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

PubMed

Moradigaravand, Danesh; Engelstädter, Jan

2014-06-20

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

Spatial dynamics of invasion: the geometry of introduced species.

PubMed

Korniss, Gyorgy; Caraco, Thomas

2005-03-07

Many exotic species combine low probability of establishment at each introduction with rapid population growth once introduction does succeed. To analyse this phenomenon, we note that invaders often cluster spatially when rare, and consequently an introduced exotic's population dynamics should depend on locally structured interactions. Ecological theory for spatially structured invasion relies on deterministic approximations, and determinism does not address the observed uncertainty of the exotic-introduction process. We take a new approach to the population dynamics of invasion and, by extension, to the general question of invasibility in any spatial ecology. We apply the physical theory for nucleation of spatial systems to a lattice-based model of competition between plant species, a resident and an invader, and the analysis reaches conclusions that differ qualitatively from the standard ecological theories. Nucleation theory distinguishes between dynamics of single- and multi-cluster invasion. Low introduction rates and small system size produce single-cluster dynamics, where success or failure of introduction is inherently stochastic. Single-cluster invasion occurs only if the cluster reaches a critical size, typically preceded by a number of failed attempts. For this case, we identify the functional form of the probability distribution of time elapsing until invasion succeeds. Although multi-cluster invasion for sufficiently large systems exhibits spatial averaging and almost-deterministic dynamics of the global densities, an analytical approximation from nucleation theory, known as Avrami's law, describes our simulation results far better than standard ecological approximations.

A general modeling framework for describing spatially structured population dynamics

USGS Publications Warehouse

Sample, Christine; Fryxell, John; Bieri, Joanna; Federico, Paula; Earl, Julia; Wiederholt, Ruscena; Mattsson, Brady; Flockhart, Tyler; Nicol, Sam; Diffendorfer, James E.; Thogmartin, Wayne E.; Erickson, Richard A.; Norris, D. Ryan

2017-01-01

Variation in movement across time and space fundamentally shapes the abundance and distribution of populations. Although a variety of approaches model structured population dynamics, they are limited to specific types of spatially structured populations and lack a unifying framework. Here, we propose a unified network-based framework sufficiently novel in its flexibility to capture a wide variety of spatiotemporal processes including metapopulations and a range of migratory patterns. It can accommodate different kinds of age structures, forms of population growth, dispersal, nomadism and migration, and alternative life-history strategies. Our objective was to link three general elements common to all spatially structured populations (space, time and movement) under a single mathematical framework. To do this, we adopt a network modeling approach. The spatial structure of a population is represented by a weighted and directed network. Each node and each edge has a set of attributes which vary through time. The dynamics of our network-based population is modeled with discrete time steps. Using both theoretical and real-world examples, we show how common elements recur across species with disparate movement strategies and how they can be combined under a unified mathematical framework. We illustrate how metapopulations, various migratory patterns, and nomadism can be represented with this modeling approach. We also apply our network-based framework to four organisms spanning a wide range of life histories, movement patterns, and carrying capacities. General computer code to implement our framework is provided, which can be applied to almost any spatially structured population. This framework contributes to our theoretical understanding of population dynamics and has practical management applications, including understanding the impact of perturbations on population size, distribution, and movement patterns. By working within a common framework, there is less chance that comparative analyses are colored by model details rather than general principles

Spatially structured superinfection and the evolution of disease virulence.

PubMed

Caraco, Thomas; Glavanakov, Stephan; Li, Shengua; Maniatty, William; Szymanski, Boleslaw K

2006-06-01

When pathogen strains differing in virulence compete for hosts, spatial structuring of disease transmission can govern both evolved levels of virulence and patterns in strain coexistence. We develop a spatially detailed model of superinfection, a form of contest competition between pathogen strains; the probability of superinfection depends explicitly on the difference in levels of virulence. We apply methods of adaptive dynamics to address the interplay of spatial dynamics and evolution. The mean-field approximation predicts evolution to criticality; any small increase in virulence capable of dynamical persistence is favored. Both pair approximation and simulation of the detailed model indicate that spatial structure constrains disease virulence. Increased spatial clustering reduces the maximal virulence capable of single-strain persistence and, more importantly, reduces the convergent-stable virulence level under strain competition. The spatially detailed model predicts that increasing the probability of superinfection, for given difference in virulence, increases the likelihood of between-strain coexistence. When strains differing in virulence can coexist ecologically, our results may suggest policies for managing diseases with localized transmission. Comparing equilibrium densities from the pair approximation, we find that introducing a more virulent strain into a host population infected by a less virulent strain can sometimes reduce total host mortality and increase global host density.

Structure and information in spatial segregation

PubMed Central

2017-01-01

Ethnoracial residential segregation is a complex, multiscalar phenomenon with immense moral and economic costs. Modeling the structure and dynamics of segregation is a pressing problem for sociology and urban planning, but existing methods have limitations. In this paper, we develop a suite of methods, grounded in information theory, for studying the spatial structure of segregation. We first advance existing profile and decomposition methods by posing two related regionalization methods, which allow for profile curves with nonconstant spatial scale and decomposition analysis with nonarbitrary areal units. We then formulate a measure of local spatial scale, which may be used for both detailed, within-city analysis and intercity comparisons. These methods highlight detailed insights in the structure and dynamics of urban segregation that would be otherwise easy to miss or difficult to quantify. They are computationally efficient, applicable to a broad range of study questions, and freely available in open source software. PMID:29078323

Structure and information in spatial segregation.

PubMed

Chodrow, Philip S

2017-10-31

Ethnoracial residential segregation is a complex, multiscalar phenomenon with immense moral and economic costs. Modeling the structure and dynamics of segregation is a pressing problem for sociology and urban planning, but existing methods have limitations. In this paper, we develop a suite of methods, grounded in information theory, for studying the spatial structure of segregation. We first advance existing profile and decomposition methods by posing two related regionalization methods, which allow for profile curves with nonconstant spatial scale and decomposition analysis with nonarbitrary areal units. We then formulate a measure of local spatial scale, which may be used for both detailed, within-city analysis and intercity comparisons. These methods highlight detailed insights in the structure and dynamics of urban segregation that would be otherwise easy to miss or difficult to quantify. They are computationally efficient, applicable to a broad range of study questions, and freely available in open source software. Published under the PNAS license.

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

PubMed

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

2012-04-22

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

Spatial and temporal synchrony in reptile population dynamics in variable environments.

PubMed

Greenville, Aaron C; Wardle, Glenda M; Nguyen, Vuong; Dickman, Chris R

2016-10-01

Resources are seldom distributed equally across space, but many species exhibit spatially synchronous population dynamics. Such synchrony suggests the operation of large-scale external drivers, such as rainfall or wildfire, or the influence of oasis sites that provide water, shelter, or other resources. However, testing the generality of these factors is not easy, especially in variable environments. Using a long-term dataset (13-22 years) from a large (8000 km(2)) study region in arid Central Australia, we tested firstly for regional synchrony in annual rainfall and the dynamics of six reptile species across nine widely separated sites. For species that showed synchronous spatial dynamics, we then used multivariate follow a multivariate auto-regressive state-space (MARSS) models to predict that regional rainfall would be positively associated with their populations. For asynchronous species, we used MARSS models to explore four other possible population structures: (1) populations were asynchronous, (2) differed between oasis and non-oasis sites, (3) differed between burnt and unburnt sites, or (4) differed between three sub-regions with different rainfall gradients. Only one species showed evidence of spatial population synchrony and our results provide little evidence that rainfall synchronizes reptile populations. The oasis or the wildfire hypotheses were the best-fitting models for the other five species. Thus, our six study species appear generally to be structured in space into one or two populations across the study region. Our findings suggest that for arid-dwelling reptile populations, spatial and temporal dynamics are structured by abiotic events, but individual responses to covariates at smaller spatial scales are complex and poorly understood.

Spatial structure and nutrients promote invasion of IncP-1 plasmids in bacterial populations

PubMed Central

Fox, Randal E; Zhong, Xue; Krone, Stephen M; Top, Eva M

2008-01-01

In spite of the importance of plasmids in bacterial adaptation, we have a poor understanding of their dynamics. It is not known if or how plasmids persist in and spread through (invade) a bacterial population when there is no selection for plasmid-encoded traits. Moreover, the differences in dynamics between spatially structured and mixed populations are poorly understood. Through a joint experimental/theoretical approach, we tested the hypothesis that self-transmissible IncP-1 plasmids can invade a bacterial population in the absence of selection when initially very rare, but only in spatially structured habitats and when nutrients are regularly replenished. Using protocols that differed in the degree of spatial structure and nutrient levels, the invasiveness of plasmid pB10 in Escherichia coli was monitored during at least 15 days, with an initial fraction of plasmid-bearing (p+) cells as low as 10−7. To further explore the mechanisms underlying plasmid dynamics, we developed a spatially explicit mathematical model. When cells were grown on filters and transferred to fresh medium daily, the p+ fraction increased to 13%, whereas almost complete invasion occurred when the population structure was disturbed daily. The plasmid was unable to invade in liquid. When carbon source levels were lower or not replenished, plasmid invasion was hampered. Simulations of the mathematical model closely matched the experimental results and produced estimates of the effects of alternative experimental parameters. This allowed us to isolate the likely mechanisms most responsible for the observations. In conclusion, spatial structure and nutrient availability can be key determinants in the invasiveness of plasmids. PMID:18528415

Organizational and Spatial Dynamics of Attentional Focusing in Hierarchically Structured Objects

ERIC Educational Resources Information Center

Yeari, Menahem; Goldsmith, Morris

2011-01-01

Is the focusing of visual attention object-based, space-based, both, or neither? Attentional focusing latencies in hierarchically structured compound-letter objects were examined, orthogonally manipulating global size (larger vs. smaller) and organizational complexity (two-level structure vs. three-level structure). In a dynamic focusing task,…

Landscape Pattern Determines Neighborhood Size and Structure within a Lizard Population

PubMed Central

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

2013-01-01

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

Simulating forest management and its effect on landscape pattern

Treesearch

Eric J. Gustafson

2017-01-01

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

GSHR-Tree: a spatial index tree based on dynamic spatial slot and hash table in grid environments

NASA Astrophysics Data System (ADS)

Chen, Zhanlong; Wu, Xin-cai; Wu, Liang

2008-12-01

Computation Grids enable the coordinated sharing of large-scale distributed heterogeneous computing resources that can be used to solve computationally intensive problems in science, engineering, and commerce. Grid spatial applications are made possible by high-speed networks and a new generation of Grid middleware that resides between networks and traditional GIS applications. The integration of the multi-sources and heterogeneous spatial information and the management of the distributed spatial resources and the sharing and cooperative of the spatial data and Grid services are the key problems to resolve in the development of the Grid GIS. The performance of the spatial index mechanism is the key technology of the Grid GIS and spatial database affects the holistic performance of the GIS in Grid Environments. In order to improve the efficiency of parallel processing of a spatial mass data under the distributed parallel computing grid environment, this paper presents a new grid slot hash parallel spatial index GSHR-Tree structure established in the parallel spatial indexing mechanism. Based on the hash table and dynamic spatial slot, this paper has improved the structure of the classical parallel R tree index. The GSHR-Tree index makes full use of the good qualities of R-Tree and hash data structure. This paper has constructed a new parallel spatial index that can meet the needs of parallel grid computing about the magnanimous spatial data in the distributed network. This arithmetic splits space in to multi-slots by multiplying and reverting and maps these slots to sites in distributed and parallel system. Each sites constructs the spatial objects in its spatial slot into an R tree. On the basis of this tree structure, the index data was distributed among multiple nodes in the grid networks by using large node R-tree method. The unbalance during process can be quickly adjusted by means of a dynamical adjusting algorithm. This tree structure has considered the distributed operation, reduplication operation transfer operation of spatial index in the grid environment. The design of GSHR-Tree has ensured the performance of the load balance in the parallel computation. This tree structure is fit for the parallel process of the spatial information in the distributed network environments. Instead of spatial object's recursive comparison where original R tree has been used, the algorithm builds the spatial index by applying binary code operation in which computer runs more efficiently, and extended dynamic hash code for bit comparison. In GSHR-Tree, a new server is assigned to the network whenever a split of a full node is required. We describe a more flexible allocation protocol which copes with a temporary shortage of storage resources. It uses a distributed balanced binary spatial tree that scales with insertions to potentially any number of storage servers through splits of the overloaded ones. The application manipulates the GSHR-Tree structure from a node in the grid environment. The node addresses the tree through its image that the splits can make outdated. This may generate addressing errors, solved by the forwarding among the servers. In this paper, a spatial index data distribution algorithm that limits the number of servers has been proposed. We improve the storage utilization at the cost of additional messages. The structure of GSHR-Tree is believed that the scheme of this grid spatial index should fit the needs of new applications using endlessly larger sets of spatial data. Our proposal constitutes a flexible storage allocation method for a distributed spatial index. The insertion policy can be tuned dynamically to cope with periods of storage shortage. In such cases storage balancing should be favored for better space utilization, at the price of extra message exchanges between servers. This structure makes a compromise in the updating of the duplicated index and the transformation of the spatial index data. Meeting the needs of the grid computing, GSHRTree has a flexible structure in order to satisfy new needs in the future. The GSHR-Tree provides the R-tree capabilities for large spatial datasets stored over interconnected servers. The analysis, including the experiments, confirmed the efficiency of our design choices. The scheme should fit the needs of new applications of spatial data, using endlessly larger datasets. Using the system response time of the parallel processing of spatial scope query algorithm as the performance evaluation factor, According to the result of the simulated the experiments, GSHR-Tree is performed to prove the reasonable design and the high performance of the indexing structure that the paper presented.

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

Treesearch

Vladimir L. Gavrikov; Valentina P. Vetrova

1991-01-01

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

Effects of spatial structure of population size on the population dynamics of barnacles across their elevational range.

PubMed

Fukaya, Keiichi; Okuda, Takehiro; Nakaoka, Masahiro; Noda, Takashi

2014-11-01

Explanations for why population dynamics vary across the range of a species reflect two contrasting hypotheses: (i) temporal variability of populations is larger in the centre of the range compared to the margins because overcompensatory density dependence destabilizes population dynamics and (ii) population variability is larger near the margins, where populations are more susceptible to environmental fluctuations. In both of these hypotheses, positions within the range are assumed to affect population variability. In contrast, the fact that population variability is often related to mean population size implies that the spatial structure of the population size within the range of a species may also be a useful predictor of the spatial variation in temporal variability of population size over the range of the species. To explore how population temporal variability varies spatially and the underlying processes responsible for the spatial variation, we focused on the intertidal barnacle Chthamalus dalli and examined differences in its population dynamics along the tidal levels it inhabits. Changes in coverage of barnacle populations were monitored for 10.5 years at 25 plots spanning the elevational range of this species. Data were analysed by fitting a population dynamics model to estimate the effects of density-dependent and density-independent processes on population growth. We also examined the temporal mean-variance relationship of population size with parameters estimated from the population dynamics model. We found that the relative variability of populations tended to increase from the centre of the elevational range towards the margins because of an increase in the magnitude of stochastic fluctuations of growth rates. Thus, our results supported hypothesis (2). We also found that spatial variations in temporal population variability were well characterized by Taylor's power law, the relative population variability being inversely related to the mean population size. Results suggest that understanding the population dynamics of a species over its range may be facilitated by taking the spatial structure of population size into account as well as by considering changes in population processes as a function of position within the range of the species. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.

High spatial resolution three-dimensional mapping of vegetation spectral dynamics using computer vision

Treesearch

Jonathan P. Dandois; Erle C. Ellis

2013-01-01

High spatial resolution three-dimensional (3D) measurements of vegetation by remote sensing are advancing ecological research and environmental management. However, substantial economic and logistical costs limit this application, especially for observing phenological dynamics in ecosystem structure and spectral traits. Here we demonstrate a new aerial remote sensing...

Source-sink dynamics sustain central stonerollers (Campostoma anomalum) in a heavily urbanized catchment

Treesearch

Eric R. Waits; Mark J. Bagley; Michael J. Blum; Frank H. McCormick; James M. Lazorchak

2008-01-01

Relating local demographic processes to spatial structure (e.g. habitat heterogeneity) is essential for understanding population and species persistence (Hanski & Gilpin, 1997; Fagan, 2002). Yet few studies have tested general hypotheses about the importance of spatial patterns in determining population dynamics within river­stream networks (Lowe, Likens &...

Light-Activated Gigahertz Ferroelectric Domain Dynamics

NASA Astrophysics Data System (ADS)

Akamatsu, Hirofumi; Yuan, Yakun; Stoica, Vladimir A.; Stone, Greg; Yang, Tiannan; Hong, Zijian; Lei, Shiming; Zhu, Yi; Haislmaier, Ryan C.; Freeland, John W.; Chen, Long-Qing; Wen, Haidan; Gopalan, Venkatraman

2018-03-01

Using time- and spatially resolved hard x-ray diffraction microscopy, the striking structural and electrical dynamics upon optical excitation of a single crystal of BaTiO3 are simultaneously captured on subnanoseconds and nanoscale within individual ferroelectric domains and across walls. A large emergent photoinduced electric field of up to 20 ×106 V /m is discovered in a surface layer of the crystal, which then drives polarization and lattice dynamics that are dramatically distinct in a surface layer versus bulk regions. A dynamical phase-field modeling method is developed that reveals the microscopic origin of these dynamics, leading to gigahertz polarization and elastic waves traveling in the crystal with sonic speeds and spatially varying frequencies. The advances in spatiotemporal imaging and dynamical modeling tools open up opportunities for disentangling ultrafast processes in complex mesoscale structures such as ferroelectric domains.

Spatial patterns and controls on historical fire regimes and forest structure in the Klamath Mountains

Treesearch

Alan H. Taylor; Carl N. Skinner

2003-01-01

Fire exclusion in mixed conifer forests has increased the risk of fire due to decades of fuel accumulation. Restoration of fire into altered forests is a challenge because of a poor understanding of the spatial and temporal dynamics of fire regimes. In this study the spatial and temporal characteristics of fire regimes and forest age structure are reconstructed in a...

Exploring space-time structure of human mobility in urban space

NASA Astrophysics Data System (ADS)

Sun, J. B.; Yuan, J.; Wang, Y.; Si, H. B.; Shan, X. M.

2011-03-01

Understanding of human mobility in urban space benefits the planning and provision of municipal facilities and services. Due to the high penetration of cell phones, mobile cellular networks provide information for urban dynamics with a large spatial extent and continuous temporal coverage in comparison with traditional approaches. The original data investigated in this paper were collected by cellular networks in a southern city of China, recording the population distribution by dividing the city into thousands of pixels. The space-time structure of urban dynamics is explored by applying Principal Component Analysis (PCA) to the original data, from temporal and spatial perspectives between which there is a dual relation. Based on the results of the analysis, we have discovered four underlying rules of urban dynamics: low intrinsic dimensionality, three categories of common patterns, dominance of periodic trends, and temporal stability. It implies that the space-time structure can be captured well by remarkably few temporal or spatial predictable periodic patterns, and the structure unearthed by PCA evolves stably over time. All these features play a critical role in the applications of forecasting and anomaly detection.

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

PubMed

Reddy, Th Dhileep N; Mallik, Bhabani S

2017-04-19

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

Graph Theoretic Foundations of Multibody Dynamics Part I: Structural Properties

PubMed Central

Jain, Abhinandan

2011-01-01

This is the first part of two papers that use concepts from graph theory to obtain a deeper understanding of the mathematical foundations of multibody dynamics. The key contribution is the development of a unifying framework that shows that key analytical results and computational algorithms in multibody dynamics are a direct consequence of structural properties and require minimal assumptions about the specific nature of the underlying multibody system. This first part focuses on identifying the abstract graph theoretic structural properties of spatial operator techniques in multibody dynamics. The second part paper exploits these structural properties to develop a broad spectrum of analytical results and computational algorithms. Towards this, we begin with the notion of graph adjacency matrices and generalize it to define block-weighted adjacency (BWA) matrices and their 1-resolvents. Previously developed spatial operators are shown to be special cases of such BWA matrices and their 1-resolvents. These properties are shown to hold broadly for serial and tree topology multibody systems. Specializations of the BWA and 1-resolvent matrices are referred to as spatial kernel operators (SKO) and spatial propagation operators (SPO). These operators and their special properties provide the foundation for the analytical and algorithmic techniques developed in the companion paper. We also use the graph theory concepts to study the topology induced sparsity structure of these operators and the system mass matrix. Similarity transformations of these operators are also studied. While the detailed development is done for the case of rigid-link multibody systems, the extension of these techniques to a broader class of systems (e.g. deformable links) are illustrated. PMID:22102790

Phage-Bacterial Dynamics with Spatial Structure: Self Organization around Phage Sinks Can Promote Increased Cell Densities

PubMed Central

Bull, James J.; Christensen, Kelly A.; Scott, Carly; Crandall, Cameron J.; Krone, Stephen M.

2018-01-01

Bacteria growing on surfaces appear to be profoundly more resistant to control by lytic bacteriophages than do the same cells grown in liquid. Here, we use simulation models to investigate whether spatial structure per se can account for this increased cell density in the presence of phages. A measure is derived for comparing cell densities between growth in spatially structured environments versus well mixed environments (known as mass action). Maintenance of sensitive cells requires some form of phage death; we invoke death mechanisms that are spatially fixed, as if produced by cells. Spatially structured phage death provides cells with a means of protection that can boost cell densities an order of magnitude above that attained under mass action, although the effect is sometimes in the opposite direction. Phage and bacteria self organize into separate refuges, and spatial structure operates so that the phage progeny from a single burst do not have independent fates (as they do with mass action). Phage incur a high loss when invading protected areas that have high cell densities, resulting in greater protection for the cells. By the same metric, mass action dynamics either show no sustained bacterial elevation or oscillate between states of low and high cell densities and an elevated average. The elevated cell densities observed in models with spatial structure do not approach the empirically observed increased density of cells in structured environments with phages (which can be many orders of magnitude), so the empirical phenomenon likely requires additional mechanisms than those analyzed here. PMID:29382134

Harmonic Brain Modes: A Unifying Framework for Linking Space and Time in Brain Dynamics.

PubMed

Atasoy, Selen; Deco, Gustavo; Kringelbach, Morten L; Pearson, Joel

2018-06-01

A fundamental characteristic of spontaneous brain activity is coherent oscillations covering a wide range of frequencies. Interestingly, these temporal oscillations are highly correlated among spatially distributed cortical areas forming structured correlation patterns known as the resting state networks, although the brain is never truly at "rest." Here, we introduce the concept of harmonic brain modes-fundamental building blocks of complex spatiotemporal patterns of neural activity. We define these elementary harmonic brain modes as harmonic modes of structural connectivity; that is, connectome harmonics, yielding fully synchronous neural activity patterns with different frequency oscillations emerging on and constrained by the particular structure of the brain. Hence, this particular definition implicitly links the hitherto poorly understood dimensions of space and time in brain dynamics and its underlying anatomy. Further we show how harmonic brain modes can explain the relationship between neurophysiological, temporal, and network-level changes in the brain across different mental states ( wakefulness, sleep, anesthesia, psychedelic). Notably, when decoded as activation of connectome harmonics, spatial and temporal characteristics of neural activity naturally emerge from the interplay between excitation and inhibition and this critical relation fits the spatial, temporal, and neurophysiological changes associated with different mental states. Thus, the introduced framework of harmonic brain modes not only establishes a relation between the spatial structure of correlation patterns and temporal oscillations (linking space and time in brain dynamics), but also enables a new dimension of tools for understanding fundamental principles underlying brain dynamics in different states of consciousness.

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

PubMed

Thummuru, Dhileep Nagi Reddy; Mallik, Bhabani S

2017-10-26

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

Object view in spatial system dynamics: a grassland farming example

PubMed Central

Neuwirth, Christian; Hofer, Barbara; Schaumberger, Andreas

2016-01-01

Abstract Spatial system dynamics (SSD) models are typically implemented by linking stock variables to raster grids while the use of object representations of human artefacts such as buildings or ownership has been limited. This limitation is addressed by this article, which demonstrates the use of object representations in SSD. The objects are parcels of land that are attributed to grassland farms. The model simulates structural change in agriculture, i.e., change in the size of farms. The aim of the model is to reveal relations between structural change, farmland fragmentation and variable farmland quality. Results show that fragmented farms tend to become consolidated by structural change, whereas consolidated initial conditions result in a significant increase of fragmentation. Consolidation is reinforced by a dynamic land market and high transportation costs. The example demonstrates the capabilities of the object-based approach for integrating object geometries (parcel shapes) and relations between objects (distances between parcels) dynamically in SSD. PMID:28190972

Lagrangian coherent structures separate dynamically distinct regions in fluid flows.

PubMed

Kelley, Douglas H; Allshouse, Michael R; Ouellette, Nicholas T

2013-07-01

Using filter-space techniques, we study the scale-to-scale transport of energy in a quasi-two-dimensional, weakly turbulent fluid flow averaged along the trajectories of fluid elements. We find that although the spatial mean of this Lagrangian-averaged flux is nearly unchanged from its Eulerian counterpart, the spatial structure of the scale-to-scale energy flux changes significantly. In particular, its features appear to correlate with the positions of Lagrangian coherent structures (LCS's). We show that the LCS's tend to lie at zeros of the scale-to-scale flux, and therefore that the LCS's separate regions that have qualitatively different dynamics. Since LCS's are also known to be impenetrable barriers to advection and mixing, we therefore find that the fluid on either side of an LCS is both kinematically and dynamically distinct. Our results extend the utility of LCS's by making clear the role they play in the flow dynamics in addition to the kinematics.

Extended generalized recurrence plot quantification of complex circular patterns

NASA Astrophysics Data System (ADS)

Riedl, Maik; Marwan, Norbert; Kurths, Jürgen

2017-03-01

The generalized recurrence plot is a modern tool for quantification of complex spatial patterns. Its application spans the analysis of trabecular bone structures, Turing patterns, turbulent spatial plankton patterns, and fractals. Determinism is a central measure in this framework quantifying the level of regularity of spatial structures. We show by basic examples of fully regular patterns of different symmetries that this measure underestimates the orderliness of circular patterns resulting from rotational symmetries. We overcome this crucial problem by checking additional structural elements of the generalized recurrence plot which is demonstrated with the examples. Furthermore, we show the potential of the extended quantity of determinism applying it to more irregular circular patterns which are generated by the complex Ginzburg-Landau-equation and which can be often observed in real spatially extended dynamical systems. So, we are able to reconstruct the main separations of the system's parameter space analyzing single snapshots of the real part only, in contrast to the use of the original quantity. This ability of the proposed method promises also an improved description of other systems with complicated spatio-temporal dynamics typically occurring in fluid dynamics, climatology, biology, ecology, social sciences, etc.

Light-activated Gigahertz Ferroelectric Domain Dynamics

DOE PAGES

Akamatsu, Hirofumii; Yuan, Yakun; Stoica, Vladimir A.; ...

2018-02-26

Using time- and spatially-resolved hard X-ray diffraction microscopy, the striking structural and electrical dynamics upon optical excitation of a single crystal of BaTiO 3 are simultaneously captured on sub-nanoseconds and nanoscale within individual ferroelectric domains and across walls. A large emergent photo-induced electric field of up to 20 million volts per meter is discovered in a surface layer of the crystal, which then drives polarization and lattice dynamics that are dramatically distinct in a surface layer versus bulk regions. A dynamical phase-field modeling (DPFM) method is developed that reveals the microscopic origin of these dynamics, leading to GHz polarization andmore » elastic waves travelling in the crystal with sonic speeds and spatially varying frequencies. The advance of spatiotemporal imaging and dynamical modeling tools open opportunities of disentangling ultrafast processes in complex mesoscale structures such as ferroelectric domains« less

Relationship between gaseous N dynamics and the hydraulic state of hierarchically structured soils

NASA Astrophysics Data System (ADS)

Schlüter, Steffen; Dörsch, Peter; Vogel, Hans-Jörg

2017-04-01

The inherent spatial heterogeneity of soil generates spatially distributed micro-sites with different local N gas (NO, N2O, N2) production and release rates. Moreover, local micro-site conditions and the pathways between them depend on soil moisture which itself is highly dynamic close to the soil surface. These relationships need to be taken into account for a quantitative understanding of soil denitrification and associated N gas dynamics. Soil structure has been recognized as a key factor to understand the high spatial variability of N gas emissions. In particular gaseous N release from soils depends on: i) the total denitrification rate, which is related to the spatial extent and distribution of anaerobic sites and ii) the probability of N2O to escape from the soil without being further reduced to N2. This impact of soil structure is typically ignored in studies with soil slurries or repacked soil. In this project we run well-defined mesocosm experiments on N gas dynamics with hierarchically structured, artificial soils in which the spatial distribution of substrate and denitrifiers is known exactly. Sintered, porous glass pellets are inoculated with strains of Paracoccus denitrificans and/or Agrobacterium tumefaciens and amended with nutrient solution. These pellets are embedded in coarse-grained sand within gas-tight columns under O2/He atmosphere. The pellets are either places in layers or randomly to create different patterns of N gas production sites and diffusion pathways. Denitrification occurs in the anaerobic centers of the porous pellets, while the partially saturated sand matrix controls the diffusive transport of N gases towards the headspace, where all relevant gas concentrations are monitored with gas chromatography. Water saturations are adjusted such that the diffusive pathways are either fully continuous or partially discontinuous. Preliminary results indicate that the water content exert a major control on the magnitude of denitrification, whereas the onset and dynamics are mainly controlled by the position of the substrate and the denitrifiers.

Spatially and temporally resolved exciton dynamics and transport in single nanostructures and assemblies

NASA Astrophysics Data System (ADS)

Huang, Libai

2015-03-01

The frontier in solar energy conversion now lies in learning how to integrate functional entities across multiple length scales to create optimal devices. To address this new frontier, I will discuss our recent efforts on elucidating multi-scale energy transfer, migration, and dissipation processes with simultaneous femtosecond temporal resolution and nanometer spatial resolution. We have developed ultrafast microscopy that combines ultrafast spectroscopy with optical microscopy to map exciton dynamics and transport with simultaneous ultrafast time resolution and diffraction-limited spatial resolution. We have employed pump-probe transient absorption microscopy to elucidate morphology and structure dependent exciton dynamics and transport in single nanostructures and molecular assemblies. More specifically, (1) We have applied transient absorption microscopy (TAM) to probe environmental and structure dependent exciton relaxation pathways in sing-walled carbon nanotubes (SWNTs) by mapping dynamics in individual pristine SWNTs with known structures. (2) We have systematically measured and modeled the optical properties of the Frenkel excitons in self-assembled porphyrin tubular aggregates that represent an analog to natural photosynthetic antennae. Using a combination of ultrafast optical microscopy and stochastic exciton modeling, we address exciton transport and relaxation pathways, especially those related to disorder.

Temporal and Spatial Dynamics of Sediment Anaerobic Ammonium Oxidation (Anammox) Bacteria in Freshwater Lakes.

PubMed

Yang, Yuyin; Dai, Yu; Li, Ningning; Li, Bingxin; Xie, Shuguang; Liu, Yong

2017-02-01

Anaerobic ammonium-oxidizing (anammox) process can play an important role in freshwater nitrogen cycle. However, the distribution of anammox bacteria in freshwater lake and the associated environmental factors remain essentially unclear. The present study investigated the temporal and spatial dynamics of sediment anammox bacterial populations in eutrotrophic Dianchi Lake and mesotrophic Erhai Lake on the Yunnan Plateau (southwestern China). The remarkable spatial change of anammox bacterial abundance was found in Dianchi Lake, while the relatively slight spatial shift occurred in Erhai Lake. Dianchi Lake had greater anammox bacterial abundance than Erhai Lake. In both Dianchi Lake and Erhai Lake, anammox bacteria were much more abundant in summer than in spring. Anammox bacterial community richness, diversity, and structure in these two freshwater lakes were subjected to temporal and spatial variations. Sediment anammox bacterial communities in Dianchi Lake and Erhai Lake were dominated by Candidatus Brocadia and a novel phylotype followed by Candidatus Kuenenia; however, these two lakes had distinct anammox bacterial community structure. In addition, trophic status determined sediment anammox bacterial community structure.

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

DTIC Science & Technology

2012-10-12

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

Social and spatial effects on genetic variation between foraging flocks in a wild bird population.

PubMed

Radersma, Reinder; Garroway, Colin J; Santure, Anna W; de Cauwer, Isabelle; Farine, Damien R; Slate, Jon; Sheldon, Ben C

2017-10-01

Social interactions are rarely random. In some instances, animals exhibit homophily or heterophily, the tendency to interact with similar or dissimilar conspecifics, respectively. Genetic homophily and heterophily influence the evolutionary dynamics of populations, because they potentially affect sexual and social selection. Here, we investigate the link between social interactions and allele frequencies in foraging flocks of great tits (Parus major) over three consecutive years. We constructed co-occurrence networks which explicitly described the splitting and merging of 85,602 flocks through time (fission-fusion dynamics), at 60 feeding sites. Of the 1,711 birds in those flocks, we genotyped 962 individuals at 4,701 autosomal single nucleotide polymorphisms (SNPs). By combining genomewide genotyping with repeated field observations of the same individuals, we were able to investigate links between social structure and allele frequencies at a much finer scale than was previously possible. We explicitly accounted for potential spatial effects underlying genetic structure at the population level. We modelled social structure and spatial configuration of great tit fission-fusion dynamics with eigenvector maps. Variance partitioning revealed that allele frequencies were strongly affected by group fidelity (explaining 27%-45% of variance) as individuals tended to maintain associations with the same conspecifics. These conspecifics were genetically more dissimilar than expected, shown by genomewide heterophily for pure social (i.e., space-independent) grouping preferences. Genomewide homophily was linked to spatial configuration, indicating spatial segregation of genotypes. We did not find evidence for homophily or heterophily for putative socially relevant candidate genes or any other SNP markers. Together, these results demonstrate the importance of distinguishing social and spatial processes in determining population structure. © 2017 John Wiley & Sons Ltd.

Living in the branches: population dynamics and ecological processes in dendritic networks

USGS Publications Warehouse

Grant, E.H.C.; Lowe, W.H.; Fagan, W.F.

2007-01-01

Spatial structure regulates and modifies processes at several levels of ecological organization (e.g. individual/genetic, population and community) and is thus a key component of complex systems, where knowledge at a small scale can be insufficient for understanding system behaviour at a larger scale. Recent syntheses outline potential applications of network theory to ecological systems, but do not address the implications of physical structure for network dynamics. There is a specific need to examine how dendritic habitat structure, such as that found in stream, hedgerow and cave networks, influences ecological processes. Although dendritic networks are one type of ecological network, they are distinguished by two fundamental characteristics: (1) both the branches and the nodes serve as habitat, and (2) the specific spatial arrangement and hierarchical organization of these elements interacts with a species' movement behaviour to alter patterns of population distribution and abundance, and community interactions. Here, we summarize existing theory relating to ecological dynamics in dendritic networks, review empirical studies examining the population- and community-level consequences of these networks, and suggest future research integrating spatial pattern and processes in dendritic systems.

Three dimensional simulation of spatial and temporal variability of stratospheric hydrogen chloride

NASA Technical Reports Server (NTRS)

Kaye, Jack A.; Rood, Richard B.; Jackman, Charles H.; Allen, Dale J.; Larson, Edmund M.

1989-01-01

Spatial and temporal variability of atmospheric HCl columns are calculated for January 1979 using a three-dimensional chemistry-transport model designed to provide the best possible representation of stratospheric transport. Large spatial and temporal variability of the HCl columns is shown to be correlated with lower stratospheric potential vorticity and thus to be of dynamical origin. Systematic longitudinal structure is correlated with planetary wave structure. These results can help place spatially and temporally isolated column and profile measurements in a regional and/or global perspective.

Tropical forest carbon balance: effects of field- and satellite-based mortality regimes on the dynamics and the spatial structure of Central Amazon forest biomass

NASA Astrophysics Data System (ADS)

Di Vittorio, Alan V.; Negrón-Juárez, Robinson I.; Higuchi, Niro; Chambers, Jeffrey Q.

2014-03-01

Debate continues over the adequacy of existing field plots to sufficiently capture Amazon forest dynamics to estimate regional forest carbon balance. Tree mortality dynamics are particularly uncertain due to the difficulty of observing large, infrequent disturbances. A recent paper (Chambers et al 2013 Proc. Natl Acad. Sci. 110 3949-54) reported that Central Amazon plots missed 9-17% of tree mortality, and here we address ‘why’ by elucidating two distinct mortality components: (1) variation in annual landscape-scale average mortality and (2) the frequency distribution of the size of clustered mortality events. Using a stochastic-empirical tree growth model we show that a power law distribution of event size (based on merged plot and satellite data) is required to generate spatial clustering of mortality that is consistent with forest gap observations. We conclude that existing plots do not sufficiently capture losses because their placement, size, and longevity assume spatially random mortality, while mortality is actually distributed among differently sized events (clusters of dead trees) that determine the spatial structure of forest canopies.

Using satellite telemetry to define spatial population structure in polar bears in the Norwegian and western Russian Arctic

USGS Publications Warehouse

Mauritzen, Mette; Derocher, Andrew E.; Wiig, Øystein; Belikov, Stanislav; Boltunov, Andrei N.; Garner, Gerald W.

2002-01-01

1. Animal populations, defined by geographical areas within a species’ distribution where population dynamics are largely regulated by births and deaths rather than by migration from surrounding areas, may be the correct unit for wildlife management. However, in heterogeneous landscapes varying habitat quality may yield subpopulations with distinct patterns in resource use and demography significant to the dynamics of populations.2. To define the spatial population structure of polar bears Ursus maritimus in the Norwegian and western Russian Arctic, and to assess the existence of a shared population between the two countries, we analysed satellite telemetry data obtained from 105 female polar bears over 12 years.3. Using both cluster analyses and home-range estimation methods, we identified five population units inhabiting areas with different sea-ice characteristics and prey availability.4. The continuous distribution of polar bear positions indicated that the different subpopulations formed one continuous polar bear population in the Norwegian and western Russian Arctic. Hence, Norway and Russia have a shared management responsibility.5. The spatial population structure identified will provide a guide for evaluating geographical patterns in polar bear ecology, the dynamics of polar bear–seal relationships and the effects of habitat alteration due to climate change. The work illustrates the importance of defining population borders and subpopulation structure in understanding the dynamics and management of larger animals.

Spatial-Temporal Dynamics of High-Resolution Animal Networks: What Can We Learn from Domestic Animals?

PubMed

Chen, Shi; Ilany, Amiyaal; White, Brad J; Sanderson, Michael W; Lanzas, Cristina

2015-01-01

Animal social network is the key to understand many ecological and epidemiological processes. We used real-time location system (RTLS) to accurately track cattle position, analyze their proximity networks, and tested the hypothesis of temporal stationarity and spatial homogeneity in these networks during different daily time periods and in different areas of the pen. The network structure was analyzed using global network characteristics (network density), subgroup clustering (modularity), triadic property (transitivity), and dyadic interactions (correlation coefficient from a quadratic assignment procedure) at hourly level. We demonstrated substantial spatial-temporal heterogeneity in these networks and potential link between indirect animal-environment contact and direct animal-animal contact. But such heterogeneity diminished if data were collected at lower spatial (aggregated at entire pen level) or temporal (aggregated at daily level) resolution. The network structure (described by the characteristics such as density, modularity, transitivity, etc.) also changed substantially at different time and locations. There were certain time (feeding) and location (hay) that the proximity network structures were more consistent based on the dyadic interaction analysis. These results reveal new insights for animal network structure and spatial-temporal dynamics, provide more accurate descriptions of animal social networks, and allow more accurate modeling of multiple (both direct and indirect) disease transmission pathways.

Impact of constrained rewiring on network structure and node dynamics

NASA Astrophysics Data System (ADS)

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

2014-11-01

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

Delineating ecological regions in marine systems: Integrating physical structure and community composition to inform spatial management in the eastern Bering Sea

NASA Astrophysics Data System (ADS)

Baker, Matthew R.; Hollowed, Anne B.

2014-11-01

Characterizing spatial structure and delineating meaningful spatial boundaries have useful applications to understanding regional dynamics in marine systems, and are integral to ecosystem approaches to fisheries management. Physical structure and drivers combine with biological responses and interactions to organize marine systems in unique ways at multiple scales. We apply multivariate statistical methods to define spatially coherent ecological units or ecoregions in the eastern Bering Sea. We also illustrate a practical approach to integrate data on species distribution, habitat structure and physical forcing mechanisms to distinguish areas with distinct biogeography as one means to define management units in large marine ecosystems. We use random forests to quantify the relative importance of habitat and environmental variables to the distribution of individual species, and to quantify shifts in multispecies assemblages or community composition along environmental gradients. Threshold shifts in community composition are used to identify regions with distinct physical and biological attributes, and to evaluate the relative importance of predictor variables to determining regional boundaries. Depth, bottom temperature and frontal boundaries were dominant factors delineating distinct biological communities in this system, with a latitudinal divide at approximately 60°N. Our results indicate that distinct climatic periods will shift habitat gradients and that dynamic physical variables such as temperature and stratification are important to understanding temporal stability of ecoregion boundaries. We note distinct distribution patterns among functional guilds and also evidence for resource partitioning among individual species within each guild. By integrating physical and biological data to determine spatial patterns in community composition, we partition ecosystems along ecologically significant gradients. This may provide a basis for defining spatial management units or serve as a baseline index for analyses of structural shifts in the physical environment, species abundance and distribution, and community dynamics over time.

Can the functional stability of forest ecosystems be evaluated from the spatial analysis of stands? A case study from the Bialowieza Primeval Forest (Poland)

Treesearch

Andrzej Bobiec

2000-01-01

Variability of external and internal factors entails specific spatial patterns and functional dynamics of communities. The study of the oak-lime-hornbeam (Quercus robur-Tilia cordata-Carpimus) forest in the Bialowieza Primeval Forest supports the concept of silvatic unit, determining the minimal structural area. To find out if the dynamics of a stand...

Life history determines genetic structure and evolutionary potential of host–parasite interactions

PubMed Central

Barrett, Luke G.; Thrall, Peter H.; Burdon, Jeremy J.; Linde, Celeste C.

2009-01-01

Measures of population genetic structure and diversity of disease-causing organisms are commonly used to draw inferences regarding their evolutionary history and potential to generate new variation in traits that determine interactions with their hosts. Parasite species exhibit a range of population structures and life-history strategies, including different transmission modes, life-cycle complexity, off-host survival mechanisms and dispersal ability. These are important determinants of the frequency and predictability of interactions with host species. Yet the complex causal relationships between spatial structure, life history and the evolutionary dynamics of parasite populations are not well understood. We demonstrate that a clear picture of the evolutionary potential of parasitic organisms and their demographic and evolutionary histories can only come from understanding the role of life history and spatial structure in influencing population dynamics and epidemiological patterns. PMID:18947899

Life history determines genetic structure and evolutionary potential of host-parasite interactions.

PubMed

Barrett, Luke G; Thrall, Peter H; Burdon, Jeremy J; Linde, Celeste C

2008-12-01

Measures of population genetic structure and diversity of disease-causing organisms are commonly used to draw inferences regarding their evolutionary history and potential to generate new variation in traits that determine interactions with their hosts. Parasite species exhibit a range of population structures and life-history strategies, including different transmission modes, life-cycle complexity, off-host survival mechanisms and dispersal ability. These are important determinants of the frequency and predictability of interactions with host species. Yet the complex causal relationships between spatial structure, life history and the evolutionary dynamics of parasite populations are not well understood. We demonstrate that a clear picture of the evolutionary potential of parasitic organisms and their demographic and evolutionary histories can only come from understanding the role of life history and spatial structure in influencing population dynamics and epidemiological patterns.

Self-Organization of Spatio-Temporal Hierarchy via Learning of Dynamic Visual Image Patterns on Action Sequences

PubMed Central

Jung, Minju; Hwang, Jungsik; Tani, Jun

2015-01-01

It is well known that the visual cortex efficiently processes high-dimensional spatial information by using a hierarchical structure. Recently, computational models that were inspired by the spatial hierarchy of the visual cortex have shown remarkable performance in image recognition. Up to now, however, most biological and computational modeling studies have mainly focused on the spatial domain and do not discuss temporal domain processing of the visual cortex. Several studies on the visual cortex and other brain areas associated with motor control support that the brain also uses its hierarchical structure as a processing mechanism for temporal information. Based on the success of previous computational models using spatial hierarchy and temporal hierarchy observed in the brain, the current report introduces a novel neural network model for the recognition of dynamic visual image patterns based solely on the learning of exemplars. This model is characterized by the application of both spatial and temporal constraints on local neural activities, resulting in the self-organization of a spatio-temporal hierarchy necessary for the recognition of complex dynamic visual image patterns. The evaluation with the Weizmann dataset in recognition of a set of prototypical human movement patterns showed that the proposed model is significantly robust in recognizing dynamically occluded visual patterns compared to other baseline models. Furthermore, an evaluation test for the recognition of concatenated sequences of those prototypical movement patterns indicated that the model is endowed with a remarkable capability for the contextual recognition of long-range dynamic visual image patterns. PMID:26147887

Self-Organization of Spatio-Temporal Hierarchy via Learning of Dynamic Visual Image Patterns on Action Sequences.

PubMed

Jung, Minju; Hwang, Jungsik; Tani, Jun

2015-01-01

It is well known that the visual cortex efficiently processes high-dimensional spatial information by using a hierarchical structure. Recently, computational models that were inspired by the spatial hierarchy of the visual cortex have shown remarkable performance in image recognition. Up to now, however, most biological and computational modeling studies have mainly focused on the spatial domain and do not discuss temporal domain processing of the visual cortex. Several studies on the visual cortex and other brain areas associated with motor control support that the brain also uses its hierarchical structure as a processing mechanism for temporal information. Based on the success of previous computational models using spatial hierarchy and temporal hierarchy observed in the brain, the current report introduces a novel neural network model for the recognition of dynamic visual image patterns based solely on the learning of exemplars. This model is characterized by the application of both spatial and temporal constraints on local neural activities, resulting in the self-organization of a spatio-temporal hierarchy necessary for the recognition of complex dynamic visual image patterns. The evaluation with the Weizmann dataset in recognition of a set of prototypical human movement patterns showed that the proposed model is significantly robust in recognizing dynamically occluded visual patterns compared to other baseline models. Furthermore, an evaluation test for the recognition of concatenated sequences of those prototypical movement patterns indicated that the model is endowed with a remarkable capability for the contextual recognition of long-range dynamic visual image patterns.

Extinction threshold for spatial forest dynamics with height structure.

PubMed

Garcia-Domingo, Josep L; Saldaña, Joan

2011-05-07

We present a pair-approximation model for spatial forest dynamics defined on a regular lattice. The model assumes three possible states for a lattice site: empty (gap site), occupied by an immature tree, and occupied by a mature tree, and considers three nonlinearities in the dynamics associated to the processes of light interference, gap expansion, and recruitment. We obtain an expression of the basic reproduction number R(0) which, in contrast to the one obtained under the mean-field approach, uses information about the spatial arrangement of individuals close to extinction. Moreover, we analyze the corresponding survival-extinction transition of the forest and the spatial correlations among gaps, immature and mature trees close to this critical point. Predictions of the pair-approximation model are compared with those of a cellular automaton. Copyright © 2011 Elsevier Ltd. All rights reserved.

Broad frequency band full field measurements for advanced applications: Point-wise comparisons between optical technologies

NASA Astrophysics Data System (ADS)

Zanarini, Alessandro

2018-01-01

The progress of optical systems gives nowadays at disposal on lightweight structures complex dynamic measurements and modal tests, each with its own advantages, drawbacks and preferred usage domains. It is thus more easy than before to obtain highly spatially defined vibration patterns for many applications in vibration engineering, testing and general product development. The potential of three completely different technologies is here benchmarked on a common test rig and advanced applications. SLDV, dynamic ESPI and hi-speed DIC are here first deployed in a complex and unique test on the estimation of FRFs with high spatial accuracy from a thin vibrating plate. The latter exhibits a broad band dynamics and high modal density in the common frequency domain where the techniques can find an operative intersection. A peculiar point-wise comparison is here addressed by means of discrete geometry transforms to put all the three technologies on trial at each physical point of the surface. Full field measurement technologies cannot estimate only displacement fields on a refined grid, but can exploit the spatial consistency of the results through neighbouring locations by means of numerical differentiation operators in the spatial domain to obtain rotational degrees of freedom and superficial dynamic strain distributions, with enhanced quality, compared to other technologies in literature. Approaching the task with the aid of superior quality receptance maps from the three different full field gears, this work calculates and compares rotational and dynamic strain FRFs. Dynamic stress FRFs can be modelled directly from the latter, by means of a constitutive model, avoiding the costly and time-consuming steps of building and tuning a numerical dynamic model of a flexible component or a structure in real life conditions. Once dynamic stress FRFs are obtained, spectral fatigue approaches can try to predict the life of a component in many excitation conditions. Different spectral shaping of the excitation can easily be used to enhance the comparison in the framework of any of the spectral approaches for fatigue life calculations, highlighting benefits and drawbacks of a direct experimental approach to failure and risk assessment in structural dynamics when dealing with complex patterns in real-life testing. Are optical measurements and spatially dense datasets really effective in advanced model updating of lightweight structures with complex structural dynamics? The noise shown in the raw signal of some experiments may pose issues in proficiently exploiting the added data in a fruitful model updating procedure. Model updating results are here compared between scanning and native full field technologies, with comments and details on the test rig, on the advantages and drawbacks of the approaches. The identification of EMA models highlights the increasing quality of shapes that can be obtained from native full field high resolution gears, against that (some time unexpectedly poor) of SLDV tested.

Hi-C First Results

NASA Technical Reports Server (NTRS)

Cirtain, Jonathan

2013-01-01

Hi-C obtained the highest spatial and temporal resolution observatoins ever taken in the solar corona. Hi-C reveals dynamics and structure at the limit of its temporal and spatial resolution. Hi-C observed ubiquitous fine-scale flows consistent with the local sound speed.

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

The problem of ecological scaling in spatially complex, nonequilibrium ecological systems [chapter 3

Treesearch

Samuel A. Cushman; Jeremy Littell; Kevin McGarigal

2010-01-01

In the previous chapter we reviewed the challenges posed by spatial complexity and temporal disequilibrium to efforts to understand and predict the structure and dynamics of ecological systems. The central theme was that spatial variability in the environment and population processes fundamentally alters the interactions between species and their environments, largely...

Extracting temporal and spatial information from remotely sensed data for mapping wildlife habitat: Tucson

USGS Publications Warehouse

Wallace, Cynthia S.A.; Advised by Marsh, Stuart E.

2002-01-01

The research accomplished in this dissertation used both mathematical and statistical techniques to extract and evaluate measures of landscape temporal dynamics and spatial structure from remotely sensed data for the purpose of mapping wildlife habitat. By coupling the landscape measures gleaned from the remotely sensed data with various sets of animal sightings and population data, effective models of habitat preference were created.Measures of temporal dynamics of vegetation greenness as measured by National Oceanographic and Atmospheric Administration’s Advanced Very High Resolution Radiometer (AVHRR) satellite were used to effectively characterize and map season specific habitat of the Sonoran pronghorn antelope, as well as produce preliminary models of potential yellow-billed cuckoo habitat in Arizona. Various measures that capture different aspects of the temporal dynamics of the landscape were derived from AVHRR Normalized Difference Vegetation Index composite data using three main classes of calculations: basic statistics, standardized principal components analysis, and Fourier analysis. Pronghorn habitat models based on the AVHRR measures correspond visually and statistically to GIS-based models produced using data that represent detailed knowledge of ground-condition.Measures of temporal dynamics also revealed statistically significant correlations with annual estimates of elk population in selected Arizona Game Management Units, suggesting elk respond to regional environmental changes that can be measured using satellite data. Such relationships, once verified and established, can be used to help indirectly monitor the population.Measures of landscape spatial structure derived from IKONOS high spatial resolution (1-m) satellite data using geostatistics effectively map details of Sonoran pronghorn antelope habitat. Local estimates of the nugget, sill, and range variogram parameters calculated within 25 x 25-meter image windows describe the spatial autocorrelation of the image, permitting classification of all pixels into coherent units whose signature graphs exhibit a classic variogram shape. The variogram parameters captured in these signatures have been shown in previous studies to discriminate between different species-specific vegetation associations.The synoptic view of the landscape provided by satellite data can inform resource management efforts. The ability to characterize the spatial structure and temporal dynamics of habitat using repeatable remote sensing data allows closer monitoring of the relationship between a species and its landscape.

Investigation of the spatial structure and developmental dynamics of near-Earth plasma perturbations under the action of powerful HF radio waves

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

Belov, A. S., E-mail: alexis-belov@yandex.ru

2015-10-15

Results of numerical simulations of the near-Earth plasma perturbations induced by powerful HF radio waves from the SURA heating facility are presented. The simulations were performed using a modified version of the SAMI2 ionospheric model for the input parameters corresponding to the series of in-situ SURA–DEMETER experiments. The spatial structure and developmental dynamics of large-scale plasma temperature and density perturbations have been investigated. The characteristic formation and relaxation times of the induced large-scale plasma perturbations at the altitudes of the Earth’s outer ionosphere have been determined.

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.

Sensorimotor coordination and the structure of space.

PubMed

McCollum, Gin

2003-01-01

Embedded in neural and behavioral organization is a structure of sensorimotor space. Both this embedded spatial structure and the structure of physical space inform sensorimotor control. This paper reviews studies in which the gravitational vertical and horizontal are crucial. The mathematical expressions of spatial geometry in these studies indicate methods for investigating sensorimotor control in freefall. In freefall, the spatial structure introduced by gravitation - the distinction between vertical and horizontal - does not exist. However, an astronaut arriving in space carries the physiologically-embedded distinction between horizontal and vertical learned on earth. The physiological organization based on this distinction collapses when the strong otolith activity and other gravitational cues for sensorimotor behavior become unavailable. The mathematical methods in this review are applicable in understanding the changes in physiological organization as an astronaut adapts to sensorimotor control in freefall. Many mathematical languages are available for characterizing the logical structures in physiological organization. Here, group theory is used to characterize basic structure of physical and physiological spaces. Dynamics and topology allow the grouping of trajectory ranges according to the outcomes or attractors. The mathematics of ordered structures express complex orderings, such as in multiphase movements in which different parts of the body are moving in different phase sequences. Conditional dynamics, which combines dynamics with the mathematics of ordered structures, accommodates the parsing of movement sequences into trajectories and transitions. Studies reviewed include those of the sit-to-stand movement and early locomotion, because of the salience of gravitation in those behaviors. Sensorimotor transitions and the conditions leading to them are characterized in conditional dynamic control structures that do not require thinking of an organism as an input-output device. Conditions leading to sensorimotor transitions on earth assume the presence of a gravitational vertical which is lacking in space. Thus, conditions used on earth for sensorimotor transitions may become ambiguous in space. A platform study in which sensorimotor transition conditions are ambiguous and are related to motion sickness is reviewed.

Space-time modeling of soil moisture

NASA Astrophysics Data System (ADS)

Chen, Zijuan; Mohanty, Binayak P.; Rodriguez-Iturbe, Ignacio

2017-11-01

A physically derived space-time mathematical representation of the soil moisture field is carried out via the soil moisture balance equation driven by stochastic rainfall forcing. The model incorporates spatial diffusion and in its original version, it is shown to be unable to reproduce the relative fast decay in the spatial correlation functions observed in empirical data. This decay resulting from variations in local topography as well as in local soil and vegetation conditions is well reproduced via a jitter process acting multiplicatively over the space-time soil moisture field. The jitter is a multiplicative noise acting on the soil moisture dynamics with the objective to deflate its correlation structure at small spatial scales which are not embedded in the probabilistic structure of the rainfall process that drives the dynamics. These scales of order of several meters to several hundred meters are of great importance in ecohydrologic dynamics. Properties of space-time correlation functions and spectral densities of the model with jitter are explored analytically, and the influence of the jitter parameters, reflecting variabilities of soil moisture at different spatial and temporal scales, is investigated. A case study fitting the derived model to a soil moisture dataset is presented in detail.

Spatial structure and distribution of small pelagic fish in the northwestern Mediterranean Sea.

PubMed

Saraux, Claire; Fromentin, Jean-Marc; Bigot, Jean-Louis; Bourdeix, Jean-Hervé; Morfin, Marie; Roos, David; Van Beveren, Elisabeth; Bez, Nicolas

2014-01-01

Understanding the ecological and anthropogenic drivers of population dynamics requires detailed studies on habitat selection and spatial distribution. Although small pelagic fish aggregate in large shoals and usually exhibit important spatial structure, their dynamics in time and space remain unpredictable and challenging. In the Gulf of Lions (north-western Mediterranean), sardine and anchovy biomasses have declined over the past 5 years causing an important fishery crisis while sprat abundance rose. Applying geostatistical tools on scientific acoustic surveys conducted in the Gulf of Lions, we investigated anchovy, sardine and sprat spatial distributions and structures over 10 years. Our results show that sardines and sprats were more coastal than anchovies. The spatial structure of the three species was fairly stable over time according to variogram outputs, while year-to-year variations in kriged maps highlighted substantial changes in their location. Support for the McCall's basin hypothesis (covariation of both population density and presence area with biomass) was found only in sprats, the most variable of the three species. An innovative method to investigate species collocation at different scales revealed that globally the three species strongly overlap. Although species often co-occurred in terms of presence/absence, their biomass density differed at local scale, suggesting potential interspecific avoidance or different sensitivity to local environmental characteristics. Persistent favourable areas were finally detected, but their environmental characteristics remain to be determined.

Predator attack rate evolution in space: the role of ecology mediated by complex emergent spatial structure and self-shading.

PubMed

Messinger, Susanna M; Ostling, Annette

2013-11-01

Predation interactions are an important element of ecological communities. Population spatial structure has been shown to influence predator evolution, resulting in the evolution of a reduced predator attack rate; however, the evolutionary role of traits governing predator and prey ecology is unknown. The evolutionary effect of spatial structure on a predator's attack rate has primarily been explored assuming a fixed metapopulation spatial structure, and understood in terms of group selection. But endogenously generated, emergent spatial structure is common in nature. Furthermore, the evolutionary influence of ecological traits may be mediated through the spatial self-structuring process. Drawing from theory on pathogens, the evolutionary effect of emergent spatial structure can be understood in terms of self-shading, where a voracious predator limits its long-term invasion potential by reducing local prey availability. Here we formalize the effects of self-shading for predators using spatial moment equations. Then, through simulations, we show that in a spatial context self-shading leads to relationships between predator-prey ecology and the predator's attack rate that are not expected in a non-spatial context. Some relationships are analogous to relationships already shown for host-pathogen interactions, but others represent new trait dimensions. Finally, since understanding the effects of ecology using existing self-shading theory requires simplifications of the emergent spatial structure that do not apply well here, we also develop metrics describing the complex spatial structure of the predator and prey populations to help us explain the evolutionary effect of predator and prey ecology in the context of self-shading. The identification of these metrics may provide a step towards expansion of the predictive domain of self-shading theory to more complex spatial dynamics. Copyright © 2013 Elsevier Inc. All rights reserved.

Frequency response function-based explicit framework for dynamic identification in human-structure systems

NASA Astrophysics Data System (ADS)

Wei, Xiaojun; Živanović, Stana

2018-05-01

The aim of this paper is to propose a novel theoretical framework for dynamic identification in a structure occupied by a single human. The framework enables the prediction of the dynamics of the human-structure system from the known properties of the individual system components, the identification of human body dynamics from the known dynamics of the empty structure and the human-structure system and the identification of the properties of the structure from the known dynamics of the human and the human-structure system. The novelty of the proposed framework is the provision of closed-form solutions in terms of frequency response functions obtained by curve fitting measured data. The advantages of the framework over existing methods are that there is neither need for nonlinear optimisation nor need for spatial/modal models of the empty structure and the human-structure system. In addition, the second-order perturbation method is employed to quantify the effect of uncertainties in human body dynamics on the dynamic identification of the empty structure and the human-structure system. The explicit formulation makes the method computationally efficient and straightforward to use. A series of numerical examples and experiments are provided to illustrate the working of the method.

Money circulation networks reveal emerging geographical communities

NASA Astrophysics Data System (ADS)

Brockmann, D.; Theis, F.; David, V.

2008-03-01

Geographical communities and their boundaries are key determinants of various spatially extended dynamical phenomena. Examples are migration dynamics of species, the spread of infectious diseases, bioinvasive processes, and the spatial evolution of language. We address the question to what extend multiscale human transportation networks encode geographical community structures, how they differ from geopolitical classifications, whether they are spatially coherent, and analyse their structure as a function of length scale. Our analysis is based on a proxy network for human transportation obtained from the geographic circulation of more than 10 million dollar bills in the United States recorded at the bill tracking website www.wheresgeorge.com. The data extends that of a previous study (Brockmann et al., Nature 2006) on the discovery of scaling laws of human travel by an order of magnitude and permits an approach to multiscale human transportation from a network perspective.

A spatial age-structured model for describing sea lamprey (Petromyzon marinus) population dynamics

USGS Publications Warehouse

Robinson, Jason M.; Wilberg, Michael J.; Adams, Jean V.; Jones, Michael L.

2013-01-01

The control of invasive sea lampreys (Petromyzon marinus) presents large scale management challenges in the Laurentian Great Lakes. No modeling approach has been developed that describes spatial dynamics of lamprey populations. We developed and validated a spatial and age-structured model and applied it to a sea lamprey population in a large river in the Great Lakes basin. We considered 75 discrete spatial areas, included a stock-recruitment function, spatial recruitment patterns, natural mortality, chemical treatment mortality, and larval metamorphosis. Recruitment was variable, and an upstream shift in recruitment location was observed over time. From 1993–2011 recruitment, larval abundance, and the abundance of metamorphosing individuals decreased by 80, 84, and 86%, respectively. The model successfully identified areas of high larval abundance and showed that areas of low larval density contribute significantly to the population. Estimated treatment mortality was less than expected but had a large population-level impact. The results and general approach of this work have applications for sea lamprey control throughout the Great Lakes and for the restoration and conservation of native lamprey species globally.

Spatial price dynamics: From complex network perspective

NASA Astrophysics Data System (ADS)

Li, Y. L.; Bi, J. T.; Sun, H. J.

2008-10-01

The spatial price problem means that if the supply price plus the transportation cost is less than the demand price, there exists a trade. Thus, after an amount of exchange, the demand price will decrease. This process is continuous until an equilibrium state is obtained. However, how the trade network structure affects this process has received little attention. In this paper, we give a evolving model to describe the levels of spatial price on different complex network structures. The simulation results show that the network with shorter path length is sensitive to the variation of prices.

Development and assessment of 30-meter pine density maps for landscape-level modeling of mountain pine beetle dynamics

Treesearch

Benjamin A. Crabb; James A. Powell; Barbara J. Bentz

2012-01-01

Forecasting spatial patterns of mountain pine beetle (MPB) population success requires spatially explicit information on host pine distribution. We developed a means of producing spatially explicit datasets of pine density at 30-m resolution using existing geospatial datasets of vegetation composition and structure. Because our ultimate goal is to model MPB population...

Collective phenomena in crowds—Where pedestrian dynamics need social psychology

PubMed Central

2017-01-01

This article is on collective phenomena in pedestrian dynamics during the assembling and dispersal of gatherings. To date pedestrian dynamics have been primarily studied in the natural and engineering sciences. Pedestrians are analyzed and modeled as driven particles revealing self-organizing phenomena and complex transport characteristics. However, pedestrians in crowds also behave as living beings according to stimulus-response mechanisms or act as human subjects on the basis of social norms, social identities or strategies. To show where pedestrian dynamics need social psychology in addition to the natural sciences we propose the application of three categories–phenomena, behavior and action. They permit a clear discrimination between situations in which minimal models from the natural sciences are appropriate and those in which sociological and psychological concepts are needed. To demonstrate the necessity of this framework, an experiment in which a large group of people (n = 270) enters a concert hall through two different spatial barrier structures is analyzed. These two structures correspond to everyday situations such as boarding trains and access to immigration desks. Methods from the natural and social sciences are applied. Firstly, physical measurements show the influence of the spatial structure on the dynamics of the entrance procedure. Density, waiting time and speed of progress show large variations. Secondly, a questionnaire study (n = 60) reveals how people perceive and evaluate these entrance situations. Markedly different expectations, social norms and strategies are associated with the two spatial structures. The results from the questionnaire study do not always conform to objective physical measures, indicating the limitations of models which are based on objective physical measures alone and which neglect subjective perspectives. PMID:28591142

Collective phenomena in crowds-Where pedestrian dynamics need social psychology.

PubMed

Sieben, Anna; Schumann, Jette; Seyfried, Armin

2017-01-01

This article is on collective phenomena in pedestrian dynamics during the assembling and dispersal of gatherings. To date pedestrian dynamics have been primarily studied in the natural and engineering sciences. Pedestrians are analyzed and modeled as driven particles revealing self-organizing phenomena and complex transport characteristics. However, pedestrians in crowds also behave as living beings according to stimulus-response mechanisms or act as human subjects on the basis of social norms, social identities or strategies. To show where pedestrian dynamics need social psychology in addition to the natural sciences we propose the application of three categories-phenomena, behavior and action. They permit a clear discrimination between situations in which minimal models from the natural sciences are appropriate and those in which sociological and psychological concepts are needed. To demonstrate the necessity of this framework, an experiment in which a large group of people (n = 270) enters a concert hall through two different spatial barrier structures is analyzed. These two structures correspond to everyday situations such as boarding trains and access to immigration desks. Methods from the natural and social sciences are applied. Firstly, physical measurements show the influence of the spatial structure on the dynamics of the entrance procedure. Density, waiting time and speed of progress show large variations. Secondly, a questionnaire study (n = 60) reveals how people perceive and evaluate these entrance situations. Markedly different expectations, social norms and strategies are associated with the two spatial structures. The results from the questionnaire study do not always conform to objective physical measures, indicating the limitations of models which are based on objective physical measures alone and which neglect subjective perspectives.

A Tour Through Shape Dynamic Black Holes

NASA Astrophysics Data System (ADS)

Herczeg, Gabriel

Shape dynamics is a classical theory of gravity which agrees with general relativity in many important cases, but possesses different gauge symmetries and constraints. Rather than spacetime diffeomorphism invariance, shape dynamics takes spatial diffeomorphism invariance and spatial Weyl invariance as the fundamental gauge symmetries associated with the gravitational field. Despite these differences, shape dynamics and general relativity generically predict the same dynamics--there exist gauge-fixings of each theory that ensure agreement with the other. However, these gauge-fixing conditions are not necessarily globally well-defined and it is therefore possible to find solutions of the shape dynamics equations of motion that agree with general relativity on some open neighborhoods, but which have different global structures. In particular, the black hole solutions of the two theories disagree globally. Understanding these novel "shape dynamic black holes" is the primary goal of this thesis.

Network structure of SiO2 and MgSiO3 in amorphous and liquid States

NASA Astrophysics Data System (ADS)

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

2017-03-01

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

Species sorting and patch dynamics in harlequin metacommunities affect the relative importance of environment and space.

PubMed

Leibold, Mathew A; Loeuille, Nicolas

2015-12-01

Metacommunity theory indicates that variation in local community structure can be partitioned into components including those related to local environmental conditions vs. spatial effects and that these can be quantified using statistical methods based on variation partitioning. It has been hypothesized that joint associations of community composition with environment and space could be due to patch dynamics involving colonization-extinction processes in environmentally heterogeneous landscapes but this has yet to be theoretically shown. We develop a two-patch, type-two, species competition model in such a "harlequin" landscape (where different patches have different environments) to evaluate how composition is related to environmental and spatial effects as a function of background extinction rate. Using spatially implicit analytical models, we find that the environmental association of community composition declines with extinction rate as expected. Using spatially explicit simulation models, we further find that there is an increase in the spatial structure with extinction due to spatial patterning into clusters that are not related to environmental conditions but that this increase is limited. Natural metacommunities often show both environment and spatial determination even under conditions of relatively high isolation and these could be more easily explained by our model than alternative metacommunity models.

Regional Population Dynamics

Treesearch

Andrew Birt

2011-01-01

The population dynamics of the southern pine beetle (SPB) exhibit characteristic fluctuations between relatively long endemic and shorter outbreak periods. Populations exhibit complex and hierarchical spatial structure with beetles and larvae aggregating within individual trees, infestations with multiple infested trees, and regional outbreaks that comprise a large...

Network evolution induced by asynchronous stimuli through spike-timing-dependent plasticity.

PubMed

Yuan, Wu-Jie; Zhou, Jian-Fang; Zhou, Changsong

2013-01-01

In sensory neural system, external asynchronous stimuli play an important role in perceptual learning, associative memory and map development. However, the organization of structure and dynamics of neural networks induced by external asynchronous stimuli are not well understood. Spike-timing-dependent plasticity (STDP) is a typical synaptic plasticity that has been extensively found in the sensory systems and that has received much theoretical attention. This synaptic plasticity is highly sensitive to correlations between pre- and postsynaptic firings. Thus, STDP is expected to play an important role in response to external asynchronous stimuli, which can induce segregative pre- and postsynaptic firings. In this paper, we study the impact of external asynchronous stimuli on the organization of structure and dynamics of neural networks through STDP. We construct a two-dimensional spatial neural network model with local connectivity and sparseness, and use external currents to stimulate alternately on different spatial layers. The adopted external currents imposed alternately on spatial layers can be here regarded as external asynchronous stimuli. Through extensive numerical simulations, we focus on the effects of stimulus number and inter-stimulus timing on synaptic connecting weights and the property of propagation dynamics in the resulting network structure. Interestingly, the resulting feedforward structure induced by stimulus-dependent asynchronous firings and its propagation dynamics reflect both the underlying property of STDP. The results imply a possible important role of STDP in generating feedforward structure and collective propagation activity required for experience-dependent map plasticity in developing in vivo sensory pathways and cortices. The relevance of the results to cue-triggered recall of learned temporal sequences, an important cognitive function, is briefly discussed as well. Furthermore, this finding suggests a potential application for examining STDP by measuring neural population activity in a cultured neural network.

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

PubMed Central

Moffatt, Ryan; Ma, Buyong; Nussinov, Ruth

2016-01-01

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

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

PubMed

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

2016-04-01

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

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.

Non-monotonic spatial distribution of the interstellar dust in astrospheres: finite gyroradius effect

NASA Astrophysics Data System (ADS)

Katushkina, O. A.; Alexashov, D. B.; Izmodenov, V. V.; Gvaramadze, V. V.

2017-02-01

High-resolution mid-infrared observations of astrospheres show that many of them have filamentary (cirrus-like) structure. Using numerical models of dust dynamics in astrospheres, we suggest that their filamentary structure might be related to specific spatial distribution of the interstellar dust around the stars, caused by a gyrorotation of charged dust grains in the interstellar magnetic field. Our numerical model describes the dust dynamics in astrospheres under an influence of the Lorentz force and assumption of a constant dust charge. Calculations are performed for the dust grains with different sizes separately. It is shown that non-monotonic spatial dust distribution (viewed as filaments) appears for dust grains with the period of gyromotion comparable with the characteristic time-scale of the dust motion in the astrosphere. Numerical modelling demonstrates that the number of filaments depends on charge-to-mass ratio of dust.

Increasing connectivity between metapopulation ecology and landscape ecology.

PubMed

Howell, Paige E; Muths, Erin; Hossack, Blake R; Sigafus, Brent H; Chandler, Richard B

2018-05-01

Metapopulation ecology and landscape ecology aim to understand how spatial structure influences ecological processes, yet these disciplines address the problem using fundamentally different modeling approaches. Metapopulation models describe how the spatial distribution of patches affects colonization and extinction, but often do not account for the heterogeneity in the landscape between patches. Models in landscape ecology use detailed descriptions of landscape structure, but often without considering colonization and extinction dynamics. We present a novel spatially explicit modeling framework for narrowing the divide between these disciplines to advance understanding of the effects of landscape structure on metapopulation dynamics. Unlike previous efforts, this framework allows for statistical inference on landscape resistance to colonization using empirical data. We demonstrate the approach using 11 yr of data on a threatened amphibian in a desert ecosystem. Occupancy data for Lithobates chiricahuensis (Chiricahua leopard frog) were collected on the Buenos Aires National Wildlife Refuge (BANWR), Arizona, USA from 2007 to 2017 following a reintroduction in 2003. Results indicated that colonization dynamics were influenced by both patch characteristics and landscape structure. Landscape resistance increased with increasing elevation and distance to the nearest streambed. Colonization rate was also influenced by patch quality, with semi-permanent and permanent ponds contributing substantially more to the colonization of neighboring ponds relative to intermittent ponds. Ponds that only hold water intermittently also had the highest extinction rate. Our modeling framework can be widely applied to understand metapopulation dynamics in complex landscapes, particularly in systems in which the environment between habitat patches influences the colonization process. © 2018 by the Ecological Society of America.

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

NASA Astrophysics Data System (ADS)

Tong, Hua; Tanaka, Hajime

2018-01-01

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

Ionic wave propagation and collision in an excitable circuit model of microtubules

NASA Astrophysics Data System (ADS)

Guemkam Ghomsi, P.; Tameh Berinyoh, J. T.; Moukam Kakmeni, F. M.

2018-02-01

In this paper, we report the propensity to excitability of the internal structure of cellular microtubules, modelled as a relatively large one-dimensional spatial array of electrical units with nonlinear resistive features. We propose a model mimicking the dynamics of a large set of such intracellular dynamical entities as an excitable medium. We show that the behavior of such lattices can be described by a complex Ginzburg-Landau equation, which admits several wave solutions, including the plane waves paradigm. A stability analysis of the plane waves solutions of our dynamical system is conducted both analytically and numerically. It is observed that perturbed plane waves will always evolve toward promoting the generation of localized periodic waves trains. These modes include both stationary and travelling spatial excitations. They encompass, on one hand, localized structures such as solitary waves embracing bright solitons, dark solitons, and bisolitonic impulses with head-on collisions phenomena, and on the other hand, the appearance of both spatially homogeneous and spatially inhomogeneous stationary patterns. This ability exhibited by our array of proteinic elements to display several states of excitability exposes their stunning biological and physical complexity and is of high relevance in the description of the developmental and informative processes occurring on the subcellular scale.

Ionic wave propagation and collision in an excitable circuit model of microtubules.

PubMed

Guemkam Ghomsi, P; Tameh Berinyoh, J T; Moukam Kakmeni, F M

2018-02-01

In this paper, we report the propensity to excitability of the internal structure of cellular microtubules, modelled as a relatively large one-dimensional spatial array of electrical units with nonlinear resistive features. We propose a model mimicking the dynamics of a large set of such intracellular dynamical entities as an excitable medium. We show that the behavior of such lattices can be described by a complex Ginzburg-Landau equation, which admits several wave solutions, including the plane waves paradigm. A stability analysis of the plane waves solutions of our dynamical system is conducted both analytically and numerically. It is observed that perturbed plane waves will always evolve toward promoting the generation of localized periodic waves trains. These modes include both stationary and travelling spatial excitations. They encompass, on one hand, localized structures such as solitary waves embracing bright solitons, dark solitons, and bisolitonic impulses with head-on collisions phenomena, and on the other hand, the appearance of both spatially homogeneous and spatially inhomogeneous stationary patterns. This ability exhibited by our array of proteinic elements to display several states of excitability exposes their stunning biological and physical complexity and is of high relevance in the description of the developmental and informative processes occurring on the subcellular scale.

Vegetation dynamics

Treesearch

Sammy L. King; Terry J. Antrobus; Sarah Billups

2000-01-01

A disturbance can be defined as "any relatively discrete event in time that disrupts ecosystem, community, or population structure and changes resources, substrate availability, or the physical environment" (Pickett and White 1985). Vegetation dynamics are a function of the temporal and spatial patterns of the disturbance regime. Natural disturbance regimes...

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.

Bent dark soliton dynamics in two spatial dimensions beyond the mean field approximation

NASA Astrophysics Data System (ADS)

Mistakidis, Simeon; Katsimiga, Garyfallia; Koutentakis, Georgios; Kevrekidis, Panagiotis; Schmelcher, Peter; Theory Group of Fundamental Processes in Quantum Physics Team

2017-04-01

The dynamics of a bented dark soliton embedded in two spatial dimensions beyond the mean-field approximation is explored. We examine the case of a single bented dark soliton comparing the mean-field approximation to a correlated approach that involves multiple orbitals. Fragmentation is generally present and significantly affects the dynamics, especially in the case of stronger interparticle interactions and in that of lower atom numbers. It is shown that the presence of fragmentation allows for the appearance of solitonic and vortex structures in the higher-orbital dynamics. In particular, a variety of excitations including dark solitons in multiple orbitals and vortex-antidark complexes is observed to arise spontaneously within the beyond mean-field dynamics. Deutsche Forschungsgemeinschaft (DFG) in the framework of the SFB 925 ``Light induced dynamics and control of correlated quantum systems''.

The Magnetospheric Constellation Mission. Dynamic Response and Coupling Observatory (DRACO): Understanding the Global Dynamics of the Structured Magnetotail

NASA Technical Reports Server (NTRS)

2001-01-01

Magnetospheric Constellation Dynamic Response and Coupling Observatory (DRACO) is the Solar Terrestrial Probe (STP) designed to understand the nonlinear dynamics, responses, and connections within the Earth's structured magnetotail, using a constellation of approximately 50 to 100 distributed vector measurement spacecraft. DRACO will reveal magnetotail processes operating within a domain extending 20 Earth radii (R(sub E)) across the tail and 40 R(sub E)down the tail, on spatial and time scales accessible to global circulation models, i.e., approximately 2 R(sub E) and 10 seconds.

Simple deterministic models and applications. Comment on "Coupled disease-behavior dynamics on complex networks: A review" by Z. Wang et al.

NASA Astrophysics Data System (ADS)

Yang, Hyun Mo

2015-12-01

Currently, discrete modellings are largely accepted due to the access to computers with huge storage capacity and high performance processors and easy implementation of algorithms, allowing to develop and simulate increasingly sophisticated models. Wang et al. [7] present a review of dynamics in complex networks, focusing on the interaction between disease dynamics and human behavioral and social dynamics. By doing an extensive review regarding to the human behavior responding to disease dynamics, the authors briefly describe the complex dynamics found in the literature: well-mixed populations networks, where spatial structure can be neglected, and other networks considering heterogeneity on spatially distributed populations. As controlling mechanisms are implemented, such as social distancing due 'social contagion', quarantine, non-pharmaceutical interventions and vaccination, adaptive behavior can occur in human population, which can be easily taken into account in the dynamics formulated by networked populations.

Hydrology Affects Environmental and Spatial Structuring of Microalgal Metacommunities in Tropical Pacific Coast Wetlands.

PubMed

Rojo, Carmen; Mesquita-Joanes, Francesc; Monrós, Juan S; Armengol, Javier; Sasa, Mahmood; Bonilla, Fabián; Rueda, Ricardo; Benavent-Corai, José; Piculo, Rubén; Segura, M Matilde

2016-01-01

The alternating climate between wet and dry periods has important effects on the hydrology and therefore on niche-based processes of water bodies in tropical areas. Additionally, assemblages of microorganism can show spatial patterns, in the form of a distance decay relationship due to their size or life form. We aimed to test spatial and environmental effects, modulated by a seasonal flooding climatic pattern, on the distribution of microalgae in 30 wetlands of a tropical dry forest region: the Pacific coast of Costa Rica and Nicaragua. Three surveys were conducted corresponding to the beginning, the highest peak, and the end of the hydrological year during the wet season, and species abundance and composition of planktonic and benthic microalgae was determined. Variation partitioning analysis (as explained by spatial distance or environmental factors) was applied to each seasonal dataset by means of partial redundancy analysis. Our results show that microalgal assemblages were structured by spatial and environmental factors depending on the hydrological period of the year. At the onset of hydroperiod and during flooding, neutral effects dominated community dynamics, but niche-based local effects resulted in more structured algal communities at the final periods of desiccating water bodies. Results suggest that climate-mediated effects on hydrology can influence the relative role of spatial and environmental factors on metacommunities of microalgae. Such variability needs to be accounted in order to describe accurately community dynamics in tropical coastal wetlands.

Hydrology Affects Environmental and Spatial Structuring of Microalgal Metacommunities in Tropical Pacific Coast Wetlands

PubMed Central

Rojo, Carmen; Mesquita-Joanes, Francesc; Monrós, Juan S.; Armengol, Javier; Sasa, Mahmood; Bonilla, Fabián; Rueda, Ricardo; Benavent-Corai, José; Piculo, Rubén; Segura, M. Matilde

2016-01-01

The alternating climate between wet and dry periods has important effects on the hydrology and therefore on niche-based processes of water bodies in tropical areas. Additionally, assemblages of microorganism can show spatial patterns, in the form of a distance decay relationship due to their size or life form. We aimed to test spatial and environmental effects, modulated by a seasonal flooding climatic pattern, on the distribution of microalgae in 30 wetlands of a tropical dry forest region: the Pacific coast of Costa Rica and Nicaragua. Three surveys were conducted corresponding to the beginning, the highest peak, and the end of the hydrological year during the wet season, and species abundance and composition of planktonic and benthic microalgae was determined. Variation partitioning analysis (as explained by spatial distance or environmental factors) was applied to each seasonal dataset by means of partial redundancy analysis. Our results show that microalgal assemblages were structured by spatial and environmental factors depending on the hydrological period of the year. At the onset of hydroperiod and during flooding, neutral effects dominated community dynamics, but niche-based local effects resulted in more structured algal communities at the final periods of desiccating water bodies. Results suggest that climate-mediated effects on hydrology can influence the relative role of spatial and environmental factors on metacommunities of microalgae. Such variability needs to be accounted in order to describe accurately community dynamics in tropical coastal wetlands. PMID:26900916

Travelling waves and spatial hierarchies in measles epidemics

NASA Astrophysics Data System (ADS)

Grenfell, B. T.; Bjørnstad, O. N.; Kappey, J.

2001-12-01

Spatio-temporal travelling waves are striking manifestations of predator-prey and host-parasite dynamics. However, few systems are well enough documented both to detect repeated waves and to explain their interaction with spatio-temporal variations in population structure and demography. Here, we demonstrate recurrent epidemic travelling waves in an exhaustive spatio-temporal data set for measles in England and Wales. We use wavelet phase analysis, which allows for dynamical non-stationarity-a complication in interpreting spatio-temporal patterns in these and many other ecological time series. In the pre-vaccination era, conspicuous hierarchical waves of infection moved regionally from large cities to small towns; the introduction of measles vaccination restricted but did not eliminate this hierarchical contagion. A mechanistic stochastic model suggests a dynamical explanation for the waves-spread via infective `sparks' from large `core' cities to smaller `satellite' towns. Thus, the spatial hierarchy of host population structure is a prerequisite for these infection waves.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Post-Fire Spatial Patterns of Soil Nitrogen Mineralization and Microbial Abundance

PubMed Central

Smithwick, Erica A. H.; Naithani, Kusum J.; Balser, Teri C.; Romme, William H.; Turner, Monica G.

2012-01-01

Stand-replacing fires influence soil nitrogen availability and microbial community composition, which may in turn mediate post-fire successional dynamics and nutrient cycling. However, fires create patchiness at both local and landscape scales and do not result in consistent patterns of ecological dynamics. The objectives of this study were to (1) quantify the spatial structure of microbial communities in forest stands recently affected by stand-replacing fire and (2) determine whether microbial variables aid predictions of in situ net nitrogen mineralization rates in recently burned stands. The study was conducted in lodgepole pine (Pinus contorta var. latifolia) and Engelmann spruce/subalpine fir (Picea engelmannii/Abies lasiocarpa) forest stands that burned during summer 2000 in Greater Yellowstone (Wyoming, USA). Using a fully probabilistic spatial process model and Bayesian kriging, the spatial structure of microbial lipid abundance and fungi-to-bacteria ratios were found to be spatially structured within plots two years following fire (for most plots, autocorrelation range varied from 1.5 to 10.5 m). Congruence of spatial patterns among microbial variables, in situ net N mineralization, and cover variables was evident. Stepwise regression resulted in significant models of in situ net N mineralization and included variables describing fungal and bacterial abundance, although explained variance was low (R2<0.29). Unraveling complex spatial patterns of nutrient cycling and the biotic factors that regulate it remains challenging but is critical for explaining post-fire ecosystem function, especially in Greater Yellowstone, which is projected to experience increased fire frequencies by mid 21st Century. PMID:23226324

Relatedness in spatially structured populations with empty sites: An approach based on spatial moment equations.

PubMed

Lion, Sébastien

2009-09-07

Taking into account the interplay between spatial ecological dynamics and selection is a major challenge in evolutionary ecology. Although inclusive fitness theory has proven to be a very useful tool to unravel the interactions between spatial genetic structuring and selection, applications of the theory usually rely on simplifying demographic assumptions. In this paper, I attempt to bridge the gap between spatial demographic models and kin selection models by providing a method to compute approximations for relatedness coefficients in a spatial model with empty sites. Using spatial moment equations, I provide an approximation of nearest-neighbour relatedness on random regular networks, and show that this approximation performs much better than the ordinary pair approximation. I discuss the connection between the relatedness coefficients I define and those used in population genetics, and sketch some potential extensions of the theory.

Drivers of Macrofungi Community Structure Differ between Soil and Rotten-Wood Substrates in a Temperate Mountain Forest in China

PubMed Central

Chen, Yun; Svenning, Jens-Christian; Wang, Xueying; Cao, Ruofan; Yuan, Zhiliang; Ye, Yongzhong

2018-01-01

The effects of environmental and dispersal processes on macrofungi community assembly remain unclear. Further, it is not well understood if community assembly differs for different functional guilds of macrofungi, e.g., soil and rotten-wood macrofungi. In this study, using 2433 macrofungi sporocarps belonging to 217 species located within a forest dynamics plot in temperate mountain forest (China), we examined the explanatory power of topography, spatial eigenvectors (representing unknown spatial processes, e.g., dispersal), plant community, and light availability for local spatial variation in the macrofungi community through variance partitioning and partial least squares path modeling. We found spatial eigenvectors and light as the most important factors for explaining species richness and composition of macrofungi. Light was negatively correlated with species richness of macrofungi. Furthermore, species richness and composition of soil macrofungi were best explained by light, and species richness and composition of rotten-wood macrofungi were best explained by spatial eigenvectors. Woody plant community structure was not an important factor for species richness and composition of macrofungi. Our findings suggest that spatial processes, perhaps dispersal limitation, and light availability were the most important factors affecting macrofungi community in temperate deciduous broad-leaved forest. Major differences in influencing factors between soil and rotten-wood macrofungi were observed, with light as the major driver for soil macrofungi and unknown spatial processes as the major driver for rotten-wood macrofungi. These findings shed new light to the processes shaping community assembly in macrofungi in temperate deciduous broad-leaved forest and point to the potential importance of both intrinsic dynamics, such as dispersal, and external forcing, such as forest dynamics, via its effect on light availability. PMID:29410660

A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy

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

Lewis, Nicholas H. C.; Dong, Hui; Oliver, Thomas A. A.

2015-09-28

Two dimensional electronic spectroscopy has proven to be a valuable experimental technique to reveal electronic excitation dynamics in photosynthetic pigment-protein complexes, nanoscale semiconductors, organic photovoltaic materials, and many other types of systems. It does not, however, provide direct information concerning the spatial structure and dynamics of excitons. 2D infrared spectroscopy has become a widely used tool for studying structural dynamics but is incapable of directly providing information concerning electronic excited states. 2D electronic-vibrational (2DEV) spectroscopy provides a link between these domains, directly connecting the electronic excitation with the vibrational structure of the system under study. In this work, we derivemore » response functions for the 2DEV spectrum of a molecular dimer and propose a method by which 2DEV spectra could be used to directly measure the electronic site populations as a function of time following the initial electronic excitation. We present results from the response function simulations which show that our proposed approach is substantially valid. This method provides, to our knowledge, the first direct experimental method for measuring the electronic excited state dynamics in the spatial domain, on the molecular scale.« less

A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy

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

Lewis, Nicholas H. C.; Dong, Hui; Oliver, Thomas A. A.

2015-09-28

Two dimensional electronic spectroscopy has proved to be a valuable experimental technique to reveal electronic excitation dynamics in photosynthetic pigment-protein complexes, nanoscale semiconductors, organic photovoltaic materials, and many other types of systems. It does not, however, provide direct information concerning the spatial structure and dynamics of excitons. 2D infrared spectroscopy has become a widely used tool for studying structural dynamics but is incapable of directly providing information concerning electronic excited states. 2D electronic-vibrational (2DEV) spectroscopy provides a link between these domains, directly connecting the electronic excitation with the vibrational structure of the system under study. In this work, we derivemore » response functions for the 2DEV spectrum of a molecular dimer and propose a method by which 2DEV spectra could be used to directly measure the electronic site populations as a function of time following the initial electronic excitation. We present results from the response function simulations which show that our proposed approach is substantially valid. This method provides, to our knowledge, the first direct experimental method for measuring the electronic excited state dynamics in the spatial domain, on the molecular scale.« less

A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy.

PubMed

Lewis, Nicholas H C; Dong, Hui; Oliver, Thomas A A; Fleming, Graham R

2015-09-28

Two dimensional electronic spectroscopy has proved to be a valuable experimental technique to reveal electronic excitation dynamics in photosynthetic pigment-protein complexes, nanoscale semiconductors, organic photovoltaic materials, and many other types of systems. It does not, however, provide direct information concerning the spatial structure and dynamics of excitons. 2D infrared spectroscopy has become a widely used tool for studying structural dynamics but is incapable of directly providing information concerning electronic excited states. 2D electronic-vibrational (2DEV) spectroscopy provides a link between these domains, directly connecting the electronic excitation with the vibrational structure of the system under study. In this work, we derive response functions for the 2DEV spectrum of a molecular dimer and propose a method by which 2DEV spectra could be used to directly measure the electronic site populations as a function of time following the initial electronic excitation. We present results from the response function simulations which show that our proposed approach is substantially valid. This method provides, to our knowledge, the first direct experimental method for measuring the electronic excited state dynamics in the spatial domain, on the molecular scale.

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

NASA Astrophysics Data System (ADS)

Pepin, Kim M.; Vercauteren, Kurt C.

2016-04-01

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

Semantic modeling of the structural and process entities during plastic deformation of crystals and rocks

NASA Astrophysics Data System (ADS)

Babaie, Hassan; Davarpanah, Armita

2016-04-01

We are semantically modeling the structural and dynamic process components of the plastic deformation of minerals and rocks in the Plastic Deformation Ontology (PDO). Applying the Ontology of Physics in Biology, the PDO classifies the spatial entities that participate in the diverse processes of plastic deformation into the Physical_Plastic_Deformation_Entity and Nonphysical_Plastic_Deformation_Entity classes. The Material_Physical_Plastic_Deformation_Entity class includes things such as microstructures, lattice defects, atoms, liquid, and grain boundaries, and the Immaterial_Physical_Plastic_Deformation_Entity class includes vacancies in crystals and voids along mineral grain boundaries. The objects under the many subclasses of these classes (e.g., crystal, lattice defect, layering) have spatial parts that are related to each other through taxonomic (e.g., Line_Defect isA Lattice_Defect), structural (mereological, e.g., Twin_Plane partOf Twin), spatial-topological (e.g., Vacancy adjacentTo Atom, Fluid locatedAlong Grain_Boundary), and domain specific (e.g., displaces, Fluid crystallizes Dissolved_Ion, Void existsAlong Grain_Boundary) relationships. The dynamic aspect of the plastic deformation is modeled under the dynamical Process_Entity class that subsumes classes such as Recrystallization and Pressure_Solution that define the flow of energy amongst the physical entities. The values of the dynamical state properties of the physical entities (e.g., Chemical_Potential, Temperature, Particle_Velocity) change while they take part in the deformational processes such as Diffusion and Dislocation_Glide. The process entities have temporal parts (phases) that are related to each other through temporal relations such as precedes, isSubprocessOf, and overlaps. The properties of the physical entities, defined under the Physical_Property class, change as they participate in the plastic deformational processes. The properties are categorized into dynamical, constitutive, spatial, temporal, statistical, and thermodynamical. The dynamical properties, categorized under the Dynamical_Rate_Property and Dynamical_State_Property classes, subsume different classes of properties (e.g., Fluid_Flow_Rate, Temperature, Chemical_Potential, Displacement, Electrical_Charge) based on the physical domain (e.g., fluid, heat, chemical, solid, electrical). The properties are related to the objects under the Physical_Entity class through diverse object type (e.g., physicalPropertyOf) and data type (e.g., Fluid_Pressure unit 'MPa') properties. The changes of the dynamical properties of the physical entities, described by the empirical laws (equations) modeled by experimental structural geologists, are modeled through the Physical_Property_Dependency class that subsumes the more specialized constitutive, kinetic, and thermodynamic expressions of the relationships among the dynamic properties. Annotation based on the PDO will make it possible to integrate and reuse experimental plastic deformation data, knowledge, and simulation models, and conduct semantic-based search of the source data originating from different rock testing laboratories.

Nanosensitive optical coherence tomography for the study of changes in static and dynamic structures

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

Alexandrov, S; Subhash, H; Leahy, M

2014-07-31

We briefly discuss the principle of image formation in Fourier domain optical coherence tomography (OCT). The theory of a new approach to improve dramatically the sensitivity of conventional OCT is described. The approach is based on spectral encoding of spatial frequency. Information about the spatial structure is directly translated from the Fourier domain to the image domain as different wavelengths, without compromising the accuracy. Axial spatial period profiles of the structure are reconstructed for any volume of interest within the 3D OCT image with nanoscale sensitivity. An example of application of the nanoscale OCT to probe the internal structure ofmore » medico-biological objects, the anterior chamber of an ex vivo rat eye, is demonstrated. (laser biophotonics)« less

Programmed coherent coupling in a synthetic DNA-based excitonic circuit

NASA Astrophysics Data System (ADS)

Boulais, Étienne; Sawaya, Nicolas P. D.; Veneziano, Rémi; Andreoni, Alessio; Banal, James L.; Kondo, Toru; Mandal, Sarthak; Lin, Su; Schlau-Cohen, Gabriela S.; Woodbury, Neal W.; Yan, Hao; Aspuru-Guzik, Alán; Bathe, Mark

2018-02-01

Natural light-harvesting systems spatially organize densely packed chromophore aggregates using rigid protein scaffolds to achieve highly efficient, directed energy transfer. Here, we report a synthetic strategy using rigid DNA scaffolds to similarly program the spatial organization of densely packed, discrete clusters of cyanine dye aggregates with tunable absorption spectra and strongly coupled exciton dynamics present in natural light-harvesting systems. We first characterize the range of dye-aggregate sizes that can be templated spatially by A-tracts of B-form DNA while retaining coherent energy transfer. We then use structure-based modelling and quantum dynamics to guide the rational design of higher-order synthetic circuits consisting of multiple discrete dye aggregates within a DX-tile. These programmed circuits exhibit excitonic transport properties with prominent circular dichroism, superradiance, and fast delocalized exciton transfer, consistent with our quantum dynamics predictions. This bottom-up strategy offers a versatile approach to the rational design of strongly coupled excitonic circuits using spatially organized dye aggregates for use in coherent nanoscale energy transport, artificial light-harvesting, and nanophotonics.

Comparison of Static and Dynamic Assessment Procedures and Their Relation to Independent Performance.

ERIC Educational Resources Information Center

Day, Jeanne D.; And Others

1997-01-01

Relationships between pretraining skills, learning, and posttest performance were studied in spatial and verbal tasks for 84 preschool children. The measurement model that fit the data best maintained separate verbal and spatial domains. The best structural model included paths from pretest and learning assessments to posttest performance within…

Harnessing Big Data to Represent 30-meter Spatial Heterogeneity in Earth System Models

NASA Astrophysics Data System (ADS)

Chaney, N.; Shevliakova, E.; Malyshev, S.; Van Huijgevoort, M.; Milly, C.; Sulman, B. N.

2016-12-01

Terrestrial land surface processes play a critical role in the Earth system; they have a profound impact on the global climate, food and energy production, freshwater resources, and biodiversity. One of the most fascinating yet challenging aspects of characterizing terrestrial ecosystems is their field-scale (˜30 m) spatial heterogeneity. It has been observed repeatedly that the water, energy, and biogeochemical cycles at multiple temporal and spatial scales have deep ties to an ecosystem's spatial structure. Current Earth system models largely disregard this important relationship leading to an inadequate representation of ecosystem dynamics. In this presentation, we will show how existing global environmental datasets can be harnessed to explicitly represent field-scale spatial heterogeneity in Earth system models. For each macroscale grid cell, these environmental data are clustered according to their field-scale soil and topographic attributes to define unique sub-grid tiles. The state-of-the-art Geophysical Fluid Dynamics Laboratory (GFDL) land model is then used to simulate these tiles and their spatial interactions via the exchange of water, energy, and nutrients along explicit topographic gradients. Using historical simulations over the contiguous United States, we will show how a robust representation of field-scale spatial heterogeneity impacts modeled ecosystem dynamics including the water, energy, and biogeochemical cycles as well as vegetation composition and distribution.

A multistate dynamic site occupancy model for spatially aggregated sessile communities

USGS Publications Warehouse

Fukaya, Keiichi; Royle, J. Andrew; Okuda, Takehiro; Nakaoka, Masahiro; Noda, Takashi

2017-01-01

Estimation of transition probabilities of sessile communities seems easy in principle but may still be difficult in practice because resampling error (i.e. a failure to resample exactly the same location at fixed points) may cause significant estimation bias. Previous studies have developed novel analytical methods to correct for this estimation bias. However, they did not consider the local structure of community composition induced by the aggregated distribution of organisms that is typically observed in sessile assemblages and is very likely to affect observations.We developed a multistate dynamic site occupancy model to estimate transition probabilities that accounts for resampling errors associated with local community structure. The model applies a nonparametric multivariate kernel smoothing methodology to the latent occupancy component to estimate the local state composition near each observation point, which is assumed to determine the probability distribution of data conditional on the occurrence of resampling error.By using computer simulations, we confirmed that an observation process that depends on local community structure may bias inferences about transition probabilities. By applying the proposed model to a real data set of intertidal sessile communities, we also showed that estimates of transition probabilities and of the properties of community dynamics may differ considerably when spatial dependence is taken into account.Results suggest the importance of accounting for resampling error and local community structure for developing management plans that are based on Markovian models. Our approach provides a solution to this problem that is applicable to broad sessile communities. It can even accommodate an anisotropic spatial correlation of species composition, and may also serve as a basis for inferring complex nonlinear ecological dynamics.

Simulated GOLD Observations of Atmospheric Waves

NASA Astrophysics Data System (ADS)

Correira, J.; Evans, J. S.; Lumpe, J. D.; Rusch, D. W.; Chandran, A.; Eastes, R.; Codrescu, M.

2016-12-01

The Global-scale Observations of the Limb and Disk (GOLD) mission will measure structures in the Earth's airglow layer due to dynamical forcing by vertically and horizontally propagating waves. These measurements focus on global-scale structures, including compositional and temperature responses resulting from dynamical forcing. Daytime observations of far-UV emissions by GOLD will be used to generate two-dimensional maps of the ratio of atomic oxygen and molecular nitrogen column densities (ΣO/N2 ) as well as neutral temperature that provide signatures of large-scale spatial structure. In this presentation, we use simulations to demonstrate GOLD's capability to deduce periodicities and spatial dimensions of large-scale waves from the spatial and temporal evolution observed in composition and temperature maps. Our simulations include sophisticated forward modeling of the upper atmospheric airglow that properly accounts for anisotropy in neutral and ion composition, temperature, and solar illumination. Neutral densities and temperatures used in the simulations are obtained from global circulation and climatology models that have been perturbed by propagating waves with a range of amplitudes, periods, and sources of excitation. Modeling of airglow emission and predictions of ΣO/N2 and neutral temperatures are performed with the Atmospheric Ultraviolet Radiance Integrated Code (AURIC) and associated derived product algorithms. Predicted structure in ΣO/N2 and neutral temperature due to dynamical forcing by propagating waves is compared to existing observations. Realistic GOLD Level 2 data products are generated from simulated airglow emission using algorithm code that will be implemented operationally at the GOLD Science Data Center.

Linking models and data on vegetation structure

NASA Astrophysics Data System (ADS)

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

2010-06-01

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

Metapopulation dynamics in a changing climate: Increasing spatial synchrony in weather conditions drives metapopulation synchrony of a butterfly inhabiting a fragmented landscape.

PubMed

Kahilainen, Aapo; van Nouhuys, Saskya; Schulz, Torsti; Saastamoinen, Marjo

2018-04-23

Habitat fragmentation and climate change are both prominent manifestations of global change, but there is little knowledge on the specific mechanisms of how climate change may modify the effects of habitat fragmentation, for example, by altering dynamics of spatially structured populations. The long-term viability of metapopulations is dependent on independent dynamics of local populations, because it mitigates fluctuations in the size of the metapopulation as a whole. Metapopulation viability will be compromised if climate change increases spatial synchrony in weather conditions associated with population growth rates. We studied a recently reported increase in metapopulation synchrony of the Glanville fritillary butterfly (Melitaea cinxia) in the Finnish archipelago, to see if it could be explained by an increase in synchrony of weather conditions. For this, we used 23 years of butterfly survey data together with monthly weather records for the same period. We first examined the associations between population growth rates within different regions of the metapopulation and weather conditions during different life-history stages of the butterfly. We then examined the association between the trends in the synchrony of the weather conditions and the synchrony of the butterfly metapopulation dynamics. We found that precipitation from spring to late summer are associated with the M. cinxia per capita growth rate, with early summer conditions being most important. We further found that the increase in metapopulation synchrony is paralleled by an increase in the synchrony of weather conditions. Alternative explanations for spatial synchrony, such as increased dispersal or trophic interactions with a specialist parasitoid, did not show paralleled trends and are not supported. The climate driven increase in M. cinxia metapopulation synchrony suggests that climate change can increase extinction risk of spatially structured populations living in fragmented landscapes by altering their dynamics. © 2018 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

Measles metapopulation dynamics: a gravity model for epidemiological coupling and dynamics.

PubMed

Xia, Yingcun; Bjørnstad, Ottar N; Grenfell, Bryan T

2004-08-01

Infectious diseases provide a particularly clear illustration of the spatiotemporal underpinnings of consumer-resource dynamics. The paradigm is provided by extremely contagious, acute, immunizing childhood infections. Partially synchronized, unstable oscillations are punctuated by local extinctions. This, in turn, can result in spatial differentiation in the timing of epidemics and, depending on the nature of spatial contagion, may result in traveling waves. Measles epidemics are one of a few systems documented well enough to reveal all of these properties and how they are affected by spatiotemporal variations in population structure and demography. On the basis of a gravity coupling model and a time series susceptible-infected-recovered (TSIR) model for local dynamics, we propose a metapopulation model for regional measles dynamics. The model can capture all the major spatiotemporal properties in prevaccination epidemics of measles in England and Wales.

A computer-assisted study of pulse dynamics in anisotropic media

NASA Astrophysics Data System (ADS)

Krishnan, J.; Engelborghs, K.; Bär, M.; Lust, K.; Roose, D.; Kevrekidis, I. G.

2001-06-01

This study focuses on the computer-assisted stability analysis of travelling pulse-like structures in spatially periodic heterogeneous reaction-diffusion media. The physical motivation comes from pulse propagation in thin annular domains on a diffusionally anisotropic catalytic surface. The study was performed by computing the travelling pulse-like structures as limit cycles of the spatially discretized PDE, which in turn is performed in two ways: a Newton method based on a pseudospectral discretization of the PDE, and a Newton-Picard method based on a finite difference discretization. Details about the spectra of these modulated pulse-like structures are discussed, including how they may be compared with the spectra of pulses in homogeneous media. The effects of anisotropy on the dynamics of pulses and pulse pairs are studied. Beyond shifting the location of bifurcations present in homogeneous media, anisotropy can also introduce certain new instabilities.

Motion-adaptive spatio-temporal regularization for accelerated dynamic MRI.

PubMed

Asif, M Salman; Hamilton, Lei; Brummer, Marijn; Romberg, Justin

2013-09-01

Accelerated magnetic resonance imaging techniques reduce signal acquisition time by undersampling k-space. A fundamental problem in accelerated magnetic resonance imaging is the recovery of quality images from undersampled k-space data. Current state-of-the-art recovery algorithms exploit the spatial and temporal structures in underlying images to improve the reconstruction quality. In recent years, compressed sensing theory has helped formulate mathematical principles and conditions that ensure recovery of (structured) sparse signals from undersampled, incoherent measurements. In this article, a new recovery algorithm, motion-adaptive spatio-temporal regularization, is presented that uses spatial and temporal structured sparsity of MR images in the compressed sensing framework to recover dynamic MR images from highly undersampled k-space data. In contrast to existing algorithms, our proposed algorithm models temporal sparsity using motion-adaptive linear transformations between neighboring images. The efficiency of motion-adaptive spatio-temporal regularization is demonstrated with experiments on cardiac magnetic resonance imaging for a range of reduction factors. Results are also compared with k-t FOCUSS with motion estimation and compensation-another recently proposed recovery algorithm for dynamic magnetic resonance imaging. . Copyright © 2012 Wiley Periodicals, Inc.

Water Quality Sensing and Spatio-Temporal Monitoring Structure with Autocorrelation Kernel Methods.

PubMed

Vizcaíno, Iván P; Carrera, Enrique V; Muñoz-Romero, Sergio; Cumbal, Luis H; Rojo-Álvarez, José Luis

2017-10-16

Pollution on water resources is usually analyzed with monitoring campaigns, which consist of programmed sampling, measurement, and recording of the most representative water quality parameters. These campaign measurements yields a non-uniform spatio-temporal sampled data structure to characterize complex dynamics phenomena. In this work, we propose an enhanced statistical interpolation method to provide water quality managers with statistically interpolated representations of spatial-temporal dynamics. Specifically, our proposal makes efficient use of the a priori available information of the quality parameter measurements through Support Vector Regression (SVR) based on Mercer's kernels. The methods are benchmarked against previously proposed methods in three segments of the Machángara River and one segment of the San Pedro River in Ecuador, and their different dynamics are shown by statistically interpolated spatial-temporal maps. The best interpolation performance in terms of mean absolute error was the SVR with Mercer's kernel given by either the Mahalanobis spatial-temporal covariance matrix or by the bivariate estimated autocorrelation function. In particular, the autocorrelation kernel provides with significant improvement of the estimation quality, consistently for all the six water quality variables, which points out the relevance of including a priori knowledge of the problem.

Water Quality Sensing and Spatio-Temporal Monitoring Structure with Autocorrelation Kernel Methods

PubMed Central

Vizcaíno, Iván P.; Muñoz-Romero, Sergio; Cumbal, Luis H.

2017-01-01

Pollution on water resources is usually analyzed with monitoring campaigns, which consist of programmed sampling, measurement, and recording of the most representative water quality parameters. These campaign measurements yields a non-uniform spatio-temporal sampled data structure to characterize complex dynamics phenomena. In this work, we propose an enhanced statistical interpolation method to provide water quality managers with statistically interpolated representations of spatial-temporal dynamics. Specifically, our proposal makes efficient use of the a priori available information of the quality parameter measurements through Support Vector Regression (SVR) based on Mercer’s kernels. The methods are benchmarked against previously proposed methods in three segments of the Machángara River and one segment of the San Pedro River in Ecuador, and their different dynamics are shown by statistically interpolated spatial-temporal maps. The best interpolation performance in terms of mean absolute error was the SVR with Mercer’s kernel given by either the Mahalanobis spatial-temporal covariance matrix or by the bivariate estimated autocorrelation function. In particular, the autocorrelation kernel provides with significant improvement of the estimation quality, consistently for all the six water quality variables, which points out the relevance of including a priori knowledge of the problem. PMID:29035333

Spatial and Temporal Dynamics of Pacific Oyster Hemolymph Microbiota across Multiple Scales

PubMed Central

Lokmer, Ana; Goedknegt, M. Anouk; Thieltges, David W.; Fiorentino, Dario; Kuenzel, Sven; Baines, John F.; Wegner, K. Mathias

2016-01-01

Unveiling the factors and processes that shape the dynamics of host associated microbial communities (microbiota) under natural conditions is an important part of understanding and predicting an organism's response to a changing environment. The microbiota is shaped by host (i.e., genetic) factors as well as by the biotic and abiotic environment. Studying natural variation of microbial community composition in multiple host genetic backgrounds across spatial as well as temporal scales represents a means to untangle this complex interplay. Here, we combined a spatially-stratified with a longitudinal sampling scheme within differentiated host genetic backgrounds by reciprocally transplanting Pacific oysters between two sites in the Wadden Sea (Sylt and Texel). To further differentiate contingent site from host genetic effects, we repeatedly sampled the same individuals over a summer season to examine structure, diversity and dynamics of individual hemolymph microbiota following experimental removal of resident microbiota by antibiotic treatment. While a large proportion of microbiome variation could be attributed to immediate environmental conditions, we observed persistent effects of antibiotic treatment and translocation suggesting that hemolymph microbial community dynamics is subject to within-microbiome interactions and host population specific factors. In addition, the analysis of spatial variation revealed that the within-site microenvironmental heterogeneity resulted in high small-scale variability, as opposed to large-scale (between-site) stability. Similarly, considerable within-individual temporal variability was in contrast with the overall temporal stability at the site level. Overall, our longitudinal, spatially-stratified sampling design revealed that variation in hemolymph microbiota is strongly influenced by site and immediate environmental conditions, whereas internal microbiome dynamics and oyster-related factors add to their long-term stability. The combination of small and large scale resolution of spatial and temporal observations therefore represents a crucial but underused tool to study host-associated microbiome dynamics. PMID:27630625

Invariant Manifolds, the Spatial Three-Body Problem and Space Mission Design

NASA Technical Reports Server (NTRS)

Gomez, G.; Koon, W. S.; Lo, Martin W.; Marsden, J. E.; Masdemont, J.; Ross, S. D.

2001-01-01

The invariant manifold structures of the collinear libration points for the spatial restricted three-body problem provide the framework for understanding complex dynamical phenomena from a geometric point of view. In particular, the stable and unstable invariant manifold 'tubes' associated to libration point orbits are the phase space structures that provide a conduit for orbits between primary bodies for separate three-body systems. These invariant manifold tubes can be used to construct new spacecraft trajectories, such as 'Petit Grand Tour' of the moons of Jupiter. Previous work focused on the planar circular restricted three-body problem. The current work extends the results to the spatial case.

Stage-structured infection transmission and a spatial epidemic: a model for Lyme disease.

PubMed

Caraco, Thomas; Glavanakov, Stephan; Chen, Gang; Flaherty, Joseph E; Ohsumi, Toshiro K; Szymanski, Boleslaw K

2002-09-01

A greater understanding of the rate at which emerging disease advances spatially has both ecological and applied significance. Analyzing the spread of vector-borne disease can be relatively complex when the vector's acquisition of a pathogen and subsequent transmission to a host occur in different life stages. A contemporary example is Lyme disease. A long-lived tick vector acquires infection during the larval blood meal and transmits it as a nymph. We present a reaction-diffusion model for the ecological dynamics governing the velocity of the current epidemic's spread. We find that the equilibrium density of infectious tick nymphs (hence the risk of human disease) can depend on density-independent survival interacting with biotic effects on the tick's stage structure. The local risk of infection reaches a maximum at an intermediate level of adult tick mortality and at an intermediate rate of juvenile tick attacks on mammalian hosts. If the juvenile tick attack rate is low, an increase generates both a greater density of infectious nymphs and an increased spatial velocity. However, if the juvenile attack rate is relatively high, nymph density may decline while the epidemic's velocity still increases. Velocities of simulated two-dimensional epidemics correlate with the model pathogen's basic reproductive number (R0), but calculating R0 involves parameters of both host infection dynamics and the vector's stage-structured dynamics.

Comment on: Polar Plumes and Fine-scale Coronal Structures - On the Interpretation of Coronal Radio Sounding Data by Patzold and Bird

NASA Technical Reports Server (NTRS)

Woo, R.; Habbal, S. R.

1998-01-01

Radio occultation measurements, which probe electron density over a wide dynamic range with high sensitivity and high spatial and temporal resolution reveal a solar corona permeated by a hierarchy of filamentary structures.

Harnessing cell-to-cell variations to probe bacterial structure and biophysics

NASA Astrophysics Data System (ADS)

Cass, Julie A.

Advances in microscopy and biotechnology have given us novel insights into cellular biology and physics. While bacteria were long considered to be relatively unstructured, the development of fluorescence microscopy techniques, and spatially and temporally resolved high-throughput quantitative studies, have uncovered that the bacterial cell is highly organized, and its structure rigorously maintained. In this thesis I will describe our gateTool software, designed to harness cell-to-cell variations to probe bacterial structure, and discuss two exciting aspects of structure that we have employed gateTool to investigate: (i) chromosome organization and the cellular mechanisms for controlling DNA dynamics, and (ii) the study of cell wall synthesis, and how the genes in the synthesis pathway impact cellular shape. In the first project, we develop a spatial and temporal mapping of cell-cycle-dependent chromosomal organization, and use this quantitative map to discover that chromosomal loci segregate from midcell with universal dynamics. In the second project, I describe preliminary time- lapse and snapshot imaging analysis suggesting phentoypical coherence across peptidoglycan synthesis pathways.

Spatial Structures of the Environment and of Dispersal Impact Species Distribution in Competitive Metacommunities

PubMed Central

Ai, Dexiecuo; Gravel, Dominique; Chu, Chengjin; Wang, Gang

2013-01-01

The correspondence between species distribution and the environment depends on species’ ability to track favorable environmental conditions (via dispersal) and to maintain competitive hierarchy against the constant influx of migrants (mass effect) and demographic stochasticity (ecological drift). Here we report a simulation study of the influence of landscape structure on species distribution. We consider lottery competition for space in a spatially heterogeneous environment, where the landscape is represented as a network of localities connected by dispersal. We quantified the contribution of neutrality and species sorting to their spatial distribution. We found that neutrality increases and the strength of species-sorting decreases with the centrality of a community in the landscape when the average dispersal among communities is low, whereas the opposite was found at elevated dispersal. We also found that the strength of species-sorting increases with environmental heterogeneity. Our results illustrate that spatial structure of the environment and of dispersal must be taken into account for understanding species distribution. We stress the importance of spatial geographic structure on the relative importance of niche vs. neutral processes in controlling community dynamics. PMID:23874815

Spatial structures of the environment and of dispersal impact species distribution in competitive metacommunities.

PubMed

Ai, Dexiecuo; Gravel, Dominique; Chu, Chengjin; Wang, Gang

2013-01-01

The correspondence between species distribution and the environment depends on species' ability to track favorable environmental conditions (via dispersal) and to maintain competitive hierarchy against the constant influx of migrants (mass effect) and demographic stochasticity (ecological drift). Here we report a simulation study of the influence of landscape structure on species distribution. We consider lottery competition for space in a spatially heterogeneous environment, where the landscape is represented as a network of localities connected by dispersal. We quantified the contribution of neutrality and species sorting to their spatial distribution. We found that neutrality increases and the strength of species-sorting decreases with the centrality of a community in the landscape when the average dispersal among communities is low, whereas the opposite was found at elevated dispersal. We also found that the strength of species-sorting increases with environmental heterogeneity. Our results illustrate that spatial structure of the environment and of dispersal must be taken into account for understanding species distribution. We stress the importance of spatial geographic structure on the relative importance of niche vs. neutral processes in controlling community dynamics.

Intermittency, nonlinear dynamics and dissipation in the solar wind and astrophysical plasmas

PubMed Central

Matthaeus, W. H.; Wan, Minping; Servidio, S.; Greco, A.; Osman, K. T.; Oughton, S.; Dmitruk, P.

2015-01-01

An overview is given of important properties of spatial and temporal intermittency, including evidence of its appearance in fluids, magnetofluids and plasmas, and its implications for understanding of heliospheric plasmas. Spatial intermittency is generally associated with formation of sharp gradients and coherent structures. The basic physics of structure generation is ideal, but when dissipation is present it is usually concentrated in regions of strong gradients. This essential feature of spatial intermittency in fluids has been shown recently to carry over to the realm of kinetic plasma, where the dissipation function is not known from first principles. Spatial structures produced in intermittent plasma influence dissipation, heating, and transport and acceleration of charged particles. Temporal intermittency can give rise to very long time correlations or a delayed approach to steady-state conditions, and has been associated with inverse cascade or quasi-inverse cascade systems, with possible implications for heliospheric prediction. PMID:25848085

The Spatial Structure of Planform Migration - Curvature Relation of Meandering Rivers

NASA Astrophysics Data System (ADS)

Guneralp, I.; Rhoads, B. L.

2005-12-01

Planform dynamics of meandering rivers have been of fundamental interest to fluvial geomorphologists and engineers because of the intriguing complexity of these dynamics, the role of planform change in floodplain development and landscape evolution, and the economic and social consequences of bank erosion and channel migration. Improved understanding of the complex spatial structure of planform change and capacity to predict these changes are important for effective stream management, engineering and restoration. The planform characteristics of a meandering river channel are integral to its planform dynamics. Active meandering rivers continually change their positions and shapes as a consequence of hydraulic forces exerted on the channel banks and bed, but as the banks and bed change through sediment transport, so do the hydraulic forces. Thus far, this complex feedback between form and process is incompletely understood, despite the fact that the characteristics and the dynamics of meandering rivers have been studied extensively. Current theoretical models aimed at predicting planform dynamics relate rates of meander migration to local and upstream planform curvature where weighting of the influence of curvature on migration rate decays exponentially over distance. This theoretical relation, however, has not been rigorously evaluated empirically. Furthermore, although models based on exponential-weighting of curvature effects yield fairly realistic predictions of meander migration, such models are incapable of reproducing complex forms of bend development, such as double heading or compound looping. This study presents the development of a new methodology based on parametric cubic spline interpolation for the characterization of channel planform and the planform curvature of meandering rivers. The use of continuous mathematical functions overcomes the reliance on bend-averaged values or piece-wise discrete approximations of planform curvature - a major limitation of previous studies. Continuous curvature series can be related to measured rates of lateral migration to explore empirically the relationship between spatially extended curvature and local bend migration. The methodology is applied to a study reach along a highly sinuous section of the Embarras River in Illinois, USA, which contains double-headed asymmetrical loops. To identify patterns of channel planform and rates of lateral migration for a study reach along Embarrass River in central Illinois, geographical information systems analysis of historical aerial photography over a period from 1936 to 1998 was conducted. Results indicate that parametric cubic spline interpolation provides excellent characterization of the complex planforms and planform curvatures of meandering rivers. The findings also indicate that the spatial structure of migration rate-curvature relation may be more complex than a simple exponential distance-decay function. The study represents a first step toward unraveling the spatial structure of planform evolution of meandering rivers and for developing models of planform dynamics that accurately relate spatially extended patterns of channel curvature to local rates of lateral migration. Such knowledge is vital for improving the capacity to accurately predict planform change of meandering rivers.

Experimental Investigation of Ultrafast Hydration Structure and Dynamics at Sub-Angstrom Lengthscales

ERIC Educational Resources Information Center

Coridan, Robert Henry

2009-01-01

This thesis outlines how meV-resolution inelastic x-ray scattering and causality-enforcing mathematics can be used to measure the dynamical density-density linear response function for liquid water with Angstrom spatial resolution and 50fs temporal resolution. The results are compared to high-resolution spectroscopic and scattering experiments and…

Transitions from trees to cycles in adaptive flow networks

NASA Astrophysics Data System (ADS)

Martens, Erik A.; Klemm, Konstantin

2017-11-01

Transport networks are crucial to the functioning of natural and technological systems. Nature features transport networks that are adaptive over a vast range of parameters, thus providing an impressive level of robustness in supply. Theoretical and experimental studies have found that real-world transport networks exhibit both tree-like motifs and cycles. When the network is subject to load fluctuations, the presence of cyclic motifs may help to reduce flow fluctuations and, thus, render supply in the network more robust. While previous studies considered network topology via optimization principles, here, we take a dynamical systems approach and study a simple model of a flow network with dynamically adapting weights (conductances). We assume a spatially non-uniform distribution of rapidly fluctuating loads in the sinks and investigate what network configurations are dynamically stable. The network converges to a spatially non-uniform stable configuration composed of both cyclic and tree-like structures. Cyclic structures emerge locally in a transcritical bifurcation as the amplitude of the load fluctuations is increased. The resulting adaptive dynamics thus partitions the network into two distinct regions with cyclic and tree-like structures. The location of the boundary between these two regions is determined by the amplitude of the fluctuations. These findings may explain why natural transport networks display cyclic structures in the micro-vascular regions near terminal nodes, but tree-like features in the regions with larger veins.

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.

THE EVOLUTION OF RESTRAINT IN BACTERIAL BIOFILMS UNDER NONTRANSITIVE COMPETITION

PubMed Central

Prado, Federico; Kerr, Benjamin

2009-01-01

Theoretical and empirical evidence indicates that competing species can coexist if dispersal, migration, and competitive interactions occur over relatively small spatial scales. In particular, spatial structure appears to be critical to certain communities with nontransitive competition. A typical nontransitive system involves three competing species that satisfy a relationship similar to the children’s game of rock–paper–scissors. Although the ecological dynamics of nontransitive systems in spatially structured communities have received some attention, fewer studies have incorporated evolutionary change. Here we investigate evolution within toxic bacterial biofilms using an agent-based simulation that represents a nontransitive community containing three populations of Escherichia coli. In structured, nontransitive communities, strains evolve that do not maximize their competitive ability: They do not reduce their probability of death to a minimum or increase their toxicity to a maximum. That is, types evolve that exercise restraint. We show that nontransitivity and spatial structure (in the form of localized interactions) are both necessary for the evolution of restraint in these biofilms. PMID:18039324

The evolution of restraint in bacterial biofilms under nontransitive competition.

PubMed

Prado, Federico; Kerr, Benjamin

2008-03-01

Theoretical and empirical evidence indicates that competing species can coexist if dispersal, migration, and competitive interactions occur over relatively small spatial scales. In particular, spatial structure appears to be critical to certain communities with nontransitive competition. A typical nontransitive system involves three competing species that satisfy a relationship similar to the children's game of rock-paper-scissors. Although the ecological dynamics of nontransitive systems in spatially structured communities have received some attention, fewer studies have incorporated evolutionary change. Here we investigate evolution within toxic bacterial biofilms using an agent-based simulation that represents a nontransitive community containing three populations of Escherichia coli. In structured, nontransitive communities, strains evolve that do not maximize their competitive ability: They do not reduce their probability of death to a minimum or increase their toxicity to a maximum. That is, types evolve that exercise restraint. We show that nontransitivity and spatial structure (in the form of localized interactions) are both necessary for the evolution of restraint in these biofilms.

Dynamic order in a surface process

NASA Astrophysics Data System (ADS)

Eiswirth, M.; Ertl, G.

1988-09-01

Under certain well-defined conditions ( p co,p_{{text{O}}_{text{2}} } , T) the rate of catalytic oxidation of CO on a Pt(110) surface may exhibit sustained temporal oscillations with an autonomous frequency v 0. Small amplitude modulation ofp_{{text{O}}_{text{2}} } with frequency v p causes a variety of phenomena characteristic for systems of nonlinear dynamics which may be identified with temporal order and show formal similarities to spatial order of surface phases: Periodic behavior for certain rational numbers of v p/v0 — corresponding to commensurate surface structures; quasiperiodic behavior characterized by an irrational ratio of the periods of perturbation and response — corresponding to incommensurate structures; and critical slowing down near the boundary of a transition to quasiperiodicity which has its counterpart in the critical fluctuations near a (spatial) phase transition.

Extended quantification of the generalized recurrence plot

NASA Astrophysics Data System (ADS)

Riedl, Maik; Marwan, Norbert; Kurths, Jürgen

2016-04-01

The generalized recurrence plot is a modern tool for quantification of complex spatial patterns. Its application spans the analysis of trabecular bone structures, Turing structures, turbulent spatial plankton patterns, and fractals. But, it is also successfully applied to the description of spatio-temporal dynamics and the detection of regime shifts, such as in the complex Ginzburg-Landau- equation. The recurrence plot based determinism is a central measure in this framework quantifying the level of regularities in temporal and spatial structures. We extend this measure for the generalized recurrence plot considering additional operations of symmetry than the simple translation. It is tested not only on two-dimensional regular patterns and noise but also on complex spatial patterns reconstructing the parameter space of the complex Ginzburg-Landau-equation. The extended version of the determinism resulted in values which are consistent to the original recurrence plot approach. Furthermore, the proposed method allows a split of the determinism into parts which based on laminar and non-laminar regions of the two-dimensional pattern of the complex Ginzburg-Landau-equation. A comparison of these parts with a standard method of image classification, the co-occurrence matrix approach, shows differences especially in the description of patterns associated with turbulence. In that case, it seems that the extended version of the determinism allows a distinction of phase turbulence and defect turbulence by means of their spatial patterns. This ability of the proposed method promise new insights in other systems with turbulent dynamics coming from climatology, biology, ecology, and social sciences, for example.

Individual differences in mental rotation: what does gesture tell us?

PubMed

Göksun, Tilbe; Goldin-Meadow, Susan; Newcombe, Nora; Shipley, Thomas

2013-05-01

Gestures are common when people convey spatial information, for example, when they give directions or describe motion in space. Here, we examine the gestures speakers produce when they explain how they solved mental rotation problems (Shepard and Meltzer in Science 171:701-703, 1971). We asked whether speakers gesture differently while describing their problems as a function of their spatial abilities. We found that low-spatial individuals (as assessed by a standard paper-and-pencil measure) gestured more to explain their solutions than high-spatial individuals. While this finding may seem surprising, finer-grained analyses showed that low-spatial participants used gestures more often than high-spatial participants to convey "static only" information but less often than high-spatial participants to convey dynamic information. Furthermore, the groups differed in the types of gestures used to convey static information: high-spatial individuals were more likely than low-spatial individuals to use gestures that captured the internal structure of the block forms. Our gesture findings thus suggest that encoding block structure may be as important as rotating the blocks in mental spatial transformation.

Cholera and shigellosis in Bangladesh: similarities and differences in population dynamics under climate forcing

NASA Astrophysics Data System (ADS)

Pascual, M.; Cash, B.; Reiner, R.; King, A.; Emch, M.; Yunus, M.; Faruque, A. S.

2012-12-01

The influence of climate variability on the population dynamics of infectious diseases is considered a large scale, regional, phenomenon, and as such, has been previously addressed for cholera with temporal models that do not incorporate fine-scale spatial structure. In our previous work, evidence for a role of ENSO (El Niño Southern Oscillation) on cholera in Bangladesh was elucidated, and shown to influence the regional climate through precipitation. With a probabilistic spatial model for cholera dynamics in the megacity of Dhaka, we found that the action of climate variability (ENSO and flooding) is localized: there is a climate-sensitive urban core that acts to propagate risk to the rest of the city. Here, we consider long-term surveillance data for shigellosis, another diarrheal disease that coexists with cholera in Bangladesh. We compare the patterns of association with climate variables for these two diseases in a rural setting, as well as the spatial structure in their spatio-temporal dynamics in an urban one. Evidence for similar patterns is presented, and discussed in the context of the differences in the routes of transmission of the two diseases and the proposed role of an environmental reservoir in cholera. The similarities provide evidence for a more general influence of hydrology and of socio-economic factors underlying human susceptibility and sanitary conditions.

Urban sprawl and fragmentation in Latin America: a dynamic quantification and characterization of spatial patterns.

PubMed

Inostroza, Luis; Baur, Rolf; Csaplovics, Elmar

2013-01-30

South America is one of the most urbanized continents in the world, where almost 84% of the total population lives in cities, more urbanized than North America (82%) and Europe (73%). Spatial dynamics, their structure, main features, land consumption rates, spatial arrangement, fragmentation degrees and comparability, remain mostly unknown for most Latin American cities. Using satellite imagery the main parameters of sprawl are quantified for 10 Latin American cities over a period of 20 years by monitoring growth patterns and identifying spatial metrics to characterize urban development and sprawling features measured with GIS tools. This quantification contributes to a better understanding of urban form in Latin America. A pervasive spatial expansion has been observed, where most of the studied cities are expanding at fast rates with falling densities trend. Although important differences in the rates of land consumption and densities exist, there is an underlying fragmentation trend towards increasing sprawl. These trends of spatial discontinuity may eventually be intensified by further economic development. Urban Sprawl/Latin America/GIS metrics/spatial development. Copyright © 2012 Elsevier Ltd. All rights reserved.

Layered Organization in the Coastal Ocean: 4-D Assessment of Thin Layer Structure, Dynamics and Impacts

DTIC Science & Technology

2009-09-30

maintenance and dissipation of layers; (2) to understand the spatial coherence and spatial properties of thin layers in the coastal ocean (especially in...ORCAS profilers at K1 South and K2 had a Nortek ADV (Acoustic Doppler Velocity meter) for simultaneously measuring centimeter- scale currents and...year will be used to (1) detect the presence, intensity, thickness, temporal persistence, and spatial coherence of thin optical and acoustical layers

Topological structure dynamics revealing collective evolution in active nematics

PubMed Central

Shi, Xia-qing; Ma, Yu-qiang

2013-01-01

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

Off-equilibrium infrared structure of self-interacting scalar fields: Universal scaling, vortex-antivortex superfluid dynamics, and Bose-Einstein condensation

NASA Astrophysics Data System (ADS)

Deng, Jian; Schlichting, Soeren; Venugopalan, Raju; Wang, Qun

2018-05-01

We map the infrared dynamics of a relativistic single-component (N =1 ) interacting scalar field theory to that of nonrelativistic complex scalar fields. The Gross-Pitaevskii (GP) equation, describing the real-time dynamics of single-component ultracold Bose gases, is obtained at first nontrivial order in an expansion proportional to the powers of λ ϕ2/m2 where λ , ϕ , and m are the coupling constant, the scalar field, and the particle mass respectively. Our analytical studies are corroborated by numerical simulations of the spatial and momentum structure of overoccupied scalar fields in (2+1)-dimensions. Universal scaling of infrared modes, vortex-antivortex superfluid dynamics, and the off-equilibrium formation of a Bose-Einstein condensate are observed. Our results for the universal scaling exponents are in agreement with those extracted in the numerical simulations of the GP equation. As in these simulations, we observe coarsening phase kinetics in the Bose superfluid with strongly anomalous scaling exponents relative to that of vertex resummed kinetic theory. Our relativistic field theory framework further allows one to study more closely the coupling between superfluid and normal fluid modes, specifically the turbulent momentum and spatial structure of the coupling between a quasiparticle cascade to the infrared and an energy cascade to the ultraviolet. We outline possible applications of the formalism to the dynamics of vortex-antivortex formation and to the off-equilibrium dynamics of the strongly interacting matter formed in heavy-ion collisions.

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.

Edge effects in game-theoretic dynamics of spatially structured tumours.

PubMed

Kaznatcheev, Artem; Scott, Jacob G; Basanta, David

2015-07-06

Cancer dynamics are an evolutionary game between cellular phenotypes. A typical assumption in this modelling paradigm is that the probability of a given phenotypic strategy interacting with another depends exclusively on the abundance of those strategies without regard for local neighbourhood structure. We address this limitation by using the Ohtsuki-Nowak transform to introduce spatial structure to the go versus grow game. We show that spatial structure can promote the invasive (go) strategy. By considering the change in neighbourhood size at a static boundary--such as a blood vessel, organ capsule or basement membrane--we show an edge effect that allows a tumour without invasive phenotypes in the bulk to have a polyclonal boundary with invasive cells. We present an example of this promotion of invasive (epithelial-mesenchymal transition-positive) cells in a metastatic colony of prostate adenocarcinoma in bone marrow. Our results caution that pathologic analyses that do not distinguish between cells in the bulk and cells at a static edge of a tumour can underestimate the number of invasive cells. Although we concentrate on applications in mathematical oncology, we expect our approach to extend to other evolutionary game models where interaction neighbourhoods change at fixed system boundaries. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

[Spatial structure analysis and distribution simulation of Therioaphis trifolii population based on geostatistics and GIS].

PubMed

Zhang, Rong; Leng, Yun-fa; Zhu, Meng-meng; Wang, Fang

2007-11-01

Based on geographic information system and geostatistics, the spatial structure of Therioaphis trifolii population of different periods in Yuanzhou district of Guyuan City, the southern Ningxia Province, was analyzed. The spatial distribution of Therioaphis trifolii population was also simulated by ordinary Kriging interpretation. The results showed that Therioaphis trifolii population of different periods was correlated spatially in the study area. The semivariograms of Therioaphis trifolii could be described by exponential model, indicating an aggregated spatial arrangement. The spatial variance varied from 34.13%-48.77%, and the range varied from 8.751-12.049 km. The degree and direction of aggregation showed that the trend was increased gradually from southwest to northeast. The dynamic change of Therioaphis trifolii population in different periods could be analyzed intuitively on the simulated maps of the spatial distribution from the two aspects of time and space, The occurrence position and degree of Therioaphis trifolii to a state of certain time could be determined easily.

Dispersal Ability Determines the Role of Environmental, Spatial and Temporal Drivers of Metacommunity Structure

PubMed Central

Padial, André A.; Ceschin, Fernanda; Declerck, Steven A. J.; De Meester, Luc; Bonecker, Cláudia C.; Lansac-Tôha, Fabio A.; Rodrigues, Liliana; Rodrigues, Luzia C.; Train, Sueli; Velho, Luiz F. M.; Bini, Luis M.

2014-01-01

Recently, community ecologists are focusing on the relative importance of local environmental factors and proxies to dispersal limitation to explain spatial variation in community structure. Albeit less explored, temporal processes may also be important in explaining species composition variation in metacommunities occupying dynamic systems. We aimed to evaluate the relative role of environmental, spatial and temporal variables on the metacommunity structure of different organism groups in the Upper Paraná River floodplain (Brazil). We used data on macrophytes, fish, benthic macroinvertebrates, zooplankton, periphyton, and phytoplankton collected in up to 36 habitats during a total of eight sampling campaigns over two years. According to variation partitioning results, the importance of predictors varied among biological groups. Spatial predictors were particularly important for organisms with comparatively lower dispersal ability, such as aquatic macrophytes and fish. On the other hand, environmental predictors were particularly important for organisms with high dispersal ability, such as microalgae, indicating the importance of species sorting processes in shaping the community structure of these organisms. The importance of watercourse distances increased when spatial variables were the main predictors of metacommunity structure. The contribution of temporal predictors was low. Our results emphasize the strength of a trait-based analysis and of better defining spatial variables. More importantly, they supported the view that “all-or- nothing” interpretations on the mechanisms structuring metacommunities are rather the exception than the rule. PMID:25340577

Spatio-temporal dynamics of turbulence trapped in geodesic acoustic modes

NASA Astrophysics Data System (ADS)

Sasaki, M.; Kobayashi, T.; Itoh, K.; Kasuya, N.; Kosuga, Y.; Fujisawa, A.; Itoh, S.-I.

2018-01-01

The spatio-temporal dynamics of turbulence with the interaction of geodesic acoustic modes (GAMs) are investigated, focusing on the phase-space structure of turbulence, where the phase-space consists of real-space and wavenumber-space. Based on the wave-kinetic framework, the coupling equation between the GAM and the turbulence is numerically solved. The turbulence trapped by the GAM velocity field is obtained. Due to the trapping effect, the turbulence intensity increases where the second derivative of the GAM velocity (curvature of the GAM) is negative. While, in the positive-curvature region, the turbulence is suppressed. Since the trapped turbulence propagates with the GAMs, this relationship is sustained spatially and temporally. The dynamics of the turbulence in the wavenumber spectrum are converted in the evolution of the frequency spectrum, and the simulation result is compared with the experimental observation in JFT-2M tokamak, where the similar patterns are obtained. The turbulence trapping effect is a key to understand the spatial structure of the turbulence in the presence of sheared flows.

In situ imaging of the dynamics of photo-induced structural phase transition at high pressures by picosecond acoustic interferometry

NASA Astrophysics Data System (ADS)

Kuriakose, Maju; Chigarev, Nikolay; Raetz, Samuel; Bulou, Alain; Tournat, Vincent; Zerr, Andreas; Gusev, Vitalyi E.

2017-05-01

Picosecond acoustic interferometry is used to monitor in time the motion of the phase transition boundary between two water ice phases, VII and VI, coexisting at a pressure of 2.15 GPa when compressed in a diamond anvil cell at room temperature. By analyzing the time-domain Brillouin scattering signals accumulated for a single incidence direction of probe laser pulses, it is possible to access ratios of sound velocity values and of the refractive indices of the involved phases, and to distinguish between the structural phase transition and a recrystallization process. Two-dimensional spatial imaging of the phase transition dynamics indicates that it is initiated by the pump and probe laser pulses, preferentially at the diamond/ice interface. This method should find applications in three-dimensional monitoring with nanometer spatial resolution of the temporal dynamics of low-contrast material inhomogeneities caused by phase transitions or chemical reactions in optically transparent media.

Killing mediated spatial structure in V. Cholerae biofilms

NASA Astrophysics Data System (ADS)

Yanni, David

Most bacteria live in biofilms, which are implicated in 60 - 80 % of microbial infections in the body. The spatial structure of a biofilm confers advantages to its member-cells, such as antibiotic resistance, and is strongly affected by competition between strains and taxa. However, A complete picture of how competition affects the self-organized structure of these complex, far-from-equilibrium systems, is yet to emerge. To that end, we investigate phase separation dynamics driven by T6SS-facilitated bacterial warfare in a system composed of two strains of mutually antagonistic V. cholerae. T6SS is a contact mediated killing mechanism present in 25 % of all gram negative bacteria, and has been shown by recent work to play a major role in the spatial assortment of biofilms. T6SS events induce lysis, causing variations in local mechanical pressure, and acting as thermalizing events. We study cells immobilized in biofilms at the air-solid interface, so our experimental system represents a different type active matter, wherein activity is due to cell death and reproduction, not mobility. Here, we show how that activity imposes a constraint of minimal curvature on strain-strain interfaces; an effective Laplace pressure is characterized which governs interfacial dynamics.

Spatial distribution of limited resources and local density regulation in juvenile Atlantic salmon.

PubMed

Finstad, Anders G; Einum, Sigurd; Ugedal, Ola; Forseth, Torbjørn

2009-01-01

1. Spatial heterogeneity of resources may influence competition among individuals and thus have a fundamental role in shaping population dynamics and carrying capacity. In the present study, we identify shelter opportunities as a limiting resource for juvenile Atlantic salmon (Salmo salar L.). Experimental and field studies are combined in order to demonstrate how the spatial distribution of shelters may influence population dynamics on both within and among population scales. 2. In closed experimental streams, fish performance scaled negatively with decreasing shelter availability and increasing densities. In contrast, the fish in open stream channels dispersed according to shelter availability and performance of fish remaining in the streams did not depend on initial density or shelters. 3. The field study confirmed that spatial variation in densities of 1-year-old juveniles was governed both by initial recruit density and shelter availability. Strength of density-dependent population regulation, measured as carrying capacity, increased with decreasing number of shelters. 4. Nine rivers were surveyed for spatial variation in shelter availability and increased shelter heterogeneity tended to decrease maximum observed population size (measured using catch statistics of adult salmon as a proxy). 5. Our studies highlight the importance of small-scale within-population spatial structure in population dynamics and demonstrate that not only the absolute amount of limiting resources but also their spatial arrangement can be an important factor influencing population carrying capacity.

The Dynamic Interplay between Spatialization of Written Units in Writing Activity and Functions of Tools on the Computer

ERIC Educational Resources Information Center

Huh, Joo Hee

2012-01-01

I criticize the typewriting model and linear writing structure of Microsoft Word software for writing in the computer. I problematize bodily movement in writing that the error of the software disregards. In this research, writing activity is viewed as bodily, spatial and mediated activity under the premise of the unity of consciousness and…

Life-stage differences in spatial genetic structure in an irruptive forest insect: implications for dispersal and spatial synchrony

Treesearch

Patrick M.A. James; Barry Cooke; Bryan M.T. Brunet; Lisa M. Lumley; Felix A.H. Sperling; Marie-Josee Fortin; Vanessa S. Quinn; Brian R. Sturtevant

2015-01-01

Dispersal determines the flux of individuals, energy and information and is therefore a key determinant of ecological and evolutionary dynamics. Yet, it remains difficult to quantify its importance relative to other factors. This is particularly true in cyclic populations in which demography, drift and dispersal contribute to spatio-temporal variability in genetic...

Temporal variation in synchrony among chinook salmon (Oncorhynchus tshawytscha) redd counts from a wilderness area in central Idaho

Treesearch

D. J. Isaak; R. F. Thurow; B. E. Rieman; J. B. Dunham

2003-01-01

Metapopulation dynamics have emerged as a key consideration in conservation planning for salmonid fishes. Implicit to many models of spatially structured populations is a degree of synchrony, or correlation, among populations. We used a spatially and temporally extensive database of chinook salmon (Oncorhynchus tshawytscha) redd counts from a wilderness area in central...

A cellular automaton implementation of a quantum battle of the sexes game with imperfect information

NASA Astrophysics Data System (ADS)

Alonso-Sanz, Ramón

2015-10-01

The dynamics of a spatial quantum formulation of the iterated battle of the sexes game with imperfect information is studied in this work. The game is played with variable entangling in a cellular automata manner, i.e. with local and synchronous interaction. The effect of spatial structure is assessed in fair and unfair scenarios.

Non-Invasive Visualization and Quantitation of Cardiovascular Structure and Function.

ERIC Educational Resources Information Center

Ritman, E. L.; And Others

1979-01-01

Described is a new approach to investigative physiology based on computerized transaxial tomography, in which visualization and measurement of the internal structure of the cardiopulmonary system is possible without postmortem, biopsy, or vivisection procedures. Examples are given for application of the Dynamic Spatial Reconstructor (DSR). (CS)

Strategy Diversity Stabilizes Mutualism through Investment Cycles, Phase Polymorphism, and Spatial Bubbles

PubMed Central

Boza, Gergely; Kun, Ádám; Scheuring, István; Dieckmann, Ulf

2012-01-01

There is continuing interest in understanding factors that facilitate the evolution and stability of cooperation within and between species. Such interactions will often involve plasticity in investment behavior, in response to the interacting partner's investments. Our aim here is to investigate the evolution and stability of reciprocal investment behavior in interspecific interactions, a key phenomenon strongly supported by experimental observations. In particular, we present a comprehensive analysis of a continuous reciprocal investment game between mutualists, both in well-mixed and spatially structured populations, and we demonstrate a series of novel mechanisms for maintaining interspecific mutualism. We demonstrate that mutualistic partners invariably follow investment cycles, during which mutualism first increases, before both partners eventually reduce their investments to zero, so that these cycles always conclude with full defection. We show that the key mechanism for stabilizing mutualism is phase polymorphism along the investment cycle. Although mutualistic partners perpetually change their strategies, the community-level distribution of investment levels becomes stationary. In spatially structured populations, the maintenance of polymorphism is further facilitated by dynamic mosaic structures, in which mutualistic partners form expanding and collapsing spatial bubbles or clusters. Additionally, we reveal strategy-diversity thresholds, both for well-mixed and spatially structured mutualistic communities, and discuss factors for meeting these thresholds, and thus maintaining mutualism. Our results demonstrate that interspecific mutualism, when considered as plastic investment behavior, can be unstable, and, in agreement with empirical observations, may involve a polymorphism of investment levels, varying both in space and in time. Identifying the mechanisms maintaining such polymorphism, and hence mutualism in natural communities, provides a significant step towards understanding the coevolution and population dynamics of mutualistic interactions. PMID:23166478

Strategy diversity stabilizes mutualism through investment cycles, phase polymorphism, and spatial bubbles.

PubMed

Boza, Gergely; Kun, Adám; Scheuring, István; Dieckmann, Ulf

2012-01-01

There is continuing interest in understanding factors that facilitate the evolution and stability of cooperation within and between species. Such interactions will often involve plasticity in investment behavior, in response to the interacting partner's investments. Our aim here is to investigate the evolution and stability of reciprocal investment behavior in interspecific interactions, a key phenomenon strongly supported by experimental observations. In particular, we present a comprehensive analysis of a continuous reciprocal investment game between mutualists, both in well-mixed and spatially structured populations, and we demonstrate a series of novel mechanisms for maintaining interspecific mutualism. We demonstrate that mutualistic partners invariably follow investment cycles, during which mutualism first increases, before both partners eventually reduce their investments to zero, so that these cycles always conclude with full defection. We show that the key mechanism for stabilizing mutualism is phase polymorphism along the investment cycle. Although mutualistic partners perpetually change their strategies, the community-level distribution of investment levels becomes stationary. In spatially structured populations, the maintenance of polymorphism is further facilitated by dynamic mosaic structures, in which mutualistic partners form expanding and collapsing spatial bubbles or clusters. Additionally, we reveal strategy-diversity thresholds, both for well-mixed and spatially structured mutualistic communities, and discuss factors for meeting these thresholds, and thus maintaining mutualism. Our results demonstrate that interspecific mutualism, when considered as plastic investment behavior, can be unstable, and, in agreement with empirical observations, may involve a polymorphism of investment levels, varying both in space and in time. Identifying the mechanisms maintaining such polymorphism, and hence mutualism in natural communities, provides a significant step towards understanding the coevolution and population dynamics of mutualistic interactions.

the Role of Species, Structure, and Biochemical Traits in the Spatial Distribution of a Woodland Community

NASA Astrophysics Data System (ADS)

Adeline, K.; Ustin, S.; Roth, K. L.; Huesca Martinez, M.; Schaaf, C.; Baldocchi, D. D.; Gastellu-Etchegorry, J. P.

2015-12-01

The assessment of canopy biochemical diversity is critical for monitoring ecological and physiological functioning and for mapping vegetation change dynamics in relation to environmental resources. For example in oak woodland savannas, these dynamics are mainly driven by water constraints. Inversion using radiative transfer theory is one method for estimating canopy biochemistry. However, this approach generally only considers relatively simple scenarios to model the canopy due to the difficulty in encompassing stand heterogeneity with spatial and temporal consistency. In this research, we compared 3 modeling strategies for estimating canopy biochemistry variables (i.e. chlorophyll, carotenoids, water, dry matter) by coupling of the PROSPECT (leaf level) and DART (canopy level) models : i) a simple forest representation made of ellipsoid trees, and two representations taking into account the tree species and structural composition, and the landscape spatial pattern, using (ii) geometric tree crown shapes and iii) detailed tree crown and wood structure retrieved from terrestrial lidar acquisitions. AVIRIS 18m remote sensing data are up-scaled to simulate HyspIRI 30m images. Both spatial resolutions are validated by measurements acquired during 2013-2014 field campaigns (cover/tree inventory, LAI, leaf sampling, optical measures). The results outline the trade-off between accurate and abstract canopy modeling for inversion purposes and may provide perspectives to assess the impact of the California drought with multi-temporal monitoring of canopy biochemistry traits.

Spatial and Temporal Extent of Ion Spectral Structures at the Inner Edge of the Plasma Sheet

NASA Astrophysics Data System (ADS)

Ferradas, C.; Reeves, G. D.; Zhang, J.; Spence, H. E.; Kistler, L. M.; Larsen, B.; Skoug, R. M.; Funsten, H. O.

2017-12-01

Several ion spectral structures are observed near the inner edge of the plasma sheet and constitute the signatures of ion drift and loss in the highly dynamic environment of the inner magnetosphere. Their study helps us understand ion access and losses in this region. Several studies have found that these structures vary with geomagnetic activity, local time, and ion species, but their spatial and temporal extent remain undetermined. We use data from the Helium, Oxygen, Proton, and Electron (HOPE) mass spectrometers onboard the Van Allen Probes to analyze the spectral structures in the energy range of 1- 50 keV. HOPE measurements on both Van Allen Probes spacecraft enable us to resolve the extent of these ion structures in space and time. As the structures respond to changes in the convection electric field on a variety of time scales, the lapping of the two spacecraft on time scales of minutes to hours helps determine their spatial and temporal evolution.

Stochastic Geometric Models with Non-stationary Spatial Correlations in Lagrangian Fluid Flows

NASA Astrophysics Data System (ADS)

Gay-Balmaz, François; Holm, Darryl D.

2018-01-01

Inspired by spatiotemporal observations from satellites of the trajectories of objects drifting near the surface of the ocean in the National Oceanic and Atmospheric Administration's "Global Drifter Program", this paper develops data-driven stochastic models of geophysical fluid dynamics (GFD) with non-stationary spatial correlations representing the dynamical behaviour of oceanic currents. Three models are considered. Model 1 from Holm (Proc R Soc A 471:20140963, 2015) is reviewed, in which the spatial correlations are time independent. Two new models, called Model 2 and Model 3, introduce two different symmetry breaking mechanisms by which the spatial correlations may be advected by the flow. These models are derived using reduction by symmetry of stochastic variational principles, leading to stochastic Hamiltonian systems, whose momentum maps, conservation laws and Lie-Poisson bracket structures are used in developing the new stochastic Hamiltonian models of GFD.

Stochastic Geometric Models with Non-stationary Spatial Correlations in Lagrangian Fluid Flows

NASA Astrophysics Data System (ADS)

Gay-Balmaz, François; Holm, Darryl D.

2018-06-01

Inspired by spatiotemporal observations from satellites of the trajectories of objects drifting near the surface of the ocean in the National Oceanic and Atmospheric Administration's "Global Drifter Program", this paper develops data-driven stochastic models of geophysical fluid dynamics (GFD) with non-stationary spatial correlations representing the dynamical behaviour of oceanic currents. Three models are considered. Model 1 from Holm (Proc R Soc A 471:20140963, 2015) is reviewed, in which the spatial correlations are time independent. Two new models, called Model 2 and Model 3, introduce two different symmetry breaking mechanisms by which the spatial correlations may be advected by the flow. These models are derived using reduction by symmetry of stochastic variational principles, leading to stochastic Hamiltonian systems, whose momentum maps, conservation laws and Lie-Poisson bracket structures are used in developing the new stochastic Hamiltonian models of GFD.

Molecular dynamics modeling of periodic nanostructuring of metals with a short UV laser pulse under spatial confinement by a water layer

NASA Astrophysics Data System (ADS)

Ivanov, D. S.; Blumenstein, A.; Ihlemann, J.; Simon, P.; Garcia, M. E.; Rethfeld, B.

2017-12-01

The possibility of material surfaces restructuring on the nanoscale due to ultrashort laser pulses has recently found a number of practical applications. It was found experimentally that under spatial confinement due to a liquid layer atop the surface, one can achieve even finer and cleaner structures as compared to that in air or in vacuum. The mechanism of the materials restructuring under the liquid confinement, however, is not clear and its experimental study is limited by the extreme conditions realized during the intense and localized laser energy deposition that takes place on nanometer spatial and picosecond time-scales. In this theoretical work, we suggest a molecular dynamics-based approach that is capable of simulating the processes of periodic nanostructuring with ultrashort UV laser pulse on metals. The theoretical results of the simulations are directly compared with the experimental data on the same spatial and temporal scales.

Dynamic, spatial models of parasite transmission in wildlife: Their structure, applications and remaining challenges.

PubMed

White, Lauren A; Forester, James D; Craft, Meggan E

2018-05-01

Individual differences in contact rate can arise from host, group and landscape heterogeneity and can result in different patterns of spatial spread for diseases in wildlife populations with concomitant implications for disease control in wildlife of conservation concern, livestock and humans. While dynamic disease models can provide a better understanding of the drivers of spatial spread, the effects of landscape heterogeneity have only been modelled in a few well-studied wildlife systems such as rabies and bovine tuberculosis. Such spatial models tend to be either purely theoretical with intrinsic limiting assumptions or individual-based models that are often highly species- and system-specific, limiting the breadth of their utility. Our goal was to review studies that have utilized dynamic, spatial models to answer questions about pathogen transmission in wildlife and identify key gaps in the literature. We begin by providing an overview of the main types of dynamic, spatial models (e.g., metapopulation, network, lattice, cellular automata, individual-based and continuous-space) and their relation to each other. We investigate different types of ecological questions that these models have been used to explore: pathogen invasion dynamics and range expansion, spatial heterogeneity and pathogen persistence, the implications of management and intervention strategies and the role of evolution in host-pathogen dynamics. We reviewed 168 studies that consider pathogen transmission in free-ranging wildlife and classify them by the model type employed, the focal host-pathogen system, and their overall research themes and motivation. We observed a significant focus on mammalian hosts, a few well-studied or purely theoretical pathogen systems, and a lack of studies occurring at the wildlife-public health or wildlife-livestock interfaces. Finally, we discuss challenges and future directions in the context of unprecedented human-mediated environmental change. Spatial models may provide new insights into understanding, for example, how global warming and habitat disturbance contribute to disease maintenance and emergence. Moving forward, better integration of dynamic, spatial disease models with approaches from movement ecology, landscape genetics/genomics and ecoimmunology may provide new avenues for investigation and aid in the control of zoonotic and emerging infectious diseases. © 2017 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.

Parallel Multiscale Algorithms for Astrophysical Fluid Dynamics Simulations

NASA Technical Reports Server (NTRS)

Norman, Michael L.

1997-01-01

Our goal is to develop software libraries and applications for astrophysical fluid dynamics simulations in multidimensions that will enable us to resolve the large spatial and temporal variations that inevitably arise due to gravity, fronts and microphysical phenomena. The software must run efficiently on parallel computers and be general enough to allow the incorporation of a wide variety of physics. Cosmological structure formation with realistic gas physics is the primary application driver in this work. Accurate simulations of e.g. galaxy formation require a spatial dynamic range (i.e., ratio of system scale to smallest resolved feature) of 104 or more in three dimensions in arbitrary topologies. We take this as our technical requirement. We have achieved, and in fact, surpassed these goals.

Controlling the influence of elastic eigenmodes on nanomagnet dynamics through pattern geometry

NASA Astrophysics Data System (ADS)

Berk, C.; Yahagi, Y.; Dhuey, S.; Cabrini, S.; Schmidt, H.

2017-03-01

The effect of the nanoscale array geometry on the interaction between optically generated surface acoustic waves (SAWs) and nanomagnet dynamics is investigated using Time-Resolved Magneto-Optical Kerr Effect Microscopy (TR-MOKE). It is demonstrated that altering the nanomagnet geometry from a periodic to a randomized aperiodic pattern effectively removes the magneto-elastic effect of SAWs on the magnetization dynamics. The efficiency of this method depends on the extent of any residual spatial correlations and is quantified by spatial Fourier analysis of the two structures. Randomization allows observation and extraction of intrinsic magnetic parameters such as spin wave frequencies and damping to be resolvable using all-optical methods, enabling the conclusion that the fabrication process does not affect the damping.

Graph Theory Roots of Spatial Operators for Kinematics and Dynamics

NASA Technical Reports Server (NTRS)

Jain, Abhinandan

2011-01-01

Spatial operators have been used to analyze the dynamics of robotic multibody systems and to develop novel computational dynamics algorithms. Mass matrix factorization, inversion, diagonalization, and linearization are among several new insights obtained using such operators. While initially developed for serial rigid body manipulators, the spatial operators and the related mathematical analysis have been shown to extend very broadly including to tree and closed topology systems, to systems with flexible joints, links, etc. This work uses concepts from graph theory to explore the mathematical foundations of spatial operators. The goal is to study and characterize the properties of the spatial operators at an abstract level so that they can be applied to a broader range of dynamics problems. The rich mathematical properties of the kinematics and dynamics of robotic multibody systems has been an area of strong research interest for several decades. These properties are important to understand the inherent physical behavior of systems, for stability and control analysis, for the development of computational algorithms, and for model development of faithful models. Recurring patterns in spatial operators leads one to ask the more abstract question about the properties and characteristics of spatial operators that make them so broadly applicable. The idea is to step back from the specific application systems, and understand more deeply the generic requirements and properties of spatial operators, so that the insights and techniques are readily available across different kinematics and dynamics problems. In this work, techniques from graph theory were used to explore the abstract basis for the spatial operators. The close relationship between the mathematical properties of adjacency matrices for graphs and those of spatial operators and their kernels were established. The connections hold across very basic requirements on the system topology, the nature of the component bodies, the indexing schemes, etc. The relationship of the underlying structure is intimately connected with efficient, recursive computational algorithms. The results provide the foundational groundwork for a much broader look at the key problems in kinematics and dynamics. The properties of general graphs and trees of nodes and edge were examined, as well as the properties of adjacency matrices that are used to describe graph connectivity. The nilpotency property of such matrices for directed trees was reviewed, and the adjacency matrices were generalized to the notion of block weighted adjacency matrices that support block matrix elements. This leads us to the development of the notion of Spatial Kernel Operator SKO kernels. These kernels provide the basis for the development of SKO resolvent operators.

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

PubMed Central

Yang, Ding-Shyue; Zewail, Ahmed H.

2009-01-01

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

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

PubMed Central

Maji, Suvrajit; Bruchez, Marcel P.

2012-01-01

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

Geocoronal Imaging from the Deep Space Gateway

NASA Astrophysics Data System (ADS)

Waldrop, L.; Immel, T.; Clarke, J.; Fillingim, M.; Rider, K.; Qin, J.; Bhattacharyya, D.; Doe, R.

2018-02-01

UV imaging of geocoronal emission at high spatial and temporal resolution from deep space would provide crucial new constraints on global exospheric structure and dynamics, significantly advancing models of space weather and atmospheric escape.

Modal decomposition of turbulent supersonic cavity

NASA Astrophysics Data System (ADS)

Soni, R. K.; Arya, N.; De, A.

2018-06-01

Self-sustained oscillations in a Mach 3 supersonic cavity with a length-to-depth ratio of three are investigated using wall-modeled large eddy simulation methodology for ReD = 3.39× 105 . The unsteady data obtained through computation are utilized to investigate the spatial and temporal evolution of the flow field, especially the second invariant of the velocity tensor, while the phase-averaged data are analyzed over a feedback cycle to study the spatial structures. This analysis is accompanied by the proper orthogonal decomposition (POD) data, which reveals the presence of discrete vortices along the shear layer. The POD analysis is performed in both the spanwise and streamwise planes to extract the coherence in flow structures. Finally, dynamic mode decomposition is performed on the data sequence to obtain the dynamic information and deeper insight into the self-sustained mechanism.

Structure and dynamics of an upland old- growth forest at Redwood National Park, California

USGS Publications Warehouse

van Mantgem, Philip J.; Stuart, John D.

2011-01-01

Many current redwood forest management targets are based on old-growth conditions, so it is critical that we understand the variability and range of conditions that constitute these forests. Here we present information on the structure and dynamics from six one-hectare forest monitoring plots in an upland old-growth forest at Redwood National Park, California. We surveyed all stems =20 cm DBH in 1995 and 2010, allowing us to estimate any systematic changes in these stands. Stem size distributions for all species and for redwood (Sequoia sempervirens (D. Don) Endl.) alone did not appreciably change over the 15 year observation interval. Recruitment and mortality rates were roughly balanced, as were basal area dynamics (gains from recruitment and growth versus losses from mortality). Similar patterns were found for Sequoia alone. The spatial structure of stems at the plots suggested a random distribution of trees, though the pattern for Sequoia alone was found to be significantly clumped at small scales (< 5 m) at three of the six plots. These results suggest that these forests, including populations of Sequoia, have been generally stable over the past 15 years at this site, though it is possible that fire exclusion may be affecting recruitment of smaller Sequoia (< 20 cm DBH). The non-uniform spatial arrangement of stems also suggests that restoration prescriptions for second-growth redwood forests that encourage uniform spatial arrangements do not appear to mimic current upland old-growth conditions.

Tropical-Forest Structure and Biomass Dynamics from TanDEM-X Radar Interferometry

Treesearch

Robert Treuhaft; Yang Lei; Fabio Gonçalves; Michael Keller; João Santos; Maxim Neumann; André Almeida

2017-01-01

Changes in tropical-forest structure and aboveground biomass (AGB) contribute directly to atmospheric changes in CO2, which, in turn, bear on global climate. This paper demonstrates the capability of radar-interferometric phase-height time series at X-band (wavelength = 3 cm) to monitor changes in vertical structure and AGB, with sub-hectare and monthly spatial and...

Finite Element Model Development and Validation for Aircraft Fuselage Structures

NASA Technical Reports Server (NTRS)

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

2000-01-01

The ability to extend the valid frequency range for finite element based structural dynamic predictions using detailed models of the structural components and attachment interfaces is examined for several stiffened aircraft fuselage structures. This extended dynamic prediction capability is needed for the integration of mid-frequency noise control technology. Beam, plate and solid element models of the stiffener components are evaluated. Attachment models between the stiffener and panel skin range from a line along the rivets of the physical structure to a constraint over the entire contact surface. The finite element models are validated using experimental modal analysis results. The increased frequency range results in a corresponding increase in the number of modes, modal density and spatial resolution requirements. In this study, conventional modal tests using accelerometers are complemented with Scanning Laser Doppler Velocimetry and Electro-Optic Holography measurements to further resolve the spatial response characteristics. Whenever possible, component and subassembly modal tests are used to validate the finite element models at lower levels of assembly. Normal mode predictions for different finite element representations of components and assemblies are compared with experimental results to assess the most accurate techniques for modeling aircraft fuselage type structures.

Modeling tree crown dynamics with 3D partial differential equations.

PubMed

Beyer, Robert; Letort, Véronique; Cournède, Paul-Henry

2014-01-01

We characterize a tree's spatial foliage distribution by the local leaf area density. Considering this spatially continuous variable allows to describe the spatiotemporal evolution of the tree crown by means of 3D partial differential equations. These offer a framework to rigorously take locally and adaptively acting effects into account, notably the growth toward light. Biomass production through photosynthesis and the allocation to foliage and wood are readily included in this model framework. The system of equations stands out due to its inherent dynamic property of self-organization and spontaneous adaptation, generating complex behavior from even only a few parameters. The density-based approach yields spatially structured tree crowns without relying on detailed geometry. We present the methodological fundamentals of such a modeling approach and discuss further prospects and applications.

Scale-dependent variation in forest structures in naturally dynamic boreal forest landscapes

NASA Astrophysics Data System (ADS)

Kulha, Niko; Pasanen, Leena; De Grandpré, Louis; Kuuluvainen, Timo; Aakala, Tuomas

2017-04-01

Natural forest structures vary at multiple spatial scales. This variation reflects the occurrence of driving factors, such as disturbances and variation in soil or topography. To explore and understand the linkages of forest structural characteristics and factors driving their variation, we need to recognize how the structural characteristics vary in relation to spatial scale. This can be achieved by identifying scale-dependent features in forest structure within unmanaged forest landscapes. By identifying these features and examining their relationship with potential driving factors, we can better understand the dynamics of forest structural development. Here, we examine the spatial variation in forest structures at multiple spatial scales, utilizing data from old-growth boreal forests in two regions with contrasting disturbance regimes: northern Finland and north-eastern Québec, Canada ( 67° 45'N, 29° 36'E, 49° 39'N, 67° 55'W, respectively). The three landscapes (4 km2 each) in Finland are dominated by Pinus sylvestris and Picea abies, whereas the two landscapes in Québec are dominated by Abies balsamea and Picea mariana. Québec's forests are a subject to cyclic outbreaks of the eastern spruce budworm, causing extensive mortality especially in A. balsamea-dominated stands. In the Finnish landscapes, gap- to patch-scale disturbances due to tree senescence, fungi and wind, as well as infrequent surface fires in areas dominated by P. sylvestris, prevail. Owing to the differences in the species compositions and the disturbance regimes, we expect differing scales of variation between the landscapes. To quantify patterns of variation, we visually interpret stereopairs of recent aerial photographs. From the photographs, we collect information on forest canopy coverage, species composition and dead wood. For the interpretation, each 4 km2 plot is divided into 0.1ha square cells (4096 per plot). Interpretations are validated against field observations and compiled to raster maps. We analyze the raster maps with Bayesian scale space approach (iBSiZer), which aims in capturing credible variations at different spatial scales. As a result, we can detect structural entities (e.g. patches with higher canopy cover), which deviate credibly from their surroundings. The detected entities can further be linked to specific drivers. Our results show that the role of a particular driving factor varies in relation to spatial scale. For example, in the Finnish landscapes, topoedaphic factors exerted a stronger control on broad-scale forest structural characteristics, whereas recent disturbances (quantified as the amount of dead wood) appeared to play an important role in explaining the smaller scale variation of forest structures. Here, we showcase the methodology used in the detection of scale-dependent forest structural entities and present the results of our analysis of the spatial scales of variation in the natural boreal forest structures.

Blind identification of full-field vibration modes of output-only structures from uniformly-sampled, possibly temporally-aliased (sub-Nyquist), video measurements

NASA Astrophysics Data System (ADS)

Yang, Yongchao; Dorn, Charles; Mancini, Tyler; Talken, Zachary; Nagarajaiah, Satish; Kenyon, Garrett; Farrar, Charles; Mascareñas, David

2017-03-01

Enhancing the spatial and temporal resolution of vibration measurements and modal analysis could significantly benefit dynamic modelling, analysis, and health monitoring of structures. For example, spatially high-density mode shapes are critical for accurate vibration-based damage localization. In experimental or operational modal analysis, higher (frequency) modes, which may be outside the frequency range of the measurement, contain local structural features that can improve damage localization as well as the construction and updating of the modal-based dynamic model of the structure. In general, the resolution of vibration measurements can be increased by enhanced hardware. Traditional vibration measurement sensors such as accelerometers have high-frequency sampling capacity; however, they are discrete point-wise sensors only providing sparse, low spatial sensing resolution measurements, while dense deployment to achieve high spatial resolution is expensive and results in the mass-loading effect and modification of structure's surface. Non-contact measurement methods such as scanning laser vibrometers provide high spatial and temporal resolution sensing capacity; however, they make measurements sequentially that requires considerable acquisition time. As an alternative non-contact method, digital video cameras are relatively low-cost, agile, and provide high spatial resolution, simultaneous, measurements. Combined with vision based algorithms (e.g., image correlation or template matching, optical flow, etc.), video camera based measurements have been successfully used for experimental and operational vibration measurement and subsequent modal analysis. However, the sampling frequency of most affordable digital cameras is limited to 30-60 Hz, while high-speed cameras for higher frequency vibration measurements are extremely costly. This work develops a computational algorithm capable of performing vibration measurement at a uniform sampling frequency lower than what is required by the Shannon-Nyquist sampling theorem for output-only modal analysis. In particular, the spatio-temporal uncoupling property of the modal expansion of structural vibration responses enables a direct modal decoupling of the temporally-aliased vibration measurements by existing output-only modal analysis methods, yielding (full-field) mode shapes estimation directly. Then the signal aliasing properties in modal analysis is exploited to estimate the modal frequencies and damping ratios. The proposed method is validated by laboratory experiments where output-only modal identification is conducted on temporally-aliased acceleration responses and particularly the temporally-aliased video measurements of bench-scale structures, including a three-story building structure and a cantilever beam.

Nitrogen (N) dynamics in the mineral soil of a Central Appalachian hardwood forest during a quarter century of whole-watershed N additions

Treesearch

Frank S. ​Gilliam; Christopher A. Walter; Mary Beth Adams; William T. Peterjohn

2018-01-01

The structure and function of terrestrial ecosystemsare maintained by processes that vary with temporal and spatial scale. This study examined temporal and spatial patterns of net nitrogen (N) mineralization and nitrification in mineral soil of three watersheds at the Fernow Experimental Forest, WV: 2 untreated watersheds and 1 watershed receiving aerial applications...

DYNAMICS OF HIGH ENERGY IONS AT A STRUCTURED COLLISIONLESS SHOCK FRONT

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

Gedalin, M.; Dröge, W.; Kartavykh, Y. Y., E-mail: gedalin@bgu.ac.il

2016-07-10

Ions undergoing first-order Fermi acceleration at a shock are scattered in the upstream and downstream regions by magnetic inhomogeneities. For high energy ions this scattering is efficient at spatial scales substantially larger than the gyroradius of the ions. The transition from one diffusive region to the other occurs via crossing the shock, and the ion dynamics during this crossing is mainly affected by the global magnetic field change between the upstream and downstream region. We study the effects of the fine structure of the shock front, such as the foot-ramp-overshoot profile and the phase-standing upstream and downstream magnetic oscillations. Wemore » also consider time dependent features, including reformation and large amplitude coherent waves. We show that the influence of the spatial and temporal structure of the shock front on the dependence of the transition and reflection on the pitch angle of the ions is already weak at ion speeds five times the speed of the upstream flow.« less

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.

Influence of the distance between target surface and focal point on the expansion dynamics of a laser-induced silicon plasma with spatial confinement

NASA Astrophysics Data System (ADS)

Zhang, Dan; Chen, Anmin; Wang, Xiaowei; Wang, Ying; Sui, Laizhi; Ke, Da; Li, Suyu; Jiang, Yuanfei; Jin, Mingxing

2018-05-01

Expansion dynamics of a laser-induced plasma plume, with spatial confinement, for various distances between the target surface and focal point were studied by the fast photography technique. A silicon wafer was ablated to induce the plasma with a Nd:YAG laser in an atmospheric environment. The expansion dynamics of the plasma plume depended on the distance between the target surface and focal point. In addition, spatially confined time-resolved images showed the different structures of the plasma plumes at different distances between the target surface and focal point. By analyzing the plume images, the optimal distance for emission enhancement was found to be approximately 6 mm away from the geometrical focus using a 10 cm focal length lens. This optimized distance resulted in the strongest compression ratio of the plasma plume by the reflected shock wave. Furthermore, the duration of the interaction between the reflected shock wave and the plasma plume was also prolonged.

Structure preserving clustering-object tracking via subgroup motion pattern segmentation

NASA Astrophysics Data System (ADS)

Fan, Zheyi; Zhu, Yixuan; Jiang, Jiao; Weng, Shuqin; Liu, Zhiwen

2018-01-01

Tracking clustering objects with similar appearances simultaneously in collective scenes is a challenging task in the field of collective motion analysis. Recent work on clustering-object tracking often suffers from poor tracking accuracy and terrible real-time performance due to the neglect or the misjudgment of the motion differences among objects. To address this problem, we propose a subgroup motion pattern segmentation framework based on a multilayer clustering structure and establish spatial constraints only among objects in the same subgroup, which entails having consistent motion direction and close spatial position. In addition, the subgroup segmentation results are updated dynamically because crowd motion patterns are changeable and affected by objects' destinations and scene structures. The spatial structure information combined with the appearance similarity information is used in the structure preserving object tracking framework to track objects. Extensive experiments conducted on several datasets containing multiple real-world crowd scenes validate the accuracy and the robustness of the presented algorithm for tracking objects in collective scenes.

Material Structure of a Graded Refractive Index Lens in Decapod Squid

NASA Astrophysics Data System (ADS)

Cai, Jing; Heiney, Paul; Sweeney, Alison

2013-03-01

Underwater vision with a camera-type eye that is simultaneously acute and sensitive requires a spherical lens with a graded distribution of refractive index. Squids have this type of lens, and our previous work has shown that its optical properties are likely achieved with radially variable densities of a single protein with multiple isoforms. Here we measure the spatial organization of this novel protein material in concentric layers of the lens and use these data to suggest possible mechanisms of self-assembly of the proteins into a graded refractive index structure. First, we performed small angle x-ray scattering (SAXS) to study how the protein is spatially organized. Then, molecular dynamic simulation allowed us to correlate structure to the possible dynamics of the system in different regions of the lens. The combination of simulation and SAXS data in this system revealed the likely protein-protein interactions, resulting material structure and its relationship to the observed and variable optical properties of this graded index system. We believe insights into the material properties of the squid lens system will inform the invention of self-assembling graded index devices.

Dynamic multiprotein assemblies shape the spatial structure of cell signaling.

PubMed

Nussinov, Ruth; Jang, Hyunbum

2014-01-01

Cell signaling underlies critical cellular decisions. Coordination, efficiency as well as fail-safe mechanisms are key elements. How the cell ensures that these hallmarks are at play are important questions. Cell signaling is often viewed as taking place through discrete and cross-talking pathways; oftentimes these are modularized to emphasize distinct functions. While simple, convenient and clear, such models largely neglect the spatial structure of cell signaling; they also convey inter-modular (or inter-protein) spatial separation that may not exist. Here our thesis is that cell signaling is shaped by a network of multiprotein assemblies. While pre-organized, the assemblies and network are loose and dynamic. They contain transiently-associated multiprotein complexes which are often mediated by scaffolding proteins. They are also typically anchored in the membrane, and their continuum may span the cell. IQGAP1 scaffolding protein which binds proteins including Raf, calmodulin, Mek, Erk, actin, and tens more, with actin shaping B-cell (and likely other) membrane-anchored nanoclusters and allosterically polymerizing in dynamic cytoskeleton formation, and Raf anchoring in the membrane along with Ras, provides a striking example. The multivalent network of dynamic proteins and lipids, with specific interactions forming and breaking, can be viewed as endowing gel-like properties. Collectively, this reasons that efficient, productive and reliable cell signaling takes place primarily through transient, preorganized and cooperative protein-protein interactions spanning the cell rather than stochastic, diffusion-controlled processes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Fishermen Follow Fine-scaled Physical Ocean Features For Finance

NASA Astrophysics Data System (ADS)

Fuller, E.; Watson, J. R.; Samhouri, J.; Castruccio, F. S.

2016-12-01

The seascapes on which many millions of people make their living and secure food have complex and dynamic spatial features - the figurative hills and valleys - that control where and how people work at sea. Here, we quantify the physical mosaic of the surface ocean by identifying Lagrangian Coherent Structures for a whole seascape - the California Current - and assess their impact on the spatial distribution of fishing. We show that there is a mixed response: some fisheries track these physical features, and others avoid them. This spatial behavior maps to economic impacts: we find that tuna fishermen can expect to make three times more revenue per trip if fishing occurs on strong coherent structures. These results highlight a connection between the physical state of the oceans, the spatial patterns of human activity and ultimately the economic prosperity of coastal communities.

Spatio-temporal dynamics of ocean conditions and forage taxa reveal regional structuring of seabird–prey relationships.

PubMed

Santora, Jarrod A; Schroeder, Isaac D; Field, John C; Wells, Brian K; Sydeman, William J

Studies of predator–prey demographic responses and the physical drivers of such relationships are rare, yet essential for predicting future changes in the structure and dynamics of marine ecosystems. Here, we hypothesize that predator–prey relationships vary spatially in association with underlying physical ocean conditions, leading to observable changes in demographic rates, such as reproduction. To test this hypothesis, we quantified spatio-temporal variability in hydrographic conditions, krill, and forage fish to model predator (seabird) demographic responses over 18 years (1990–2007). We used principal component analysis and spatial correlation maps to assess coherence among ocean conditions, krill, and forage fish, and generalized additive models to quantify interannual variability in seabird breeding success relative to prey abundance. The first principal component of four hydrographic measurements yielded an index that partitioned “warm/weak upwelling” and “cool/strong upwelling” years. Partitioning of krill and forage fish time series among shelf and oceanic regions yielded spatially explicit indicators of prey availability. Krill abundance within the oceanic region was remarkably consistent between years, whereas krill over the shelf showed marked interannual fluctuations in relation to ocean conditions. Anchovy abundance varied on the shelf, and was greater in years of strong stratification, weak upwelling and warmer temperatures. Spatio-temporal variability of juvenile forage fish co-varied strongly with each other and with krill, but was weakly correlated with hydrographic conditions. Demographic responses between seabirds and prey availability revealed spatially variable associations indicative of the dynamic nature of “predator–habitat” relationships. Quantification of spatially explicit demographic responses, and their variability through time, demonstrate the possibility of delineating specific critical areas where the implementation of protective measures could maintain functions and productivity of central place foraging predators.

Investigation of Optical Cavity Modes and Ultrafast Carrier Dynamics in Zinc Oxide Rods Using Second-Harmonic Generation and Transient Absorption Pump-Probe Microscopy

NASA Astrophysics Data System (ADS)

Mehl, Brian Peter

The polydispersity intrinsic to nanoscale and microscale semiconductor materials poses a major challenge to using individual objects as building blocks for device applications. The ability to manipulate the shape of ZnO structures is enormous, making it an ideal material for studying shape-dependent phenomena. We have built a nonlinear microscope used to directly image optical cavity modes in ZnO rods using second-harmonic generation. Images of second-harmonic generation in needle-shaped ZnO rods obtained from individual structures show areas of enhanced second-harmonic intensity along the longitudinal axis of the rod that are periodically distributed and symmetrically situated relative to the rod midpoint. The spatial modulation is a direct consequence of the fundamental optical field coupling into standing wave resonator modes of the ZnO structure, leading to an enhanced backscattered second-harmonic condition that cannot be achieved in bulk ZnO. A more complicated second-harmonic image is observed when excitation is below the band gap, which is attributed to whispering gallery modes. Additionally, the nonlinear microscope was combined with transient absorption pump-probe to follow the electron-hole recombination dynamics at different points within individual needle-shaped ZnO rods to characterize spatial differences in dynamical behavior. The results from pump-probe experiments are correlated with spatially resolved ultrafast emission measurements, and scanning electron microscopy provides structural details. Dramatically different electron-hole recombination dynamics are observed in the narrow tips compared to the interior, with the ends exhibiting a greater propensity for electron-hole plasma formation and faster recombination of carriers across the band gap that stem from a physical confinement of the charge carriers. In the interior of the rod, a greater fraction of the electron-hole recombination is trap-mediated and occurs on a significantly longer time scale.

Phase Synchronization and Desynchronization of Structural Response Induced by Turbulent and External Sound

NASA Technical Reports Server (NTRS)

Maestrello, Lucio

2002-01-01

Acoustic and turbulent boundary layer flow loadings over a flexible structure are used to study the spatial-temporal dynamics of the response of the structure. The stability of the spatial synchronization and desynchronization by an active external force is investigated with an array of coupled transducers on the structure. In the synchronous state, the structural phase is locked, which leads to the formation of spatial patterns while the amplitude peaks exhibit chaotic behaviors. Large amplitude, spatially symmetric loading is superimposed on broadband, but in the desynchronized state, the spectrum broadens and the phase space is lost. The resulting pattern bears a striking resemblance to phase turbulence. The transition is achieved by using a low power external actuator to trigger broadband behaviors from the knowledge of the external acoustic load inducing synchronization. The changes are made favorably and efficiently to alter the frequency distribution of power, not the total power level. Before synchronization effects are seen, the panel response to the turbulent boundary layer loading is discontinuously spatio-temporally correlated. The stability develops from different competing wavelengths; the spatial scale is significantly shorter than when forced with the superimposed external sound. When the external sound level decreases and the synchronized phases are lost, changes in the character of the spectra can be linked to the occurrence of spatial phase transition. These changes can develop broadband response. Synchronized responses of fuselage structure panels have been observed in subsonic and supersonic aircraft; results from two flights tests are discussed.

Historical fire and vegetation dynamics in dry forests of the interior Pacific Northwest, USA, and relationships to northern spotted owl (Strix occidentalis caurina) habitat conservation

Treesearch

Rebecca S.H. Kennedy; Michael C. Wimberly

2009-01-01

Regional conservation planning frequently relies on general assumptions about historical disturbance regimes to inform decisions about landscape restoration, reserve allocations, and landscape management. Spatially explicit simulations of landscape dynamics provide quantitative estimates of landscape structure and allow for the testing of alternative scenarios. We used...

Dynamic design of ecological monitoring networks for non-Gaussian spatio-temporal data

USGS Publications Warehouse

Wikle, C.K.; Royle, J. Andrew

2005-01-01

Many ecological processes exhibit spatial structure that changes over time in a coherent, dynamical fashion. This dynamical component is often ignored in the design of spatial monitoring networks. Furthermore, ecological variables related to processes such as habitat are often non-Gaussian (e.g. Poisson or log-normal). We demonstrate that a simulation-based design approach can be used in settings where the data distribution is from a spatio-temporal exponential family. The key random component in the conditional mean function from this distribution is then a spatio-temporal dynamic process. Given the computational burden of estimating the expected utility of various designs in this setting, we utilize an extended Kalman filter approximation to facilitate implementation. The approach is motivated by, and demonstrated on, the problem of selecting sampling locations to estimate July brood counts in the prairie pothole region of the U.S.

Bidimensional nano-optomechanics and topological backaction in a non-conservative radiation force field.

PubMed

Gloppe, A; Verlot, P; Dupont-Ferrier, E; Siria, A; Poncharal, P; Bachelier, G; Vincent, P; Arcizet, O

2014-11-01

Optomechanics, which explores the fundamental coupling between light and mechanical motion, has made important advances in manipulating macroscopic mechanical oscillators down to the quantum level. However, dynamical effects related to the vectorial nature of the optomechanical interaction remain to be investigated. Here we study a nanowire with subwavelength dimensions coupled strongly to a tightly focused beam of light, enabling an ultrasensitive readout of the nanoresonator dynamics. We determine experimentally the vectorial structure of the optomechanical interaction and demonstrate that a bidimensional dynamical backaction governs the nanowire dynamics. Moreover, the spatial topology of the optomechanical interaction is responsible for novel canonical signatures of strong coupling between mechanical modes, which leads to a topological instability that underlies the non-conservative nature of the optomechanical interaction. These results have a universal character and illustrate the increased sensitivity of nanomechanical devices towards spatially varying interactions, opening fundamental perspectives in nanomechanics, optomechanics, ultrasensitive scanning force microscopy and nano-optics.

Stochastic population dynamics in spatially extended predator-prey systems

NASA Astrophysics Data System (ADS)

Dobramysl, Ulrich; Mobilia, Mauro; Pleimling, Michel; Täuber, Uwe C.

2018-02-01

Spatially extended population dynamics models that incorporate demographic noise serve as case studies for the crucial role of fluctuations and correlations in biological systems. Numerical and analytic tools from non-equilibrium statistical physics capture the stochastic kinetics of these complex interacting many-particle systems beyond rate equation approximations. Including spatial structure and stochastic noise in models for predator-prey competition invalidates the neutral Lotka-Volterra population cycles. Stochastic models yield long-lived erratic oscillations stemming from a resonant amplification mechanism. Spatially extended predator-prey systems display noise-stabilized activity fronts that generate persistent correlations. Fluctuation-induced renormalizations of the oscillation parameters can be analyzed perturbatively via a Doi-Peliti field theory mapping of the master equation; related tools allow detailed characterization of extinction pathways. The critical steady-state and non-equilibrium relaxation dynamics at the predator extinction threshold are governed by the directed percolation universality class. Spatial predation rate variability results in more localized clusters, enhancing both competing species’ population densities. Affixing variable interaction rates to individual particles and allowing for trait inheritance subject to mutations induces fast evolutionary dynamics for the rate distributions. Stochastic spatial variants of three-species competition with ‘rock-paper-scissors’ interactions metaphorically describe cyclic dominance. These models illustrate intimate connections between population dynamics and evolutionary game theory, underscore the role of fluctuations to drive populations toward extinction, and demonstrate how space can support species diversity. Two-dimensional cyclic three-species May-Leonard models are characterized by the emergence of spiraling patterns whose properties are elucidated by a mapping onto a complex Ginzburg-Landau equation. Multiple-species extensions to general ‘food networks’ can be classified on the mean-field level, providing both fundamental understanding of ensuing cooperativity and profound insight into the rich spatio-temporal features and coarsening kinetics in the corresponding spatially extended systems. Novel space-time patterns emerge as a result of the formation of competing alliances; e.g. coarsening domains that each incorporate rock-paper-scissors competition games.

Four millennia of woodland structure and dynamics at the Arctic treeline of eastern Canada.

PubMed

Auger, Sarah; Payette, Serge

2010-05-01

Paleoecological analysis using complementary indicators of vegetation and soil can provide spatially explicit information on ecological processes influencing trajectories of long-term ecosystem change. Here we document the structure and dynamics of an old-growth woodland before and after its inception 1000 years ago. We infer vegetation and soil characteristics from size and age distributions of black spruce (Picea mariana (Mill.) B.S.P.), soil properties, plant fossils, and paleosols. Radiocarbon ages of charcoal on the ground and in the soil indicate that the fire return interval was approximately 300 years between 2750 and 1000 cal. yr BP. No fire evidence was found before and after this period despite the presence of spruce since 4200 cal. yr BP. The size structures of living and dead spruce suggest that the woodland is in equilibrium with present climate in absence of fire. Tree establishment and mortality occurred regularly since the last fire event around 950 cal. yr BP. Both layering and occasional seeding have contributed to stabilize the spatial distribution of spruce over the past 1000 years. Since initial afforestation, soil development has been homogenized by the changing spatial distribution of spruce following each fire. We conclude that the history of the woodland is characterized by vegetation shifts associated with fire and soil disturbances and by millennial-scale maintenance of the woodland's structure despite changing climatic conditions.

Dissipative structure in the photo-induced phase under steady light irradiation in the spin crossover complex.

PubMed

Nishihara, Taishi; Bousseksou, Azzdine; Tanaka, Koichiro

2013-12-16

We report the spatial and temporal dynamics of the photo-induced phase in the iron (II) spin crossover complex Fe(ptz)(6)(BF(4))(2) studied by image measurement under steady light irradiation and transient absorption measurement. The dynamic factors are derived from the spatial and temporal fluctuation of the image in the steady state under light irradiation between 65 and 100 K. The dynamic factors clearly indicate that the fluctuation has a resonant frequency that strongly depends on the temperature, and is proportional to the relaxation rate of the photo-induced phase. This oscillation of the speckle pattern under steady light irradiation is ascribed to the nonlinear interaction between the spin state and the lattice volume at the surface.

Spatio-Temporal Structure, Path Characteristics, and Perceptual Grouping in Immediate Serial Spatial Recall

PubMed Central

De Lillo, Carlo; Kirby, Melissa; Poole, Daniel

2016-01-01

Immediate serial spatial recall measures the ability to retain sequences of locations in short-term memory and is considered the spatial equivalent of digit span. It is tested by requiring participants to reproduce sequences of movements performed by an experimenter or displayed on a monitor. Different organizational factors dramatically affect serial spatial recall but they are often confounded or underspecified. Untangling them is crucial for the characterization of working-memory models and for establishing the contribution of structure and memory capacity to spatial span. We report five experiments assessing the relative role and independence of factors that have been reported in the literature. Experiment 1 disentangled the effects of spatial clustering and path-length by manipulating the distance of items displayed on a touchscreen monitor. Long-path sequences segregated by spatial clusters were compared with short-path sequences not segregated by clusters. Recall was more accurate for sequences segregated by clusters independently from path-length. Experiment 2 featured conditions where temporal pauses were introduced between or within cluster boundaries during the presentation of sequences with the same paths. Thus, the temporal structure of the sequences was either consistent or inconsistent with a hierarchical representation based on segmentation by spatial clusters but the effect of structure could not be confounded with effects of path-characteristics. Pauses at cluster boundaries yielded more accurate recall, as predicted by a hierarchical model. In Experiment 3, the systematic manipulation of sequence structure, path-length, and presence of path-crossings of sequences showed that structure explained most of the variance, followed by the presence/absence of path-crossings, and path-length. Experiments 4 and 5 replicated the results of the previous experiments in immersive virtual reality navigation tasks where the viewpoint of the observer changed dynamically during encoding and recall. This suggested that the effects of structure in spatial span are not dependent on perceptual grouping processes induced by the aerial view of the stimulus array typically afforded by spatial recall tasks. These results demonstrate the independence of coding strategies based on structure from effects of path characteristics and perceptual grouping in immediate serial spatial recall. PMID:27891101

Delay-induced depinning of localized structures in a spatially inhomogeneous Swift-Hohenberg model

NASA Astrophysics Data System (ADS)

Tabbert, Felix; Schelte, Christian; Tlidi, Mustapha; Gurevich, Svetlana V.

2017-03-01

We report on the dynamics of localized structures in an inhomogeneous Swift-Hohenberg model describing pattern formation in the transverse plane of an optical cavity. This real order parameter equation is valid close to the second-order critical point associated with bistability. The optical cavity is illuminated by an inhomogeneous spatial Gaussian pumping beam and subjected to time-delayed feedback. The Gaussian injection beam breaks the translational symmetry of the system by exerting an attracting force on the localized structure. We show that the localized structure can be pinned to the center of the inhomogeneity, suppressing the delay-induced drift bifurcation that has been reported in the particular case where the injection is homogeneous, assuming a continuous wave operation. Under an inhomogeneous spatial pumping beam, we perform the stability analysis of localized solutions to identify different instability regimes induced by time-delayed feedback. In particular, we predict the formation of two-arm spirals, as well as oscillating and depinning dynamics caused by the interplay of an attracting inhomogeneity and destabilizing time-delayed feedback. The transition from oscillating to depinning solutions is investigated by means of numerical continuation techniques. Analytically, we use an order parameter approach to derive a normal form of the delay-induced Hopf bifurcation leading to an oscillating solution. Additionally we model the interplay of an attracting inhomogeneity and destabilizing time delay by describing the localized solution as an overdamped particle in a potential well generated by the inhomogeneity. In this case, the time-delayed feedback acts as a driving force. Comparing results from the later approach with the full Swift-Hohenberg model, we show that the approach not only provides an instructive description of the depinning dynamics, but also is numerically accurate throughout most of the parameter regime.

Exploring the Spatial and Temporal Organization of a Cell’s Proteome

PubMed Central

Beck, Martin; Topf, Maya; Frazier, Zachary; Tjong, Harianto; Xu, Min; Zhang, Shihua; Alber, Frank

2013-01-01

To increase our current understanding of cellular processes, such as cell signaling and division, knowledge is needed about the spatial and temporal organization of the proteome at different organizational levels. These levels cover a wide range of length and time scales: from the atomic structures of macromolecules for inferring their molecular function, to the quantitative description of their abundance, and distribution in the cell. Emerging new experimental technologies are greatly increasing the availability of such spatial information on the molecular organization in living cells. This review addresses three fields that have significantly contributed to our understanding of the proteome’s spatial and temporal organization: first, methods for the structure determination of individual macromolecular assemblies, specifically the fitting of atomic structures into density maps generated from electron microscopy techniques; second, research that visualizes the spatial distributions of these complexes within the cellular context using cryo electron tomography techniques combined with computational image processing; and third, methods for the spatial modeling of the dynamic organization of the proteome, specifically those methods for simulating reaction and diffusion of proteins and complexes in crowded intracellular fluids. The long-term goal is to integrate the varied data about a proteome’s organization into a spatially explicit, predictive model of cellular processes. PMID:21094684

The Third Solar Wind Conference: A summary

NASA Technical Reports Server (NTRS)

Russell, C. T.

1974-01-01

The Third Solar Wind Conference consisted of nine sessions. The following subjects were discussed: (1) solar abundances; (2) the history and evolution of the solar wind; (3) the structure and dynamics of the solar corona; (4) macroscopic and microscopic properties of the solar wind; (5) cosmic rays as a probe of the solar wind; (6) the structure and dynamics of the solar wind; (7) spatial gradients; (8) stellar winds; and (9) interactions with objects in the solar wind. The invited and contributed talks presented at the conference are summarized.

Spatial Memory in the Morris Water Maze and Activation of Cyclic AMP Response Element-Binding (CREB) Protein within the Mouse Hippocampus

ERIC Educational Resources Information Center

Porte, Yves; Buhot, Marie Christine; Mons, Nicole E.

2008-01-01

We investigated the spatio-temporal dynamics of learning-induced cAMP response element-binding protein activation/phosphorylation (pCREB) in mice trained in a spatial reference memory task in the water maze. Using immunohistochemistry, we examined pCREB immunoreactivity (pCREB-ir) in hippocampal CA1 and CA3 and related brain structures. During the…

Laser-combined scanning tunnelling microscopy for probing ultrafast transient dynamics.

PubMed

Terada, Yasuhiko; Yoshida, Shoji; Takeuchi, Osamu; Shigekawa, Hidemi

2010-07-07

The development of time-resolved scanning tunnelling microscopy (STM), in particular, attempts to combine STM with ultrafast laser technology, is reviewed with emphasis on observed physical quantities and spatiotemporal resolution. Ultrashort optical pulse technology has allowed us to observe transient phenomena in the femtosecond range, which, however, has the drawback of a relatively low spatial resolution due to the electromagnetic wavelength used. In contrast, STM and its related techniques, although the time resolution is limited by the circuit bandwidth (∼100 kHz), enable us to observe structures at the atomic level in real space. Our purpose has been to combine these two techniques to achieve a new technology that satisfies the requirements for exploring the ultrafast transient dynamics of the local quantum functions in organized small structures, which will advance the pursuit of future nanoscale scientific research in terms of the ultimate temporal and spatial resolutions. © 2010 IOP Publishing Ltd

Probing Atomic Dynamics and Structures Using Optical Patterns

NASA Astrophysics Data System (ADS)

Schmittberger, Bonnie L.; Gauthier, Daniel J.

2015-05-01

Pattern formation is a widely studied phenomenon that can provide fundamental insights into nonlinear systems. Emergent patterns in cold atoms are of particular interest in condensed matter physics and quantum information science because one can relate optical patterns to spatial structures in the atoms. In our experimental system, we study multimode optical patterns generated from a sample of cold, thermal atoms. We observe this nonlinear optical phenomenon at record low input powers due to the highly nonlinear nature of the spatial bunching of atoms in an optical lattice. We present a detailed study of the dynamics of these bunched atoms during optical pattern formation. We show how small changes in the atomic density distribution affect the symmetry of the generated patterns as well as the nature of the nonlinearity that describes the light-atom interaction. We gratefully acknowledge the financial support of the National Science Foundation through Grant #PHY-1206040.

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

Dispersal responses override density effects on genetic diversity during post-disturbance succession

PubMed Central

Landguth, Erin L.; Bull, C. Michael; Banks, Sam C.; Gardner, Michael G.; Driscoll, Don A.

2016-01-01

Dispersal fundamentally influences spatial population dynamics but little is known about dispersal variation in landscapes where spatial heterogeneity is generated predominantly by disturbance and succession. We tested the hypothesis that habitat succession following fire inhibits dispersal, leading to declines over time in genetic diversity in the early successional gecko Nephrurus stellatus. We combined a landscape genetics field study with a spatially explicit simulation experiment to determine whether successional patterns in genetic diversity were driven by habitat-mediated dispersal or demographic effects (declines in population density leading to genetic drift). Initial increases in genetic structure following fire were likely driven by direct mortality and rapid population expansion. Subsequent habitat succession increased resistance to gene flow and decreased dispersal and genetic diversity in N. stellatus. Simulated changes in population density alone did not reproduce these results. Habitat-mediated reductions in dispersal, combined with changes in population density, were essential to drive the field-observed patterns. Our study provides a framework for combining demographic, movement and genetic data with simulations to discover the relative influence of demography and dispersal on patterns of landscape genetic structure. Our results suggest that succession can inhibit connectivity among individuals, opening new avenues for understanding how disturbance regimes influence spatial population dynamics. PMID:27009225

Dynamical structure of extreme ultraviolet macrospicules

NASA Technical Reports Server (NTRS)

Karovska, Margarita; Habbal, Shadia Rifai

1994-01-01

We describe the substructures forming the macrospicules and their temporal evolution, as revealed by the application of an image enhancement algorithm to extreme ultraviolet (EUV) observations of macrospicules. The enhanced images uncover, for the first time, the substructures forming the column-like structures within the macrospicules and the low-lying arches at their base. The spatial and temporal evolution of macrospicules clearly show continuous interaction between these substructures with occasional ejection of plasma following a ballistic trajectory. We comment on the importance of these results for planning near future space observations of macrospicules with better temporal and spatial resolution.

Synthesis of dynamic phase profile by the correlation technique for spatial control of optical beams in multiplexing and switching

NASA Astrophysics Data System (ADS)

Bugaychuk, Svitlana A.; Gnatovskyy, Vladimir O.; Sidorenko, Andrey V.; Pryadko, Igor I.; Negriyko, Anatoliy M.

2015-11-01

New approach for the correlation technique, which is based on multiple periodic structures to create a controllable angular spectrum, is proposed and investigated both theoretically and experimentally. The transformation of an initial laser beam occurs due to the actions of consecutive phase periodic structures, which may differ by their parameters. Then, after the Fourier transformation of a complex diffraction field, the output diffraction orders will be changed both by their intensities and by their spatial position. The controllable change of output angular spectrum is carried out by a simple control of the parameters of the periodic structures. We investigate several simple examples of such management.

Quantifying seascape structure: Extending terrestrial spatial pattern metrics to the marine realm

USGS Publications Warehouse

Wedding, L.M.; Christopher, L.A.; Pittman, S.J.; Friedlander, A.M.; Jorgensen, S.

2011-01-01

Spatial pattern metrics have routinely been applied to characterize and quantify structural features of terrestrial landscapes and have demonstrated great utility in landscape ecology and conservation planning. The important role of spatial structure in ecology and management is now commonly recognized, and recent advances in marine remote sensing technology have facilitated the application of spatial pattern metrics to the marine environment. However, it is not yet clear whether concepts, metrics, and statistical techniques developed for terrestrial ecosystems are relevant for marine species and seascapes. To address this gap in our knowledge, we reviewed, synthesized, and evaluated the utility and application of spatial pattern metrics in the marine science literature over the past 30 yr (1980 to 2010). In total, 23 studies characterized seascape structure, of which 17 quantified spatial patterns using a 2-dimensional patch-mosaic model and 5 used a continuously varying 3-dimensional surface model. Most seascape studies followed terrestrial-based studies in their search for ecological patterns and applied or modified existing metrics. Only 1 truly unique metric was found (hydrodynamic aperture applied to Pacific atolls). While there are still relatively few studies using spatial pattern metrics in the marine environment, they have suffered from similar misuse as reported for terrestrial studies, such as the lack of a priori considerations or the problem of collinearity between metrics. Spatial pattern metrics offer great potential for ecological research and environmental management in marine systems, and future studies should focus on (1) the dynamic boundary between the land and sea; (2) quantifying 3-dimensional spatial patterns; and (3) assessing and monitoring seascape change. ?? Inter-Research 2011.

Palmitoylation of LIM Kinase-1 ensures spine-specific actin polymerization and morphological plasticity

PubMed Central

George, Joju; Soares, Cary; Montersino, Audrey; Beique, Jean-Claude; Thomas, Gareth M

2015-01-01

Precise regulation of the dendritic spine actin cytoskeleton is critical for neurodevelopment and neuronal plasticity, but how neurons spatially control actin dynamics is not well defined. Here, we identify direct palmitoylation of the actin regulator LIM kinase-1 (LIMK1) as a novel mechanism to control spine-specific actin dynamics. A conserved palmitoyl-motif is necessary and sufficient to target LIMK1 to spines and to anchor LIMK1 in spines. ShRNA knockdown/rescue experiments reveal that LIMK1 palmitoylation is essential for normal spine actin polymerization, for spine-specific structural plasticity and for long-term spine stability. Palmitoylation is critical for LIMK1 function because this modification not only controls LIMK1 targeting, but is also essential for LIMK1 activation by its membrane-localized upstream activator PAK. These novel roles for palmitoylation in the spatial control of actin dynamics and kinase signaling provide new insights into structural plasticity mechanisms and strengthen links between dendritic spine impairments and neuropathological conditions. DOI: http://dx.doi.org/10.7554/eLife.06327.001 PMID:25884247

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

NASA Astrophysics Data System (ADS)

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

2009-04-01

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

Atomic Scale Medium Range Order and Relaxation Dynamics in Metallic Glass

NASA Astrophysics Data System (ADS)

Zhang, Pei

We studied the atomic scale structure of bulk metallic glass (BMG) with the combination of fluctuation electron microscopy (FEM) and hybrid reverse Monte Carlo (HRMC) simulation. Medium range order (MRO), which occupies the length scale between short range order (SRO) and long-range order, plays an important role on the properties of metallic glass, but the characterization of MRO in experiment is difficult because conventional techniques are not sensitive to the structure at MRO scale. Compared with the X-ray and neutron which can measure SRO by two-body correlation functions, FEM is an effective way to detect MRO structure through three and four-body correlation functions, providing information about the size, distribution, and internal structure of MRO combing HRMC modeling. Thickness estimation is necessary in FEM experiment and HRMC calculation, so in Chapter 3, we measured the elastic and inelastic mean free paths of metallic glass alloys based on focused ion beam prepared thin samples with measured thickness gradients. We developed a model based on the Wentzel atomic model to predict the elastic mean free path for other amorphous materials. In Chapter 4, we studied the correlation of MRO and glass forming ability ZrCuAl alloy. Results from Variable resolution fluctuation microscopy show that in Zr50Cu35Al15 the crystal-like clusters shrink but become more ordered, while icosahedral-like clusters grow. Compared with Zr50Cu45Al5, Zr50Cu35Al15 with poorer glass forming ability exhibits more stable crystal-like structure under annealing, indicating that destabilizing crystal-like structures is important to achieve better glass forming ability in this alloy. In Chapter 5, we studied the crystallization and MRO structural in deformed and quenched Ni60Nb40 metallic glass. The deformed Ni60Nb40 contains fewer icosahedral-like Voronoi clusters and more crystal-like and bcc-like Voronoi clusters. The crystal-like and bcc-like medium range order clusters may be the structural origin for its lower crystallization temperature compared with quenched alloy. Dynamics heterogeneity is proposed to be the microscopic origin of the dynamic nature of glass transition. Some experimental evidence and simulation have indicated that different regions of materials indeed relax at fast or slow rate. However, the spatial distribution of relaxation time visualized from the experiment as the direct evidence of heterogeneous dynamics is still challenging. We proposed to measure the structural dynamics of supercooled metallic glasses with electron correlation microscopy (ECM) technique at the nanometer scale. ECM was developed as a way to measure structural relaxation times of liquids with nanometer-scale spatial resolution using the coherent electron scattering equivalent of photon correlation spectroscopy. In chapter 6, we studied the experimental requirements of ECM to obtain reliable results. For example, the trajectory length must be at least 40 times the relaxation time to obtain a well-converged g2( t), and the time per frame must be less than 0.1 time the relaxation time to obtain sufficient sampling. ECM experiment was firstly realized in scanning transmission electron microscopy (STEM) mode and applied to measure the structural relaxation time of Pd based metallic glass. In order to overcome the drift problem and capture the spatial information, we developed ECM experiment in dark field (DF) mode. In Chapter 7, through DF-ECM, we visualized the spatially heterogeneous dynamics by in-situ heating Pt57.5Cu14.7Ni 5.3P22.5 nanowire into supercooled liquid state, and quantify the size of the heterogeneity by four-point correlation function. The thickness effect and temporal evolution of the heterogeneous domain were also discussed. Additionally, a fast near-surface dynamics was discovered, providing an effective mechanism for surface crystallization of liquids by homogeneous nucleation.

Microbial Life in Soil - Linking Biophysical Models with Observations

NASA Astrophysics Data System (ADS)

Or, Dani; Tecon, Robin; Ebrahimi, Ali; Kleyer, Hannah; Ilie, Olga; Wang, Gang

2015-04-01

Microbial life in soil occurs within fragmented aquatic habitats formed in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools that enable new mechanistic insights into how differences in substrate affinities among microbial species and soil micro-hydrological conditions may give rise to a remarkable spatial and functional order in an extremely heterogeneous soil microbial world

Microbial Life in Soil - Linking Biophysical Models with Observations

NASA Astrophysics Data System (ADS)

Or, D.; Tecon, R.; Ebrahimi, A.; Kleyer, H.; Ilie, O.; Wang, G.

2014-12-01

Microbial life in soil occurs within fragmented aquatic habitats in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools that enable new mechanistic insights into how differences in substrate affinities among microbial species and soil micro-hydrological conditions may give rise to a remarkable spatial and functional order in an extremely heterogeneous soil microbial world.

The roles of competition and habitat in the dynamics of populations and species distributions Ecology

Treesearch

Charles B. Yackulic; Janice Reid; James D. Nichols; James E. Hines; Raymond Davis; Eric Forsman

2014-01-01

The role of competition in structuring biotic communities at fine spatial scales is well known from detailed process-based studies. Our understanding of competition’s importance at broader scales is less resolved and mainly based on static species distribution maps. Here, we bridge this gap by examining the joint occupancy dynamics of an invading species (Barred Owl,...

On species persistence-time distributions.

PubMed

Suweis, S; Bertuzzo, E; Mari, L; Rodriguez-Iturbe, I; Maritan, A; Rinaldo, A

2012-06-21

We present new theoretical and empirical results on the probability distributions of species persistence times in natural ecosystems. Persistence times, defined as the timespans occurring between species' colonization and local extinction in a given geographic region, are empirically estimated from local observations of species' presence/absence. A connected sampling problem is presented, generalized and solved analytically. Species persistence is shown to provide a direct connection with key spatial macroecological patterns like species-area and endemics-area relationships. Our empirical analysis pertains to two different ecosystems and taxa: a herbaceous plant community and a estuarine fish database. Despite the substantial differences in ecological interactions and spatial scales, we confirm earlier evidence on the general properties of the scaling of persistence times, including the predicted effects of the structure of the spatial interaction network. The framework tested here allows to investigate directly nature and extent of spatial effects in the context of ecosystem dynamics. The notable coherence between spatial and temporal macroecological patterns, theoretically derived and empirically verified, is suggested to underlie general features of the dynamic evolution of ecosystems. Copyright © 2012 Elsevier Ltd. All rights reserved.

Spatial Statistics of atmospheric particulate matter in China

NASA Astrophysics Data System (ADS)

Huang, Yongxiang; Wang, Yangjun; Liu, Yulu

2017-04-01

In this work, the spatial dynamics of the atmospheric particulate matters (resp. PM10 and PM2.5) are studied using turbulence methodologies. The hourly concentrations of particulate matter were released by the Chinese government (http://www.cnemc.cn). We first processed these data into daily average concentrations. Totally, there are 305 monitor stations with an observations period of 425 days. It is found experimentally that the spatial correlation function ρ(r) shows a log-law on the mesoscale range, i.e., 50 ≤ r ≤ 500 km, with an experimental scaling exponent β = 0.45. The spatial structure function shows a power-law behavior on the mesoscale range 90 ≤ r ≤ 500 km. The experimental scaling exponent ζ(q) is convex, showing that the intermittent correction is relevant in characterizing the spatial dynamics of particulate matter. The measured singularity spectrum f(α) also shows its multifractal nature. Experimentally, the particulate matter is more intermittent than the passive scalar, which could be partially due to the mesoscale movements of the atmosphere, and also due to local sources, such as local industry activities.

Dynamical Heterogeneity in Granular Fluids and Structural Glasses

NASA Astrophysics Data System (ADS)

Avila, Karina E.

Our current understanding of the dynamics of supercooled liquids and other similar slowly evolving (glassy) systems is rather limited. One aspect that is particularly poorly understood is the origin and behavior of the strong non trivial fluctuations that appear in the relaxation process toward equilibrium. Glassy systems and granular systems both present regions of particles moving cooperatively and at different rates from other regions. This phenomenon is known as spatially heterogeneous dynamics. A detailed explanation of this phenomenon may lead to a better understanding of the slow relaxation process, and perhaps it could even help to explain the presence of the glass transition. This dissertation concentrates on studying dynamical heterogeneity by analyzing simulation data for models of granular materials and structural glasses. For dissipative granular fluids, the growing behavior of dynamical heterogeneities is studied for different densities and different degrees of inelasticity in the particle collisions. The correlated regions are found to grow rapidly as the system approaches dynamical arrest. Their geometry is conserved even when probing at different cutoff length in the correlation function or when the energy dissipation in the system is increased. For structural glasses, I test a theoretical framework that models dynamical heterogeneity as originated in the presence of Goldstone modes, which emerge from a broken continuous time reparametrization symmetry. This analysis is based on quantifying the size and the spatial correlations of fluctuations in the time variable and of other kinds of fluctuations. The results obtained here agree with the predictions of the hypothesis. In particular, the fluctuations associated to the time reparametrization invariance become stronger for low temperatures, long timescales, and large coarse graining lengths. Overall, this research points to dynamical heterogeneity to be described for granular systems similarly than for other glassy systems and it provides evidence in favor of a particular theory for the origin of dynamical heterogeneity.

Modeling the Spatial Dynamics of Regional Land Use: The CLUE-S Model

NASA Astrophysics Data System (ADS)

Verburg, Peter H.; Soepboer, Welmoed; Veldkamp, A.; Limpiada, Ramil; Espaldon, Victoria; Mastura, Sharifah S. A.

2002-09-01

Land-use change models are important tools for integrated environmental management. Through scenario analysis they can help to identify near-future critical locations in the face of environmental change. A dynamic, spatially explicit, land-use change model is presented for the regional scale: CLUE-S. The model is specifically developed for the analysis of land use in small regions (e.g., a watershed or province) at a fine spatial resolution. The model structure is based on systems theory to allow the integrated analysis of land-use change in relation to socio-economic and biophysical driving factors. The model explicitly addresses the hierarchical organization of land use systems, spatial connectivity between locations and stability. Stability is incorporated by a set of variables that define the relative elasticity of the actual land-use type to conversion. The user can specify these settings based on expert knowledge or survey data. Two applications of the model in the Philippines and Malaysia are used to illustrate the functioning of the model and its validation.

Modeling the spatial dynamics of regional land use: the CLUE-S model.

PubMed

Verburg, Peter H; Soepboer, Welmoed; Veldkamp, A; Limpiada, Ramil; Espaldon, Victoria; Mastura, Sharifah S A

2002-09-01

Land-use change models are important tools for integrated environmental management. Through scenario analysis they can help to identify near-future critical locations in the face of environmental change. A dynamic, spatially explicit, land-use change model is presented for the regional scale: CLUE-S. The model is specifically developed for the analysis of land use in small regions (e.g., a watershed or province) at a fine spatial resolution. The model structure is based on systems theory to allow the integrated analysis of land-use change in relation to socio-economic and biophysical driving factors. The model explicitly addresses the hierarchical organization of land use systems, spatial connectivity between locations and stability. Stability is incorporated by a set of variables that define the relative elasticity of the actual land-use type to conversion. The user can specify these settings based on expert knowledge or survey data. Two applications of the model in the Philippines and Malaysia are used to illustrate the functioning of the model and its validation.

Spatially encoded phase-contrast MRI-3D MRI movies of 1D and 2D structures at millisecond resolution.

PubMed

Merboldt, Klaus-Dietmar; Uecker, Martin; Voit, Dirk; Frahm, Jens

2011-10-01

This work demonstrates that the principles underlying phase-contrast MRI may be used to encode spatial rather than flow information along a perpendicular dimension, if this dimension contains an MRI-visible object at only one spatial location. In particular, the situation applies to 3D mapping of curved 2D structures which requires only two projection images with different spatial phase-encoding gradients. These phase-contrast gradients define the field of view and mean spin-density positions of the object in the perpendicular dimension by respective phase differences. When combined with highly undersampled radial fast low angle shot (FLASH) and image reconstruction by regularized nonlinear inversion, spatial phase-contrast MRI allows for dynamic 3D mapping of 2D structures in real time. First examples include 3D MRI movies of the acting human hand at a temporal resolution of 50 ms. With an even simpler technique, 3D maps of curved 1D structures may be obtained from only three acquisitions of a frequency-encoded MRI signal with two perpendicular phase encodings. Here, 3D MRI movies of a rapidly rotating banana were obtained at 5 ms resolution or 200 frames per second. In conclusion, spatial phase-contrast 3D MRI of 2D or 1D structures is respective two or four orders of magnitude faster than conventional 3D MRI. Copyright © 2011 Wiley-Liss, Inc.

Ecotoxicology and spatial modeling in population dynamics: an illustration with brown trout.

PubMed

Chaumot, Arnaud; Charles, Sandrine; Flammarion, Patrick; Auger, Pierre

2003-05-01

We developed a multiregion matrix population model to explore how the demography of a hypothetical brown trout population living in a river network varies in response to different spatial scenarios of cadmium contamination. Age structure, spatial distribution, and demographic and migration processes are taken into account in the model. Chronic or acute cadmium concentrations affect the demographic parameters at the scale of the river range. The outputs of the model constitute population-level end points (the asymptotic population growth rate, the stable age structure, and the asymptotic spatial distribution) that allow comparing the different spatial scenarios of contamination regarding the demographic response at the scale of the whole river network. An analysis of the sensitivity of these end points to lower order parameters enables us to link the local effects of cadmium to the global demographic behavior of the brown trout population. Such a link is of broad interest in the point of view of ecotoxicological management.

Up, Down, and All Around: Scale-Dependent Spatial Variation in Rocky-Shore Communities of Fildes Peninsula, King George Island, Antarctica

PubMed Central

Valdivia, Nelson; Díaz, María J.; Holtheuer, Jorge; Garrido, Ignacio; Huovinen, Pirjo; Gómez, Iván

2014-01-01

Understanding the variation of biodiversity along environmental gradients and multiple spatial scales is relevant for theoretical and management purposes. Hereby, we analysed the spatial variability in diversity and structure of intertidal and subtidal macrobenthic Antarctic communities along vertical environmental stress gradients and across multiple horizontal spatial scales. Since biotic interactions and local topographic features are likely major factors for coastal assemblages, we tested the hypothesis that fine-scale processes influence the effects of the vertical environmental stress gradients on the macrobenthic diversity and structure. We used nested sampling designs in the intertidal and subtidal habitats, including horizontal spatial scales ranging from few centimetres to 1000s of metres along the rocky shore of Fildes Peninsula, King George Island. In both intertidal and subtidal habitats, univariate and multivariate analyses showed a marked vertical zonation in taxon richness and community structure. These patterns depended on the horizontal spatial scale of observation, as all analyses showed a significant interaction between height (or depth) and the finer spatial scale analysed. Variance and pseudo-variance components supported our prediction for taxon richness, community structure, and the abundance of dominant species such as the filamentous green alga Urospora penicilliformis (intertidal), the herbivore Nacella concinna (intertidal), the large kelp-like Himantothallus grandifolius (subtidal), and the red crustose red alga Lithothamnion spp. (subtidal). We suggest that in coastal ecosystems strongly governed by physical factors, fine-scale processes (e.g. biotic interactions and refugia availability) are still relevant for the structuring and maintenance of the local communities. The spatial patterns found in this study serve as a necessary benchmark to understand the dynamics and adaptation of natural assemblages in response to observed and predicted environmental changes in Antarctica. PMID:24956114

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

PubMed

Deco, Gustavo; Ponce-Alvarez, Adrián; Mantini, Dante; Romani, Gian Luca; Hagmann, Patric; Corbetta, Maurizio

2013-07-03

Brain fluctuations at rest are not random but are structured in spatial patterns of correlated activity across different brain areas. The question of how resting-state functional connectivity (FC) emerges from the brain's anatomical connections has motivated several experimental and computational studies to understand structure-function relationships. However, the mechanistic origin of resting state is obscured by large-scale models' complexity, and a close structure-function relation is still an open problem. Thus, a realistic but simple enough description of relevant brain dynamics is needed. Here, we derived a dynamic mean field model that consistently summarizes the realistic dynamics of a detailed spiking and conductance-based synaptic large-scale network, in which connectivity is constrained by diffusion imaging data from human subjects. The dynamic mean field approximates the ensemble dynamics, whose temporal evolution is dominated by the longest time scale of the system. With this reduction, we demonstrated that FC emerges as structured linear fluctuations around a stable low firing activity state close to destabilization. Moreover, the model can be further and crucially simplified into a set of motion equations for statistical moments, providing a direct analytical link between anatomical structure, neural network dynamics, and FC. Our study suggests that FC arises from noise propagation and dynamical slowing down of fluctuations in an anatomically constrained dynamical system. Altogether, the reduction from spiking models to statistical moments presented here provides a new framework to explicitly understand the building up of FC through neuronal dynamics underpinned by anatomical connections and to drive hypotheses in task-evoked studies and for clinical applications.

Functional connectivity dynamically evolves on multiple time-scales over a static structural connectome: Models and mechanisms.

PubMed

Cabral, Joana; Kringelbach, Morten L; Deco, Gustavo

2017-10-15

Over the last decade, we have observed a revolution in brain structural and functional Connectomics. On one hand, we have an ever-more detailed characterization of the brain's white matter structural connectome. On the other, we have a repertoire of consistent functional networks that form and dissipate over time during rest. Despite the evident spatial similarities between structural and functional connectivity, understanding how different time-evolving functional networks spontaneously emerge from a single structural network requires analyzing the problem from the perspective of complex network dynamics and dynamical system's theory. In that direction, bottom-up computational models are useful tools to test theoretical scenarios and depict the mechanisms at the genesis of resting-state activity. Here, we provide an overview of the different mechanistic scenarios proposed over the last decade via computational models. Importantly, we highlight the need of incorporating additional model constraints considering the properties observed at finer temporal scales with MEG and the dynamical properties of FC in order to refresh the list of candidate scenarios. Copyright © 2017 Elsevier Inc. All rights reserved.

Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase

PubMed Central

Mittag, Tanja; Marsh, Joseph; Grishaev, Alexander; Orlicky, Stephen; Lin, Hong; Sicheri, Frank; Tyers, Mike; Forman-Kay, Julie D.

2010-01-01

Summary Intrinsically disordered proteins can form highly dynamic complexes with partner proteins. One such dynamic complex involves the intrinsically disordered Sic1 with its partner Cdc4 in regulation of yeast cell cycle progression. Phosphorylation of six N-terminal Sic1 sites leads to equilibrium engagement of each phosphorylation site with the primary binding pocket in Cdc4, the substrate recognition subunit of a ubiquitin ligase. ENSEMBLE calculations utilizing experimental NMR and small-angle x-ray scattering data reveal significant transient structure in both phosphorylation states of the isolated ensembles (Sic1 and pSic1) that modulates their electrostatic potential, suggesting a structural basis for the proposed strong contribution of electrostatics to binding. A structural model of the dynamic pSic1-Cdc4 complex demonstrates the spatial arrangements in the ubiquitin ligase complex. These results provide a physical picture of a protein that is predominantly disordered in both its free and bound states, enabling aspects of its structure/function relationship to be elucidated. PMID:20399186

Spatio-Temporal Patterning in Primary Motor Cortex at Movement Onset.

PubMed

Best, Matthew D; Suminski, Aaron J; Takahashi, Kazutaka; Brown, Kevin A; Hatsopoulos, Nicholas G

2017-02-01

Voluntary movement initiation involves the engagement of large populations of motor cortical neurons around movement onset. Despite knowledge of the temporal dynamics that lead to movement, the spatial structure of these dynamics across the cortical surface remains unknown. In data from 4 rhesus macaques, we show that the timing of attenuation of beta frequency local field potential oscillations, a correlate of locally activated cortex, forms a spatial gradient across primary motor cortex (MI). We show that these spatio-temporal dynamics are recapitulated in the engagement order of ensembles of MI neurons. We demonstrate that these patterns are unique to movement onset and suggest that movement initiation requires a precise spatio-temporal sequential activation of neurons in MI. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Trading strategy based on dynamic mode decomposition: Tested in Chinese stock market

NASA Astrophysics Data System (ADS)

Cui, Ling-xiao; Long, Wen

2016-11-01

Dynamic mode decomposition (DMD) is an effective method to capture the intrinsic dynamical modes of complex system. In this work, we adopt DMD method to discover the evolutionary patterns in stock market and apply it to Chinese A-share stock market. We design two strategies based on DMD algorithm. The strategy which considers only timing problem can make reliable profits in a choppy market with no prominent trend while fails to beat the benchmark moving-average strategy in bull market. After considering the spatial information from spatial-temporal coherent structure of DMD modes, we improved the trading strategy remarkably. Then the DMD strategies profitability is quantitatively evaluated by performing SPA test to correct the data-snooping effect. The results further prove that DMD algorithm can model the market patterns well in sideways market.

High Annular Resolution Stellar Interferometry.

DTIC Science & Technology

1985-07-31

correlation is separable, C3 (Ax,At) = C1 (Ax) C2 (At), then the spatial structure and time evolution are uncorrelated and under these conditions one would...the following one. Reference 6 points out the bias obtained on the shape of the normalised spatial correlation function of dynamic speckle under the...MS student) 1982 H Daum (U1 assistant) 1981 C S ________ 20. 6. MUPID This appendix oontains oopies of the 20 publioations produced under this

Time-dependent spectral analysis of interactions within groups of walking pedestrians and vertical structural motion using wavelets

NASA Astrophysics Data System (ADS)

Bocian, M.; Brownjohn, J. M. W.; Racic, V.; Hester, D.; Quattrone, A.; Gilbert, L.; Beasley, R.

2018-05-01

A multi-scale and multi-object interaction phenomena can arise when a group of walking pedestrians crosses a structure capable of exhibiting dynamic response. This is because each pedestrian is an autonomous dynamic system capable of displaying intricate behaviour affected by social, psychological, biomechanical and environmental factors, including adaptations to the structural motion. Despite a wealth of mathematical models attempting to describe and simulate coupled crowd-structure system, their applicability can generally be considered uncertain. This can be assigned to a number of assumptions made in their development and the scarcity or unavailability of data suitable for their validation, in particular those associated with pedestrian-pedestrian and pedestrian-structure interaction. To alleviate this problem, data on behaviour of individual pedestrians within groups of six walkers with different spatial arrangements are gathered simultaneously with data on dynamic structural response of a footbridge, from a series of measurements utilising wireless motion monitors. Unlike in previous studies on coordination of pedestrian behaviour, the collected data can serve as a proxy for pedestrian vertical force, which is of critical importance from the point of view of structural stability. A bivariate analysis framework is proposed and applied to these data, encompassing wavelet transform, synchronisation measures based on Shannon entropy and circular statistics. A topological pedestrian map is contrived showing the strength and directionality of between-subjects interactions. It is found that the coordination in pedestrians' vertical force depends on the spatial collocation within a group, but it is generally weak. The relationship between the bridge and pedestrian behaviour is also analysed, revealing stronger propensity for pedestrians to coordinate their force with the structural motion rather than with each other.

Transoceanic migration, spatial dynamics, and population linkages of white sharks.

PubMed

Bonfil, Ramón; Meÿer, Michael; Scholl, Michael C; Johnson, Ryan; O'Brien, Shannon; Oosthuizen, Herman; Swanson, Stephan; Kotze, Deon; Paterson, Michael

2005-10-07

The large-scale spatial dynamics and population structure of marine top predators are poorly known. We present electronic tag and photographic identification data showing a complex suite of behavioral patterns in white sharks. These include coastal return migrations and the fastest known transoceanic return migration among swimming fauna, which provide direct evidence of a link between widely separated populations in South Africa and Australia. Transoceanic return migration involved a return to the original capture location, dives to depths of 980 meters, and the tolerance of water temperatures as low as 3.4 degrees C. These findings contradict previous ideas that female white sharks do not make transoceanic migrations, and they suggest natal homing behavior.

Blind identification of full-field vibration modes of output-only structures from uniformly-sampled, possibly temporally-aliased (sub-Nyquist), video measurements

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

Yang, Yongchao; Dorn, Charles; Mancini, Tyler

Enhancing the spatial and temporal resolution of vibration measurements and modal analysis could significantly benefit dynamic modelling, analysis, and health monitoring of structures. For example, spatially high-density mode shapes are critical for accurate vibration-based damage localization. In experimental or operational modal analysis, higher (frequency) modes, which may be outside the frequency range of the measurement, contain local structural features that can improve damage localization as well as the construction and updating of the modal-based dynamic model of the structure. In general, the resolution of vibration measurements can be increased by enhanced hardware. Traditional vibration measurement sensors such as accelerometers havemore » high-frequency sampling capacity; however, they are discrete point-wise sensors only providing sparse, low spatial sensing resolution measurements, while dense deployment to achieve high spatial resolution is expensive and results in the mass-loading effect and modification of structure's surface. Non-contact measurement methods such as scanning laser vibrometers provide high spatial and temporal resolution sensing capacity; however, they make measurements sequentially that requires considerable acquisition time. As an alternative non-contact method, digital video cameras are relatively low-cost, agile, and provide high spatial resolution, simultaneous, measurements. Combined with vision based algorithms (e.g., image correlation or template matching, optical flow, etc.), video camera based measurements have been successfully used for experimental and operational vibration measurement and subsequent modal analysis. However, the sampling frequency of most affordable digital cameras is limited to 30–60 Hz, while high-speed cameras for higher frequency vibration measurements are extremely costly. This work develops a computational algorithm capable of performing vibration measurement at a uniform sampling frequency lower than what is required by the Shannon-Nyquist sampling theorem for output-only modal analysis. In particular, the spatio-temporal uncoupling property of the modal expansion of structural vibration responses enables a direct modal decoupling of the temporally-aliased vibration measurements by existing output-only modal analysis methods, yielding (full-field) mode shapes estimation directly. Then the signal aliasing properties in modal analysis is exploited to estimate the modal frequencies and damping ratios. Furthermore, the proposed method is validated by laboratory experiments where output-only modal identification is conducted on temporally-aliased acceleration responses and particularly the temporally-aliased video measurements of bench-scale structures, including a three-story building structure and a cantilever beam.« less

Blind identification of full-field vibration modes of output-only structures from uniformly-sampled, possibly temporally-aliased (sub-Nyquist), video measurements

DOE PAGES

Yang, Yongchao; Dorn, Charles; Mancini, Tyler; ...

2016-12-05

Enhancing the spatial and temporal resolution of vibration measurements and modal analysis could significantly benefit dynamic modelling, analysis, and health monitoring of structures. For example, spatially high-density mode shapes are critical for accurate vibration-based damage localization. In experimental or operational modal analysis, higher (frequency) modes, which may be outside the frequency range of the measurement, contain local structural features that can improve damage localization as well as the construction and updating of the modal-based dynamic model of the structure. In general, the resolution of vibration measurements can be increased by enhanced hardware. Traditional vibration measurement sensors such as accelerometers havemore » high-frequency sampling capacity; however, they are discrete point-wise sensors only providing sparse, low spatial sensing resolution measurements, while dense deployment to achieve high spatial resolution is expensive and results in the mass-loading effect and modification of structure's surface. Non-contact measurement methods such as scanning laser vibrometers provide high spatial and temporal resolution sensing capacity; however, they make measurements sequentially that requires considerable acquisition time. As an alternative non-contact method, digital video cameras are relatively low-cost, agile, and provide high spatial resolution, simultaneous, measurements. Combined with vision based algorithms (e.g., image correlation or template matching, optical flow, etc.), video camera based measurements have been successfully used for experimental and operational vibration measurement and subsequent modal analysis. However, the sampling frequency of most affordable digital cameras is limited to 30–60 Hz, while high-speed cameras for higher frequency vibration measurements are extremely costly. This work develops a computational algorithm capable of performing vibration measurement at a uniform sampling frequency lower than what is required by the Shannon-Nyquist sampling theorem for output-only modal analysis. In particular, the spatio-temporal uncoupling property of the modal expansion of structural vibration responses enables a direct modal decoupling of the temporally-aliased vibration measurements by existing output-only modal analysis methods, yielding (full-field) mode shapes estimation directly. Then the signal aliasing properties in modal analysis is exploited to estimate the modal frequencies and damping ratios. Furthermore, the proposed method is validated by laboratory experiments where output-only modal identification is conducted on temporally-aliased acceleration responses and particularly the temporally-aliased video measurements of bench-scale structures, including a three-story building structure and a cantilever beam.« less

The Sun at high spatial resolution: The physics of small spatial structures in a magnetized medium

NASA Technical Reports Server (NTRS)

Rosner, R. T.

1986-01-01

An attempt is made to provide a perspective on the problem of spatial structuring on scales smaller than can presently be directly and regularly observed from the ground or with which current space-based instrumentation can be anticipated. There is abundant evidence from both observations and theory that such spatial structuring of the solar outer atmosphere is ubiquitous not only on the observed scales, but also on spatial scales down to (at least) the subarcsecond range. This is not to say that the results to be obtained from observations on these small scales can be anticipated: quite the opposite. What is clear instead is that many of the classic problems of coronal and chromospheric activity - involving the basic dissipative nature of magnetized plasmas - will be seen from a novel perspective at these scales, and that there are reasons for believing that dynamical processes of importance to activity on presently-resolved scales will themselves begin to be resolved on the sub-arcsecond level. Since the Sun is the only astrophysical laboratory for which there is any hope of studying these processes in any detail, this observatioinal opportunity is an exciting prospect for any student of magnetic activity in astrophysics.

A Malthusian curb on spatial structure in microorganism populations.

PubMed

Martin, A P

2004-10-07

That all organisms are born in the company of a parent but die alone is a fundamental biological asymmetry. It has been suggested that this provides a deep-rooted source of spatial pattern formation for microorganisms even at the scale of the population. Such a theory, however, neglects the strong influence in nature of the limited and spatially variable availability of food. The tendency, first recognized by Thomas Malthus in the 18th century, of a population to out-strip its food resources will eventually lead, through local starvation, to the suppression of a heterogeneity growing within a population. Using a generic model it is demonstrated that including local food limitation of breeding strongly dampens spatial structure otherwise resulting from birth and death. The extent of this damping is shown to be a function of the strength of the coupling between organisms and their food and of the total abundance of organic material. Moreover, this work provides an example of a density-dependent process acting to diminish spatial structure rather than to create it and highlights the rich variety of behaviour that is missed by continuum models which fail to represent such local dynamics.

The role of social and ecological processes in structuring animal populations: a case study from automated tracking of wild birds

PubMed Central

Farine, Damien R.; Firth, Josh A.; Aplin, Lucy M.; Crates, Ross A.; Culina, Antica; Garroway, Colin J.; Hinde, Camilla A.; Kidd, Lindall R.; Milligan, Nicole D.; Psorakis, Ioannis; Radersma, Reinder; Verhelst, Brecht; Voelkl, Bernhard; Sheldon, Ben C.

2015-01-01

Both social and ecological factors influence population process and structure, with resultant consequences for phenotypic selection on individuals. Understanding the scale and relative contribution of these two factors is thus a central aim in evolutionary ecology. In this study, we develop a framework using null models to identify the social and spatial patterns that contribute to phenotypic structure in a wild population of songbirds. We used automated technologies to track 1053 individuals that formed 73 737 groups from which we inferred a social network. Our framework identified that both social and spatial drivers contributed to assortment in the network. In particular, groups had a more even sex ratio than expected and exhibited a consistent age structure that suggested local association preferences, such as preferential attachment or avoidance. By contrast, recent immigrants were spatially partitioned from locally born individuals, suggesting differential dispersal strategies by phenotype. Our results highlight how different scales of social decision-making, ranging from post-natal dispersal settlement to fission–fusion dynamics, can interact to drive phenotypic structure in animal populations. PMID:26064644

Hierarchical spatial structure of stream fish colonization and extinction

USGS Publications Warehouse

Hitt, N.P.; Roberts, J.H.

2012-01-01

Spatial variation in extinction and colonization is expected to influence community composition over time. In stream fish communities, local species richness (alpha diversity) and species turnover (beta diversity) are thought to be regulated by high extinction rates in headwater streams and high colonization rates in downstream areas. We evaluated the spatiotemporal structure of fish communities in streams originally surveyed by Burton and Odum 1945 (Ecology 26: 182-194) in Virginia, USA and explored the effects of species traits on extinction and colonization dynamics. We documented dramatic changes in fish community structure at both the site and stream scales. Of the 34 fish species observed, 20 (59%) were present in both time periods, but 11 (32%) colonized the study area and three (9%) were extirpated over time. Within streams, alpha diversity increased in two of three streams but beta diversity decreased dramatically in all streams due to fish community homogenization caused by colonization of common species and extirpation of rare species. Among streams, however, fish communities differentiated over time. Regression trees indicated that reproductive life-history traits such as spawning mound construction, associations with mound-building species, and high fecundity were important predictors of species persistence or colonization. Conversely, native fishes not associated with mound-building exhibited the highest rates of extirpation from streams. Our results demonstrate that stream fish colonization and extinction dynamics exhibit hierarchical spatial structure and suggest that mound-building fishes serve as keystone species for colonization of headwater streams.

Decoupled ARX and RBF Neural Network Modeling Using PCA and GA Optimization for Nonlinear Distributed Parameter Systems.

PubMed

Zhang, Ridong; Tao, Jili; Lu, Renquan; Jin, Qibing

2018-02-01

Modeling of distributed parameter systems is difficult because of their nonlinearity and infinite-dimensional characteristics. Based on principal component analysis (PCA), a hybrid modeling strategy that consists of a decoupled linear autoregressive exogenous (ARX) model and a nonlinear radial basis function (RBF) neural network model are proposed. The spatial-temporal output is first divided into a few dominant spatial basis functions and finite-dimensional temporal series by PCA. Then, a decoupled ARX model is designed to model the linear dynamics of the dominant modes of the time series. The nonlinear residual part is subsequently parameterized by RBFs, where genetic algorithm is utilized to optimize their hidden layer structure and the parameters. Finally, the nonlinear spatial-temporal dynamic system is obtained after the time/space reconstruction. Simulation results of a catalytic rod and a heat conduction equation demonstrate the effectiveness of the proposed strategy compared to several other methods.

Aspiration dynamics in structured population acts as if in a well-mixed one.

PubMed

Du, Jinming; Wu, Bin; Wang, Long

2015-01-26

Understanding the evolution of human interactive behaviors is important. Recent experimental results suggest that human cooperation in spatial structured population is not enhanced as predicted in previous works, when payoff-dependent imitation updating rules are used. This constraint opens up an avenue to shed light on how humans update their strategies in real life. Studies via simulations show that, instead of comparison rules, self-evaluation driven updating rules may explain why spatial structure does not alter the evolutionary outcome. Though inspiring, there is a lack of theoretical result to show the existence of such evolutionary updating rule. Here we study the aspiration dynamics, and show that it does not alter the evolutionary outcome in various population structures. Under weak selection, by analytical approximation, we find that the favored strategy in regular graphs is invariant. Further, we show that this is because the criterion under which a strategy is favored is the same as that of a well-mixed population. By simulation, we show that this holds for random networks. Although how humans update their strategies is an open question to be studied, our results provide a theoretical foundation of the updating rules that may capture the real human updating rules.

Magnetic field sensing with nitrogen-vacancy color centers in diamond

NASA Astrophysics Data System (ADS)

Pham, Linh My

In recent years, the nitrogen-vacancy (NV) center has emerged as a promising magnetic sensor capable of measuring magnetic fields with high sensitivity and spatial resolution under ambient conditions. This combination of characteristics allows NV magnetometers to probe magnetic structures and systems that were previously inaccessible with alternative magnetic sensing technologies This dissertation presents and discusses a number of the initial efforts to demonstrate and improve NV magnetometry. In particular, a wide-field CCD based NV magnetic field imager capable of micron-scale spatial resolution is demonstrated; and magnetic field alignment, preferential NV orientation, and multipulse dynamical decoupling techniques are explored for enhancing magnetic sensitivity. The further application of dynamical decoupling control sequences as a spectral probe to extract information about the dynamics of the NV spin environment is also discussed; such information may be useful for determining optimal diamond sample parameters for different applications. Finally, several proposed and recently demonstrated applications which take advantage of NV magnetometers' sensitivity and spatial resolution at room temperature are presented, with particular focus on bio-magnetic field imaging.

Self-Induced Switchings between Multiple Space-Time Patterns on Complex Networks of Excitable Units

NASA Astrophysics Data System (ADS)

Ansmann, Gerrit; Lehnertz, Klaus; Feudel, Ulrike

2016-01-01

We report on self-induced switchings between multiple distinct space-time patterns in the dynamics of a spatially extended excitable system. These switchings between low-amplitude oscillations, nonlinear waves, and extreme events strongly resemble a random process, although the system is deterministic. We show that a chaotic saddle—which contains all the patterns as well as channel-like structures that mediate the transitions between them—is the backbone of such a pattern-switching dynamics. Our analyses indicate that essential ingredients for the observed phenomena are that the system behaves like an inhomogeneous oscillatory medium that is capable of self-generating spatially localized excitations and that is dominated by short-range connections but also features long-range connections. With our findings, we present an alternative to the well-known ways to obtain self-induced pattern switching, namely, noise-induced attractor hopping, heteroclinic orbits, and adaptation to an external signal. This alternative way can be expected to improve our understanding of pattern switchings in spatially extended natural dynamical systems like the brain and the heart.

Landscape structure, groundwater dynamics, and soil water content influence soil respiration across riparian-hillslope transitions in the Tenderfoot Creek Experimental Forest, Montana

Treesearch

Vincent J. Pacific; Brian L. McGlynn; Diego A. Riveros-Iregui; Daniel L. Welsch; Howard E. Epstein

2011-01-01

Variability in soil respiration at various spatial and temporal scales has been the focus of much research over the last decade aimed to improve our understanding and parameterization of physical and environmental controls on this flux. However, few studies have assessed the control of landscape position and groundwater table dynamics on the spatiotemporal variability...

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

DTIC Science & Technology

2012-09-15

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

A Deep-Structured Conditional Random Field Model for Object Silhouette Tracking

PubMed Central

Shafiee, Mohammad Javad; Azimifar, Zohreh; Wong, Alexander

2015-01-01

In this work, we introduce a deep-structured conditional random field (DS-CRF) model for the purpose of state-based object silhouette tracking. The proposed DS-CRF model consists of a series of state layers, where each state layer spatially characterizes the object silhouette at a particular point in time. The interactions between adjacent state layers are established by inter-layer connectivity dynamically determined based on inter-frame optical flow. By incorporate both spatial and temporal context in a dynamic fashion within such a deep-structured probabilistic graphical model, the proposed DS-CRF model allows us to develop a framework that can accurately and efficiently track object silhouettes that can change greatly over time, as well as under different situations such as occlusion and multiple targets within the scene. Experiment results using video surveillance datasets containing different scenarios such as occlusion and multiple targets showed that the proposed DS-CRF approach provides strong object silhouette tracking performance when compared to baseline methods such as mean-shift tracking, as well as state-of-the-art methods such as context tracking and boosted particle filtering. PMID:26313943

Evolutionary dynamics on graphs

NASA Astrophysics Data System (ADS)

Lieberman, Erez; Hauert, Christoph; Nowak, Martin A.

2005-01-01

Evolutionary dynamics have been traditionally studied in the context of homogeneous or spatially extended populations. Here we generalize population structure by arranging individuals on a graph. Each vertex represents an individual. The weighted edges denote reproductive rates which govern how often individuals place offspring into adjacent vertices. The homogeneous population, described by the Moran process, is the special case of a fully connected graph with evenly weighted edges. Spatial structures are described by graphs where vertices are connected with their nearest neighbours. We also explore evolution on random and scale-free networks. We determine the fixation probability of mutants, and characterize those graphs for which fixation behaviour is identical to that of a homogeneous population. Furthermore, some graphs act as suppressors and others as amplifiers of selection. It is even possible to find graphs that guarantee the fixation of any advantageous mutant. We also study frequency-dependent selection and show that the outcome of evolutionary games can depend entirely on the structure of the underlying graph. Evolutionary graph theory has many fascinating applications ranging from ecology to multi-cellular organization and economics.

The role of landscape-dependent disturbance and dispersal in metapopulation persistence.

PubMed

Elkin, Ché M; Possingham, Hugh

2008-10-01

The fundamental processes that influence metapopulation dynamics (extinction and recolonization) will often depend on landscape structure. Disturbances that increase patch extinction rates will frequently be landscape dependent such that they are spatially aggregated and have an increased likelihood of occurring in some areas. Similarly, landscape structure can influence organism movement, producing asymmetric dispersal between patches. Using a stochastic, spatially explicit model, we examine how landscape-dependent correlations between dispersal and disturbance rates influence metapopulation dynamics. Habitat patches that are situated in areas where the likelihood of disturbance is low will experience lower extinction rates and will function as partial refuges. We discovered that the presence of partial refuges increases metapopulation viability and that the value of partial refuges was contingent on whether dispersal was also landscape dependent. Somewhat counterintuitively, metapopulation viability was reduced when individuals had a preponderance to disperse away from refuges and was highest when there was biased dispersal toward refuges. Our work demonstrates that landscape structure needs to be incorporated into metapopulation models when there is either empirical data or ecological rationale for extinction and/or dispersal rates being landscape dependent.

Electron-hole liquid in semiconductors and low-dimensional structures

NASA Astrophysics Data System (ADS)

Sibeldin, N. N.

2017-11-01

The condensation of excitons into an electron-hole liquid (EHL) and the main EHL properties in bulk semiconductors and low-dimensional structures are considered. The EHL properties in bulk materials are discussed primarily in qualitative terms based on the experimental results obtained for germanium and silicon. Some of the experiments in which the main EHL thermodynamic parameters (density and binding energy) have been obtained are described and the basic factors that determine these parameters are considered. Topics covered include the effect of external perturbations (uniaxial strain and magnetic field) on EHL stability; phase diagrams for a nonequilibrium exciton-gas-EHL system; information on the size and concentration of electron-hole drops (EHDs) under various experimental conditions; the kinetics of exciton condensation and of recombination in the exciton-gas-EHD system; dynamic EHD properties and the motion of EHDs under the action of external forces; the properties of giant EHDs that form in potential wells produced by applying an inhomogeneous strain to the crystal; and effects associated with the drag of EHDs by nonequilibrium phonons (phonon wind), including the dynamics and formation of an anisotropic spatial structure of the EHD cloud. In discussing EHLs in low-dimensional structures, a number of studies are reviewed on the observation and experimental investigation of phenomena such as spatially indirect (dipolar) electron-hole and exciton (dielectric) liquids in GaAs/AlGaAs structures with double quantum wells (QWs), EHDs containing only a few electron-hole pairs (dropletons), EHLs in type-I silicon QWs, and spatially direct and dipolar EHLs in type-II silicon-germanium heterostructures.

Nucleon structure in lattice QCD with dynamical domain-wall fermions quarks

NASA Astrophysics Data System (ADS)

Ohta, Shigemi

2006-12-01

We report RBC and RBC/UKQCD lattice QCD numerical calculations of nucleon electroweak matrix elements with dynamical domain-wall fermions (DWF) quarks. The first, RBC, set of dynamical DWF ensembles employs two degenerate flavors of DWF quarks and the DBW2 gauge action. Three sea quark mass values of 0.04, 0.03 and 0.02 in lattice units are used with about 200 gauge configurations each. The lattice cutoff is a-1 ˜ 1.7GeV and the spatial volume is about (1.9fm)3 . Despite the small volume, the ratio of the isovector vector and axial charges gA /gV and that of structure function moments x u-d / x u- d are in agreement with experiment, and show only very mild quark mass dependence. The second, RBC/UK, set of ensembles employs one strange and two degenerate (up and down) dynamical DWF quarks and Iwasaki gauge action. The strange quark mass is set at 0.04, and three up/down mass values of 0.03, 0.02 and 0.01 in lattice units are used. The lattice cutoff is a-1 ˜ 1.6GeV and the spatial volume is about (3.0fm)3 . Even with preliminary statistics of 25-30 gauge configurations, the ratios gA /gV and x u-d / x u- d are consistent with experiment and show only very mild quark mass dependence. Another structure function moment, d1 , though yet to be renormalized, appears small in both sets.

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.

Application of biospeckles for assessment of structural and cellular changes in muscle tissue

NASA Astrophysics Data System (ADS)

Maksymenko, Oleksandr P.; Muravsky, Leonid I.; Berezyuk, Mykola I.

2015-09-01

A modified spatial-temporal speckle correlation technique for operational assessment of structural changes in muscle tissues after slaughtering is considered. Coefficient of biological activity as a quantitative indicator of structural changes of biochemical processes in biological tissues is proposed. The experimental results have shown that this coefficient properly evaluates the biological activity of pig and chicken muscle tissue samples. Studying the degradation processes in muscle tissue during long-time storage in a refrigerator by measuring the spatial-temporal dynamics of biospeckle patterns is carried out. The reduction of the bioactivity level of refrigerated muscle tissue samples connected with the initiation of muscle fiber cracks and ruptures, reduction of sarcomeres, nuclei deformation, nuclear chromatin diminishing, and destruction of mitochondria is analyzed.

Palms, peccaries and perturbations: widespread effects of small-scale disturbance in tropical forests

PubMed Central

2012-01-01

Background Disturbance is an important process structuring ecosystems worldwide and has long been thought to be a significant driver of diversity and dynamics. In forests, most studies of disturbance have focused on large-scale disturbance such as hurricanes or tree-falls. However, smaller sub-canopy disturbances could also have significant impacts on community structure. One such sub-canopy disturbance in tropical forests is abscising leaves of large arborescent palm (Arececeae) trees. These leaves can weigh up to 15 kg and cause physical damage and mortality to juvenile plants. Previous studies examining this question suffered from the use of static data at small spatial scales. Here we use data from a large permanent forest plot combined with dynamic data on the survival and growth of > 66,000 individuals over a seven-year period to address whether falling palm fronds do impact neighboring seedling and sapling communities, or whether there is an interaction between the palms and peccaries rooting for fallen palm fruit in the same area as falling leaves. We tested the wider generalisation of these hypotheses by comparing seedling and sapling survival under fruiting and non-fruiting trees in another family, the Myristicaceae. Results We found a spatially-restricted but significant effect of large arborescent fruiting palms on the spatial structure, population dynamics and species diversity of neighbouring sapling and seedling communities. However, these effects were not found around slightly smaller non-fruiting palm trees, suggesting it is seed predators such as peccaries rather than falling leaves that impact on the communities around palm trees. Conversely, this hypothesis was not supported in data from other edible species, such as those in the family Myristicaceae. Conclusions Given the abundance of arborescent palm trees in Amazonian forests, it is reasonable to conclude that their presence does have a significant, if spatially-restricted, impact on juvenile plants, most likely on the survival and growth of seedlings and saplings damaged by foraging peccaries. Given the abundance of fruit produced by each palm, the widespread effects of these small-scale disturbances appear, over long time-scales, to cause directional changes in community structure at larger scales. PMID:22429883

Palms, peccaries and perturbations: widespread effects of small-scale disturbance in tropical forests.

PubMed

Queenborough, Simon A; Metz, Margaret R; Wiegand, Thorsten; Valencia, Renato

2012-03-19

Disturbance is an important process structuring ecosystems worldwide and has long been thought to be a significant driver of diversity and dynamics. In forests, most studies of disturbance have focused on large-scale disturbance such as hurricanes or tree-falls. However, smaller sub-canopy disturbances could also have significant impacts on community structure. One such sub-canopy disturbance in tropical forests is abscising leaves of large arborescent palm (Arececeae) trees. These leaves can weigh up to 15 kg and cause physical damage and mortality to juvenile plants. Previous studies examining this question suffered from the use of static data at small spatial scales. Here we use data from a large permanent forest plot combined with dynamic data on the survival and growth of > 66,000 individuals over a seven-year period to address whether falling palm fronds do impact neighboring seedling and sapling communities, or whether there is an interaction between the palms and peccaries rooting for fallen palm fruit in the same area as falling leaves. We tested the wider generalisation of these hypotheses by comparing seedling and sapling survival under fruiting and non-fruiting trees in another family, the Myristicaceae. We found a spatially-restricted but significant effect of large arborescent fruiting palms on the spatial structure, population dynamics and species diversity of neighbouring sapling and seedling communities. However, these effects were not found around slightly smaller non-fruiting palm trees, suggesting it is seed predators such as peccaries rather than falling leaves that impact on the communities around palm trees. Conversely, this hypothesis was not supported in data from other edible species, such as those in the family Myristicaceae. Given the abundance of arborescent palm trees in Amazonian forests, it is reasonable to conclude that their presence does have a significant, if spatially-restricted, impact on juvenile plants, most likely on the survival and growth of seedlings and saplings damaged by foraging peccaries. Given the abundance of fruit produced by each palm, the widespread effects of these small-scale disturbances appear, over long time-scales, to cause directional changes in community structure at larger scales.

Recent Structural Change in Remote Sensing Data Time Series Linked to Farm Management in Horn of Africa (1999-2009)

NASA Astrophysics Data System (ADS)

Crisci, A.; Vignaroli, P.; Genesio, L.; Grasso, V.; Bacci, M.; Tarchiani, V.; Capecchi, V.

2011-01-01

Food security in East Africa region essentially depends on the stability of rain-fed crops farming, which renders its society vulnerable to climatic fluctuations. These ones in Africa are most widely and directly related to rainfall. In this study, the relation between recent spatial rainfall variability and vegetation dynamics has been investigated for East Africa territories. Satellite raster products SPOT-4 Vegetation 1 km resolution (Saint, 1995) and RFE (rainfall estimates) from Famine Early Warning Systems Network (FEWS NET) are used. The survey is carried out at administrative level scale using 10-day summaries extracted from raster data for each spatial area unit thanks to specific polygonal layers. Time series covers two different periods: 1996-2009 for rainfall estimates and 1999-2009 for NDVI. The first step of the analysis has been to build for each administrative unit a coherent set of data, along the time series, suitable to be processed with state-of-art statistical tools. The analysis is based on the assumption that every structural break in vegetation dynamics could be caused by two alternative/complementary causes, namely: (i) modifications in crop farming systems (adaptation strategy) related to eventual break-shift in rainfall regime and/or (ii) other socio-economic factors. BFAST (Verbesselt et al, 2010) R package are employed to lead a comprehensive breakpoint analysis on 10-day RFE (spatial mean and standard deviation) and 10-day NDVI ones (spatial mean, mode and standard deviation). The cross-viewing of the years where significant breaks have occurred, throughout opportune GIS layering, provides an explorative interpretation of spatial climate/vegetation dynamics in the whole area. Moreover, the spatial and temporal pattern of ecosystem dynamics in response to climatic variability has been investigated using wavelet coherency by SOWAS R package (Maraun, 2007). The wavelet coherency (WCOH) is a normalized time and scale resolved measure for the relationship between two time series (Maraun and Kurths, 2004). This kind of multi-scale temporal investigation provides an explanation of break detected in time series, confirming or not their climatic linkage; results of the analysis are shown. Finally, in order to support the dissemination and sharing of information, interactive vegetation maps have been implemented with Google Earth mash-up. The maturity of Web-based GIS enables the generation of thematic maps dynamically and efficiently, with a thin/thick client or hybrid architectures. This could be a great support for the understanding environmental phenomena.

Structure of mangrove meiofaunal assemblages associated with local sediment conditions in subtropical eastern australia

NASA Astrophysics Data System (ADS)

Abdullah, Maizah M.; Lee, S. Y.

2017-11-01

Meiofauna are ubiquitous but poorly-studied components of soft-bottom marine habitats around the world, including mangroves. The dynamic environmental conditions and heterogeneous sediments of mangroves present challenges to understanding the structure of mangrove meiofaunal assemblages at various spatial and temporal scales. In this study, we investigated the meiofaunal assemblage structure of sediments colonised by three mangrove species, namely, Avicennia marina, Rhizophora stylosa and Aegiceras corniculatum, at three locations in subtropical eastern Australia. Spatial and temporal variations were tested by sampling at the three mangrove locations (i.e. Tallebudgera, Currumbin and Terranora) in autumn, with samplings repeated at Tallebudgera at two other times broadly representing during dry/cool winter and wet/hot summer seasons. We examined the variability of the sediment environments within each of the different mangrove species, and investigated how meiofaunal assemblages would respond to the particular changes in their habitats to result in differences in assemblage structure between and within sites. Total meiofaunal density was highest in Tallebudgera and Currumbin and lowest in Terranora (mean density of 424, 393 and 239 ind.10 cm-2, respectively). In Tallebudgera, the density was higher in winter and summer (mean density of 546 and 530 ind.10 cm-2, respectively). The meiofaunal assemblage in this study shows a trend and association with the environmental variables. High availability of food proxies such phaeopigments, Chl a or TOC, with moderate tannin content and appropriate habitat structure (sediment particle size, belowground root biomass and/or moisture content provide the best condition for the meiofauna to achieve the highest density. However, given the complex dynamic habitats and the spatial heterogeneity of the mangrove environments across different locations and seasons, no clear generalization could be made regarding the key environmental variables that predominantly shape the meiofaunal assemblages' structure.

Bacterial predator–prey dynamics in microscale patchy landscapes

PubMed Central

Rotem, Or; Jurkevitch, Edouard; Dekker, Cees

2016-01-01

Soil is a microenvironment with a fragmented (patchy) spatial structure in which many bacterial species interact. Here, we explore the interaction between the predatory bacterium Bdellovibrio bacteriovorus and its prey Escherichia coli in microfabricated landscapes. We ask how fragmentation influences the prey dynamics at the microscale and compare two landscape geometries: a patchy landscape and a continuous landscape. By following the dynamics of prey populations with high spatial and temporal resolution for many generations, we found that the variation in predation rates was twice as large in the patchy landscape and the dynamics was correlated over shorter length scales. We also found that while the prey population in the continuous landscape was almost entirely driven to extinction, a significant part of the prey population in the fragmented landscape persisted over time. We observed significant surface-associated growth, especially in the fragmented landscape and we surmise that this sub-population is more resistant to predation. Our results thus show that microscale fragmentation can significantly influence bacterial interactions. PMID:26865299

Estimation of skeletal movement of human locomotion from body surface shapes using dynamic spatial video camera (DSVC) and 4D human model.

PubMed

Saito, Toshikuni; Suzuki, Naoki; Hattori, Asaki; Suzuki, Shigeyuki; Hayashibe, Mitsuhiro; Otake, Yoshito

2006-01-01

We have been developing a DSVC (Dynamic Spatial Video Camera) system to measure and observe human locomotion quantitatively and freely. A 4D (four-dimensional) human model with detailed skeletal structure, joint, muscle, and motor functionality has been built. The purpose of our research was to estimate skeletal movements from body surface shapes using DSVC and the 4D human model. For this purpose, we constructed a body surface model of a subject and resized the standard 4D human model to match with geometrical features of the subject's body surface model. Software that integrates the DSVC system and the 4D human model, and allows dynamic skeletal state analysis from body surface movement data was also developed. We practically applied the developed system in dynamic skeletal state analysis of a lower limb in motion and were able to visualize the motion using geometrically resized standard 4D human model.

Evolution in action: Climate change, biodiversity dynamics and emerging infectious disease

USDA-ARS?s Scientific Manuscript database

Climatological variation and ecological perturbation have been pervasive drivers of faunal assembly, structure and diversification for parasites and pathogens through recurrent events of geographic and host colonization at varying spatial and temporal scales of Earth history. Episodic shifts in clim...

Seismic Study of the Subsurface Structure and Dynamics of the Solar Interior from High Spatial Resolution Observations

NASA Technical Reports Server (NTRS)

Korzennik, Sylvain G.

1997-01-01

We have carried out the data reduction and analysis of Mt. Wilson 60' solar tower high spatial resolution observations. The reduction of the 100-day-long summer of 1990 observation campaign in terms of rotational splittings was completed leading to an excess of 600,000 splittings. The analysis of these splittings lead to a new inference of the solar internal rotation rate as a function of depth and latitude.

Spatial and Temporal Dynamics in Air Pollution Exposure Assessment

PubMed Central

Dias, Daniela; Tchepel, Oxana

2018-01-01

Analyzing individual exposure in urban areas offers several challenges where both the individual’s activities and air pollution levels demonstrate a large degree of spatial and temporal dynamics. This review article discusses the concepts, key elements, current developments in assessing personal exposure to urban air pollution (seventy-two studies reviewed) and respective advantages and disadvantages. A new conceptual structure to organize personal exposure assessment methods is proposed according to two classification criteria: (i) spatial-temporal variations of individuals’ activities (point-fixed or trajectory based) and (ii) characterization of air quality (variable or uniform). This review suggests that the spatial and temporal variability of urban air pollution levels in combination with indoor exposures and individual’s time-activity patterns are key elements of personal exposure assessment. In the literature review, the majority of revised studies (44 studies) indicate that the trajectory based with variable air quality approach provides a promising framework for tackling the important question of inter- and intra-variability of individual exposure. However, future quantitative comparison between the different approaches should be performed, and the selection of the most appropriate approach for exposure quantification should take into account the purpose of the health study. This review provides a structured basis for the intercomparing of different methodologies and to make their advantages and limitations more transparent in addressing specific research objectives. PMID:29558426

Soil respiration across a permafrost transition zone: spatial structure and environmental correlates

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

Stegen, James C.; Anderson, Carolyn G.; Bond-Lamberty, Ben

Soil respiration is a key ecosystem function whereby shifts in respiration rates can shift systems from carbon sinks to sources. Soil respiration in permafrost-associated systems is particularly important given climate change driven permafrost thaw that leads to significant uncertainty in resulting ecosystem carbon dynamics. Here we characterize the spatial structure and environmental drivers of soil respiration across a permafrost transition zone. We find that soil respiration is characterized by a non-linear threshold that occurs at active-layer depths greater than 140 cm. We also find that within each season, tree basal area is a dominant driver of soil respiration regardless of spatial scale, but onlymore » in spatial domains with significant spatial variability in basal area. Our analyses further show that spatial variation (the coefficient of variation) and mean-variance power-law scaling of soil respiration in our boreal system are consistent with previous work in other ecosystems (e.g., tropical forests) and in population ecology, respectively. Comparing our results to those in other ecosystems suggests that temporally stable features such as tree-stand structure are often primary drivers of spatial variation in soil respiration. If so, this provides an opportunity to better estimate the magnitude and spatial variation in soil respiration through remote sensing. Finally, combining such an approach with broader knowledge of thresholding behavior – here related to active layer depth – would provide empirical constraints on models aimed at predicting ecosystem responses to ongoing permafrost thaw.« less

Soil respiration across a permafrost transition zone: spatial structure and environmental correlates

DOE PAGES

Stegen, James C.; Anderson, Carolyn G.; Bond-Lamberty, Ben; ...

2017-09-28

Soil respiration is a key ecosystem function whereby shifts in respiration rates can shift systems from carbon sinks to sources. Soil respiration in permafrost-associated systems is particularly important given climate change driven permafrost thaw that leads to significant uncertainty in resulting ecosystem carbon dynamics. Here we characterize the spatial structure and environmental drivers of soil respiration across a permafrost transition zone. We find that soil respiration is characterized by a non-linear threshold that occurs at active-layer depths greater than 140 cm. We also find that within each season, tree basal area is a dominant driver of soil respiration regardless of spatial scale, but onlymore » in spatial domains with significant spatial variability in basal area. Our analyses further show that spatial variation (the coefficient of variation) and mean-variance power-law scaling of soil respiration in our boreal system are consistent with previous work in other ecosystems (e.g., tropical forests) and in population ecology, respectively. Comparing our results to those in other ecosystems suggests that temporally stable features such as tree-stand structure are often primary drivers of spatial variation in soil respiration. If so, this provides an opportunity to better estimate the magnitude and spatial variation in soil respiration through remote sensing. Finally, combining such an approach with broader knowledge of thresholding behavior – here related to active layer depth – would provide empirical constraints on models aimed at predicting ecosystem responses to ongoing permafrost thaw.« less

Soil respiration across a permafrost transition zone: spatial structure and environmental correlates

NASA Astrophysics Data System (ADS)

Stegen, James C.; Anderson, Carolyn G.; Bond-Lamberty, Ben; Crump, Alex R.; Chen, Xingyuan; Hess, Nancy

2017-09-01

Soil respiration is a key ecosystem function whereby shifts in respiration rates can shift systems from carbon sinks to sources. Soil respiration in permafrost-associated systems is particularly important given climate change driven permafrost thaw that leads to significant uncertainty in resulting ecosystem carbon dynamics. Here we characterize the spatial structure and environmental drivers of soil respiration across a permafrost transition zone. We find that soil respiration is characterized by a non-linear threshold that occurs at active-layer depths greater than 140 cm. We also find that within each season, tree basal area is a dominant driver of soil respiration regardless of spatial scale, but only in spatial domains with significant spatial variability in basal area. Our analyses further show that spatial variation (the coefficient of variation) and mean-variance power-law scaling of soil respiration in our boreal system are consistent with previous work in other ecosystems (e.g., tropical forests) and in population ecology, respectively. Comparing our results to those in other ecosystems suggests that temporally stable features such as tree-stand structure are often primary drivers of spatial variation in soil respiration. If so, this provides an opportunity to better estimate the magnitude and spatial variation in soil respiration through remote sensing. Combining such an approach with broader knowledge of thresholding behavior - here related to active layer depth - would provide empirical constraints on models aimed at predicting ecosystem responses to ongoing permafrost thaw.

Modeling the spatial and temporal population dynamics of the copepod Centropages typicus in the northwestern Mediterranean Sea during the year 2001 using a 3D ecosystem model

NASA Astrophysics Data System (ADS)

Carlotti, F.; Eisenhauer, L.; Campbell, R.; Diaz, F.

2014-07-01

The spatio-temporal dynamics of a simulated Centropages typicus (Kröyer) population during the year 2001 at the regional scale of the northwestern Mediterranean Sea are addressed using a 3D coupled physical-biogeochemical model. The setup of the coupled biological model comprises a pelagic plankton ecosystem model and a stage-structured population model forced by the 3D velocity and temperature fields provided by an eddy-resolving regional circulation model. The population model for C. typicus (C. t. below) represents demographic processes through five groups of developmental stages, which depend on underlying individual growth and development processes and are forced by both biotic (prey and predator fields) and abiotic (temperature, advection) factors from the coupled physical-biogeochemical model. The objective is to characterize C. t. ontogenic habitats driven by physical and trophic processes. The annual dynamics are presented for two of the main oceanographic stations in the Gulf of Lions, which are representative of shelf and open sea conditions, while the spatial distributions over the whole area are presented for three dates during the year, in early and late spring and in winter. The simulated spatial patterns of C. t. developmental stages are closely related to mesoscale hydrodynamic features and circulation patterns. The seasonal and spatial distributions on the Gulf of Lions shelf depend on the seasonal interplay between the Rhône river plume, the mesoscale eddies on the shelf and the Northern Current acting as either as a dynamic barrier between the shelf and the open sea or allowing cross-shelf exchanges. In the central gyre of the northwestern Mediterranean Sea, the patchiness of plankton is tightly linked to mesoscale frontal systems, surface eddies and filaments and deep gradients. Due to its flexibility in terms of its diet, C. t. succeeds in maintaining its population in both coastal and offshore areas year round. The simulations suggest that the winte-spring food conditions are more favorable on the shelf for C. t., whereas in late summer and fall, the offshore depth-integrated food biomasses represent a larger resource for C. t., particularly when mesoscale structures and vertical discontinuities increase food patchiness. The development and reproduction of C. t. depend on the prey field within the mesoscale structures that induce a contrasting spatial distribution of successive developmental stages on a given observation date. In late fall and winter, the results of the model suggest the existence of three refuge areas where the population maintains winter generations near the coast and within the Rhone River plume, or offshore within canyons within the shelf break, or in the frontal system related to the Northern Current. The simulated spatial and temporal distributions as well as the life cycle and physiological features of C. t. are discussed in light of recent reviews on the dynamics of C. t. in the northwestern Mediterranean Sea.

The Importance of Large-Diameter Trees to Forest Structural Heterogeneity

PubMed Central

Lutz, James A.; Larson, Andrew J.; Freund, James A.; Swanson, Mark E.; Bible, Kenneth J.

2013-01-01

Large-diameter trees dominate the structure, dynamics and function of many temperate and tropical forests. However, their attendant contributions to forest heterogeneity are rarely addressed. We established the Wind River Forest Dynamics Plot, a 25.6 ha permanent plot within which we tagged and mapped all 30,973 woody stems ≥1 cm dbh, all 1,966 snags ≥10 cm dbh, and all shrub patches ≥2 m2. Basal area of the 26 woody species was 62.18 m2/ha, of which 61.60 m2/ha was trees and 0.58 m2/ha was tall shrubs. Large-diameter trees (≥100 cm dbh) comprised 1.5% of stems, 31.8% of basal area, and 17.6% of the heterogeneity of basal area, with basal area dominated by Tsuga heterophylla and Pseudotsuga menziesii. Small-diameter subpopulations of Pseudotsuga menziesii, Tsuga heterophylla and Thuja plicata, as well as all tree species combined, exhibited significant aggregation relative to the null model of complete spatial randomness (CSR) up to 9 m (P≤0.001). Patterns of large-diameter trees were either not different from CSR (Tsuga heterophylla), or exhibited slight aggregation (Pseudotsuga menziesii and Thuja plicata). Significant spatial repulsion between large-diameter and small-diameter Tsuga heterophylla suggests that large-diameter Tsuga heterophylla function as organizers of tree demography over decadal timescales through competitive interactions. Comparison among two forest dynamics plots suggests that forest structural diversity responds to intermediate-scale environmental heterogeneity and disturbances, similar to hypotheses about patterns of species richness, and richness- ecosystem function. Large mapped plots with detailed within-plot environmental spatial covariates will be required to test these hypotheses. PMID:24376579

The importance of large-diameter trees to forest structural heterogeneity.

PubMed

Lutz, James A; Larson, Andrew J; Freund, James A; Swanson, Mark E; Bible, Kenneth J

2013-01-01

Large-diameter trees dominate the structure, dynamics and function of many temperate and tropical forests. However, their attendant contributions to forest heterogeneity are rarely addressed. We established the Wind River Forest Dynamics Plot, a 25.6 ha permanent plot within which we tagged and mapped all 30,973 woody stems ≥ 1 cm dbh, all 1,966 snags ≥ 10 cm dbh, and all shrub patches ≥ 2 m(2). Basal area of the 26 woody species was 62.18 m(2)/ha, of which 61.60 m(2)/ha was trees and 0.58 m(2)/ha was tall shrubs. Large-diameter trees (≥ 100 cm dbh) comprised 1.5% of stems, 31.8% of basal area, and 17.6% of the heterogeneity of basal area, with basal area dominated by Tsuga heterophylla and Pseudotsuga menziesii. Small-diameter subpopulations of Pseudotsuga menziesii, Tsuga heterophylla and Thuja plicata, as well as all tree species combined, exhibited significant aggregation relative to the null model of complete spatial randomness (CSR) up to 9 m (P ≤ 0.001). Patterns of large-diameter trees were either not different from CSR (Tsuga heterophylla), or exhibited slight aggregation (Pseudotsuga menziesii and Thuja plicata). Significant spatial repulsion between large-diameter and small-diameter Tsuga heterophylla suggests that large-diameter Tsuga heterophylla function as organizers of tree demography over decadal timescales through competitive interactions. Comparison among two forest dynamics plots suggests that forest structural diversity responds to intermediate-scale environmental heterogeneity and disturbances, similar to hypotheses about patterns of species richness, and richness- ecosystem function. Large mapped plots with detailed within-plot environmental spatial covariates will be required to test these hypotheses.

The microtubule lattice and plus-end association of Drosophila Mini spindles is spatially regulated to fine-tune microtubule dynamics.

PubMed

Currie, Joshua D; Stewman, Shannon; Schimizzi, Gregory; Slep, Kevin C; Ma, Ao; Rogers, Stephen L

2011-11-01

Individual microtubules (MTs) exhibit dynamic instability, a behavior in which they cycle between phases of growth and shrinkage while the total amount of MT polymer remains constant. Dynamic instability is promoted by the conserved XMAP215/Dis1 family of microtubule-associated proteins (MAPs). In this study, we conducted an in vivo structure-function analysis of the Drosophila homologue Mini spindles (Msps). Msps exhibits EB1-dependent and spatially regulated MT localization, targeting to microtubule plus ends in the cell interior and decorating the lattice of growing and shrinking microtubules in the cell periphery. RNA interference rescue experiments revealed that the NH(2)-terminal four TOG domains of Msps function as paired units and were sufficient to promote microtubule dynamics and EB1 comet formation. We also identified TOG5 and novel inter-TOG linker motifs that are required for targeting Msps to the microtubule lattice. These novel microtubule contact sites are necessary for the interplay between the conserved TOG domains and inter-TOG MT binding that underlies the ability of Msps to promote MT dynamic instability.

Static and dynamic properties of two-dimensional Coulomb clusters.

PubMed

Ash, Biswarup; Chakrabarti, J; Ghosal, Amit

2017-10-01

We study the temperature dependence of static and dynamic responses of Coulomb interacting particles in two-dimensional confinements across the crossover from solid- to liquid-like behaviors. While static correlations that investigate the translational and bond orientational order in the confinements show the footprints of hexatic-like phase at low temperatures, dynamics of the particles slow down considerably in this phase, reminiscent of a supercooled liquid. Using density correlations, we probe long-lived heterogeneities arising from the interplay of the irregularity in the confinement and long-range Coulomb interactions. The relaxation at multiple time scales show stretched-exponential decay of spatial correlations in irregular traps. Temperature dependence of characteristic time scales, depicting the structural relaxation of the system, show striking similarities with those observed for the glassy systems, indicating that some of the key signatures of supercooled liquids emerge in confinements with lower spatial symmetries.

PROPERTIES AND MODELING OF UNRESOLVED FINE STRUCTURE LOOPS OBSERVED IN THE SOLAR TRANSITION REGION BY IRIS

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

Brooks, David H.; Reep, Jeffrey W.; Warren, Harry P.

Recent observations from the Interface Region Imaging Spectrograph ( IRIS ) have discovered a new class of numerous low-lying dynamic loop structures, and it has been argued that they are the long-postulated unresolved fine structures (UFSs) that dominate the emission of the solar transition region. In this letter, we combine IRIS measurements of the properties of a sample of 108 UFSs (intensities, lengths, widths, lifetimes) with one-dimensional non-equilibrium ionization simulations, using the HYDRAD hydrodynamic model to examine whether the UFSs are now truly spatially resolved in the sense of being individual structures rather than being composed of multiple magnetic threads.more » We find that a simulation of an impulsively heated single strand can reproduce most of the observed properties, suggesting that the UFSs may be resolved, and the distribution of UFS widths implies that they are structured on a spatial scale of 133 km on average. Spatial scales of a few hundred kilometers appear to be typical for a range of chromospheric and coronal structures, and we conjecture that this could be an important clue for understanding the coronal heating process.« less

Contrasting patterns of fine-scale herb layer species composition in temperate forests

NASA Astrophysics Data System (ADS)

Chudomelová, Markéta; Zelený, David; Li, Ching-Feng

2017-04-01

Although being well described at the landscape level, patterns in species composition of forest herb layer are rarely studied at smaller scales. Here, we examined fine-scale environmental determinants and spatial structures of herb layer communities in thermophilous oak- and hornbeam dominated forests of the south-eastern part of the Czech Republic. Species composition of herb layer vegetation and environmental variables were recorded within a fixed grid of 2 × 2 m subplots regularly distributed within 1-ha quadrate plots in three forest stands. For each site, environmental models best explaining species composition were constructed using constrained ordination analysis. Spatial eigenvector mapping was used to model and account for spatial structures in community variation. Mean Ellenberg indicator values calculated for each subplot were used for ecological interpretation of spatially structured residual variation. The amount of variation explained by environmental and spatial models as well as the selection of variables with the best explanatory power differed among sites. As an important environmental factor, relative elevation was common to all three sites, while pH and canopy openness were shared by two sites. Both environmental and community variation was mostly coarse-scaled, as was the spatially structured portion of residual variation. When corrected for bias due to spatial autocorrelation, those environmental factors with already weak explanatory power lost their significance. Only a weak evidence of possibly omitted environmental predictor was found for autocorrelated residuals of site models using mean Ellenberg indicator values. Community structure was determined by different factors at different sites. The relative importance of environmental filtering vs. spatial processes was also site specific, implying that results of fine-scale studies tend to be shaped by local conditions. Contrary to expectations based on other studies, overall dominance of spatial processes at fine scale has not been detected. Ecologists should keep this in mind when making generalizations about community dynamics.

Distributed dynamic strain measurement using long-gauge FBG and DTR3 interrogator based on delayed transmission/reflection ratiometric reflectometry

NASA Astrophysics Data System (ADS)

Nishiyama, M.; Igawa, H.; Kasai, T.; Watanabe, N.

2013-09-01

In this paper, we reveal characteristics of static and dynamic distributed strain measurement using a long-gauge fiber Bragg grating (FBG) and a Delayed Transmission/Reflection Ratiometric Reflectometry (DTR3) scheme. The DTR3 scheme has capability of detecting distributed strain using the long-gauge FBG with 50-cm spatial resolution. Additionally, dynamic strain measurement can be achieved using this technique in 100-Hz sampling rate. We evaluated strain sensing characteristics of the long-gauge FBG attached on 2.5-m aluminum bar by a four-point bending equipment. Experimental results showed that the DTR3 using the long-gauge FBG could detect distributed strain in static tests and resonance frequency of structure in free vibration tests. As a result, it is suggested that the DTR3 scheme using the longgauge FBG is attractive to structural health monitoring (SHM) as dynamic deformation detection of a few and tensmeters structure such as the airplane wing and the helicopter blade.

Capturing Structural Dynamics in Crystalline Silicon Using Chirped Electrons from a Laser Wakefield Accelerator

PubMed Central

He, Z.-H.; Beaurepaire, B.; Nees, J. A.; Gallé, G.; Scott, S. A.; Pérez, J. R. Sánchez; Lagally, M. G.; Krushelnick, K.; Thomas, A. G. R.; Faure, J.

2016-01-01

Recent progress in laser wakefield acceleration has led to the emergence of a new generation of electron and X-ray sources that may have enormous benefits for ultrafast science. These novel sources promise to become indispensable tools for the investigation of structural dynamics on the femtosecond time scale, with spatial resolution on the atomic scale. Here, we demonstrate the use of laser-wakefield-accelerated electron bunches for time-resolved electron diffraction measurements of the structural dynamics of single-crystal silicon nano-membranes pumped by an ultrafast laser pulse. In our proof-of-concept study, we resolve the silicon lattice dynamics on a picosecond time scale by deflecting the momentum-time correlated electrons in the diffraction peaks with a static magnetic field to obtain the time-dependent diffraction efficiency. Further improvements may lead to femtosecond temporal resolution, with negligible pump-probe jitter being possible with future laser-wakefield-accelerator ultrafast-electron-diffraction schemes. PMID:27824086

Capturing Structural Dynamics in Crystalline Silicon Using Chirped Electrons from a Laser Wakefield Accelerator

DOE PAGES

He, Z. -H.; Beaurepaire, B.; Nees, J. A.; ...

2016-11-08

Recent progress in laser wakefield acceleration has led to the emergence of a new generation of electron and X-ray sources that may have enormous benefits for ultrafast science. These novel sources promise to become indispensable tools for the investigation of structural dynamics on the femtosecond time scale, with spatial resolution on the atomic scale. Here in this paper, we demonstrate the use of laser-wakefield-accelerated electron bunches for time-resolved electron diffraction measurements of the structural dynamics of single-crystal silicon nano-membranes pumped by an ultrafast laser pulse. In our proof-of-concept study, we resolve the silicon lattice dynamics on a picosecond time scalemore » by deflecting the momentum-time correlated electrons in the diffraction peaks with a static magnetic field to obtain the time-dependent diffraction efficiency. Further improvements may lead to femtosecond temporal resolution, with negligible pump-probe jitter being possible with future laser-wakefield-accelerator ultrafast-electron-diffraction schemes.« less

Unravel the submesoscale dynamics of the phytoplanktonic community in the NW Mediterranean Sea by in situ observations: the 2015 OSCAHR cruise

NASA Astrophysics Data System (ADS)

Marrec, Pierre; Doglioli, Andrea M.; Grégori, Gérald; Della Penna, Alice; Wagener, Thibaut; Rougier, Gille; Bhairy, Nagib; Dugenne, Mathilde; Lahbib, Soumaya; Thyssen, Melilotus

2017-04-01

Submesoscale phenomena have been recently recognized as a key factor in physical-biological-biogeochemical interactions, even if it remains unclear how these processes affect the global state of the ocean. Significant large-scale impacts of submesoscale structures on primary production and influence on the phytoplankton community structure and diversity have also been reported. In the past decade submesoscale dynamics have been predominately studied through the analysis of numerical simulations. Observing the coupled physical and biogeochemical variability at this scale remains challenging due to the ephemeral nature of submesoscale structures. The in-situ study of such structures necessitates multidisciplinary approaches involving in situ observations, remote sensing and modeling. Last progresses in biogeochemical sensor development and advanced methodology including Lagrangian real-time adaptative strategies represent outstanding opportunities. The OSCAHR (Observing Submesoscale Coupling At High Resolution) campaign has been conducted thanks to a multidisciplinary approach in order to improve the understanding of submesoscale processes. An ephemeral submesoscale structure was first identified in the Ligurian Sea in fall 2015 using both satellite and numerical modeling data before the campaign. Afterwards, advanced observing systems for the physical, biological and biogeochemical characterization of the sea surface layer at a high spatial and temporal frequency were deployed during a 10-days cruise. A MVP (Moving Vessel Profiler) was used to obtain high resolution CTD profiles associated to a new pumping system with 1-m vertical resolution. Moreover, along the ship track, in addition to the standard measurements of seawater surface samples (Chl-a, nutrients, O2, SST, SSS …), we deployed an automated flow cytometer for near real-time characterization of phytoplankton functional groups (from micro-phytoplankton down to cyanobacteria). The observed submesoscale feature presented a cyclonic structure with a relatively cold core surrounded by warmer waters. Six phytoplankton groups were identified across the structure with an unprecedented spatial and temporal resolution. According to our observations, we could quantify the influence of the fast established physical structure on the spatial distribution of the phytoplankton functional groups, giving coherence to the observed community structuration. Moreover, the high resolution of our observations allows us to estimate the growth rate of the main phytoplankton groups. Our innovative adaptative strategy with a multidisciplinary and transversal approach provides a deeper understanding of the marine biogeochemical dynamics through the first trophic levels.

Structural response of existing spatial truss roof construction based on Cosserat rod theory

NASA Astrophysics Data System (ADS)

Miśkiewicz, Mikołaj

2018-04-01

Paper presents the application of the Cosserat rod theory and newly developed associated finite elements code as the tools that support in the expert-designing engineering practice. Mechanical principles of the 3D spatially curved rods, dynamics (statics) laws, principle of virtual work are discussed. Corresponding FEM approach with interpolation and accumulation techniques of state variables are shown that enable the formulation of the C0 Lagrangian rod elements with 6-degrees of freedom per node. Two test examples are shown proving the correctness and suitability of the proposed formulation. Next, the developed FEM code is applied to assess the structural response of the spatial truss roof of the "Olivia" Sports Arena Gdansk, Poland. The numerical results are compared with load test results. It is shown that the proposed FEM approach yields correct results.

Nonlinear amplification of coherent waves in media with soliton-type refractive index pattern.

PubMed

Bugaychuk, S; Conte, R

2012-08-01

We derive the complex Ginzburg-Landau equation for the dynamical self-diffraction of optical waves in a nonlinear cavity. The case of the reflection geometry of wave interaction as well as a medium that possesses the cubic nonlinearity (including a local and a nonlocal nonlinear responses) and the relaxation is considered. A stable localized spatial structure in the form of a "dark" dissipative soliton is formed in the cavity in the steady state. The envelope of the intensity pattern, as well as of the dynamical grating amplitude, takes the shape of a tanh function. The obtained complex Ginzburg-Landau equation describes the dynamics of this envelope; at the same time, the evolution of this spatial structure changes the parameters of the output waves. New effects are predicted in this system due to the transformation of the dissipative soliton which takes place during the interaction of a pulse with a continuous wave, such as retention of the pulse shape during the transmission of impulses in a long nonlinear cavity, and giant amplification of a seed pulse, which takes energy due to redistribution of the pump continuous energy into the signal.

Ecological and evolutionary consequences of explicit spatial structure in exploiter-victim systems

NASA Astrophysics Data System (ADS)

Klopfer, Eric David

One class of spatial model which has been widely used in ecology has been termed "pseudo-spatial models" and classically employs various types of aggregation in studying the coexistence of competing parasitoids. Yet, little is known about the relative effects of each of these aggregation behaviors. Thus, in Chapter 1 I chose to examine three types of aggregation and explore their relative strengths in promoting coexistence of two competing parasitoids. A striking shortcoming of spatial models in ecology to date is that there is a relative lack of use of spatial models to investigate problems on the evolutionary as opposed to ecological time scale. Consequently, in Chapter 2 I chose to start with a classic problem of evolutionary time scale--the evolution of virulence and predation rates. Debate about this problem has continued through several decades, yet many instances are not adequately explained by current models. In this study I explored the effect of explicit spatial structure on exploitation rates by comparing a cellular automata (CA) exploiter-victim model which incorporates local dynamics to a metapopulation model which does not include such dynamics. One advantage of CA models is that they are defined by simple rules rather than the often complex equations of other types of spatial models. This is an extremely useful attribute when one wants to convey results of models to an audience with an applied bent that is often uncomfortable with hard-to-understand equations. Thus, in Chapter 3, through the use of CA models I show that there are spatial phenomena which alter the impact of introduced predators and that these phenomena are potentially important in the implementation of biocontrol programs. The relatively recent incorporation of spatial models into the ecological literature has left most ecologists and evolutionary biologists without the ability to understand, let alone employ, spatial models in evolutionary problems. In order to give the next generation of potential ecologists a better understanding of these models, in Chapter 4 I present an interactive tutorial in which students are able to explore the most well studied of these models (the evolution of cooperation in a spatial environment).

The Voronoi spatio-temporal data structure

NASA Astrophysics Data System (ADS)

Mioc, Darka

2002-04-01

Current GIS models cannot integrate the temporal dimension of spatial data easily. Indeed, current GISs do not support incremental (local) addition and deletion of spatial objects, and they can not support the temporal evolution of spatial data. Spatio-temporal facilities would be very useful in many GIS applications: harvesting and forest planning, cadastre, urban and regional planning, and emergency planning. The spatio-temporal model that can overcome these problems is based on a topological model---the Voronoi data structure. Voronoi diagrams are irregular tessellations of space, that adapt to spatial objects and therefore they are a synthesis of raster and vector spatial data models. The main advantage of the Voronoi data structure is its local and sequential map updates, which allows us to automatically record each event and performed map updates within the system. These map updates are executed through map construction commands that are composed of atomic actions (geometric algorithms for addition, deletion, and motion of spatial objects) on the dynamic Voronoi data structure. The formalization of map commands led to the development of a spatial language comprising a set of atomic operations or constructs on spatial primitives (points and lines), powerful enough to define the complex operations. This resulted in a new formal model for spatio-temporal change representation, where each update is uniquely characterized by the numbers of newly created and inactivated Voronoi regions. This is used for the extension of the model towards the hierarchical Voronoi data structure. In this model, spatio-temporal changes induced by map updates are preserved in a hierarchical data structure that combines events and corresponding changes in topology. This hierarchical Voronoi data structure has an implicit time ordering of events visible through changes in topology, and it is equivalent to an event structure that can support temporal data without precise temporal information. This formal model of spatio-temporal change representation is currently applied to retroactive map updates and visualization of map evolution. It offers new possibilities in the domains of temporal GIS, transaction processing, spatio-temporal queries, spatio-temporal analysis, map animation and map visualization.

Imaging the Subsurface of the Thuringian Basin (Germany) on Different Spatial Scales

NASA Astrophysics Data System (ADS)

Goepel, A.; Krause, M.; Methe, P.; Kukowski, N.

2014-12-01

Understanding the coupled dynamics of near surface and deep fluid flow patterns is essential to characterize the properties of sedimentary basins, to identify the processes of compaction, diagenesis, and transport of mass and energy. The multidisciplinary project INFLUINS (Integrated FLUid dynamics IN Sedimentary basins) aims for investigating the behavior of fluids in the Thuringian Basin, a small intra-continental sedimentary basin in Germany, at different spatial scales, ranging from the pore scale to the extent of the entire basin. As hydraulic properties often significantly vary with spatial scales, e.g. seismic data using different frequencies are required to gain information about the spatial variability of elastic and hydraulic subsurface properties. For the Thuringian Basin, we use seismic and borehole data acquired in the framework of INFLUINS. Basin-wide structural imaging data are available from 2D reflection seismic profiles as well as 2.5D and 3D seismic travel time tomography. Further, core material from a 1,179 m deep drill hole completed in 2013 is available for laboratory seismic experiments on mm- to cm-scale. The data are complemented with logging data along the entire drill hole. This campaign yielded e.g. sonic and density logs allowing the estimation of in-situ P-velocity and acoustic impedance with a spatial resolution on the cm-scale and provides improved information about petrologic and stratigraphic variability at different scales. Joint interpretation of basin scale structural and elastic properties data with laboratory scale data from ultrasound experiments using core samples enables a detailed and realistic imaging of the subsurface properties on different spatial scales. Combining seismic travel time tomography with stratigraphic interpretation provides useful information of variations in the elastic properties for certain geological units and therefore gives indications for changes in hydraulic properties.

Quantitative three-dimensional dynamic imaging of structure and function of the cardiopulmonary and circulatory systems in all regions of the body

NASA Technical Reports Server (NTRS)

Sturm, R. E.; Ritman, E. L.; Wood, E. H.

1975-01-01

The background for, and design of a third generation, general purpose, all electronic spatial scanning system, the DSR is described. Its specified performance capabilities provide dynamic and stop action three dimensional spatial reconstructions of any portion of the body based on a minimum exposure time of 0.01 second for each 28 multiplanar 180 deg scanning set, a maximum scan repetition rate of sixty 28 multiplane scan sets per second, each scan set consisting of a maximum of 240 parallel cross sections of a minimum thickness of 0.9 mm, and encompassing a maximum cylindrical volume about 23 cm in length and up to 38 cm in diameter.

Controlling shockwave dynamics using architecture in periodic porous materials

DOE PAGES

Branch, Brittany; Ionita, Axinte; Clements, Bradford E.; ...

2017-04-07

Additive manufacturing (AM) is an attractive approach for the design and fabrication of structures capable of achieving controlled mechanical response of the underlying deformation mechanisms. While there are numerous examples illustrating how the quasi-static mechanical responses of polymer foams have been tailored by additive manufacturing, there is limited understanding of the response of these materials under shockwave compression. Dynamic compression experiments coupled with time-resolved X-ray imaging were performed to obtain insights into the in situ evolution of shockwave coupling to porous, periodic polymer foams. We further demonstrate shock wave modulation or “spatially graded-flow” in shock-driven experiments via the spatial controlmore » of layer symmetries afforded by additive manufacturing techniques at the micron scale.« less

Estimation of Spatial Dynamic Nonparametric Durbin Models with Fixed Effects

ERIC Educational Resources Information Center

Qian, Minghui; Hu, Ridong; Chen, Jianwei

2016-01-01

Spatial panel data models have been widely studied and applied in both scientific and social science disciplines, especially in the analysis of spatial influence. In this paper, we consider the spatial dynamic nonparametric Durbin model (SDNDM) with fixed effects, which takes the nonlinear factors into account base on the spatial dynamic panel…

Effects of landscape and patch-level attributes on regional population persistence

EPA Science Inventory

Habitat patch size and isolation are often described as the key habitat variables influencing population dynamics. Yet habitat quality may also play an important role in influencing the regional persistence of spatially structured populations as the value or density of resources ...

Static sampling of dynamic processes - a paradox?

NASA Astrophysics Data System (ADS)

Mälicke, Mirko; Neuper, Malte; Jackisch, Conrad; Hassler, Sibylle; Zehe, Erwin

2017-04-01

Environmental systems monitoring aims at its core at the detection of spatio-temporal patterns of processes and system states, which is a pre-requisite for understanding and explaining their baffling heterogeneity. Most observation networks rely on distributed point sampling of states and fluxes of interest, which is combined with proxy-variables from either remote sensing or near surface geophysics. The cardinal question on the appropriate experimental design of such a monitoring network has up to now been answered in many different ways. Suggested approaches range from sampling in a dense regular grid using for the so-called green machine, transects along typical catenas, clustering of several observations sensors in presumed functional units or HRUs, arrangements of those cluster along presumed lateral flow paths to last not least a nested, randomized stratified arrangement of sensors or samples. Common to all these approaches is that they provide a rather static spatial sampling, while state variables and their spatial covariance structure dynamically change in time. It is hence of key interest how much of our still incomplete understanding stems from inappropriate sampling and how much needs to be attributed to an inappropriate analysis of spatial data sets. We suggest that it is much more promising to analyze the spatial variability of processes, for instance changes in soil moisture values, than to investigate the spatial variability of soil moisture states themselves. This is because wetting of the soil, reflected in a soil moisture increase, is causes by a totally different meteorological driver - rainfall - than drying of the soil. We hence propose that the rising and the falling limbs of soil moisture time series belong essentially to different ensembles, as they are influenced by different drivers. Positive and negative temporal changes in soil moisture need, hence, to be analyzed separately. We test this idea using the CAOS data set as a benchmark. Specifically, we expect the covariance structure of the positive temporal changes of soil moisture to be dominated by the spatial structure of rain- and through-fall and saturated hydraulic conductivity. The covariance in temporarily decreasing soil moisture during radiation driven conditions is expect to be dominated by the spatial structure of retention properties and plant transpiration. An analysis of soil moisture changes has furthermore the advantage that those are free from systematic measurement errors.

Evolution of spatial and temporal correlations in the solar wind - Observations and interpretation

NASA Technical Reports Server (NTRS)

Klein, L. W.; Matthaeus, W. H.; Roberts, D. A.; Goldstein, M. L.

1992-01-01

Observations of solar wind magnetic field spectra from 1-22 AU indicate a distinctive structure in frequency which evolves with increasing heliocentric distance. At 1 AU extremely low frequency correlations are associated with temporal variations at the solar period and its first few harmonics. For periods of l2-96 hours, a l/f distribution is observed, which we interpret as an aggregate of uncorrelated coronal structures which have not dynamically interacted by 1 AU. At higher frequencies the familiar Kolmogorov-like power law is seen. Farther from the sun the frequency break point between the shallow l/f and the steeper Kolmogorov spectrum evolves systematically towards lower frequencies. We suggest that the Kolmogorov-like spectra emerge due to in situ turbulence that generates spatial correlations associated with the turbulent cascade and that the background l/f noise is a largely temporal phenomenon, not associated with in situ dynamical processes. In this paper we discuss these ideas from the standpoint of observations from several interplanetary spacecraft.

Criticality of forcing directions on the fragmentation and resilience of grid networks.

PubMed

Abundo, Cheryl; Monterola, Christopher; Legara, Erika Fille

2014-08-27

A general framework for probing the dynamic evolution of spatial networks comprised of nodes applying force amongst each other is presented. Aside from the already reported magnitude of forces and elongation thresholds, we show that preservation of links in a network is also crucially dependent on how nodes are connected and how edges are directed. We demonstrate that the time it takes for the networks to reach its equilibrium network structure follows a robust power law relationship consistent with Basquin's law with an exponent that can be tuned by changing only the force directions. Further, we illustrate that networks with different connection structures, node positions and edge directions have different Basquin's exponent which can be used to distinguish spatial directed networks from each other. Using an extensive waiting time simulation that spans up to over 16 orders of magnitude, we establish that the presence of memory combined with the scale-free bursty dynamics of edge breaking at the micro level leads to the evident macroscopic power law distribution of network lifetime.

Spatio-temporal evolution of perturbations in ensembles initialized by bred, Lyapunov and singular vectors

NASA Astrophysics Data System (ADS)

Pazó, Diego; Rodríguez, Miguel A.; López, Juan M.

2010-05-01

We study the evolution of finite perturbations in the Lorenz ‘96 model, a meteorological toy model of the atmosphere. The initial perturbations are chosen to be aligned along different dynamic vectors: bred, Lyapunov, and singular vectors. Using a particular vector determines not only the amplification rate of the perturbation but also the spatial structure of the perturbation and its stability under the evolution of the flow. The evolution of perturbations is systematically studied by means of the so-called mean-variance of logarithms diagram that provides in a very compact way the basic information to analyse the spatial structure. We discuss the corresponding advantages of using those different vectors for preparing initial perturbations to be used in ensemble prediction systems, focusing on key properties: dynamic adaptation to the flow, robustness, equivalence between members of the ensemble, etc. Among all the vectors considered here, the so-called characteristic Lyapunov vectors are possibly optimal, in the sense that they are both perfectly adapted to the flow and extremely robust.

Spatio-temporal evolution of perturbations in ensembles initialized by bred, Lyapunov and singular vectors

NASA Astrophysics Data System (ADS)

Pazó, Diego; Rodríguez, Miguel A.; López, Juan M.

2010-01-01

We study the evolution of finite perturbations in the Lorenz `96 model, a meteorological toy model of the atmosphere. The initial perturbations are chosen to be aligned along different dynamic vectors: bred, Lyapunov, and singular vectors. Using a particular vector determines not only the amplification rate of the perturbation but also the spatial structure of the perturbation and its stability under the evolution of the flow. The evolution of perturbations is systematically studied by means of the so-called mean-variance of logarithms diagram that provides in a very compact way the basic information to analyse the spatial structure. We discuss the corresponding advantages of using those different vectors for preparing initial perturbations to be used in ensemble prediction systems, focusing on key properties: dynamic adaptation to the flow, robustness, equivalence between members of the ensemble, etc. Among all the vectors considered here, the so-called characteristic Lyapunov vectors are possibly optimal, in the sense that they are both perfectly adapted to the flow and extremely robust.

Strain measurement using a Brillouin optical time domain reflectometer for development of aircraft structure health monitoring system

NASA Astrophysics Data System (ADS)

Shimizu, Takayuki; Yari, Takashi; Nagai, Kanehiro; Takeda, Nobuo

2001-07-01

We conducted theoretical and experimental approaches for applying Brillouin optical time domain reflectometer (BOTDR) to aircraft and spacecraft structure health monitoring system. Firstly, distributed strain was measured by BOTDR under 3-point bending test and a spatial resolution was enhanced up to 0.5m using Brillouin spectrum analysis and processing though the device used in this experiment had a spatial resolution of 2m normally. Secondly, dynamic strain measurement was executed under cyclic loading conditions. Brillouin spectrum measured under dynamic conditions is equivalent to superposed spectrum using many spectra measured under static loading conditions. As the measured spectrum was decomposed into many spectra in static loading state, the strain amplitude and its ratio could be estimated. Thirdly, strain and temperature could be measured independently using combined system of BOTDR and fiber Bragg grating (FBG) with wavelength division multiplexing (WDM). Additionally, the application of BOTDR sensing system was shown for a prototype carbon fiber reinforced plastic (CFRP) liquid hydrogen (LH2) tank under cryogenic condition.

Compressibility effect on thermal coherent structures in spatially-developing turbulent boundary layers via DNS

NASA Astrophysics Data System (ADS)

Araya, Guillermo; Jansen, Kenneth

2017-11-01

DNS of compressible spatially-developing turbulent boundary layers is performed at a Mach number of 2.5 over an isothermal flat plate. Turbulent inflow information is generated by following the concept of the rescaling-recycling approach introduced by Lund et al. (J. Comp. Phys. 140, 233-258, 1998); although, the proposed methodology is extended to compressible flows. Furthermore, a dynamic approach is employed to connect the friction velocities at the inlet and recycle stations (i.e., there is no need of an empirical correlation as in Lund et al.). Additionally, the Morkovin's Strong Reynolds Analogy (SRA) is used in the rescaling process of the thermal fluctuations from the recycle plane. Low/high order flow statistics is compared with direct simulations of an incompressible isothermal ZPG boundary layer at similar Reynolds numbers and temperature regarded as a passive scalar. Focus is given to the effect assessment of flow compressibility on the dynamics of thermal coherent structures. AFOSR #FA9550-17-1-0051.

Community ecology in 3D: Tensor decomposition reveals spatio-temporal dynamics of large ecological communities.

PubMed

Frelat, Romain; Lindegren, Martin; Denker, Tim Spaanheden; Floeter, Jens; Fock, Heino O; Sguotti, Camilla; Stäbler, Moritz; Otto, Saskia A; Möllmann, Christian

2017-01-01

Understanding spatio-temporal dynamics of biotic communities containing large numbers of species is crucial to guide ecosystem management and conservation efforts. However, traditional approaches usually focus on studying community dynamics either in space or in time, often failing to fully account for interlinked spatio-temporal changes. In this study, we demonstrate and promote the use of tensor decomposition for disentangling spatio-temporal community dynamics in long-term monitoring data. Tensor decomposition builds on traditional multivariate statistics (e.g. Principal Component Analysis) but extends it to multiple dimensions. This extension allows for the synchronized study of multiple ecological variables measured repeatedly in time and space. We applied this comprehensive approach to explore the spatio-temporal dynamics of 65 demersal fish species in the North Sea, a marine ecosystem strongly altered by human activities and climate change. Our case study demonstrates how tensor decomposition can successfully (i) characterize the main spatio-temporal patterns and trends in species abundances, (ii) identify sub-communities of species that share similar spatial distribution and temporal dynamics, and (iii) reveal external drivers of change. Our results revealed a strong spatial structure in fish assemblages persistent over time and linked to differences in depth, primary production and seasonality. Furthermore, we simultaneously characterized important temporal distribution changes related to the low frequency temperature variability inherent in the Atlantic Multidecadal Oscillation. Finally, we identified six major sub-communities composed of species sharing similar spatial distribution patterns and temporal dynamics. Our case study demonstrates the application and benefits of using tensor decomposition for studying complex community data sets usually derived from large-scale monitoring programs.

Membrane Driven Spatial Organization of GPCRs

NASA Astrophysics Data System (ADS)

Mondal, Sayan; Johnston, Jennifer M.; Wang, Hao; Khelashvili, George; Filizola, Marta; Weinstein, Harel

2013-10-01

Spatial organization of G-protein coupled receptors (GPCRs) into dimers and higher order oligomers has been demonstrated in vitro and in vivo. The pharmacological readout was shown to depend on the specific interfaces, but why particular regions of the GPCR structure are involved, and how ligand-determined states change them remains unknown. Here we show why protein-membrane hydrophobic matching is attained upon oligomerization at specific interfaces from an analysis of coarse-grained molecular dynamics simulations of the spontaneous diffusion-interaction of the prototypical beta2-adrenergic (β2AR) receptors in a POPC lipid bilayer. The energy penalty from mismatch is significantly reduced in the spontaneously emerging oligomeric arrays, making the spatial organization of the GPCRs dependent on the pattern of mismatch in the monomer. This mismatch pattern is very different for β2AR compared to the highly homologous and structurally similar β1AR, consonant with experimentally observed oligomerization patterns of β2AR and β1AR. The results provide a mechanistic understanding of the structural context of oligomerization.

Study of diffusion and local structure of sodium-silicate liquid: the molecular dynamic simulation

NASA Astrophysics Data System (ADS)

Hung, Pham Khac; Noritake, Fumiya; San, Luyen Thi; Van, To Ba; Vinh, Le The

2017-10-01

A systematic analysis on sodium-silicate melt with various silica contents was carried out. The simulation revealed two diffusion mechanisms occurred in the melt: the bond-breaking and hopping between sites. The local structure was analyzed through T-simplexes. It was revealed that T-clusters have a non-spherical shape and represent the diffusion channel, in which Na atoms are dominant, but no any O atoms are located. The SiO2-poor melt acquires a long channel. In contrast, the SiO2-rich melt consists of unconnected short channels. The simulation also revealed the immobile and mobile regions which differ in local structure and constituent composition. We propose a new CL-function to characterizing the spatial distribution of different atom component. The spatial distribution of mobile and immobile atoms is found quite different. In particular, the immobile atoms are concentrated in high-density regions possessing very large density of immobile atoms. The spatial distribution of mobile atoms in contrast is more homogeneous.

Molecular dynamics simulation of geminal dicationic ionic liquids [Cn(mim)2][NTf2]2 - structural and dynamical properties.

PubMed

Moosavi, Majid; Khashei, Fatemeh; Sedghamiz, Elaheh

2017-12-20

In this work, the structural and dynamical properties of two imidazolium-based geminal dicationic ionic liquids (GDILs), i.e. [C n (mim) 2 ][NTf 2 ] 2 with n = 3 and 5, have been studied to obtain a fundamental understanding of the molecular basis of the macroscopic and microscopic properties of the bulk liquid phase. To achieve this purpose, molecular dynamics (MD) simulation, density functional theory (DFT) and atoms in molecule (AIM) methods were used. Interaction energies, charge transfers and hydrogen bonds between the cation and anions of each studied GDIL were investigated by DFT calculations and also AIM. The mean square displacement (MSD), self-diffusion coefficient, and transference number of the cation and anions, and also the density, viscosity and electrical conductivity of the studied GDILs, were computed at 333.15 K and at 1 atm. The simulated values were in good agreement with the experimental data. The effect of linkage alkyl chain length on the thermodynamic, transport and structural properties of these GDILs has been investigated. The structural features of these GDILs were characterized by calculating the partial site-site radial distribution functions (RDFs) and spatial distribution functions (SDFs). The heterogeneity order parameter (HOP) has been used to describe the spatial structures of these GDILs and the distribution of the angles formed between two cation heads and the middle carbon atom of the linkage alkyl chain was analyzed in these ILs. To investigate the temporal heterogeneity of the studied GDILs, the deviation of the self-part of the van Hove correlation function, G s (r[combining right harpoon above],t), from the Gaussian distribution of particle displacement and also the second-order non-Gaussian parameter, α 2 (t), were used. Since, the transport and interfacial properties and ionic characteristics of these GDILs were studied experimentally in our previous studies as a function of linkage chain length and temperature, in this work, we try to give a better perspective of the structure and dynamics of these systems at a molecular level.

Control of hierarchical polymer mechanics with bioinspired metal-coordination dynamics

PubMed Central

Grindy, Scott C.; Learsch, Robert; Mozhdehi, Davoud; Cheng, Jing; Barrett, Devin G.; Guan, Zhibin; Messersmith, Phillip B.; Holten-Andersen, Niels

2015-01-01

In conventional polymer materials, mechanical performance is traditionally engineered via material structure, using motifs such as polymer molecular weight, polymer branching, or copolymer-block design1. Here, by means of a model system of 4-arm poly(ethylene glycol) hydrogels crosslinked with multiple, kinetically distinct dynamic metal-ligand coordinate complexes, we show that polymer materials with decoupled spatial structure and mechanical performance can be designed. By tuning the relative concentration of two types of metal-ligand crosslinks, we demonstrate control over the material’s mechanical hierarchy of energy-dissipating modes under dynamic mechanical loading, and therefore the ability to engineer a priori the viscoelastic properties of these materials by controlling the types of crosslinks rather than by modifying the polymer itself. This strategy to decouple material mechanics from structure may inform the design of soft materials for use in complex mechanical environments. PMID:26322715

Imaging multi-scale dynamics in vivo with spiral volumetric optoacoustic tomography

NASA Astrophysics Data System (ADS)

Deán-Ben, X. Luís.; Fehm, Thomas F.; Ford, Steven J.; Gottschalk, Sven; Razansky, Daniel

2017-03-01

Imaging dynamics in living organisms is essential for the understanding of biological complexity. While multiple imaging modalities are often required to cover both microscopic and macroscopic spatial scales, dynamic phenomena may also extend over different temporal scales, necessitating the use of different imaging technologies based on the trade-off between temporal resolution and effective field of view. Optoacoustic (photoacoustic) imaging has been shown to offer the exclusive capability to link multiple spatial scales ranging from organelles to entire organs of small animals. Yet, efficient visualization of multi-scale dynamics remained difficult with state-of-the-art systems due to inefficient trade-offs between image acquisition and effective field of view. Herein, we introduce a spiral volumetric optoacoustic tomography (SVOT) technique that provides spectrally-enriched high-resolution optical absorption contrast across multiple spatio-temporal scales. We demonstrate that SVOT can be used to monitor various in vivo dynamics, from video-rate volumetric visualization of cardiac-associated motion in whole organs to high-resolution imaging of pharmacokinetics in larger regions. The multi-scale dynamic imaging capability thus emerges as a powerful and unique feature of the optoacoustic technology that adds to the multiple advantages of this technology for structural, functional and molecular imaging.

Fine-scale spatial genetic dynamics over the life cycle of the tropical tree Prunus africana.

PubMed

Berens, D G; Braun, C; González-Martínez, S C; Griebeler, E M; Nathan, R; Böhning-Gaese, K

2014-11-01

Studying fine-scale spatial genetic patterns across life stages is a powerful approach to identify ecological processes acting within tree populations. We investigated spatial genetic dynamics across five life stages in the insect-pollinated and vertebrate-dispersed tropical tree Prunus africana in Kakamega Forest, Kenya. Using six highly polymorphic microsatellite loci, we assessed genetic diversity and spatial genetic structure (SGS) from seed rain and seedlings, and different sapling stages to adult trees. We found significant SGS in all stages, potentially caused by limited seed dispersal and high recruitment rates in areas with high light availability. SGS decreased from seed and early seedling stages to older juvenile stages. Interestingly, SGS was stronger in adults than in late juveniles. The initial decrease in SGS was probably driven by both random and non-random thinning of offspring clusters during recruitment. Intergenerational variation in SGS could have been driven by variation in gene flow processes, overlapping generations in the adult stage or local selection. Our study shows that complex sequential processes during recruitment contribute to SGS of tree populations.

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.

Imaging nanoscale spatial modulation of a relativistic electron beam with a MeV ultrafast electron microscope

NASA Astrophysics Data System (ADS)

Lu, Chao; Jiang, Tao; Liu, Shengguang; Wang, Rui; Zhao, Lingrong; Zhu, Pengfei; Liu, Yaqi; Xu, Jun; Yu, Dapeng; Wan, Weishi; Zhu, Yimei; Xiang, Dao; Zhang, Jie

2018-03-01

An accelerator-based MeV ultrafast electron microscope (MUEM) has been proposed as a promising tool to the study structural dynamics at the nanometer spatial scale and the picosecond temporal scale. Here, we report experimental tests of a prototype MUEM where high quality images with nanoscale fine structures were recorded with a pulsed ˜3 MeV picosecond electron beam. The temporal and spatial resolutions of the MUEM operating in the single-shot mode are about 4 ps (FWHM) and 100 nm (FWHM), corresponding to a temporal-spatial resolution of 4 × 10-19 s m, about 2 orders of magnitude higher than that achieved with state-of-the-art single-shot keV UEM. Using this instrument, we offer the demonstration of visualizing the nanoscale periodic spatial modulation of an electron beam, which may be converted into longitudinal density modulation through emittance exchange to enable production of high-power coherent radiation at short wavelengths. Our results mark a great step towards single-shot nanometer-resolution MUEMs and compact intense x-ray sources that may have widespread applications in many areas of science.

Effects of spatial variability of soil hydraulic properties on water dynamics

NASA Astrophysics Data System (ADS)

Gumiere, Silvio Jose; Caron, Jean; Périard, Yann; Lafond, Jonathan

2013-04-01

Soil hydraulic properties may present spatial variability and dependence at the scale of watersheds or fields even in man-made single soil structures, such as cranberry fields. The saturated hydraulic conductivity (Ksat) and soil moisture curves were measured at two depths for three cranberry fields (about 2 ha) at three different sites near Québec city, Canada. Two of the three studied fields indicate strong spatial dependence for Ksat values and soil moisture curves both in horizontal and vertical directions. In the summer of 2012, the three fields were equipped with 55 tensiometers installed at a depth of 0.10 m in a regular grid. About 20 mm of irrigation water were applied uniformly by aspersion to the fields, raising soil water content to near saturation condition. Soil water tension was measured once every hour during seven days. Geostatistical techniques such as co-kriging and cross-correlograms estimations were used to investigate the spatial dependence between variables. The results show that soil tension varied faster in high Ksat zones than in low Ksatones in the cranberry fields. These results indicate that soil water dynamic is strongly affected by the variability of saturated soil hydraulic conductivity, even in a supposed homogenous anthropogenic soil. This information may have a strong impact in irrigation management and subsurface drainage efficiency as well as other water conservation issues. Future work will involve 3D numerical modeling of the field water dynamics with HYDRUS software. The anticipated outcome will provide valuable information for the understanding of the effect of spatial variability of soil hydraulic properties on soil water dynamics and its relationship with crop production and water conservation.

Remote sensing and spatial analysis based study for detecting deforestation and the associated drivers

NASA Astrophysics Data System (ADS)

El-Abbas, Mustafa M.; Csaplovics, Elmar; Deafalla, Taisser H.

2013-10-01

Nowadays, remote-sensing technologies are becoming increasingly interlinked to the issue of deforestation. They offer a systematized and objective strategy to document, understand and simulate the deforestation process and its associated causes. In this context, the main goal of this study, conducted in the Blue Nile region of Sudan, in which most of the natural habitats were dramatically destroyed, was to develop spatial methodologies to assess the deforestation dynamics and its associated factors. To achieve that, optical multispectral satellite scenes (i.e., ASTER and LANDSAT) integrated with field survey in addition to multiple data sources were used for the analyses. Spatiotemporal Object Based Image Analysis (STOBIA) was applied to assess the change dynamics within the period of study. Broadly, the above mentioned analyses include; Object Based (OB) classifications, post-classification change detection, data fusion, information extraction and spatial analysis. Hierarchical multi-scale segmentation thresholds were applied and each class was delimited with semantic meanings by a set of rules associated with membership functions. Consequently, the fused multi-temporal data were introduced to create detailed objects of change classes from the input LU/LC classes. The dynamic changes were quantified and spatially located as well as the spatial and contextual relations from adjacent areas were analyzed. The main finding of the present study is that, the forest areas were drastically decreased, while the agrarian structure in conversion of forest into agricultural fields and grassland was the main force of deforestation. In contrast, the capability of the area to recover was clearly observed. The study concludes with a brief assessment of an 'oriented' framework, focused on the alarming areas where serious dynamics are located and where urgent plans and interventions are most critical, guided with potential solutions based on the identified driving forces.

Effective 3-D surface modeling for geographic information systems

NASA Astrophysics Data System (ADS)

Yüksek, K.; Alparslan, M.; Mendi, E.

2013-11-01

In this work, we propose a dynamic, flexible and interactive urban digital terrain platform (DTP) with spatial data and query processing capabilities of Geographic Information Systems (GIS), multimedia database functionality and graphical modeling infrastructure. A new data element, called Geo-Node, which stores image, spatial data and 3-D CAD objects is developed using an efficient data structure. The system effectively handles data transfer of Geo-Nodes between main memory and secondary storage with an optimized Directional Replacement Policy (DRP) based buffer management scheme. Polyhedron structures are used in Digital Surface Modeling (DSM) and smoothing process is performed by interpolation. The experimental results show that our framework achieves high performance and works effectively with urban scenes independent from the amount of spatial data and image size. The proposed platform may contribute to the development of various applications such as Web GIS systems based on 3-D graphics standards (e.g. X3-D and VRML) and services which integrate multi-dimensional spatial information and satellite/aerial imagery.

Effective 3-D surface modeling for geographic information systems

NASA Astrophysics Data System (ADS)

Yüksek, K.; Alparslan, M.; Mendi, E.

2016-01-01

In this work, we propose a dynamic, flexible and interactive urban digital terrain platform with spatial data and query processing capabilities of geographic information systems, multimedia database functionality and graphical modeling infrastructure. A new data element, called Geo-Node, which stores image, spatial data and 3-D CAD objects is developed using an efficient data structure. The system effectively handles data transfer of Geo-Nodes between main memory and secondary storage with an optimized directional replacement policy (DRP) based buffer management scheme. Polyhedron structures are used in digital surface modeling and smoothing process is performed by interpolation. The experimental results show that our framework achieves high performance and works effectively with urban scenes independent from the amount of spatial data and image size. The proposed platform may contribute to the development of various applications such as Web GIS systems based on 3-D graphics standards (e.g., X3-D and VRML) and services which integrate multi-dimensional spatial information and satellite/aerial imagery.

A quantum relativistic battle of the sexes cellular automaton

NASA Astrophysics Data System (ADS)

Alonso-Sanz, Ramón; Situ, Haozhen

2017-02-01

The effect of variable entangling on the dynamics of a spatial quantum relativistic formulation of the iterated battle of the sexes game is studied in this work. The game is played in the cellular automata manner, i.e., with local and synchronous interaction. The game is assessed in fair and unfair contests. Despite the full range of quantum parameters initially accessible, they promptly converge into fairly stable configurations, that often show rich spatial structures in simulations with no negligible entanglement.

Structure and dynamics of a silica melt in neutral confinement

NASA Astrophysics Data System (ADS)

Geske, Julian; Drossel, Barbara; Vogel, Michael

2017-04-01

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

Structure and dynamics of a silica melt in neutral confinement.

PubMed

Geske, Julian; Drossel, Barbara; Vogel, Michael

2017-04-07

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

Biophysical controls on cluster dynamics and architectural differentiation of microbial biofilms in contrasting flow environments

PubMed Central

Hödl, Iris; Mari, Lorenzo; Bertuzzo, Enrico; Suweis, Samir; Besemer, Katharina; Rinaldo, Andrea; Battin, Tom J

2014-01-01

Ecology, with a traditional focus on plants and animals, seeks to understand the mechanisms underlying structure and dynamics of communities. In microbial ecology, the focus is changing from planktonic communities to attached biofilms that dominate microbial life in numerous systems. Therefore, interest in the structure and function of biofilms is on the rise. Biofilms can form reproducible physical structures (i.e. architecture) at the millimetre-scale, which are central to their functioning. However, the spatial dynamics of the clusters conferring physical structure to biofilms remains often elusive. By experimenting with complex microbial communities forming biofilms in contrasting hydrodynamic microenvironments in stream mesocosms, we show that morphogenesis results in ‘ripple-like’ and ‘star-like’ architectures – as they have also been reported from monospecies bacterial biofilms, for instance. To explore the potential contribution of demographic processes to these architectures, we propose a size-structured population model to simulate the dynamics of biofilm growth and cluster size distribution. Our findings establish that basic physical and demographic processes are key forces that shape apparently universal biofilm architectures as they occur in diverse microbial but also in single-species bacterial biofilms. PMID:23879839

Spatial and seasonal dynamics of brook trout populations inhabiting a central Appalachian watershed

USGS Publications Warehouse

Petty, J.T.; Lamothe, P.J.; Mazik, P.M.

2005-01-01

We quantified the watershed-scale spatial population dynamics of brook trout Salvelinus fontinalis in the Second Fork, a third-order tributary of Shavers Fork in eastern West Virginia. We used visual surveys, electrofishing, and mark-recapture techniques to quantify brook trout spawning intensity, population density, size structure, and demographic rates (apparent survival and immigration) throughout the watershed. Our analyses produced the following results. Spawning by brook trout was concentrated in streams with small basin areas (i.e., segments draining less than 3 km2), relatively high alkalinity (>10 mg CaCO3/L), and high amounts of instream cover. The spatial distribution of juvenile and small-adult brook trout within the watershed was relatively stable and was significantly correlated with spawning intensity. However, no such relationship was observed for large adults, which exhibited highly variable distribution patterns related to seasonally important habitat features, including instream cover, stream depth and width, and riparian canopy cover. Brook trout survival and immigration rates varied seasonally, spatially, and among size-classes. Differential survival and immigration tended to concentrate juveniles and small adults in small, alkaline streams, whereas dispersal tended to redistribute large adults at the watershed scale. Our results suggest that spatial and temporal variations in spawning, survival, and movement interact to determine the distribution, abundance, and size structure of brook trout populations at a watershed scale. These results underscore the importance of small tributaries for the persistence of brook trout in this watershed and the need to consider watershed-scale processes when designing management plans for Appalachian brook trout populations. ?? Copyright by the American Fisheries Society 2005.

Diagnosing the Dynamics of Observed and Simulated Ecosystem Gross Primary Productivity with Time Causal Information Theory Quantifiers

DOE PAGES

Sippel, Sebastian; Lange, Holger; Mahecha, Miguel D.; ...

2016-10-20

Data analysis and model-data comparisons in the environmental sciences require diagnostic measures that quantify time series dynamics and structure, and are robust to noise in observational data. This paper investigates the temporal dynamics of environmental time series using measures quantifying their information content and complexity. The measures are used to classify natural processes on one hand, and to compare models with observations on the other. The present analysis focuses on the global carbon cycle as an area of research in which model-data integration and comparisons are key to improving our understanding of natural phenomena. We investigate the dynamics of observedmore » and simulated time series of Gross Primary Productivity (GPP), a key variable in terrestrial ecosystems that quantifies ecosystem carbon uptake. However, the dynamics, patterns and magnitudes of GPP time series, both observed and simulated, vary substantially on different temporal and spatial scales. Here we demonstrate that information content and complexity, or Information Theory Quantifiers (ITQ) for short, serve as robust and efficient data-analytical and model benchmarking tools for evaluating the temporal structure and dynamical properties of simulated or observed time series at various spatial scales. At continental scale, we compare GPP time series simulated with two models and an observations-based product. This analysis reveals qualitative differences between model evaluation based on ITQ compared to traditional model performance metrics, indicating that good model performance in terms of absolute or relative error does not imply that the dynamics of the observations is captured well. Furthermore, we show, using an ensemble of site-scale measurements obtained from the FLUXNET archive in the Mediterranean, that model-data or model-model mismatches as indicated by ITQ can be attributed to and interpreted as differences in the temporal structure of the respective ecological time series. At global scale, our understanding of C fluxes relies on the use of consistently applied land models. Here, we use ITQ to evaluate model structure: The measures are largely insensitive to climatic scenarios, land use and atmospheric gas concentrations used to drive them, but clearly separate the structure of 13 different land models taken from the CMIP5 archive and an observations-based product. In conclusion, diagnostic measures of this kind provide data-analytical tools that distinguish different types of natural processes based solely on their dynamics, and are thus highly suitable for environmental science applications such as model structural diagnostics.« less

Diagnosing the Dynamics of Observed and Simulated Ecosystem Gross Primary Productivity with Time Causal Information Theory Quantifiers

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

Sippel, Sebastian; Lange, Holger; Mahecha, Miguel D.

Data analysis and model-data comparisons in the environmental sciences require diagnostic measures that quantify time series dynamics and structure, and are robust to noise in observational data. This paper investigates the temporal dynamics of environmental time series using measures quantifying their information content and complexity. The measures are used to classify natural processes on one hand, and to compare models with observations on the other. The present analysis focuses on the global carbon cycle as an area of research in which model-data integration and comparisons are key to improving our understanding of natural phenomena. We investigate the dynamics of observedmore » and simulated time series of Gross Primary Productivity (GPP), a key variable in terrestrial ecosystems that quantifies ecosystem carbon uptake. However, the dynamics, patterns and magnitudes of GPP time series, both observed and simulated, vary substantially on different temporal and spatial scales. Here we demonstrate that information content and complexity, or Information Theory Quantifiers (ITQ) for short, serve as robust and efficient data-analytical and model benchmarking tools for evaluating the temporal structure and dynamical properties of simulated or observed time series at various spatial scales. At continental scale, we compare GPP time series simulated with two models and an observations-based product. This analysis reveals qualitative differences between model evaluation based on ITQ compared to traditional model performance metrics, indicating that good model performance in terms of absolute or relative error does not imply that the dynamics of the observations is captured well. Furthermore, we show, using an ensemble of site-scale measurements obtained from the FLUXNET archive in the Mediterranean, that model-data or model-model mismatches as indicated by ITQ can be attributed to and interpreted as differences in the temporal structure of the respective ecological time series. At global scale, our understanding of C fluxes relies on the use of consistently applied land models. Here, we use ITQ to evaluate model structure: The measures are largely insensitive to climatic scenarios, land use and atmospheric gas concentrations used to drive them, but clearly separate the structure of 13 different land models taken from the CMIP5 archive and an observations-based product. In conclusion, diagnostic measures of this kind provide data-analytical tools that distinguish different types of natural processes based solely on their dynamics, and are thus highly suitable for environmental science applications such as model structural diagnostics.« less

Diagnosing the Dynamics of Observed and Simulated Ecosystem Gross Primary Productivity with Time Causal Information Theory Quantifiers

PubMed Central

Sippel, Sebastian; Mahecha, Miguel D.; Hauhs, Michael; Bodesheim, Paul; Kaminski, Thomas; Gans, Fabian; Rosso, Osvaldo A.

2016-01-01

Data analysis and model-data comparisons in the environmental sciences require diagnostic measures that quantify time series dynamics and structure, and are robust to noise in observational data. This paper investigates the temporal dynamics of environmental time series using measures quantifying their information content and complexity. The measures are used to classify natural processes on one hand, and to compare models with observations on the other. The present analysis focuses on the global carbon cycle as an area of research in which model-data integration and comparisons are key to improving our understanding of natural phenomena. We investigate the dynamics of observed and simulated time series of Gross Primary Productivity (GPP), a key variable in terrestrial ecosystems that quantifies ecosystem carbon uptake. However, the dynamics, patterns and magnitudes of GPP time series, both observed and simulated, vary substantially on different temporal and spatial scales. We demonstrate here that information content and complexity, or Information Theory Quantifiers (ITQ) for short, serve as robust and efficient data-analytical and model benchmarking tools for evaluating the temporal structure and dynamical properties of simulated or observed time series at various spatial scales. At continental scale, we compare GPP time series simulated with two models and an observations-based product. This analysis reveals qualitative differences between model evaluation based on ITQ compared to traditional model performance metrics, indicating that good model performance in terms of absolute or relative error does not imply that the dynamics of the observations is captured well. Furthermore, we show, using an ensemble of site-scale measurements obtained from the FLUXNET archive in the Mediterranean, that model-data or model-model mismatches as indicated by ITQ can be attributed to and interpreted as differences in the temporal structure of the respective ecological time series. At global scale, our understanding of C fluxes relies on the use of consistently applied land models. Here, we use ITQ to evaluate model structure: The measures are largely insensitive to climatic scenarios, land use and atmospheric gas concentrations used to drive them, but clearly separate the structure of 13 different land models taken from the CMIP5 archive and an observations-based product. In conclusion, diagnostic measures of this kind provide data-analytical tools that distinguish different types of natural processes based solely on their dynamics, and are thus highly suitable for environmental science applications such as model structural diagnostics. PMID:27764187

Modeling the Impact of Spatial Structure on Growth Dynamics of Invasive Plant Species

NASA Astrophysics Data System (ADS)

Murphy, James T.; Johnson, Mark P.; Walshe, Ray

2013-07-01

Invasive nonindigenous plant species can have potentially serious detrimental effects on local ecosystems and, as a result, costly control efforts often have to be put in place to protect habitats. An example of an invasive problem on a global scale involves the salt marsh grass species from the genus Spartina. The spread of Spartina anglica in Europe and Asia has drawn much concern due to its ability to convert coastal habitats into cord-grass monocultures and to alter the native food webs. However, the patterns of invasion of Spartina species are amenable to spatially-explicit modeling strategies that take into account both temporal and spatio-temporal processes. In this study, an agent-based model of Spartina growth on a simulated mud flat environment was developed in order to study the effects of spatial pattern and initial seedling placement on the invasion dynamics of the population. The spatial pattern of an invasion plays a key role in the rate of spread of the species and understanding this can lead to significant cost savings when designing efficient control strategies. We present here a model framework that can be used to explicitly represent complex spatial and temporal patterns of invasion in order to be able to predict quantitatively the impact of these factors on invasion dynamics. This would be a useful tool for assessing eradication strategies and choosing optimal control solutions in order to be able to minimize future control costs.

Modifying a dynamic global vegetation model for simulating large spatial scale land surface water balance

NASA Astrophysics Data System (ADS)

Tang, G.; Bartlein, P. J.

2012-01-01

Water balance models of simple structure are easier to grasp and more clearly connect cause and effect than models of complex structure. Such models are essential for studying large spatial scale land surface water balance in the context of climate and land cover change, both natural and anthropogenic. This study aims to (i) develop a large spatial scale water balance model by modifying a dynamic global vegetation model (DGVM), and (ii) test the model's performance in simulating actual evapotranspiration (ET), soil moisture and surface runoff for the coterminous United States (US). Toward these ends, we first introduced development of the "LPJ-Hydrology" (LH) model by incorporating satellite-based land covers into the Lund-Potsdam-Jena (LPJ) DGVM instead of dynamically simulating them. We then ran LH using historical (1982-2006) climate data and satellite-based land covers at 2.5 arc-min grid cells. The simulated ET, soil moisture and surface runoff were compared to existing sets of observed or simulated data for the US. The results indicated that LH captures well the variation of monthly actual ET (R2 = 0.61, p < 0.01) in the Everglades of Florida over the years 1996-2001. The modeled monthly soil moisture for Illinois of the US agrees well (R2 = 0.79, p < 0.01) with the observed over the years 1984-2001. The modeled monthly stream flow for most 12 major rivers in the US is consistent R2 > 0.46, p < 0.01; Nash-Sutcliffe Coefficients >0.52) with observed values over the years 1982-2006, respectively. The modeled spatial patterns of annual ET and surface runoff are in accordance with previously published data. Compared to its predecessor, LH simulates better monthly stream flow in winter and early spring by incorporating effects of solar radiation on snowmelt. Overall, this study proves the feasibility of incorporating satellite-based land-covers into a DGVM for simulating large spatial scale land surface water balance. LH developed in this study should be a useful tool for studying effects of climate and land cover change on land surface hydrology at large spatial scales.

Watching proteins function with picosecond X-ray crystallography and molecular dynamics simulations.

NASA Astrophysics Data System (ADS)

Anfinrud, Philip

2006-03-01

Time-resolved electron density maps of myoglobin, a ligand-binding heme protein, have been stitched together into movies that unveil with < 2-å spatial resolution and 150-ps time-resolution the correlated protein motions that accompany and/or mediate ligand migration within the hydrophobic interior of a protein. A joint analysis of all-atom molecular dynamics (MD) calculations and picosecond time-resolved X-ray structures provides single-molecule insights into mechanisms of protein function. Ensemble-averaged MD simulations of the L29F mutant of myoglobin following ligand dissociation reproduce the direction, amplitude, and timescales of crystallographically-determined structural changes. This close agreement with experiments at comparable resolution in space and time validates the individual MD trajectories, which identify and structurally characterize a conformational switch that directs dissociated ligands to one of two nearby protein cavities. This unique combination of simulation and experiment unveils functional protein motions and illustrates at an atomic level relationships among protein structure, dynamics, and function. In collaboration with Friedrich Schotte and Gerhard Hummer, NIH.

Influence of wing tip morphology on vortex dynamics of flapping flight

NASA Astrophysics Data System (ADS)

Krishna, Swathi; Mulleners, Karen

2013-11-01

The mechanism of flapping wing flight provides insects with extraordinary flight capabilities. The uniquely shaped wing tips give insects an edge in flight performance and the interaction between the leading edge vortices and wing tip vortices enhance their propelling efficiencies and manoeuvrability. These are qualities that are sought after in current-day Micro Air Vehicles. A detailed understanding of the vortex dynamics of flapping flight and the influence of the wing tip planform is imperative for technical application. An experimental study is conducted to investigate the effects of different wing tip planforms on the formation, evolution and interaction of vortical structures. We thereby focus on the interaction between the coherent structures evolving from the leading edge and the wing tip during pitching and flapping motions.The spatial and temporal evolution of the three-dimensional flow structures are determined using Scanning (Stereo) Particle Image Velocimetry and an in-depth coherent structure analysis. By comparing the vortex dynamics, the aerodynamic performance of various wing tip planforms are evaluated.

Environmental filtering structures tree functional traits combination and lineages across space in tropical tree assemblages.

PubMed

Asefa, Mengesha; Cao, Min; Zhang, Guocheng; Ci, Xiuqin; Li, Jie; Yang, Jie

2017-03-09

Environmental filtering consistently shapes the functional and phylogenetic structure of species across space within diverse forests. However, poor descriptions of community functional and lineage distributions across space hamper the accurate understanding of coexistence mechanisms. We combined environmental variables and geographic space to explore how traits and lineages are filtered by environmental factors using extended RLQ and fourth-corner analyses across different spatial scales. The dispersion patterns of traits and lineages were also examined in a 20-ha tropical rainforest dynamics plot in southwest China. We found that environmental filtering was detected across all spatial scales except the largest scale (100 × 100 m). Generally, the associations between functional traits and environmental variables were more or less consistent across spatial scales. Species with high resource acquisition-related traits were associated with the resource-rich part of the plot across the different spatial scales, whereas resource-conserving functional traits were distributed in limited-resource environments. Furthermore, we found phylogenetic and functional clustering at all spatial scales. Similar functional strategies were also detected among distantly related species, suggesting that phylogenetic distance is not necessarily a proxy for functional distance. In summary, environmental filtering considerably structured the trait and lineage assemblages in this species-rich tropical rainforest.

Large Variations in HIV-1 Viral Load Explained by Shifting-Mosaic Metapopulation Dynamics

PubMed Central

Lythgoe, Katrina A.; Blanquart, François

2016-01-01

The viral population of HIV-1, like many pathogens that cause systemic infection, is structured and differentiated within the body. The dynamics of cellular immune trafficking through the blood and within compartments of the body has also received wide attention. Despite these advances, mathematical models, which are widely used to interpret and predict viral and immune dynamics in infection, typically treat the infected host as a well-mixed homogeneous environment. Here, we present mathematical, analytical, and computational results that demonstrate that consideration of the spatial structure of the viral population within the host radically alters predictions of previous models. We study the dynamics of virus replication and cytotoxic T lymphocytes (CTLs) within a metapopulation of spatially segregated patches, representing T cell areas connected by circulating blood and lymph. The dynamics of the system depend critically on the interaction between CTLs and infected cells at the within-patch level. We show that for a wide range of parameters, the system admits an unexpected outcome called the shifting-mosaic steady state. In this state, the whole body’s viral population is stable over time, but the equilibrium results from an underlying, highly dynamic process of local infection and clearance within T-cell centers. Notably, and in contrast to previous models, this new model can explain the large differences in set-point viral load (SPVL) observed between patients and their distribution, as well as the relatively low proportion of cells infected at any one time, and alters the predicted determinants of viral load variation. PMID:27706164

Farm-scale variation of soil quality indices and association with edaphic properties

USDA-ARS?s Scientific Manuscript database

Soil organisms are indicators of dynamic soil quality because their community structure and population density are sensitive to management changes. However, edaphic properties can also affect soil organisms and high spatial variability can confound their utility for soil evaluation. In the present...

Femtosecond diffraction dynamics of laser-induced periodic surface structures on fused silica

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

Hoehm, S.; Rosenfeld, A.; Krueger, J.

2013-02-04

The formation of laser-induced periodic surface structures (LIPSS) on fused silica upon irradiation with linearly polarized fs-laser pulses (50 fs pulse duration, 800 nm center wavelength) is studied experimentally using a transillumination femtosecond time-resolved (0.1 ps-1 ns) pump-probe diffraction approach. This allows to reveal the generation dynamics of near-wavelength-sized LIPSS showing a transient diffraction at specific spatial frequencies even before a corresponding permanent surface relief was observed. The results confirm that the ultrafast energy deposition to the materials surface plays a key role and triggers subsequent physical mechanisms such as carrier scattering into self-trapped excitons.

Monitoring hillslope moisture dynamics with surface ERT for enhancing spatial significance of hydrometric point measurements

NASA Astrophysics Data System (ADS)

Hübner, R.; Heller, K.; Günther, T.; Kleber, A.

2015-01-01

Besides floodplains, hillslopes are basic units that mainly control water movement and flow pathways within catchments of subdued mountain ranges. The structure of their shallow subsurface affects water balance, e.g. infiltration, retention, and runoff. Nevertheless, there is still a gap in the knowledge of the hydrological dynamics on hillslopes, notably due to the lack of generalization and transferability. This study presents a robust multi-method framework of electrical resistivity tomography (ERT) in addition to hydrometric point measurements, transferring hydrometric data into higher spatial scales to obtain additional patterns of distribution and dynamics of soil moisture on a hillslope. A geoelectrical monitoring in a small catchment in the eastern Ore Mountains was carried out at weekly intervals from May to December 2008 to image seasonal moisture dynamics on the hillslope scale. To link water content and electrical resistivity, the parameters of Archie's law were determined using different core samples. To optimize inversion parameters and methods, the derived spatial and temporal water content distribution was compared to tensiometer data. The results from ERT measurements show a strong correlation with the hydrometric data. The response is congruent to the soil tension data. Water content calculated from the ERT profile shows similar variations as that of water content from soil moisture sensors. Consequently, soil moisture dynamics on the hillslope scale may be determined not only by expensive invasive punctual hydrometric measurements, but also by minimally invasive time-lapse ERT, provided that pedo-/petrophysical relationships are known. Since ERT integrates larger spatial scales, a combination with hydrometric point measurements improves the understanding of the ongoing hydrological processes and better suits identification of heterogeneities.

Spatial structures in a simple model of population dynamics for parasite-host interactions

NASA Astrophysics Data System (ADS)

Dong, J. J.; Skinner, B.; Breecher, N.; Schmittmann, B.; Zia, R. K. P.

2015-08-01

Spatial patterning can be crucially important for understanding the behavior of interacting populations. Here we investigate a simple model of parasite and host populations in which parasites are random walkers that must come into contact with a host in order to reproduce. We focus on the spatial arrangement of parasites around a single host, and we derive using analytics and numerical simulations the necessary conditions placed on the parasite fecundity and lifetime for the population's long-term survival. We also show that the parasite population can be pushed to extinction by a large drift velocity, but, counterintuitively, a small drift velocity generally increases the parasite population.

Heterogeneous chain dynamics and aggregate lifetimes in precise acid-containing polyethylenes: Experiments and simulations

DOE PAGES

Middleton, L. Robert; Tarver, Jacob D.; Cordaro, Joseph; ...

2016-11-10

Melt state dynamics for a series of strictly linear polyethylenes with precisely spaced associating functional groups were investigated. The periodic pendant acrylic acid groups form hydrogen-bonded acid aggregates within the polyethylene (PE) matrix. The dynamics of these nanoscale heterogeneous morphologies were investigated from picosecond to nanosecond timescales by both quasi-elastic neutron scattering (QENS) measurements and fully atomistic molecular dynamics (MD) simulations. Two dynamic processes were observed. The faster dynamic processes which occur at the picosecond timescales are compositionally insensitive and indicative of spatially restricted local motions. The slower dynamic processes are highly composition dependent and indicate the structural relaxation ofmore » the polymer backbone. Higher acid contents, or shorter PE spacers between pendant acid groups, slow the structural relaxation timescale and increase the stretching parameter (β) of the structural relaxation. Additionally, the dynamics of specific hydrogen atom positions along the backbone correlate structural heterogeneity imposed by the associating acid groups with a mobility gradient along the polymer backbone. At time intervals (<2 ns), the mean-squared displacements for the four methylene groups closest to the acid groups are up to 10 times smaller than those of methylene groups further from the acid groups. At longer timescales acid aggregates rearrange and the chain dynamics of the slow, near-aggregate regions and the faster bridge regions converge, implying a characteristic timescale for the passage of chains between aggregates. As a result, the characterization of the nanoscale chain dynamics in these associating polymer systems both provides validation of simulation force fields and provides understanding of heterogeneous chain dynamics in associating polymers.« less

Reserve size and fragmentation alter community assembly, diversity, and dynamics.

PubMed

Lasky, Jesse R; Keitt, Timothy H

2013-11-01

Researchers have disputed whether a single large habitat reserve will support more species than many small reserves. However, relatively little is known from a theoretical perspective about how reserve size affects competitive communities structured by spatial abiotic gradients. We investigate how reserve size affects theoretical communities whose assembly is governed by dispersal limitation, abiotic niche differentiation, and source-sink dynamics. Simulations were conducted with varying scales of dispersal across landscapes with variable environmental spatial autocorrelation. Landscapes were inhabited by simulated trees with seedling and adult stages. For a fixed total area in reserves, we found that small reserve systems increased the distance between environments dominated by different species, diminishing the effects of source-sink dynamics. As reserve size decreased, environmental limitations to community assembly became stronger, α species richness decreased, and γ richness increased. When dispersal occurred across short distances, a large reserve strategy caused greater stochastic community variation, greater α richness, and lower γ richness than in small reserve systems. We found that reserve size variation trades off between preserving different aspects of natural communities, including α diversity versus γ diversity. Optimal reserve size will depend on the importance of source-sink dynamics and the value placed on different characteristics of natural communities. Anthropogenic changes to the size and separation of remnant habitats can have far-reaching effects on community structure and assembly.

Nonintegrable semidiscrete Hirota equation: gauge-equivalent structures and dynamical properties.

PubMed

Ma, Li-Yuan; Zhu, Zuo-Nong

2014-09-01

In this paper, we investigate nonintegrable semidiscrete Hirota equations, including the nonintegrable semidiscrete Hirota(-) equation and the nonintegrable semidiscrete Hirota(+) equation. We focus on the topics on gauge-equivalent structures and dynamical behaviors for the two nonintegrable semidiscrete equations. By using the concept of the prescribed discrete curvature, we show that, under the discrete gauge transformations, the nonintegrable semidiscrete Hirota(-) equation and the nonintegrable semidiscrete Hirota(+) equation are, respectively, gauge equivalent to the nonintegrable generalized semidiscrete modified Heisenberg ferromagnet equation and the nonintegrable generalized semidiscrete Heisenberg ferromagnet equation. We prove that the two discrete gauge transformations are reversible. We study the dynamical properties for the two nonintegrable semidiscrete Hirota equations. The exact spatial period solutions of the two nonintegrable semidiscrete Hirota equations are obtained through the constructions of period orbits of the stationary discrete Hirota equations. We discuss the topic regarding whether the spatial period property of the solution to the nonintegrable semidiscrete Hirota equation is preserved to that of the corresponding gauge-equivalent nonintegrable semidiscrete equations under the action of discrete gauge transformation. By using the gauge equivalent, we obtain the exact solutions to the nonintegrable generalized semidiscrete modified Heisenberg ferromagnet equation and the nonintegrable generalized semidiscrete Heisenberg ferromagnet equation. We also give the numerical simulations for the stationary discrete Hirota equations. We find that their dynamics are much richer than the ones of stationary discrete nonlinear Schrödinger equations.

Study of the dynamic of motion landing vehicles in the planet's atmosphere using inflatable braking device

NASA Astrophysics Data System (ADS)

Koryanov, Vsevolod; Harri, Ari-Matti; Kazakovtcev, Victor

At present paper analyzes the dynamics of movement of the landing vehicle (LV) with an inflatable braking device (IBD). During the movement in the planet's atmosphere with LV with IBD are significant aerodynamic loads, which can lead to a change in a non-rigid shape and appearance of the shell IBD current asymmetries LV with IBD. The presence arising in the manufacture of structural LV asymmetry results in a stabilized descent in the process of turning the LV with IBD various dynamic phenomena, such as the vibrational-rotational resonance, the resonance autorotation, altering the dynamics of angular motion of the LV. As a result of work carried out, among others, the following conclusions: 1. In the first step of descent of landing vehicle possible high angles of attack, however, the very small quantities of the velocity head. 2. In the second phase of descent arise spatial angles of attack, caused by small structural asymmetries of LV. These angles of attack, together with increasing magnitude of the velocity head cause these significant increase in lateral load. The increase in the transverse load leads to an increase in the asymmetry of the external form, which causes an additional increase in the spatial angle of attack. Depending on the magnitude of the transverse stiffness IBD or leads to a certain additional increase in the spatial angle of attack, or a possible buckling landing vehicle. 3. In the third (final) stage of the descent at subsonic speed landing vehicle with additional inflatable braking device does not influence the stiffness braking, changing the dynamics of angular motion slightly. This is due to the small size of the ram on the subsonic long trajectory and, accordingly, small deformation additional inflatable braking device. This research was supported by the European Commission Seventh Framework Programme FP7/2007-2013 under grant agreement n 263255 RITD.

Contrasting spatial structures of Atlantic Multidecadal Oscillation between observations and slab ocean model simulations

NASA Astrophysics Data System (ADS)

Sun, Cheng; Li, Jianping; Kucharski, Fred; Xue, Jiaqing; Li, Xiang

2018-04-01

The spatial structure of Atlantic multidecadal oscillation (AMO) is analyzed and compared between the observations and simulations from slab ocean models (SOMs) and fully coupled models. The observed sea surface temperature (SST) pattern of AMO is characterized by a basin-wide monopole structure, and there is a significantly high degree of spatial coherence of decadal SST variations across the entire North Atlantic basin. The observed SST anomalies share a common decadal-scale signal, corresponding to the basin-wide average (i. e., the AMO). In contrast, the simulated AMO in SOMs (AMOs) exhibits a tripole-like structure, with the mid-latitude North Atlantic SST showing an inverse relationship with other parts of the basin, and the SOMs fail to reproduce the observed strong spatial coherence of decadal SST variations associated with the AMO. The observed spatial coherence of AMO SST anomalies is identified as a key feature that can be used to distinguish the AMO mechanism. The tripole-like SST pattern of AMOs in SOMs can be largely explained by the atmosphere-forced thermodynamics mechanism due to the surface heat flux changes associated with the North Atlantic Oscillation (NAO). The thermodynamic forcing of AMOs by the NAO gives rise to a simultaneous inverse NAO-AMOs relationship at both interannual and decadal timescales and a seasonal phase locking of the AMOs variability to the cold season. However, the NAO-forced thermodynamics mechanism cannot explain the observed NAO-AMO relationship and the seasonal phase locking of observed AMO variability to the warm season. At decadal timescales, a strong lagged relationship between NAO and AMO is observed, with the NAO leading by up to two decades, while the simultaneous correlation of NAO with AMO is weak. This lagged relationship and the spatial coherence of AMO can be well understood from the view point of ocean dynamics. A time-integrated NAO index, which reflects the variations in Atlantic meridional overturning circulation (AMOC) and northward ocean heat transport caused by the accumulated effect of NAO forcing, reasonably well captures the observed multidecadal fluctuations in the AMO. Further analysis using the fully coupled model simulations provides direct modeling evidence that the observed spatial coherence of decadal SST variations across North Atlantic basin can be reproduced only by including the AMOC-related ocean dynamics, and the AMOC acts as a common forcing signal that results in a spatially coherent variation of North Atlantic SST.

Modular and hierarchical structure of social contact networks

NASA Astrophysics Data System (ADS)

Ge, Yuanzheng; Song, Zhichao; Qiu, Xiaogang; Song, Hongbin; Wang, Yong

2013-10-01

Social contact networks exhibit overlapping qualities of communities, hierarchical structure and spatial-correlated nature. We propose a mixing pattern of modular and growing hierarchical structures to reconstruct social contact networks by using an individual’s geospatial distribution information in the real world. The hierarchical structure of social contact networks is defined based on the spatial distance between individuals, and edges among individuals are added in turn from the modular layer to the highest layer. It is a gradual process to construct the hierarchical structure: from the basic modular model up to the global network. The proposed model not only shows hierarchically increasing degree distribution and large clustering coefficients in communities, but also exhibits spatial clustering features of individual distributions. As an evaluation of the method, we reconstruct a hierarchical contact network based on the investigation data of a university. Transmission experiments of influenza H1N1 are carried out on the generated social contact networks, and results show that the constructed network is efficient to reproduce the dynamic process of an outbreak and evaluate interventions. The reproduced spread process exhibits that the spatial clustering of infection is accordant with the clustering of network topology. Moreover, the effect of individual topological character on the spread of influenza is analyzed, and the experiment results indicate that the spread is limited by individual daily contact patterns and local clustering topology rather than individual degree.

Structural organization of process zones in upland watersheds of central Nevada and its influence on basin connectivity, dynamics, and wet meadow complexes

Treesearch

Jerry R. Miller; Mark L. Lord; Lionel F. Villarroel; Dru Germanoski; Jeanne C. Chambers

2012-01-01

The drainage network within upland watersheds in central Nevada can be subdivided into distinct zones each dominated by a unique set of processes on the basis of valley form, the geological materials that comprise the valley floor, and the presence or absence of surficial channels. On hillslopes, the type and structure (frequency, length, and spatial arrangement) of...

Global Rice Watch: Spatial-temporal dynamics, driving factors, and impacts of paddy rice agriculture in the world

NASA Astrophysics Data System (ADS)

Xiao, X.; Dong, J.; Zhang, G.; Xin, F.; Li, X.

2017-12-01

Paddy rice croplands account for more than 12% of the global cropland areas, and provide food to feed more than 50% of the world population. Spatial patterns and temporal dynamics of paddy rice croplands have changed remarkably in the past decades, driven by growing human population and their changing diet structure, land use (e.g., urbanization, industrialization), climate, markets, and technologies. In this presentation, we will provide a comprehensive review of our current knowledge on (1) the spatial patterns and temporal dynamics of paddy rice croplands from agricultural statistics data and remote sensing approaches; (2) major driving factors for the observed changes in paddy rice areas, including social, economic, climate, land use, markets, crop breeding technology, and farming technology; and (3) major impacts on atmospheric methane concentration, land surface temperature, water resources and use, and so on. We will highlight the results from a few case studies in China and monsoon Asia. We will also call for a global synthesis analysis of paddy rice agriculture, and invite researchers to join the effort to write and edit a book that provides comprehensive and updated knowledge on paddy rice agriculture.

Semiclassical dynamics of spin density waves

NASA Astrophysics Data System (ADS)

Chern, Gia-Wei; Barros, Kipton; Wang, Zhentao; Suwa, Hidemaro; Batista, Cristian D.

2018-01-01

We present a theoretical framework for equilibrium and nonequilibrium dynamical simulation of quantum states with spin-density-wave (SDW) order. Within a semiclassical adiabatic approximation that retains electron degrees of freedom, we demonstrate that the SDW order parameter obeys a generalized Landau-Lifshitz equation. With the aid of an enhanced kernel polynomial method, our linear-scaling quantum Landau-Lifshitz dynamics (QLLD) method enables dynamical SDW simulations with N ≃105 lattice sites. Our real-space formulation can be used to compute dynamical responses, such as the dynamical structure factor, of complex and even inhomogeneous SDW configurations at zero or finite temperatures. Applying the QLLD to study the relaxation of a noncoplanar topological SDW under the excitation of a short pulse, we further demonstrate the crucial role of spatial correlations and fluctuations in the SDW dynamics.

Deconstruction of spatial integrity in visual stimulus detected by modulation of synchronized activity in cat visual cortex.

PubMed

Zhou, Zhiyi; Bernard, Melanie R; Bonds, A B

2008-04-02

Spatiotemporal relationships among contour segments can influence synchronization of neural responses in the primary visual cortex. We performed a systematic study to dissociate the impact of spatial and temporal factors in the signaling of contour integration via synchrony. In addition, we characterized the temporal evolution of this process to clarify potential underlying mechanisms. With a 10 x 10 microelectrode array, we recorded the simultaneous activity of multiple cells in the cat primary visual cortex while stimulating with drifting sine-wave gratings. We preserved temporal integrity and systematically degraded spatial integrity of the sine-wave gratings by adding spatial noise. Neural synchronization was analyzed in the time and frequency domains by conducting cross-correlation and coherence analyses. The general association between neural spike trains depends strongly on spatial integrity, with coherence in the gamma band (35-70 Hz) showing greater sensitivity to the change of spatial structure than other frequency bands. Analysis of the temporal dynamics of synchronization in both time and frequency domains suggests that spike timing synchronization is triggered nearly instantaneously by coherent structure in the stimuli, whereas frequency-specific oscillatory components develop more slowly, presumably through network interactions. Our results suggest that, whereas temporal integrity is required for the generation of synchrony, spatial integrity is critical in triggering subsequent gamma band synchronization.

Modeling oscillations and spiral waves in Dictyostelium populations

NASA Astrophysics Data System (ADS)

Noorbakhsh, Javad; Schwab, David J.; Sgro, Allyson E.; Gregor, Thomas; Mehta, Pankaj

2015-06-01

Unicellular organisms exhibit elaborate collective behaviors in response to environmental cues. These behaviors are controlled by complex biochemical networks within individual cells and coordinated through cell-to-cell communication. Describing these behaviors requires new mathematical models that can bridge scales—from biochemical networks within individual cells to spatially structured cellular populations. Here we present a family of "multiscale" models for the emergence of spiral waves in the social amoeba Dictyostelium discoideum. Our models exploit new experimental advances that allow for the direct measurement and manipulation of the small signaling molecule cyclic adenosine monophosphate (cAMP) used by Dictyostelium cells to coordinate behavior in cellular populations. Inspired by recent experiments, we model the Dictyostelium signaling network as an excitable system coupled to various preprocessing modules. We use this family of models to study spatially unstructured populations of "fixed" cells by constructing phase diagrams that relate the properties of population-level oscillations to parameters in the underlying biochemical network. We then briefly discuss an extension of our model that includes spatial structure and show how this naturally gives rise to spiral waves. Our models exhibit a wide range of novel phenomena. including a density-dependent frequency change, bistability, and dynamic death due to slow cAMP dynamics. Our modeling approach provides a powerful tool for bridging scales in modeling of Dictyostelium populations.

Space, time, and host evolution facilitate coexistence of competing bacteriophages: theory and experiment.

PubMed

Coberly, L Caitlin; Wei, Wei; Sampson, Koffi Y; Millstein, Jack; Wichman, Holly A; Krone, Stephen M

2009-04-01

We present a joint experimental/theoretical investigation into the roles of spatial structure and time in the competition between two pathogens for a single host. We suggest a natural mechanism by which competing pathogens can coexist when host evolution and competitive dynamics occur on similar timescales. Our experimental system consisted of a single bacterial host species and two competing bacteriophage strains grown on agar plates, with a serial transfer of samples of the bacteriophage population to fresh host populations after each incubation cycle. The experiments included two incubation times and two transfer protocols that either maintained or disrupted the spatial structure of the viruses at each transfer. The same bacteriophage acted as the dominant competitor under both transfer protocols. A striking difference between the treatments is that the weak competitor was able to persist in the long-incubation experiments but not in the short-incubation experiments. Mathematical and experimental evidence suggest that coexistence is due to the appearance of resistant mutant host cells that provide a transient "spatiotemporal refuge" for the weaker competitor. Our mathematical model is individual based, captures the stochastic spatial dynamics down to the level of individual cells, and helps to explain the differences in behavior under the various experimental conditions.

Molecular dynamics simulations of viral RNA polymerases link conserved and correlated motions of functional elements to fidelity

PubMed Central

Moustafa, Ibrahim M.; Shen, Hujun; Morton, Brandon; Colina, Coray M.; Cameron, Craig E.

2011-01-01

The viral RNA-dependent RNA polymerase (RdRp) is essential for multiplication of all RNA viruses. The sequence diversity of an RNA virus population contributes to its ability to infect the host. This diversity emanates from errors made by the RdRp during RNA synthesis. The physical basis for RdRp fidelity is unclear but is linked to conformational changes occurring during the nucleotide-addition cycle. To understand RdRp dynamics that might influence RdRp function, we have analyzed all-atom molecular dynamics (MD) simulations on the nanosecond timescale of four RdRps from the picornavirus family that exhibit 30–74% sequence identity. Principal component analysis showed that the major motions observed during the simulations derived from conserved structural motifs and regions of known function. Dynamics of residues participating in the same biochemical property, for example RNA binding, nucleotide binding or catalysis, were correlated even when spatially distant on the RdRp structure. The conserved and correlated dynamics of functional, structural elements suggest co-evolution of dynamics with structure and function of the RdRp. Crystal structures of all picornavirus RdRps exhibit a template-nascent RNA duplex channel too small to fully accommodate duplex RNA. Simulations revealed opening and closing motions of the RNA and NTP channels, which might be relevant to NTP entry, PPi exit and translocation. A role for nanosecond timescale dynamics in RdRp fidelity is supported by altered dynamics of the high-fidelity G64S derivative of PV RdRp relative to wild-type enzyme. PMID:21575642

Nucleon Structure from 2+1 Flavor Domain Wall QCD at Nearly Physical Pion Mass

NASA Astrophysics Data System (ADS)

Ohta, Shigemi

2011-05-01

The RBC and UKQCD collaborations have been investigating hadron physics in numerical lattice quantum chromodynamics (QCD) with (2+1) flavors of dynamical domain wall fermions (DWF) quarks that preserves continuum-like chiral and flavor symmetries. The strange quark mass is adjusted to physical value via reweighting and degenerate up and down quark masses are set as light as possible. In a recent study of nucleon structure we found a strong dependence on pion mass and lattice spatial extent in isovector axialvector-current form factors. This is likely the first credible evidence for the pion cloud surrounding nucleon. Here we report the status of nucleon structure calculations with a new (2+1)-flavor dynamical DWF ensembles with much lighter pion mass of 180 and 250 MeV and a much larger lattice spatial exent of 4.6 fm. A combination of the Iwasaki and dislocation-suppressing-determinant-ratio (I+DSDR) gauge action and DWF fermion action allows us to generate these ensembles at cutoff of about 1.4 GeV while keeping the residual breaking of chiral symmetry sufficiently small. Nucleon source Gaussian smearing has been optimized. Preliminary nucleon mass estimates are 0.98 and 1.05 GeV.

Spatial Organization Plasticity as an Adaptive Driver of Surface Microbial Communities

PubMed Central

Bridier, Arnaud; Piard, Jean-Christophe; Pandin, Caroline; Labarthe, Simon; Dubois-Brissonnet, Florence; Briandet, Romain

2017-01-01

Biofilms are dynamic habitats which constantly evolve in response to environmental fluctuations and thereby constitute remarkable survival strategies for microorganisms. The modulation of biofilm functional properties is largely governed by the active remodeling of their three-dimensional structure and involves an arsenal of microbial self-produced components and interconnected mechanisms. The production of matrix components, the spatial reorganization of ecological interactions, the generation of physiological heterogeneity, the regulation of motility, the production of actives enzymes are for instance some of the processes enabling such spatial organization plasticity. In this contribution, we discussed the foundations of architectural plasticity as an adaptive driver of biofilms through the review of the different microbial strategies involved. Moreover, the possibility to harness such characteristics to sculpt biofilm structure as an attractive approach to control their functional properties, whether beneficial or deleterious, is also discussed. PMID:28775718

Mapping and modeling the urban landscape in Bangkok, Thailand: Physical-spectral-spatial relations of population-environmental interactions

NASA Astrophysics Data System (ADS)

Shao, Yang

This research focuses on the application of remote sensing, geographic information systems, statistical modeling, and spatial analysis to examine the dynamics of urban land cover, urban structure, and population-environment interactions in Bangkok, Thailand, with an emphasis on rural-to-urban migration from rural Nang Rong District, Northeast Thailand to the primate city of Bangkok. The dissertation consists of four main sections: (1) development of remote sensing image classification and change-detection methods for characterizing imperviousness for Bangkok, Thailand from 1993-2002; (2) development of 3-D urban mapping methods, using high spatial resolution IKONOS satellite images, to assess high-rises and other urban structures; (3) assessment of urban spatial structure from 2-D and 3-D perspectives; and (4) an analysis of the spatial clustering of migrants from Nang Rong District in Bangkok and the neighborhood environments of migrants' locations. Techniques are developed to improve the accuracy of the neural network classification approach for the analysis of remote sensing data, with an emphasis on the spectral unmixing problem. The 3-D building heights are derived using the shadow information on the high-resolution IKONOS image. The results from the 2-D and 3-D mapping are further examined to assess urban structure and urban feature identification. This research contributes to image processing of remotely-sensed images and urban studies. The rural-urban migration process and migrants' settlement patterns are examined using spatial statistics, GIS, and remote sensing perspectives. The results show that migrants' spatial clustering in urban space is associated with the source village and a number of socio-demographic variables. In addition, the migrants' neighborhood environments in urban setting are modeled using a set of geographic and socio-demographic variables, and the results are scale-dependent.

Spatial patterns of native freshwater mussels in the Upper Mississippi River

USGS Publications Warehouse

Ries, Patricia R.; DeJager, Nathan R.; Zigler, Steven J.; Newton, Teresa

2016-01-01

Multiple physical and biological factors structure freshwater mussel communities in large rivers, and their distributions have been described as clumped or patchy. However, few surveys of mussel populations have been conducted over areas large enough and at resolutions fine enough to quantify spatial patterns in their distribution. We used global and local indicators of spatial autocorrelation (i.e., Moran’s I) to quantify spatial patterns of adult and juvenile (≤5 y of age) freshwater mussels across multiple scales based on survey data from 4 reaches (navigation pools 3, 5, 6, and 18) of the Upper Mississippi River, USA. Native mussel densities were sampled at a resolution of ∼300 m and across distances ranging from 21 to 37 km, making these some of the most spatially extensive surveys conducted in a large river. Patch density and the degree and scale of patchiness varied by river reach, age group, and the scale of analysis. In all 4 pools, some patches of adults overlapped patches of juveniles, suggesting spatial and temporal persistence of adequate habitat. In pools 3 and 5, patches of juveniles were found where there were few adults, suggesting recent emergence of positive structuring mechanisms. Last, in pools 3, 5, and 6, some patches of adults were found where there were few juveniles, suggesting that negative structuring mechanisms may have replaced positive ones, leading to a lack of localized recruitment. Our results suggest that: 1) the detection of patches of freshwater mussels requires a multiscaled approach, 2) insights into the spatial and temporal dynamics of structuring mechanisms can be gained by conducting independent analyses of adults and juveniles, and 3) maps of patch distributions can be used to guide restoration and management actions and identify areas where mussels are most likely to influence ecosystem function.

Exceptional-point Dynamics in Photonic Honeycomb Lattices with PT Symmetry

DTIC Science & Technology

2012-01-17

coherent perfect laser absorber [25], spatial optical switches [26], and nonlinear switching structures [27]. Despite the wealth of results on...Petermann, IEEE J. Quantum Electron. 15, 566 (1979); A. E. Siegman , Phys. Rev. A 39, 1264 (1989). [36] M. V. Berry, J. Mod. Opt. 50, 63 (2003); S.-Y

Considerations for achieving cross-platform point cloud data fusion across different dryland ecosystem structural states

USDA-ARS?s Scientific Manuscript database

Dryland ecosystems undergo long periods of senescence punctuated by rapid growth following seasonal precipitation events. Remote sensing of vegetation dynamics which capture new growth as well as herbivory and disturbance require both high spatial and temporal resolution data acquired by various op...

Spatial-area selective retrieval of multiple object-place associations in a hierarchical cognitive map formed by theta phase coding.

PubMed

Sato, Naoyuki; Yamaguchi, Yoko

2009-06-01

The human cognitive map is known to be hierarchically organized consisting of a set of perceptually clustered landmarks. Patient studies have demonstrated that these cognitive maps are maintained by the hippocampus, while the neural dynamics are still poorly understood. The authors have shown that the neural dynamic "theta phase precession" observed in the rodent hippocampus may be capable of forming hierarchical cognitive maps in humans. In the model, a visual input sequence consisting of object and scene features in the central and peripheral visual fields, respectively, results in the formation of a hierarchical cognitive map for object-place associations. Surprisingly, it is possible for such a complex memory structure to be formed in a few seconds. In this paper, we evaluate the memory retrieval of object-place associations in the hierarchical network formed by theta phase precession. The results show that multiple object-place associations can be retrieved with the initial cue of a scene input. Importantly, according to the wide-to-narrow unidirectional connections among scene units, the spatial area for object-place retrieval can be controlled by the spatial area of the initial cue input. These results indicate that the hierarchical cognitive maps have computational advantages on a spatial-area selective retrieval of multiple object-place associations. Theta phase precession dynamics is suggested as a fundamental neural mechanism of the human cognitive map.

Spatial and temporal distribution of the vibrionaceae in coastal waters of Hawaii, Australia, and France.

PubMed

Jones, B W; Maruyama, A; Ouverney, C C; Nishiguchi, M K

2007-08-01

Relatively little is known about large-scale spatial and temporal fluctuations in bacterioplankton, especially within the bacterial families. In general, however, a number of abiotic factors (namely, nutrients and temperature) appear to influence distribution. Community dynamics within the Vibrionaceae are of particular interest to biologists because this family contains a number of important pathogenic, commensal, and mutualist species. Of special interest to this study is the mutualism between sepiolid squids and Vibrio fischeri and Vibrio logei, where host squids seed surrounding waters daily with their bacterial partners. This study seeks to examine the spatial and temporal distribution of the Vibrionaceae with respect to V. fischeri and V. logei in Hawaii, southeastern Australia, and southern France sampling sites. In particular, we examine how the presence of sepiolid squid hosts influences community population structure within the Vibrionaceae. We found that abiotic (temperature) and biotic (host distribution) factors both influence population dynamics. In Hawaii, three sites within squid host habitat contained communities of Vibrionaceae with higher proportions of V. fischeri. In Australia, V. fischeri numbers at host collection sites were greater than other populations; however, there were no spatial or temporal patterns seen at other sample sites. In France, host presence did not appear to influence Vibrio communities, although sampled populations were significantly greater in the winter than summer sampling periods. Results of this study demonstrate the importance of understanding how both abiotic and biotic factors interact to influence bacterial community structure within the Vibrionaceae.

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.

Dynamics of a neural system with a multiscale architecture

PubMed Central

Breakspear, Michael; Stam, Cornelis J

2005-01-01

The architecture of the brain is characterized by a modular organization repeated across a hierarchy of spatial scales—neurons, minicolumns, cortical columns, functional brain regions, and so on. It is important to consider that the processes governing neural dynamics at any given scale are not only determined by the behaviour of other neural structures at that scale, but also by the emergent behaviour of smaller scales, and the constraining influence of activity at larger scales. In this paper, we introduce a theoretical framework for neural systems in which the dynamics are nested within a multiscale architecture. In essence, the dynamics at each scale are determined by a coupled ensemble of nonlinear oscillators, which embody the principle scale-specific neurobiological processes. The dynamics at larger scales are ‘slaved’ to the emergent behaviour of smaller scales through a coupling function that depends on a multiscale wavelet decomposition. The approach is first explicated mathematically. Numerical examples are then given to illustrate phenomena such as between-scale bifurcations, and how synchronization in small-scale structures influences the dynamics in larger structures in an intuitive manner that cannot be captured by existing modelling approaches. A framework for relating the dynamical behaviour of the system to measured observables is presented and further extensions to capture wave phenomena and mode coupling are suggested. PMID:16087448

Environment and Spatial Influences on Aquatic Insect Communities in Cerrado Streams: the Relative Importance of Conductivity, Altitude, and Conservation Areas.

PubMed

Godoy, B S; Queiroz, L L; Lodi, S; Oliveira, L G

2017-04-01

The aquatic insect community is an important element for stream functionality and diversity, but the effects of altitude and conservation areas on the aquatic insect community have been poorly explored in neotropical ecozone. The lack of studies about the relative importance of space and environment on community structure is another obstacle within aquatic insect ecology, which precludes the inclusion of these studies in more current frameworks, like the metacommunity dynamics. We evaluated the relationship between the aquatic insect community structure at 19 streams in the Brazilian Cerrado and spatial and environmental variables, namely geographical distance among sites, stream altitude, chemical variables, and environmental protection areas. We partitioned the variance explained by spatial and environmental components using a partial redundancy analysis. The environment exhibited a strong spatial structure for abundance and number of genera, increasing these community parameters with elevated water conductivity. Only community composition had a large unexplained portion of variance, with a small portion constrained by environmental (altitude and conductivity) and spatial factors. A relevant point in the result was the streams with high conductivity were located outside of the conservation areas. These results suggest that the relationship between number of genera and abundance with environmental conditions is always associated with spatial configuration of streams. Our study shows that altitude is an important determinant of community structure, as it exerts indirect influences, and electrical conductivity directly determines community composition, and that some national parks may be inefficient in maintaining the diversity of aquatic insects in the Cerrado region.

Temporal-spatial distribution of American bison (Bison bison) in a tallgrass prairie fire mosaic

USGS Publications Warehouse

Schuler, K.L.; Leslie, David M.; Shaw, J.H.; Maichak, E.J.

2006-01-01

Fire and bison (Bison bison) are thought to be historically responsible for shaping prairie vegetation in North America. Interactions between temporal-spatial distributions of bison and prescribed burning protocols are important in current restoration of tallgrass prairies. We examined dynamics of bison distribution in a patch-burned tallgrass prairie in the south-central United States relative to bison group size and composition, and burn age and temporal distribution. Bison formed larger mixed groups during summer and smaller sexually segregated groups the rest of the year, and bison selected dormant-season burn patches in the 1st posture growing season most often during spring and summer. Large bison herds selecting recently burned areas resulted in seasonally variable and concentrated grazing pressure that may substantially alter site-specific vegetation. These dynamics must be considered when reintroducing bison and fire into tallgrass prairie because variable outcomes of floral richness and structural complexity are likely depending on temporal-spatial distribution of bison. ?? 2006 American Society of Mammalogists.

Resting-State Functional Connectivity Emerges from Structurally and Dynamically Shaped Slow Linear Fluctuations

PubMed Central

Deco, Gustavo; Mantini, Dante; Romani, Gian Luca; Hagmann, Patric; Corbetta, Maurizio

2013-01-01

Brain fluctuations at rest are not random but are structured in spatial patterns of correlated activity across different brain areas. The question of how resting-state functional connectivity (FC) emerges from the brain's anatomical connections has motivated several experimental and computational studies to understand structure–function relationships. However, the mechanistic origin of resting state is obscured by large-scale models' complexity, and a close structure–function relation is still an open problem. Thus, a realistic but simple enough description of relevant brain dynamics is needed. Here, we derived a dynamic mean field model that consistently summarizes the realistic dynamics of a detailed spiking and conductance-based synaptic large-scale network, in which connectivity is constrained by diffusion imaging data from human subjects. The dynamic mean field approximates the ensemble dynamics, whose temporal evolution is dominated by the longest time scale of the system. With this reduction, we demonstrated that FC emerges as structured linear fluctuations around a stable low firing activity state close to destabilization. Moreover, the model can be further and crucially simplified into a set of motion equations for statistical moments, providing a direct analytical link between anatomical structure, neural network dynamics, and FC. Our study suggests that FC arises from noise propagation and dynamical slowing down of fluctuations in an anatomically constrained dynamical system. Altogether, the reduction from spiking models to statistical moments presented here provides a new framework to explicitly understand the building up of FC through neuronal dynamics underpinned by anatomical connections and to drive hypotheses in task-evoked studies and for clinical applications. PMID:23825427

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

Middleton, L. Robert; Tarver, Jacob D.; Cordaro, Joseph

Melt state dynamics for a series of strictly linear polyethylenes with precisely spaced associating functional groups were investigated. The periodic pendant acrylic acid groups form hydrogen-bonded acid aggregates within the polyethylene (PE) matrix. The dynamics of these nanoscale heterogeneous morphologies were investigated from picosecond to nanosecond timescales by both quasi-elastic neutron scattering (QENS) measurements and fully atomistic molecular dynamics (MD) simulations. Two dynamic processes were observed. The faster dynamic processes which occur at the picosecond timescales are compositionally insensitive and indicative of spatially restricted local motions. The slower dynamic processes are highly composition dependent and indicate the structural relaxation ofmore » the polymer backbone. Higher acid contents, or shorter PE spacers between pendant acid groups, slow the structural relaxation timescale and increase the stretching parameter (β) of the structural relaxation. Additionally, the dynamics of specific hydrogen atom positions along the backbone correlate structural heterogeneity imposed by the associating acid groups with a mobility gradient along the polymer backbone. At time intervals (<2 ns), the mean-squared displacements for the four methylene groups closest to the acid groups are up to 10 times smaller than those of methylene groups further from the acid groups. At longer timescales acid aggregates rearrange and the chain dynamics of the slow, near-aggregate regions and the faster bridge regions converge, implying a characteristic timescale for the passage of chains between aggregates. As a result, the characterization of the nanoscale chain dynamics in these associating polymer systems both provides validation of simulation force fields and provides understanding of heterogeneous chain dynamics in associating polymers.« less

The unifying role of dissipative action in the dynamic failure of solids

DOE PAGES

Grady, Dennis

2015-05-19

Dissipative action, the product of dissipation energy and transport time, is fundamental to the dynamic failure of solids. Invariance of the dissipative action underlies the fourth-power nature of structured shock waves observed in selected solid metals and compounds. Dynamic failure through shock compaction, tensile spall and adiabatic shear are also governed by a constancy of the dissipative action. This commonality underlying the various modes of dynamic failure is described and leads to deeper insights into failure of solids in the intense shock wave event. These insights are in turn leading to a better understanding of the shock deformation processes underlyingmore » the fourth-power law. Experimental result and material models encompassing the dynamic failure of solids are explored for the purpose of demonstrating commonalities leading to invariance of the dissipation action. As a result, calculations are extended to aluminum and uranium metals with the intent of predicting micro-scale energetics and spatial scales in the structured shock wave.« less

Quantitative, depth-resolved determination of particle motion using multi-exposure, spatial frequency domain laser speckle imaging.

PubMed

Rice, Tyler B; Kwan, Elliott; Hayakawa, Carole K; Durkin, Anthony J; Choi, Bernard; Tromberg, Bruce J

2013-01-01

Laser Speckle Imaging (LSI) is a simple, noninvasive technique for rapid imaging of particle motion in scattering media such as biological tissue. LSI is generally used to derive a qualitative index of relative blood flow due to unknown impact from several variables that affect speckle contrast. These variables may include optical absorption and scattering coefficients, multi-layer dynamics including static, non-ergodic regions, and systematic effects such as laser coherence length. In order to account for these effects and move toward quantitative, depth-resolved LSI, we have developed a method that combines Monte Carlo modeling, multi-exposure speckle imaging (MESI), spatial frequency domain imaging (SFDI), and careful instrument calibration. Monte Carlo models were used to generate total and layer-specific fractional momentum transfer distributions. This information was used to predict speckle contrast as a function of exposure time, spatial frequency, layer thickness, and layer dynamics. To verify with experimental data, controlled phantom experiments with characteristic tissue optical properties were performed using a structured light speckle imaging system. Three main geometries were explored: 1) diffusive dynamic layer beneath a static layer, 2) static layer beneath a diffuse dynamic layer, and 3) directed flow (tube) submerged in a dynamic scattering layer. Data fits were performed using the Monte Carlo model, which accurately reconstructed the type of particle flow (diffusive or directed) in each layer, the layer thickness, and absolute flow speeds to within 15% or better.

Data Mining of NASA Boeing 737 Flight Data: Frequency Analysis of In-Flight Recorded Data

NASA Technical Reports Server (NTRS)

Butterfield, Ansel J.

2001-01-01

Data recorded during flights of the NASA Trailblazer Boeing 737 have been analyzed to ascertain the presence of aircraft structural responses from various excitations such as the engine, aerodynamic effects, wind gusts, and control system operations. The NASA Trailblazer Boeing 737 was chosen as a focus of the study because of a large quantity of its flight data records. The goal of this study was to determine if any aircraft structural characteristics could be identified from flight data collected for measuring non-structural phenomena. A number of such data were examined for spatial and frequency correlation as a means of discovering hidden knowledge of the dynamic behavior of the aircraft. Data recorded from on-board dynamic sensors over a range of flight conditions showed consistently appearing frequencies. Those frequencies were attributed to aircraft structural vibrations.

On-Line Modal State Monitoring of Slowly Time-Varying Structures

NASA Technical Reports Server (NTRS)

Johnson, Erik A.; Bergman, Lawrence A.; Voulgaris, Petros G.

1997-01-01

Monitoring the dynamic response of structures is often performed for a variety of reasons. These reasons include condition-based maintenance, health monitoring, performance improvements, and control. In many cases the data analysis that is performed is part of a repetitive decision-making process, and in these cases the development of effective on-line monitoring schemes help to speed the decision-making process and reduce the risk of erroneous decisions. This report investigates the use of spatial modal filters for tracking the dynamics of slowly time-varying linear structures. The report includes an overview of modal filter theory followed by an overview of several structural system identification methods. Included in this discussion and comparison are H-infinity, eigensystem realization, and several time-domain least squares approaches. Finally, a two-stage adaptive on-line monitoring scheme is developed and evaluated.

The effect of climatic forcing on population synchrony and genetic structuring of the Canadian lynx

PubMed Central

Stenseth, Nils Chr.; Ehrich, Dorothee; Rueness, Eli Knispel; Lingjærde, Ole Chr.; Chan, Kung-Sik; Boutin, Stan; O'Donoghue, Mark; Robinson, David A.; Viljugrein, Hildegunn; Jakobsen, Kjetill S.

2004-01-01

The abundance of Canadian lynx follows 10-year density fluctuations across the Canadian subcontinent. These cyclic fluctuations have earlier been shown to be geographically structured into three climatic regions: the Atlantic, Continental, and Pacific zones. Recent genetic evidence revealed an essentially similar spatial structuring. Introducing a new population model, the “climate forcing of ecological and evolutionary patterns” model, we link the observed ecological and evolutionary patterns. Specifically, we demonstrate that there is greater phase synchrony within climatic zones than between them and show that external climatic forcing may act as a synchronizer. We simulated genetic drift by using data on population dynamics generated by the climate forcing of ecological and evolutionary patterns model, and we demonstrate that the observed genetic structuring can be seen as an emerging property of the spatiotemporal ecological dynamics. PMID:15067131

The effect of the dynamic wet troposphere on radio interferometric measurements

NASA Technical Reports Server (NTRS)

Treuhaft, R. N.; Lanyi, G. E.

1987-01-01

A statistical model of water vapor fluctuations is used to describe the effect of the dynamic wet troposphere on radio interferometric measurements. It is assumed that the spatial structure of refractivity is approximated by Kolmogorov turbulence theory, and that the temporal fluctuations are caused by spatial patterns moved over a site by the wind, and these assumptions are examined for the VLBI delay and delay rate observables. The results suggest that the delay rate measurement error is usually dominated by water vapor fluctuations, and water vapor induced VLBI parameter errors and correlations are determined as a function of the delay observable errors. A method is proposed for including the water vapor fluctuations in the parameter estimation method to obtain improved parameter estimates and parameter covariances.

Dynamically assisted Schwinger effect beyond the spatially-uniform-field approximation

NASA Astrophysics Data System (ADS)

Aleksandrov, I. A.; Plunien, G.; Shabaev, V. M.

2018-06-01

We investigate the phenomenon of electron-positron pair production from vacuum in the presence of a strong electric field superimposed by a weak but fast varying pulse which substantially increases the total particle yield. We employ a nonperturbative numerical technique and perform the calculations beyond the spatially-uniform-field approximation, i.e., dipole approximation, taking into account the coordinate dependence of the fast component. The analysis of the main characteristics of the pair-production process (momentum spectra of particles and total amount of pairs) reveals a number of important features which are absent within the previously used approximation. In particular, the structure of the momentum distribution is modified both qualitatively and quantitatively, and the total number of pairs created as well as the enhancement factor due to dynamical assistance become significantly smaller.

Regional processes in mangrove ecosystems: Spatial scaling relationships, biomass, and turnover rates following catastrophic disturbance

USGS Publications Warehouse

Ward, G.A.; Smith, T. J.; Whelan, K.R.T.; Doyle, T.W.

2006-01-01

Physiological processes and local-scale structural dynamics of mangroves are relatively well studied. Regional-scale processes, however, are not as well understood. Here we provide long-term data on trends in structure and forest turnover at a large scale, following hurricane damage in mangrove ecosystems of South Florida, U.S.A. Twelve mangrove vegetation plots were monitored at periodic intervals, between October 1992 and March 2005. Mangrove forests of this region are defined by a -1.5 scaling relationship between mean stem diameter and stem density, mirroring self-thinning theory for mono-specific stands. This relationship is reflected in tree size frequency scaling exponents which, through time, have exhibited trends toward a community average that is indicative of full spatial resource utilization. These trends, together with an asymptotic standing biomass accumulation, indicate that coastal mangrove ecosystems do adhere to size-structured organizing principles as described for upland tree communities. Regenerative dynamics are different between areas inside and outside of the primary wind-path of Hurricane Andrew which occurred in 1992. Forest dynamic turnover rates, however, are steady through time. This suggests that ecological, more-so than structural factors, control forest productivity. In agreement, the relative mean rate of biomass growth exhibits an inverse relationship with the seasonal range of porewater salinities. The ecosystem average in forest scaling relationships may provide a useful investigative tool of mangrove community biomass relationships, as well as offer a robust indicator of general ecosystem health for use in mangrove forest ecosystem management and restoration. ?? Springer 2006.

Quantifying stream thermal regimes at management-pertinent scales: combining thermal infrared and stationary stream temperature data in a novel modeling framework.

USGS Publications Warehouse

Vatland, Shane J.; Gresswell, Robert E.; Poole, Geoffrey C.

2015-01-01

Accurately quantifying stream thermal regimes can be challenging because stream temperatures are often spatially and temporally heterogeneous. In this study, we present a novel modeling framework that combines stream temperature data sets that are continuous in either space or time. Specifically, we merged the fine spatial resolution of thermal infrared (TIR) imagery with hourly data from 10 stationary temperature loggers in a 100 km portion of the Big Hole River, MT, USA. This combination allowed us to estimate summer thermal conditions at a relatively fine spatial resolution (every 100 m of stream length) over a large extent of stream (100 km of stream) during during the warmest part of the summer. Rigorous evaluation, including internal validation, external validation with spatially continuous instream temperature measurements collected from a Langrangian frame of reference, and sensitivity analyses, suggests the model was capable of accurately estimating longitudinal patterns in summer stream temperatures for this system Results revealed considerable spatial and temporal heterogeneity in summer stream temperatures and highlighted the value of assessing thermal regimes at relatively fine spatial and temporal scales. Preserving spatial and temporal variability and structure in abiotic stream data provides a critical foundation for understanding the dynamic, multiscale habitat needs of mobile stream organisms. Similarly, enhanced understanding of spatial and temporal variation in dynamic water quality attributes, including temporal sequence and spatial arrangement, can guide strategic placement of monitoring equipment that will subsequently capture variation in environmental conditions directly pertinent to research and management objectives.

The walk is never random: subtle landscape effects shape gene flow in a continuous white-tailed deer population in the Midwestern United States

USGS Publications Warehouse

Robinson, Stacie J.; Samuel, Michael D.; Lopez, Davin L.; Shelton, Paul

2012-01-01

One of the pervasive challenges in landscape genetics is detecting gene flow patterns within continuous populations of highly mobile wildlife. Understanding population genetic structure within a continuous population can give insights into social structure, movement across the landscape and contact between populations, which influence ecological interactions, reproductive dynamics or pathogen transmission. We investigated the genetic structure of a large population of deer spanning the area of Wisconsin and Illinois, USA, affected by chronic wasting disease. We combined multiscale investigation, landscape genetic techniques and spatial statistical modelling to address the complex questions of landscape factors influencing population structure. We sampled over 2000 deer and used spatial autocorrelation and a spatial principal components analysis to describe the population genetic structure. We evaluated landscape effects on this pattern using a spatial autoregressive model within a model selection framework to test alternative hypotheses about gene flow. We found high levels of genetic connectivity, with gradients of variation across the large continuous population of white-tailed deer. At the fine scale, spatial clustering of related animals was correlated with the amount and arrangement of forested habitat. At the broader scale, impediments to dispersal were important to shaping genetic connectivity within the population. We found significant barrier effects of individual state and interstate highways and rivers. Our results offer an important understanding of deer biology and movement that will help inform the management of this species in an area where overabundance and disease spread are primary concerns.

Dynamic mode decomposition for plasma diagnostics and validation.

PubMed

Taylor, Roy; Kutz, J Nathan; Morgan, Kyle; Nelson, Brian A

2018-05-01

We demonstrate the application of the Dynamic Mode Decomposition (DMD) for the diagnostic analysis of the nonlinear dynamics of a magnetized plasma in resistive magnetohydrodynamics. The DMD method is an ideal spatio-temporal matrix decomposition that correlates spatial features of computational or experimental data while simultaneously associating the spatial activity with periodic temporal behavior. DMD can produce low-rank, reduced order surrogate models that can be used to reconstruct the state of the system with high fidelity. This allows for a reduction in the computational cost and, at the same time, accurate approximations of the problem, even if the data are sparsely sampled. We demonstrate the use of the method on both numerical and experimental data, showing that it is a successful mathematical architecture for characterizing the helicity injected torus with steady inductive (HIT-SI) magnetohydrodynamics. Importantly, the DMD produces interpretable, dominant mode structures, including a stationary mode consistent with our understanding of a HIT-SI spheromak accompanied by a pair of injector-driven modes. In combination, the 3-mode DMD model produces excellent dynamic reconstructions across the domain of analyzed data.

Dynamic mode decomposition for plasma diagnostics and validation

NASA Astrophysics Data System (ADS)

Taylor, Roy; Kutz, J. Nathan; Morgan, Kyle; Nelson, Brian A.

2018-05-01

We demonstrate the application of the Dynamic Mode Decomposition (DMD) for the diagnostic analysis of the nonlinear dynamics of a magnetized plasma in resistive magnetohydrodynamics. The DMD method is an ideal spatio-temporal matrix decomposition that correlates spatial features of computational or experimental data while simultaneously associating the spatial activity with periodic temporal behavior. DMD can produce low-rank, reduced order surrogate models that can be used to reconstruct the state of the system with high fidelity. This allows for a reduction in the computational cost and, at the same time, accurate approximations of the problem, even if the data are sparsely sampled. We demonstrate the use of the method on both numerical and experimental data, showing that it is a successful mathematical architecture for characterizing the helicity injected torus with steady inductive (HIT-SI) magnetohydrodynamics. Importantly, the DMD produces interpretable, dominant mode structures, including a stationary mode consistent with our understanding of a HIT-SI spheromak accompanied by a pair of injector-driven modes. In combination, the 3-mode DMD model produces excellent dynamic reconstructions across the domain of analyzed data.

Failure and recovery in dynamical networks.

PubMed

Böttcher, L; Luković, M; Nagler, J; Havlin, S; Herrmann, H J

2017-02-03

Failure, damage spread and recovery crucially underlie many spatially embedded networked systems ranging from transportation structures to the human body. Here we study the interplay between spontaneous damage, induced failure and recovery in both embedded and non-embedded networks. In our model the network's components follow three realistic processes that capture these features: (i) spontaneous failure of a component independent of the neighborhood (internal failure), (ii) failure induced by failed neighboring nodes (external failure) and (iii) spontaneous recovery of a component. We identify a metastable domain in the global network phase diagram spanned by the model's control parameters where dramatic hysteresis effects and random switching between two coexisting states are observed. This dynamics depends on the characteristic link length of the embedded system. For the Euclidean lattice in particular, hysteresis and switching only occur in an extremely narrow region of the parameter space compared to random networks. We develop a unifying theory which links the dynamics of our model to contact processes. Our unifying framework may help to better understand controllability in spatially embedded and random networks where spontaneous recovery of components can mitigate spontaneous failure and damage spread in dynamical networks.

Community ecology in 3D: Tensor decomposition reveals spatio-temporal dynamics of large ecological communities

PubMed Central

Lindegren, Martin; Denker, Tim Spaanheden; Floeter, Jens; Fock, Heino O.; Sguotti, Camilla; Stäbler, Moritz; Otto, Saskia A.; Möllmann, Christian

2017-01-01

Understanding spatio-temporal dynamics of biotic communities containing large numbers of species is crucial to guide ecosystem management and conservation efforts. However, traditional approaches usually focus on studying community dynamics either in space or in time, often failing to fully account for interlinked spatio-temporal changes. In this study, we demonstrate and promote the use of tensor decomposition for disentangling spatio-temporal community dynamics in long-term monitoring data. Tensor decomposition builds on traditional multivariate statistics (e.g. Principal Component Analysis) but extends it to multiple dimensions. This extension allows for the synchronized study of multiple ecological variables measured repeatedly in time and space. We applied this comprehensive approach to explore the spatio-temporal dynamics of 65 demersal fish species in the North Sea, a marine ecosystem strongly altered by human activities and climate change. Our case study demonstrates how tensor decomposition can successfully (i) characterize the main spatio-temporal patterns and trends in species abundances, (ii) identify sub-communities of species that share similar spatial distribution and temporal dynamics, and (iii) reveal external drivers of change. Our results revealed a strong spatial structure in fish assemblages persistent over time and linked to differences in depth, primary production and seasonality. Furthermore, we simultaneously characterized important temporal distribution changes related to the low frequency temperature variability inherent in the Atlantic Multidecadal Oscillation. Finally, we identified six major sub-communities composed of species sharing similar spatial distribution patterns and temporal dynamics. Our case study demonstrates the application and benefits of using tensor decomposition for studying complex community data sets usually derived from large-scale monitoring programs. PMID:29136658

On the evolution of specialization with a mechanistic underpinning in structured metapopulations.

PubMed

Nurmi, Tuomas; Parvinen, Kalle

2008-03-01

We analyze the evolution of specialization in resource utilization in a discrete-time metapopulation model using the adaptive dynamics approach. The local dynamics in the metapopulation are based on the Beverton-Holt model with mechanistic underpinnings. The consumer faces a trade-off in the abilities to consume two resources that are spatially heterogeneously distributed to patches that are prone to local catastrophes. We explore the factors favoring the spread of generalist or specialist strategies. Increasing fecundity or decreasing catastrophe probability favors the spread of the generalist strategy and increasing environmental heterogeneity enlarges the parameter domain where the evolutionary branching is possible. When there are no catastrophes, increasing emigration diminishes the parameter domain where the evolutionary branching may occur. Otherwise, the effect of emigration on evolutionary dynamics is non-monotonous: both small and large values of emigration probability favor the spread of the specialist strategies whereas the parameter domain where evolutionary branching may occur is largest when the emigration probability has intermediate values. We compare how different forms of spatial heterogeneity and different models of local growth affect the evolutionary dynamics. We show that even small changes in the resource dynamics may have outstanding evolutionary effects to the consumers.

Surface and finite size effect on fluctuations dynamics in nanoparticles with long-range order

NASA Astrophysics Data System (ADS)

Morozovska, A. N.; Eliseev, E. A.

2010-02-01

The influence of surface and finite size on the dynamics of the order parameter fluctuations and critical phenomena in the three-dimensional (3D)-confined systems with long-range order was not considered theoretically. In this paper, we study the influence of surface and finite size on the dynamics of the order parameter fluctuations in the particles of arbitrary shape. We consider concrete examples of the spherical and cylindrical ferroic nanoparticles within Landau-Ginzburg-Devonshire phenomenological approach. Allowing for the strong surface energy contribution in micro and nanoparticles, the analytical expressions derived for the Ornstein-Zernike correlator of the long-range order parameter spatial-temporal fluctuations, dynamic generalized susceptibility, relaxation times, and correlation radii discrete spectra are different from those known for bulk systems. Obtained analytical expressions for the correlation function of the order parameter spatial-temporal fluctuations in micro and nanosized systems can be useful for the quantitative analysis of the dynamical structural factors determined from magnetic resonance diffraction and scattering spectra. Besides the practical importance of the correlation function for the analysis of the experimental data, derived expressions for the fluctuations strength determine the fundamental limits of phenomenological theories applicability for 3D-confined systems.

Temporal and spatial constraints on community assembly during microbial colonization of wood in seawater.

PubMed

Kalenitchenko, Dimitri; Fagervold, Sonja K; Pruski, Audrey M; Vétion, Gilles; Yücel, Mustafa; Le Bris, Nadine; Galand, Pierre E

2015-12-01

Wood falls on the ocean floor form chemosynthetic ecosystems that remain poorly studied compared with features such as hydrothermal vents or whale falls. In particular, the microbes forming the base of this unique ecosystem are not well characterized and the ecology of communities is not known. Here we use wood as a model to study microorganisms that establish and maintain a chemosynthetic ecosystem. We conducted both aquaria and in situ deep-sea experiments to test how different environmental constraints structure the assembly of bacterial, archaeal and fungal communities. We also measured changes in wood lipid concentrations and monitored sulfide production as a way to detect potential microbial activity. We show that wood falls are dynamic ecosystems with high spatial and temporal community turnover, and that the patterns of microbial colonization change depending on the scale of observation. The most illustrative example was the difference observed between pine and oak wood community dynamics. In pine, communities changed spatially, with strong differences in community composition between wood microhabitats, whereas in oak, communities changed more significantly with time of incubation. Changes in community assembly were reflected by changes in phylogenetic diversity that could be interpreted as shifts between assemblies ruled by species sorting to assemblies structured by competitive exclusion. These ecological interactions followed the dynamics of the potential microbial metabolisms accompanying wood degradation in the sea. Our work showed that wood is a good model for creating and manipulating chemosynthetic ecosystems in the laboratory, and attracting not only typical chemosynthetic microbes but also emblematic macrofaunal species.

Lifestyle as an Influential Factor to Urban Mobility Transport: a Case Study of Semarang City, Indonesia

NASA Astrophysics Data System (ADS)

Ismiyati, I.; Hermawan, F.

2018-02-01

Most of urban spatial structures in developing countries apparently face a typical phenomenon, as well as in Indonesia. The development of the urban spatial structure has the effects, namely to create polycentric pattern (sprawl). Moreover, communication technology believes that the factors of distance and density are highly considered in the organization of the urban structure. In other words, a distance problem is overcome by communication technology, in terms of interaction among people; in running their activities, mobility or distance is not a problem at all. Urban structure as path which is dependent is unable to intervene for an optimum form of urban structure because of dynamic of development objectives. In facts, lifestyle of inhabitant particularly concerning residential and vehicle ownership influences the mobility transport on the tremendous changes in developing countries. On the contrary, this research points out that mobility transport contributes to transportation problems as it becomes increasingly inefficient. Therefore, a sporadic traffic jam and increasing carbon emission issues have risen on the urban phenomenon. It is important to investigate the lifestyle, in terms of residential choice and vehicle ownership to reshape the urban spatial structure. The research aims to draw the urban spatial growth which extends to the phenomenon process toward polycentric pattern and inefficient transport mobility patterns triggering transportation problems in the context of Indonesia. The results confirm that lifestyle regarding residential choices to suburban area and vehicle ownership preference are unable to create the efficient mobility transport, either by cost, density consequences or vehicle ownership as orientation. This research recommends the local authority from multi-disciplinary sector, in particular public policy making to issue permission for authority of land use; residential area and transport agencies for reconciliation with regard to life style aspects in urban spatial planning.

A dynamic landscape model for fish in the Everglades and its application to restoration

USGS Publications Warehouse

Gaff, H.D.; DeAngelis, D.L.; Gross, L.J.; Salinas, R.; Shorrosh, M.

2000-01-01

A model (ALFISH) for fish functional groups in freshwater marshes of the greater Everglades area of southern Florida has been developed. Its main objective is to assess the spatial pattern of fish densities through time across freshwater marshes. This model has the capability of providing a dynamic measure of the spatially-explicit food resources available to wading birds. ALFISH simulates two functional groups, large and small fish, where the larger ones can prey on the small fish type. Both functional groups are size-structured. The marsh landscape is modeled as 500×500 m spatial cells on a grid across southern Florida. A hydrology model predicts water levels in the spatial cells on 5-day time steps. Fish populations spread across the marsh during flooded conditions and either retreat into refugia (alligator ponds), move to other spatial cells, or die if their cell dries out. ALFISH has been applied to the evaluation of alternative water regulation scenarios under the Central and South Florida Comprehensive Project Review Study. The objective of this Review Study is to compare alternative methods for restoring historical ecological conditions in southern Florida. ALFISH has provided information on which plans are most are likely to increase fish biomass and its availability to wading bird populations.

Quasistationary areas of NDVI trend dynamics is a powerful research tool for studying spatial patterns of land vegetation

NASA Astrophysics Data System (ADS)

Shevyrnogov, Anatoly; Larko, Aleksandr

The most important task for humankind is to study and understand global processes on Earth. Large factual material on the dynamics of the optical spectral characteristics of the land surface has been accumulated in recent decades. This has been only made possible due to the use of satellite information. The development of satellite measurement technologies and new methods for pre-processing and interpretation of satellite data allowed the research adequate to the scale of the Earth. This adequacy includes the compliance of scale terrestrial objects to the scale of satellite measurements. Research is not limited by any latitude or longitude of the objects studied. The second most important quality is the adequacy of the technologies used to velocities of processes on Earth. This is enabled by long-term continuous satellite measurements at almost all latitudes. Effectiveness of this approach to the study of natural systems has been shown by the authors in ASR publications (AP Shevyrnogov, GS Vysotskaya, JI Gitelson, Quasistationary areas of chlorophyll concentration in the world ocean as observed satellite data Advances in Space Research, Volume 18, Issue 7, Pages 129-132, 1996), which reported a method for determining the ocean surface quasistationary zones. This approach allowed us to identify different types of phytopigment dynamics and the hydrological structure of the ocean. We proposed a similar approach for the study of land vegetation. In some aspects, it is similar to the previously published approach, despite the different nature of terrestrial and aquatic ecosystems. The results are based on the processing of satellite data from 1981 to 2006. Dynamics is the most interesting and important parameter of ecosystems, especially their trends. Therefore, it has been chosen for the analysis of spatial patterns of plant biota. The first results showed great heterogeneity of variances in nonlinear trends of the study areas of the Earth's surface. They corresponded to different natural systems. Various scales of temporal and spatial windows highlight different features of land vegetation. Methods for normalization of the initial information are also effective for highlighting the features of the spatial structure of vegetation. Thus, we have a powerful tool to analyze the spatial distribution and dynamics of terrestrial vegetation based on satellite data. This approach provides a great opportunity to get fundamental knowledge on the functioning of the biosphere. This is global warming, shifts in permafrost boundaries, global gas exchange, etc. It can be used for practical applications in various fields of human activity: forestry, environmental protection, agriculture, etc. We show the illustration of this method: the global maps of land surface dynamics of trends with different parameters of data processing.

From structure to structural dynamics: Ahmed Zewail's legacy.

PubMed

Chergui, Majed; Thomas, John Meurig

2017-07-01

In this brief tribute to Ahmed Zewail, we highlight and place in the historical context, several of the major achievements that he and his colleagues have made in Femtochemistry (of which he was the principal instigator) and his introduction of ultrafast electron scattering, diffraction, microscopy and spectroscopy. By achieving a sub-picosecond temporal resolution, coupled with a picometer spatial resolution, he revolutionised our understanding of the corpus of chemical, physical, biological and materials science systems.

Stress state reassessment of Romanian offshore structures taking into account corrosion influence

NASA Astrophysics Data System (ADS)

Joavină, R.; Zăgan, S.; Zăgan, R.; Popa, M.

2017-08-01

Progressive degradation analysis for extraction or exploration offshore structure, with appraisal of failure potential and the causes that can be correlated with the service age, depends on the various sources of uncertainty that require particular attention in design, construction and exploitation phases. Romanian self erecting platforms are spatial lattice structures consist of tubular steel joints, forming a continuous system with an infinite number of dynamic degrees of freedom. Reassessment of a structure at fixed intervals of time, recorrelation of initial design elements with the actual situation encountered in location and with structural behaviour represents a major asset in lowering vulnerabilities of offshore structure. This paper proposes a comparative reassessment of the stress state for an offshore structure Gloria type, when leaving the shipyard and at the end of that interval corresponding to capital revision, taking into account sectional changes due to marine environment corrosion. The calculation was done using Newmark integration method on a 3D model, asses of the dynamic loads was made through probabilistic spectral method.

Accelerated high-resolution photoacoustic tomography via compressed sensing

NASA Astrophysics Data System (ADS)

Arridge, Simon; Beard, Paul; Betcke, Marta; Cox, Ben; Huynh, Nam; Lucka, Felix; Ogunlade, Olumide; Zhang, Edward

2016-12-01

Current 3D photoacoustic tomography (PAT) systems offer either high image quality or high frame rates but are not able to deliver high spatial and temporal resolution simultaneously, which limits their ability to image dynamic processes in living tissue (4D PAT). A particular example is the planar Fabry-Pérot (FP) photoacoustic scanner, which yields high-resolution 3D images but takes several minutes to sequentially map the incident photoacoustic field on the 2D sensor plane, point-by-point. However, as the spatio-temporal complexity of many absorbing tissue structures is rather low, the data recorded in such a conventional, regularly sampled fashion is often highly redundant. We demonstrate that combining model-based, variational image reconstruction methods using spatial sparsity constraints with the development of novel PAT acquisition systems capable of sub-sampling the acoustic wave field can dramatically increase the acquisition speed while maintaining a good spatial resolution: first, we describe and model two general spatial sub-sampling schemes. Then, we discuss how to implement them using the FP interferometer and demonstrate the potential of these novel compressed sensing PAT devices through simulated data from a realistic numerical phantom and through measured data from a dynamic experimental phantom as well as from in vivo experiments. Our results show that images with good spatial resolution and contrast can be obtained from highly sub-sampled PAT data if variational image reconstruction techniques that describe the tissues structures with suitable sparsity-constraints are used. In particular, we examine the use of total variation (TV) regularization enhanced by Bregman iterations. These novel reconstruction strategies offer new opportunities to dramatically increase the acquisition speed of photoacoustic scanners that employ point-by-point sequential scanning as well as reducing the channel count of parallelized schemes that use detector arrays.

The Central Italy Seismic Sequence (2016): Spatial Patterns and Dynamic Fingerprints

NASA Astrophysics Data System (ADS)

Suteanu, Cristian; Liucci, Luisa; Melelli, Laura

2018-01-01

The paper investigates spatio-temporal aspects of the seismic sequence that started in Central Italy (Amatrice, Lazio region) in August 2016, causing hundreds of fatalities and producing major damage to settlements. On one hand, scaling properties of the landscape topography are identified and related to geomorphological processes, supporting the identification of preferential spatial directions in tectonic activity and confirming the role of the past tectonic periods and ongoing processes with respect to the driving of the geomorphological evolution of the area. On the other hand, relations between the spatio-temporal evolution of the sequence and the seismogenic fault systems are studied. The dynamic fingerprints of seismicity are established with the help of events thread analysis (ETA), which characterizes anisotropy in spatio-temporal earthquake patterns. ETA confirms the fact that the direction of the seismogenic normal fault-oriented (N)NW-(S)SE is characterized by persistent seismic activity. More importantly, it also highlights the role of the pre-existing compressive structures, Neogenic thrust and transpressive regional fronts, with a trend-oriented (N)NE-(S)SW, in the stress transfer. Both the fractal features of the topographic surface and the dynamic fingerprint of the recent seismic sequence point to the hypothesis of an active interaction between the Quaternary fault systems and the pre-existing compressional structures.

Label-free nanoscale characterization of red blood cell structure and dynamics using single-shot transport of intensity equation

NASA Astrophysics Data System (ADS)

Poola, Praveen Kumar; John, Renu

2017-10-01

We report the results of characterization of red blood cell (RBC) structure and its dynamics with nanometric sensitivity using transport of intensity equation microscopy (TIEM). Conventional transport of intensity technique requires three intensity images and hence is not suitable for studying real-time dynamics of live biological samples. However, assuming the sample to be homogeneous, phase retrieval using transport of intensity equation has been demonstrated with single defocused measurement with x-rays. We adopt this technique for quantitative phase light microscopy of homogenous cells like RBCs. The main merits of this technique are its simplicity, cost-effectiveness, and ease of implementation on a conventional microscope. The phase information can be easily merged with regular bright-field and fluorescence images to provide multidimensional (three-dimensional spatial and temporal) information without any extra complexity in the setup. The phase measurement from the TIEM has been characterized using polymeric microbeads and the noise stability of the system has been analyzed. We explore the structure and real-time dynamics of RBCs and the subdomain membrane fluctuations using this technique.

An online input force time history reconstruction algorithm using dynamic principal component analysis

NASA Astrophysics Data System (ADS)

Prawin, J.; Rama Mohan Rao, A.

2018-01-01

The knowledge of dynamic loads acting on a structure is always required for many practical engineering problems, such as structural strength analysis, health monitoring and fault diagnosis, and vibration isolation. In this paper, we present an online input force time history reconstruction algorithm using Dynamic Principal Component Analysis (DPCA) from the acceleration time history response measurements using moving windows. We also present an optimal sensor placement algorithm to place limited sensors at dynamically sensitive spatial locations. The major advantage of the proposed input force identification algorithm is that it does not require finite element idealization of structure unlike the earlier formulations and therefore free from physical modelling errors. We have considered three numerical examples to validate the accuracy of the proposed DPCA based method. Effects of measurement noise, multiple force identification, different kinds of loading, incomplete measurements, and high noise levels are investigated in detail. Parametric studies have been carried out to arrive at optimal window size and also the percentage of window overlap. Studies presented in this paper clearly establish the merits of the proposed algorithm for online load identification.

Metacommunity ecology meets biogeography: effects of geographical region, spatial dynamics and environmental filtering on community structure in aquatic organisms.

PubMed

Heino, Jani; Soininen, Janne; Alahuhta, Janne; Lappalainen, Jyrki; Virtanen, Risto

2017-01-01

Metacommunity patterns and underlying processes in aquatic organisms have typically been studied within a drainage basin. We examined variation in the composition of six freshwater organismal groups across various drainage basins in Finland. We first modelled spatial structures within each drainage basin using Moran eigenvector maps. Second, we partitioned variation in community structure among three groups of predictors using constrained ordination: (1) local environmental variables, (2) spatial variables, and (3) dummy variable drainage basin identity. Third, we examined turnover and nestedness components of multiple-site beta diversity, and tested the best fit patterns of our datasets using the "elements of metacommunity structure" analysis. Our results showed that basin identity and local environmental variables were significant predictors of community structure, whereas within-basin spatial effects were typically negligible. In half of the organismal groups (diatoms, bryophytes, zooplankton), basin identity was a slightly better predictor of community structure than local environmental variables, whereas the opposite was true for the remaining three organismal groups (insects, macrophytes, fish). Both pure basin and local environmental fractions were, however, significant after accounting for the effects of the other predictor variable sets. All organismal groups exhibited high levels of beta diversity, which was mostly attributable to the turnover component. Our results showed consistent Clementsian-type metacommunity structures, suggesting that subgroups of species responded similarly to environmental factors or drainage basin limits. We conclude that aquatic communities across large scales are mostly determined by environmental and basin effects, which leads to high beta diversity and prevalence of Clementsian community types.

4D PET iterative deconvolution with spatiotemporal regularization for quantitative dynamic PET imaging.

PubMed

Reilhac, Anthonin; Charil, Arnaud; Wimberley, Catriona; Angelis, Georgios; Hamze, Hasar; Callaghan, Paul; Garcia, Marie-Paule; Boisson, Frederic; Ryder, Will; Meikle, Steven R; Gregoire, Marie-Claude

2015-09-01

Quantitative measurements in dynamic PET imaging are usually limited by the poor counting statistics particularly in short dynamic frames and by the low spatial resolution of the detection system, resulting in partial volume effects (PVEs). In this work, we present a fast and easy to implement method for the restoration of dynamic PET images that have suffered from both PVE and noise degradation. It is based on a weighted least squares iterative deconvolution approach of the dynamic PET image with spatial and temporal regularization. Using simulated dynamic [(11)C] Raclopride PET data with controlled biological variations in the striata between scans, we showed that the restoration method provides images which exhibit less noise and better contrast between emitting structures than the original images. In addition, the method is able to recover the true time activity curve in the striata region with an error below 3% while it was underestimated by more than 20% without correction. As a result, the method improves the accuracy and reduces the variability of the kinetic parameter estimates calculated from the corrected images. More importantly it increases the accuracy (from less than 66% to more than 95%) of measured biological variations as well as their statistical detectivity. Crown Copyright © 2015. Published by Elsevier Inc. All rights reserved.

The 7BM beamline at the APS: a facility for time-resolved fluid dynamics measurements

PubMed Central

Kastengren, Alan; Powell, Christopher F.; Arms, Dohn; Dufresne, Eric M.; Gibson, Harold; Wang, Jin

2012-01-01

In recent years, X-ray radiography has been used to probe the internal structure of dense sprays with microsecond time resolution and a spatial resolution of 15 µm even in high-pressure environments. Recently, the 7BM beamline at the Advanced Photon Source (APS) has been commissioned to focus on the needs of X-ray spray radiography measurements. The spatial resolution and X-ray intensity at this beamline represent a significant improvement over previous time-resolved X-ray radiography measurements at the APS. PMID:22713903

Exploring the Moon and Mars Using an Orbiting Superconducting Gravity Gradiometer

NASA Technical Reports Server (NTRS)

Paik, Ho Jung; Strayer, Donald M.

2004-01-01

Gravity measurement is fundamental to understanding the interior structure, dynamics, and evolution of planets. High-resolution gravity maps will also help locating natural resources, including subsurface water, and underground cavities for astronaut habitation on the Moon and Mars. Detecting the second spatial derivative of the potential, a gravity gradiometer mission tends to give the highest spatial resolution and has the advantage of requiring only a single satellite. We discuss gravity missions to the Moon and Mars using an orbiting Superconducting Gravity Gradiometer and discuss the instrument and spacecraft control requirements.

Dynamic nano-imaging of label-free living cells using electron beam excitation-assisted optical microscope

PubMed Central

Fukuta, Masahiro; Kanamori, Satoshi; Furukawa, Taichi; Nawa, Yasunori; Inami, Wataru; Lin, Sheng; Kawata, Yoshimasa; Terakawa, Susumu

2015-01-01

Optical microscopes are effective tools for cellular function analysis because biological cells can be observed non-destructively and non-invasively in the living state in either water or atmosphere condition. Label-free optical imaging technique such as phase-contrast microscopy has been analysed many cellular functions, and it is essential technology for bioscience field. However, the diffraction limit of light makes it is difficult to image nano-structures in a label-free living cell, for example the endoplasmic reticulum, the Golgi body and the localization of proteins. Here we demonstrate the dynamic imaging of a label-free cell with high spatial resolution by using an electron beam excitation-assisted optical (EXA) microscope. We observed the dynamic movement of the nucleus and nano-scale granules in living cells with better than 100 nm spatial resolution and a signal-to-noise ratio (SNR) around 10. Our results contribute to the development of cellular function analysis and open up new bioscience applications. PMID:26525841

Dynamic nano-imaging of label-free living cells using electron beam excitation-assisted optical microscope.

PubMed

Fukuta, Masahiro; Kanamori, Satoshi; Furukawa, Taichi; Nawa, Yasunori; Inami, Wataru; Lin, Sheng; Kawata, Yoshimasa; Terakawa, Susumu

2015-11-03

Optical microscopes are effective tools for cellular function analysis because biological cells can be observed non-destructively and non-invasively in the living state in either water or atmosphere condition. Label-free optical imaging technique such as phase-contrast microscopy has been analysed many cellular functions, and it is essential technology for bioscience field. However, the diffraction limit of light makes it is difficult to image nano-structures in a label-free living cell, for example the endoplasmic reticulum, the Golgi body and the localization of proteins. Here we demonstrate the dynamic imaging of a label-free cell with high spatial resolution by using an electron beam excitation-assisted optical (EXA) microscope. We observed the dynamic movement of the nucleus and nano-scale granules in living cells with better than 100 nm spatial resolution and a signal-to-noise ratio (SNR) around 10. Our results contribute to the development of cellular function analysis and open up new bioscience applications.

Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics

PubMed Central

Harcombe, William R.; Riehl, William J.; Dukovski, Ilija; Granger, Brian R.; Betts, Alex; Lang, Alex H.; Bonilla, Gracia; Kar, Amrita; Leiby, Nicholas; Mehta, Pankaj; Marx, Christopher J.; Segrè, Daniel

2014-01-01

Summary The inter-species exchange of metabolites plays a key role in the spatio-temporal dynamics of microbial communities. This raises the question whether ecosystem-level behavior of structured communities can be predicted using genome-scale models of metabolism for multiple organisms. We developed a modeling framework that integrates dynamic flux balance analysis with diffusion on a lattice, and applied it to engineered consortia. First, we predicted, and experimentally confirmed, the species-ratio to which a 2-species mutualistic consortium converges, and the equilibrium composition of a newly engineered 3-member community. We next identified a specific spatial arrangement of colonies, which gives rise to what we term the “eclipse dilemma”: does a competitor placed between a colony and its cross-feeding partner benefit or hurt growth of the original colony? Our experimentally validated finding, that the net outcome is beneficial, highlights the complex nature of metabolic interactions in microbial communities, while at the same time demonstrating their predictability. PMID:24794435

Dynamic nano-imaging of label-free living cells using electron beam excitation-assisted optical microscope

NASA Astrophysics Data System (ADS)

Fukuta, Masahiro; Kanamori, Satoshi; Furukawa, Taichi; Nawa, Yasunori; Inami, Wataru; Lin, Sheng; Kawata, Yoshimasa; Terakawa, Susumu

2015-11-01

Optical microscopes are effective tools for cellular function analysis because biological cells can be observed non-destructively and non-invasively in the living state in either water or atmosphere condition. Label-free optical imaging technique such as phase-contrast microscopy has been analysed many cellular functions, and it is essential technology for bioscience field. However, the diffraction limit of light makes it is difficult to image nano-structures in a label-free living cell, for example the endoplasmic reticulum, the Golgi body and the localization of proteins. Here we demonstrate the dynamic imaging of a label-free cell with high spatial resolution by using an electron beam excitation-assisted optical (EXA) microscope. We observed the dynamic movement of the nucleus and nano-scale granules in living cells with better than 100 nm spatial resolution and a signal-to-noise ratio (SNR) around 10. Our results contribute to the development of cellular function analysis and open up new bioscience applications.

Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover

DOE PAGES

Stegen, James C.; Fredrickson, James K.; Wilkins, Michael J.; ...

2016-04-07

Environmental transition zones are associated with geochemical gradients that overcome energy limitations to microbial metabolism, resulting in biogeochemical hot spots and moments. Riverine systems where groundwater mixes with surface water (the hyporheic zone) are spatially complex and temporally dynamic, making development of predictive models challenging. Spatial and temporal variations in hyporheic zone microbial communities are a key, but understudied, component of riverine biogeochemical function. To investigate the coupling among groundwater-surface water mixing, microbial communities, and biogeochemistry we applied ecological theory, aqueous biogeochemistry, DNA sequencing, and ultra-high resolution organic carbon profiling to field samples collected across times and locations representing amore » broad range of mixing conditions. Mixing of groundwater and surface water resulted in a shift from transport-driven stochastic dynamics to a deterministic microbial structure associated with elevated biogeochemical rates. While the dynamics of the hyporheic make predictive modeling a challenge, we provide new knowledge that can improve the tractability of such models.« less

Fusion of multichannel local and global structural cues for photo aesthetics evaluation.

PubMed

Luming Zhang; Yue Gao; Zimmermann, Roger; Qi Tian; Xuelong Li

2014-03-01

Photo aesthetic quality evaluation is a fundamental yet under addressed task in computer vision and image processing fields. Conventional approaches are frustrated by the following two drawbacks. First, both the local and global spatial arrangements of image regions play an important role in photo aesthetics. However, existing rules, e.g., visual balance, heuristically define which spatial distribution among the salient regions of a photo is aesthetically pleasing. Second, it is difficult to adjust visual cues from multiple channels automatically in photo aesthetics assessment. To solve these problems, we propose a new photo aesthetics evaluation framework, focusing on learning the image descriptors that characterize local and global structural aesthetics from multiple visual channels. In particular, to describe the spatial structure of the image local regions, we construct graphlets small-sized connected graphs by connecting spatially adjacent atomic regions. Since spatially adjacent graphlets distribute closely in their feature space, we project them onto a manifold and subsequently propose an embedding algorithm. The embedding algorithm encodes the photo global spatial layout into graphlets. Simultaneously, the importance of graphlets from multiple visual channels are dynamically adjusted. Finally, these post-embedding graphlets are integrated for photo aesthetics evaluation using a probabilistic model. Experimental results show that: 1) the visualized graphlets explicitly capture the aesthetically arranged atomic regions; 2) the proposed approach generalizes and improves four prominent aesthetic rules; and 3) our approach significantly outperforms state-of-the-art algorithms in photo aesthetics prediction.

Computational Modeling of Airway and Pulmonary Vascular Structure and Function: Development of a “Lung Physiome”

PubMed Central

Tawhai, M. H.; Clark, A. R.; Donovan, G. M.; Burrowes, K. S.

2011-01-01

Computational models of lung structure and function necessarily span multiple spatial and temporal scales, i.e., dynamic molecular interactions give rise to whole organ function, and the link between these scales cannot be fully understood if only molecular or organ-level function is considered. Here, we review progress in constructing multiscale finite element models of lung structure and function that are aimed at providing a computational framework for bridging the spatial scales from molecular to whole organ. These include structural models of the intact lung, embedded models of the pulmonary airways that couple to model lung tissue, and models of the pulmonary vasculature that account for distinct structural differences at the extra- and intra-acinar levels. Biophysically based functional models for tissue deformation, pulmonary blood flow, and airway bronchoconstriction are also described. The development of these advanced multiscale models has led to a better understanding of complex physiological mechanisms that govern regional lung perfusion and emergent heterogeneity during bronchoconstriction. PMID:22011236

High efficiency all-optical plasmonic diode based on a nonlinear side-coupled waveguide-cavity structure with broken symmetry

NASA Astrophysics Data System (ADS)

Liang, Hong-Qin; Liu, Bin; Hu, Jin-Feng; He, Xing-Dao

2018-05-01

An all-optical plasmonic diode, comprising a metal-insulator-metal waveguide coupled with a stub cavity, is proposed based on a nonlinear Fano structure. The key technique used is to break structural spatial symmetry by a simple reflector layer in the waveguide. The spatial asymmetry of the structure gives rise to the nonreciprocity of coupling efficiencies between the Fano cavity and waveguides on both sides of the reflector layer, leading to a nonreciprocal nonlinear response. Transmission properties and dynamic responses are numerically simulated and investigated by the nonlinear finite-difference time-domain method. In the proposed structure, high-efficiency nonreciprocal transmission can be achieved with a low power threshold and an ultrafast response time (subpicosecond level). A high maximum transmittance of 89.3% and an ultra-high transmission contrast ratio of 99.6% can also be obtained. The device can be flexibly adjusted for working wavebands by altering the stub cavity length.

Scaling view by the Virtual Nature Systems

NASA Astrophysics Data System (ADS)

Klenov, Valeriy

2010-05-01

The Actual Nature Systems (ANS) continually are under spatial-temporal governing external influences from other systems (Meteorology and Geophysics). This influences provide own spatial temporal patterns on the Earth Nature Systems, which reforms these influences by own manner and scales. These at last three systems belong to the Open Non Equilibrium Nature Systems (ONES). The Geophysics and Meteorology Systems are both governing for the ANS on the Earth. They provide as continual energetic pressure and impacts, and direct Extremes from the both systems to the ANS on Earth surface (earthquakes, storms, and others). The Geodynamics of the ANS is under mixing of influence for both systems, on their scales and on dynamics of their spatial-temporal structures, and by own ANS properties, as the ONES. To select influences of external systems on the Earth systems always is among major tasks of the Geomorphology. Mixing of the Systems scales and dynamics provide specific properties for the memory of Earth system. The memory of the ANS has practical value for their multi-purpose management. The knowledge of these properties is the key for research spatial-temporal GeoDynamics and Trends of Earth Nature Systems. Selection of the influences in time and space requires for special tool, requires elaboration and action of the Virtual Nature Systems (VNS), which are enliven computer doubles for analysis Geodynamics of the ANS. The Experience on the VNS enables to assess influence of each and both external factors on the ANS. It is source of knowledge for regional tectonic and climate oscillations, trends, and threats. Research by the VNS for spatial-temporal dynamics and structures of stochastic regimes of governing systems and processes results in stochastic GeoDynamics of environmental processes, in forming of false trends and blanks in natural records. This ‘wild dance' of 2D stochastic patterns and their interaction each other and generates acting structures of river nets, and of river basins, in multi-layer, multi-scale, and multi-driven structures of surface processes. It results in the Information Loss Law for observed memory of the VNS (and of external drivers) which gradually cut off own Past and distort own history. This view on the GeoDynamics appeared after long time field measurements thousand of terrace levels, hundreds of terrace ranks, and many terrace complexes in river basins of all scales - for the purpose to recognize their deforming by climatic and tectonic spatial-temporal influences. The method for following up of terrace levels along valleys was used in the Geomorphology and Geology for a long time, by linking fragments of level to ‘cycles'. It gradually linked them by heights above riverbed. The understanding of this logical mistake was happened (as insight) during observing from upstream a valley. All fragmental levels downstream were good visible, without chances for their correlation ‘by height' or ‘by number'. Instead of link of fragments, this explains process of river valleys' stochastic GeoDynamics by properties of the ONES (I. Prigogine et al., 1984) to generate oscillations. Is only first view, but later it turned to simple mechanic of Information Loss Law action in the GeoInformatics for Nature Systems (Klenov, 1980, et al.). The Information Loss distorts and destroys natural records (sources for data on the Past exogenous and endogenous rivers). This simple equation was received by multiple measures of terrace rank, and other natural records. It explains origin of false trend in natural records, destroys most own history by stochastic dynamics of the ONES. It prevents to restore of nature records as a memory of the Past. Non-disturbed is only small time between the Past and the Future, which looks like a peak between two non-linear losses. The history of Past (of the ANS, and of external drivers) are destroyed by the ANS. The Future becomes none determined due unknown 2D data of future external influences. However, the effect is the reliable Outstripping Monitoring for impending disasters and of other processes with satisfactory exactness. It was proved by direct validations (by use observed records). The conclusions are as follows: The ILL is mechanics for dissipation the Past and indeterminism the Future of the Nature. Moving back along the VNS' Phase Trajectory changes a view on natural records, and is chance to restore history of the ANS and its external drivers.

Basins of coexistence and extinction in spatially extended ecosystems of cyclically competing species.

PubMed

Ni, Xuan; Yang, Rui; Wang, Wen-Xu; Lai, Ying-Cheng; Grebogi, Celso

2010-12-01

Microscopic models based on evolutionary games on spatially extended scales have recently been developed to address the fundamental issue of species coexistence. In this pursuit almost all existing works focus on the relevant dynamical behaviors originated from a single but physically reasonable initial condition. To gain comprehensive and global insights into the dynamics of coexistence, here we explore the basins of coexistence and extinction and investigate how they evolve as a basic parameter of the system is varied. Our model is cyclic competitions among three species as described by the classical rock-paper-scissors game, and we consider both discrete lattice and continuous space, incorporating species mobility and intraspecific competitions. Our results reveal that, for all cases considered, a basin of coexistence always emerges and persists in a substantial part of the parameter space, indicating that coexistence is a robust phenomenon. Factors such as intraspecific competition can, in fact, promote coexistence by facilitating the emergence of the coexistence basin. In addition, we find that the extinction basins can exhibit quite complex structures in terms of the convergence time toward the final state for different initial conditions. We have also developed models based on partial differential equations, which yield basin structures that are in good agreement with those from microscopic stochastic simulations. To understand the origin and emergence of the observed complicated basin structures is challenging at the present due to the extremely high dimensional nature of the underlying dynamical system. © 2010 American Institute of Physics.

An introduction to NMR-based approaches for measuring protein dynamics

PubMed Central

Kleckner, Ian R; Foster, Mark P

2010-01-01

Proteins are inherently flexible at ambient temperature. At equilibrium, they are characterized by a set of conformations that undergo continuous exchange within a hierarchy of spatial and temporal scales ranging from nanometers to micrometers and femtoseconds to hours. Dynamic properties of proteins are essential for describing the structural bases of their biological functions including catalysis, binding, regulation and cellular structure. Nuclear magnetic resonance (NMR) spectroscopy represents a powerful technique for measuring these essential features of proteins. Here we provide an introduction to NMR-based approaches for studying protein dynamics, highlighting eight distinct methods with recent examples, contextualized within a common experimental and analytical framework. The selected methods are (1) Real-time NMR, (2) Exchange spectroscopy, (3) Lineshape analysis, (4) CPMG relaxation dispersion, (5) Rotating frame relaxation dispersion, (6) Nuclear spin relaxation, (7) Residual dipolar coupling, (8) Paramagnetic relaxation enhancement. PMID:21059410

Dynamic displacement monitoring of long-span bridges with a microwave radar interferometer

NASA Astrophysics Data System (ADS)

Zhang, Bochen; Ding, Xiaoli; Werner, Charles; Tan, Kai; Zhang, Bin; Jiang, Mi; Zhao, Jingwen; Xu, Youlin

2018-04-01

Structural health monitoring of long-span bridges is a critical process in ensuring the operational safety of the structures. In this paper, we present experimental results of monitoring the displacements of two long-span bridges in Hong Kong Ting Kau Bridge (TKB) and Tsing Ma Bridge (TMB) with a terrestrial microwave radar interferometer named the GAMMA Portable Radar Interferometer (GPRI). A technique for fusing the measurements from two receiving antennas of the radar instrument is proposed. In addition, a two-step phase unwrapping approach is also tested. The results reveal the bridge dynamic responses under different loading conditions, including winds, vehicle traffic, and passing trains. The results also show that the terrestrial microwave radar interferometer can be used to monitor the dynamics of long-span bridges with unprecedented spatial and temporal resolutions.

The impact of resource dependence of the mechanisms of life on the spatial population dynamics of an in silico microbial community

NASA Astrophysics Data System (ADS)

Daly, Aisling J.; Baetens, Jan M.; De Baets, Bernard

2016-12-01

Biodiversity has a critical impact on ecosystem functionality and stability, and thus the current biodiversity crisis has motivated many studies of the mechanisms that sustain biodiversity, a notable example being non-transitive or cyclic competition. We therefore extend existing microscopic models of communities with cyclic competition by incorporating resource dependence in demographic processes, characteristics of natural systems often oversimplified or overlooked by modellers. The spatially explicit nature of our individual-based model of three interacting species results in the formation of stable spatial structures, which have significant effects on community functioning, in agreement with experimental observations of pattern formation in microbial communities.

A nonlocal spatial model for Lyme disease

NASA Astrophysics Data System (ADS)

Yu, Xiao; Zhao, Xiao-Qiang

2016-07-01

This paper is devoted to the study of a nonlocal and time-delayed reaction-diffusion model for Lyme disease with a spatially heterogeneous structure. In the case of a bounded domain, we first prove the existence of the positive steady state and a threshold type result for the disease-free system, and then establish the global dynamics for the model system in terms of the basic reproduction number. In the case of an unbound domain, we obtain the existence of the disease spreading speed and its coincidence with the minimal wave speed. At last, we use numerical simulations to verify our analytic results and investigate the influence of model parameters and spatial heterogeneity on the disease infection risk.

Femtosecond movies of water near interfaces at sub-Angstrom resolution

NASA Astrophysics Data System (ADS)

Coridan, Robert; Hwee Lai, Ghee; Schmidt, Nathan; Abbamonte, Peter; Wong, Gerard C. L.

2010-03-01

The behavior of liquid water near interfaces with nanoscopic variations in chemistry influences a broad range of phenomena in biology. Using inelastic x-ray scattering (IXS) data from 3rd-generation synchrotron x-ray sources, we reconstruct the Greens function of liquid water, which describes the å-scale spatial and femtosecond-scale temporal evolution of density fluctuations. We extend this response function formalism to reconstruct the evolution of hydration structures near dynamic surfaces with different charge distributions, in order to define more precisely the molecular signature of hydrophilicity and hydrophobicity. Moreover, we investigate modifications to surface hydration structures and dynamics as the size of hydrophilic and hydrophobic patches are varied.

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.

Imaging nanoscale spatial modulation of a relativistic electron beam with a MeV ultrafast electron microscope

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

Lu, Chao; Jiang, Tao; Liu, Shengguang

Here, an accelerator-based MeV ultrafast electron microscope (MUEM) has been proposed as a promising tool to the study structural dynamics at the nanometer spatial scale and the picosecond temporal scale. Here, we report experimental tests of a prototype MUEM where high quality images with nanoscale fine structures were recorded with a pulsed ~3 MeV picosecond electron beam. The temporal and spatial resolutions of the MUEM operating in the single-shot mode are about 4 ps (FWHM) and 100 nm (FWHM), corresponding to a temporal-spatial resolution of 4 × 10 –19 sm, about 2 orders of magnitude higher than that achieved withmore » state-of-the-art single-shot keV UEM. Using this instrument, we offer the demonstration of visualizing the nanoscale periodic spatial modulation of an electron beam, which may be converted into longitudinal density modulation through emittance exchange to enable production of high-power coherent radiation at short wavelengths. Our results mark a great step towards single-shot nanometer-resolution MUEMs and compact intense x-ray sources that may have widespread applications in many areas of science.« less

Imaging nanoscale spatial modulation of a relativistic electron beam with a MeV ultrafast electron microscope

DOE PAGES

Lu, Chao; Jiang, Tao; Liu, Shengguang; ...

2018-03-12

Here, an accelerator-based MeV ultrafast electron microscope (MUEM) has been proposed as a promising tool to the study structural dynamics at the nanometer spatial scale and the picosecond temporal scale. Here, we report experimental tests of a prototype MUEM where high quality images with nanoscale fine structures were recorded with a pulsed ~3 MeV picosecond electron beam. The temporal and spatial resolutions of the MUEM operating in the single-shot mode are about 4 ps (FWHM) and 100 nm (FWHM), corresponding to a temporal-spatial resolution of 4 × 10 –19 sm, about 2 orders of magnitude higher than that achieved withmore » state-of-the-art single-shot keV UEM. Using this instrument, we offer the demonstration of visualizing the nanoscale periodic spatial modulation of an electron beam, which may be converted into longitudinal density modulation through emittance exchange to enable production of high-power coherent radiation at short wavelengths. Our results mark a great step towards single-shot nanometer-resolution MUEMs and compact intense x-ray sources that may have widespread applications in many areas of science.« less

Deployable robotic woven wire structures and joints for space applications

NASA Technical Reports Server (NTRS)

Shahinpoor, MO; Smith, Bradford

1991-01-01

Deployable robotic structures are basically expandable and contractable structures that may be transported or launched to space in a compact form. These structures may then be intelligently deployed by suitable actuators. The deployment may also be done by means of either airbag or spring-loaded typed mechanisms. The actuators may be pneumatic, hydraulic, ball-screw type, or electromagnetic. The means to trigger actuation may be on-board EPROMS, programmable logic controllers (PLCs) that trigger actuation based on some input caused by the placement of the structure in the space environment. The actuation may also be performed remotely by suitable remote triggering devices. Several deployable woven wire structures are examined. These woven wire structures possess a unique form of joint, the woven wire joint, which is capable of moving and changing its position and orientation with respect to the structure itself. Due to the highly dynamic and articulate nature of these joints the 3-D structures built using them are uniquely and highly expandable, deployable, and dynamic. The 3-D structure naturally gives rise to a new generation of deployable three-dimensional spatial structures.

Dynamics and spatial structure of ENSO from re-analyses versus CMIP5 models

NASA Astrophysics Data System (ADS)

Serykh, Ilya; Sonechkin, Dmitry

2016-04-01

Basing on a mathematical idea about the so-called strange nonchaotic attractor (SNA) in the quasi-periodically forced dynamical systems, the currently available re-analyses data are considered. It is found that the El Niño - Southern Oscillation (ENSO) is driven not only by the seasonal heating, but also by three more external periodicities (incommensurate to the annual period) associated with the ~18.6-year lunar-solar nutation of the Earth rotation axis, ~11-year sunspot activity cycle and the ~14-month Chandler wobble in the Earth's pole motion. Because of the incommensurability of their periods all four forces affect the system in inappropriate time moments. As a result, the ENSO time series look to be very complex (strange in mathematical terms) but nonchaotic. The power spectra of ENSO indices reveal numerous peaks located at the periods that are multiples of the above periodicities as well as at their sub- and super-harmonic. In spite of the above ENSO complexity, a mutual order seems to be inherent to the ENSO time series and their spectra. This order reveals itself in the existence of a scaling of the power spectrum peaks and respective rhythms in the ENSO dynamics that look like the power spectrum and dynamics of the SNA. It means there are no limits to forecast ENSO, in principle. In practice, it opens a possibility to forecast ENSO for several years ahead. Global spatial structures of anomalies during El Niño and power spectra of ENSO indices from re-analyses are compared with the respective output quantities in the CMIP5 climate models (the Historical experiment). It is found that the models reproduce global spatial structures of the near surface temperature and sea level pressure anomalies during El Niño very similar to these fields in the re-analyses considered. But the power spectra of the ENSO indices from the CMIP5 models show no peaks at the same periods as the re-analyses power spectra. We suppose that it is possible to improve modeled rhythms if the afore-mentioned external periodicities are taken in an explicit consideration in the models.

Automatic reconstruction of fault networks from seismicity catalogs: Three-dimensional optimal anisotropic dynamic clustering

NASA Astrophysics Data System (ADS)

Ouillon, G.; Ducorbier, C.; Sornette, D.

2008-01-01

We propose a new pattern recognition method that is able to reconstruct the three-dimensional structure of the active part of a fault network using the spatial location of earthquakes. The method is a generalization of the so-called dynamic clustering (or k means) method, that partitions a set of data points into clusters, using a global minimization criterion of the variance of the hypocenters locations about their center of mass. The new method improves on the original k means method by taking into account the full spatial covariance tensor of each cluster in order to partition the data set into fault-like, anisotropic clusters. Given a catalog of seismic events, the output is the optimal set of plane segments that fits the spatial structure of the data. Each plane segment is fully characterized by its location, size, and orientation. The main tunable parameter is the accuracy of the earthquake locations, which fixes the resolution, i.e., the residual variance of the fit. The resolution determines the number of fault segments needed to describe the earthquake catalog: the better the resolution, the finer the structure of the reconstructed fault segments. The algorithm successfully reconstructs the fault segments of synthetic earthquake catalogs. Applied to the real catalog constituted of a subset of the aftershock sequence of the 28 June 1992 Landers earthquake in southern California, the reconstructed plane segments fully agree with faults already known on geological maps or with blind faults that appear quite obvious in longer-term catalogs. Future improvements of the method are discussed, as well as its potential use in the multiscale study of the inner structure of fault zones.

Effects of Heterogeneous Diffuse Fibrosis on Arrhythmia Dynamics and Mechanism

PubMed Central

Kazbanov, Ivan V.; ten Tusscher, Kirsten H. W. J.; Panfilov, Alexander V.

2016-01-01

Myocardial fibrosis is an important risk factor for cardiac arrhythmias. Previous experimental and numerical studies have shown that the texture and spatial distribution of fibrosis may play an important role in arrhythmia onset. Here, we investigate how spatial heterogeneity of fibrosis affects arrhythmia onset using numerical methods. We generate various tissue textures that differ by the mean amount of fibrosis, the degree of heterogeneity and the characteristic size of heterogeneity. We study the onset of arrhythmias using a burst pacing protocol. We confirm that spatial heterogeneity of fibrosis increases the probability of arrhythmia induction. This effect is more pronounced with the increase of both the spatial size and the degree of heterogeneity. The induced arrhythmias have a regular structure with the period being mostly determined by the maximal local fibrosis level. We perform ablations of the induced fibrillatory patterns to classify their type. We show that in fibrotic tissue fibrillation is usually of the mother rotor type but becomes of the multiple wavelet type with increase in tissue size. Overall, we conclude that the most important factor determining the formation and dynamics of arrhythmia in heterogeneous fibrotic tissue is the value of maximal local fibrosis. PMID:26861111

Spatial and Temporal Patterns of Throughfall Amounts and Solutes in a Tropical Montane Forest - Comparisons with Findings From Lowland Rain Forests

NASA Astrophysics Data System (ADS)

Zimmermann, A.

2007-05-01

The diverse tree species composition, irregular shaped tree crowns and a multi-layered forest structure affect the redistribution of rainfall in lower montane rain forests. In addition, abundant epiphyte biomass and associated canopy humus influence spatial patterns of throughfall. The spatial variability of throughfall amounts controls spatial patterns of solute concentrations and deposition. Moreover, the living and dead biomass interacts with the rainwater during the passage through the canopy and creates a chemical variability of its own. Since spatial and temporal patterns are intimately linked, the analysis of temporal solute concentration dynamics is an important step to understand the emerging spatial patterns. I hypothesized that: (1) the spatial variability of volumes and chemical composition of throughfall is particularly high compared with other forests because of the high biodiversity and epiphytism, (2) the temporal stability of the spatial pattern is high because of stable structures in the canopy (e.g. large epiphytes) that show only minor changes during the short term observation period, and (3) the element concentrations decrease with increasing rainfall because of exhausting element pools in the canopy. The study area at 1950 m above sea level is located in the south Ecuadorian Andes far away from anthropogenic emission sources and marine influences. Rain and throughfall were collected from August to October 2005 on an event and within-event basis for five precipitation periods and analyzed for pH, K, Na, Ca, Mg, NH4+, Cl-, NO3-, PO43-, TN, TP and TOC. Throughfall amounts and most of the solutes showed a high spatial variability, thereby the variability of H+, K, Ca, Mg, Cl- and NO3- exceeded those from a Brazilian tropical rain forest. The temporal persistence of the spatial patterns was high for throughfall amounts and varied depending on the solute. Highly persistent time stability patterns were detected for K, Mg and TOC concentrations. Time stability patterns of solute deposition were somewhat weaker than for concentrations for most of the solutes. Epiphytes strongly affected time stability patterns in that collectors situated below thick moss mats or arboreal bromeliads were in large part responsible for the extreme persistence with low throughfall amounts and high ion concentrations (H+ showed low concentrations). Rainfall solute concentrations were low compared with a variety of other tropical lowland and montane forest sites and showed a small temporal variability during the study period for both between and within-event dynamics, respectively. Throughfall solute concentrations were more within the range when compared with other sites and showed highly variable within-event dynamics. For most of the solutes, within-event concentrations did not reach low, constant concentrations in later event stages, rather concentrations fluctuated (e.g. Cl-) or increased (e.g. K and TOC). The within-event throughfall solute concentration dynamics in this lower montane rain forest contrast to recent observations from lowland tropical rain forests in Panama and Brazil. The observed within-event patterns are attributed (1) to the influence of epiphytes and associated canopy humus, and (2) to low rainfall intensities.

Virtual Embryo: Cell-Agent Based Modeling of Developmental Processes and Toxicities (CSS BOSC)

EPA Science Inventory

Spatial regulation of cellular dynamics is fundamental to morphological development. As such, chemical disruption of spatial dynamics is a determinant of developmental toxicity. Incorporating spatial dynamics into AOPs for developmental toxicity is desired but constrained by the ...

4D ground penetrating radar measurements as non-invasive means for hydrological process investigation

NASA Astrophysics Data System (ADS)

Jackisch, Conrad; Allroggen, Niklas

2017-04-01

The missing vision into the subsurface appears to be a major limiting factor for our hydrological process understanding and theory development. Today, hydrology-related sciences have collected tremendous evidence for soils acting as drainage network and retention stores simultaneously in structured and self-organising domains. However, our present observation technology relies mainly on point-scale sensors, which integrate over a volume of unknown structures and is blind for their distribution. Although heterogeneity is acknowledged at all scales, it is rarely seen as inherent system property. At small scales (soil moisture probe) and at large scales (neutron probe) our measurements leave quite some ambiguity. Consequently, spatially and temporally continuous measurement of soil water states is essential for advancing our understanding and development of subsurface process theories. We present results from several irrigation experiments accompanied by 2D and 3D time-lapse GPR for the development of a novel technique to visualise and quantify water dynamics in the subsurface. Through the comparison of TDR, tracer and gravimetric measurement of soil moisture it becomes apparent that all sensor-based techniques are capable to record temporal dynamics, but are challenged to precisely quantify the measurements and to extrapolate them in space. At the same time excavative methods are very limited in temporal and spatial resolution. The application of non-invasive 4D GPR measurements complements the existing techniques and reveals structural and temporal dynamics simultaneously. By consequently increasing the density of the GPR data recordings in time and space, we find means to process the data also in the time-dimension. This opens ways to quantitatively analyse soil water dynamics in complex settings.

NUCLEON STRUCTURE IN LATTICE QCD WITH DYNAMICAL DOMAIN--WALL FERMIONS QUARKS.

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

LIN H.-W.; OHTA, S.

2006-10-02

We report RBC and RBC/UKQCD lattice QCD numerical calculations of nucleon electroweak matrix elements with dynamical domain-wall fermions (DWF) quarks. The first, RBC, set of dynamical DWF ensembles employs two degenerate flavors of DWF quarks and the DBW2 gauge action. Three sea quark mass values of 0.04, 0.03 and 0.02 in lattice units are used with 220 gauge configurations each. The lattice cutoff is a{sup -1} {approx} 1.7GeV and the spatial volume is about (1.9fm){sup 3}. Despite the small volume, the ratio of the isovector vector and axial charges g{sub A}/g{sub V} and that of structure function moments {sub u-d}/{submore » {Delta}u-{Delta}d} are in agreement with experiment, and show only very mild quark mass dependence. The second, RBC/UK, set of ensembles employs one strange and two degenerate (up and down) dynamical DWF quarks and Iwasaki gauge action. The strange quark mass is set at 0.04, and three up/down mass values of 0.03, 0.02 and 0.01 in lattice units are used. The lattice cutoff is a{sup -1} {approx} 1.6GeV and the spatial volume is about (3.0fm){sup 3}. Even with preliminary statistics of 25-30 gauge configurations, the ratios g{sub A}/g{sub V} and {sub u-d}/{sub {Delta}u-{Delta}d} are consistent with experiment and show only very mild quark mass dependence. Another structure function moment, d{sub 1}, though yet to be renormalized, appears small in both sets.« less

Growth and demography of Pinaleno high elevation forests

Treesearch

Christopher O' Connor; Donald A. Falk; Ann M. Lynch; Craig P. Wilcox; Thomas W. Swetnam; Tyson L. Swetnam

2010-01-01

The project goal is to understand how multiple disturbance events including fire, insect outbreaks, and climate variability interact in space and time, and how they combine to influence forest species composition, spatial structure, and tree population dynamics in high elevation forests of the Pinaleno Mountains. Information from each of these components is needed in...

Region-Specific Involvement of Actin Rearrangement-Related Synaptic Structure Alterations in Conditioned Taste Aversion Memory

ERIC Educational Resources Information Center

Bi, Ai-Ling; Wang, Yue; Li, Bo-Qin; Wang, Qian-Qian; Ma, Ling; Yu, Hui; Zhao, Ling; Chen, Zhe-Yu

2010-01-01

Actin rearrangement plays an essential role in learning and memory; however, the spatial and temporal regulation of actin dynamics in different phases of associative memory has not been fully understood. Here, using the conditioned taste aversion (CTA) paradigm, we investigated the region-specific involvement of actin rearrangement-related…

Disturbance patterns in a socio-ecological system at multiple scales

Treesearch

G. Zurlini; Kurt H. Riitters; N. Zaccarelli; I. Petrosillo; K.B. Jones; L. Rossi

2006-01-01

Ecological systems with hierarchical organization and non-equilibrium dynamics require multiple-scale analyses to comprehend how a system is structured and to formulate hypotheses about regulatory mechanisms. Characteristic scales in real landscapes are determined by, or at least reflect, the spatial patterns and scales of constraining human interactions with the...

The Architecture, Dynamics, and Development of Mental Processing: Greek, Chinese, or Universal?

ERIC Educational Resources Information Center

Demetriou, A.; Kui, Z.X.; Spanoudis, G.; Christou, C.; Kyriakides, L.; Platsidou, M.

2005-01-01

This study compared Greeks with Chinese, from 8 to 14 years of age, on measures of processing efficiency, working memory, and reasoning. All processes were addressed through three domains of relations: verbal/propositional, quantitative, and visuo/spatial. Structural equations modelling and rating scale analysis showed that the architecture and…

North American pulp & paper model (NAPAP)

Treesearch

Peter J. Ince; Joseph Buongiorno

2007-01-01

This chapter describes the development and structure of the NAPAP model and compares it to other forest sector models. The NAPAP model was based on PELPS and adapted to describe paper and paperboard product demand, pulpwood and recovered paper supply, and production capacity and technology, with spatially dynamic market equilibria. We describe how the model predicts...

Preface to spatial and temporal reflections of disturbances in boreal and temperate forests

Treesearch

Kalev Jogiste; Timo Kuuluvainen; W. Keith Moser

2009-01-01

Disturbances are a natural part of all ecosystems and they are important for the maintenance of biodiversity in forest ecosystems (Attiwill 1994). Periodicity and intensity of disturbances shape the structural characteristics and dynamics of forest landscape mosaics (Turner et al. 2001). Natural disturbances increase habitat availability and diversity, particularly for...

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...

[Spatial point pattern analysis of main trees and flowering Fargesia qinlingensis in Abies fargesii forests in Mt Taibai of the Qinling Mountains, China].

PubMed

Li, Guo Chun; Song, Hua Dong; Li, Qi; Bu, Shu Hai

2017-11-01

In Abies fargesii forests of the giant panda's habitats in Mt. Taibai, the spatial distribution patterns and interspecific associations of main tree species and their spatial associations with the understory flowering Fargesia qinlingensis were analyzed at multiple scales by univariate and bivaria-te O-ring function in point pattern analysis. The results showed that in the A. fargesii forest, the number of A. fargesii was largest but its population structure was in decline. The population of Betula platyphylla was relatively young, with a stable population structure, while the population of B. albo-sinensis declined. The three populations showed aggregated distributions at small scales and gradually showed random distributions with increasing spatial scales. Spatial associations among tree species were mainly showed at small scales and gradually became not spatially associated with increasing scale. A. fargesii and B. platyphylla were positively associated with flowering F. qinlingensis at large and medium scales, whereas B. albo-sinensis showed negatively associated with flowering F. qinlingensis at large and medium scales. The interaction between trees and F. qinlingensis in the habitats of giant panda promoted the dynamic succession and development of forests, which changed the environment of giant panda's habitats in Qinling.

Direct Patlak Reconstruction From Dynamic PET Data Using the Kernel Method With MRI Information Based on Structural Similarity.

PubMed

Gong, Kuang; Cheng-Liao, Jinxiu; Wang, Guobao; Chen, Kevin T; Catana, Ciprian; Qi, Jinyi

2018-04-01

Positron emission tomography (PET) is a functional imaging modality widely used in oncology, cardiology, and neuroscience. It is highly sensitive, but suffers from relatively poor spatial resolution, as compared with anatomical imaging modalities, such as magnetic resonance imaging (MRI). With the recent development of combined PET/MR systems, we can improve the PET image quality by incorporating MR information into image reconstruction. Previously, kernel learning has been successfully embedded into static and dynamic PET image reconstruction using either PET temporal or MRI information. Here, we combine both PET temporal and MRI information adaptively to improve the quality of direct Patlak reconstruction. We examined different approaches to combine the PET and MRI information in kernel learning to address the issue of potential mismatches between MRI and PET signals. Computer simulations and hybrid real-patient data acquired on a simultaneous PET/MR scanner were used to evaluate the proposed methods. Results show that the method that combines PET temporal information and MRI spatial information adaptively based on the structure similarity index has the best performance in terms of noise reduction and resolution improvement.

Enhancement of carrier lifetimes in type-II quantum dot/quantum well hybrid structures

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

Couto, O. D. D., E-mail: odilon@ifi.unicamp.br; Almeida, P. T. de; Santos, G. E. dos

We investigate optical transitions and carrier dynamics in hybrid structures containing type-I GaAs/AlGaAs quantum wells (QWs) and type-II GaSb/AlGaAs quantum dots (QDs). We show that the optical recombination of photocreated electrons confined in the QWs with holes in the QDs and wetting layer can be modified according to the QW/QD spatial separation. In particular, for low spacer thicknesses, the QW optical emission can be suppressed due to the transference of holes from the QW to the GaSb layer, favoring the optical recombination of spatially separated carriers, which can be useful for optical memory and solar cell applications. Time-resolved photoluminescence (PL)more » measurements reveal non-exponential recombination dynamics. We demonstrate that the PL transients can only be quantitatively described by considering both linear and quadratic terms of the carrier density in the bimolecular recombination approximation for type-II semiconductor nanostructures. We extract long exciton lifetimes from 700 ns to 5 μs for QDs depending on the spacer layer thickness.« less

Spatially Resolved Quantification of Chromatin Condensation through Differential Local Rheology in Cell Nuclei Fluorescence Lifetime Imaging

PubMed Central

Spagnol, Stephen T.; Dahl, Kris Noel

2016-01-01

The linear sequence of DNA encodes access to the complete set of proteins that carry out cellular functions. Yet, much of the functionality appropriate for each cell is nested within layers of dynamic regulation and organization, including a hierarchy of chromatin structural states and spatial arrangement within the nucleus. There remain limitations in our understanding of gene expression within the context of nuclear organization from an inability to characterize hierarchical chromatin organization in situ. Here we demonstrate the use of fluorescence lifetime imaging microscopy (FLIM) to quantify and spatially resolve chromatin condensation state using cell-permeable, DNA-binding dyes (Hoechst 33342 and PicoGreen). Through in vitro and in situ experiments we demonstrate the sensitivity of fluorescence lifetime to condensation state through the mechanical effects that accompany the structural changes and are reflected through altered viscosity. The establishment of FLIM for resolving and quantifying chromatin condensation state opens the door for single-measurement mechanical studies of the nucleus and for characterizing the role of genome structure and organization in nuclear processes that accompany physiological and pathological changes. PMID:26765322

Effects of population succession on demographic and genetic processes: predictions and tests in the daylily Hemerocallis thunbergii (Liliaceae).

PubMed

Chung, Mi Yoon; Nason, John D; Chung, Myong Gi

2007-07-01

Spatial genetic structure within plant populations is influenced by variation in demographic processes through space and time, including a population's successional status. To determine how demographic structure and fine-scale genetic structure (FSGS) change with stages in a population's successional history, we studied Hemerocallis thunbergii (Liliaceae), a nocturnal flowering and hawkmoth-pollinated herbaceous perennial with rapid population turnover dynamics. We examined nine populations assigned to three successive stages of population succession: expansion, maturation, and senescence. We developed stage-specific expectations for within-population demographic and genetic structure, and then for each population quantified the spatial aggregation of individuals and genotypes using spatial autocorrelation methods (nonaccumulative O-ring and kinship statistics, respectively), and at the landscape level measured inbreeding and genetic structure using Wright's F-statistics. Analyses using the O-ring statistic revealed significant aggregation of individuals at short spatial scales in expanding and senescing populations, in particular, which may reflect restricted seed dispersal around maternal individuals combined with relatively low local population densities at these stages. Significant FSGS was found for three of four expanding, no mature, and only one senescing population, a pattern generally consistent with expectations of successional processes. Although allozyme genetic diversity was high within populations (mean %P = 78.9 and H(E) = 0.281), landscape-level differentiation among sites was also high (F(ST) = 0.166) and all populations exhibited a significant deficit of heterozygotes relative to Hardy-Weinberg expectations (range F = 0.201-0.424, mean F(IS) = 0.321). Within populations, F was not correlated with the degree of FSGS, thus suggesting inbreeding due primarily to selfing as opposed to mating among close relatives in spatially structured populations. Our results demonstrate considerable variation in the spatial distribution of individuals and patterns and magnitude of FSGS in H. thunbergii populations across the landscape. This variation is generally consistent with succession-stage-specific differences in ecological processes operating within these populations.

From mobile phone data to the spatial structure of cities

PubMed Central

Louail, Thomas; Lenormand, Maxime; Cantu Ros, Oliva G.; Picornell, Miguel; Herranz, Ricardo; Frias-Martinez, Enrique; Ramasco, José J.; Barthelemy, Marc

2014-01-01

Pervasive infrastructures, such as cell phone networks, enable to capture large amounts of human behavioral data but also provide information about the structure of cities and their dynamical properties. In this article, we focus on these last aspects by studying phone data recorded during 55 days in 31 Spanish cities. We first define an urban dilatation index which measures how the average distance between individuals evolves during the day, allowing us to highlight different types of city structure. We then focus on hotspots, the most crowded places in the city. We propose a parameter free method to detect them and to test the robustness of our results. The number of these hotspots scales sublinearly with the population size, a result in agreement with previous theoretical arguments and measures on employment datasets. We study the lifetime of these hotspots and show in particular that the hierarchy of permanent ones, which constitute the ‘heart' of the city, is very stable whatever the size of the city. The spatial structure of these hotspots is also of interest and allows us to distinguish different categories of cities, from monocentric and “segregated” where the spatial distribution is very dependent on land use, to polycentric where the spatial mixing between land uses is much more important. These results point towards the possibility of a new, quantitative classification of cities using high resolution spatio-temporal data. PMID:24923248

Heterogeneous environments shape invader impacts: integrating environmental, structural and functional effects by isoscapes and remote sensing.

PubMed

Hellmann, Christine; Große-Stoltenberg, André; Thiele, Jan; Oldeland, Jens; Werner, Christiane

2017-06-23

Spatial heterogeneity of ecosystems crucially influences plant performance, while in return plant feedbacks on their environment may increase heterogeneous patterns. This is of particular relevance for exotic plant invaders that transform native ecosystems, yet, approaches integrating geospatial information of environmental heterogeneity and plant-plant interaction are lacking. Here, we combined remotely sensed information of site topography and vegetation cover with a functional tracer of the N cycle, δ 15 N. Based on the case study of the invasion of an N 2 -fixing acacia in a nutrient-poor dune ecosystem, we present the first model that can successfully predict (R 2  = 0.6) small-scale spatial variation of foliar δ 15 N in a non-fixing native species from observed geospatial data. Thereby, the generalized additive mixed model revealed modulating effects of heterogeneous environments on invader impacts. Hence, linking remote sensing techniques with tracers of biological processes will advance our understanding of the dynamics and functioning of spatially structured heterogeneous systems from small to large spatial scales.

Dynamical Structure of a Traditional Amazonian Social Network

PubMed Central

Hooper, Paul L.; DeDeo, Simon; Caldwell Hooper, Ann E.; Gurven, Michael; Kaplan, Hillard S.

2014-01-01

Reciprocity is a vital feature of social networks, but relatively little is known about its temporal structure or the mechanisms underlying its persistence in real world behavior. In pursuit of these two questions, we study the stationary and dynamical signals of reciprocity in a network of manioc beer (Spanish: chicha; Tsimane’: shocdye’) drinking events in a Tsimane’ village in lowland Bolivia. At the stationary level, our analysis reveals that social exchange within the community is heterogeneously patterned according to kinship and spatial proximity. A positive relationship between the frequencies at which two families host each other, controlling for kinship and proximity, provides evidence for stationary reciprocity. Our analysis of the dynamical structure of this network presents a novel method for the study of conditional, or non-stationary, reciprocity effects. We find evidence that short-timescale reciprocity (within three days) is present among non- and distant-kin pairs; conversely, we find that levels of cooperation among close kin can be accounted for on the stationary hypothesis alone. PMID:25053880

Correlative live and super-resolution imaging reveals the dynamic structure of replication domains.

PubMed

Xiang, Wanqing; Roberti, M Julia; Hériché, Jean-Karim; Huet, Sébastien; Alexander, Stephanie; Ellenberg, Jan

2018-06-04

Chromosome organization in higher eukaryotes controls gene expression, DNA replication, and DNA repair. Genome mapping has revealed the functional units of chromatin at the submegabase scale as self-interacting regions called topologically associating domains (TADs) and showed they correspond to replication domains (RDs). A quantitative structural and dynamic description of RD behavior in the nucleus is, however, missing because visualization of dynamic subdiffraction-sized RDs remains challenging. Using fluorescence labeling of RDs combined with correlative live and super-resolution microscopy in situ, we determined biophysical parameters to characterize the internal organization, spacing, and mechanical coupling of RDs. We found that RDs are typically 150 nm in size and contain four co-replicating regions spaced 60 nm apart. Spatially neighboring RDs are spaced 300 nm apart and connected by highly flexible linker regions that couple their motion only <550 nm. Our pipeline allows a robust quantitative characterization of chromosome structure in situ and provides important biophysical parameters to understand general principles of chromatin organization. © 2018 Xiang et al.

Dynamical Structure of a Traditional Amazonian Social Network.

PubMed

Hooper, Paul L; DeDeo, Simon; Caldwell Hooper, Ann E; Gurven, Michael; Kaplan, Hillard S

2013-11-13

Reciprocity is a vital feature of social networks, but relatively little is known about its temporal structure or the mechanisms underlying its persistence in real world behavior. In pursuit of these two questions, we study the stationary and dynamical signals of reciprocity in a network of manioc beer (Spanish: chicha ; Tsimane': shocdye' ) drinking events in a Tsimane' village in lowland Bolivia. At the stationary level, our analysis reveals that social exchange within the community is heterogeneously patterned according to kinship and spatial proximity. A positive relationship between the frequencies at which two families host each other, controlling for kinship and proximity, provides evidence for stationary reciprocity. Our analysis of the dynamical structure of this network presents a novel method for the study of conditional, or non-stationary, reciprocity effects. We find evidence that short-timescale reciprocity (within three days) is present among non- and distant-kin pairs; conversely, we find that levels of cooperation among close kin can be accounted for on the stationary hypothesis alone.

Investigating dynamical information transfer in the brain following a TMS pulse: Insights from structural architecture.

PubMed

Amico, Enrico; Van Mierlo, Pieter; Marinazzo, Daniele; Laureys, Steven

2015-01-01

Transcranial magnetic stimulation (TMS) has been used for more than 20 years to investigate connectivity and plasticity in the human cortex. By combining TMS with high-density electroencephalography (hd-EEG), one can stimulate any cortical area and measure the effects produced by this perturbation in the rest of the cerebral cortex. The purpose of this paper is to investigate changes of information flow in the brain after TMS from a functional and structural perspective, using multimodal modeling of source reconstructed TMS/hd-EEG recordings and DTI tractography. We prove how brain dynamics induced by TMS is constrained and driven by its structure, at different spatial and temporal scales, especially when considering cross-frequency interactions. These results shed light on the function-structure organization of the brain network at the global level, and on the huge variety of information contained in it.

Investigation of magnetization dynamics in 2D Ni80Fe20 diatomic nanodot arrays

NASA Astrophysics Data System (ADS)

De, Anulekha; Mondal, Sucheta; Banerjee, Chandrima; Chaurasiya, Avinash K.; Mandal, Ruma; Otani, Yoshichika; Mitra, Rajib K.; Barman, Anjan

2017-09-01

Magnetization dynamics in Ni80Fe20 (Py) diatomic nanodots (nanodots of the same thickness but with large and small diameters that are closely placed to each other so as to act as a diatomic basis structure) embedded in 2D arrays have been investigated by the Brillouin light scattering technique. A distinct variation of resonant mode characteristics for different in-plane bias magnetic field applied along two different orientations of the lattice has been observed. Micromagnetic simulations reproduced the observed dynamical behaviour and revealed the variation of spatial distribution of collective modes of constituent single nanodots with different diameter and a diatomic unit forming the large array to understand the evolution of the magnetization dynamics from a single dot to the large array via a diatomic unit. The changes in mode frequency, spatial profiles of the modes, and appearance of new modes in a diatomic unit and its array from that of the constituent single dots indicate the strong magnetostatic interaction among the dots within the diatomic unit. Also, the occurrence of the new interacting mode at different frequencies for different orientations of the bias field indicates the change in the nature of interaction among the dots within the diatomic unit with bias magnetic field. The mode profiles also show distinct behaviour for smooth and rough-edged dots. This work motivates the study of magnonic band structure formation of such a dipolarly coupled nanodot array containing a complex double-dot unit cell.

Nonlinear electric field structures in the inner magnetosphere

DOE PAGES

Malaspina, D. M.; Andersson, L.; Ergun, R. E.; ...

2014-08-28

Recent observations by the Van Allen Probes spacecraft have demonstrated that a variety of electric field structures and nonlinear waves frequently occur in the inner terrestrial magnetosphere, including phase space holes, kinetic field-line resonances, nonlinear whistler-mode waves, and several types of double layer. However, it is nuclear whether such structures and waves have a significant impact on the dynamics of the inner magnetosphere, including the radiation belts and ring current. To make progress toward quantifying their importance, this study statistically evaluates the correlation of such structures and waves with plasma boundaries. A strong correlation is found. These statistical results, combinedmore » with observations of electric field activity at propagating plasma boundaries, are consistent with the identification of these boundaries as the source of free energy responsible for generating the electric field structures and nonlinear waves of interest. Therefore, the ability of these structures and waves to influence plasma in the inner magnetosphere is governed by the spatial extent and dynamics of macroscopic plasma boundaries in that region.« less

A mini-review on econophysics: Comparative study of Chinese and western financial markets

NASA Astrophysics Data System (ADS)

Zheng, Bo; Jiang, Xiong-Fei; Ni, Peng-Yun

2014-07-01

We present a review of our recent research in econophysics, and focus on the comparative study of Chinese and western financial markets. By virtue of concepts and methods in statistical physics, we investigate the time correlations and spatial structure of financial markets based on empirical high-frequency data. We discover that the Chinese stock market shares common basic properties with the western stock markets, such as the fat-tail probability distribution of price returns, the long-range auto-correlation of volatilities, and the persistence probability of volatilities, while it exhibits very different higher-order time correlations of price returns and volatilities, spatial correlations of individual stock prices, and large-fluctuation dynamic behaviors. Furthermore, multi-agent-based models are developed to simulate the microscopic interaction and dynamic evolution of the stock markets.

A Low-Cost PC-Based Image Workstation for Dynamic Interactive Display of Three-Dimensional Anatomy

NASA Astrophysics Data System (ADS)

Barrett, William A.; Raya, Sai P.; Udupa, Jayaram K.

1989-05-01

A system for interactive definition, automated extraction, and dynamic interactive display of three-dimensional anatomy has been developed and implemented on a low-cost PC-based image workstation. An iconic display is used for staging predefined image sequences through specified increments of tilt and rotation over a solid viewing angle. Use of a fast processor facilitates rapid extraction and rendering of the anatomy into predefined image views. These views are formatted into a display matrix in a large image memory for rapid interactive selection and display of arbitrary spatially adjacent images within the viewing angle, thereby providing motion parallax depth cueing for efficient and accurate perception of true three-dimensional shape, size, structure, and spatial interrelationships of the imaged anatomy. The visual effect is that of holding and rotating the anatomy in the hand.

Precisely cyclic sand: self-organization of periodically sheared frictional grains.

PubMed

Royer, John R; Chaikin, Paul M

2015-01-06

The disordered static structure and chaotic dynamics of frictional granular matter has occupied scientists for centuries, yet there are few organizational principles or guiding rules for this highly hysteretic, dissipative material. We show that cyclic shear of a granular material leads to dynamic self-organization into several phases with different spatial and temporal order. Using numerical simulations, we present a phase diagram in strain-friction space that shows chaotic dispersion, crystal formation, vortex patterns, and most unusually a disordered phase in which each particle precisely retraces its unique path. However, the system is not reversible. Rather, the trajectory of each particle, and the entire frictional, many-degrees-of-freedom system, organizes itself into a limit cycle absorbing state. Of particular note is that fact that the cyclic states are spatially disordered, whereas the ordered states are chaotic.

Spectra- and temperature-dependent dynamics of directly end-pumped holmium lasers

NASA Astrophysics Data System (ADS)

Ji, Encai; Shen, Yijie; Nie, Mingming; Fu, Xing; Liu, Qiang

2017-04-01

We develop a theoretical model with high accuracy for directly end-pumped Ho3+ laser system considering the influences of ground-state depletion, energy transfer up-conversion, temperature-dependent cross sections, and pump spectra shift. The heat generation in our model is precisely evaluated by calculating the transition rates of non-radiation relaxation processes among manifolds and in-band relaxation processes based on a detailed analysis of energy levels structure of holmium ions. A spatial dynamic thermal iteration method, just developed by our group, is applied to describe the coupled influences between spatial thermal effects and pump spectra. This model is verified to both adapt to the narrow-band good beam-quality pumped case and the broad-band bad beam-quality pumped case, which is in accordance with our previous reported experimental results.

Human mobility in an emerging epidemic: a key aspect for response planning

NASA Astrophysics Data System (ADS)

Poletto, Chiara; Bajardi, Paolo; Colizza, Vittoria; Ramasco, Jose J.; Tizzoni, Michele; Vespignani, Alessandro

2010-03-01

Human mobility and interactions represent key ingredients in the spreading dynamics of an infectious disease. The flows of traveling people form a network characterized by complex features, such as strong topological and traffic heterogeneities, that unfolds at different temporal and spatial scales, from short ranges to the global scale. Computational models can be developed that integrate detailed network structures based on demographic and mobility data, in order to simulate the spatial evolution of an epidemic. Focusing on the recent A(H1N1) influenza pandemic as a paradigmatic example, these approaches allow the assessment of the interplay between individual mobility and epidemic dynamics, quantifying the effects of travel restrictions in delaying the epidemic spread and the role of mobility as an additional source of information for the understanding of the early outbreak.

Precisely cyclic sand: Self-organization of periodically sheared frictional grains

PubMed Central

Royer, John R.; Chaikin, Paul M.

2015-01-01

The disordered static structure and chaotic dynamics of frictional granular matter has occupied scientists for centuries, yet there are few organizational principles or guiding rules for this highly hysteretic, dissipative material. We show that cyclic shear of a granular material leads to dynamic self-organization into several phases with different spatial and temporal order. Using numerical simulations, we present a phase diagram in strain–friction space that shows chaotic dispersion, crystal formation, vortex patterns, and most unusually a disordered phase in which each particle precisely retraces its unique path. However, the system is not reversible. Rather, the trajectory of each particle, and the entire frictional, many–degrees-of-freedom system, organizes itself into a limit cycle absorbing state. Of particular note is that fact that the cyclic states are spatially disordered, whereas the ordered states are chaotic. PMID:25538298

The “unreasonable effectiveness” of stratigraphic and geomorphic experiments

NASA Astrophysics Data System (ADS)

Paola, Chris; Straub, Kyle; Mohrig, David; Reinhardt, Liam

2009-12-01

The growth of quantitative analysis and prediction in Earth-surface science has been accompanied by growth in experimental stratigraphy and geomorphology. Experimenters have grown increasingly bold in targeting landscape elements from channel reaches up to the entire erosional networks and depositional basins, often using very small facilities. The experiments produce spatial structure and kinematics that, although imperfect, compare well with natural systems despite differences of spatial scale, time scale, material properties, and number of active processes. Experiments have been particularly useful in studying a wide range of forms of self-organized (autogenic) complexity that occur in morphodynamic systems. Autogenic dynamics creates much of the spatial structure we see in the landscape and in preserved strata, and is strongly associated with sediment storage and release. The observed consistency between experimental and field systems despite large differences in governing dimensionless numbers is what we mean by "unreasonable effectiveness". We suggest that unreasonable experimental effectiveness arises from natural scale independence. We generalize existing ideas to relate internal similarity, in which a small part of a system is similar to the larger system, to external similarity, in which a small copy of a system is similar to the larger system. We propose that internal similarity implies external similarity, though not the converse. The external similarity of landscape experiments to natural landscapes suggests that natural scale independence may be even more characteristic of morphodynamics than it is of better studied cases such as turbulence. We urge a shift in emphasis in experimental stratigraphy and geomorphology away from classical dynamical scaling and towards a quantitative understanding of the origins and limits of scale independence. Other research areas with strong growth potential in experimental surface dynamics include physical-biotic interactions, cohesive effects, stochastic processes, the interplay of structural and geomorphic self-organization, extraction of quantitative process information from landscape and stratigraphic records, and closer interaction between experimentation and theory.

Impacts of large dams on the complexity of suspended sediment dynamics in the Yangtze River

NASA Astrophysics Data System (ADS)

Wang, Yuankun; Rhoads, Bruce L.; Wang, Dong; Wu, Jichun; Zhang, Xiao

2018-03-01

The Yangtze River is one of the largest and most important rivers in the world. Over the past several decades, the natural sediment regime of the Yangtze River has been altered by the construction of dams. This paper uses multi-scale entropy analysis to ascertain the impacts of large dams on the complexity of high-frequency suspended sediment dynamics in the Yangtze River system, especially after impoundment of the Three Gorges Dam (TGD). In this study, the complexity of sediment dynamics is quantified by framing it within the context of entropy analysis of time series. Data on daily sediment loads for four stations located in the mainstem are analyzed for the past 60 years. The results indicate that dam construction has reduced the complexity of short-term (1-30 days) variation in sediment dynamics near the structures, but that complexity has actually increased farther downstream. This spatial pattern seems to reflect a filtering effect of the dams on the on the temporal pattern of sediment loads as well as decreased longitudinal connectivity of sediment transfer through the river system, resulting in downstream enhancement of the influence of local sediment inputs by tributaries on sediment dynamics. The TGD has had a substantial impact on the complexity of sediment series in the mainstem of the Yangtze River, especially after it became fully operational. This enhanced impact is attributed to the high trapping efficiency of this dam and its associated large reservoir. The sediment dynamics "signal" becomes more spatially variable after dam construction. This study demonstrates the spatial influence of dams on the high-frequency temporal complexity of sediment regimes and provides valuable information that can be used to guide environmental conservation of the Yangtze River.

Habitat fragmentation effects depend on complex interactions between population size and dispersal ability: Modeling influences of roads, agriculture and residential development across a range of life-history characteristics [chapter 20

Treesearch

Samuel A. Cushman; Bradley W. Compton; Kevin McGarigal

2010-01-01

Habitat loss and fragmentation are widely believed to be the most important drivers of extinction (Leakey and Lewin 1995). The habitats in which organisms live are spatially structured at a number of scales, and these patterns interact with organism perception and behavior to drive population dynamics and community structure (Johnson et al. 1992). Anthropogenic habitat...

Knowledge representation of rock plastic deformation

NASA Astrophysics Data System (ADS)

Davarpanah, Armita; Babaie, Hassan

2017-04-01

The first iteration of the Rock Plastic Deformation (RPD) ontology models the semantics of the dynamic physical and chemical processes and mechanisms that occur during the deformation of the generally inhomogeneous polycrystalline rocks. The ontology represents the knowledge about the production, reconfiguration, displacement, and consumption of the structural components that participate in these processes. It also formalizes the properties that are known by the structural geology and metamorphic petrology communities to hold between the instances of the spatial components and the dynamic processes, the state and system variables, the empirical flow laws that relate the variables, and the laboratory testing conditions and procedures. The modeling of some of the complex physio-chemical, mathematical, and informational concepts and relations of the RPD ontology is based on the class and property structure of some well-established top-level ontologies. The flexible and extensible design of the initial version of the RPD ontology allows it to develop into a model that more fully represents the knowledge of plastic deformation of rocks under different spatial and temporal scales in the laboratory and in solid Earth. The ontology will be used to annotate the datasets related to the microstructures and physical-chemical processes that involve them. This will help the autonomous and globally distributed communities of experimental structural geologists and metamorphic petrologists to coherently and uniformly distribute, discover, access, share, and use their data through automated reasoning and enhanced data integration and software interoperability.

Long-gauge FBGs interrogated by DTR3 for dynamic distributed strain measurement of helicopter blade model

NASA Astrophysics Data System (ADS)

Nishiyama, M.; Igawa, H.; Kasai, T.; Watanabe, N.

2014-05-01

In this paper, we describe characteristics of distributed strain sensing based on a Delayed Transmission/Reflection Ratiometric Reflectometry (DTR3) scheme with a long-gauge Fiber Bragg Grating (FBG), which is attractive to dynamic structural deformation monitoring such as a helicopter blade and an airplane wing. The DTR3 interrogator using the longgauge FBG has capability of detecting distributed strain with 50 cm spatial resolution in 100 Hz sampling rate. We evaluated distributed strain sensing characteristics of the long-gauge FBG attached on a 5.5 m helicopter blade model in static tests and free vibration dynamic tests.

High spatial resolution three-dimensional mapping of vegetation spectral dynamics using computer vision and hobbyist unmanned aerial vehicles

NASA Astrophysics Data System (ADS)

Dandois, J. P.; Ellis, E. C.

2013-12-01

High spatial resolution three-dimensional (3D) measurements of vegetation by remote sensing are advancing ecological research and environmental management. However, substantial economic and logistical costs limit this application, especially for observing phenological dynamics in ecosystem structure and spectral traits. Here we demonstrate a new aerial remote sensing system enabling routine and inexpensive aerial 3D measurements of canopy structure and spectral attributes, with properties similar to those of LIDAR, but with RGB (red-green-blue) spectral attributes for each point, enabling high frequency observations within a single growing season. This 'Ecosynth' methodology applies photogrammetric ''Structure from Motion'' computer vision algorithms to large sets of highly overlapping low altitude (< 130 m) aerial photographs acquired using off-the-shelf digital cameras mounted on an inexpensive (< USD$4000), lightweight (< 2 kg), hobbyist-grade unmanned aerial system (UAS). Ecosynth 3D point clouds with densities of 30 - 67 points m-2 were produced using commercial computer vision software from digital photographs acquired repeatedly by UAS over three 6.25 ha (250 m x 250 m) Temperate Deciduous forest sites in Maryland USA. Ecosynth canopy height maps (CHMs) were strong predictors of field-measured tree heights (R2 0.63 to 0.84) and were highly correlated with a LIDAR CHM (R 0.87) acquired 4 days earlier, though Ecosynth-based estimates of aboveground biomass densities included significant errors (31 - 36% of field-based estimates). Repeated scanning of a 0.25 ha forested area at six different times across a 16 month period revealed ecologically significant dynamics in canopy color at different heights and a structural shift upward in canopy density, as demonstrated by changes in vertical height profiles of point density and relative RGB brightness. Changes in canopy relative greenness were highly correlated (R2 = 0.88) with MODIS NDVI time series for the same area and vertical differences in canopy color revealed the early green up of the dominant canopy species, Liriodendron tulipifera, strong evidence that Ecosynth time series measurements capture vegetation structural and spectral dynamics at the spatial scale of individual trees. Observing canopy phenology in 3D at high temporal resolutions represents a breakthrough in forest ecology. Inexpensive user-deployed technologies for multispectral 3D scanning of vegetation at landscape scales (< 1 km2) heralds a new era of participatory remote sensing by field ecologists, community foresters and the interested public.

Modelling the development and arrangement of the primary vascular structure in plants.

PubMed

Cartenì, Fabrizio; Giannino, Francesco; Schweingruber, Fritz Hans; Mazzoleni, Stefano

2014-09-01

The process of vascular development in plants results in the formation of a specific array of bundles that run throughout the plant in a characteristic spatial arrangement. Although much is known about the genes involved in the specification of procambium, phloem and xylem, the dynamic processes and interactions that define the development of the radial arrangement of such tissues remain elusive. This study presents a spatially explicit reaction-diffusion model defining a set of logical and functional rules to simulate the differentiation of procambium, phloem and xylem and their spatial patterns, starting from a homogeneous group of undifferentiated cells. Simulation results showed that the model is capable of reproducing most vascular patterns observed in plants, from primitive and simple structures made up of a single strand of vascular bundles (protostele), to more complex and evolved structures, with separated vascular bundles arranged in an ordered pattern within the plant section (e.g. eustele). The results presented demonstrate, as a proof of concept, that a common genetic-molecular machinery can be the basis of different spatial patterns of plant vascular development. Moreover, the model has the potential to become a useful tool to test different hypotheses of genetic and molecular interactions involved in the specification of vascular tissues.

A management-oriented framework for selecting metrics used to assess habitat- and path-specific quality in spatially structured populations

USGS Publications Warehouse

Nicol, Sam; Wiederholt, Ruscena; Diffendorfer, James E.; Mattsson, Brady; Thogmartin, Wayne E.; Semmens, Darius J.; Laura Lopez-Hoffman,; Norris, Ryan

2016-01-01

Mobile species with complex spatial dynamics can be difficult to manage because their population distributions vary across space and time, and because the consequences of managing particular habitats are uncertain when evaluated at the level of the entire population. Metrics to assess the importance of habitats and pathways connecting habitats in a network are necessary to guide a variety of management decisions. Given the many metrics developed for spatially structured models, it can be challenging to select the most appropriate one for a particular decision. To guide the management of spatially structured populations, we define three classes of metrics describing habitat and pathway quality based on their data requirements (graph-based, occupancy-based, and demographic-based metrics) and synopsize the ecological literature relating to these classes. Applying the first steps of a formal decision-making approach (problem framing, objectives, and management actions), we assess the utility of metrics for particular types of management decisions. Our framework can help managers with problem framing, choosing metrics of habitat and pathway quality, and to elucidate the data needs for a particular metric. Our goal is to help managers to narrow the range of suitable metrics for a management project, and aid in decision-making to make the best use of limited resources.

Atomic-Scale Nuclear Spin Imaging Using Quantum-Assisted Sensors in Diamond

NASA Astrophysics Data System (ADS)

Ajoy, A.; Bissbort, U.; Lukin, M. D.; Walsworth, R. L.; Cappellaro, P.

2015-01-01

Nuclear spin imaging at the atomic level is essential for the understanding of fundamental biological phenomena and for applications such as drug discovery. The advent of novel nanoscale sensors promises to achieve the long-standing goal of single-protein, high spatial-resolution structure determination under ambient conditions. In particular, quantum sensors based on the spin-dependent photoluminescence of nitrogen-vacancy (NV) centers in diamond have recently been used to detect nanoscale ensembles of external nuclear spins. While NV sensitivity is approaching single-spin levels, extracting relevant information from a very complex structure is a further challenge since it requires not only the ability to sense the magnetic field of an isolated nuclear spin but also to achieve atomic-scale spatial resolution. Here, we propose a method that, by exploiting the coupling of the NV center to an intrinsic quantum memory associated with the nitrogen nuclear spin, can reach a tenfold improvement in spatial resolution, down to atomic scales. The spatial resolution enhancement is achieved through coherent control of the sensor spin, which creates a dynamic frequency filter selecting only a few nuclear spins at a time. We propose and analyze a protocol that would allow not only sensing individual spins in a complex biomolecule, but also unraveling couplings among them, thus elucidating local characteristics of the molecule structure.

A simulation analysis to characterize the dynamics of vaccinating behaviour on contact networks.

PubMed

Perisic, Ana; Bauch, Chris T

2009-05-28

Human behavior influences infectious disease transmission, and numerous "prevalence-behavior" models have analyzed this interplay. These previous analyses assumed homogeneously mixing populations without spatial or social structure. However, spatial and social heterogeneity are known to significantly impact transmission dynamics and are particularly relevant for certain diseases. Previous work has demonstrated that social contact structure can change the individual incentive to vaccinate, thus enabling eradication of a disease under a voluntary vaccination policy when the corresponding homogeneous mixing model predicts that eradication is impossible due to free rider effects. Here, we extend this work and characterize the range of possible behavior-prevalence dynamics on a network. We simulate transmission of a vaccine-preventable infection through a random, static contact network. Individuals choose whether or not to vaccinate on any given day according to perceived risks of vaccination and infection. We find three possible outcomes for behavior-prevalence dynamics on this type of network: small final number vaccinated and final epidemic size (due to rapid control through voluntary ring vaccination); large final number vaccinated and significant final epidemic size (due to imperfect voluntary ring vaccination), and little or no vaccination and large final epidemic size (corresponding to little or no voluntary ring vaccination). We also show that the social contact structure enables eradication under a broad range of assumptions, except when vaccine risk is sufficiently high, the disease risk is sufficiently low, or individuals vaccinate too late for the vaccine to be effective. For populations where infection can spread only through social contact network, relatively small differences in parameter values relating to perceived risk or vaccination behavior at the individual level can translate into large differences in population-level outcomes such as final size and final number vaccinated. The qualitative outcome of rational, self interested behaviour under a voluntary vaccination policy can vary substantially depending on interactions between social contact structure, perceived vaccine and disease risks, and the way that individual vaccination decision-making is modelled.

A simulation analysis to characterize the dynamics of vaccinating behaviour on contact networks

PubMed Central

2009-01-01

Background Human behavior influences infectious disease transmission, and numerous "prevalence-behavior" models have analyzed this interplay. These previous analyses assumed homogeneously mixing populations without spatial or social structure. However, spatial and social heterogeneity are known to significantly impact transmission dynamics and are particularly relevant for certain diseases. Previous work has demonstrated that social contact structure can change the individual incentive to vaccinate, thus enabling eradication of a disease under a voluntary vaccination policy when the corresponding homogeneous mixing model predicts that eradication is impossible due to free rider effects. Here, we extend this work and characterize the range of possible behavior-prevalence dynamics on a network. Methods We simulate transmission of a vaccine-prevetable infection through a random, static contact network. Individuals choose whether or not to vaccinate on any given day according to perceived risks of vaccination and infection. Results We find three possible outcomes for behavior-prevalence dynamics on this type of network: small final number vaccinated and final epidemic size (due to rapid control through voluntary ring vaccination); large final number vaccinated and significant final epidemic size (due to imperfect voluntary ring vaccination), and little or no vaccination and large final epidemic size (corresponding to little or no voluntary ring vaccination). We also show that the social contact structure enables eradication under a broad range of assumptions, except when vaccine risk is sufficiently high, the disease risk is sufficiently low, or individuals vaccinate too late for the vaccine to be effective. Conclusion For populations where infection can spread only through social contact network, relatively small differences in parameter values relating to perceived risk or vaccination behavior at the individual level can translate into large differences in population-level outcomes such as final size and final number vaccinated. The qualitative outcome of rational, self interested behaviour under a voluntary vaccination policy can vary substantially depending on interactions between social contact structure, perceived vaccine and disease risks, and the way that individual vaccination decision-making is modelled. PMID:19476616

Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota.

PubMed

de Muinck, Eric J; Lundin, Knut E A; Trosvik, Pål

2017-01-01

The gastrointestinal (GI) microbiome is a densely populated ecosystem where dynamics are determined by interactions between microbial community members, as well as host factors. The spatial organization of this system is thought to be important in human health, yet this aspect of our resident microbiome is still poorly understood. In this study, we report significant spatial structure of the GI microbiota, and we identify general categories of spatial patterning in the distribution of microbial taxa along a healthy human GI tract. We further estimate the biotic interaction structure in the GI microbiota, both through time series and cooccurrence modeling of microbial community data derived from a large number of sequentially collected fecal samples. Comparison of these two approaches showed that species pairs involved in significant negative interactions had strong positive contemporaneous correlations and vice versa, while for species pairs without significant interactions, contemporaneous correlations were distributed around zero. We observed similar patterns when comparing these models to the spatial correlations between taxa identified in the adherent microbiota. This suggests that colocalization of microbial taxon pairs, and thus the spatial organization of the GI microbiota, is driven, at least in part, by direct or indirect biotic interactions. Thus, our study can provide a basis for an ecological interpretation of the biogeography of the human gut. IMPORTANCE The human gut microbiome is the subject of intense study due to its importance in health and disease. The majority of these studies have been based on the analysis of feces. However, little is known about how the microbial composition in fecal samples relates to the spatial distribution of microbial taxa along the gastrointestinal tract. By characterizing the microbial content both in intestinal tissue samples and in fecal samples obtained daily, we provide a conceptual framework for how the spatial structure relates to biotic interactions on the community level. We further describe general categories of spatial distribution patterns and identify taxa conforming to these categories. To our knowledge, this is the first study combining spatial and temporal analyses of the human gut microbiome. This type of analysis can be used for identifying candidate probiotics and designing strategies for clinical intervention.

The ambivalent effect of lattice structure on a spatial game

NASA Astrophysics Data System (ADS)

Zhang, Hui; Gao, Meng; Li, Zizhen; Maa, Zhihui; Wang, Hailong

2011-06-01

The evolution of cooperation is studied in lattice-structured populations, in which each individual who adopts one of the following strategies ‘always defect' (ALLD), ‘tit-for-tat' (TFT), and ‘always cooperate' (ALLC) plays the repeated Prisoner's Dilemma game with its neighbors according to an asynchronous update rule. Computer simulations are applied to analyse the dynamics depending on major parameters. Mathematical analyses based on invasion probability analysis, mean-field approximation, as well as pair approximation are also used. We find that the lattice structure promotes the evolution of cooperation compared with a non-spatial population, this is also confirmed by invasion probability analysis in one dimension. Meanwhile, it also inhibits the evolution of cooperation due to the advantage of being spiteful, which indicates the key role of specific life-history assumptions. Mean-field approximation fails to predict the outcome of computer simulations. Pair approximation is accurate in two dimensions but fails in one dimension.

Submarine slope failures due to pipe structure formation.

PubMed

Elger, Judith; Berndt, Christian; Rüpke, Lars; Krastel, Sebastian; Gross, Felix; Geissler, Wolfram H

2018-02-19

There is a strong spatial correlation between submarine slope failures and the occurrence of gas hydrates. This has been attributed to the dynamic nature of gas hydrate systems and the potential reduction of slope stability due to bottom water warming or sea level drop. However, 30 years of research into this process found no solid supporting evidence. Here we present new reflection seismic data from the Arctic Ocean and numerical modelling results supporting a different link between hydrates and slope stability. Hydrates reduce sediment permeability and cause build-up of overpressure at the base of the gas hydrate stability zone. Resulting hydro-fracturing forms pipe structures as pathways for overpressured fluids to migrate upward. Where these pipe structures reach shallow permeable beds, this overpressure transfers laterally and destabilises the slope. This process reconciles the spatial correlation of submarine landslides and gas hydrate, and it is independent of environmental change and water depth.

Chromatin Insulators and Topological Domains: Adding New Dimensions to 3D Genome Architecture

PubMed Central

Matharu, Navneet K.; Ahanger, Sajad H.

2015-01-01

The spatial organization of metazoan genomes has a direct influence on fundamental nuclear processes that include transcription, replication, and DNA repair. It is imperative to understand the mechanisms that shape the 3D organization of the eukaryotic genomes. Chromatin insulators have emerged as one of the central components of the genome organization tool-kit across species. Recent advancements in chromatin conformation capture technologies have provided important insights into the architectural role of insulators in genomic structuring. Insulators are involved in 3D genome organization at multiple spatial scales and are important for dynamic reorganization of chromatin structure during reprogramming and differentiation. In this review, we will discuss the classical view and our renewed understanding of insulators as global genome organizers. We will also discuss the plasticity of chromatin structure and its re-organization during pluripotency and differentiation and in situations of cellular stress. PMID:26340639

Spatial and temporal features of the growth of a bacterial species colonizing the zebrafish gut.

PubMed

Jemielita, Matthew; Taormina, Michael J; Burns, Adam R; Hampton, Jennifer S; Rolig, Annah S; Guillemin, Karen; Parthasarathy, Raghuveer

2014-12-16

The vertebrate intestine is home to microbial ecosystems that play key roles in host development and health. Little is known about the spatial and temporal dynamics of these microbial communities, limiting our understanding of fundamental properties, such as their mechanisms of growth, propagation, and persistence. To address this, we inoculated initially germ-free zebrafish larvae with fluorescently labeled strains of an Aeromonas species, representing an abundant genus in the zebrafish gut. Using light sheet fluorescence microscopy to obtain three-dimensional images spanning the gut, we quantified the entire bacterial load, as founding populations grew from tens to tens of thousands of cells over several hours. The data yield the first ever measurements of the growth kinetics of a microbial species inside a live vertebrate intestine and show dynamics that robustly fit a logistic growth model. Intriguingly, bacteria were nonuniformly distributed throughout the gut, and bacterial aggregates showed considerably higher growth rates than did discrete individuals. The form of aggregate growth indicates intrinsically higher division rates for clustered bacteria, rather than surface-mediated agglomeration onto clusters. Thus, the spatial organization of gut bacteria both relative to the host and to each other impacts overall growth kinetics, suggesting that spatial characterizations will be an important input to predictive models of host-associated microbial community assembly. Our intestines are home to vast numbers of microbes that influence many aspects of health and disease. Though we now know a great deal about the constituents of the gut microbiota, we understand very little about their spatial structure and temporal dynamics in humans or in any animal: how microbial populations establish themselves, grow, fluctuate, and persist. To address this, we made use of a model organism, the zebrafish, and a new optical imaging technique, light sheet fluorescence microscopy, to visualize for the first time the colonization of a live, vertebrate gut by specific bacteria with sufficient resolution to quantify the population over a range from a few individuals to tens of thousands of bacterial cells. Our results provide unprecedented measures of bacterial growth kinetics and also show the influence of spatial structure on bacterial populations, which can be revealed only by direct imaging. Copyright © 2014 Jemielita et al.

Motion-Dependent Filling-In of Spatiotemporal Information at the Blind Spot

PubMed Central

Maus, Gerrit W.; Whitney, David

2016-01-01

We usually do not notice the blind spot, a receptor-free region on the retina. Stimuli extending through the blind spot appear filled in. However, if an object does not reach through but ends in the blind spot, it is perceived as “cut off” at the boundary. Here we show that even when there is no corresponding stimulation at opposing edges of the blind spot, well known motion-induced position shifts also extend into the blind spot and elicit a dynamic filling-in process that allows spatial structure to be extrapolated into the blind spot. We presented observers with sinusoidal gratings that drifted into or out of the blind spot, or flickered in counterphase. Gratings moving into the blind spot were perceived to be longer than those moving out of the blind spot or flickering, revealing motion-dependent filling-in. Further, observers could perceive more of a grating’s spatial structure inside the blind spot than would be predicted from simple filling-in of luminance information from the blind spot edge. This is evidence for a dynamic filling-in process that uses spatiotemporal information from the motion system to extrapolate visual percepts into the scotoma of the blind spot. Our findings also provide further support for the notion that an explicit spatial shift of topographic representations contributes to motion-induced position illusions. PMID:27100795

Motion-Dependent Filling-In of Spatiotemporal Information at the Blind Spot.

PubMed

Maus, Gerrit W; Whitney, David

2016-01-01

We usually do not notice the blind spot, a receptor-free region on the retina. Stimuli extending through the blind spot appear filled in. However, if an object does not reach through but ends in the blind spot, it is perceived as "cut off" at the boundary. Here we show that even when there is no corresponding stimulation at opposing edges of the blind spot, well known motion-induced position shifts also extend into the blind spot and elicit a dynamic filling-in process that allows spatial structure to be extrapolated into the blind spot. We presented observers with sinusoidal gratings that drifted into or out of the blind spot, or flickered in counterphase. Gratings moving into the blind spot were perceived to be longer than those moving out of the blind spot or flickering, revealing motion-dependent filling-in. Further, observers could perceive more of a grating's spatial structure inside the blind spot than would be predicted from simple filling-in of luminance information from the blind spot edge. This is evidence for a dynamic filling-in process that uses spatiotemporal information from the motion system to extrapolate visual percepts into the scotoma of the blind spot. Our findings also provide further support for the notion that an explicit spatial shift of topographic representations contributes to motion-induced position illusions.

HESS Opinions: Functional units: a novel framework to explore the link between spatial organization and hydrological functioning of intermediate scale catchments

NASA Astrophysics Data System (ADS)

Zehe, E.; Ehret, U.; Pfister, L.; Blume, T.; Schröder, B.; Westhoff, M.; Jackisch, C.; Schymanski, S. J.; Weiler, M.; Schulz, K.; Allroggen, N.; Tronicke, J.; Dietrich, P.; Scherer, U.; Eccard, J.; Wulfmeyer, V.; Kleidon, A.

2014-03-01

This opinion paper proposes a novel framework for exploring how spatial organization alongside with spatial heterogeneity controls functioning of intermediate scale catchments of organized complexity. Key idea is that spatial organization in landscapes implies that functioning of intermediate scale catchments is controlled by a hierarchy of functional units: hillslope scale lead topologies and embedded elementary functional units (EFUs). We argue that similar soils and vegetation communities and thus also soil structures "co-developed" within EFUs in an adaptive, self-organizing manner as they have been exposed to similar flows of energy, water and nutrients from the past to the present. Class members of the same EFU (class) are thus deemed to belong to the same ensemble with respect to controls of the energy balance and related vertical flows of capillary bounded soil water and heat. Class members of superordinate lead topologies are characterized by the same spatially organized arrangement of EFUs along the gradient driving lateral flows of free water as well as a similar surface and bedrock topography. We hence postulate that they belong to the same ensemble with respect to controls on rainfall runoff transformation and related vertical and lateral fluxes of free water. We expect class members of these functional units to have a distinct way how their architecture controls the interplay of state dynamics and integral flows, which is typical for all members of one class but dissimilar among the classes. This implies that we might infer on the typical dynamic behavior of the most important classes of EFU and lead topologies in a catchment, by thoroughly characterizing a few members of each class. A major asset of the proposed framework, which steps beyond the concept of hydrological response units, is that it can be tested experimentally. In this respect, we reflect on suitable strategies based on stratified observations drawing from process hydrology, soil physics, geophysics, ecology and remote sensing which are currently conducted in replicates of candidate functional units in the Attert basin (Luxembourg), to search for typical and similar functional and structural characteristics. A second asset of this framework is that it blueprints a way towards a structurally more adequate model concept for water and energy cycles in intermediate scale catchments, which balances necessary complexity with falsifiability. This is because EFU and lead topologies are deemed to mark a hierarchy of "scale breaks" where simplicity with respect to the energy balance and stream flow generation emerges from spatially organized process-structure interactions. This offers the opportunity for simplified descriptions of these processes that are nevertheless physically and thermodynamically consistent. In this respect we reflect on a candidate model structure that (a) may accommodate distributed observations of states and especially terrestrial controls on driving gradients to constrain the space of feasible model structures and (b) allows testing the possible added value of organizing principles to understand the role of spatial organization from an optimality perspective.

Modelling Southern Ocean ecosystems: krill, the food-web, and the impacts of harvesting.

PubMed

Hill, S L; Murphy, E J; Reid, K; Trathan, P N; Constable, A J

2006-11-01

The ecosystem approach to fisheries recognises the interdependence between harvested species and other ecosystem components. It aims to account for the propagation of the effects of harvesting through the food-web. The formulation and evaluation of ecosystem-based management strategies requires reliable models of ecosystem dynamics to predict these effects. The krill-based system in the Southern Ocean was the focus of some of the earliest models exploring such effects. It is also a suitable example for the development of models to support the ecosystem approach to fisheries because it has a relatively simple food-web structure and progress has been made in developing models of the key species and interactions, some of which has been motivated by the need to develop ecosystem-based management. Antarctic krill, Euphausia superba, is the main target species for the fishery and the main prey of many top predators. It is therefore critical to capture the processes affecting the dynamics and distribution of krill in ecosystem dynamics models. These processes include environmental influences on recruitment and the spatially variable influence of advection. Models must also capture the interactions between krill and its consumers, which are mediated by the spatial structure of the environment. Various models have explored predator-prey population dynamics with simplistic representations of these interactions, while others have focused on specific details of the interactions. There is now a pressing need to develop plausible and practical models of ecosystem dynamics that link processes occurring at these different scales. Many studies have highlighted uncertainties in our understanding of the system, which indicates future priorities in terms of both data collection and developing methods to evaluate the effects of these uncertainties on model predictions. We propose a modelling approach that focuses on harvested species and their monitored consumers and that evaluates model uncertainty by using alternative structures and functional forms in a Monte Carlo framework.

Dynamic Connectivity Patterns in Conscious and Unconscious Brain

PubMed Central

Ma, Yuncong; Hamilton, Christina

2017-01-01

Abstract Brain functional connectivity undergoes dynamic changes from the awake to unconscious states. However, how the dynamics of functional connectivity patterns are linked to consciousness at the behavioral level remains elusive. In this study, we acquired resting-state functional magnetic resonance imaging data during wakefulness and graded levels of consciousness in rats. Data were analyzed using a dynamic approach combining the sliding window method and k-means clustering. Our results demonstrate that whole-brain networks contained several quasi-stable patterns that dynamically recurred from the awake state into anesthetized states. Remarkably, two brain connectivity states with distinct spatial similarity to the structure of anatomical connectivity were strongly biased toward high and low consciousness levels, respectively. These results provide compelling neuroimaging evidence linking the dynamics of whole-brain functional connectivity patterns and states of consciousness at the behavioral level. PMID:27846731

Decomposing risk: landscape structure and wolf behavior generate different predation patterns in two sympatric ungulates.

PubMed

Gervasi, Vincenzo; Sand, Hakan; Zimmermann, Barbara; Mattisson, Jenny; Wabakken, Petter; Linnell, John D C

2013-10-01

Recolonizing carnivores can have a large impact on the status of wild ungulates, which have often modified their behavior in the absence of predation. Therefore, understanding the dynamics of reestablished predator-prey systems is crucial to predict their potential ecosystem effects. We decomposed the spatial structure of predation by recolonizing wolves (Canis lupus) on two sympatric ungulates, moose (Alces alces) and roe deer (Capreolus capreolus), in Scandinavia during a 10-year study. We monitored 18 wolves with GPS collars, distributed over 12 territories, and collected records from predation events. By using conditional logistic regression, we assessed the contributions of three main factors, the utilization patterns of each wolf territory, the spatial distribution of both prey species, and fine-scale landscape structure, in determining the spatial structure of moose and roe deer predation risk. The reestablished predator-prey system showed a remarkable spatial variation in kill occurrence at the intra-territorial level, with kill probabilities varying by several orders of magnitude inside the same territory. Variation in predation risk was evident also when a spatially homogeneous probability for a wolf to encounter a prey was simulated. Even inside the same territory, with the same landscape structure, and when exposed to predation by the same wolves, the two prey species experienced an opposite spatial distribution of predation risk. In particular, increased predation risk for moose was associated with open areas, especially clearcuts and young forest stands, whereas risk was lowered for roe deer in the same habitat types. Thus, fine-scale landscape structure can generate contrasting predation risk patterns in sympatric ungulates, so that they can experience large differences in the spatial distribution of risk and refuge areas when exposed to predation by a recolonizing predator. Territories with an earlier recolonization were not associated with a lower hunting success for wolves. Such constant efficiency in wolf predation during the recolonization process is in line with previous findings about the naive nature of Scandinavian moose to wolf predation. This, together with the human-dominated nature of the Scandinavian ecosystem, seems to limit the possibility for wolves to have large ecosystem effects and to establish a behaviorally mediated trophic cascade in Scandinavia.

Dynamical modeling and free vibration analysis of spinning pipes conveying fluid with axial deployment

NASA Astrophysics Data System (ADS)

Liang, Feng; Yang, Xiao-Dong; Zhang, Wei; Qian, Ying-Jing

2018-03-01

In this paper, a dynamical model of simply-supported spinning pipes conveying fluid with axial deployment is proposed and the transverse free vibration and stability for such a doubly gyroscopic system involving time-dependent parameters are investigated. The partial differential equations of motion are derived by the extended Hamilton principle and then truncated by the Galerkin technique. The time-variant frequencies, mode shapes and responses to initial conditions are comprehensively investigated to reveal the dynamical essence of the system. It is indicated that the qualitative stability evolution of the system mainly depends on the effect of fluid-structure interaction (FSI), while the spinning motion will enhance the pipe rigidity and eliminate the buckling instability. The dynamical evolution of a retracting pipe is almost inverse to that of the deploying one. The pipe possesses different mode configurations of spatial curves as the pipe length increases and some modal and response characteristics of the present system are found rather distinct from those of deploying cantilevered structures.

FATE-HD: A spatially and temporally explicit integrated model for predicting vegetation structure and diversity at regional scale

PubMed Central

Isabelle, Boulangeat; Damien, Georges; Wilfried, Thuiller

2014-01-01

During the last decade, despite strenuous efforts to develop new models and compare different approaches, few conclusions have been drawn on their ability to provide robust biodiversity projections in an environmental change context. The recurring suggestions are that models should explicitly (i) include spatiotemporal dynamics; (ii) consider multiple species in interactions; and (iii) account for the processes shaping biodiversity distribution. This paper presents a biodiversity model (FATE-HD) that meets this challenge at regional scale by combining phenomenological and process-based approaches and using well-defined plant functional groups. FATE-HD has been tested and validated in a French National Park, demonstrating its ability to simulate vegetation dynamics, structure and diversity in response to disturbances and climate change. The analysis demonstrated the importance of considering biotic interactions, spatio-temporal dynamics, and disturbances in addition to abiotic drivers to simulate vegetation dynamics. The distribution of pioneer trees was particularly improved, as were all undergrowth functional groups. PMID:24214499

Detecting spatial ontogenetic niche shifts in complex dendritic ecological networks

USGS Publications Warehouse

Fields, William R.; Grant, Evan H. Campbell; Lowe, Winsor H.

2017-01-01

Ontogenetic niche shifts (ONS) are important drivers of population and community dynamics, but they can be difficult to identify for species with prolonged larval or juvenile stages, or for species that inhabit continuous habitats. Most studies of ONS focus on single transitions among discrete habitat patches at local scales. However, for species with long larval or juvenile periods, affinity for particular locations within connected habitat networks may differ among cohorts. The resulting spatial patterns of distribution can result from a combination of landscape-scale habitat structure, position of a habitat patch within a network, and local habitat characteristics—all of which may interact and change as individuals grow. We estimated such spatial ONS for spring salamanders (Gyrinophilus porphyriticus), which have a larval period that can last 4 years or more. Using mixture models to identify larval cohorts from size frequency data, we fit occupancy models for each age class using two measures of the branching structure of stream networks and three measures of stream network position. Larval salamander cohorts showed different preferences for the position of a site within the stream network, and the strength of these responses depended on the basin-wide spatial structure of the stream network. The isolation of a site had a stronger effect on occupancy in watersheds with more isolated headwater streams, while the catchment area, which is associated with gradients in stream habitat, had a stronger effect on occupancy in watersheds with more paired headwater streams. Our results show that considering the spatial structure of habitat networks can provide new insights on ONS in long-lived species.

Dynamic decoupling and local atomic order of a model multicomponent metallic glass-former.

PubMed

Kim, Jeongmin; Sung, Bong June

2015-06-17

The dynamics of multicomponent metallic alloys is spatially heterogeneous near glass transition. The diffusion coefficient of one component of the metallic alloys may also decouple from those of other components, i.e., the diffusion coefficient of each component depends differently on the viscosity of metallic alloys. In this work we investigate the dynamic heterogeneity and decoupling of a model system for multicomponent Pd43Cu27Ni10P20 melts by using a hard sphere model that considers the size disparity of alloys but does not take chemical effects into account. We also study how such dynamic behaviors would relate to the local atomic structure of metallic alloys. We find, from molecular dynamics simulations, that the smallest component P of multicomponent Pd43Cu27Ni10P20 melts becomes dynamically heterogeneous at a translational relaxation time scale and that the largest major component Pd forms a slow subsystem, which has been considered mainly responsible for the stabilization of amorphous state of alloys. The heterogeneous dynamics of P atoms accounts for the breakdown of Stokes-Einstein relation and also leads to the dynamic decoupling of P and Pd atoms. The dynamically heterogeneous P atoms decrease the lifetime of the local short-range atomic orders of both icosahedral and close-packed structures by orders of magnitude.

Mapping atomic motions with ultrabright electrons: towards fundamental limits in space-time resolution.

PubMed

Manz, Stephanie; Casandruc, Albert; Zhang, Dongfang; Zhong, Yinpeng; Loch, Rolf A; Marx, Alexander; Hasegawa, Taisuke; Liu, Lai Chung; Bayesteh, Shima; Delsim-Hashemi, Hossein; Hoffmann, Matthias; Felber, Matthias; Hachmann, Max; Mayet, Frank; Hirscht, Julian; Keskin, Sercan; Hada, Masaki; Epp, Sascha W; Flöttmann, Klaus; Miller, R J Dwayne

2015-01-01

The long held objective of directly observing atomic motions during the defining moments of chemistry has been achieved based on ultrabright electron sources that have given rise to a new field of atomically resolved structural dynamics. This class of experiments requires not only simultaneous sub-atomic spatial resolution with temporal resolution on the 100 femtosecond time scale but also has brightness requirements approaching single shot atomic resolution conditions. The brightness condition is in recognition that chemistry leads generally to irreversible changes in structure during the experimental conditions and that the nanoscale thin samples needed for electron structural probes pose upper limits to the available sample or "film" for atomic movies. Even in the case of reversible systems, the degree of excitation and thermal effects require the brightest sources possible for a given space-time resolution to observe the structural changes above background. Further progress in the field, particularly to the study of biological systems and solution reaction chemistry, requires increased brightness and spatial coherence, as well as an ability to tune the electron scattering cross-section to meet sample constraints. The electron bunch density or intensity depends directly on the magnitude of the extraction field for photoemitted electron sources and electron energy distribution in the transverse and longitudinal planes of electron propagation. This work examines the fundamental limits to optimizing these parameters based on relativistic electron sources using re-bunching cavity concepts that are now capable of achieving 10 femtosecond time scale resolution to capture the fastest nuclear motions. This analysis is given for both diffraction and real space imaging of structural dynamics in which there are several orders of magnitude higher space-time resolution with diffraction methods. The first experimental results from the Relativistic Electron Gun for Atomic Exploration (REGAE) are given that show the significantly reduced multiple electron scattering problem in this regime, which opens up micron scale systems, notably solution phase chemistry, to atomically resolved structural dynamics.

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

Sadovnikov, A. V., E-mail: sadovnikovav@gmail.com; Nikitov, S. A.; Kotel'nikov Institute of Radioengineering and Electronics, Russian Academy of Sciences, Moscow 125009

Using the space-resolved Brillouin light scattering spectroscopy we study the transformation of dynamic magnetization patterns in a bilayer multiferroic structure. We show that in the comparison with a single yttrium iron garnet (YIG) film magnetization distribution is transformed in the bilayer structure due to the coupling of waves propagating both in an YIG film (magnetic layer) and in a barium strontium titanate slab (ferroelectric layer). We present a simple electrodynamic model using the numerical finite element method to show the transformation of eigenmode spectrum of confined multiferroic. In particular, we demonstrate that the control over the dynamic magnetization and themore » transformation of spatial profiles of transverse modes in magnetic film of the bilayer structure can be performed by the tuning of the wavevectors of transverse modes. The studied confined multiferroic stripe can be utilized for fabrication of integrated dual tunable functional devices for magnonic applications.« less

The structural origin of the hard-sphere glass transition in granular packing

DOE PAGES

Xia, Chengjie; Li, Jindong; Cao, Yixin; ...

2015-09-28

Glass transition is accompanied by a rapid growth of the structural relaxation time and a concomitant decrease of configurational entropy. It remains unclear whether the transition has a thermodynamic origin, and whether the dynamic arrest is associated with the growth of a certain static order. Using granular packing as a model hard-sphere glass, we show the glass transition as a thermodynamic phase transition with a ‘hidden’ polytetrahedral order. This polytetrahedral order is spatially correlated with the slow dynamics. It is geometrically frustrated and has a peculiar fractal dimension. Additionally, as the packing fraction increases, its growth follows an entropy-driven nucleationmore » process, similar to that of the random first-order transition theory. In conclusion, our study essentially identifies a long-sought-after structural glass order in hard-sphere glasses.« less

Modeling the Dynamics of Soil Structure and Water in Agricultural Soil

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

A Unified Picture of Mass Segregation in Globular Clusters

NASA Astrophysics Data System (ADS)

Watkins, Laura

2017-08-01

The sensitivity, stability and longevity of HST have opened up an exciting new parameter space: we now have velocity measurements, in the form of proper motions (PMs), for stars from the tip of the red giant branch to a few magnitudes below the main-sequence turn off for a large sample of globular clusters (GCs). For the very first time, we have the opportunity to measure both kinematic and spatial dependences on stellar mass in GCs.The formation and evolution histories of GCs are poorly understood, so too are their intermediate-mass black hole populations and binary fractions. However, the current structure and dynamical state of a GC is directly determined by its past history and its components, so by understanding the former we can gain insight into the latter. Quantifying variations in spatial structure for stars of different mass is extremely difficult with photometry alone as datasets are inhomogenous and incomplete. We require kinematic data for stars that span a range of stellar masses, combined with proper dynamical modelling. We now have the data in hand, but still lack the models needed to maximise the scientific potential of our HST datasets.Here, we propose to extend existing single-mass discrete dynamical-modelling tools to include kinematic and spatial variations with stellar mass, and verify the upgrades using mock data generated from N-body models. We will then apply the models to HST PM data and directly quantify energy equipartition and mass segregation in the GCs. The theoretical phase of the project is vital for the success of the subsequent data analysis, and will serve as a benchmark for future observational campaigns with HST, JWST and beyond.

Spatial constraints of stereopsis in video displays

NASA Technical Reports Server (NTRS)

Schor, Clifton

1989-01-01

Recent development in video technology, such as the liquid crystal displays and shutters, have made it feasible to incorporate stereoscopic depth into the 3-D representations on 2-D displays. However, depth has already been vividly portrayed in video displays without stereopsis using the classical artists' depth cues described by Helmholtz (1866) and the dynamic depth cues described in detail by Ittleson (1952). Successful static depth cues include overlap, size, linear perspective, texture gradients, and shading. Effective dynamic cues include looming (Regan and Beverly, 1979) and motion parallax (Rogers and Graham, 1982). Stereoscopic depth is superior to the monocular distance cues under certain circumstances. It is most useful at portraying depth intervals as small as 5 to 10 arc secs. For this reason it is extremely useful in user-video interactions such as telepresence. Objects can be manipulated in 3-D space, for example, while a person who controls the operations views a virtual image of the manipulated object on a remote 2-D video display. Stereopsis also provides structure and form information in camouflaged surfaces such as tree foliage. Motion parallax also reveals form; however, without other monocular cues such as overlap, motion parallax can yield an ambiguous perception. For example, a turning sphere, portrayed as solid by parallax can appear to rotate either leftward or rightward. However, only one direction of rotation is perceived when stereo-depth is included. If the scene is static, then stereopsis is the principal cue for revealing the camouflaged surface structure. Finally, dynamic stereopsis provides information about the direction of motion in depth (Regan and Beverly, 1979). Clearly there are many spatial constraints, including spatial frequency content, retinal eccentricity, exposure duration, target spacing, and disparity gradient, which - when properly adjusted - can greatly enhance stereodepth in video displays.

Self-sustaining dynamical nuclear polarization oscillations in quantum dots.

PubMed

Rudner, M S; Levitov, L S

2013-02-22

Early experiments on spin-blockaded double quantum dots revealed robust, large-amplitude current oscillations in the presence of a static (dc) source-drain bias. Despite experimental evidence implicating dynamical nuclear polarization, the mechanism has remained a mystery. Here we introduce a minimal albeit realistic model of coupled electron and nuclear spin dynamics which supports self-sustained oscillations. Our mechanism relies on a nuclear spin analog of the tunneling magnetoresistance phenomenon (spin-dependent tunneling rates in the presence of an inhomogeneous Overhauser field) and nuclear spin diffusion, which governs dynamics of the spatial profile of nuclear polarization. The proposed framework naturally explains the differences in phenomenology between vertical and lateral quantum dot structures as well as the extremely long oscillation periods.

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.

Operationalizing Dynamic Ocean Management (DOM): Understanding the Incentive Structure, Policy and Regulatory Context for DOM in Practice

NASA Astrophysics Data System (ADS)

Lewison, R. L.; Saumweber, W. J.; Erickson, A.; Martone, R. G.

2016-12-01

Dynamic ocean management, or management that uses near real-time data to guide the spatial distribution of commercial activities, is an emerging approach to balance ocean resource use and conservation. Employing a wide range of data types, dynamic ocean management in a fisheries context can be used to meet multiple objectives - managing target quota, bycatch reduction, and reducing interactions with species of conservation concern. There is a growing list of DOM applications currently in practice in fisheries around the world, yet the approach is new enough that both fishers and fisheries managers are unclear how DOM can be applied to their fishery. Here, we use the experience from dynamic ocean management applications that are currently in practice to address the commonly asked question "How can dynamic management approaches be implemented in a traditionally managed fishery?". Combining knowledge from the DOM participants with a review of regulatory frameworks and incentive structures, stakeholder participation, and technological requirements of DOM in practice, we identify ingredients that have supported successful implementation of this new management approach.

Modeling landscape net ecosystem productivity (LandNEP) under alternative management regimes

Treesearch

Eugenie S. Euskirchen; Jiquan Chen; Harbin Li; Eric J. Gustafson; Thomas R. Crow

2002-01-01

Forests have been considered as a major carbon sink within the global carbon budget. However, a fragmented forest landscape varies significantly in its composition and age structure, and the amount of carbon sequestered at this level remains generally unknown to the scientific community. More precisely, the temporal dynamics and spatial distribution of net ecosystem...

Momentum Flux Increases and Coherent-Structure Dynamics in a Subsonic Axisymmetric Free Jet

DTIC Science & Technology

1988-08-19

CONTENTS I1. INTRODUCTION ....................................... .. 2. THE NUMERICAL MODEL ...used to study both planar and axisymmetric shear layers. A number of these have modeled temporally developing mixing layers (Patnaik et al. 1976...Riley & Metcalfe 1980; Moin et al. 1985). Others have modeled spatially developing layers (Ashurst 1979: Davis & Moore 1985; Grinstein et al. 1986), which

Correlations among stand ages and forest strata in mixed-oak forests of southeastern Ohio

Treesearch

P. Charles Goebel; David M. Hix

1997-01-01

Many models of landscape ecosystem development, as well as of forest stand dynamics, are based upon spatial and temporal changes in the species composition and structure of various forest strata. However, few document the interrelationships among forest strata, or the response of different strata to alterations of natural disturbance regimes. To examine how...

Ecohydrology of an outbreak: Mountain pine beetle impacts trees in drier landscape positions first

Treesearch

Kendra E. Kaiser; Ryan E. Emanuel

2013-01-01

Vegetation pattern and landscape structure intersect to exert strong control over ecohydrological dynamics at the watershed scale. The hydrologic implications of vegetation disturbance (e.g. fire, disease) depend on the spatial pattern and form of environmental change. Here, we investigate this intersection at Tenderfoot Creek Experimental Forest (TCEF), Montana, with...

Self Diagnostic Adhesive for Bonded Joints in Aircraft Structures

DTIC Science & Technology

2016-10-04

validated under the fatigue/dynamic loading condition. 3) Both SEM (Spectral Element Modeling) and FEM ( Finite Element Modeling) simulation of the...Sensors ..................................................................... 22 Parametric Study of Sensor Performance via Finite Element Simulation...The frequency range that we are interested is around 800 kHz. Conventional linear finite element method (FEM) requires a very fine spatial

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.…

Cordilleran forest scaling dynamics and disturbance regimes quantified by aerial LiDAR

Treesearch

Tyson L. Swetnam

2013-01-01

Semi-arid forests are in a period of rapid transition as a result of unprecedented landscape scale fires, insect outbreaks, drought, and anthropogenic land use practices. Understanding how historically episodic disturbances led to coherent forest structural and spatial patterns that promoted resilience and resistance is a critical part of addressing change. Here my...

A Head in Virtual Reality: Development of A Dynamic Head and Neck Model

ERIC Educational Resources Information Center

Nguyen, Ngan; Wilson, Timothy D.

2009-01-01

Advances in computer and interface technologies have made it possible to create three-dimensional (3D) computerized models of anatomical structures for visualization, manipulation, and interaction in a virtual 3D environment. In the past few decades, a multitude of digital models have been developed to facilitate complex spatial learning of the…

Abundance and production of riparian trees in the lowland floodplain of the Queets River, Washington.

Treesearch

Estelle V. Balian; Robert J. Naiman

2005-01-01

Riparian zones associated with alluvial rivers are spatially dynamic, forming distinct vegetative mosaics that exhibit sharp contrasts in structure and processes related to the underlying biophysical template. The productivity of riparian plants, especially trees, influences streamside community characteristics as, well as the forms and fluxes of organic matter to...

Understanding and responding to earthquake hazards

NASA Technical Reports Server (NTRS)

Raymond, C. A.; Lundgren, P. R.; Madsen, S. N.; Rundle, J. B.

2002-01-01

Advances in understanding of the earthquake cycle and in assessing earthquake hazards is a topic of great importance. Dynamic earthquake hazard assessments resolved for a range of spatial scales and time scales will allow a more systematic approach to prioritizing the retrofitting of vulnerable structures, relocating populations at risk, protecting lifelines, preparing for disasters, and educating the public.

Spatiotemporal variation in survival rates: implications for population dynamics of yellow-bellied marmots.

PubMed

Ozgul, Arpat; Armitage, Kenneth B; Blumstein, Daniel T; Oli, Madan K

2006-04-01

Spatiotemporal variation in age-specific survival rates can profoundly influence population dynamics, but few studies of vertebrates have thoroughly investigated both spatial and temporal variability in age-specific survival rates. We used 28 years (1976-2003) of capture-mark-recapture (CMR) data from 17 locations to parameterize an age-structured Cormack-Jolly-Seber model, and investigated spatial and temporal variation in age-specific annual survival rates of yellow-bellied marmots (Marmota flaviventris). Survival rates varied both spatially and temporally, with survival of younger animals exhibiting the highest degree of variation. Juvenile survival rates varied from 0.52 +/- 0.05 to 0.78 +/- 0.10 among sites and from 0.15 +/- 0.14 to 0.89 +/- 0.06 over time. Adult survival rates varied from 0.62 +/- 0.09 to 0.80 +/- 0.03 among sites, but did not vary significantly over time. We used reverse-time CMR models to estimate the realized population growth rate (lamda), and to investigate the influence of the observed variation in age-specific survival rates on lamda. The realized growth rate of the population closely covaried with, and was significantly influenced by, spatiotemporal variation in juvenile survival rate. High variability in juvenile survival rates over space and time clearly influenced the dynamics of our study population and is also likely to be an important determinant of the spatiotemporal variation in the population dynamics of other mammals with similar life history characteristics.

Experimental Research Regarding The Motion Capacity Of A Robotic Arm

NASA Astrophysics Data System (ADS)

Dumitru, Violeta Cristina

2015-09-01

This paper refers to the development of necessary experiments which obtained dynamic parameters (force, displacement) for a modular mechanism with multiple vertebrae. This mechanism performs functions of inspection and intervention in small spaces. Mechanical structure allows functional parameters to achieve precise movements to an imposed target. Will be analyzed the dynamic of the mechanisms using simulation instruments DimamicaRobot.tst under TestPoint programming environment and the elasticity of the tension cables. It will be changes on the mechanism so that spatial movement of the robotic arm is optimal.

Approaching the molecular origins of collective dynamics in oscillating cell populations

PubMed Central

Mehta, Pankaj; Gregor, Thomas

2011-01-01

From flocking birds, to organ generation, to swarming bacterial colonies, biological systems often exhibit collective behaviors. Here, we review recent advances in our understanding of collective dynamics in cell populations. We argue that understanding population-level oscillations requires examining the system under consideration at three different levels of complexity: at the level of isolated cells, homogenous populations, and spatially structured populations. We discuss the experimental and theoretical challenges this poses and highlight how new experimental techniques, when combined with conceptual tools adapted from physics, may help us overcome these challenges. PMID:20934869

The Emergence of Temporal Structures in Dynamical Systems

NASA Astrophysics Data System (ADS)

Mainzer, Klaus

2010-10-01

Dynamical systems in classical, relativistic and quantum physics are ruled by laws with time reversibility. Complex dynamical systems with time-irreversibility are known from thermodynamics, biological evolution, growth of organisms, brain research, aging of people, and historical processes in social sciences. Complex systems are systems that compromise many interacting parts with the ability to generate a new quality of macroscopic collective behavior the manifestations of which are the spontaneous emergence of distinctive temporal, spatial or functional structures. But, emergence is no mystery. In a general meaning, the emergence of macroscopic features results from the nonlinear interactions of the elements in a complex system. Mathematically, the emergence of irreversible structures is modelled by phase transitions in non-equilibrium dynamics of complex systems. These methods have been modified even for chemical, biological, economic and societal applications (e.g., econophysics). Emergence of irreversible structures can also be simulated by computational systems. The question arises how the emergence of irreversible structures is compatible with the reversibility of fundamental physical laws. It is argued that, according to quantum cosmology, cosmic evolution leads from symmetry to complexity of irreversible structures by symmetry breaking and phase transitions. Thus, arrows of time and aging processes are not only subjective experiences or even contradictions to natural laws, but they can be explained by quantum cosmology and the nonlinear dynamics of complex systems. Human experiences and religious concepts of arrows of time are considered in a modern scientific framework. Platonic ideas of eternity are at least understandable with respect to mathematical invariance and symmetry of physical laws. Heraclit’s world of change and dynamics can be mapped onto our daily real-life experiences of arrows of time.

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

Method and apparatus for optical Doppler tomographic imaging of fluid flow velocity in highly scattering media

DOEpatents

Nelson, John Stuart; Milner, Thomas Edward; Chen, Zhongping

1999-01-01

Optical Doppler tomography permits imaging of fluid flow velocity in highly scattering media. The tomography system combines Doppler velocimetry with high spatial resolution of partially coherent optical interferometry to measure fluid flow velocity at discrete spatial locations. Noninvasive in vivo imaging of blood flow dynamics and tissue structures with high spatial resolutions of the order of 2 to 10 microns is achieved in biological systems. The backscattered interference signals derived from the interferometer may be analyzed either through power spectrum determination to obtain the position and velocity of each particle in the fluid flow sample at each pixel, or the interference spectral density may be analyzed at each frequency in the spectrum to obtain the positions and velocities of the particles in a cross-section to which the interference spectral density corresponds. The realized resolutions of optical Doppler tomography allows noninvasive in vivo imaging of both blood microcirculation and tissue structure surrounding the vessel which has significance for biomedical research and clinical applications.

Modeling Global Spatial-Temporal Evolution of Society: Hyperbolic Growth and Historical Cycles

NASA Astrophysics Data System (ADS)

Kurkina, E. S.

2011-09-01

The global historical processes are under consideration; and laws of global evolution of the world community are studied. The world community is considered as a united complex self-developing and self-organizing system. It supposed that the main driving force of social-economical evolution was the positive feedback between the population size and the level of technological development, which was a cause of growth in blow-up regime both of population and of global economic indexes. The study is supported by the results of mathematical modeling founded on a nonlinear heat equation with a source. Every social-economical epoch characterizes by own specific spatial distributed structures. So the global dynamics of world community during the whole history is investigated throughout the prism of the developing of spatial-temporal structures. The model parameters have been chosen so that 1) total population follows stable hyperbolic growth, consistently with the demographic data; 2) the evolution of the World-System goes through 11 stages corresponding to the main historical epochs.

[Compartmentalization of the cell nucleus and spatial organization of the genome].

PubMed

Gavrilov, A A; Razin, S V

2015-01-01

The eukaryotic cell nucleus is one of the most complex cell organelles. Despite the absence of membranes, the nuclear space is divided into numerous compartments where different processes in- volved in the genome activity take place. The most important nuclear compartments include nucleoli, nuclear speckles, PML bodies, Cajal bodies, histone locus bodies, Polycomb bodies, insulator bodies, transcription and replication factories. The structural basis for the nuclear compartmentalization is provided by genomic DNA that occupies most of the nuclear volume. Nuclear compartments, in turn, guide the chromosome folding by providing a platform for the spatial interaction of individual genomic loci. In this review, we discuss fundamental principles of higher order genome organization with a focus on chromosome territories and chromosome domains, as well as consider the structure and function of the key nuclear compartments. We show that the func- tional compartmentalization of the cell nucleus and genome spatial organization are tightly interconnected, and that this form of organization is highly dynamic and is based on stochastic processes.

A high-resolution genetic signature of demographic and spatial expansion in epizootic rabies virus

PubMed Central

Biek, Roman; Henderson, J. Caroline; Waller, Lance A.; Rupprecht, Charles E.; Real, Leslie A.

2007-01-01

Emerging pathogens potentially undergo rapid evolution while expanding in population size and geographic range during the course of invasion, yet it is generally difficult to demonstrate how these processes interact. Our analysis of a 30-yr data set covering a large-scale rabies virus outbreak among North American raccoons reveals the long lasting effect of the initial infection wave in determining how viral populations are genetically structured in space. We further find that coalescent-based estimates derived from the genetic data yielded an amazingly accurate reconstruction of the known spatial and demographic dynamics of the virus over time. Our study demonstrates the combined evolutionary and population dynamic processes characterizing the spread of pathogen after its introduction into a fully susceptible host population. Furthermore, the results provide important insights regarding the spatial scale of rabies persistence and validate the use of coalescent approaches for uncovering even relatively complex population histories. Such approaches will be of increasing relevance for understanding the epidemiology of emerging zoonotic diseases in a landscape context. PMID:17470818

Context-dependent colonization dynamics: Regional reward contagion drives local compression in aquatic beetles.

PubMed

Pintar, Matthew R; Resetarits, William J

2017-09-01

Habitat selection by colonizing organisms is an important factor in determining species abundance and community dynamics at multiple spatial scales. Many organisms select habitat patches based on intrinsic patch quality, but patches exist in complex landscapes linked by dispersal and colonization, forming metapopulations and metacommunities. Perceived patch quality can be influenced by neighbouring patches through spatial contagion, wherein perceived quality of one patch can extend beyond its borders and either increase or decrease the colonization of neighbouring patches and localities. These spatially explicit colonization dynamics can result in habitat compression, wherein more colonists occupy a patch or locality than in the absence of spatial context dependence. Previous work on contagion/compression focused primarily on the role of predators in driving colonization patterns. Our goal was to determine whether resource abundance can drive multi-scale colonization dynamics of aquatic beetles through the processes of contagion and compression in naturally colonized experimental pools. We established two levels (high/low quality) of within-patch resource abundances (leaf litter) using an experimental landscape of mesocosms, and assayed colonization by 35 species of aquatic beetles. Patches were arranged in localities (sets of two patches), which consisted of a combination of two patch-level resource levels in a 2 × 2 factorial design, allowing us to assay colonization at both locality and patch levels. We demonstrate that patterns of species abundance and richness of colonizing aquatic beetles are determined by patch quality and context-dependent processes at multiple spatial scales. Localities that consisted of at least one high-quality patch were colonized at equivalent rates that were higher than localities containing only low-quality patches, displaying regional reward contagion. In localities that consisted of one high- and one low-quality patch, reward contagion produced by higher leaf litter levels resulted in greater abundance of beetles in such localities, which then compressed into the highest quality patches. Our results provide further support for the critical roles of habitat selection and spatial context, particularly the quality of neighbouring habitat patches, in generating patterns of species abundances and community structure across landscapes. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

Rubella metapopulation dynamics and importance of spatial coupling to the risk of congenital rubella syndrome in Peru

PubMed Central

Metcalf, C. J. E.; Munayco, C. V.; Chowell, G.; Grenfell, B. T.; Bjørnstad, O. N.

2011-01-01

Rubella is generally a mild childhood disease, but infection during early pregnancy may cause spontaneous abortion or congenital rubella syndrome (CRS), which may entail a variety of birth defects. Consequently, understanding the age-structured dynamics of this infection has considerable public health value. Vaccination short of the threshold for local elimination of transmission will increase the average age of infection. Accordingly, the classic concern for this infection is the potential for vaccination to increase incidence in individuals of childbearing age. A neglected aspect of rubella dynamics is how age incidence patterns may be moulded by the spatial dynamics inherent to epidemic metapopulations. Here, we use a uniquely detailed dataset from Peru to explore the implications of this for the burden of CRS. Our results show that the risk of CRS may be particularly severe in small remote regions, a prediction at odds with expectations in the endemic situation, and with implications for the outcome of vaccination. This outcome results directly from the metapopulation context: specifically, extinction–re-colonization dynamics are crucial because they allow for significant leakage of susceptible individuals into the older age classes during inter-epidemic periods with the potential to increase CRS risk by as much as fivefold. PMID:20659931

A MODELING AND SIMULATION LANGUAGE FOR BIOLOGICAL CELLS WITH COUPLED MECHANICAL AND CHEMICAL PROCESSES

PubMed Central

Somogyi, Endre; Glazier, James A.

2017-01-01

Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, and migration. Modeling and simulation of such dynamic phenomena poses a number of computational challenges. A modeling language describing cellular dynamics must naturally represent complex intra and extra-cellular spatial structures and coupled mechanical, chemical and electrical processes. Domain experts will find a modeling language most useful when it is based on concepts, terms and principles native to the problem domain. A compiler must then be able to generate an executable model from this physically motivated description. Finally, an executable model must efficiently calculate the time evolution of such dynamic and inhomogeneous phenomena. We present a spatial hybrid systems modeling language, compiler and mesh-free Lagrangian based simulation engine which will enable domain experts to define models using natural, biologically motivated constructs and to simulate time evolution of coupled cellular, mechanical and chemical processes acting on a time varying number of cells and their environment. PMID:29303160

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

Higa, Kenneth; Zhao, Hui; Parkinson, Dilworth Y.

The internal structure of a porous electrode strongly influences battery performance. Understanding the dynamics of electrode slurry drying could aid in engineering electrodes with desired properties. For instance, one might monitor the dynamic, spatially-varying thickness near the edge of a slurry coating, as it should lead to non-uniform thickness of the dried film. This work examines the dynamic behavior of drying slurry drops consisting of SiO x and carbon black particles in a solution of carboxymethylcellulose and deionized water, as an experimental model of drying behavior near the edge of a slurry coating. An X-ray radiography-based procedure is developed tomore » calculate the evolving spatial distribution of active material particles from images of the drying slurry drops. To the authors’ knowledge, this study is the first to use radiography to investigate battery slurry drying, as well as the first to determine particle distributions from radiography images of drying suspensions. The dynamic results are consistent with tomography reconstructions of the static, fully-dried films. It is found that active material particles can rapidly become non-uniformly distributed within the drops. Heating can promote distribution uniformity, but seemingly must be applied very soon after slurry deposition. Higher slurry viscosity is found to strongly restrain particle redistribution.« less

A MODELING AND SIMULATION LANGUAGE FOR BIOLOGICAL CELLS WITH COUPLED MECHANICAL AND CHEMICAL PROCESSES.

PubMed

Somogyi, Endre; Glazier, James A

2017-04-01

Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, and migration. Modeling and simulation of such dynamic phenomena poses a number of computational challenges. A modeling language describing cellular dynamics must naturally represent complex intra and extra-cellular spatial structures and coupled mechanical, chemical and electrical processes. Domain experts will find a modeling language most useful when it is based on concepts, terms and principles native to the problem domain. A compiler must then be able to generate an executable model from this physically motivated description. Finally, an executable model must efficiently calculate the time evolution of such dynamic and inhomogeneous phenomena. We present a spatial hybrid systems modeling language, compiler and mesh-free Lagrangian based simulation engine which will enable domain experts to define models using natural, biologically motivated constructs and to simulate time evolution of coupled cellular, mechanical and chemical processes acting on a time varying number of cells and their environment.

Habitat continuity and stepping-stone oceanographic distances explain population genetic connectivity of the brown alga Cystoseira amentacea.

PubMed

Buonomo, Roberto; Assis, Jorge; Fernandes, Francisco; Engelen, Aschwin H; Airoldi, Laura; Serrão, Ester A

2017-02-01

Effective predictive and management approaches for species occurring in a metapopulation structure require good understanding of interpopulation connectivity. In this study, we ask whether population genetic structure of marine species with fragmented distributions can be predicted by stepping-stone oceanographic transport and habitat continuity, using as model an ecosystem-structuring brown alga, Cystoseira amentacea var. stricta. To answer this question, we analysed the genetic structure and estimated the connectivity of populations along discontinuous rocky habitat patches in southern Italy, using microsatellite markers at multiple scales. In addition, we modelled the effect of rocky habitat continuity and ocean circulation on gene flow by simulating Lagrangian particle dispersal based on ocean surface currents allowing multigenerational stepping-stone dynamics. Populations were highly differentiated, at scales from few metres up to thousands of kilometres. The best possible model fit to explain the genetic results combined current direction, rocky habitat extension and distance along the coast among rocky sites. We conclude that a combination of variable suitable habitat and oceanographic transport is a useful predictor of genetic structure. This relationship provides insight into the mechanisms of dispersal and the role of life-history traits. Our results highlight the importance of spatially explicit modelling of stepping-stone dynamics and oceanographic directional transport coupled with habitat suitability, to better describe and predict marine population structure and differentiation. This study also suggests the appropriate spatial scales for the conservation, restoration and management of species that are increasingly affected by habitat modifications. © 2016 John Wiley & Sons Ltd.

Climate and Edaphic Controls on Humid Tropical Forest Tree Height

NASA Astrophysics Data System (ADS)

Yang, Y.; Saatchi, S. S.; Xu, L.

2014-12-01

Uncertainty in the magnitude and spatial variations of forest carbon density in tropical regions is due to under sampling of forest structure from inventory plots and the lack of regional allometry to estimate the carbon density from structure. Here we quantify the variation of tropical forest structure by using more than 2.5 million measurements of canopy height from systematic sampling of Geoscience Laser Altimeter System (GLAS) satellite observations between 2004 to 2008 and examine the climate and edaphic variables influencing the variations. We used top canopy height of GLAS footprints (~ 0.25 ha) to grid the statistical mean and 90 percentile of samples at 0.5 degrees to capture the regional variability of large trees in tropics. GLAS heights were also aggregated based on a stratification of tropical regions using soil, elevation, and forest types. Both approaches provided consistent patterns of statistically dominant large trees and the least heterogeneity, both as strong drivers of distribution of high biomass forests. Statistical models accounting for spatial autocorrelation suggest that climate, soil and spatial features together can explain more than 60% of the variations in observed tree height information, while climate-only variables explains about one third of the first-order changes in tree height. Soil basics, including physical compositions such as clay and sand contents, chemical properties such as PH values and cation-exchange capacity, as well as biological variables such as organic matters, all present independent but statistically significant relationships to tree height variations. The results confirm other landscape and regional studies that soil fertility, geology and climate may jointly control a majority of the regional variations of forest structure in pan-tropics and influencing both biomass stocks and dynamics. Consequently, other factors such as biotic and disturbance regimes, not included in this study, may have less influence on regional variations but strongly mediate landscape and small-scale forest structure and dynamics.

Regimes of Flow over Complex Structures of Endothelial Glycocalyx: A Molecular Dynamics Simulation Study.

PubMed

Jiang, Xi Zhuo; Feng, Muye; Ventikos, Yiannis; Luo, Kai H

2018-04-10

Flow patterns on surfaces grafted with complex structures play a pivotal role in many engineering and biomedical applications. In this research, large-scale molecular dynamics (MD) simulations are conducted to study the flow over complex surface structures of an endothelial glycocalyx layer. A detailed structure of glycocalyx has been adopted and the flow/glycocalyx system comprises about 5,800,000 atoms. Four cases involving varying external forces and modified glycocalyx configurations are constructed to reveal intricate fluid behaviour. Flow profiles including temporal evolutions and spatial distributions of velocity are illustrated. Moreover, streamline length and vorticity distributions under the four scenarios are compared and discussed to elucidate the effects of external forces and glycocalyx configurations on flow patterns. Results show that sugar chain configurations affect streamline length distributions but their impact on vorticity distributions is statistically insignificant, whilst the influence of the external forces on both streamline length and vorticity distributions are trivial. Finally, a regime diagram for flow over complex surface structures is proposed to categorise flow patterns.

Scale invariance in natural and artificial collective systems: a review

PubMed Central

Huepe, Cristián

2017-01-01

Self-organized collective coordinated behaviour is an impressive phenomenon, observed in a variety of natural and artificial systems, in which coherent global structures or dynamics emerge from local interactions between individual parts. If the degree of collective integration of a system does not depend on size, its level of robustness and adaptivity is typically increased and we refer to it as scale-invariant. In this review, we first identify three main types of self-organized scale-invariant systems: scale-invariant spatial structures, scale-invariant topologies and scale-invariant dynamics. We then provide examples of scale invariance from different domains in science, describe their origins and main features and discuss potential challenges and approaches for designing and engineering artificial systems with scale-invariant properties. PMID:29093130

Construction of 4D high-definition cortical surface atlases of infants: Methods and applications.

PubMed

Li, Gang; Wang, Li; Shi, Feng; Gilmore, John H; Lin, Weili; Shen, Dinggang

2015-10-01

In neuroimaging, cortical surface atlases play a fundamental role for spatial normalization, analysis, visualization, and comparison of results across individuals and different studies. However, existing cortical surface atlases created for adults are not suitable for infant brains during the first two postnatal years, which is the most dynamic period of postnatal structural and functional development of the highly-folded cerebral cortex. Therefore, spatiotemporal cortical surface atlases for infant brains are highly desired yet still lacking for accurate mapping of early dynamic brain development. To bridge this significant gap, leveraging our infant-dedicated computational pipeline for cortical surface-based analysis and the unique longitudinal infant MRI dataset acquired in our research center, in this paper, we construct the first spatiotemporal (4D) high-definition cortical surface atlases for the dynamic developing infant cortical structures at seven time points, including 1, 3, 6, 9, 12, 18, and 24 months of age, based on 202 serial MRI scans from 35 healthy infants. For this purpose, we develop a novel method to ensure the longitudinal consistency and unbiasedness to any specific subject and age in our 4D infant cortical surface atlases. Specifically, we first compute the within-subject mean cortical folding by unbiased groupwise registration of longitudinal cortical surfaces of each infant. Then we establish longitudinally-consistent and unbiased inter-subject cortical correspondences by groupwise registration of the geometric features of within-subject mean cortical folding across all infants. Our 4D surface atlases capture both longitudinally-consistent dynamic mean shape changes and the individual variability of cortical folding during early brain development. Experimental results on two independent infant MRI datasets show that using our 4D infant cortical surface atlases as templates leads to significantly improved accuracy for spatial normalization of cortical surfaces across infant individuals, in comparison to the infant surface atlases constructed without longitudinal consistency and also the FreeSurfer adult surface atlas. Moreover, based on our 4D infant surface atlases, for the first time, we reveal the spatially-detailed, region-specific correlation patterns of the dynamic cortical developmental trajectories between different cortical regions during early brain development. Copyright © 2015 Elsevier B.V. All rights reserved.

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

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

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

Caustic Skeleton & Cosmic Web

NASA Astrophysics Data System (ADS)

Feldbrugge, Job; van de Weygaert, Rien; Hidding, Johan; Feldbrugge, Joost

2018-05-01

We present a general formalism for identifying the caustic structure of a dynamically evolving mass distribution, in an arbitrary dimensional space. The identification of caustics in fluids with Hamiltonian dynamics, viewed in Lagrangian space, corresponds to the classification of singularities in Lagrangian catastrophe theory. On the basis of this formalism we develop a theoretical framework for the dynamics of the formation of the cosmic web, and specifically those aspects that characterize its unique nature: its complex topological connectivity and multiscale spinal structure of sheetlike membranes, elongated filaments and compact cluster nodes. Given the collisionless nature of the gravitationally dominant dark matter component in the universe, the presented formalism entails an accurate description of the spatial organization of matter resulting from the gravitationally driven formation of cosmic structure. The present work represents a significant extension of the work by Arnol'd et al. [1], who classified the caustics that develop in one- and two-dimensional systems that evolve according to the Zel'dovich approximation. His seminal work established the defining role of emerging singularities in the formation of nonlinear structures in the universe. At the transition from the linear to nonlinear structure evolution, the first complex features emerge at locations where different fluid elements cross to establish multistream regions. Involving a complex folding of the 6-D sheetlike phase-space distribution, it manifests itself in the appearance of infinite density caustic features. The classification and characterization of these mass element foldings can be encapsulated in caustic conditions on the eigenvalue and eigenvector fields of the deformation tensor field. In this study we introduce an alternative and transparent proof for Lagrangian catastrophe theory. This facilitates the derivation of the caustic conditions for general Lagrangian fluids, with arbitrary dynamics. Most important in the present context is that it allows us to follow and describe the full three-dimensional geometric and topological complexity of the purely gravitationally evolving nonlinear cosmic matter field. While generic and statistical results can be based on the eigenvalue characteristics, one of our key findings is that of the significance of the eigenvector field of the deformation field for outlining the entire spatial structure of the caustic skeleton emerging from a primordial density field. In this paper we explicitly consider the caustic conditions for the three-dimensional Zel'dovich approximation, extending earlier work on those for one- and two-dimensional fluids towards the full spatial richness of the cosmic web. In an accompanying publication, we apply this towards a full three-dimensional study of caustics in the formation of the cosmic web and evaluate in how far it manages to outline and identify the intricate skeletal features in the corresponding N-body simulations.

Strategies of offspring investment and dispersal in a spatially structured environment: a theoretical study using ants.

PubMed

Cronin, Adam L; Loeuille, Nicolas; Monnin, Thibaud

2016-02-05

Offspring investment strategies vary markedly between and within taxa, and much of this variation is thought to stem from the trade-off between offspring size and number. While producing larger offspring can increase their competitive ability, this often comes at a cost to their colonization ability. This competition-colonization trade-off (CCTO) is thought to be an important mechanism supporting coexistence of alternative strategies in a wide range of taxa. However, the relative importance of an alternative and possibly synergistic mechanism-spatial structuring of the environment-remains the topic of some debate. In this study, we explore the influence of these mechanisms on metacommunity structure using an agent-based model built around variable life-history traits. Our model combines explicit resource competition and spatial dynamics, allowing us to tease-apart the influence of, and explore the interaction between, the CCTO and the spatial structure of the environment. We test our model using two reproductive strategies which represent extremes of the CCTO and are common in ants. Our simulations show that colonisers outperform competitors in environments subject to higher temporal and spatial heterogeneity and are favoured when agents mature late and invest heavily in reproduction, whereas competitors dominate in low-disturbance, high resource environments and when maintenance costs are low. Varying life-history parameters has a marked influence on coexistence conditions and yields evolutionary stable strategies for both modes of reproduction. Nonetheless, we show that these strategies can coexist over a wide range of life-history and environmental parameter values, and that coexistence can in most cases be explained by a CCTO. By explicitly considering space, we are also able to demonstrate the importance of the interaction between dispersal and landscape structure. The CCTO permits species employing different reproductive strategies to coexist over a wide range of life-history and environmental parameters, and is likely to be an important factor in structuring ant communities. Our consideration of space highlights the importance of dispersal, which can limit the success of low-dispersers through kin competition, and enhance coexistence conditions for different strategies in spatially structured environments.