowed with the derived synaptic dynamics can be utilized for the neural behavior control of autonomous mobile agents. The resulting behavior depends also on the underlying network structure, which is either engineered or developed by evolutionary techniques. The effectiveness of these self-regulating units is demonstrated by controlling locomotion of a hexapod with 18 degrees of freedom, and obstacle-avoidance of a wheel-driven robot. PMID:24904403

Characterization of the geometry and topology of DNA pictured as a discrete collection of atoms

PubMed Central

Olson, Wilma K.

2014-01-01

The structural and physical properties of DNA are closely related to its geometry and topology. The classical mathematical treatment of DNA geometry and topology in terms of ideal smooth space curves was not designed to characterize the spatial arrangements of atoms found in high-resolution and simulated double-helical structures. We present here new and rigorous numerical methods for the rapid and accurate assessment of the geometry and topology of double-helical DNA structures in terms of the constituent atoms. These methods are well designed for large DNA datasets obtained in detailed numerical simulations or determined experimentally at high-resolution. We illustrate the usefulness of our methodology by applying it to the analysis of three canonical double-helical DNA chains, a 65-bp minicircle obtained in recent molecular dynamics simulations, and a crystallographic array of protein-bound DNA duplexes. Although we focus on fully base-paired DNA structures, our methods can be extended to treat the geometry and topology of melted DNA structures as well as to characterize the folding of arbitrary molecules such as RNA and cyclic peptides. PMID:24791158

Formulation d'un modele mathematique par des techniques d'estimation de parametres a partir de donnees de vol pour l'helicoptere Bell 427 et l'avion F/A-18 servant a la recherches en aeroservoelasticite

NASA Astrophysics Data System (ADS)

Nadeau-Beaulieu, Michel

In this thesis, three mathematical models are built from flight test data for different aircraft design applications: a ground dynamics model for the Bell 427 helicopter, a prediction model for the rotor and engine parameters for the same helicopter type and a simulation model for the aeroelastic deflections of the F/A-18. In the ground dynamics application, the model structure is derived from physics where the normal force between the helicopter and the ground is modelled as a vertical spring and the frictional force is modelled with static and dynamic friction coefficients. The ground dynamics model coefficients are optimized to ensure that the model matches the landing data within the FAA (Federal Aviation Administration) tolerance bands for a level D flight simulator. In the rotor and engine application, rotors torques (main and tail), the engine torque and main rotor speed are estimated using a state-space model. The model inputs are nonlinear terms derived from the pilot control inputs and the helicopter states. The model parameters are identified using the subspace method and are further optimised with the Levenberg-Marquardt minimisation algorithm. The model built with the subspace method provides an excellent estimate of the outputs within the FAA tolerance bands. The F/A-18 aeroelastic state-space model is built from flight test. The research concerning this model is divided in two parts. Firstly, the deflection of a given structural surface on the aircraft following a differential ailerons control input is represented by a Multiple Inputs Single Outputs linear model whose inputs are the ailerons positions and the structural surfaces deflections. Secondly, a single state-space model is used to represent the deflection of the aircraft wings and trailing edge flaps following any control input. In this case the model is made non-linear by multiplying model inputs into higher order terms and using these terms as the inputs of the state-space equations. In both cases, the identification method is the subspace method. Most fit coefficients between the estimated and the measured signals are above 73% and most correlation coefficient are higher than 90%.

Structures and mechanisms - Streamlining for fuel economy

NASA Technical Reports Server (NTRS)

Card, M. F.

1983-01-01

The design of prospective NASA space station components which inherently possess the means for structural growth without compromising initial system characteristics is considered. In structural design terms, space station growth can be achieved by increasing design safety factors, introducing dynamic isolators to prevent loads from reaching the initial components, or preplanning the refurbishment of the original structure with stronger elements. Design tradeoffs will be based on the definition of on-orbit loads, including docking and maneuvering, whose derived load spectra will allow the estimation of fatigue life. Improvements must be made in structural materials selection in order to reduce contamination, slow degradation, and extend the life of coatings. To minimize on-orbit maintenance, long service life lubrication systems with advanced sealing devices must be developed.

Numerical damage models using a structural approach: application in bones and ligaments

NASA Astrophysics Data System (ADS)

Arnoux, P. J.; Bonnoit, J.; Chabrand, P.; Jean, M.; Pithioux, M.

2002-01-01

The purpose of the present study was to apply knowledge of structural properties to perform numerical simulations with models of bones and knee ligaments exposed to dynamic tensile loading leading to tissue damage. Compact bones and knee ligaments exhibit the same geometrical pattern in their different levels of structural hierarchy from the tropocollagen molecule to the fibre. Nevertheless, their mechanical behaviours differ considerably at the fibril level. These differences are due to the contribution of the joints in the microfibril-fibril-fibre assembly and to the mechanical properties of the structural components. Two finite element models of the fibrous bone and ligament structure were used to describe damage in terms of elastoplastic laws or joint decohesion processes.

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.

Control of Spin Wave Dynamics in Spatially Twisted Magnetic Structures

DTIC Science & Technology

2017-06-27

realize high-performance spintronic and magnetic storage devices. 15. SUBJECT TERMS nano- electronics , spin, wave, magnetic, multi-functional, device 16... electronics has required us to develop high-performance and multi-functional electronic devices driven with extremely low power consumption...Spintronics”, simultaneously utilizing the charge and the spin of electrons , provides us with solutions to essential problems for semiconductor-based

A preliminary riparian/wetland vegetation community classification of the Upper and Middle Rio Grande watersheds in New Mexico

Treesearch

Paula Durkin; Esteban Muldavin; Mike Bradley; Stacey E. Carr

1996-01-01

The riparian wetland vegetation communities of the upper and middle Rio Grande watersheds in New Mexico were surveyed in 1992 through 1994. The communities are hierarchically classified in terms of species composition and vegetation structure. The resulting Community Types are related to soil conditions, hydrological regime, and temporal dynamics. The classification is...

Long-term effects of fire severity on oak–conifer dynamics in the southern Cascades

Treesearch

Matthew I. Cocking; J. Morgan Varner; Eric E. Knapp

2014-01-01

We studied vegetation composition and structure in a mixed conifer–oak ecosystem across a range of fire severity 10 years following wildfire. Sample plots centered on focal California black oaks (Quercus kelloggii) were established to evaluate oak and neighboring tree and shrub recovery across a gradient of fire severity in the southern Cascade...

Dynamics of a temperate deciduous forest under landscape-scale management: Implications for adaptability to climate change

Treesearch

Matthew G. Olson; Benjamin O. Knapp; John M. Kabrick

2017-01-01

Landscape forest management is an approach to meeting diverse objectives that collectively span multiple spatial scales. It is critical that we understand the long-term effects of landscape management on the structure and composition of forest tree communities to ensure that these practices are sustainable. Furthermore, it is increasingly important to also consider...

A molecular dynamics approach to barrodiffusion

NASA Astrophysics Data System (ADS)

Cooley, James; Marciante, Mathieu; Murillo, Michael

2016-10-01

Unexpected phenomena in the reaction rates for Inertial Confinement Fusion (ICF) capsules have led to a renewed interest in the thermo-dynamically driven diffusion process for the past 10 years, often described collectively as barodiffusion. In the current context, barodiffusion would manifest as a process that separates ions of differing mass and charge ratios due to pressure and temperature gradients set-up through shock structures in the capsule core. Barrodiffusion includes additional mass transfer terms that account for the irreversible transport of species due to gradients in the system, both thermodynamic and electric e.g, i = - ρD [ ∇c +kp ∇ln(pi) +kT(i) ∇ln(Ti) +kt(e) ∇ln(Te) +eke/Ti ∇ϕ ] . Several groups have attacked this phenomena using continuum scale models and supplemented with kinetic theory to derive coefficients for the different diffusion terms based on assumptions about the collisional processes. In contrast, we have applied a molecular dynamics (MD) simulation to this system to gain a first-principle understanding of the rate kinetics and to assess the accuracy of the differin

Dynamics of a new family of iterative processes for quadratic polynomials

NASA Astrophysics Data System (ADS)

Gutiérrez, J. M.; Hernández, M. A.; Romero, N.

2010-03-01

In this work we show the presence of the well-known Catalan numbers in the study of the convergence and the dynamical behavior of a family of iterative methods for solving nonlinear equations. In fact, we introduce a family of methods, depending on a parameter . These methods reach the order of convergence m+2 when they are applied to quadratic polynomials with different roots. Newton's and Chebyshev's methods appear as particular choices of the family appear for m=0 and m=1, respectively. We make both analytical and graphical studies of these methods, which give rise to rational functions defined in the extended complex plane. Firstly, we prove that the coefficients of the aforementioned family of iterative processes can be written in terms of the Catalan numbers. Secondly, we make an incursion into its dynamical behavior. In fact, we show that the rational maps related to these methods can be written in terms of the entries of the Catalan triangle. Next we analyze its general convergence, by including some computer plots showing the intricate structure of the Universal Julia sets associated with the methods.

Modulational instability and dynamics of implicit higher-order rogue wave solutions for the Kundu equation

NASA Astrophysics Data System (ADS)

Wen, Xiao-Yong; Zhang, Guoqiang

2018-01-01

Under investigation in this paper is the Kundu equation, which may be used to describe the propagation process of ultrashort optical pulses in nonlinear optics. The modulational instability of the plane-wave for the possible reason of the formation of the rogue wave (RW) is studied for the system. Based on our proposed generalized perturbation (n,N - n)-fold Darboux transformation (DT), some new higher-order implicit RW solutions in terms of determinants are obtained by means of the generalized perturbation (1,N - 1)-fold DT, when choosing different special parameters, these results will reduce to the RW solutions of the Kaup-Newell (KN) equation, Chen-Lee-Liu (CLL) equation and Gerjikov-Ivanov (GI) equation, respectively. The relevant wave structures are shown graphically, which display abundant interesting wave structures. The dynamical behaviors and propagation stability of the first-order and second-order RW solutions are discussed by using numerical simulations, the higher-order nonlinear terms for the Kundu equation have an impact on the propagation instability of the RW. The method can also be extended to find the higher-order RW or rational solutions of other integrable nonlinear equations.

Acceleration and torque feedback for robotic control - Experimental results

NASA Technical Reports Server (NTRS)

Mclnroy, John E.; Saridis, George N.

1990-01-01

Gross motion control of robotic manipulators typically requires significant on-line computations to compensate for nonlinear dynamics due to gravity, Coriolis, centripetal, and friction nonlinearities. One controller proposed by Luo and Saridis avoids these computations by feeding back joint acceleration and torque. This study implements the controller on a Puma 600 robotic manipulator. Joint acceleration measurement is obtained by measuring linear accelerations of each joint, and deriving a computationally efficient transformation from the linear measurements to the angular accelerations. Torque feedback is obtained by using the previous torque sent to the joints. The implementation has stability problems on the Puma 600 due to the extremely high gains inherent in the feedback structure. Since these high gains excite frequency modes in the Puma 600, the algorithm is modified to decrease the gain inherent in the feedback structure. The resulting compensator is stable and insensitive to high frequency unmodeled dynamics. Moreover, a second compensator is proposed which uses acceleration and torque feedback, but still allows nonlinear terms to be fed forward. Thus, by feeding the increment in the easily calculated gravity terms forward, improved responses are obtained. Both proposed compensators are implemented, and the real time results are compared to those obtained with the computed torque algorithm.

Molecular dynamics simulation reveals how phosphorylation of tyrosine 26 of phosphoglycerate mutase 1 upregulates glycolysis and promotes tumor growth.

PubMed

Wang, Yan; Cai, Wen-Sheng; Chen, Luonan; Wang, Guanyu

2017-02-14

Phosphoglycerate mutase 1 (PGAM1) catalyzes the eighth step of glycolysis and is often found upregulated in cancer cells. To test the hypothesis that the phosphorylation of tyrosine 26 residue of PGAM1 greatly enhances its activity, we performed both conventional and steered molecular dynamics simulations on the binding and unbinding of PGAM1 to its substrates, with tyrosine 26 either phosphorylated or not. We analyzed the simulated data in terms of structural stability, hydrogen bond formation, binding free energy, etc. We found that tyrosine 26 phosphorylation enhances the binding of PGAM1 to its substrates through generating electrostatic environment and structural features that are advantageous to the binding. Our results may provide valuable insights into computer-aided design of drugs that specifically target cancer cells with PGAM1 tyrosine 26 phosphorylated.

Six-component semi-discrete integrable nonlinear Schrödinger system

NASA Astrophysics Data System (ADS)

Vakhnenko, Oleksiy O.

2018-01-01

We suggest the six-component integrable nonlinear system on a quasi-one-dimensional lattice. Due to its symmetrical form, the general system permits a number of reductions; one of which treated as the semi-discrete integrable nonlinear Schrödinger system on a lattice with three structural elements in the unit cell is considered in considerable details. Besides six truly independent basic field variables, the system is characterized by four concomitant fields whose background values produce three additional types of inter-site resonant interactions between the basic fields. As a result, the system dynamics becomes associated with the highly nonstandard form of Poisson structure. The elementary Poisson brackets between all field variables are calculated and presented explicitly. The richness of system dynamics is demonstrated on the multi-component soliton solution written in terms of properly parameterized soliton characteristics.

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

Improved nonorthogonal tight-binding Hamiltonian for molecular-dynamics simulations of silicon clusters

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

Ordejon, P.; Lebedenko, D.; Menon, M.

1994-08-15

We present an improvement over the nonorthogonal tight-binding molecular-dynamics scheme recently proposed by Menon and Subbaswamy [Phys. Rev. B 47, 12 754 (1993)]. The proper treatment of the nonorthogonality and its effect on the Hamiltonian matrix elements has been found to obviate the need for a bond-counting term, leaving only two adjustable parameters in the formalism. With the improved parametrization we obtain values of the energies and bonding distances which are in better agreement with the available [ital ab] [ital initio] results for clusters of size up to [ital N]=10. Additionally, we have identified a lowest energy structure for themore » Si[sub 9] cluster, which to our knowledge has not been considered to date. We show that this structure (a distorted tricapped trigonal prism with [ital C][sub 2[ital v

On the hydration of subnanometric antifouling organosilane adlayers: a molecular dynamics simulation.

PubMed

Sheikh, Sonia; Blaszykowski, Christophe; Nolan, Robert; Thompson, Damien; Thompson, Michael

2015-01-01

The connection between antifouling and surface hydration is a fascinating but daunting question to answer. Herein, we use molecular dynamics (MD) computer simulations to gain further insight into the role of surface functionalities in the molecular-level structuration of water (surface kosmotropicity)--within and atop subnanometric organosilane adlayers that were shown in previous experimental work to display varied antifouling behavior. Our simulations support the hypothesized intimate link between surface hydration and antifouling, in particular the importance of both internal and interfacial hydrophilicity and kosmotropicity. The antifouling mechanism is also discussed in terms of surface dehydration energy and water dynamicity (lability and mobility), notably the crucial requirement for clustered water molecules to remain tightly bound for extensive periods of time--i.e. exhibit slow exchange dynamics. A substrate effect on surface hydration, which would also participate in endowing antifouling adlayers with hydrogel-like characteristics, is also proposed. In contrast, the role of adlayer flexibility, if any, is assigned a secondary role in these ultrathin structures made of short building blocks. The conclusions from this work are well in line with those previously drawn in the literature. Copyright © 2014 Elsevier Inc. All rights reserved.

Bond lifetime and diffusion coefficient in colloids with short-range interactions.

PubMed

Ndong Mintsa, E; Germain, Ph; Amokrane, S

2015-03-01

We use molecular dynamics simulations to study the influence of short-range structures in the interaction potential between hard-sphere-like colloidal particles. Starting from model potentials and effective potentials in binary mixtures computed from the Ornstein-Zernike equations, we investigate the influence of the range and strength of a possible tail beyond the usual core repulsion or the presence of repulsive barriers. The diffusion coefficient and mean "bond" lifetimes are used as indicators of the effect of this structure on the dynamics. The existence of correlations between the variations of these quantities with the physical parameters is discussed to assess the interpretation of dynamics slowing down in terms of long-lived bonds. We also discuss the question of a universal behaviour determined by the second virial coefficient B ((2)) and the interplay of attraction and repulsion. While the diffusion coefficient follows the B ((2)) law for purely attractive tails, this is no longer true in the presence of repulsive barriers. Furthermore, the bond lifetime shows a dependence on the physical parameters that differs from that of the diffusion coefficient. This raises the question of the precise role of bonds on the dynamics slowing down in colloidal gels.

A magnetic fluid seal for rotary blood pumps: effects of seal structure on long-term performance in liquid.

PubMed

Mitamura, Yoshinori; Takahashi, Sayaka; Amari, Shuichi; Okamoto, Eiji; Murabayashi, Shun; Nishimura, Ikuya

2011-03-01

A magnetic fluid (MF) seal enables mechanical contact-free rotation of the shaft and hence has excellent durability. The performance of an MF seal, however, has been reported to decrease in liquids. We developed an MF seal that has a "shield" mechanism, and a new MF with a higher magnetization of 47.9 kA/m. The sealing performance of the MF seal installed in a rotary blood pump was studied. Three types of MF seals were used. Seal A was a conventional seal without a shield. Seal B had the same structure as that of Seal A, but the seal was installed at 1 mm below liquid level. Seal C was a seal with a shield and the MF was set at 1 mm below liquid level. Seal A failed after 6 and 11 days. Seal B showed better results (20 and 73 days). Seal C showed long-term durability (217 and 275 days). The reason for different results in different seal structures was considered to be different flow conditions near the magnetic fluid. Fluid dynamics near the MF in the pump were analyzed using computational fluid dynamics (CFD) software. We have developed an MF seal with a shield that works in liquid for >275 days. The MF seal is promising as a shaft seal for rotary blood pumps.

Federal funding for syringe exchange in the US: Explaining a long-term policy failure.

PubMed

Showalter, David

2018-05-01

The United States prohibited federal funding for syringe exchange programs for people who inject drugs nearly continuously from 1988 to 2015, despite growing scientific evidence, diminishing AIDS-related controversy, and tens of thousands of deaths from injection-related AIDS. This study investigates the political and institutional bases of this long-term failure to support lifesaving public policy. This study draws on national, regional, and local media coverage, archival sources, and semi-structured, in-depth interviews with 6 long-time syringe exchange researchers and activists from California. I use case-oriented process tracing methods to explain the persistence and reform of the federal funding ban. Though previous studies focus on the symbolic clash between conservative morality and empirical science, I find that changing demographic and regional inequalities in the effects of the AIDS epidemic and dynamics produced by the federal structure of US government were more important factors in the creation and persistence of the funding ban. The persistence and eventual repeal of the ban on federal funding for syringe exchange was a product of the changing demographic, geographic, and political effects of the AIDS epidemic within the federal structure of US government, rather than a consequence of intractable morality politics. These contextual dynamics continue to shape AIDS and public health policy at all levels of government. Copyright © 2018. Published by Elsevier B.V.

Solution-state structure and affinities of cyclodextrin: Fentanyl complexes by nuclear magnetic resonance spectroscopy and molecular dynamics simulation

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

Mayer, Brian P.; Kennedy, Daniel J.; Lau, Edmond Y.

Cyclodextrins (CDs) are investigated for their ability to form inclusion complexes with the analgesic fentanyl and three similar molecules: acetylfentanyl, thiofentanyl, and acetylthiofentanyl. Stoichiometry, binding strength, and complex structure are revealed through nuclear magnetic resonance (NMR) techniques and discussed in terms of molecular dynamics (MD) simulations. It was found that β-cyclodextrin is generally capable of forming the strongest complexes with the fentanyl panel. Two-dimensional NMR data and computational chemical calculations are used to derive solution-state structures of the complexes. Binding of the fentanyls to the CDs occurs at the amide phenyl ring, leaving the majority of the molecule solvated bymore » water, an observation common to all four fentanyls. This finding suggests a universal binding behavior, as the vast majority of previously synthesized fentanyl analogues contain this structural moiety. Furthermore, this baseline study serves as the most complete work on CD:fentanyl complexes to date and provides the insights into strategies for producing future generations of designer cyclodextrins capable of stronger and more selective complexation of fentanyl and its analogues.« less

Solution-state structure and affinities of cyclodextrin: Fentanyl complexes by nuclear magnetic resonance spectroscopy and molecular dynamics simulation

DOE PAGES

Mayer, Brian P.; Kennedy, Daniel J.; Lau, Edmond Y.; ...

2016-02-04

Cyclodextrins (CDs) are investigated for their ability to form inclusion complexes with the analgesic fentanyl and three similar molecules: acetylfentanyl, thiofentanyl, and acetylthiofentanyl. Stoichiometry, binding strength, and complex structure are revealed through nuclear magnetic resonance (NMR) techniques and discussed in terms of molecular dynamics (MD) simulations. It was found that β-cyclodextrin is generally capable of forming the strongest complexes with the fentanyl panel. Two-dimensional NMR data and computational chemical calculations are used to derive solution-state structures of the complexes. Binding of the fentanyls to the CDs occurs at the amide phenyl ring, leaving the majority of the molecule solvated bymore » water, an observation common to all four fentanyls. This finding suggests a universal binding behavior, as the vast majority of previously synthesized fentanyl analogues contain this structural moiety. Furthermore, this baseline study serves as the most complete work on CD:fentanyl complexes to date and provides the insights into strategies for producing future generations of designer cyclodextrins capable of stronger and more selective complexation of fentanyl and its analogues.« less

Protein simulation using coarse-grained two-bead multipole force field with polarizable water models.

PubMed

Li, Min; Zhang, John Z H

2017-02-14

A recently developed two-bead multipole force field (TMFF) is employed in coarse-grained (CG) molecular dynamics (MD) simulation of proteins in combination with polarizable CG water models, the Martini polarizable water model, and modified big multipole water model. Significant improvement in simulated structures and dynamics of proteins is observed in terms of both the root-mean-square deviations (RMSDs) of the structures and residue root-mean-square fluctuations (RMSFs) from the native ones in the present simulation compared with the simulation result with Martini's non-polarizable water model. Our result shows that TMFF simulation using CG water models gives much stable secondary structures of proteins without the need for adding extra interaction potentials to constrain the secondary structures. Our result also shows that by increasing the MD time step from 2 fs to 6 fs, the RMSD and RMSF results are still in excellent agreement with those from all-atom simulations. The current study demonstrated clearly that the application of TMFF together with a polarizable CG water model significantly improves the accuracy and efficiency for CG simulation of proteins.

Protein simulation using coarse-grained two-bead multipole force field with polarizable water models

NASA Astrophysics Data System (ADS)

Li, Min; Zhang, John Z. H.

2017-02-01

A recently developed two-bead multipole force field (TMFF) is employed in coarse-grained (CG) molecular dynamics (MD) simulation of proteins in combination with polarizable CG water models, the Martini polarizable water model, and modified big multipole water model. Significant improvement in simulated structures and dynamics of proteins is observed in terms of both the root-mean-square deviations (RMSDs) of the structures and residue root-mean-square fluctuations (RMSFs) from the native ones in the present simulation compared with the simulation result with Martini's non-polarizable water model. Our result shows that TMFF simulation using CG water models gives much stable secondary structures of proteins without the need for adding extra interaction potentials to constrain the secondary structures. Our result also shows that by increasing the MD time step from 2 fs to 6 fs, the RMSD and RMSF results are still in excellent agreement with those from all-atom simulations. The current study demonstrated clearly that the application of TMFF together with a polarizable CG water model significantly improves the accuracy and efficiency for CG simulation of proteins.

The function of neurocognitive networks. Comment on “Understanding brain networks and brain organization” by Pessoa

NASA Astrophysics Data System (ADS)

Bressler, Steven L.

2014-09-01

Pessoa [5] has performed a valuable service by reviewing the extant literature on brain networks and making a number of interesting proposals about their cognitive function. The term function is at the core of understanding the brain networks of cognition, or neurocognitive networks (NCNs) [1]. The great Russian neuropsychologist, Luria [4], defined brain function as the common task executed by a distributed brain network of complex dynamic structures united by the demands of cognition. Casting Luria in a modern light, we can say that function emerges from the interactions of brain regions in NCNs as they dynamically self-organize according to cognitive demands. Pessoa rightly details the mapping between brain function and structure, emphasizing both its pluripotency (one structure having multiple functions) and degeneracy (many structures having the same function). However, he fails to consider the potential importance of a one-to-one mapping between NCNs and function. If NCNs are uniquely composed of specific collections of brain areas, then each NCN has a unique function determined by that composition.

Hydrostatic pressure effects on the structural and electronicproperties of carbon nanotubes

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

Capaz,Rodrigo B.; Spataru, Catalin D.; Tangney, Paul

2004-03-15

We study the structural and electronic properties ofisolated single-wall carbon nanotubes (SWNTs) under hydrostatic pressureusing a combination of theoretical techniques: continuum elasticitymodels, classical molecular dynamics simulations, tight-bindingelectronic structure methods, and first-principles total energycalculations within the density-functional and pseudopotentialframeworks. For pressures below a certain critica pressure Pc, the SWNTs'structure remains cylindrical and the Kohn-Sham energy gaps ofsemiconducting SWNTs have either positive or negative pressurecoefficients depending on the value of (n,m) with a distinct "family" (ofthe same n-m) behavior. The diameter and chirality dependence of thepressure coefficients can be described by a simple analytical expression.At Pc, molecular-dynamics simulations predict that isolated SWNTsmore » undergoa pressure-induced symmetry-breaking transformation from a cylindricalshape to a collapsed geometry. This transition is described by a simpleelastic model as arising from the competition between the bond-bendingand PV terms in the enthalpy. The good agreement between calculated andexperimental values of Pc provides a strong support to the "collapse"interpretation of the experimental transitions in bundles.« less

Computational structures technology and UVA Center for CST

NASA Technical Reports Server (NTRS)

Noor, Ahmed K.

1992-01-01

Rapid advances in computer hardware have had a profound effect on various engineering and mechanics disciplines, including the materials, structures, and dynamics disciplines. A new technology, computational structures technology (CST), has recently emerged as an insightful blend between material modeling, structural and dynamic analysis and synthesis on the one hand, and other disciplines such as computer science, numerical analysis, and approximation theory, on the other hand. CST is an outgrowth of finite element methods developed over the last three decades. The focus of this presentation is on some aspects of CST which can impact future airframes and propulsion systems, as well as on the newly established University of Virginia (UVA) Center for CST. The background and goals for CST are described along with the motivations for developing CST, and a brief discussion is made on computational material modeling. We look at the future in terms of technical needs, computing environment, and research directions. The newly established UVA Center for CST is described. One of the research projects of the Center is described, and a brief summary of the presentation is given.

Solvent effect on the folding dynamics and structure of E6-associated protein characterized from ab initio protein folding simulations

NASA Astrophysics Data System (ADS)

Xu, Zhijun; Lazim, Raudah; Sun, Tiedong; Mei, Ye; Zhang, Dawei

2012-04-01

Solvent effect on protein conformation and folding mechanism of E6-associated protein (E6ap) peptide are investigated using a recently developed charge update scheme termed as adaptive hydrogen bond-specific charge (AHBC). On the basis of the close agreement between the calculated helix contents from AHBC simulations and experimental results, we observed based on the presented simulations that the two ends of the peptide may simultaneously take part in the formation of the helical structure at the early stage of folding and finally merge to form a helix with lowest backbone RMSD of about 0.9 Å in 40% 2,2,2-trifluoroethanol solution. However, in pure water, the folding may start at the center of the peptide sequence instead of at the two opposite ends. The analysis of the free energy landscape indicates that the solvent may determine the folding clusters of E6ap, which subsequently leads to the different final folded structure. The current study demonstrates new insight to the role of solvent in the determination of protein structure and folding dynamics.

Ising model with conserved magnetization on the human connectome: Implications on the relation structure-function in wakefulness and anesthesia

NASA Astrophysics Data System (ADS)

Stramaglia, S.; Pellicoro, M.; Angelini, L.; Amico, E.; Aerts, H.; Cortés, J. M.; Laureys, S.; Marinazzo, D.

2017-04-01

Dynamical models implemented on the large scale architecture of the human brain may shed light on how a function arises from the underlying structure. This is the case notably for simple abstract models, such as the Ising model. We compare the spin correlations of the Ising model and the empirical functional brain correlations, both at the single link level and at the modular level, and show that their match increases at the modular level in anesthesia, in line with recent results and theories. Moreover, we show that at the peak of the specific heat (the critical state), the spin correlations are minimally shaped by the underlying structural network, explaining how the best match between the structure and function is obtained at the onset of criticality, as previously observed. These findings confirm that brain dynamics under anesthesia shows a departure from criticality and could open the way to novel perspectives when the conserved magnetization is interpreted in terms of a homeostatic principle imposed to neural activity.

Simulating market dynamics: interactions between consumer psychology and social networks.

PubMed

Janssen, Marco A; Jager, Wander

2003-01-01

Markets can show different types of dynamics, from quiet markets dominated by one or a few products, to markets with continual penetration of new and reintroduced products. In a previous article we explored the dynamics of markets from a psychological perspective using a multi-agent simulation model. The main results indicated that the behavioral rules dominating the artificial consumer's decision making determine the resulting market dynamics, such as fashions, lock-in, and unstable renewal. Results also show the importance of psychological variables like social networks, preferences, and the need for identity to explain the dynamics of markets. In this article we extend this work in two directions. First, we will focus on a more systematic investigation of the effects of different network structures. The previous article was based on Watts and Strogatz's approach, which describes the small-world and clustering characteristics in networks. More recent research demonstrated that many large networks display a scale-free power-law distribution for node connectivity. In terms of market dynamics this may imply that a small proportion of consumers may have an exceptional influence on the consumptive behavior of others (hubs, or early adapters). We show that market dynamics is a self-organized property depending on the interaction between the agents' decision-making process (heuristics), the product characteristics (degree of satisfaction of unit of consumption, visibility), and the structure of interactions between agents (size of network and hubs in a social network).

A generative spike train model with time-structured higher order correlations.

PubMed

Trousdale, James; Hu, Yu; Shea-Brown, Eric; Josić, Krešimir

2013-01-01

Emerging technologies are revealing the spiking activity in ever larger neural ensembles. Frequently, this spiking is far from independent, with correlations in the spike times of different cells. Understanding how such correlations impact the dynamics and function of neural ensembles remains an important open problem. Here we describe a new, generative model for correlated spike trains that can exhibit many of the features observed in data. Extending prior work in mathematical finance, this generalized thinning and shift (GTaS) model creates marginally Poisson spike trains with diverse temporal correlation structures. We give several examples which highlight the model's flexibility and utility. For instance, we use it to examine how a neural network responds to highly structured patterns of inputs. We then show that the GTaS model is analytically tractable, and derive cumulant densities of all orders in terms of model parameters. The GTaS framework can therefore be an important tool in the experimental and theoretical exploration of neural dynamics.

Langevin dynamics for ramified structures

NASA Astrophysics Data System (ADS)

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

2017-06-01

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

The CLAIR model: Extension of Brodmann areas based on brain oscillations and connectivity.

PubMed

Başar, Erol; Düzgün, Aysel

2016-05-01

Since the beginning of the last century, the localization of brain function has been represented by Brodmann areas, maps of the anatomic organization of the brain. They are used to broadly represent cortical structures with their given sensory-cognitive functions. In recent decades, the analysis of brain oscillations has become important in the correlation of brain functions. Moreover, spectral connectivity can provide further information on the dynamic connectivity between various structures. In addition, brain responses are dynamic in nature and structural localization is almost impossible, according to Luria (1966). Therefore, brain functions are very difficult to localize; hence, a combined analysis of oscillation and event-related coherences is required. In this study, a model termed as "CLAIR" is described to enrich and possibly replace the concept of the Brodmann areas. A CLAIR model with optimum function may take several years to develop, but this study sets out to lay its foundation. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Reversible and Irreversible Behavior of Glass-forming Materials from the Standpoint of Hierarchical Dynamical Facilitation

NASA Astrophysics Data System (ADS)

Keys, Aaron

2013-03-01

Using molecular simulation and coarse-grained lattice models, we study the dynamics of glass-forming liquids above and below the glass transition temperature. In the supercooled regime, we study the structure, statistics, and dynamics of excitations responsible for structural relaxation for several atomistic models of glass-formers. Excitations (or soft spots) are detected in terms of persistent particle displacements. At supercooled conditions, we find that excitations are associated with correlated particle motions that are sparse and localized, and the statistics and dynamics of these excitations are facilitated and hierarchical. Excitations at one point in space facilitate the birth and death of excitations at neighboring locations, and space-time excitation structures are microcosms of heterogeneous dynamics at larger scales. Excitation-energy scales grow logarithmically with the characteristic size of the excitation, giving structural-relaxation times that can be predicted quantitatively from dynamics at short time scales. We demonstrate that these same physical principles govern the dynamics of glass-forming systems driven out-of-equilibrium by time-dependent protocols. For a system cooled and re-heated through the glass transition, non-equilibrium response functions, such as heat capacities, are notably asymmetric in time, and the response to melting a glass depends markedly on the cooling protocol by which the glass was formed. We introduce a quantitative description of this behavior based on the East model, with parameters determined from reversible transport data, that agrees well with irreversible differential scanning calorimetry. We find that the observed hysteresis and asymmetric response is a signature of an underlying dynamical transition between equilibrium melts with no trivial spatial correlations and non-equilibrium glasses with correlation lengths that are both large and dependent upon the rate at which the glass is prepared. The correlation length corresponds to the size of amorphous domains bounded by excitations that remain frozen on the observation time scale, thus forming stripes when viewed in space and time. We elucidate properties of the striped phase and show that glasses of this type, traditionally prepared through cooling, can be considered a finite-size realization of the inactive phase formed by the s-ensemble in the space-time thermodynamic limit.

Nonlinear bending-torsional vibration and stability of rotating, pretwisted, preconed blades including Coriolis effects

NASA Technical Reports Server (NTRS)

Subrahmanyam, K. B.; Kaza, K. R. V.; Brown, G. V.; Lawrence, C.

1986-01-01

The coupled bending-bending-torsional equations of dynamic motion of rotating, linearly pretwisted blades are derived including large precone, second degree geometric nonlinearities and Coriolis effects. The equations are solved by the Galerkin method and a linear perturbation technique. Accuracy of the present method is verified by comparisons of predicted frequencies and steady state deflections with those from MSC/NASTRAN and from experiments. Parametric results are generated to establish where inclusion of only the second degree geometric nonlinearities is adequate. The nonlinear terms causing torsional divergence in thin blades are identified. The effects of Coriolis terms and several other structurally nonlinear terms are studied, and their relative importance is examined.

Nonlinear vibration and stability of rotating, pretwisted, preconed blades including Coriolis effects

NASA Technical Reports Server (NTRS)

Subrahmanyam, K. B.; Kaza, K. R. V.; Brown, G. V.; Lawrence, C.

1987-01-01

The coupled bending-bending-torsional equations of dynamic motion of rotating, linearly pretwisted blades are derived including large precone, second degree geometric nonlinearities and Coriolis effects. The equations are solved by the Galerkin method and a linear perturbation technique. Accuracy of the present method is verified by conparisons of predicted frequencies and steady state deflections with those from MSC/NASTRAN and from experiments. Parametric results are generated to establish where inclusion of only the second degree geometric nonlinearities is adequate. The nonlinear terms causing torsional divergence in thin blades are identified. The effects of Coriolis terms and several other structurally nonlinear terms are studied, and their relative importance is examined.

Molecular Dynamics Simulations of Carbon Nanotubes in Water

NASA Technical Reports Server (NTRS)

Walther, J. H.; Jaffe, R.; Halicioglu, T.; Koumoutsakos, P.

2000-01-01

We study the hydrophobic/hydrophilic behavior of carbon nanotubes using molecular dynamics simulations. The energetics of the carbon-water interface are mainly dispersive but in the present study augmented with a carbon quadrupole term acting on the charge sites of the water. The simulations indicate that this contribution is negligible in terms of modifying the structural properties of water at the interface. Simulations of two carbon nanotubes in water display a wetting and drying of the interface between the nanotubes depending on their initial spacing. Thus, initial tube spacings of 7 and 8 A resulted in a drying of the interface whereas spacing of > 9 A remain wet during the course of the simulation. Finally, we present a novel particle-particle-particle-mesh algorithm for long range potentials which allows for general (curvilinear) meshes and "black-box" fast solvers by adopting an influence matrix technique.

Adiabatic Coupling Constant of Nitrobenzene- n-Alkane Critical Mixtures. Evidence from Ultrasonic Spectra and Thermodynamic Data

NASA Astrophysics Data System (ADS)

Mirzaev, Sirojiddin Z.; Kaatze, Udo

2016-09-01

Ultrasonic spectra of mixtures of nitrobenzene with n-alkanes, from n-hexane to n-nonane, are analyzed. They feature up to two Debye-type relaxation terms with discrete relaxation times and, near the critical point, an additional relaxation term due to the fluctuations in the local concentration. The latter can be well represented by the dynamic scaling theory. Its amplitude parameter reveals the adiabatic coupling constant of the mixtures of critical composition. The dependence of this thermodynamic parameter upon the length of the n-alkanes corresponds to that of the slope in the pressure dependence of the critical temperature and is thus taken another confirmation of the dynamic scaling model. The change in the variation of the coupling constant and of several other mixture parameters with alkane length probably reflects a structural change in the nitrobenzene- n-alkane mixtures when the number of carbon atoms per alkane exceeds eight.

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction.

PubMed

Zhang, Ping; Wu, Wei-Min; Van Nostrand, Joy D; Deng, Ye; He, Zhili; Gihring, Thomas; Zhang, Gengxin; Schadt, Chris W; Watson, David; Jardine, Phil; Criddle, Craig S; Brooks, Scott; Marsh, Terence L; Tiedje, James M; Arkin, Adam P; Zhou, Jizhong

2015-06-15

A pilot-scale field experiment demonstrated that a one-time amendment of emulsified vegetable oil (EVO) reduced groundwater U(VI) concentrations for 1 year in a fast-flowing aquifer. However, little is known about how EVO amendment stimulates the functional gene composition, structure, and dynamics of groundwater microbial communities toward prolonged U(VI) reduction. In this study, we hypothesized that EVO amendment would shift the functional gene composition and structure of groundwater microbial communities and stimulate key functional genes/groups involved in EVO biodegradation and reduction of electron acceptors in the aquifer. To test these hypotheses, groundwater microbial communities after EVO amendment were analyzed using a comprehensive functional gene microarray. Our results showed that EVO amendment stimulated sequential shifts in the functional composition and structure of groundwater microbial communities. Particularly, the relative abundance of key functional genes/groups involved in EVO biodegradation and the reduction of NO3 (-), Mn(IV), Fe(III), U(VI), and SO4 (2-) significantly increased, especially during the active U(VI) reduction period. The relative abundance for some of these key functional genes/groups remained elevated over 9 months. Montel tests suggested that the dynamics in the abundance, composition, and structure of these key functional genes/groups were significantly correlated with groundwater concentrations of acetate, NO3 (-), Mn(II), Fe(II), U(VI), and SO4 (2-). Our results suggest that EVO amendment stimulated dynamic succession of key functional microbial communities. This study improves our understanding of the composition, structure, and function changes needed for groundwater microbial communities to sustain a long-term U(VI) reduction. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction

PubMed Central

Zhang, Ping; Wu, Wei-Min; Van Nostrand, Joy D.; Deng, Ye; He, Zhili; Gihring, Thomas; Zhang, Gengxin; Schadt, Chris W.; Watson, David; Jardine, Phil; Criddle, Craig S.; Brooks, Scott; Marsh, Terence L.; Tiedje, James M.; Arkin, Adam P.

2015-01-01

A pilot-scale field experiment demonstrated that a one-time amendment of emulsified vegetable oil (EVO) reduced groundwater U(VI) concentrations for 1 year in a fast-flowing aquifer. However, little is known about how EVO amendment stimulates the functional gene composition, structure, and dynamics of groundwater microbial communities toward prolonged U(VI) reduction. In this study, we hypothesized that EVO amendment would shift the functional gene composition and structure of groundwater microbial communities and stimulate key functional genes/groups involved in EVO biodegradation and reduction of electron acceptors in the aquifer. To test these hypotheses, groundwater microbial communities after EVO amendment were analyzed using a comprehensive functional gene microarray. Our results showed that EVO amendment stimulated sequential shifts in the functional composition and structure of groundwater microbial communities. Particularly, the relative abundance of key functional genes/groups involved in EVO biodegradation and the reduction of NO3−, Mn(IV), Fe(III), U(VI), and SO42− significantly increased, especially during the active U(VI) reduction period. The relative abundance for some of these key functional genes/groups remained elevated over 9 months. Montel tests suggested that the dynamics in the abundance, composition, and structure of these key functional genes/groups were significantly correlated with groundwater concentrations of acetate, NO3−, Mn(II), Fe(II), U(VI), and SO42−. Our results suggest that EVO amendment stimulated dynamic succession of key functional microbial communities. This study improves our understanding of the composition, structure, and function changes needed for groundwater microbial communities to sustain a long-term U(VI) reduction. PMID:25862231

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction

DOE PAGES

Zhang, Ping; Wu, Wei-Min; Van Nostrand, Joy D.; ...

2015-04-10

A pilot-scale field experiment demonstrated that a one-time amendment of emulsified vegetable oil (EVO) reduced groundwater U(VI) concentrations for 1 year in a fast-flowing aquifer. However, little is known about how EVO amendment stimulates the functional gene composition, structure, and dynamics of groundwater microbial communities toward prolonged U(VI) reduction. In this paper, we hypothesized that EVO amendment would shift the functional gene composition and structure of groundwater microbial communities and stimulate key functional genes/groups involved in EVO biodegradation and reduction of electron acceptors in the aquifer. To test these hypotheses, groundwater microbial communities after EVO amendment were analyzed using amore » comprehensive functional gene microarray. Our results showed that EVO amendment stimulated sequential shifts in the functional composition and structure of groundwater microbial communities. Particularly, the relative abundance of key functional genes/groups involved in EVO biodegradation and the reduction of NO 3 -, Mn(IV), Fe(III), U(VI), and SO 4 2- significantly increased, especially during the active U(VI) reduction period. The relative abundance for some of these key functional genes/groups remained elevated over 9 months. Montel tests suggested that the dynamics in the abundance, composition, and structure of these key functional genes/groups were significantly correlated with groundwater concentrations of acetate, NO 3 -, Mn(II), Fe(II), U(VI), and SO 4 2-. Our results suggest that EVO amendment stimulated dynamic succession of key functional microbial communities. Finally, this study improves our understanding of the composition, structure, and function changes needed for groundwater microbial communities to sustain a long-term U(VI) reduction.« less

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction

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

Zhang, Ping; Wu, Wei-Min; Van Nostrand, Joy D.

A pilot-scale field experiment demonstrated that a one-time amendment of emulsified vegetable oil (EVO) reduced groundwater U(VI) concentrations for 1 year in a fast-flowing aquifer. However, little is known about how EVO amendment stimulates the functional gene composition, structure, and dynamics of groundwater microbial communities toward prolonged U(VI) reduction. In this paper, we hypothesized that EVO amendment would shift the functional gene composition and structure of groundwater microbial communities and stimulate key functional genes/groups involved in EVO biodegradation and reduction of electron acceptors in the aquifer. To test these hypotheses, groundwater microbial communities after EVO amendment were analyzed using amore » comprehensive functional gene microarray. Our results showed that EVO amendment stimulated sequential shifts in the functional composition and structure of groundwater microbial communities. Particularly, the relative abundance of key functional genes/groups involved in EVO biodegradation and the reduction of NO 3 -, Mn(IV), Fe(III), U(VI), and SO 4 2- significantly increased, especially during the active U(VI) reduction period. The relative abundance for some of these key functional genes/groups remained elevated over 9 months. Montel tests suggested that the dynamics in the abundance, composition, and structure of these key functional genes/groups were significantly correlated with groundwater concentrations of acetate, NO 3 -, Mn(II), Fe(II), U(VI), and SO 4 2-. Our results suggest that EVO amendment stimulated dynamic succession of key functional microbial communities. Finally, this study improves our understanding of the composition, structure, and function changes needed for groundwater microbial communities to sustain a long-term U(VI) reduction.« less

Agricultural resources investigations in northern Italy and southern France (Agreste Project)

NASA Technical Reports Server (NTRS)

1976-01-01

The author has identified the following significant results. The vegetation structure of rice was investigated and interpreted in dynamic terms as a significant factor governing the distribution of solar energy thoughout the canopy and therefore conditions the final yield. Radiometric characteristics of rice culture were described for various stages of development in relation to the vegetation structure in an attempt to establish correlations between data of total biomass and of grain yield. Qualitative classification results were encouraging although the discrimination achieved was far from complete.

Fluid-membrane tethers: minimal surfaces and elastic boundary layers.

PubMed

Powers, Thomas R; Huber, Greg; Goldstein, Raymond E

2002-04-01

Thin cylindrical tethers are common lipid bilayer membrane structures, arising in situations ranging from micromanipulation experiments on artificial vesicles to the dynamic structure of the Golgi apparatus. We study the shape and formation of a tether in terms of the classical soap-film problem, which is applied to the case of a membrane disk under tension subject to a point force. A tether forms from the elastic boundary layer near the point of application of the force, for sufficiently large displacement. Analytic results for various aspects of the membrane shape are given.

Hydrological conditions in the straits of the Ryukyu archipelago and adjacent basins

NASA Astrophysics Data System (ADS)

Moroz, V. V.; Bogdanov, K. T.

2007-10-01

The structure and dynamics of the water are studied on the basis of hydrological and meteorological long-term data combined with the materials of field observations over a period longer than half a century in the region of the Ryukyu archipelago. New data about the hydrological characteristics of the waters were obtained. Characteristic differences of waters of various modifications in the main straits between the islands are demonstrated. The dependence of the water structure formation in the straits on the seasonal variability of the water exchange through the straits is distinguished.

Distance matrix-based approach to protein structure prediction.

PubMed

Kloczkowski, Andrzej; Jernigan, Robert L; Wu, Zhijun; Song, Guang; Yang, Lei; Kolinski, Andrzej; Pokarowski, Piotr

2009-03-01

Much structural information is encoded in the internal distances; a distance matrix-based approach can be used to predict protein structure and dynamics, and for structural refinement. Our approach is based on the square distance matrix D = [r(ij)(2)] containing all square distances between residues in proteins. This distance matrix contains more information than the contact matrix C, that has elements of either 0 or 1 depending on whether the distance r (ij) is greater or less than a cutoff value r (cutoff). We have performed spectral decomposition of the distance matrices D = sigma lambda(k)V(k)V(kT), in terms of eigenvalues lambda kappa and the corresponding eigenvectors v kappa and found that it contains at most five nonzero terms. A dominant eigenvector is proportional to r (2)--the square distance of points from the center of mass, with the next three being the principal components of the system of points. By predicting r (2) from the sequence we can approximate a distance matrix of a protein with an expected RMSD value of about 7.3 A, and by combining it with the prediction of the first principal component we can improve this approximation to 4.0 A. We can also explain the role of hydrophobic interactions for the protein structure, because r is highly correlated with the hydrophobic profile of the sequence. Moreover, r is highly correlated with several sequence profiles which are useful in protein structure prediction, such as contact number, the residue-wise contact order (RWCO) or mean square fluctuations (i.e. crystallographic temperature factors). We have also shown that the next three components are related to spatial directionality of the secondary structure elements, and they may be also predicted from the sequence, improving overall structure prediction. We have also shown that the large number of available HIV-1 protease structures provides a remarkable sampling of conformations, which can be viewed as direct structural information about the dynamics. After structure matching, we apply principal component analysis (PCA) to obtain the important apparent motions for both bound and unbound structures. There are significant similarities between the first few key motions and the first few low-frequency normal modes calculated from a static representative structure with an elastic network model (ENM) that is based on the contact matrix C (related to D), strongly suggesting that the variations among the observed structures and the corresponding conformational changes are facilitated by the low-frequency, global motions intrinsic to the structure. Similarities are also found when the approach is applied to an NMR ensemble, as well as to atomic molecular dynamics (MD) trajectories. Thus, a sufficiently large number of experimental structures can directly provide important information about protein dynamics, but ENM can also provide a similar sampling of conformations. Finally, we use distance constraints from databases of known protein structures for structure refinement. We use the distributions of distances of various types in known protein structures to obtain the most probable ranges or the mean-force potentials for the distances. We then impose these constraints on structures to be refined or include the mean-force potentials directly in the energy minimization so that more plausible structural models can be built. This approach has been successfully used by us in 2006 in the CASPR structure refinement (http://predictioncenter.org/caspR).

Postsynaptic density 95 (PSD-95) serine 561 phosphorylation regulates a conformational switch and bidirectional dendritic spine structural plasticity.

PubMed

Wu, Qian; Sun, Miao; Bernard, Laura P; Zhang, Huaye

2017-09-29

Postsynaptic density 95 (PSD-95) is a major synaptic scaffolding protein that plays a key role in bidirectional synaptic plasticity, which is a process important for learning and memory. It is known that PSD-95 shows increased dynamics upon induction of plasticity. However, the underlying structural and functional changes in PSD-95 that mediate its role in plasticity remain unclear. Here we show that phosphorylation of PSD-95 at Ser-561 in its guanylate kinase (GK) domain, which is mediated by the partitioning-defective 1 (Par1) kinases, regulates a conformational switch and is important for bidirectional plasticity. Using a fluorescence resonance energy transfer (FRET) biosensor, we show that a phosphomimetic mutation of Ser-561 promotes an intramolecular interaction between GK and the nearby Src homology 3 (SH3) domain, leading to a closed conformation, whereas a non-phosphorylatable S561A mutation or inhibition of Par1 kinase activity decreases SH3-GK interaction, causing PSD-95 to adopt an open conformation. In addition, S561A mutation facilitates the interaction between PSD-95 and its binding partners. Fluorescence recovery after photobleaching imaging reveals that the S561A mutant shows increased stability, whereas the phosphomimetic S561D mutation increases PSD-95 dynamics at the synapse. Moreover, molecular replacement of endogenous PSD-95 with the S561A mutant blocks dendritic spine structural plasticity during chemical long-term potentiation and long-term depression. Endogenous Ser-561 phosphorylation is induced by synaptic NMDA receptor activation, and the SH3-GK domains exhibit a Ser-561 phosphorylation-dependent switch to a closed conformation during synaptic plasticity. Our results provide novel mechanistic insight into the regulation of PSD-95 in dendritic spine structural plasticity through phosphorylation-mediated regulation of protein dynamics and conformation. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

The polarized Debye sheath effect on Kadomtsev-Petviashvili electrostatic structures in strongly coupled dusty plasma

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

Shahmansouri, M.; Alinejad, H.

2015-04-15

We give a theoretical investigation on the dynamics of nonlinear electrostatic waves in a strongly coupled dusty plasma with strong electrostatic interaction between dust grains in the presence of the polarization force (i.e., the force due to the polarized Debye sheath). Adopting a reductive perturbation method, we derived a three-dimensional Kadomtsev-Petviashvili equation that describes the evolution of weakly nonlinear electrostatic localized waves. The energy integral equation is used to study the existence domains of the localized structures. The analysis provides the localized structure existence region, in terms of the effects of strong interaction between the dust particles and polarization force.

A slewing control experiment for flexible structures

NASA Technical Reports Server (NTRS)

Juang, J.-N.; Horta, L. G.; Robertshaw, H. H.

1985-01-01

A hardware set-up has been developed to study slewing control for flexible structures including a steel beam and a solar panel. The linear optimal terminal control law is used to design active controllers which are implemented in an analog computer. The objective of this experiment is to demonstrate and verify the dynamics and optimal terminal control laws as applied to flexible structures for large angle maneuver. Actuation is provided by an electric motor while sensing is given by strain gages and angle potentiometer. Experimental measurements are compared with analytical predictions in terms of modal parameters of the system stability matrix and sufficient agreement is achieved to validate the theory.

Numerical modeling of interaction in the dynamic system "gas-structure" with harmonic motion of the piston in the variable section pipe

NASA Astrophysics Data System (ADS)

Butymova, L. N.; Modorskii, V. Ya.; Petrov, V. Yu.

2016-10-01

The Helmholtz resonator is an instrument to create low-frequency natural oscillations whose wavelength is substantially larger than the dimensions of the resonator itself. Some modern insulating materials are a set of Helmholtz resonators made in the form of a multilayer composite structure with a layer of cells between the carrier layers. The cells have an outlet hole drilled in the support layer. Improving effectiveness of such structures in terms of noise reduction is an urgent task [1 - 7]. It is found that the resonator with a throat of higher surface roughness damps noise more effectively.