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Sample records for landscapes exact dynamics

  1. Landscape Construction in Dynamical Systems

    NASA Astrophysics Data System (ADS)

    Tang, Ying; Yuan, Ruoshi; Wang, Gaowei; Ao, Ping

    The idea of landscape has been recently applied to study various of biological problems. We demonstrate that a dynamical structure built into nonlinear dynamical systems allows us to construct such a global optimization landscape, which serves as the Lyapunov function for the ordinary differential equation. We find exact constructions on the landscape for a class of dynamical systems, including a van der Pol type oscillator, competitive Lotka-Volterra systems, and a chaotic system. The landscape constructed provides a new angle for understanding and modelling biological network dynamics.

  2. Exact results for amplitude spectra of fitness landscapes.

    PubMed

    Neidhart, Johannes; Szendro, Ivan G; Krug, Joachim

    2013-09-01

    Starting from fitness correlation functions, we calculate exact expressions for the amplitude spectra of fitness landscapes as defined by Stadler [1996. Landscapes and their correlation functions. J. Math. Chem. 20, 1] for common landscape models, including Kauffman's NK-model, rough Mount Fuji landscapes and general linear superpositions of such landscapes. We further show that correlations decaying exponentially with the Hamming distance yield exponentially decaying spectra similar to those reported recently for a model of molecular signal transduction. Finally, we compare our results for the model systems to the spectra of various experimentally measured fitness landscapes. We claim that our analytical results should be helpful when trying to interpret empirical data and guide the search for improved fitness landscape models.

  3. Reserves, resilience and dynamic landscapes.

    PubMed

    Bengtsson, Janne; Angelstam, Per; Elmqvist, Thomas; Emanuelsson, Urban; Folke, Carl; Ihse, Margareta; Moberg, Fredrik; Nyström, Magnus

    2003-09-01

    In a world increasingly modified by human activities, the conservation of biodiversity is essential as insurance to maintain resilient ecosystems and ensure a sustainable flow of ecosystem goods and services to society. However, existing reserves and national parks are unlikely to incorporate the long-term and large-scale dynamics of ecosystems. Hence, conservation strategies have to actively incorporate the large areas of land that are managed for human use. For ecosystems to reorganize after large-scale natural and human-induced disturbances, spatial resilience in the form of ecological memory is a prerequisite. The ecological memory is composed of the species, interactions and structures that make ecosystem reorganization possible, and its components may be found within disturbed patches as well in the surrounding landscape. Present static reserves should be complemented with dynamic reserves, such as ecological fallows and dynamic successional reserves, that are part of ecosystem management mimicking natural disturbance regimes at the landscape level.

  4. Reserves, resilience and dynamic landscapes.

    PubMed

    Bengtsson, Janne; Angelstam, Per; Elmqvist, Thomas; Emanuelsson, Urban; Folke, Carl; Ihse, Margareta; Moberg, Fredrik; Nyström, Magnus

    2003-09-01

    In a world increasingly modified by human activities, the conservation of biodiversity is essential as insurance to maintain resilient ecosystems and ensure a sustainable flow of ecosystem goods and services to society. However, existing reserves and national parks are unlikely to incorporate the long-term and large-scale dynamics of ecosystems. Hence, conservation strategies have to actively incorporate the large areas of land that are managed for human use. For ecosystems to reorganize after large-scale natural and human-induced disturbances, spatial resilience in the form of ecological memory is a prerequisite. The ecological memory is composed of the species, interactions and structures that make ecosystem reorganization possible, and its components may be found within disturbed patches as well in the surrounding landscape. Present static reserves should be complemented with dynamic reserves, such as ecological fallows and dynamic successional reserves, that are part of ecosystem management mimicking natural disturbance regimes at the landscape level. PMID:14627367

  5. Understanding Patchy Landscape Dynamics: Towards a Landscape Language

    PubMed Central

    Gaucherel, Cédric; Boudon, Frédéric; Houet, Thomas; Castets, Mathieu; Godin, Christophe

    2012-01-01

    Patchy landscapes driven by human decisions and/or natural forces are still a challenge to be understood and modelled. No attempt has been made up to now to describe them by a coherent framework and to formalize landscape changing rules. Overcoming this lacuna was our first objective here, and this was largely based on the notion of Rewriting Systems, also called Formal Grammars. We used complicated scenarios of agricultural dynamics to model landscapes and to write their corresponding driving rule equations. Our second objective was to illustrate the relevance of this landscape language concept for landscape modelling through various grassland managements, with the final aim to assess their respective impacts on biological conservation. For this purpose, we made the assumptions that a higher grassland appearance frequency and higher land cover connectivity are favourable to species conservation. Ecological results revealed that dairy and beef livestock production systems are more favourable to wild species than is hog farming, although in different ways. Methodological results allowed us to efficiently model and formalize these landscape dynamics. This study demonstrates the applicability of the Rewriting System framework to the modelling of agricultural landscapes and, hopefully, to other patchy landscapes. The newly defined grammar is able to explain changes that are neither necessarily local nor Markovian, and opens a way to analytical modelling of landscape dynamics. PMID:23049935

  6. Mathematical Models of Quasi-Species Theory and Exact Results for the Dynamics.

    PubMed

    Saakian, David B; Hu, Chin-Kun

    2016-01-01

    We formulate the Crow-Kimura, discrete-time Eigen model, and continuous-time Eigen model. These models are interrelated and we established an exact mapping between them. We consider the evolutionary dynamics for the single-peak fitness and symmetric smooth fitness. We applied the quantum mechanical methods to find the exact dynamics of the evolution model with a single-peak fitness. For the smooth symmetric fitness landscape, we map exactly the evolution equations into Hamilton-Jacobi equation (HJE). We apply the method to the Crow-Kimura (parallel) and Eigen models. We get simple formulas to calculate the dynamics of the maximum of distribution and the variance. We review the existing mathematical tools of quasi-species theory.

  7. Mathematical Models of Quasi-Species Theory and Exact Results for the Dynamics.

    PubMed

    Saakian, David B; Hu, Chin-Kun

    2016-01-01

    We formulate the Crow-Kimura, discrete-time Eigen model, and continuous-time Eigen model. These models are interrelated and we established an exact mapping between them. We consider the evolutionary dynamics for the single-peak fitness and symmetric smooth fitness. We applied the quantum mechanical methods to find the exact dynamics of the evolution model with a single-peak fitness. For the smooth symmetric fitness landscape, we map exactly the evolution equations into Hamilton-Jacobi equation (HJE). We apply the method to the Crow-Kimura (parallel) and Eigen models. We get simple formulas to calculate the dynamics of the maximum of distribution and the variance. We review the existing mathematical tools of quasi-species theory. PMID:26342705

  8. An exact factorization perspective on quantum interferences in nonadiabatic dynamics.

    PubMed

    Curchod, Basile F E; Agostini, Federica; Gross, E K U

    2016-07-21

    Nonadiabatic quantum interferences emerge whenever nuclear wavefunctions in different electronic states meet and interact in a nonadiabatic region. In this work, we analyze how nonadiabatic quantum interferences translate in the context of the exact factorization of the molecular wavefunction. In particular, we focus our attention on the shape of the time-dependent potential energy surface-the exact surface on which the nuclear dynamics takes place. We use a one-dimensional exactly solvable model to reproduce different conditions for quantum interferences, whose characteristic features already appear in one-dimension. The time-dependent potential energy surface develops complex features when strong interferences are present, in clear contrast to the observed behavior in simple nonadiabatic crossing cases. Nevertheless, independent classical trajectories propagated on the exact time-dependent potential energy surface reasonably conserve a distribution in configuration space that mimics one of the exact nuclear probability densities. PMID:27448870

  9. An exact factorization perspective on quantum interferences in nonadiabatic dynamics

    NASA Astrophysics Data System (ADS)

    Curchod, Basile F. E.; Agostini, Federica; Gross, E. K. U.

    2016-07-01

    Nonadiabatic quantum interferences emerge whenever nuclear wavefunctions in different electronic states meet and interact in a nonadiabatic region. In this work, we analyze how nonadiabatic quantum interferences translate in the context of the exact factorization of the molecular wavefunction. In particular, we focus our attention on the shape of the time-dependent potential energy surface—the exact surface on which the nuclear dynamics takes place. We use a one-dimensional exactly solvable model to reproduce different conditions for quantum interferences, whose characteristic features already appear in one-dimension. The time-dependent potential energy surface develops complex features when strong interferences are present, in clear contrast to the observed behavior in simple nonadiabatic crossing cases. Nevertheless, independent classical trajectories propagated on the exact time-dependent potential energy surface reasonably conserve a distribution in configuration space that mimics one of the exact nuclear probability densities.

  10. Exact dynamic properties of molecular motors

    NASA Astrophysics Data System (ADS)

    Boon, N. J.; Hoyle, R. B.

    2012-08-01

    Molecular motors play important roles within a biological cell, performing functions such as intracellular transport and gene transcription. Recent experimental work suggests that there are many plausible biochemical mechanisms that molecules such as myosin-V could use to achieve motion. To account for the abundance of possible discrete-stochastic frameworks that can arise when modeling molecular motor walks, a generalized and straightforward graphical method for calculating their dynamic properties is presented. It allows the calculation of the velocity, dispersion, and randomness ratio for any proposed system through analysis of its structure. This article extends work of King and Altman ["A schematic method of deriving the rate laws of enzyme-catalyzed reactions," J. Phys. Chem. 60, 1375-1378 (1956)], 10.1021/j150544a010 on networks of enzymatic reactions by calculating additional dynamic properties for spatially hopping systems. Results for n-state systems are presented: single chain, parallel pathway, divided pathway, and divided pathway with a chain. A novel technique for combining multiple system architectures coupled at a reference state is also demonstrated. Four-state examples illustrate the effectiveness and simplicity of these methods.

  11. Brownian motion on random dynamical landscapes

    NASA Astrophysics Data System (ADS)

    Suñé Simon, Marc; Sancho, José María; Lindenberg, Katja

    2016-03-01

    We present a study of overdamped Brownian particles moving on a random landscape of dynamic and deformable obstacles (spatio-temporal disorder). The obstacles move randomly, assemble, and dissociate following their own dynamics. This landscape may account for a soft matter or liquid environment in which large obstacles, such as macromolecules and organelles in the cytoplasm of a living cell, or colloids or polymers in a liquid, move slowly leading to crowding effects. This representation also constitutes a novel approach to the macroscopic dynamics exhibited by active matter media. We present numerical results on the transport and diffusion properties of Brownian particles under this disorder biased by a constant external force. The landscape dynamics are characterized by a Gaussian spatio-temporal correlation, with fixed time and spatial scales, and controlled obstacle concentrations.

  12. Exact dynamical coarse-graining without time-scale separation

    NASA Astrophysics Data System (ADS)

    Lu, Jianfeng; Vanden-Eijnden, Eric

    2014-07-01

    A family of collective variables is proposed to perform exact dynamical coarse-graining even in systems without time scale separation. More precisely, it is shown that these variables are not slow in general, yet satisfy an overdamped Langevin equation that statistically preserves the sequence in which any regions in collective variable space are visited and permits to calculate exactly the mean first passage times from any such region to another. The role of the free energy and diffusion coefficient in this overdamped Langevin equation is discussed, along with the way they transform under any change of variable in collective variable space. These results apply both to systems with and without inertia, and they can be generalized to using several collective variables simultaneously. The view they offer on what makes collective variables and reaction coordinates optimal breaks from the standard notion that good collective variable must be slow variable, and it suggests new ways to interpret data from molecular dynamics simulations and experiments.

  13. Global view of bionetwork dynamics: adaptive landscape.

    PubMed

    Ao, Ping

    2009-02-01

    Based on recent work, I will give a nontechnical brief review of a powerful quantitative concept in biology, adaptive landscape, initially proposed by S. Wright over 70 years ago, reintroduced by one of the founders of molecular biology and by others in different biological contexts, but apparently forgotten by modern biologists for many years. Nevertheless, this concept finds an increasingly important role in the development of systems biology and bionetwork dynamics modeling, from phage lambda genetic switch to endogenous network for cancer genesis and progression. It is an ideal quantification to describe the robustness and stability of bionetworks. Here, I will first introduce five landmark proposals in biology on this concept, to demonstrate an important common thread in theoretical biology. Then I will discuss a few recent results, focusing on the studies showing theoretical consistency of adaptive landscape. From the perspective of a working scientist and of what is needed logically for a dynamical theory when confronting empirical data, the adaptive landscape is useful both metaphorically and quantitatively, and has captured an essential aspect of biological dynamical processes. Though at the theoretical level the adaptive landscape must exist and it can be used across hierarchical boundaries in biology, many associated issues are indeed vague in their initial formulations and their quantitative realizations are not easy, and are good research topics for quantitative biologists. I will discuss three types of open problems associated with the adaptive landscape in a broader perspective.

  14. Dynamical Response of Networks Under External Perturbations: Exact Results

    NASA Astrophysics Data System (ADS)

    Chinellato, David D.; Epstein, Irving R.; Braha, Dan; Bar-Yam, Yaneer; de Aguiar, Marcus A. M.

    2015-04-01

    We give exact statistical distributions for the dynamic response of influence networks subjected to external perturbations. We consider networks whose nodes have two internal states labeled 0 and 1. We let nodes be frozen in state 0, in state 1, and the remaining nodes change by adopting the state of a connected node with a fixed probability per time step. The frozen nodes can be interpreted as external perturbations to the subnetwork of free nodes. Analytically extending and to be smaller than 1 enables modeling the case of weak coupling. We solve the dynamical equations exactly for fully connected networks, obtaining the equilibrium distribution, transition probabilities between any two states and the characteristic time to equilibration. Our exact results are excellent approximations for other topologies, including random, regular lattice, scale-free and small world networks, when the numbers of fixed nodes are adjusted to take account of the effect of topology on coupling to the environment. This model can describe a variety of complex systems, from magnetic spins to social networks to population genetics, and was recently applied as a framework for early warning signals for real-world self-organized economic market crises.

  15. Exact dynamics of a class of aggregation models

    NASA Astrophysics Data System (ADS)

    Majumdar, Satya N.; Sire, Clément

    1993-11-01

    The dynamics of a class of aggregation models proposed by Takayasu and co-workers are solved exactly in one dimension and in the mean field limit. These models describe the aggregation of positive and negative charges. In one dimension, we find the dynamical cluster-size exponents z=3/2 and zc=3/4 when the average flux of injected charges is nonzero and zero, respectively. We also find the crossover exponent near the transition to be φ=4/3. Within mean field theory, we find these exponents to be z=2, zc=1, and φ=1. Assuming dynamic scaling, we show that in any dimension, these exponents are related to one single static exponent.

  16. Dynamic landscapes in human evolution and dispersal

    NASA Astrophysics Data System (ADS)

    Devès, Maud; King, Geoffrey; Bailey, Geoffrey; Inglis, Robyn; Williams, Matthew; Winder, Isabelle

    2013-04-01

    Archaeological studies of human settlement in its wider landscape setting usually focus on climate change as the principal environmental driver of change in the physical features of the landscape, even on the long time scales of early human evolution. We emphasize that landscapes evolve dynamically due to an interplay of processes occurring over different timescales. Tectonic deformation, volcanism, sea level changes, by acting on the topography, the lithology and on the patterns of erosion-deposition in a given area, can moderate or amplify the influence of climate at the regional and local scale. These processes impose or alleviate physical barriers to movement, and modify the distribution and accessibility of plant and animal resources in ways critical to human ecological and evolutionary success (King and Bailey, JHE 2006; Bailey and King, Antiquity 2011, Winder et al. Antiquity in press). The DISPERSE project, an ERC-funded collaboration between the University of York and the Institut de Physique du Globe de Paris, aims to develop systematic methods for reconstructing landscapes associated with active tectonics, volcanism and sea level change at a variety of scales in order to study their potential impact on patterns of human evolution and dispersal. Examples are shown to illustrate the ways in which changes of significance to human settlement can occur at a range of geographical scales and on time scales that range from lifetimes to tens of millennia, creating and sustaining attractive conditions for human settlement and exercising powerful selective pressures on human development.

  17. Waves on a vortex filament: exact solutions of dynamical equations

    NASA Astrophysics Data System (ADS)

    Brugarino, Tommaso; Mongiovi, Maria Stella; Sciacca, Michele

    2014-09-01

    In this paper, we take into account the dynamical equations of a vortex filament in superfluid helium at finite temperature (1 K < T < 2.17 K) and at very low temperature, which is called Biot-Savart law. The last equation is also valid for a vortex tube in a frictionless, unbounded, and incompressible fluid. Both the equations are approximated by the Local Induction Approximation (LIA) and Fukumoto's approximation. The obtained equations are then considered in the extrinsic frame of reference, where exact solutions (Kelvin waves) are shown. These waves are then compared one to each other in terms of their dispersion relations in the frictionless case. The same equations are then investigated for a quantized vortex line in superfluid helium at higher temperature, where friction terms are needed for a full description of the motion.

  18. Waves on a vortex filament: exact solutions of dynamical equations

    NASA Astrophysics Data System (ADS)

    Brugarino, Tommaso; Mongiovi, Maria Stella; Sciacca, Michele

    2015-06-01

    In this paper, we take into account the dynamical equations of a vortex filament in superfluid helium at finite temperature (1 K < T < 2.17 K) and at very low temperature, which is called Biot-Savart law. The last equation is also valid for a vortex tube in a frictionless, unbounded, and incompressible fluid. Both the equations are approximated by the Local Induction Approximation (LIA) and Fukumoto's approximation. The obtained equations are then considered in the extrinsic frame of reference, where exact solutions (Kelvin waves) are shown. These waves are then compared one to each other in terms of their dispersion relations in the frictionless case. The same equations are then investigated for a quantized vortex line in superfluid helium at higher temperature, where friction terms are needed for a full description of the motion.

  19. Exact Quantum Dynamics Calculations Using Phase Space Wavelets

    NASA Astrophysics Data System (ADS)

    Halverson, Thomas; Poirier, Bill

    2013-06-01

    In a series of earlier papers, the authors introduced the first exact quantum dynamics method that defeats the exponential scaling of CPU effort with system dimensionality. The method used a ``weylet'' basis set (orthogonalized Weyl-Heisenberg wavelets), combined with a phase space truncation scheme first proposed by M. Davis and E. Heller. Here, we use a related, but much simpler, wavelet basis consisting of momentum-symmetrized phase space Gaussians. Despite being non-orthogonal, symmetrized Gaussians exhibit collective locality, allowing for effective phase space truncation and the defeat of exponential scaling. A ``universal'' and remarkably simple code has been written, which is dimensionally independent, and which also exploits massively parallel algorithms. The codes have been used to calculate the vibrational spectra of several molecules of varying dimensionality.

  20. Global structure of exact scalar hairy dynamical black holes

    NASA Astrophysics Data System (ADS)

    Fan, Zhong-Ying; Chen, Bin; Lü, H.

    2016-05-01

    We study the global structure of some exact scalar hairy dynamical black holes which were constructed in Einstein gravity either minimally or non-minimally coupled to a scalar field. We find that both the apparent horizon and the local event horizon (measured in luminosity coordinate) monotonically increase with the advanced time as well as the Vaidya mass. At late advanced times, the apparent horizon approaches the event horizon and gradually becomes future outer. Correspondingly, the space-time arrives at stationary black hole states with the relaxation time inversely proportional to the 1/( n-1) power of the final black hole mass, where n is the space-time dimension. These results strongly support the solutions describing the formation of black holes with scalar hair. We also obtain new charged dynamical solutions in the non-minimal theory by introducing an Maxwell field which is non-minimally coupled to the scalar. The presence of the electric charge strongly modifies the dynamical evolution of the space-time.

  1. Mutator Dynamics on a Smooth Evolutionary Landscape

    NASA Astrophysics Data System (ADS)

    Kessler, David A.; Levine, Herbert

    1998-03-01

    We investigate a model of evolutionary dynamics on a smooth landscape which features a ``mutator'' allele which increases the mutation rate. We show that when the fitness is far from its equilibrium value the expected proportion of mutators approaches a value governed solely by the transition rates into and out of the mutator state, resulting in a much faster fitness increase than would be the case without the mutator allele. Near the fitness equilibrium, the mutators are severely suppressed, due to the detrimental effects of a large mutation rate near the fitness maximum. We discuss the results of a recent experiment on natural selection of E. coli in the light of our model.

  2. Exact Dynamics via Poisson Process: a unifying Monte Carlo paradigm

    NASA Astrophysics Data System (ADS)

    Gubernatis, James

    2014-03-01

    A common computational task is solving a set of ordinary differential equations (o.d.e.'s). A little known theorem says that the solution of any set of o.d.e.'s is exactly solved by the expectation value over a set of arbitary Poisson processes of a particular function of the elements of the matrix that defines the o.d.e.'s. The theorem thus provides a new starting point to develop real and imaginary-time continous-time solvers for quantum Monte Carlo algorithms, and several simple observations enable various quantum Monte Carlo techniques and variance reduction methods to transfer to a new context. I will state the theorem, note a transformation to a very simple computational scheme, and illustrate the use of some techniques from the directed-loop algorithm in context of the wavefunction Monte Carlo method that is used to solve the Lindblad master equation for the dynamics of open quantum systems. I will end by noting that as the theorem does not depend on the source of the o.d.e.'s coming from quantum mechanics, it also enables the transfer of continuous-time methods from quantum Monte Carlo to the simulation of various classical equations of motion heretofore only solved deterministically.

  3. Connecting exact coherent states to turbulent dynamics in channel flow

    NASA Astrophysics Data System (ADS)

    Park, Jae Sung; Graham, Michael D.

    2015-11-01

    The discovery of nonlinear traveling wave solutions to the Navier-Stokes equations or exact coherent states has greatly advanced the understanding of the nature of turbulent shear flows. These solutions are unstable saddle points in state space, while the time evolution of a turbulent flow is a dynamical trajectory wandering around them. In this regard, it is of interest to investigate how closely the turbulent trajectories approach these invariant states. Here, we present connections between turbulent trajectories and one intriguing solution family in channel flow. A state space visualization of turbulent trajectories is presented in a three-dimensional space. The lifetime of the trajectories is well represented by closeness to two distinct solutions resembling in many ways the active and hibernating phases of minimal channel turbulence (Xi & Graham PRL 2010). The connections are then examined by comparing mean profiles and flow structures. More importantly, the connections are confirmed by calculating the L2 distance between the trajectories and the traveling waves. Lastly, paths of an intermittent bursting phenomenon are identified in state space and the relationship between bursting paths and the traveling waves or hibernating turbulence is further discussed. This work was supported by the Air Force Office of Scientific Research through grant FA9550-15-1-0062 (Flow Interactions and Control Program).

  4. Spacetime dynamics of spinning particles: Exact electromagnetic analogies

    NASA Astrophysics Data System (ADS)

    Costa, L. Filipe O.; Natário, José; Zilhão, Miguel

    2016-05-01

    We compare the rigorous equations describing the motion of spinning test particles in gravitational and electromagnetic fields, and show that if the Mathisson-Pirani spin condition holds then exact gravito-electromagnetic analogies emerge. These analogies provide a familiar formalism to treat gravitational problems, as well as a means for comparing the two interactions. Fundamental differences are manifest in the symmetries and time projections of the electromagnetic and gravitational tidal tensors. The physical consequences of the symmetries of the tidal tensors are explored comparing the following analogous setups: magnetic dipoles in the field of nonspinning/spinning charges, and gyroscopes in the Schwarzschild, Kerr, and Kerr-de Sitter spacetimes. The implications of the time projections of the tidal tensors are illustrated by the work done on the particle in various frames; in particular, a reciprocity is found to exist: in a frame comoving with the particle, the electromagnetic (but not the gravitational) field does work on it, causing a variation of its proper mass; conversely, for "static observers," a stationary gravitomagnetic (but not a magnetic) field does work on the particle, and the associated potential energy is seen to embody the Hawking-Wald spin-spin interaction energy. The issue of hidden momentum, and its counterintuitive dynamical implications, is also analyzed. Finally, a number of issues regarding the electromagnetic interaction and the physical meaning of Dixon's equations are clarified.

  5. The dynamical landscape of marine phytoplankton diversity.

    PubMed

    Lévy, Marina; Jahn, Oliver; Dutkiewicz, Stephanie; Follows, Michael J; d'Ovidio, Francesco

    2015-10-01

    Observations suggest that the landscape of marine phytoplankton assemblage might be strongly heterogeneous at the dynamical mesoscale and submesoscale (10-100 km, days to months), with potential consequences in terms of global diversity and carbon export. But these variations are not well documented as synoptic taxonomic data are difficult to acquire. Here, we examine how phytoplankton assemblage and diversity vary between mesoscale eddies and submesoscale fronts. We use a multi-phytoplankton numerical model embedded in a mesoscale flow representative of the North Atlantic. Our model results suggest that the mesoscale flow dynamically distorts the niches predefined by environmental contrasts at the basin scale and that the phytoplankton diversity landscape varies over temporal and spatial scales that are one order of magnitude smaller than those of the basin-scale environmental conditions. We find that any assemblage and any level of diversity can occur in eddies and fronts. However, on a statistical level, the results suggest a tendency for larger diversity and more fast-growing types at fronts, where nutrient supplies are larger and where populations of adjacent water masses are constantly brought into contact; and lower diversity in the core of eddies, where water masses are kept isolated long enough to enable competitive exclusion.

  6. The dynamical landscape of marine phytoplankton diversity

    PubMed Central

    Lévy, Marina; Jahn, Oliver; Dutkiewicz, Stephanie; Follows, Michael J.; d'Ovidio, Francesco

    2015-01-01

    Observations suggest that the landscape of marine phytoplankton assemblage might be strongly heterogeneous at the dynamical mesoscale and submesoscale (10–100 km, days to months), with potential consequences in terms of global diversity and carbon export. But these variations are not well documented as synoptic taxonomic data are difficult to acquire. Here, we examine how phytoplankton assemblage and diversity vary between mesoscale eddies and submesoscale fronts. We use a multi-phytoplankton numerical model embedded in a mesoscale flow representative of the North Atlantic. Our model results suggest that the mesoscale flow dynamically distorts the niches predefined by environmental contrasts at the basin scale and that the phytoplankton diversity landscape varies over temporal and spatial scales that are one order of magnitude smaller than those of the basin-scale environmental conditions. We find that any assemblage and any level of diversity can occur in eddies and fronts. However, on a statistical level, the results suggest a tendency for larger diversity and more fast-growing types at fronts, where nutrient supplies are larger and where populations of adjacent water masses are constantly brought into contact; and lower diversity in the core of eddies, where water masses are kept isolated long enough to enable competitive exclusion. PMID:26400196

  7. The dynamical landscape of marine phytoplankton diversity.

    PubMed

    Lévy, Marina; Jahn, Oliver; Dutkiewicz, Stephanie; Follows, Michael J; d'Ovidio, Francesco

    2015-10-01

    Observations suggest that the landscape of marine phytoplankton assemblage might be strongly heterogeneous at the dynamical mesoscale and submesoscale (10-100 km, days to months), with potential consequences in terms of global diversity and carbon export. But these variations are not well documented as synoptic taxonomic data are difficult to acquire. Here, we examine how phytoplankton assemblage and diversity vary between mesoscale eddies and submesoscale fronts. We use a multi-phytoplankton numerical model embedded in a mesoscale flow representative of the North Atlantic. Our model results suggest that the mesoscale flow dynamically distorts the niches predefined by environmental contrasts at the basin scale and that the phytoplankton diversity landscape varies over temporal and spatial scales that are one order of magnitude smaller than those of the basin-scale environmental conditions. We find that any assemblage and any level of diversity can occur in eddies and fronts. However, on a statistical level, the results suggest a tendency for larger diversity and more fast-growing types at fronts, where nutrient supplies are larger and where populations of adjacent water masses are constantly brought into contact; and lower diversity in the core of eddies, where water masses are kept isolated long enough to enable competitive exclusion. PMID:26400196

  8. Metapopulation dynamics in a complex ecological landscape

    NASA Astrophysics Data System (ADS)

    Colombo, E. H.; Anteneodo, C.

    2015-08-01

    We propose a general model to study the interplay between spatial dispersal and environment spatiotemporal fluctuations in metapopulation dynamics. An ecological landscape of favorable patches is generated like a Lévy dust, which allows to build a range of patterns, from dispersed to clustered ones. Locally, the dynamics is driven by a canonical model for the time evolution of the population density, consisting of a logistic expression plus multiplicative noises. Spatial coupling is introduced by means of two spreading mechanisms: diffusion and selective dispersal driven by patch suitability. We focus on the long-time population size as a function of habitat configurations, environment fluctuations, and coupling schemes. We obtain the conditions, that the spatial distribution of favorable patches and the coupling mechanisms must fulfill, to grant population survival. The fundamental phenomenon that we observe is the positive feedback between environment fluctuations and spatial spread preventing extinction.

  9. Metapopulation dynamics in a complex ecological landscape.

    PubMed

    Colombo, E H; Anteneodo, C

    2015-08-01

    We propose a general model to study the interplay between spatial dispersal and environment spatiotemporal fluctuations in metapopulation dynamics. An ecological landscape of favorable patches is generated like a Lévy dust, which allows to build a range of patterns, from dispersed to clustered ones. Locally, the dynamics is driven by a canonical model for the time evolution of the population density, consisting of a logistic expression plus multiplicative noises. Spatial coupling is introduced by means of two spreading mechanisms: diffusion and selective dispersal driven by patch suitability. We focus on the long-time population size as a function of habitat configurations, environment fluctuations, and coupling schemes. We obtain the conditions, that the spatial distribution of favorable patches and the coupling mechanisms must fulfill, to grant population survival. The fundamental phenomenon that we observe is the positive feedback between environment fluctuations and spatial spread preventing extinction. PMID:26382439

  10. Landscape pattern and successional dynamics in the boreal forest

    NASA Technical Reports Server (NTRS)

    Hall, Forrest G.; Strebel, Donald E.; Goetz, Scott J.; Woods, Kerry D.; Botkin, Daniel B.

    1987-01-01

    The landscape-scale community dynamics of a boreal forest ecosystem was investigated using the Landsat MSS data record form 1973 to 1983 to generate a stochastic description of the key life cycle states of the community landscape elements. Such descriptions can provide input and verification for models of community development and landscape dynamics. It is anticipated that the proposed approach may be extended to measure, monitor, and model ecosystems at continental and planetary scales.

  11. Exact milestoning

    SciTech Connect

    Bello-Rivas, Juan M.; Elber, Ron

    2015-03-07

    A new theory and an exact computer algorithm for calculating kinetics and thermodynamic properties of a particle system are described. The algorithm avoids trapping in metastable states, which are typical challenges for Molecular Dynamics (MD) simulations on rough energy landscapes. It is based on the division of the full space into Voronoi cells. Prior knowledge or coarse sampling of space points provides the centers of the Voronoi cells. Short time trajectories are computed between the boundaries of the cells that we call milestones and are used to determine fluxes at the milestones. The flux function, an essential component of the new theory, provides a complete description of the statistical mechanics of the system at the resolution of the milestones. We illustrate the accuracy and efficiency of the exact Milestoning approach by comparing numerical results obtained on a model system using exact Milestoning with the results of long trajectories and with a solution of the corresponding Fokker-Planck equation. The theory uses an equation that resembles the approximate Milestoning method that was introduced in 2004 [A. K. Faradjian and R. Elber, J. Chem. Phys. 120(23), 10880-10889 (2004)]. However, the current formulation is exact and is still significantly more efficient than straightforward MD simulations on the system studied.

  12. Feedbacks and landscape-level vegetation dynamics.

    PubMed

    Bowman, David M J S; Perry, George L W; Marston, J B

    2015-05-01

    Alternative stable-state theory (ASS) is widely accepted as explaining landscape-level vegetation dynamics, such as switches between forest and grassland. This theory argues that webs of feedbacks stabilise vegetation composition and structure, and that abrupt state shifts can occur if stabilising feedbacks are weakened. However, it is difficult to identify stabilising feedback loops and the disturbance thresholds beyond which state changes occur. Here, we argue that doing this requires a synthetic approach blending observation, experimentation, simulation, conceptual models, and narratives. Using forest boundaries and large mammal extinctions, we illustrate how a multifaceted research program can advance understanding of feedback-driven ecosystem change. Our integrative approach has applicability to other complex macroecological systems controlled by numerous feedbacks where controlled experimentation is impossible.

  13. Universality in exact quantum state population dynamics and control

    SciTech Connect

    Wu, Lian-Ao; Segal, Dvira; Brumer, Paul; Egusquiza, Inigo L.

    2010-09-15

    We consider an exact population transition, defined as the probability of finding a state at a final time that is exactly equal to the probability of another state at the initial time. We prove that, given a Hamiltonian, there always exists a complete set of orthogonal states that can be employed as time-zero states for which this exact population transition occurs. The result is general: It holds for arbitrary systems, arbitrary pairs of initial and final states, and for any time interval. The proposition is illustrated with several analytic models. In particular, we demonstrate that in some cases, by tuning the control parameters, a complete transition might occur, where a target state, vacant at t=0, is fully populated at time {tau}.

  14. [Dynamics of forest landscape boundary at Changbai Mountain].

    PubMed

    Chang, Yu; Bu, Rencang; Hu, Yuanman; Xu, Chonggang; Wang, Qingli

    2004-01-01

    By using Geographic Information System (GIS) and Remote Sensing (RS) technology combined with field investigation and correlation analysis, this study was aimed to explore the dynamics of forest landscape boundary at Changbai Mountain, and to reveal the relationships among landscape fragmentation and changes of landscape boundary indices. The results showed that in the last 20 years or so, tundra decreased by 3694.8 hm2, spruce and fir forest reduced by 130482.03 hm2, and Korean pine-hardwood and mountain birch forest increased by 41610.4 hm2 and 669.78 hm2, respectively. The forest landscapes at Changbai Mountain tended to be more fragmented, and the shape of the landscape boundary became more complicated due to timber harvesting, forest cutting for cropping, and other human activities such as tourism. The changes of landscape shape index (LSI), contrast weighted edge density (CWED), total weighted edge length (TE-WGT) and weighted landscape shape index (LSI-WGT) could be used as good indicators for the degrees of forest landscape fragmentations, which was approved by correlation analysis among landscape fragmentation and changes of landscape boundary indices. The degree of human activities on landscape could be reflected by landscape shape index.

  15. Landscape Disturbance History and Belowground Carbon Dynamics.

    NASA Astrophysics Data System (ADS)

    Marin-Spiotta, E.; Smith, A. P.; Atkinson, E. E.; Chaopricha, N. T.

    2014-12-01

    Earth system models vary in their predictions of carbon (C) uptake and release by the terrestrial biosphere, partly due to great uncertainties in the response of soils, one of the largest C reservoirs. The world's soils play a major role in the exchange of greenhouse gases with the atmosphere, in sustaining primary production, and in providing food security. Despite this, the sensitivity of soils to disturbance is highly uncertain. One reason for this is geographic variability in the importance of different mechanisms regulating soil C turnover. Most of our understanding of factors influencing soil organic C dynamics comes from research in temperate soils, despite the major role of tropical soils in the global C cycle. Even in the tropics, the diversity of soil environments is grossly underrepresented in the literature. This has important implications for predictions of soil C change across latitudes. We discuss results from the response of soil C pools and microbial communities to land use legacies on two contrasting tropical soil environments. Uncertainties in the response of soil C to disturbance also stem from a historic focus on shallow depths and the assumption that deep soil C is unreactive to landscape change. Growing evidence indicates that soil C pools in deep mineral horizons can be sensitive to changes in land cover and climate. This realization highlights the need to reassess the source of soil C at depth and the processes contributing to its stabilization. We discuss results from the interaction between multiple disturbances: drought, fire and erosion, on the accumulation of soil C at depths beyond those typically included in regional or global inventories. Our data show that deep soil C can be reactive and be a potential source of C if reconnected to the atmosphere. A deeper, mechanistic appreciation for a landscape's history of disturbance is critical for predicting feedbacks between the terrestrial biosphere and the climate system.

  16. Biodiversity and ecosystem functioning in dynamic landscapes.

    PubMed

    Brose, Ulrich; Hillebrand, Helmut

    2016-05-19

    in dynamic communities of real-world landscapes. PMID:27114570

  17. Biodiversity and ecosystem functioning in dynamic landscapes

    PubMed Central

    Brose, Ulrich; Hillebrand, Helmut

    2016-01-01

    in dynamic communities of real-world landscapes. PMID:27114570

  18. How vegetation patterning affects sediment dynamics in complex landscapes

    NASA Astrophysics Data System (ADS)

    Baartman, Jantiene; Temme, Arnaud; Saco, Patricia

    2016-04-01

    Semi-arid ecosystems are often spatially self-organized in typical patterns of vegetation bands with high plant cover interspersed with bare soil areas, also known as 'tigerbush'. Tigerbush dynamics have been studied using model simulations on flat synthetic landscapes, although in some cases straight slopes were used. The feedbacks between vegetation and more realistic and complex landscapes have not been studied yet, even though these landscapes are much more prevalent. Hence, our objective was to determine the effect of landform variation on vegetation patterning and sediment dynamics. We linked two existing models that simulate (a) plant growth, death and dispersal of vegetation, and (b) erosion and sedimentation. The model was calibrated on a straight planar hillslope and then applied to (i) a set of synthetic but more complex topographies and (ii) three real-world landscapes. Furthermore, sediment dynamics were evaluated by comparing simulated sediment output with and without vegetation dynamics. Results show banded vegetation patterning on all synthetic topographies, always perpendicular to the slope gradient. For real topographies, banded vegetation was simulated in the relatively flat, rolling landscape and in the dissected landscape when slopes were gentle. In the steep dissected landscape and the alluvial fan, vegetation was simulated to grow in local depressions where moisture is present whereas hilltops were bare. Including vegetation dynamics resulted in significantly less simulated erosion and relatively more deposition compared to simulations with uniformly distributed vegetation.

  19. Dynamic Shade and Irradiance Simulation of Aquatic Landscapes and Watersheds

    EPA Science Inventory

    Penumbra is a landscape shade and irradiance simulation model that simulates how solar energy spatially and temporally interacts within dynamic ecosystems such as riparian zones, forests, and other terrain that cast topological shadows. Direct and indirect solar energy accumulate...

  20. Bacterial predator-prey dynamics in microscale patchy landscapes.

    PubMed

    Hol, Felix J H; Rotem, Or; Jurkevitch, Edouard; Dekker, Cees; Koster, Daniel A

    2016-02-10

    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.

  1. Soil erosion dynamics response to landscape pattern.

    PubMed

    Ouyang, Wei; Skidmore, Andrew K; Hao, Fanghua; Wang, Tiejun

    2010-02-15

    Simulating soil erosion variation with a temporal land use database reveals long-term fluctuations in landscape patterns, as well as priority needs for soil erosion conservation. The application of a multi-year land use database in support of a Soil Water Assessment Tool (SWAT) led to an accurate assessment, from 1977 to 2006, of erosion in the upper watershed of the Yellow River. At same time, the impacts of land use and landscape service features on soil erosion load were assessed. A series of supervised land use classifications of Landsat images characterized variations in land use and landscape patterns over three decades. The SWAT database was constructed with soil properties, climate and elevation data. Using water flow and sand density data as parameters, regional soil erosion load was simulated. A numerical statistical model was used to relate soil erosion to land use and landscape. The results indicated that decadal decrease of grassland areas did not pose a significant threat to soil erosion, while the continual increase of bare land, water area and farmland increased soil erosion. Regional landscape variation also had a strong relationship with erosion. Patch level landscape analyses demonstrated that larger water area led to more soil erosion. The patch correlation indicated that contagious grassland patches reduced soil erosion yield. The increased grassland patches led to more patch edges, in turn increasing the sediment transportation from the patch edges. The findings increase understanding of the temporal variation in soil erosion processes, which is the basis for preventing local pollution.

  2. Criticality in conserved dynamical systems: Experimental observation vs. exact properties

    NASA Astrophysics Data System (ADS)

    Marković, Dimitrije; Gros, Claudius; Schuelein, André

    2013-03-01

    Conserved dynamical systems are generally considered to be critical. We study a class of critical routing models, equivalent to random maps, which can be solved rigorously in the thermodynamic limit. The information flow is conserved for these routing models and governed by cyclic attractors. We consider two classes of information flow, Markovian routing without memory and vertex routing involving a one-step routing memory. Investigating the respective cycle length distributions for complete graphs, we find log corrections to power-law scaling for the mean cycle length, as a function of the number of vertices, and a sub-polynomial growth for the overall number of cycles. When observing experimentally a real-world dynamical system one normally samples stochastically its phase space. The number and the length of the attractors are then weighted by the size of their respective basins of attraction. This situation is equivalent, for theory studies, to "on the fly" generation of the dynamical transition probabilities. For the case of vertex routing models, we find in this case power law scaling for the weighted average length of attractors, for both conserved routing models. These results show that the critical dynamical systems are generically not scale-invariant but may show power-law scaling when sampled stochastically. It is hence important to distinguish between intrinsic properties of a critical dynamical system and its behavior that one would observe when randomly probing its phase space.

  3. An Exact Solvable Model of Rocket Dynamics in Atmosphere

    ERIC Educational Resources Information Center

    Rodrigues, H.; Pinho, M. O.; Portes, D., Jr.; Santiago, A.

    2009-01-01

    In basic physics courses at undergraduate level, the dynamics of self-propelled bodies is presented as an example of momentum conservation law applied to systems with time-varying mass. However, is often studied the simple situation of free motion or the motion under the action of a constant gravitational field. In this work, we investigate the…

  4. Locally dispersing populations in heterogeneous dynamic landscapes with spatiotemporal correlations. I. Block disturbance.

    PubMed

    Hiebeler, David E; Houle, Jennifer; Drummond, Frank; Bilodeau, Peter; Merckens, Jeffery

    2016-10-21

    Locally dispersing populations are generally favorably affected by increasing the scale of habitat heterogeneity because they can exploit contiguous patches of suitable habitat. Increasing the spatial scale of landscape disturbances (such as by applying a pesticide to control an unwanted species) drives down population density because of reasons including dispersal-limited recolonization and the resulting increase in temporal variability. Here, we examine how population density changes as the spatial scale of landscape disturbance increases: does it increase due to increases in spatial correlations in landscape habitat type, or does it decrease due to the various spatial and temporal effects of larger-scale disturbances? We use simulations, mean field approximations, pair approximations, landscape-improved pair approximations (LIPA), and block probabilities to investigate a model of a locally dispersing species on a dynamic landscape with spatiotemporally structured heterogeneous habitat. Pesticide is applied at a given spatial scale, leaving habitat unsuitable for some time before dissipating and allowing the habitat to revert to a suitable state. We found that increasing the spatial scale of disturbances (while keeping the overall disturbance rate fixed) can increase population density, but generally only when landscape turnover is slow relative to population dynamics and when the population is somewhat close to its extinction threshold. Applying control measures at larger spatial scales may allow them to be more effective with the same overall treatment rate. The optimal spatial strategy for applying disturbances depends on both habitat availability as well as the turnover rate of the control measure being used. For the large-scale habitat dynamics in our model, it is possible to analytically calculate spatial correlations in habitat types over arbitrary scales. However, including exact habitat correlations at the triplet scale but approximating population

  5. Locally dispersing populations in heterogeneous dynamic landscapes with spatiotemporal correlations. I. Block disturbance.

    PubMed

    Hiebeler, David E; Houle, Jennifer; Drummond, Frank; Bilodeau, Peter; Merckens, Jeffery

    2016-10-21

    Locally dispersing populations are generally favorably affected by increasing the scale of habitat heterogeneity because they can exploit contiguous patches of suitable habitat. Increasing the spatial scale of landscape disturbances (such as by applying a pesticide to control an unwanted species) drives down population density because of reasons including dispersal-limited recolonization and the resulting increase in temporal variability. Here, we examine how population density changes as the spatial scale of landscape disturbance increases: does it increase due to increases in spatial correlations in landscape habitat type, or does it decrease due to the various spatial and temporal effects of larger-scale disturbances? We use simulations, mean field approximations, pair approximations, landscape-improved pair approximations (LIPA), and block probabilities to investigate a model of a locally dispersing species on a dynamic landscape with spatiotemporally structured heterogeneous habitat. Pesticide is applied at a given spatial scale, leaving habitat unsuitable for some time before dissipating and allowing the habitat to revert to a suitable state. We found that increasing the spatial scale of disturbances (while keeping the overall disturbance rate fixed) can increase population density, but generally only when landscape turnover is slow relative to population dynamics and when the population is somewhat close to its extinction threshold. Applying control measures at larger spatial scales may allow them to be more effective with the same overall treatment rate. The optimal spatial strategy for applying disturbances depends on both habitat availability as well as the turnover rate of the control measure being used. For the large-scale habitat dynamics in our model, it is possible to analytically calculate spatial correlations in habitat types over arbitrary scales. However, including exact habitat correlations at the triplet scale but approximating population

  6. Dynamic homotopy and landscape dynamical set topology in quantum control

    SciTech Connect

    Dominy, Jason; Rabitz, Herschel

    2012-08-15

    We examine the topology of the subset of controls taking a given initial state to a given final state in quantum control, where 'state' may mean a pure state Double-Vertical-Line {psi}>, an ensemble density matrix {rho}, or a unitary propagator U(0, T). The analysis consists in showing that the endpoint map acting on control space is a Hurewicz fibration for a large class of affine control systems with vector controls. Exploiting the resulting fibration sequence and the long exact sequence of basepoint-preserving homotopy classes of maps, we show that the indicated subset of controls is homotopy equivalent to the loopspace of the state manifold. This not only allows us to understand the connectedness of 'dynamical sets' realized as preimages of subsets of the state space through this endpoint map, but also provides a wealth of additional topological information about such subsets of control space.

  7. Nonlinear dynamics, Waddington landscape and stem cells

    NASA Astrophysics Data System (ADS)

    Tang, Chao

    There are hundreds of different cell types (skin, neuron, muscle, etc.) in human body, all derived from the stem cell and all have the same genetic information. About 60 years ago, Waddington speculated that the different cell types correspond to different minima in a landscape emerged from genetic interactions. Recently, biologists succeeded in transforming one cell type to another by perturbing the genetic interactions in a cell. I will discuss the experiments and a mathematical model of a set of such cell type transformations in mice, in which we can see an actual example of the Waddington landscape and ways to alter it to facilitate cell type transformation - in particular, to reprogram a differentiated cell back into a stem cell.

  8. Exploring the control landscape for nonlinear quantum dynamics

    NASA Astrophysics Data System (ADS)

    Yan, Julia; Hocker, David; Long, Ruixing; Ho, Tak-San; Rabitz, Herschel

    2014-06-01

    Manipulation of a quantum system can be viewed in the framework of a control landscape defined as the physical objective as a functional of the control. Control landscape analyses have thus far considered linear quantum dynamics. This paper extends the analysis of control landscape topology to nonlinear quantum dynamics with the objective of steering a finite-level quantum system from an initial state to a final target state. The analysis rests on the assumptions that (i) the final state is reachable from the initial state, (ii) the differential mapping from the control to the state is surjective, and (iii) the control resources are unconstrained. Under these assumptions, landscape critical points (i.e., where the slope vanishes) for nonlinear quantum dynamics only appear as the global maximum and minimum; thus, the landscape is free of traps. Moreover, the landscape Hessian (i.e., the second derivative with respect to the control) at the global maximum has finite rank, indicating the presence of a large level set of optimal controls that preserve the value of the maximum. Extensive numerical simulations on finite-level models of the Gross-Pitaevskii equation confirm the trap-free nature of the landscape as well as the Hessian rank analysis, using either an applied electric field or a tunable condensate two-body interaction strength as the control. In addition, the control mechanisms arising in the numerical simulations are qualitatively assessed. These results are a generalization of previous findings for the linear Schrödinger equation, and show promise for successful control in a wide range of nonlinear quantum dynamics applications.

  9. Landscape matrix mediates occupancy dynamics of Neotropical avian insectivores

    USGS Publications Warehouse

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

    2011-01-01

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

  10. Communication: Relation of centroid molecular dynamics and ring-polymer molecular dynamics to exact quantum dynamics.

    PubMed

    Hele, Timothy J H; Willatt, Michael J; Muolo, Andrea; Althorpe, Stuart C

    2015-05-21

    We recently obtained a quantum-Boltzmann-conserving classical dynamics by making a single change to the derivation of the "Classical Wigner" approximation. Here, we show that the further approximation of this "Matsubara dynamics" gives rise to two popular heuristic methods for treating quantum Boltzmann time-correlation functions: centroid molecular dynamics (CMD) and ring-polymer molecular dynamics (RPMD). We show that CMD is a mean-field approximation to Matsubara dynamics, obtained by discarding (classical) fluctuations around the centroid, and that RPMD is the result of discarding a term in the Matsubara Liouvillian which shifts the frequencies of these fluctuations. These findings are consistent with previous numerical results and give explicit formulae for the terms that CMD and RPMD leave out.

  11. Land Cover Applications, Landscape Dynamics, and Global Change

    USGS Publications Warehouse

    Tieszen, Larry L.

    2007-01-01

    The Land Cover Applications, Landscape Dynamics, and Global Change project at U.S. Geological Survey (USGS) Center for Earth Resources Observation and Science (EROS) seeks to integrate remote sensing and simulation models to better understand and seek solutions to national and global issues. Modeling processes related to population impacts, natural resource management, climate change, invasive species, land use changes, energy development, and climate mitigation all pose significant scientific opportunities. The project activities use remotely sensed data to support spatial monitoring, provide sensitivity analyses across landscapes and large regions, and make the data and results available on the Internet with data access and distribution, decision support systems, and on-line modeling. Applications support sustainable natural resource use, carbon cycle science, biodiversity conservation, climate change mitigation, and robust simulation modeling approaches that evaluate ecosystem and landscape dynamics.

  12. Exact quantum dynamics of spin systems using the positive-P representation

    NASA Astrophysics Data System (ADS)

    Ng, Ray; Sorensen, Erik

    2011-03-01

    We discuss a scheme for simulating the exact real time quantum dynamics of interacting quantum spin systems within the positive-P formalism. As model systems we study the transverse field Ising model as well as the Heisenberg model undergoing a quench away from the classical ferromagnetic ordered state. In using the positive-P representation (PPR), the dynamics of the interacting quantum spin system is mapped onto a set of stochastic differential equations (SDEs). The number of which scales linearly with the number of spins, N, compared to an exact solution through diagonalization that in the case of the Heisenberg model would require matrices exponentially large in N. This mapping is exact and can in principle be extended to higher dimensional interacting systems as well as to systems with an explicit coupling to the environment. We compare the results from using a PPR approach based on both the optical coherent states as well as SU(2) Radcliff coherent states.

  13. Pathogen population dynamics in agricultural landscapes: the Ddal modelling framework.

    PubMed

    Papaïx, Julien; Adamczyk-Chauvat, Katarzyna; Bouvier, Annie; Kiêu, Kiên; Touzeau, Suzanne; Lannou, Christian; Monod, Hervé

    2014-10-01

    Modelling processes that occur at the landscape scale is gaining more and more attention from theoretical ecologists to agricultural managers. Most of the approaches found in the literature lack applicability for managers or, on the opposite, lack a sound theoretical basis. Based on the metapopulation concept, we propose here a modelling approach for landscape epidemiology that takes advantage of theoretical results developed in the metapopulation context while considering realistic landscapes structures. A landscape simulator makes it possible to represent both the field pattern and the spatial distribution of crops. The pathogen population dynamics are then described through a matrix population model both stage- and space-structured. In addition to a classical invasion analysis we present a stochastic simulation experiment and provide a complete framework for performing a sensitivity analysis integrating the landscape as an input factor. We illustrate our approach using an example to evaluate whether the agricultural landscape composition and structure may prevent and mitigate the development of an epidemic. Although designed for a fungal foliar disease, our modelling approach is easily adaptable to other organisms.

  14. Communication: Relation of centroid molecular dynamics and ring-polymer molecular dynamics to exact quantum dynamics

    SciTech Connect

    Hele, Timothy J. H.; Willatt, Michael J.; Muolo, Andrea; Althorpe, Stuart C.

    2015-05-21

    We recently obtained a quantum-Boltzmann-conserving classical dynamics by making a single change to the derivation of the “Classical Wigner” approximation. Here, we show that the further approximation of this “Matsubara dynamics” gives rise to two popular heuristic methods for treating quantum Boltzmann time-correlation functions: centroid molecular dynamics (CMD) and ring-polymer molecular dynamics (RPMD). We show that CMD is a mean-field approximation to Matsubara dynamics, obtained by discarding (classical) fluctuations around the centroid, and that RPMD is the result of discarding a term in the Matsubara Liouvillian which shifts the frequencies of these fluctuations. These findings are consistent with previous numerical results and give explicit formulae for the terms that CMD and RPMD leave out.

  15. Exact diagonalization of the Bohr Hamiltonian for rotational nuclei: Dynamical {gamma} softness and triaxiality

    SciTech Connect

    Caprio, M. A.

    2011-06-15

    Detailed quantitative predictions are obtained for phonon and multiphonon excitations in well-deformed rotor nuclei within the geometric framework, by exact numerical diagonalization of the Bohr Hamiltonian in an SO(5) basis. Dynamical {gamma} deformation is found to significantly influence the predictions through its coupling to the rotational motion. Basic signatures for the onset of rigid triaxial deformation are also obtained.

  16. Field dynamics and tunneling in a flux landscape

    SciTech Connect

    Johnson, Matthew C.; Larfors, Magdalena

    2008-10-15

    We investigate field dynamics and tunneling between metastable minima in a landscape of type IIB flux compactifications, utilizing monodromies of the complex structure moduli space to continuously connect flux vacua. After describing the generic features of a flux-induced potential for the complex structure and type IIB axiodilaton, we specialize to the mirror quintic Calabi-Yau to obtain an example landscape. Studying the cosmological dynamics of the complex structure moduli, we find that the potential generically does not support slow-roll inflation and that in general the landscape separates neatly into basins of attraction of the various minima. We then discuss tunneling, with the inclusion of gravitational effects, in many-dimensional field spaces. A set of constraints on the form of the Euclidean paths through field space are presented, and then applied to construct approximate instantons mediating the transition between de Sitter vacua in the flux landscape. We find that these instantons are generically thick wall and that the tunneling rate is suppressed in the large-volume limit. We also consider examples where supersymmetry is not broken by fluxes, in which case near-Bogomolnyi-Prasad-Sommerfeld thin-wall bubbles can be constructed. We calculate the bubble-wall tension, finding that it scales like a D- or NS-brane bubble, and comment on the implications of this correspondence. Finally, we present a brief discussion of eternal inflation in the flux landscape.

  17. Introduction to special issue on carbon and landscape dynamics

    USGS Publications Warehouse

    Madej, Mary Ann; Wohl, Ellen E.

    2016-01-01

    In October, 2013, at the Geological Society of America annual meeting, a theme session focused on carbon and landscape dynamics.  That event led to interest in producing a special issue in ESPL compiling papers on this subject.  The 13 papers collected for this special issue reflect the diversity of recent geomorphic research, across a range of climatic and geomorphic settings, addressing some aspect of carbon dynamics.

  18. Spatial dynamics and genetics of infectious diseases on heterogeneous landscapes.

    PubMed

    Real, Leslie A; Biek, Roman

    2007-10-22

    Explicit spatial analysis of infectious disease processes recognizes that host-pathogen interactions occur in specific locations at specific times and that often the nature, direction, intensity and outcome of these interactions depend upon the particular location and identity of both host and pathogen. Spatial context and geographical landscape contribute to the probability of initial disease establishment, direction and velocity of disease spread, the genetic organization of resistance and susceptibility, and the design of appropriate control and management strategies. In this paper, we review the manner in which the physical organization of the landscape has been shown to influence the population dynamics and spatial genetic structure of host-pathogen interactions, and how we might incorporate landscape architecture into spatially explicit population models of the infectious disease process to increase our ability to predict patterns of disease occurrence and optimally design vaccination and control policies.

  19. Using multistate dynamical corrections to compute classically exact diffusion constants at arbitrary temperature

    SciTech Connect

    Voter, A.F.; Doll, J.D.; Cohen, J.M.

    1989-02-01

    A method is presented for computing the classically exact, surface or bulk diffusion constant of a point defect at arbitrary temperature. The thermal diffusion constant is expressed using the squared jump length averaged over all possible final states to which the atom can jump. The rate constants that weight this sum are computed using transition state theory and molecular dynamics within a recently developed many-state dynamical corrections formalism. While these rate constants are valid only in the rare-event regime (i.e., at low temperature), it is shown that for a periodic lattice of equivalent binding sites, the resulting diffusion contants is valid at any temperature for which the lattice sites remain well defined. It is thus possible to compute classically exact surface or bulk diffusion constant for an arbitrary interatomic potential, without the time scale limitations of direct molecular dynamics.

  20. Sediment dynamics in flat landscapes - insights from central Australia

    NASA Astrophysics Data System (ADS)

    Struck, Martin; Jansen, John D.; Codilean, Alexandru T.; Fujioka, Toshiyuki; Fink, David; Kotevski, Steven

    2015-04-01

    Erosion and sediment routing are key to understanding landscape evolution. In this regard, steep mountain regions have been the focus of most research efforts, leaving flat landscapes effectively unstudied in spite of their vast global extent. However, the timescales of material transfer and storage in regions of low relief are considered much longer than in their steep counterparts. Here we apply in situ-produced cosmogenic nuclides (CNs) to examine the sediment transport and storage history of a low-gradient catchment, Peake River, in arid central Australia. Previous work in central Australia has been restricted to mainly local measurements of landscape lowering and bedrock erosion; however, to better understand the processes shaping these landscapes, we adopt a source-to-sink approach coupling bedrock and hillslope colluvium measurements of CNs with basin-wide measurements in fluvial sediment. Variation in concentrations and ratios of cosmogenic 10Be and 26Al in sediment provide insights to rates of sediment residence times and burial history as grains are transmitted through the bedrock-hillslope-stream sediment conveyor. We present our preliminary CN results from sediments and bedrock, and discuss basin-wide sediment dynamics in flat landscapes, emphasizing the contrast with well-studied mountainous regions.

  1. Exact dynamical state of the exclusive queueing process with deterministic hopping.

    PubMed

    Arita, Chikashi; Schadschneider, Andreas

    2011-11-01

    The exclusive queueing process (EQP) has recently been introduced as a model for the dynamics of queues that takes into account the spatial structure of the queue. It can be interpreted as a totally asymmetric exclusion process of varying length. Here we investigate the case of deterministic bulk hopping p=1 that turns out to be one of the rare cases where exact nontrivial results for the dynamical properties can be obtained. Using a time-dependent matrix product form we calculate several dynamical properties, e.g., the density profile of the system.

  2. The F-Landscape: Dynamically Determining The Multiverse

    NASA Astrophysics Data System (ADS)

    Li, Tianjun; Maxin, James A.; Nanopoulos, Dimitri V.; Walker, Joel W.

    2012-09-01

    We evolve our Multiverse Blueprints to characterize our local neighborhood of the String Landscape and the Multiverse of plausible string, M- and F-theory vacua. Building upon the tripodal foundations of (i) the Flipped SU(5) Grand Unified Theory (GUT), (ii) extra TeV-Scale vector-like multiplets derived out of F-theory, and (iii) the dynamics of No-Scale supergravity, together dubbed No-Scale F-SU(5), we demonstrate the existence of a continuous family of solutions which might adeptly describe the dynamics of distinctive universes. This Multiverse landscape of F-SU(5) solutions, which we shall refer to as the F-Landscape, accommodates a subset of universes compatible with the presently known experimental uncertainties of our own universe. We show that by secondarily minimizing the minimum of the scalar Higgs potential of each solution within the F-Landscape, a continuous hypervolume of distinct minimum minimorum can be engineered which comprise a regional dominion of universes, with our own universe cast as the bellwether. We conjecture that an experimental signal at the LHC of the No-Scale F-SU(5) framework's applicability to our own universe might sensibly be extrapolated as corroborating evidence for the role of string, M- and F-theory as a master theory of the Multiverse, with No-Scale supergravity as a crucial and pervasive reinforcing structure.

  3. The dynamic landscape of the cell nucleus.

    PubMed

    Austin, Christopher M; Bellini, Michel

    2010-01-01

    While the cell nucleus was described for the first time almost two centuries ago, our modern view of the nuclear architecture is primarily based on studies from the last two decades. This surprising late start coincides with the development of new, powerful strategies to probe for the spatial organization of nuclear activities in both fixed and live cells. As a result, three major principles have emerged: first, the nucleus is not just a bag filled with nucleic acids and proteins. Rather, many distinct functional domains, including the chromosomes, resides within the confines of the nuclear envelope. Second, all these nuclear domains are highly dynamic, with molecules exchanging rapidly between them and the surrounding nucleoplasm. Finally, the motion of molecules within the nucleoplasm appears to be mostly driven by random diffusion. Here, the emerging roles of several subnuclear domains are discussed in the context of the dynamic functions of the cell nucleus.

  4. Event-driven Monte Carlo: Exact dynamics at all time scales for discrete-variable models

    NASA Astrophysics Data System (ADS)

    Mendoza-Coto, Alejandro; Díaz-Méndez, Rogelio; Pupillo, Guido

    2016-06-01

    We present an algorithm for the simulation of the exact real-time dynamics of classical many-body systems with discrete energy levels. In the same spirit of kinetic Monte Carlo methods, a stochastic solution of the master equation is found, with no need to define any other phase-space construction. However, unlike existing methods, the present algorithm does not assume any particular statistical distribution to perform moves or to advance the time, and thus is a unique tool for the numerical exploration of fast and ultra-fast dynamical regimes. By decomposing the problem in a set of two-level subsystems, we find a natural variable step size, that is well defined from the normalization condition of the transition probabilities between the levels. We successfully test the algorithm with known exact solutions for non-equilibrium dynamics and equilibrium thermodynamical properties of Ising-spin models in one and two dimensions, and compare to standard implementations of kinetic Monte Carlo methods. The present algorithm is directly applicable to the study of the real-time dynamics of a large class of classical Markovian chains, and particularly to short-time situations where the exact evolution is relevant.

  5. The dynamic landscape of exceptional language development.

    PubMed

    Peltzer-Karpf, Annemarie

    2012-06-01

    Developmental neurocognitive studies have shown that the brain systems supporting the emergence of sensory and cognitive abilities display different profiles of neuroplasticity. The research question posed here is to what extent sensory deprivation influences the dynamics of language development. The findings reported are grounded in studies with vision-impaired children with sighted peers featured as controls (age range 18 months to 3 years). Their data are matched against findings on advanced language development in blind children (age range: from 6 to 10 years; N = 12) and hearing-impaired and deaf children (age range: from 5 to 11 years; N = 20). The data give evidence that language acquisition in sensory-impaired children follows the same overall developmental path with respect to macrostructural changes and the succession of phase-shifts. System-specific temporal discrepancies expressed in protracted phase-shifts and delayed increases of variability are most evident in the early phases. Self-organizing maps (SOMs) help to visualize individual and group-specific variation. The dynamic framework used (1) shows a higher sensibility to system-specific changes, (2) enhances the informative value of the data assessed, and (3) facilitates reliable prognoses concerning the child's cognitive and linguistic future.

  6. Exact dynamics and squeezing in two harmonic modes coupled through angular momentum

    NASA Astrophysics Data System (ADS)

    Canosa, N.; Mandal, Swapan; Rossignoli, R.

    2015-08-01

    We investigate the exact dynamics of a system of two independent harmonic oscillators coupled through their angular momentum. The exact analytic solution of the equations of motion for the field operators is derived, and the conditions for dynamical stability are obtained. As for the application, we examine the emergence of squeezing and mode entanglement for an arbitrary separable coherent initial state. It is shown that close to instability, the system develops considerable entanglement, which is accompanied with simultaneous squeezing in the coordinate of one oscillator and the momentum of the other oscillator. In contrast, for weak coupling away from instability, the generated entanglement is small, with weak alternating squeezing in the coordinate and momentum of each oscillator. Approximate expressions describing these regimes are also provided.

  7. Exact analysis of the dynamic properties of a 2-2 cement based piezoelectric transducer

    NASA Astrophysics Data System (ADS)

    Zhang, Taotao; Shi, Zhifei

    2011-08-01

    An analytical model of the dynamic properties of the 2-2 cement based piezoelectric transducer is proposed using the piezoelectric effect, based on Li's experiments. Then, the exact solutions are obtained by using the displacement method; comparison and discussion with Li's experimental results in related literature are also given and good agreement is found, which could be used for better understanding of Li's experiment. A theoretical method for applying the cement based piezoelectric composite in civil engineering is provided.

  8. Trends of forest dynamics in tiger landscapes across Asia.

    PubMed

    Mondal, Pinki; Nagendra, Harini

    2011-10-01

    Protected areas (PAs) are cornerstones of biodiversity conservation, but small parks alone cannot support wide-ranging species, such as the tiger. Hence, forest dynamics in the surrounding landscapes of PAs are also important to tiger conservation. Tiger landscapes often support considerable human population in proximity of the PA, sometimes within the core itself, and thus are subject to various land use activities (such as agricultural expansion and road development) driving habitat loss and fragmentation. We synthesize information from 27 journal articles in 24 tiger landscapes to assess forest-cover dynamics in tiger-range countries. Although 29% of the PAs considered in this study have negligible change in overall forest cover, approximately 71% are undergoing deforestation and fragmentation. Approximately 58% of the total case studies have human settlements within the core area. Most changes-including agricultural expansion, plantation, and farming (52%), fuelwood and fodder collection (43%), logging (38%), grazing (38%), and tourism and development (10%)-can be attributed to human impacts largely linked to the nature of the management regime. This study highlights the need for incorporating new perspectives, ideas, and lessons learned locally and across borders into management plans to ensure tiger conservation in landscapes dominated by human activities. Given the increasing isolation of most parks due to agricultural, infrastructural, and commercial developments at the periphery, it is imperative to conduct planning and evaluation at the landscape level, as well as incorporate multiple actors and institutions in planning, instead of focusing solely on conservation within the PAs as is currently the case in most tiger parks.

  9. Trends of Forest Dynamics in Tiger Landscapes Across Asia

    NASA Astrophysics Data System (ADS)

    Mondal, Pinki; Nagendra, Harini

    2011-10-01

    Protected areas (PAs) are cornerstones of biodiversity conservation, but small parks alone cannot support wide-ranging species, such as the tiger. Hence, forest dynamics in the surrounding landscapes of PAs are also important to tiger conservation. Tiger landscapes often support considerable human population in proximity of the PA, sometimes within the core itself, and thus are subject to various land use activities (such as agricultural expansion and road development) driving habitat loss and fragmentation. We synthesize information from 27 journal articles in 24 tiger landscapes to assess forest-cover dynamics in tiger-range countries. Although 29% of the PAs considered in this study have negligible change in overall forest cover, approximately 71% are undergoing deforestation and fragmentation. Approximately 58% of the total case studies have human settlements within the core area. Most changes—including agricultural expansion, plantation, and farming (52%), fuelwood and fodder collection (43%), logging (38%), grazing (38%), and tourism and development (10%)—can be attributed to human impacts largely linked to the nature of the management regime. This study highlights the need for incorporating new perspectives, ideas, and lessons learned locally and across borders into management plans to ensure tiger conservation in landscapes dominated by human activities. Given the increasing isolation of most parks due to agricultural, infrastructural, and commercial developments at the periphery, it is imperative to conduct planning and evaluation at the landscape level, as well as incorporate multiple actors and institutions in planning, instead of focusing solely on conservation within the PAs as is currently the case in most tiger parks.

  10. Trends of forest dynamics in tiger landscapes across Asia.

    PubMed

    Mondal, Pinki; Nagendra, Harini

    2011-10-01

    Protected areas (PAs) are cornerstones of biodiversity conservation, but small parks alone cannot support wide-ranging species, such as the tiger. Hence, forest dynamics in the surrounding landscapes of PAs are also important to tiger conservation. Tiger landscapes often support considerable human population in proximity of the PA, sometimes within the core itself, and thus are subject to various land use activities (such as agricultural expansion and road development) driving habitat loss and fragmentation. We synthesize information from 27 journal articles in 24 tiger landscapes to assess forest-cover dynamics in tiger-range countries. Although 29% of the PAs considered in this study have negligible change in overall forest cover, approximately 71% are undergoing deforestation and fragmentation. Approximately 58% of the total case studies have human settlements within the core area. Most changes-including agricultural expansion, plantation, and farming (52%), fuelwood and fodder collection (43%), logging (38%), grazing (38%), and tourism and development (10%)-can be attributed to human impacts largely linked to the nature of the management regime. This study highlights the need for incorporating new perspectives, ideas, and lessons learned locally and across borders into management plans to ensure tiger conservation in landscapes dominated by human activities. Given the increasing isolation of most parks due to agricultural, infrastructural, and commercial developments at the periphery, it is imperative to conduct planning and evaluation at the landscape level, as well as incorporate multiple actors and institutions in planning, instead of focusing solely on conservation within the PAs as is currently the case in most tiger parks. PMID:21786183

  11. How Ecology and Landscape Dynamics Shape Phylogenetic Trees.

    PubMed

    Gascuel, Fanny; Ferrière, Régis; Aguilée, Robin; Lambert, Amaury

    2015-07-01

    Whether biotic or abiotic factors are the dominant drivers of clade diversification is a long-standing question in evolutionary biology. The ubiquitous patterns of phylogenetic imbalance and branching slowdown have been taken as supporting the role of ecological niche filling and spatial heterogeneity in ecological features, and thus of biotic processes, in diversification. However, a proper theoretical assessment of the relative roles of biotic and abiotic factors in macroevolution requires models that integrate both types of factors, and such models have been lacking. In this study, we use an individual-based model to investigate the temporal patterns of diversification driven by ecological speciation in a stochastically fluctuating geographic landscape. The model generates phylogenies whose shape evolves as the clade ages. Stabilization of tree shape often occurs after ecological saturation, revealing species turnover caused by competition and demographic stochasticity. In the initial phase of diversification (allopatric radiation into an empty landscape), trees tend to be unbalanced and branching slows down. As diversification proceeds further due to landscape dynamics, balance and branching tempo may increase and become positive. Three main conclusions follow. First, the phylogenies of ecologically saturated clades do not always exhibit branching slowdown. Branching slowdown requires that competition be wide or heterogeneous across the landscape, or that the characteristics of landscape dynamics vary geographically. Conversely, branching acceleration is predicted under narrow competition or frequent local catastrophes. Second, ecological heterogeneity does not necessarily cause phylogenies to be unbalanced--short time in geographical isolation or frequent local catastrophes may lead to balanced trees despite spatial heterogeneity. Conversely, unbalanced trees can emerge without spatial heterogeneity, notably if competition is wide. Third, short isolation time

  12. Classically exact overlayer dynamics: Diffusion of rhodium clusters on Rh(100)

    SciTech Connect

    Voter, A.F.

    1986-11-15

    A new method is presented for describing the classical dynamics (e.g., diffusion, desorption) of adsorbed overlayers of atoms or molecules, starting from arbitrary interatomic potentials. Provided that a certain dynamical criterion is met, the method yields classically exact results, but with many orders of magnitude less computation than direct molecular dynamics. The approach provides, for what we believe to be the first time, a connection between stochastic lattice-gas dynamical methods and the interatomic potential function. As a sample application, the diffusion constants are computed for two-dimensional rhodium clusters of up to 75 atoms on the Rh(100) surface at T = 2000 K. For clusters larger than n = 15 atoms, the diffusion constant scales as n/sup -1.76//sup +- //sup 0.06/, and the dominant mechanism for the diffusion is found to be atoms running along the edges of the cluster blocks.

  13. Entanglement dynamics in a non-Markovian environment: An exactly solvable model

    NASA Astrophysics Data System (ADS)

    Wilson, Justin H.; Fregoso, Benjamin M.; Galitski, Victor M.

    2012-05-01

    We study the non-Markovian effects on the dynamics of entanglement in an exactly solvable model that involves two independent oscillators, each coupled to its own stochastic noise source. First, we develop Lie algebraic and functional integral methods to find an exact solution to the single-oscillator problem which includes an analytic expression for the density matrix and the complete statistics, i.e., the probability distribution functions for observables. For long bath time correlations, we see nonmonotonic evolution of the uncertainties in observables. Further, we extend this exact solution to the two-particle problem and find the dynamics of entanglement in a subspace. We find the phenomena of “sudden death” and “rebirth” of entanglement. Interestingly, all memory effects enter via the functional form of the energy and hence the time of death and rebirth is controlled by the amount of noisy energy added into each oscillator. If this energy increases above (decreases below) a threshold, we obtain sudden death (rebirth) of entanglement.

  14. Exact dynamic stiffness matrix for flexural vibration of three-layered sandwich beams

    NASA Astrophysics Data System (ADS)

    Howson, W. P.; Zare, A.

    2005-04-01

    An exact dynamic member stiffness matrix (exact finite element), which defines the flexural motion of a three-layered sandwich beam with unequal faceplates, is developed from the closed form solution of the governing differential equation. This enables the powerful modelling features associated with the finite element technique to be utilised, including the ability to account for nodal masses, spring support stiffnesses and non-classical boundary conditions. However, such a formulation necessitates the solution of a transcendental eigenvalue problem. This is accomplished using the Wittrick-Williams algorithm, which enables the required natural frequencies to be converged upon to any required accuracy with the certain knowledge that none have been missed. The accuracy of the method is confirmed by comparison with three sets of published results and a final example indicates its range of application.

  15. Exact stochastic unraveling of an optical coherence dynamics by cumulant expansion

    SciTech Connect

    Olšina, Jan; Mančal, Tomáš; Kramer, Tobias; Kreisbeck, Christoph

    2014-10-28

    A numerically exact Monte Carlo scheme for calculation of open quantum system dynamics is proposed and implemented. The method consists of a Monte Carlo summation of a perturbation expansion in terms of trajectories in Liouville phase-space with respect to the coupling between the excited states of the molecule. The trajectories are weighted by a complex decoherence factor based on the second-order cumulant expansion of the environmental evolution. The method can be used with an arbitrary environment characterized by a general correlation function and arbitrary coupling strength. It is formally exact for harmonic environments, and it can be used with arbitrary temperature. Time evolution of an optically excited Frenkel exciton dimer representing a molecular exciton interacting with a charge transfer state is calculated by the proposed method. We calculate the evolution of the optical coherence elements of the density matrix and linear absorption spectrum, and compare them with the predictions of standard simulation methods.

  16. Detecting Quantum Dissonance and Discord in Exact Dynamics of qubit Systems

    NASA Astrophysics Data System (ADS)

    Berrada, K.

    2016-08-01

    In this paper, we evaluate the quantum and classical correlations in exact dynamics of qubit systems interacting with a common dephasing environment. We show the existence of a sharp transition between the classical and quantum loss of correlations during the time evolution. We show that it is possible to exploit a large class of initial states in different tasks of quantum information and processing without any perturbation of the correlations from the environment noisy for large time intervals. On the other hand, we include the dynamics of a new kind of correlation so-called quantum dissonance, which contains the rest of the nonclassical correlations. We show that the quantum dissonance can be considered as an indicator to expect the behavior of the dynamics of classical and quantum correlations in composite open quantum systems.

  17. Feedbacks Between Channel Adjustment, Sediment Calibre and Landscape Dynamics in Tectonically Perturbed Landscapes (Invited)

    NASA Astrophysics Data System (ADS)

    Attal, M.; Cowie, P. A.; Whittaker, A. C.; Tucker, G. E.; Mudd, S. M.; Hurst, M. D.

    2010-12-01

    Knowledge of the coupling between channel geometry and sediment input to rivers is central to understanding the mechanisms and timescales over which landscapes respond to a tectonic perturbation. Here, we document changes to channel geometry and sediment calibre in catchments experiencing a well-constrained increase in relative uplift rate in the Central Apennines (Italy) and the Sierra Nevada (California). In both landscapes, channels and hillslopes steepen and knickpoints propagate upstream through the catchments, leading to the formation of a break in both hillslope and channel gradient that separates the steepened landscape from lower relief topography which has not yet responded to the change in uplift rate. Downstream of this break in slope, channels narrow markedly as river gradient increases. In addition, they are supplied with coarser sediment from the steepened hillslopes, in particular when sediment is supplied via landslides and debris fans. In Italy, channel narrowing can be explained using the equation proposed by Finnegan et al. [2005]: W = kQ3/8S-3/16, where W is channel width, k is a constant, Q is river discharge and S is channel slope. However, to model our field data, the prefactor k must be strongly dependent on uplift rate: the higher the uplift rate, the smaller the prefactor k. Using the Channel-Hillslope Integrated Landscape Development (CHILD) model, we show that the location of the main break in slope along the river profiles in Italy (in terms of height and along stream distance) can be fitted using a detachment-limited model with dynamic channel adjustment (equation above), k dependent on uplift rate and a threshold for erosion. A threshold corresponding to the shear stress required to entrain the median grain size of the sediment along the steepened reaches of the channels best fits the data. Our modelling results show that the response time of the landscape in this setting is strongly dependent on relative uplift rate, since

  18. Modelling rogue waves through exact dynamical lump soliton controlled by ocean currents.

    PubMed

    Kundu, Anjan; Mukherjee, Abhik; Naskar, Tapan

    2014-04-01

    Rogue waves are extraordinarily high and steep isolated waves, which appear suddenly in a calm sea and disappear equally fast. However, though the rogue waves are localized surface waves, their theoretical models and experimental observations are available mostly in one dimension, with the majority of them admitting only limited and fixed amplitude and modular inclination of the wave. We propose two dimensions, exactly solvable nonlinear Schrödinger (NLS) equation derivable from the basic hydrodynamic equations and endowed with integrable structures. The proposed two-dimensional equation exhibits modulation instability and frequency correction induced by the nonlinear effect, with a directional preference, all of which can be determined through precise analytic result. The two-dimensional NLS equation allows also an exact lump soliton which can model a full-grown surface rogue wave with adjustable height and modular inclination. The lump soliton under the influence of an ocean current appears and disappears preceded by a hole state, with its dynamics controlled by the current term. These desirable properties make our exact model promising for describing ocean rogue waves.

  19. Modelling rogue waves through exact dynamical lump soliton controlled by ocean currents

    PubMed Central

    Kundu, Anjan; Mukherjee, Abhik; Naskar, Tapan

    2014-01-01

    Rogue waves are extraordinarily high and steep isolated waves, which appear suddenly in a calm sea and disappear equally fast. However, though the rogue waves are localized surface waves, their theoretical models and experimental observations are available mostly in one dimension, with the majority of them admitting only limited and fixed amplitude and modular inclination of the wave. We propose two dimensions, exactly solvable nonlinear Schrödinger (NLS) equation derivable from the basic hydrodynamic equations and endowed with integrable structures. The proposed two-dimensional equation exhibits modulation instability and frequency correction induced by the nonlinear effect, with a directional preference, all of which can be determined through precise analytic result. The two-dimensional NLS equation allows also an exact lump soliton which can model a full-grown surface rogue wave with adjustable height and modular inclination. The lump soliton under the influence of an ocean current appears and disappears preceded by a hole state, with its dynamics controlled by the current term. These desirable properties make our exact model promising for describing ocean rogue waves. PMID:24711719

  20. Exact-exchange time-dependent density-functional theory for static and dynamic polarizabilities

    SciTech Connect

    Hirata, So; Ivanov, Stanislav; Bartlett, Rodney J.; Grabowski, Ireneusz

    2005-03-01

    Time-dependent density-functional theory (TDDFT) employing the exact-exchange functional has been formulated on the basis of the optimized-effective-potential (OEP) method of Talman and Shadwick for second-order molecular properties and implemented into a Gaussian-basis-set, trial-vector algorithm. The only approximation involved, apart from the lack of correlation effects and the use of Gaussian-type basis functions, was the consistent use of the adiabatic approximation in the exchange kernel and in the linear response function. The static and dynamic polarizabilities and their anisotropy predicted by the TDDFT with exact exchange (TDOEP) agree accurately with the corresponding values from time-dependent Hartree-Fock theory, the exact-exchange counterpart in the wave function theory. The TDOEP is free from the nonphysical asymptotic decay of the exchange potential of most conventional density functionals or from any other manifestations of the incomplete cancellation of the self-interaction energy. The systematic overestimation of the absolute values and dispersion of polarizabilities that plagues most conventional TDDFT cannot be seen in the TDOEP.

  1. Dynamic landscapes: a model of context and contingency in evolution.

    PubMed

    Foster, David V; Rorick, Mary M; Gesell, Tanja; Feeney, Laura M; Foster, Jacob G

    2013-10-01

    Although the basic mechanics of evolution have been understood since Darwin, debate continues over whether macroevolutionary phenomena are driven by the fitness structure of genotype space or by ecological interaction. In this paper we propose a simple model capturing key features of fitness-landscape and ecological models of evolution. Our model describes evolutionary dynamics in a high-dimensional, structured genotype space with interspecies interaction. We find promising qualitative similarity with the empirical facts about macroevolution, including broadly distributed extinction sizes and realistic exploration of the genotype space. The abstraction of our model permits numerous applications beyond macroevolution, including protein and RNA evolution.

  2. Exact dynamics for optical coherent-state qubits subject to environmental noise

    NASA Astrophysics Data System (ADS)

    Yang, Ming-Jay; Wu, Shin-Tza

    2014-02-01

    We study the exact dynamics of optical qubits encoded via coherent states with opposite phases which are interacting with an environment modeled as a collection of simple harmonic oscillators. Making use of a coherent-state path-integral formulation, we are able to study memory effects on the dynamics of the coherent-state qubits due to strong environment coupling. We apply this formulation to examine the time evolution of a noisy quantum channel formed by two coherent-state qubits that are subject to uncorrelated local environment noises. In particular, we examine the time evolution of entanglement and maximal teleportation fidelity of the noisy quantum channel and show that at strong coupling, due to large feedback effects from the environment noise, it is possible to maintain a robust quantum channel in the long-time limit if an appropriate error-correcting code is applied.

  3. Stroboscopic phenomena in superconductors with dynamic pinning landscape.

    PubMed

    Jelić, Ž L; Milošević, M V; Van de Vondel, J; Silhanek, A V

    2015-01-01

    Introducing artificial pinning centers is a well established strategy to trap quantum vortices and increase the maximal magnetic field and applied electric current that a superconductor can sustain without dissipation. In case of spatially periodic pinning, a clear enhancement of the superconducting critical current arises when commensurability between the vortex configurations and the pinning landscape occurs. With recent achievements in (ultrafast) optics and nanoengineered plasmonics it has become possible to exploit the interaction of light with superconductivity, and create not only spatially periodic imprints on the superconducting condensate, but also temporally periodic ones. Here we show that in the latter case, temporal matching phenomena develop, caused by stroboscopic commensurability between the characteristic frequency of the vortex motion under applied current and the frequency of the dynamic pinning. The matching resonances persist in a broad parameter space, including magnetic field, driving current, or material purity, giving rise to unusual features such as externally variable resistance/impedance and Shapiro steps in current-voltage characteristics. All features are tunable by the frequency of the dynamic pinning landscape. These findings open further exploration avenues for using flashing, spatially engineered, and/or mobile excitations on superconductors, permitting us to achieve advanced functionalities. PMID:26423610

  4. Stroboscopic phenomena in superconductors with dynamic pinning landscape

    PubMed Central

    Jelić, Ž. L.; Milošević, M. V.; Van de Vondel, J.; Silhanek, A. V.

    2015-01-01

    Introducing artificial pinning centers is a well established strategy to trap quantum vortices and increase the maximal magnetic field and applied electric current that a superconductor can sustain without dissipation. In case of spatially periodic pinning, a clear enhancement of the superconducting critical current arises when commensurability between the vortex configurations and the pinning landscape occurs. With recent achievements in (ultrafast) optics and nanoengineered plasmonics it has become possible to exploit the interaction of light with superconductivity, and create not only spatially periodic imprints on the superconducting condensate, but also temporally periodic ones. Here we show that in the latter case, temporal matching phenomena develop, caused by stroboscopic commensurability between the characteristic frequency of the vortex motion under applied current and the frequency of the dynamic pinning. The matching resonances persist in a broad parameter space, including magnetic field, driving current, or material purity, giving rise to unusual features such as externally variable resistance/impedance and Shapiro steps in current-voltage characteristics. All features are tunable by the frequency of the dynamic pinning landscape. These findings open further exploration avenues for using flashing, spatially engineered, and/or mobile excitations on superconductors, permitting us to achieve advanced functionalities. PMID:26423610

  5. Stroboscopic phenomena in superconductors with dynamic pinning landscape

    NASA Astrophysics Data System (ADS)

    Jelić, Ž. L.; Milošević, M. V.; van de Vondel, J.; Silhanek, A. V.

    2015-10-01

    Introducing artificial pinning centers is a well established strategy to trap quantum vortices and increase the maximal magnetic field and applied electric current that a superconductor can sustain without dissipation. In case of spatially periodic pinning, a clear enhancement of the superconducting critical current arises when commensurability between the vortex configurations and the pinning landscape occurs. With recent achievements in (ultrafast) optics and nanoengineered plasmonics it has become possible to exploit the interaction of light with superconductivity, and create not only spatially periodic imprints on the superconducting condensate, but also temporally periodic ones. Here we show that in the latter case, temporal matching phenomena develop, caused by stroboscopic commensurability between the characteristic frequency of the vortex motion under applied current and the frequency of the dynamic pinning. The matching resonances persist in a broad parameter space, including magnetic field, driving current, or material purity, giving rise to unusual features such as externally variable resistance/impedance and Shapiro steps in current-voltage characteristics. All features are tunable by the frequency of the dynamic pinning landscape. These findings open further exploration avenues for using flashing, spatially engineered, and/or mobile excitations on superconductors, permitting us to achieve advanced functionalities.

  6. Interactions among bioenergy feedstock choices, landscape dynamics, and land use

    SciTech Connect

    Dale, Virginia H; Kline, Keith L; Wright, Lynn L; Perlack, Robert D; Downing, Mark; Graham, Robin Lambert

    2011-01-01

    Landscape implications of bioenergy feedstock choices are significant and depend on land-use practices and their environmental impacts. Although land-use changes and carbon emissions associated with bioenergy feedstock production are dynamic and complicated, lignocellulosic feedstocks may offer opportunities that enhance sustainability when compared to other transportation fuel alternatives. For bioenergy sustainability, major drivers and concerns revolve around energy security, food production, land productivity, soil carbon and erosion, greenhouse gas emissions, biodiversity, air quality, and water quantity and quality. The many implications of bioenergy feedstock choices require several indicators at multiple scales to provide a more complete accounting of effects. Ultimately, the long-term sustainability of bioenergy feedstock resources (as well as food supplies) throughout the world depends on land-use practices and landscape dynamics. Land-management decisions often invoke trade-offs among potential environmental effects and social and economic factors as well as future opportunities for resource use. The hypothesis being addressed in this paper is that sustainability of bioenergy feedstock production can be achieved via appropriately designed crop residue and perennial lignocellulosic systems. We find that decision makers need scientific advancements and adequate data that both provide quantitative and qualitative measures of the effects of bioenergy feedstock choices at different spatial and temporal scales and allow fair comparisons among available options for renewable liquid fuels.

  7. Evolution and Extinction Dynamics in Rugged Fitness Landscapes

    NASA Astrophysics Data System (ADS)

    Sibani, Paolo; Brandt, Michael; Alstrøm, Preben

    After an introductory section summarizing the paleontological data and some of their theoretical descriptions, we describe the "reset" model and its (in part analytically soluble) mean field version, which have been briefly introduced in Letters.1,2 Macroevolution is considered as a problem of stochastic dynamics in a system with many competing agents. Evolutionary events (speciations and extinctions) are triggered by fitness records found by random exploration of the agents' fitness landscapes. As a consequence, the average fitness in the system increases logarithmically with time, while the rate of extinction steadily decreases. This non-stationary dynamics is studied by numerical simulations and, in a simpler mean field version, analytically. We also consider the effect of externally added "mass" extinctions. The predictions for various quantities of paleontological interest (life-time distribution, distribution of event sizes and behavior of the rate of extinction) are robust and in good agreement with available data.

  8. EDISON-WMW: Exact Dynamic Programing Solution of the Wilcoxon-Mann-Whitney Test.

    PubMed

    Marx, Alexander; Backes, Christina; Meese, Eckart; Lenhof, Hans-Peter; Keller, Andreas

    2016-02-01

    In many research disciplines, hypothesis tests are applied to evaluate whether findings are statistically significant or could be explained by chance. The Wilcoxon-Mann-Whitney (WMW) test is among the most popular hypothesis tests in medicine and life science to analyze if two groups of samples are equally distributed. This nonparametric statistical homogeneity test is commonly applied in molecular diagnosis. Generally, the solution of the WMW test takes a high combinatorial effort for large sample cohorts containing a significant number of ties. Hence, P value is frequently approximated by a normal distribution. We developed EDISON-WMW, a new approach to calculate the exact permutation of the two-tailed unpaired WMW test without any corrections required and allowing for ties. The method relies on dynamic programing to solve the combinatorial problem of the WMW test efficiently. Beyond a straightforward implementation of the algorithm, we presented different optimization strategies and developed a parallel solution. Using our program, the exact P value for large cohorts containing more than 1000 samples with ties can be calculated within minutes. We demonstrate the performance of this novel approach on randomly-generated data, benchmark it against 13 other commonly-applied approaches and moreover evaluate molecular biomarkers for lung carcinoma and chronic obstructive pulmonary disease (COPD). We found that approximated P values were generally higher than the exact solution provided by EDISON-WMW. Importantly, the algorithm can also be applied to high-throughput omics datasets, where hundreds or thousands of features are included. To provide easy access to the multi-threaded version of EDISON-WMW, a web-based solution of our algorithm is freely available at http://www.ccb.uni-saarland.de/software/wtest/. PMID:26829645

  9. EDISON-WMW: Exact Dynamic Programing Solution of the Wilcoxon–Mann–Whitney Test

    PubMed Central

    Marx, Alexander; Backes, Christina; Meese, Eckart; Lenhof, Hans-Peter; Keller, Andreas

    2016-01-01

    In many research disciplines, hypothesis tests are applied to evaluate whether findings are statistically significant or could be explained by chance. The Wilcoxon–Mann–Whitney (WMW) test is among the most popular hypothesis tests in medicine and life science to analyze if two groups of samples are equally distributed. This nonparametric statistical homogeneity test is commonly applied in molecular diagnosis. Generally, the solution of the WMW test takes a high combinatorial effort for large sample cohorts containing a significant number of ties. Hence, P value is frequently approximated by a normal distribution. We developed EDISON-WMW, a new approach to calculate the exact permutation of the two-tailed unpaired WMW test without any corrections required and allowing for ties. The method relies on dynamic programing to solve the combinatorial problem of the WMW test efficiently. Beyond a straightforward implementation of the algorithm, we presented different optimization strategies and developed a parallel solution. Using our program, the exact P value for large cohorts containing more than 1000 samples with ties can be calculated within minutes. We demonstrate the performance of this novel approach on randomly-generated data, benchmark it against 13 other commonly-applied approaches and moreover evaluate molecular biomarkers for lung carcinoma and chronic obstructive pulmonary disease (COPD). We found that approximated P values were generally higher than the exact solution provided by EDISON-WMW. Importantly, the algorithm can also be applied to high-throughput omics datasets, where hundreds or thousands of features are included. To provide easy access to the multi-threaded version of EDISON-WMW, a web-based solution of our algorithm is freely available at http://www.ccb.uni-saarland.de/software/wtest/. PMID:26829645

  10. The exact explicit dynamic stiffness matrix of multi-cracked Euler-Bernoulli beam and applications to damaged frame structures

    NASA Astrophysics Data System (ADS)

    Caddemi, S.; Caliò, I.

    2013-06-01

    In this paper the closed form expression of the exact dynamic stiffness matrix of an Euler-Bernoulli beam in the presence of an arbitrary number of concentrated cracks is derived. The procedure adopted for the evaluation of the dynamic stiffness matrix is based on the availability of the exact closed form solution of the vibration modes of the multi-cracked beam, derived by the same authors in a previous paper. The knowledge of the exact explicit dynamic stiffness matrix of the multi-cracked beam makes the direct evaluation of the exact global dynamic stiffness matrix of damaged frame structures possible. Furthermore, it allows the exact evaluation of the frequencies and the corresponding vibration modes, consistent with the distributed parameter model, through the application of the well-known Wittrick-Williams algorithm. Some numerical applications, relative to the evaluation of frequencies and the corresponding mode shapes of multi-cracked framed structure, are reported. Furthermore, the closed-form solution has been validated by comparing with some exact results available in the literature, for a simple single cracked frame. Finally, further new results for a multi-cracked frame have been compared with those obtained by a finite element simulation.

  11. Biomolecular Dynamics: Order-Disorder Transitions and Energy Landscapes

    PubMed Central

    Whitford, Paul C.; Sanbonmatsu, Karissa Y.; Onuchic, José N.

    2013-01-01

    While the energy landscape theory of protein folding is now a widely accepted view for understanding how relatively-weak molecular interactions lead to rapid and cooperative protein folding, such a framework must be extended to describe the large-scale functional motions observed in molecular machines. In this review, we discuss 1) the development of the energy landscape theory of biomolecular folding, 2) recent advances towards establishing a consistent understanding of folding and function, and 3) emerging themes in the functional motions of enzymes, biomolecular motors, and other biomolecular machines. Recent theoretical, computational, and experimental lines of investigation are providing a very dynamic picture of biomolecular motion. In contrast to earlier ideas, where molecular machines were thought to function similarly to macroscopic machines, with rigid components that move along a few degrees of freedom in a deterministic fashion, biomolecular complexes are only marginally stable. Since the stabilizing contribution of each atomic interaction is on the order of the thermal fluctuations in solution, the rigid body description of molecular function must be revisited. An emerging theme is that functional motions encompass order-disorder transitions and structural flexibility provide significant contributions to the free-energy. In this review, we describe the biological importance of order-disorder transitions and discuss the statistical-mechanical foundation of theoretical approaches that can characterize such transitions. PMID:22790780

  12. Enrichment Ratio and Aggregate Stability Dynamics in Intensely Managed Landscapes

    NASA Astrophysics Data System (ADS)

    Wacha, K.; Papanicolaou, T.; Filley, T. R.; Hou, T.; Abban, B. K.; Wilson, C. G.; Boys, J.

    2015-12-01

    Challenges in understanding the soil carbon dynamics within intensely managed landscapes (IMLs), found throughout much the US Midwest, is highly complex due to the presence of heterogeneous landscape features and properties, as well as a mosaic of physical and biogeochemical processes occurring at different time scales. In addition, rainfall events exacerbate the effects of tillage by the impact of raindrops, which break down aggregates that encase carbon and dislodge and entrain soil particles and aggregates along the downslope. The redistribution of soil and carbon can have huge implications on biogeochemical cycling and overall carbon budgeting. In this study, we provide some rare field data on the mechanisms impacting aggregate stability, enrichment ratio values to estimate fluxes of carbon, as well as lignin chemistry to see influences on oxidation/mineralization rates. Rainfall simulation experiments were conducted within agricultural fields. Experiments were performed on the midslope (eroding) and toeslope (depositional) sections of representative hillslopes, under a variety of land managements, including row crop (conventional and conservation) and restored grasslands. Sensors were utilized to capture the evolution of soil moisture, temperature, microbial respiration pulses, and discharge rates to identify pseudo-steady state conditions. Samples collected at the weir outlet were tested for sediment concentrations and size fractions, as well as carbon and lignin fluxes. Preliminary findings show that conservation management practices have higher aggregate stability and decreased mass fluxes of carbon in the downslope than conventional tillage techniques.

  13. The spectral gap and the dynamical critical exponent of an exact solvable probabilistic cellular automaton

    NASA Astrophysics Data System (ADS)

    Lazo, M. J.; Ferreira, A. A.; Alcaraz, F. C.

    2015-11-01

    We obtained the exact solution of a probabilistic cellular automaton related to the diagonal-to-diagonal transfer matrix of the six-vertex model on a square lattice. The model describes the flow of ants (or particles), traveling on a one-dimensional lattice whose sites are small craters containing sleeping or awake ants (two kinds of particles). We found the Bethe ansatz equations and the spectral gap for the time-evolution operator of the cellular automaton. From the spectral gap we show that in the asymmetric case it belongs to the Kardar-Parisi-Zhang (KPZ) universality class, exhibiting a dynamical critical exponent value z = 3/2. This result is also obtained from a direct Monte Carlo simulation, by evaluating the lattice-size dependence of the decay time to the stationary state.

  14. The landscape of nonlinear structural dynamics: an introduction.

    PubMed

    Butlin, T; Woodhouse, J; Champneys, A R

    2015-09-28

    Nonlinear behaviour is ever-present in vibrations and other dynamical motions of engineering structures. Manifestations of nonlinearity include amplitude-dependent natural frequencies, buzz, squeak and rattle, self-excited oscillation and non-repeatability. This article primarily serves as an extended introduction to a theme issue in which such nonlinear phenomena are highlighted through diverse case studies. More ambitiously though, there is another goal. Both the engineering context and the mathematical techniques that can be used to identify, analyse, control or exploit these phenomena in practice are placed in the context of a mind-map, which has been created through expert elicitation. This map, which is available in software through the electronic supplementary material, attempts to provide a practitioner's guide to what hitherto might seem like a vast and complex research landscape.

  15. The landscape of nonlinear structural dynamics: an introduction

    PubMed Central

    Butlin, T.; Woodhouse, J.; Champneys, A. R.

    2015-01-01

    Nonlinear behaviour is ever-present in vibrations and other dynamical motions of engineering structures. Manifestations of nonlinearity include amplitude-dependent natural frequencies, buzz, squeak and rattle, self-excited oscillation and non-repeatability. This article primarily serves as an extended introduction to a theme issue in which such nonlinear phenomena are highlighted through diverse case studies. More ambitiously though, there is another goal. Both the engineering context and the mathematical techniques that can be used to identify, analyse, control or exploit these phenomena in practice are placed in the context of a mind-map, which has been created through expert elicitation. This map, which is available in software through the electronic supplementary material, attempts to provide a practitioner’s guide to what hitherto might seem like a vast and complex research landscape. PMID:26303925

  16. Insights to urban dynamics through landscape spatial pattern analysis

    NASA Astrophysics Data System (ADS)

    TV, Ramachandra; Aithal, Bharath H.; Sanna, Durgappa D.

    2012-08-01

    Urbanisation is a dynamic complex phenomenon involving large scale changes in the land uses at local levels. Analyses of changes in land uses in urban environments provide a historical perspective of land use and give an opportunity to assess the spatial patterns, correlation, trends, rate and impacts of the change, which would help in better regional planning and good governance of the region. Main objective of this research is to quantify the urban dynamics using temporal remote sensing data with the help of well-established landscape metrics. Bangalore being one of the rapidly urbanising landscapes in India has been chosen for this investigation. Complex process of urban sprawl was modelled using spatio temporal analysis. Land use analyses show 584% growth in built-up area during the last four decades with the decline of vegetation by 66% and water bodies by 74%. Analyses of the temporal data reveals an increase in urban built up area of 342.83% (during 1973-1992), 129.56% (during 1992-1999), 106.7% (1999-2002), 114.51% (2002-2006) and 126.19% from 2006 to 2010. The Study area was divided into four zones and each zone is further divided into 17 concentric circles of 1 km incrementing radius to understand the patterns and extent of the urbanisation at local levels. The urban density gradient illustrates radial pattern of urbanisation for the period 1973-2010. Bangalore grew radially from 1973 to 2010 indicating that the urbanisation is intensifying from the central core and has reached the periphery of the Greater Bangalore. Shannon's entropy, alpha and beta population densities were computed to understand the level of urbanisation at local levels. Shannon's entropy values of recent time confirms dispersed haphazard urban growth in the city, particularly in the outskirts of the city. This also illustrates the extent of influence of drivers of urbanisation in various directions. Landscape metrics provided in depth knowledge about the sprawl. Principal component

  17. Dynamic LiDAR-NDVI classification of fluvial landscape units

    NASA Astrophysics Data System (ADS)

    Ramírez-Núñez, Carolina; Parrot, Jean-François

    2015-04-01

    The lower basin of the Coatzacoalcos River is a wide floodplain in which, during the wet season, local and major flooding are distinguished. Both types of floods, intermittent and regional, are important in terms of resources; the regional flood sediments enrich the soils of the plains and intermittent floods allow obtaining aquatic resources for subsistence during the heatwave. In the floodplain different abandoned meanders and intermittent streams are quickly colonized by aquatic vegetation. However, from the 1990s, the Coatzacoalcos River floodplain has important topographic changes due to mining, road and bridges construction; erosion and sedimentation requires continuous parcel boundaries along with the increasing demand of channel reparation, embankments, levees and bridges associated to tributaries. NDVI data, LiDAR point cloud and various types of flood simulations taking into account the DTM are used to classify the dynamic landscape units. These units are associated to floods in relation with water resources, agriculture and livestock. In the study area, the first returns of the point cloud allow extracting vegetation strata. The last returns correspond to the bare earth surface, especially in this area with few human settlements. The surface that is not covered by trees or by aquatic vegetation, correspond to crops, pastures and bare soils. The classification is obtained by using the NDVI index coupled with vegetation strata and water bodies. The result shows that 47.96% of the area does not present active vegetation and it includes 31.53% of bare soils. Concerning the active vegetation, pastures, bushes and trees represent respectively 25.59%, 11.14% and 13.25%. The remaining 1.25% is distributed between water bodies with aquatic vegetation, trees and shrubs. Dynamic landscape units' classification represents a tool for monitoring water resources in a fluvial plain. This approach can be also applied to forest management, environmental services and

  18. Locally dispersing populations in heterogeneous dynamic landscapes with spatiotemporal correlations. II. Habitat driven by voter dynamics.

    PubMed

    Hiebeler, David E; Hill, Jack L

    2016-10-21

    We examine a spatially explicit population model on a dynamic landscape with suitable and unsuitable habitat driven by voter or contagion dynamics. We consider four cases, consisting of all combinations of local and global interactions for both population dispersal and habitat dynamics. For both local and global population dispersal, using local habitat dynamics always increases population density relative to the case with global habitat dynamics, due to the resulting segregation of habitat turnover, decrease in effective habitat turnover rate, and presence of stable habitat corridors. With global habitat dynamics, a population using local dispersal exhibits lower density than one with global dispersal due to local crowding as well as frequent disturbance due to habitat transitions. On the other hand, with local habitat dynamics, a population using local dispersal can exploit suitable habitat patches and use dynamic corridors to colonize new regions. The latter effect is not seen with static landscapes, where clustered habitat can lead to the isolation of suitable patches due to surrounding unsuitable habitat.

  19. Locally dispersing populations in heterogeneous dynamic landscapes with spatiotemporal correlations. II. Habitat driven by voter dynamics.

    PubMed

    Hiebeler, David E; Hill, Jack L

    2016-10-21

    We examine a spatially explicit population model on a dynamic landscape with suitable and unsuitable habitat driven by voter or contagion dynamics. We consider four cases, consisting of all combinations of local and global interactions for both population dispersal and habitat dynamics. For both local and global population dispersal, using local habitat dynamics always increases population density relative to the case with global habitat dynamics, due to the resulting segregation of habitat turnover, decrease in effective habitat turnover rate, and presence of stable habitat corridors. With global habitat dynamics, a population using local dispersal exhibits lower density than one with global dispersal due to local crowding as well as frequent disturbance due to habitat transitions. On the other hand, with local habitat dynamics, a population using local dispersal can exploit suitable habitat patches and use dynamic corridors to colonize new regions. The latter effect is not seen with static landscapes, where clustered habitat can lead to the isolation of suitable patches due to surrounding unsuitable habitat. PMID:27457095

  20. Exact coherent structures and chaotic dynamics in a model of cardiac tissue.

    PubMed

    Byrne, Greg; Marcotte, Christopher D; Grigoriev, Roman O

    2015-03-01

    Unstable nonchaotic solutions embedded in the chaotic attractor can provide significant new insight into chaotic dynamics of both low- and high-dimensional systems. In particular, in turbulent fluid flows, such unstable solutions are referred to as exact coherent structures (ECS) and play an important role in both initiating and sustaining turbulence. The nature of ECS and their role in organizing spatiotemporally chaotic dynamics, however, is reasonably well understood only for systems on relatively small spatial domains lacking continuous Euclidean symmetries. Construction of ECS on large domains and in the presence of continuous translational and/or rotational symmetries remains a challenge. This is especially true for models of excitable media which display spiral turbulence and for which the standard approach to computing ECS completely breaks down. This paper uses the Karma model of cardiac tissue to illustrate a potential approach that could allow computing a new class of ECS on large domains of arbitrary shape by decomposing them into a patchwork of solutions on smaller domains, or tiles, which retain Euclidean symmetries locally. PMID:25833430

  1. Exact coherent structures and chaotic dynamics in a model of cardiac tissue

    SciTech Connect

    Byrne, Greg; Marcotte, Christopher D.; Grigoriev, Roman O.

    2015-03-15

    Unstable nonchaotic solutions embedded in the chaotic attractor can provide significant new insight into chaotic dynamics of both low- and high-dimensional systems. In particular, in turbulent fluid flows, such unstable solutions are referred to as exact coherent structures (ECS) and play an important role in both initiating and sustaining turbulence. The nature of ECS and their role in organizing spatiotemporally chaotic dynamics, however, is reasonably well understood only for systems on relatively small spatial domains lacking continuous Euclidean symmetries. Construction of ECS on large domains and in the presence of continuous translational and/or rotational symmetries remains a challenge. This is especially true for models of excitable media which display spiral turbulence and for which the standard approach to computing ECS completely breaks down. This paper uses the Karma model of cardiac tissue to illustrate a potential approach that could allow computing a new class of ECS on large domains of arbitrary shape by decomposing them into a patchwork of solutions on smaller domains, or tiles, which retain Euclidean symmetries locally.

  2. Exact dynamics of stochastic linear delayed systems: Application to spatiotemporal coordination of comoving agents

    NASA Astrophysics Data System (ADS)

    McKetterick, Thomas John; Giuggioli, Luca

    2014-10-01

    Delayed dynamics result from finite transmission speeds of a signal in the form of energy, mass, or information. In stochastic systems the resulting lagged dynamics challenge our understanding due to the rich behavioral repertoire encompassing monotonic, oscillatory, and unstable evolution. Despite the vast literature, quantifying this rich behavior is limited by a lack of explicit analytic studies of high-dimensional stochastic delay systems. Here we fill this gap for systems governed by a linear Langevin equation of any number of delays and spatial dimensions with additive Gaussian noise. By exploiting Laplace transforms we are able to derive an exact time-dependent analytic solution of the Langevin equation. By using characteristic functionals we are able to construct the full time dependence of the multivariate probability distribution of the stochastic process as a function of the delayed and nondelayed random variables. As an application we consider interactions in animal collective movement that go beyond the traditional assumption of instantaneous alignment. We propose models for coordinated maneuvers of comoving agents applicable to recent empirical findings in pigeons and bats whereby individuals copy the heading of their neighbors with some delay. We highlight possible strategies that individual pairs may adopt to reduce the variance in their velocity difference and/or in their spatial separation. We also show that a minimum in the variance of the spatial separation at long times can be achieved with certain ratios of measurement to reaction delay.

  3. Sinks without borders: Snowshoe hare dynamics in a complex landscape

    USGS Publications Warehouse

    Griffin, P.C.; Scott, Mills L.

    2009-01-01

    A full understanding of population dynamics of wide-ranging animals should account for the effects that movement and habitat use have on individual contributions to population growth or decline. Quantifying the per-capita, habitat-specific contribution to population growth can clarify the value of different patch types, and help to differentiate population sources from population sinks. Snowshoe hares, Lepus americanus, routinely use various habitat types in the landscapes they inhabit in the contiguous US, where managing forests for high snowshoe hare density is a priority for conservation of Canada lynx, Lynx canadensis. We estimated density and demographic rates via mark-recapture live trapping and radio-telemetry within four forest stand structure (FSS) types at three study areas within heterogeneous managed forests in western Montana. We found support for known fate survival models with time-varying individual covariates representing the proportion of locations in each of the FSS types, with survival rates decreasing as use of open young and open mature FSS types increased. The per-capita contribution to overall population growth increased with use of the dense mature or dense young FSS types and decreased with use of the open young or open mature FSS types, and relatively high levels of immigration appear to be necessary to sustain hares in the open FSS types. Our results support a conceptual model for snowshoe hares in the southern range in which sink habitats (open areas) prevent the buildup of high hare densities. More broadly, we use this system to develop a novel approach to quantify demographic sources and sinks for animals making routine movements through complex fragmented landscapes. ?? 2009 Oikos.

  4. Airborne Measurement of Ecosystem Carbon Dynamics over Heterogeneous Landscapes

    NASA Astrophysics Data System (ADS)

    Wade, T. J.; Hill, T. C.; Clement, R.; Moncrieff, J.; Disney, M.; Nichol, C. J.; Williams, M. D.

    2009-12-01

    Terrestrial carbon sinks are currently believed to account for the removal and storage of approximately 25% of anthropogenic carbon emissions from the atmosphere. The processes involved are numerous and complex and many feedbacks are at play. The ability to study the dynamics of different ecosystems at scales meaningful to climatic forcing is essential for understanding the key processes involved and identifying crucial sensitivities and thresholds. Airborne platforms with the requisite instrumentation offer the opportunity to directly measure biological processes and atmospheric structures at scales that are not achievable by ground measurements alone. The current generation of small research aircraft such as the University of Edinburgh’s Diamond HK36TTC ECO Dimona present excellent platforms for measurement of both the atmosphere and terrestrial surface. In this study we present results from airborne CO2/H2O flux measuring campaigns in contrasting climatic systems to quantify spatial patterns in ecosystem photosynthesis. Several airborne campaigns were undertaken in Arctic Finland, as part of the Arctic Biosphere Atmosphere Coupling at Multiple Scales (ABACUS) project (2008), and mainland UK as part of the UK Population Biology Network (UKPopNet) 2009 project, to explore the variability in surface CO2 flux across spatial scales larger than captured using conventional ground based eddy covariance. We discuss the application of our aircraft platform as a tool to address the challenge of understanding carbon dynamics within landscapes of heterogeneous vegetation class, terrain and hydrology using complementary datasets acquired from airborne eddy covariance and remote sensing.

  5. Protocol for Landsat-Based Monitoring of Landscape Dynamics at North Coast and Cascades Network Parks

    USGS Publications Warehouse

    Kennedy, Robert E.; Cohen, Warren B.; Kirschbaum, Alan A.; Haunreiter, Erik

    2007-01-01

    Background and Objectives As part of the National Park Service's larger goal of developing long-term monitoring programs in response to the Natural Resource Challenge of 2000, the parks of the North Coast and Cascades Network (NCCN) have determined that monitoring of landscape dynamics is necessary to track ecosystem health (Weber and others, 2005). Landscape dynamics refer to a broad suite of ecological, geomorphological, and anthropogenic processes occurring across broad spatial scales. The NCCN has sought protocols that would leverage remote-sensing technologies to aid in monitoring landscape dynamics.

  6. A novel simulation methodology merging source-sink dynamics and landscape connectivity

    EPA Science Inventory

    Source-sink dynamics are an emergent property of complex species-landscape interactions. This study explores the patterns of source and sink behavior that become established across a large landscape, using a simulation model for the northern spotted owl (Strix occidentalis cauri...

  7. Integrated dynamic landscape analysis and modeling system (IDLAMS) : programmer's manual.

    SciTech Connect

    Klaus, C. M.; Li, Z.; Majerus, K. A.; Sundell, R. C.; Sydelko, P. J.; Vogt, M. C.

    1999-02-24

    The Integrated Dynamic Landscape Analysis and Modeling System (IDLAMS) is a prototype, integrated land management technology developed through a joint effort between Argonne National Laboratory (ANL) and the US Army Corps of Engineers Construction Engineering Research Laboratories (USACERL). Dr. Ronald C. Sundell, Ms. Pamela J. Sydelko, and Ms. Kimberly A. Majerus were the principal investigators (PIs) for this project. Dr. Zhian Li was the primary software developer. Dr. Jeffrey M. Keisler, Mr. Christopher M. Klaus, and Mr. Michael C. Vogt developed the decision analysis component of this project. It was developed with funding support from the Strategic Environmental Research and Development Program (SERDP), a land/environmental stewardship research program with participation from the US Department of Defense (DoD), the US Department of Energy (DOE), and the US Environmental Protection Agency (EPA). IDLAMS predicts land conditions (e.g., vegetation, wildlife habitats, and erosion status) by simulating changes in military land ecosystems for given training intensities and land management practices. It can be used by military land managers to help predict the future ecological condition for a given land use based on land management scenarios of various levels of training intensity. It also can be used as a tool to help land managers compare different land management practices and further determine a set of land management activities and prescriptions that best suit the needs of a specific military installation.

  8. Integrated dynamic landscape analysis and modeling system (IDLAMS) : installation manual.

    SciTech Connect

    Li, Z.; Majerus, K. A.; Sundell, R. C.; Sydelko, P. J.; Vogt, M. C.

    1999-02-24

    The Integrated Dynamic Landscape Analysis and Modeling System (IDLAMS) is a prototype, integrated land management technology developed through a joint effort between Argonne National Laboratory (ANL) and the US Army Corps of Engineers Construction Engineering Research Laboratories (USACERL). Dr. Ronald C. Sundell, Ms. Pamela J. Sydelko, and Ms. Kimberly A. Majerus were the principal investigators (PIs) for this project. Dr. Zhian Li was the primary software developer. Dr. Jeffrey M. Keisler, Mr. Christopher M. Klaus, and Mr. Michael C. Vogt developed the decision analysis component of this project. It was developed with funding support from the Strategic Environmental Research and Development Program (SERDP), a land/environmental stewardship research program with participation from the US Department of Defense (DoD), the US Department of Energy (DOE), and the US Environmental Protection Agency (EPA). IDLAMS predicts land conditions (e.g., vegetation, wildlife habitats, and erosion status) by simulating changes in military land ecosystems for given training intensities and land management practices. It can be used by military land managers to help predict the future ecological condition for a given land use based on land management scenarios of various levels of training intensity. It also can be used as a tool to help land managers compare different land management practices and further determine a set of land management activities and prescriptions that best suit the needs of a specific military installation.

  9. System dynamic modelling of industrial growth and landscape ecology in China.

    PubMed

    Xu, Jian; Kang, Jian; Shao, Long; Zhao, Tianyu

    2015-09-15

    With the rapid development of large industrial corridors in China, the landscape ecology of the country is currently being affected. Therefore, in this study, a system dynamic model with multi-dimensional nonlinear dynamic prediction function that considers industrial growth and landscape ecology is developed and verified to allow for more sustainable development. Firstly, relationships between industrial development and landscape ecology in China are examined, and five subsystems are then established: industry, population, urban economy, environment and landscape ecology. The main influencing factors are then examined for each subsystem to establish flow charts connecting those factors. Consequently, by connecting the subsystems, an overall industry growth and landscape ecology model is established. Using actual data and landscape index calculated based on GIS of the Ha-Da-Qi industrial corridor, a typical industrial corridor in China, over the period 2005-2009, the model is validated in terms of historical behaviour, logical structure and future prediction, where for 84.8% of the factors, the error rate of the model is less than 5%, the mean error rate of all factors is 2.96% and the error of the simulation test for the landscape ecology subsystem is less than 2%. Moreover, a model application has been made to consider the changes in landscape indices under four industrial development modes, and the optimal industrial growth plan has been examined for landscape ecological protection through the simulation prediction results over 2015-2020.

  10. [Dynamic changes of landscape pattern and hemeroby in Ximen Island wetland, Zhejiang Province, China].

    PubMed

    Xiao, Cui; Xie, Xue-Fen; Wu, Tao; Jiang, Guo-Jun; Bian, Hua-Jing; Xu, Wei

    2014-11-01

    Abstract: The hemeroby type classification system of Ximen Island wetland of Zhejiang Province was established based on the multiple datasets: SOPT-5 image data with a spatial resolution of 5 m in 2007 and 2010, its wetland land cover and land use status, the National Land Use Classification (on trail), and sea area use classification of marine industry standards as well as remote sensing data features. Meanwhile, the dynamic relationship between the landscape pattern and the degree of hemeroby in Ximen Island was investigated with the landscape indices and hemeroby index (HI) derived from the landscape pattern index and GIS spatial analysis. The results showed that the wetland landscape spatial heterogeneity, fragmentation and dominance index dropped, and the landscape shape index complexity was low. The human disturbance center developed from a dispersion type to a concentration type. The landscape type of the disturbance center was bare land and settlement. The HI rose up from the sea to the land. Settlement, wharf and traffic land had the highest HI. The HI of the mudflat cultivation, mudflats and raft-cultivation dramatically changed. Marine-terrestrial interlaced zone showed a low total HI with unstable characteristics. The number of patches declined of undisturbed, partially disturbed and completely disturbed landscapes. Mean patch areas of partially disturbed and completely disturbed landscapes increased, and that of the undisturbed decreased. Mean shape index of the undisturbed landscape decreased, while the partially disturbed and completely disturbed landscapes showed a trend of shape complication. PMID:25898624

  11. [Landscape pattern gradient dynamics and desakota features in rapid urbanization area: a case study in Panyu of Guangzhou].

    PubMed

    Yu, Long-Sheng; Fu, Yi-Fu; Yu, Huai-Yi; Li, Zhi-Qin

    2011-01-01

    In order to understand the landscape pattern gradient dynamics and desakota features in rapid urbanization area, this paper took the rapidly urbanizing Panyu District of Guangzhou City as a case, and analyzed its land use and land cover data, based on four Landsat TM images from 1990 to 2008. With the combination of gradient analysis and landscape pattern analysis, and by using the landscape indices in both class and landscape scales, the spatial dynamics and desakota feature of this rapidly urbanizing district were quantified. In the study district, there was a significant change in the landscape pattern, and a typical desakota feature presented along buffer gradient zones. Urban landscape increased and expanded annually, accompanied with serious fragmentation of agricultural landscape. The indices patch density, contagion, and landscape diversity, etc., changed regularly in the urbanization gradient, and the peak of landscape indices appeared in the gradient zone of 4-6 km away from the urban center. The landscape patterns at time series also reflected the differences among the dynamics in different gradient zones. The landscape pattern in desakota region was characterized by complex patch shape, high landscape diversity and fragmentation, and remarkable landscape dynamics. The peaks of landscape indices spread from the urban center to border areas, and desakota region was expanding gradually. The general trend of spatiotemporal dynamics in desakota region and its driving forces were discussed, which could be benefit to the regional land use policy-making and sustainable development planning.

  12. Direct simulation of electron transfer using ring polymer molecular dynamics: comparison with semiclassical instanton theory and exact quantum methods.

    PubMed

    Menzeleev, Artur R; Ananth, Nandini; Miller, Thomas F

    2011-08-21

    The use of ring polymer molecular dynamics (RPMD) for the direct simulation of electron transfer (ET) reaction dynamics is analyzed in the context of Marcus theory, semiclassical instanton theory, and exact quantum dynamics approaches. For both fully atomistic and system-bath representations of condensed-phase ET, we demonstrate that RPMD accurately predicts both ET reaction rates and mechanisms throughout the normal and activationless regimes of the thermodynamic driving force. Analysis of the ensemble of reactive RPMD trajectories reveals the solvent reorganization mechanism for ET that is anticipated in the Marcus rate theory, and the accuracy of the RPMD rate calculation is understood in terms of its exact description of statistical fluctuations and its formal connection to semiclassical instanton theory for deep-tunneling processes. In the inverted regime of the thermodynamic driving force, neither RPMD nor a related formulation of semiclassical instanton theory capture the characteristic turnover in the reaction rate; comparison with exact quantum dynamics simulations reveals that these methods provide inadequate quantization of the real-time electronic-state dynamics in the inverted regime.

  13. Organic fields sustain weed metacommunity dynamics in farmland landscapes.

    PubMed

    Henckel, Laura; Börger, Luca; Meiss, Helmut; Gaba, Sabrina; Bretagnolle, Vincent

    2015-06-01

    Agro-ecosystems constitute essential habitat for many organisms. Agricultural intensification, however, has caused a strong decline of farmland biodiversity. Organic farming (OF) is often presented as a more biodiversity-friendly practice, but the generality of the beneficial effects of OF is debated as the effects appear often species- and context-dependent, and current research has highlighted the need to quantify the relative effects of local- and landscape-scale management on farmland biodiversity. Yet very few studies have investigated the landscape-level effects of OF; that is to say, how the biodiversity of a field is affected by the presence or density of organically farmed fields in the surrounding landscape. We addressed this issue using the metacommunity framework, with weed species richness in winter wheat within an intensively farmed landscape in France as model system. Controlling for the effects of local and landscape structure, we showed that OF leads to higher local weed diversity and that the presence of OF in the landscape is associated with higher local weed biodiversity also for conventionally farmed fields, and may reach a similar biodiversity level to organic fields in field margins. Based on these results, we derive indications for improving the sustainable management of farming systems.

  14. Organic fields sustain weed metacommunity dynamics in farmland landscapes

    PubMed Central

    Henckel, Laura; Börger, Luca; Meiss, Helmut; Gaba, Sabrina; Bretagnolle, Vincent

    2015-01-01

    Agro-ecosystems constitute essential habitat for many organisms. Agricultural intensification, however, has caused a strong decline of farmland biodiversity. Organic farming (OF) is often presented as a more biodiversity-friendly practice, but the generality of the beneficial effects of OF is debated as the effects appear often species- and context-dependent, and current research has highlighted the need to quantify the relative effects of local- and landscape-scale management on farmland biodiversity. Yet very few studies have investigated the landscape-level effects of OF; that is to say, how the biodiversity of a field is affected by the presence or density of organically farmed fields in the surrounding landscape. We addressed this issue using the metacommunity framework, with weed species richness in winter wheat within an intensively farmed landscape in France as model system. Controlling for the effects of local and landscape structure, we showed that OF leads to higher local weed diversity and that the presence of OF in the landscape is associated with higher local weed biodiversity also for conventionally farmed fields, and may reach a similar biodiversity level to organic fields in field margins. Based on these results, we derive indications for improving the sustainable management of farming systems. PMID:25994672

  15. Organic fields sustain weed metacommunity dynamics in farmland landscapes.

    PubMed

    Henckel, Laura; Börger, Luca; Meiss, Helmut; Gaba, Sabrina; Bretagnolle, Vincent

    2015-06-01

    Agro-ecosystems constitute essential habitat for many organisms. Agricultural intensification, however, has caused a strong decline of farmland biodiversity. Organic farming (OF) is often presented as a more biodiversity-friendly practice, but the generality of the beneficial effects of OF is debated as the effects appear often species- and context-dependent, and current research has highlighted the need to quantify the relative effects of local- and landscape-scale management on farmland biodiversity. Yet very few studies have investigated the landscape-level effects of OF; that is to say, how the biodiversity of a field is affected by the presence or density of organically farmed fields in the surrounding landscape. We addressed this issue using the metacommunity framework, with weed species richness in winter wheat within an intensively farmed landscape in France as model system. Controlling for the effects of local and landscape structure, we showed that OF leads to higher local weed diversity and that the presence of OF in the landscape is associated with higher local weed biodiversity also for conventionally farmed fields, and may reach a similar biodiversity level to organic fields in field margins. Based on these results, we derive indications for improving the sustainable management of farming systems. PMID:25994672

  16. A technology to analyze spatiotemporal landscape dynamics: Application to Cadiz Township (Wisconsin)

    SciTech Connect

    Krummel, J.R.; Dunn, C.P.; Eckert, T.C.; Ayers, A.J.

    1993-09-01

    As landscape ecology has matured, it has gone beyond description of land-use changes, to examining the functional relationships between spatial patterns of landscapes and ecological processes. Attempts to describe these relationships at larger scales or in complex landscapes have been hampered by the lack of spatially explicit distributed parameter models linked dynamically to geographical information systems (GIS). This paper describes developments we have made to link such models to GIS and to develop visualization methods (a graphical interface) that permits the user to readily manipulate large element files containing model parameters. We then present preliminary results illustrating the effects of pattern (in an agricultural landscape) on water and material flow across a heterogeneous landscape composed of multiple watersheds. These dynamics are driven in large measure by the location, size, and number of forest patches. By use of soil, hydrologic, and vegetation data from a real landscape, the effects of spatial relocation of vegetation on water and sediment dynamics are explored through the model-GIS combination. The spatiotemporal modeling approach described here could be useful in effectively managing ecosystem restoration and rehabilitation at the landscape scale.

  17. The effects of large herbivores on the landscape dynamics of a perennial herb

    PubMed Central

    Hemrová, Lucie; Červenková, Zita; Münzbergová, Zuzana

    2012-01-01

    Background and Aims Models assessing the prospects of plant species at the landscape level often focus primarily on the relationship between species dynamics and landscape structure. However, the short-term prospects of species with slow responses to landscape changes depend on the factors affecting local population dynamics. In this study it is hypothesized that large herbivores may be a major factor affecting the short-term prospects of slow-responding species in the European landscape, because large herbivores have increased in number in this region in recent decades and can strongly influence local population dynamics. Methods The impact of browsing by large herbivores was simulated on the landscape-level dynamics of the dry grassland perennial polycarpic herb Scorzonera hispanica. A dynamic, spatially explicit model was used that incorporated information on the location of patches suitable for S. hispanica, local population dynamics (matrices including the impact of large herbivores), initial population sizes and dispersal rate of the species. Simulations were performed relating to the prospects of S. hispanica over the next 30 years under different rates of herbivory (browsing intensity) and varying frequencies of population destruction (e.g. by human activity). Key Results Although a high rate of herbivory was detected in most populations of S. hispanica, current landscape-level dynamics of S. hispanica were approximately in equilibrium. A decline or increase of over 20 % in the herbivory rate promoted rapid expansion or decline of S. hispanica, respectively. This effect was much stronger in the presence of population destruction. Conclusions Browsing by large herbivores can have a dramatic effect on the landscape dynamics of plant species. Changes in the density of large herbivores and the probability of population destruction should be incorporated into models predicting species abundance and distribution. PMID:22492260

  18. Exactly Computing the Parsimony Scores on Phylogenetic Networks Using Dynamic Programming

    PubMed Central

    Wheeler, Ward C.

    2014-01-01

    Abstract Scoring a given phylogenetic network is the first step that is required in searching for the best evolutionary framework for a given dataset. Using the principle of maximum parsimony, we can score phylogenetic networks based on the minimum number of state changes across a subset of edges of the network for each character that are required for a given set of characters to realize the input states at the leaves of the networks. Two such subsets of edges of networks are interesting in light of studying evolutionary histories of datasets: (i) the set of all edges of the network, and (ii) the set of all edges of a spanning tree that minimizes the score. The problems of finding the parsimony scores under these two criteria define slightly different mathematical problems that are both NP-hard. In this article, we show that both problems, with scores generalized to adding substitution costs between states on the endpoints of the edges, can be solved exactly using dynamic programming. We show that our algorithms require O(mpk) storage at each vertex (per character), where k is the number of states the character can take, p is the number of reticulate vertices in the network, m = k for the problem with edge set (i), and m = 2 for the problem with edge set (ii). This establishes an O(nmpk2) algorithm for both the problems (n is the number of leaves in the network), which are extensions of Sankoff's algorithm for finding the parsimony scores for phylogenetic trees. We will discuss improvements in the complexities and show that for phylogenetic networks whose underlying undirected graphs have disjoint cycles, the storage at each vertex can be reduced to O(mk), thus making the algorithm polynomial for this class of networks. We will present some properties of the two approaches and guidance on choosing between the criteria, as well as traverse through the network space using either of the definitions. We show that our methodology provides an effective means to

  19. Origin of static and dynamic steps in exact Kohn-Sham potentials

    NASA Astrophysics Data System (ADS)

    Hodgson, M. J. P.; Ramsden, J. D.; Godby, R. W.

    2016-04-01

    Knowledge of exact properties of the exchange-correlation (xc) functional is important for improving the approximations made within density functional theory. Features such as steps in the exact xc potential are known to be necessary for yielding accurate densities, yet little is understood regarding their shape, magnitude, and location. We use systems of a few electrons, where the exact electron density is known, to demonstrate general properties of steps. We find that steps occur at points in the electron density where there is a change in the `local effective ionization energy' of the electrons. We provide practical arguments, based on the electron density, for determining the position, shape, and height of steps for ground-state systems, and extend the concepts to time-dependent systems. These arguments are intended to inform the development of approximate functionals, such as the mixed localization potential (MLP), which already demonstrate their capability to produce steps in the Kohn-Sham potential.

  20. Tbilisi's climatic-landscape peculiarities and their dynamics.

    PubMed

    Salukvadze, Elene; Mumladze, Dali; Chaladze, Tamila; Lomidze, Nino; Khechikashvili, Maia; Chikharadze, Nino; Janelidze, Zurab

    2012-04-01

    The current condition and development tendencies of natural environment of capital of Georgia - Tbilisi are directly connected with the anthropogenesis. Analyze of changing of environment peculiarities of rapid expansion of Tbilisi city and according to it revealing its landscape-climatic changes is the aim of the research paper. The diverse landscape of Tbilisi suburbs is represented by forests, forest-steppes, steppes, shrubs, etc. The variety can be attributed to complex reliefs geological structure, diversity of climate, flora and fauna, and to the location between two different geostructural areas - the mountain system (Trialeti, Saguramo-Ialno) and intermountain valleys (Mameuli and Gardabani lowlands). Natural landscapes have been partly preserved in the city suburbs, but even they are gradually being replaced by new anthropogenic landscapes: new roads and residential and industrial zones. According to the data prior to 2007, the city territory totaled 372 km2, while presently, under the modified municipal decree, it is 504 km2. Transformation of natural landscape of territory of Tbilisi into the anthropogenic one, has changed the physical condition of underlying surface. Especially, heat balance of the city was changed, which was followed by increase in air mean temperature (0.4-0.5 degrees C) and precipitation and reduction of wind speed.

  1. Quantitative Microfluidic Dynamics Of Spheroidal Particles Within Periodic Optical Landscapes

    NASA Astrophysics Data System (ADS)

    Conover, Brandon Lee

    2011-12-01

    Over the past 4 decades, research and development of optical manipulation techniques has been primarily focused on observable phenomena. Trapping, sorting, mixing, aligning, and organizing particles---often times spheres on the order of 1 -- 100mum---has been shown by several groups using many different optical trapping and optical potential techniques. However, relatively little been reported on either the quantification of the various forces on the particles or on the theoretical aspects of the motion of the particles. Even less has been reported regarding the theoretical aspects of the motion of non-spherical particles within optical traps and landscapes. It is the objective of this dissertation to address these deficits by means of modeling and experimentally verifying the behavior of particles within periodic optical landscapes. First, we report on our development of a quantifiable analysis of these phenomena by means of a form factor model of spheroidal particle motion in periodic optical landscapes. Using this model, we show that shape does indeed have a quantifiable impact on a particle's motion in an optical landscape. We conclude that a collection of particles will all traverse an optical landscape differently based directly on their respective sizes, refractive indices, and shapes, sometimes with a high degree of dispersion. Next, we report on our development of a second model of spheroidal particle motion in periodic optical landscapes. Based on the T-matrix scattering approach, this model addresses the scattering forces and the electric field polarization effects on the particles' motion. We conclude that as the particle size gets larger, the scattering forces become greater and very quickly rise above an order of magnitude larger than the gradient forces of the optical landscape. Our conclusions provide quantifiable conditions for when scattering forces and electric field-induced torques within an optical landscape are significant and should not be

  2. Λ polarization in an exact fluid dynamical model for heavy-ion collisions

    NASA Astrophysics Data System (ADS)

    Xie, Yilong

    2016-05-01

    Λ polarization is calculated in an exact analytical, rotating model based on parameters from a high resolution (3+1)D Particle-in-Cell Relativistic hydrodynamics calculation. The polarization is attributed to effects from thermal vorticity and for the first time the effects of the radial and axial acceleration are also studied separately.

  3. Dynamic Tracking: The Study of Changes in Landscape.

    ERIC Educational Resources Information Center

    Strang, Carl A.

    1996-01-01

    States that tracking, or the study of changes in landscapes, offers clues that give us a direct experiential connection to the past and consequently enriches our appreciation of how the present came to be. Discusses tracking animals and footprints, tree tracking, and geomorphology or landforms. (AIM)

  4. Effects of Collective Histone State Dynamics on Epigenetic Landscape and Kinetics of Cell Reprogramming

    NASA Astrophysics Data System (ADS)

    Ashwin, S. S.; Sasai, Masaki

    2015-11-01

    Cell reprogramming is a process of transitions from differentiated to pluripotent cell states via transient intermediate states. Within the epigenetic landscape framework, such a process is regarded as a sequence of transitions among basins on the landscape; therefore, theoretical construction of a model landscape which exhibits experimentally consistent dynamics can provide clues to understanding epigenetic mechanism of reprogramming. We propose a minimal gene-network model of the landscape, in which each gene is regulated by an integrated mechanism of transcription-factor binding/unbinding and the collective chemical modification of histones. We show that the slow collective variation of many histones around each gene locus alters topology of the landscape and significantly affects transition dynamics between basins. Differentiation and reprogramming follow different transition pathways on the calculated landscape, which should be verified experimentally via single-cell pursuit of the reprogramming process. Effects of modulation in collective histone state kinetics on transition dynamics and pathway are examined in search for an efficient protocol of reprogramming.

  5. Effects of Collective Histone State Dynamics on Epigenetic Landscape and Kinetics of Cell Reprogramming

    PubMed Central

    Ashwin, S. S.; Sasai, Masaki

    2015-01-01

    Cell reprogramming is a process of transitions from differentiated to pluripotent cell states via transient intermediate states. Within the epigenetic landscape framework, such a process is regarded as a sequence of transitions among basins on the landscape; therefore, theoretical construction of a model landscape which exhibits experimentally consistent dynamics can provide clues to understanding epigenetic mechanism of reprogramming. We propose a minimal gene-network model of the landscape, in which each gene is regulated by an integrated mechanism of transcription-factor binding/unbinding and the collective chemical modification of histones. We show that the slow collective variation of many histones around each gene locus alters topology of the landscape and significantly affects transition dynamics between basins. Differentiation and reprogramming follow different transition pathways on the calculated landscape, which should be verified experimentally via single-cell pursuit of the reprogramming process. Effects of modulation in collective histone state kinetics on transition dynamics and pathway are examined in search for an efficient protocol of reprogramming. PMID:26581803

  6. Effects of Collective Histone State Dynamics on Epigenetic Landscape and Kinetics of Cell Reprogramming.

    PubMed

    Ashwin, S S; Sasai, Masaki

    2015-01-01

    Cell reprogramming is a process of transitions from differentiated to pluripotent cell states via transient intermediate states. Within the epigenetic landscape framework, such a process is regarded as a sequence of transitions among basins on the landscape; therefore, theoretical construction of a model landscape which exhibits experimentally consistent dynamics can provide clues to understanding epigenetic mechanism of reprogramming. We propose a minimal gene-network model of the landscape, in which each gene is regulated by an integrated mechanism of transcription-factor binding/unbinding and the collective chemical modification of histones. We show that the slow collective variation of many histones around each gene locus alters topology of the landscape and significantly affects transition dynamics between basins. Differentiation and reprogramming follow different transition pathways on the calculated landscape, which should be verified experimentally via single-cell pursuit of the reprogramming process. Effects of modulation in collective histone state kinetics on transition dynamics and pathway are examined in search for an efficient protocol of reprogramming. PMID:26581803

  7. Landscape-scale modelling of soil carbon dynamics under land use and climate change

    NASA Astrophysics Data System (ADS)

    Lacoste, Marine; Viaud, Valérie; Michot, Didier; Christian, Walter

    2013-04-01

    Soil organic carbon (SOC) sequestration is highly linked to soil use and farming practices, but also to soil redistributions, soil properties, and climate. In a global change context, landscape, farming practice and climate changes are expected; and they will most probably impact SOC dynamics. To assess their respective impacts, we modelled the SOC contents and stocks evolution at the scale of an agricultural landscape, by taking into account the soil redistribution by tillage and water processes. The simulations were conducted from 2010 to 2100 under different scenarios of landscape and climate. These scenarios combined different land uses associated to specific farming practices (mixed dairy with rotations of crops and grasslands, intensive cropping with only crops rotations or permanent grasslands), landscape managements (hedges planting or removal), and climates (business-as-usual climate and climate change, with temperature and precipitations increase). We used a spatially SOC dynamic model (adapted from RothC), coupled to a soil redistribution model (LandSoil). SOC dynamics were spatially modelled with a lateral resolution of 2-m and for soil organic layers up to 105 cm. Initial SOC stocks were described with a 2-m resolution map based on field data and produced with digital soil mapping methods. The major factor of change in SOC stocks was land use change, the second factor of importance was climate change, and finally landscape management: for the total SOC stocks (0-to-105 cm soil layer) the change of land use, climate and landscape management induced a respective mean absolute variation of 10 to 20 tC ha-1, 9 tC ha-1 and 0.4 tC ha-1. When considering the 0-to-105 cm soil layer, the different modelled landscapes showed the same sensitivity to climate change, with induced a mean decrease of 10 tC ha-1. However, the impact of climate change was found different according to the different modelled landscape when considering the 0-to-7.5 and 0-to-30 cm soil

  8. Fuel dynamics by using Landscape Ecology Indices in the Alto Mijares, Spain

    NASA Astrophysics Data System (ADS)

    Iqbal, J.; Garcia, C. V.

    2009-04-01

    Land abandonment in Mediterranean regions has brought about a number of management problems, being an increased wildfire activity prevalent among them. Agricultural neglect in highlands resulted in reduced anthropogenic disturbances and greater landscape homogeneity in areas such as the Alto Mijares in Spain. It is widely accepted that processes like forest fires, influence structure of the landscape and vice versa. Fire-prone Mediterranean flora is well adapted to this disturbance, exhibiting excellent succession capabilities; but higher fuel loads and homogeneous conditions may ally to promote vegetation recession when the fire regime is altered by land abandonment. Both succession and recession make changes to the landscape structure and configuration. However, these changes are difficult to quantify and characterize. If landscape restoration of these forests is a management objective, then developing a quantitative knowledge base for landscape fuel dynamics is a prerequisite. Four classified LandsatTM satellite images were compared to quantify changes in landscape structure between 1984 and 1998. An attempt is made to define landscape level dynamics for fuel development after reduced disturbance and fuel accumulation that leads to catastrophic fires by using landscape ecology indices. By doing so, indices that best describe the fuel dynamics are pointed. The results indicate that low-level disturbance increases heterogeneity, thus lowers fire hazard. No disturbance or severe disturbance increases homogeneity because of vegetation succession and may lead to devastating fires. These fires could be avoided by human induced disturbance like controlled burning, harvesting, mechanical works for fuel reduction and other silviculture measures; thus bringing in more heterogeneity in the region. The Alto Mijares landscape appears to be in an unstable equilibrium where succession and recession are at tug of war. The effects are evident in the general absence of the climax

  9. Modeling fluvial incision and transient landscape evolution: Influence of dynamic channel adjustment

    NASA Astrophysics Data System (ADS)

    Attal, M.; Tucker, G. E.; Whittaker, A. C.; Cowie, P. A.; Roberts, G. P.

    2008-09-01

    Channel geometry exerts a fundamental control on fluvial processes. Recent work has shown that bedrock channel width depends on a number of parameters, including channel slope, and is not solely a function of drainage area as is commonly assumed. The present work represents the first attempt to investigate the consequences of dynamic, gradient-sensitive channel adjustment for drainage-basin evolution. We use the Channel-Hillslope Integrated Landscape Development (CHILD) model to analyze the response of a catchment to a given tectonic perturbation, using, as a template, the topography of a well-documented catchment in the footwall of an active normal fault in the Apennines (Italy) that is known to be undergoing a transient response to tectonic forcing. We show that the observed transient response can be reproduced to first order with a simple detachment-limited fluvial incision law. Transient landscape is characterized by gentler gradients and a shorter response time when dynamic channel adjustment is allowed. The differences in predicted channel geometry between the static case (width dependent solely on upstream area) and dynamic case (width dependent on both drainage area and channel slope) lead to contrasting landscape morphologies when integrated at the scale of a whole catchment, particularly in presence of strong tilting and/or pronounced slip-rate acceleration. Our results emphasize the importance of channel width in controlling fluvial processes and landscape evolution. They stress the need for using a dynamic hydraulic scaling law when modeling landscape evolution, particularly when the relative uplift field is nonuniform.

  10. Agricultural landscapes dynamic at the North-West of Russia

    NASA Astrophysics Data System (ADS)

    Guzel, N.

    2012-04-01

    The process of reduction of agrolandscapes has taken place some decades in the North-Western European Russia. During 100 last years the area of agricultural lands have reduced in 1,4 times on the Karelian Isthmus. The most part of it had been abandoned after change of State border after of the Second World War. The processes of overgrowing of the former agricultural lands are studied on the landscapes base. The types of landscapes are distinguished on the based of the morphological relief symptoms, characteristics of the structure rock and the humid regime. Agricultural lands occupy landscapes such as kames, sandy, sandy-loam, clayey plains, sometimes with excess moistening, sandy fluvioglacial plains, loamy morainic plains, mesotrophic and evtrophic peat-bogs. Four stages can be revealed. I - (period to 20 years after termination of agricultural use) - grass-herb meadow with unclosed brush II - (20 - 40) - shrub layer with closed or low-closed canopy and unclosed or low closed small-leaved regrowth III - (40 - 80) - closed small-leaved forest, sometime including the coniferous trees IY - predomination of the coniferous on small-leaved trees Reestablish vegetation successions can be realised by different ways, with different rate, including various trees and ecological groups of species in different landscapes. In the different sites many traits in common are discovered during this processes. The processes taking place in soil of abandoned agricultural lands are expressed more poorly than in vegetation as soil is more "conservative" element of landscape. Now most area occupies former agricultural lands, inhering on III stage and presenting itself small-leaved forest. Over the last decade because of a change in the socio-political situation there has emerged a tendency towards an increase in the area of the cultivated land in the Karelian Isthmus including the secondary development of previously abandoned lands. However, this process is going on spontaneously; there

  11. Doing arithmetic by hand: hand movements during exact arithmetic reveal systematic, dynamic spatial processing.

    PubMed

    Marghetis, Tyler; Núñez, Rafael; Bergen, Benjamin K

    2014-01-01

    Mathematics requires precise inferences about abstract objects inaccessible to perception. How is this possible? One proposal is that mathematical reasoning, while concerned with entirely abstract objects, nevertheless relies on neural resources specialized for interacting with the world-in other words, mathematics may be grounded in spatial or sensorimotor systems. Mental arithmetic, for instance, could involve shifts in spatial attention along a mental "number-line", the product of cultural artefacts and practices that systematically spatialize number and arithmetic. Here, we investigate this hypothesized spatial processing during exact, symbolic arithmetic (e.g., 4 + 3 = 7). Participants added and subtracted single-digit numbers and selected the exact solution from responses in the top corners of a computer monitor. While they made their selections using a computer mouse, we recorded the movement of their hand as indexed by the streaming x, y coordinates of the computer mouse cursor. As predicted, hand movements during addition and subtraction were systematically deflected toward the right and the left, respectively, as if calculation involved simultaneously simulating motion along a left-to-right mental number-line. This spatial-arithmetical bias, moreover, was distinct from-but correlated with-individuals' spatial-numerical biases (i.e., spatial-numerical association of response codes, SNARC, effect). These results are the first evidence that exact, symbolic arithmetic prompts systematic spatial processing associated with mental calculation. We discuss the possibility that mathematical calculation relies, in part, on an integrated system of spatial processes. PMID:25051274

  12. Landscape complexity and vegetation dynamics in Riding Mountain National Park, Canada

    NASA Astrophysics Data System (ADS)

    Walker, David John

    The primary focus of landscape ecology is the interrelationship between spatial pattern and processes within an ecosystem. It is through their mutual interaction that landscape structure and complexity are ultimately determined. Complexity, which includes both the horizontal and vertical arrangement of vegetation structure on the landscape, is an emergent property of dynamic systems. In the boreal forest, landscape complexity is a product of successional dynamics, physiography and environmental variability. The objective of this study was to examine spatial and temporal changes to landscape complexity in the boreal mixedwood of Riding Mountain National Park (RMNP), Canada. Using remotely sensed Landsat data and scale invariant fractal measures of spatial pattern, change in landscape complexity under natural and human induced fragmentation regimes was examined. The importance of structure as an emergent property of boreal canopies and its influence on landscape mapping using satellite data was addressed. It was found that landscape-level spatial pattern became increasingly entropic during succession. Old landscapes (120 years post-fire) were typified by a landscape matrix dominated by small scale patches and low spatial persistence. Physiography was also found to influence scale invariant landscape complexity. Landscapes typified by simple physiographies (well-drained, topographically simple sites) were characterized by a few dominant over-dispersed land-cover classes. Complex landscapes (variably drained, topographically complex sites), patches were under-dispersed and contagious, however complex gradients resulted in high pattern complexity (increased juxapositioning of landscape elements). It is suggested that the accumulation of small-scale disturbances over time and species turnover along complex environmental gradient affect high landscape complexity in the boreal forest. In contrast, human driven disturbance processes in the boreal forest resulted in lower

  13. A new class of exact solutions with shock waves in gas dynamics

    NASA Astrophysics Data System (ADS)

    Poslavskii, S. A.

    1985-10-01

    New exact solutions are obtained for one-dimensional gasdynamic equations with strong shock waves propagating in a moving medium, with gas flow behind the shock wave described by a solution with uniform deformation. Solutions are then presented for a problem concerning explosion without counterpressure in a uniformly expanding (contracting) gas with an arbitrary adiabatic exponent and a nonuniform initial density distribution. A solution is also presented for the problem of cavity collapse in a dust cloud with the formation of a shock wave.

  14. Emergence of spatio-temporal dynamics from exact coherent solutions in pipe flow

    NASA Astrophysics Data System (ADS)

    Ritter, Paul; Mellibovsky, Fernando; Avila, Marc

    2016-08-01

    Turbulent-laminar patterns are ubiquitous near transition in wall-bounded shear flows. Despite recent progress in describing their dynamics in analogy to non-equilibrium phase transitions, there is no theory explaining their emergence. Dynamical-system approaches suggest that invariant solutions to the Navier–Stokes equations, such as traveling waves and relative periodic orbits in pipe flow, act as building blocks of the disordered dynamics. While recent studies have shown how transient chaos arises from such solutions, the ensuing dynamics lacks the strong fluctuations in size, shape and speed of the turbulent spots observed in experiments. We here show that chaotic spots with distinct dynamical and kinematic properties merge in phase space and give rise to the enhanced spatio-temporal patterns observed in pipe flow. This paves the way for a dynamical-system foundation to the phenomenology of turbulent-laminar patterns in wall-bounded extended shear flows.

  15. Emergence of spatio-temporal dynamics from exact coherent solutions in pipe flow

    NASA Astrophysics Data System (ADS)

    Ritter, Paul; Mellibovsky, Fernando; Avila, Marc

    2016-08-01

    Turbulent-laminar patterns are ubiquitous near transition in wall-bounded shear flows. Despite recent progress in describing their dynamics in analogy to non-equilibrium phase transitions, there is no theory explaining their emergence. Dynamical-system approaches suggest that invariant solutions to the Navier-Stokes equations, such as traveling waves and relative periodic orbits in pipe flow, act as building blocks of the disordered dynamics. While recent studies have shown how transient chaos arises from such solutions, the ensuing dynamics lacks the strong fluctuations in size, shape and speed of the turbulent spots observed in experiments. We here show that chaotic spots with distinct dynamical and kinematic properties merge in phase space and give rise to the enhanced spatio-temporal patterns observed in pipe flow. This paves the way for a dynamical-system foundation to the phenomenology of turbulent-laminar patterns in wall-bounded extended shear flows.

  16. An exact representation of the fermion dynamics in terms of Poisson processes and its connection with Monte Carlo algorithms

    NASA Astrophysics Data System (ADS)

    Beccaria, M.; Presilla, C.; DeAngelis, G. F.; Jona-Lasinio, G.

    1999-11-01

    We present a simple derivation of a Feynman-Kac type formula to study fermionic systems. In this approach the real time or the imaginary time dynamics is expressed in terms of the evolution of a collection of Poisson processes. This formula leads to a family of algorithms parametrized by the values of the jump rates of the Poisson processes. From these an optimal algorithm can be chosen which coincides with the Green Function Monte Carlo method in the limit when the latter becomes exact.

  17. Landscapes of non-gradient dynamics without detailed balance: Stable limit cycles and multiple attractors

    NASA Astrophysics Data System (ADS)

    Ge, Hao; Qian, Hong

    2012-06-01

    Landscape is one of the key notions in literature on biological processes and physics of complex systems with both deterministic and stochastic dynamics. The large deviation theory (LDT) provides a possible mathematical basis for the scientists' intuition. In terms of Freidlin-Wentzell's LDT, we discuss explicitly two issues in singularly perturbed stationary diffusion processes arisen from nonlinear differential equations: (1) For a process whose corresponding ordinary differential equation has a stable limit cycle, the stationary solution exhibits a clear separation of time scales: an exponential terms and an algebraic prefactor. The large deviation rate function attains its minimum zero on the entire stable limit cycle, while the leading term of the prefactor is inversely proportional to the velocity of the non-uniform periodic oscillation on the cycle. (2) For dynamics with multiple stable fixed points and saddles, there is in general a breakdown of detailed balance among the corresponding attractors. Two landscapes, a local and a global, arise in LDT, and a Markov jumping process with cycle flux emerges in the low-noise limit. A local landscape is pertinent to the transition rates between neighboring stable fixed points; and the global landscape defines a nonequilibrium steady state. There would be nondifferentiable points in the latter for a stationary dynamics with cycle flux. LDT serving as the mathematical foundation for emergent landscapes deserves further investigations.

  18. Mapping, monitoring, and modeling Western Gateway Community landscape dynamics

    USGS Publications Warehouse

    Hester, David J.

    2013-01-01

    Federal public lands in the western United States are becoming increasingly surrounded by Gateway Communities. These communities are undergoing landscape change due to population growth, economic growth, and the resulting land-use development. Socioeconomic, demographic, and land-use changes in Gateway Communities are often perceived as threats to Federal land resources, natural amenities, cultural resources, and recreational opportunities. However, land-surface disturbances on Federal public lands, such as conventional and alternative energy development (which impact surrounding Gateway Communities), are also environmental and societal issues that Federal land and adjacent regional community planners need to consider in their long-range land-use planning.

  19. The Dynamic Response of an Euler-Bernoulli Beam on an Elastic Foundation by Finite Element Analysis using the Exact Stiffness Matrix

    NASA Astrophysics Data System (ADS)

    Kim, Jeong Soo; Kyum Kim, Moon

    2012-08-01

    In this study, finite element analysis of beam on elastic foundation, which received great attention of researchers due to its wide applications in engineering, is performed for estimating dynamic responses of shallow foundation using exact stiffness matrix. First, element stiffness matrix based on the closed solution of beam on elastic foundation is derived. Then, we performed static finite element analysis included exact stiffness matrix numerically, comparing results from the analysis with some exact analysis solutions well known for verification. Finally, dynamic finite element analysis is performed for a shallow foundation structure under rectangular pulse loading using trapezoidal method. The dynamic analysis results exist in the reasonable range comparing solution of single degree of freedom problem under a similar condition. The results show that finite element analysis using exact stiffness matrix is evaluated as a good tool of estimating the dynamic response of structures on elastic foundation.

  20. Dynamic fitness landscapes: expansions for small mutation rates

    NASA Astrophysics Data System (ADS)

    Wilke, Claus O.; Ronnewinkel, Christopher

    2001-02-01

    We study the evolution of asexual microorganisms with small mutation rate in fluctuating environments, and develop techniques that allow us to expand the formal solution of the evolution equations to first order in the mutation rate. Our method can be applied to both discrete time and continuous time systems. While the behavior of continuous time systems is dominated by the average fitness landscape for small mutation rates, in discrete time systems it is instead the geometric mean fitness that determines the system's properties. In both cases, we find that in situations in which the arithmetic (resp. geometric) mean of the fitness landscape is degenerate, regions in which the fitness fluctuates around the mean value present a selective advantage over regions in which the fitness stays at the mean. This effect is caused by the vanishing genetic diffusion at low mutation rates. In the absence of strong diffusion, a population can stay close to a fluctuating peak when the peak's height is below average, and take advantage of the peak when its height is above average.

  1. Experimental evidence of dynamic re-organization of evolving landscapes under changing climatic forcing

    NASA Astrophysics Data System (ADS)

    Singh, Arvind; Tejedor, Alejandro; Zaliapin, Ilya; Reinhardt, Liam; Foufoula-Georgiou, Efi

    2015-04-01

    The aim of this study is to better understand the dynamic re-organization of an evolving landscape under a scenario of changing climatic forcing for improving our knowledge of geomorphic transport laws under transient conditions and developing predictive models of landscape response to external perturbations. Real landscape observations for long-term analysis are limited and to this end a high resolution controlled laboratory experiment was conducted at the St. Anthony Falls laboratory at the University of Minnesota. Elevation data were collected at temporal resolution of 5 mins and spatial resolution of 0.5 mm as the landscape approached steady state (constant uplift and precipitation rate) and in the transient state (under the same uplift and 5x precipitation). The results reveal rapid topographic re-organization under a five-fold precipitation increase with the fluvial regime expanding into the previously debris dominated regime, accelerated erosion happening at hillslope scales, and rivers shifting from an erosion-limited to a transport-limited regime. From a connectivity and clustering analysis of the erosional and depositional events, we demonstrate the strikingly different spatial patterns of landscape evolution under steady-state (SS) and transient-state (TS), even when the time under SS is "stretched" compared to that under TS such as to match the total volume and PDF of erosional and depositional amounts. We quantify the spatial coupling of hillslopes and channels and demonstrate that hillslopes lead and channels follow in re-organizing the whole landscape under such an amplified precipitation regime.

  2. Landscape dynamics in the Arctic foothills: Landscape evolution and vegetation succession on disturbances

    SciTech Connect

    Walker, D.A.; Walker, M.D.

    1990-10-20

    This document contains a summary of research accomplished by the University of Colorado's Institute of Arctic and Alpine Research (INSTAAR) Joint Facility for Regional Ecosystem Analysis (JFREA) for the Department of Energy's R D research program for 1989--1990. Aerial photographs, orthophoto topographic maps, and digital elevation models (DEMs) of the Toolik Lake region site were prepared by Aeromap US at 1:500 and 1:5000 scales. During August 1990, the region surrounding Toolik Lake was mapped at 1:5000 scale, and the intensive research grid was mapped at 1:500 scale. Mapped variables include vegetation, landforms, surface forms, and percentage surface water. Soil data from the Imnavait Creek and Toolik Lake sites are central to the analysis of landscape evolution. Soils were collected from the base of the O horizon at 72 gridpoints on the 1:500-scale map area at Imnavait Creek, and 85 grid points at Toolik Lake. Soils are being analyzed for percentage moisture, pH (saturated paste), electrical conductivity, percentage organic matter, nitrate, nitrogen, phosphorus, potassium, iron, manganese, copper. Soils were also collected from 81 permanent plots (199 horizons) which will be used for vegetation-environmental analyses. Permanent 1 {times} 1-meter point-quadrat plots were established at 85 points of the Toolik Lake grid. Data from the plots will be stratified according to slope position and terrain unit and used to compare vegetation structure and cover on different aged surfaces. Work continued on the study of the effects of road dust on tundra vegetation. 28 figs.

  3. MODELING THE DYNAMICS OF WILDLIFE HABITAT AND POPULATIONS AT THE LANDSCAPE SCALE

    EPA Science Inventory

    A forest dynamics model (FORCLIM) was linked to a spatial wildlife population model (PATCH) to assess the effects of habitat change in a landscape on selected wildlife species. The habitat changes included forest responses to harvesting, development, and climate change on a west...

  4. Spatial analyses of soil properties, terrain, and water dynamics in a semi-arid agricultural landscape

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Quantification of soil-water patterns in space and time is essential for understanding soil hydrological processes and to aid land management decisions. In undulating terrain, dynamics of profile soil water can vary by landscape position in relation to terrain attributes, soil properties, and plant ...

  5. DYNAMICS OF A SUBTIDAL SEAGRASS LANDSCAPE: SEASONAL AND ANNUAL CHANGE IN RELATION TO WATER DEPTH

    EPA Science Inventory

    The spatial heterogeneity of a subtidal marine landscape and the areal extent of both monospecific and mixed patches of seagrass species were studied in Tampa Bay, FL. Specifically, we examined the temporal dynamics of seagrass distribution and its relationship to water depth an...

  6. Measuring Effects of Metaphor in a Dynamic Opinion Landscape

    PubMed Central

    Thibodeau, Paul H.; Boroditsky, Lera

    2015-01-01

    Metaphors pervade discussions of critical issues, making up as much as 10–20% of natural discourse. Recent work has suggested that these conventional and systematic metaphors influence the way people reason about the issues they describe. For instance, previous work has found that people were more likely to want to fight back against a crime beast by increasing the police force but more likely to want to diagnose and treat a crime virus through social reform. Here, we report the results of three norming tasks and two experiments that reveal a shift in the overall landscape of opinion on the topic of crime. Importantly, we find that the metaphors continue to have an influence on people’s reasoning about crime. Our results and analyses highlight the importance of up-to-date opinion norms and carefully controlled materials in metaphor research. PMID:26218229

  7. Fitness of multidimensional phenotypes in dynamic adaptive landscapes.

    PubMed

    Laughlin, Daniel C; Messier, Julie

    2015-08-01

    Phenotypic traits influence species distributions, but ecology lacks established links between multidimensional phenotypes and fitness for predicting species responses to environmental change. The common focus on single traits rather than multiple trait combinations limits our understanding of their adaptive value, and intraspecific trait covariation has been neglected in ecology despite its importance in evolutionary theory and its likely impact on species distributions. Here, we extend the adaptive landscape framework to ecological sorting of multidimensional phenotypes across environments and discuss how two analytical approaches can be used to quantify fitness as a function of the interaction between the phenotype and the environment. We encourage ecologists to consider how phenotypic integration will constrain species responses to environmental change.

  8. Measuring Effects of Metaphor in a Dynamic Opinion Landscape.

    PubMed

    Thibodeau, Paul H; Boroditsky, Lera

    2015-01-01

    Metaphors pervade discussions of critical issues, making up as much as 10-20% of natural discourse. Recent work has suggested that these conventional and systematic metaphors influence the way people reason about the issues they describe. For instance, previous work has found that people were more likely to want to fight back against a crime beast by increasing the police force but more likely to want to diagnose and treat a crime virus through social reform. Here, we report the results of three norming tasks and two experiments that reveal a shift in the overall landscape of opinion on the topic of crime. Importantly, we find that the metaphors continue to have an influence on people's reasoning about crime. Our results and analyses highlight the importance of up-to-date opinion norms and carefully controlled materials in metaphor research.

  9. An Experimental Fluid dynamics Study of Exact-Replica Atherosclerotic Carotid Bifurcations

    NASA Astrophysics Data System (ADS)

    Bale-Glickman, Jocelyn; Selby, Kathy; Saloner, David; Savas, Omer

    2003-11-01

    Physiological flow studies are carried out in two different models of atherosclerotic carotid bifurcations using flow visualization and particle image velocimetry (PIV). The flow models exactly replicate the lumen of plaques excised intact from patients with severe atherosclerosis. A boundary treatment technique is employed in PIV processing to estimate the flow strain rate near the wall, hence to estimate the wall shear stresses (WSS) to a first order accuracy. The systolic and diastolic Reynolds numbers are about 900 and 300, respectively, which match Doppler Ultrasound scans done on the patients just before surgery. The complex internal geometry of the diseased artery combined with the pulsatile input flows gives exceedingly complex flow patterns. The flows are highly three-dimensional and chaotic in which the details vary from cycle to cycle. The flow patterns include internal jets, three-dimensional shear layers, stagnation lines, separation zones and recirculation zones. The vorticity and streamline maps confirm the highly complex and three-dimensional nature of the flow. WSS are estimated to range from -7 Pa to 30 Pa at the stenotic neck over time. Companion experiments are also carried out with sinusoidal and steady CCA input flows for comparison.

  10. An exact renormalization model for earthquakes and material failure: Statics and dynamics

    SciTech Connect

    Newman, W.I. |; Gabrielov, A.M. |; Durand, T.A.; Phoenix, S.L.; Turcotte, D.L.

    1993-09-12

    Earthquake events are well-known to prams a variety of empirical scaling laws. Accordingly, renormalization methods offer some hope for understanding why earthquake statistics behave in a similar way over orders of magnitude of energy. We review the progress made in the use of renormalization methods in approaching the earthquake problem. In particular, earthquake events have been modeled by previous investigators as hierarchically organized bundles of fibers with equal load sharing. We consider by computational and analytic means the failure properties of such bundles of fibers, a problem that may be treated exactly by renormalization methods. We show, independent of the specific properties of an individual fiber, that the stress and time thresholds for failure of fiber bundles obey universal, albeit different, staling laws with respect to the size of the bundles. The application of these results to fracture processes in earthquake events and in engineering materials helps to provide insight into some of the observed patterns and scaling-in particular, the apparent weakening of earthquake faults and composite materials with respect to size, and the apparent emergence of relatively well-defined stresses and times when failure is seemingly assured.

  11. The DYNAFLUX / DYNACOLD Network: Dynamics, Fluxes, Stability, Succession and Landscape Formation in Cold Environments

    NASA Astrophysics Data System (ADS)

    Beylich, A. A.; Molau, U.

    2012-04-01

    Within Europe there is a wide array of high-latitude and high-altitude landscapes, covering a significant proportion of the total land area. These cold climate landscapes represent a variety of stages of deglaciation history and landscape formation. We find landscapes at different levels of postglacial stabilization providing the unique possibility to study the interactions between geo-, bio-, social and socio-economic systems at the land surface. The DYNAFLUX / DYNACOLD Network (2004 - ) bridges across geo-, bio-, social and socio-economic sciences in order to investigate the complex dynamics of stabilization, succession and landscape formation during and after ice retreat and under human impact. DYNAFLUX / DYNACOLD provides a multidisciplinary forum where research groups come together. The integrated approach provides - in addition to newly generated disciplinary knowledge - the qualitative and quantitative linkages of findings from geo-, bio- and socio-work groups to develop a systems-based holistic level-of-understanding about the dynamics of environmental fluxes in high-latitude and high-altitude geo-ecosystems and landscapes. This knowledge can be used to assess the risks and potentials of the future development with reference to land use intensity / changes and climatic dynamics. DYNAFLUX / DYNACOLD is since 2004 linking and integrating a number of networks and programmes and creates an umbrella programme and a forum for sharing knowledge. The focus of the Network is relevant for different end users, including risk and vulnerability assessment, sustainable land use, land management and conservation. Also questions with regards to Global Change are addressed (hazards, permafrost degradation, loss of biodiversity, etc.).

  12. Stochastic models for mainland-island metapopulations in static and dynamic landscapes.

    PubMed

    Ross, J V

    2006-02-01

    This paper has three primary aims: to establish an effective means for modelling mainland-island metapopulations inhabiting a dynamic landscape; to investigate the effect of immigration and dynamic changes in habitat on metapopulation patch occupancy dynamics; and to illustrate the implications of our results for decision-making and population management. We first extend the mainland-island metapopulation model of Alonso and McKane [Bull. Math. Biol. 64:913-958, 2002] to incorporate a dynamic landscape. It is shown, for both the static and the dynamic landscape models, that a suitably scaled version of the process converges to a unique deterministic model as the size of the system becomes large. We also establish that, under quite general conditions, the density of occupied patches, and the densities of suitable and occupied patches, for the respective models, have approximate normal distributions. Our results not only provide us with estimates for the means and variances that are valid at all stages in the evolution of the population, but also provide a tool for fitting the models to real metapopulations. We discuss the effect of immigration and habitat dynamics on metapopulations, showing that mainland-like patches heavily influence metapopulation persistence, and we argue for adopting measures to increase connectivity between this large patch and the other island-like patches. We illustrate our results with specific reference to examples of populations of butterfly and the grasshopper Bryodema tuberculata.

  13. The dynamics of a coupled soilscape-landscape evolution model

    NASA Astrophysics Data System (ADS)

    Welivitiya, Dimuth; Willgoose, Garry; Hancock, Greg

    2016-04-01

    In this study we present results obtained from a landform evolution model coupled with SSSPAM5D soilscape evolution model. This presentation will show a number of computer animations with this coupled model using a range of widely accepted soil profile weathering models, and erosion/armouring models. The animations clearly show that subtle changes in process can result in dramatic changes in long-term equilibrium hillslope and soilscape form. We will discuss the reasons for these differences, arguing from the various mathematical and physical assumptions modelled, and infer how observed hillslope form may provide identifiable (and perhaps quantifiable) landform and soilscape signatures of landscape and soilscape process, and in particular the coupling between the landscape and the soilscape. Specifically we have simulated soilscapes using 3 depth dependent weathering functions: 1) Exponential, 2) Humped and 3) Reversed exponential. The Exponential weathering function simulates physical weathering due to thermal effects, and the weathering rate exponentially decreases with depth. The Humped function simulates chemical and/or physical weathering with moisture feedbacks, where the highest weathering rate is at a finite depth below the surface and exponentially declines with depth. The Reversed exponential function simulates chemical weathering, and the highest weathering rate is at the soil-saprolite interface and exponentially decreases both above and below the interface. Both the Humped and Reversed exponential functions can be used as approximations to chemical weathering as they can be derived analytically by solving widely accepted geochemical weathering equations. The Humped function can arise where the weathering fluid is introduced at the top of the soil profile (e.g. rainfall equilibrated with carbon dioxide in the atmosphere), while the Reversed exponential can be derived when carbon dioxide is generated within the profile (e.g. by biodegradation of soil

  14. Landscape and Flux Framework for Non-Equilibrium Networks: Kinetic Paths and Rate Dynamics

    NASA Astrophysics Data System (ADS)

    Wang, Jin

    2012-02-01

    We developed a general framework to quantify three key ingredients for dynamics of nonequilibrium systems through path integrals in length space. First, we identify dominant kinetic paths as the ones with optimal weights, leading to effective reduction of dimensionality or degrees of freedom from exponential to polynomial so large systems can be treated. Second, we uncover the underlying nonequilibrium potential landscapes from the explorations of the state space through kinetic paths. We apply our framework to a specific example of nonequilibrium network system: lambda phage genetic switch. Two distinct basins of attractions emerge. The dominant kinetic paths from one basin to another are irreversible and do not follow the usual steepest descent or gradient path along the landscape. It reflects the fact that the dynamics of nonequilibrium systems is not just determined by potential gradient but also the residual curl flux force, suggesting experiments to test theoretical predictions. Third, we have calculated dynamic transition time scales from one basin to another critical for stability of the system through instantons. Theoretical predictions are in good agreements with wild type and mutant experiments.We further uncover the correlations between the kinetic transition time scales and the underlying landscape topography: the barrier heights along the dominant paths. We found that both the dominant paths and the landscape are relatively robust against the influences of external environmental perturbations and the system tends to dissipate less with less fluctuations. Our theoretical framework is general and can be applied to other nonequilibrium systems.

  15. Dynamics of observables and exactly solvable quantum problems: Using time-dependent density-functional theory to control quantum systems

    NASA Astrophysics Data System (ADS)

    Farzanehpour, M.; Tokatly, I. V.

    2016-05-01

    We use analytic (current) density-potential maps of time-dependent (current) density-functional theory [TD(C)DFT] to inverse engineer analytically solvable time-dependent quantum problems. In this approach the driving potential (the control signal) and the corresponding solution of the Schrödinger equation are parametrized analytically in terms of the basic TD(C)DFT observables. We describe the general reconstruction strategy and illustrate it with a number of explicit examples. First we consider the real space one-particle dynamics driven by a time-dependent electromagnetic field and recover, from the general TDDFT reconstruction formulas, the known exact solution for a driven oscillator with a time-dependent frequency. Then we use analytic maps of the lattice TD(C)DFT to control quantum dynamics in a discrete space. As a first example we construct a time-dependent potential which generates prescribed dynamics on a tight-binding chain. Then our method is applied to the dynamics of spin-1/2 driven by a time-dependent magnetic field. We design an analytic control pulse that transfers the system from the ground to excited state and vice versa. This pulse generates the spin flip thus operating as a quantum not gate.

  16. Spatiotemporal dynamics of wetted soils across a polar desert landscape

    SciTech Connect

    Langford, Zachary L.; Gooseff, Michael N.; Lampkin, Derrick J.

    2014-10-30

    Liquid water is scarce across the landscape of the McMurdo Dry Valleys (MDV), Antarctica, a 3800 km2 ice-free region, and is chiefly associated with soils that are adjacent to streams and lakes (i.e. wetted margins) during the annual thaw season. However, isolated wetted soils have been observed at locations distal from water bodies. The source of water for the isolated patches of wet soil is potentially generated by a combination of infiltration from melting snowpacks, melting of pore ice at the ice table, and melting of buried segregation ice formed during winter freezing. In this paper, high resolution remote sensing data gathered several times per summer in the MDV region were used to determine the spatial and temporal distribution of wet soils. The spatial consistency with which the wet soils occurred was assessed for the 2009–10 to 2011–12 summers. The remote sensing analyses reveal that cumulative area and number of wet soil patches varies among summers. The 2010–11 summer provided the most wetted soil area (10.21 km2) and 2009–10 covered the least (5.38 km2). Finally, these data suggest that wet soils are a significant component of the MDV cold desert land system and may become more prevalent as regional climate changes.

  17. Spatiotemporal dynamics of wetted soils across a polar desert landscape

    DOE PAGES

    Langford, Zachary L.; Gooseff, Michael N.; Lampkin, Derrick J.

    2014-10-30

    Liquid water is scarce across the landscape of the McMurdo Dry Valleys (MDV), Antarctica, a 3800 km2 ice-free region, and is chiefly associated with soils that are adjacent to streams and lakes (i.e. wetted margins) during the annual thaw season. However, isolated wetted soils have been observed at locations distal from water bodies. The source of water for the isolated patches of wet soil is potentially generated by a combination of infiltration from melting snowpacks, melting of pore ice at the ice table, and melting of buried segregation ice formed during winter freezing. In this paper, high resolution remote sensingmore » data gathered several times per summer in the MDV region were used to determine the spatial and temporal distribution of wet soils. The spatial consistency with which the wet soils occurred was assessed for the 2009–10 to 2011–12 summers. The remote sensing analyses reveal that cumulative area and number of wet soil patches varies among summers. The 2010–11 summer provided the most wetted soil area (10.21 km2) and 2009–10 covered the least (5.38 km2). Finally, these data suggest that wet soils are a significant component of the MDV cold desert land system and may become more prevalent as regional climate changes.« less

  18. Exact and approximate dynamics of the quantum mechanical O(N) model

    SciTech Connect

    Mihaila, Bogdan; Athan, Tara; Cooper, Fred; Dawson, John; Habib, Salman

    2000-12-15

    We study the dynamics of the quantum mechanical O(N) model as a specific example to investigate the systematics of a 1/N expansion. The closed time path formalism melded with an expansion in 1/N is used to derive time evolution equations valid to order 1/N (next-to-leading order). The effective potential is also obtained to this order and its properties are elucidated. In order to compare theoretical predictions against numerical solutions of the time-dependent Schro''dinger equation, we consider two initial conditions consistent with O(N) symmetry, one of them a quantum roll, the other a wave packet initially to one side of the potential minimum, whose center has all coordinates equal. For the case of the quantum roll we map out the domain of validity of the large-N expansion. We also discuss the existence of unitarity violation in this expansion, a well-known problem faced by moment truncation techniques. The 1/N results, both static and dynamic, are contrasted with those given by a Hartree variational ansatz at given values of N. A comparison against numerical results leads us to conclude that late-time dynamical behavior, where nonlinear effects are significant, is not well described by either approximation.

  19. Dynamics of sea level rise and coastal flooding on a changing landscape

    NASA Astrophysics Data System (ADS)

    Bilskie, M. V.; Hagen, S. C.; Medeiros, S. C.; Passeri, D. L.

    2014-02-01

    Standard approaches to determining the impacts of sea level rise (SLR) on storm surge flooding employ numerical models reflecting present conditions with modified sea states for a given SLR scenario. In this study, we advance this paradigm by adjusting the model framework so that it reflects not only a change in sea state but also variations to the landscape (morphologic changes and urbanization of coastal cities). We utilize a numerical model of the Mississippi and Alabama coast to simulate the response of hurricane storm surge to changes in sea level, land use/land cover, and land surface elevation for past (1960), present (2005), and future (2050) conditions. The results show that the storm surge response to SLR is dynamic and sensitive to changes in the landscape. We introduce a new modeling framework that includes modification of the landscape when producing storm surge models for future conditions.

  20. The effects of landscape fragmentation on pollination dynamics: absence of evidence not evidence of absence.

    PubMed

    Hadley, Adam S; Betts, Matthew G

    2012-08-01

    Animal-mediated pollination is essential for both ecosystem services and conservation of global biodiversity, but a growing body of work reveals that it is negatively affected by anthropogenic disturbance. Landscape-scale disturbance results in two often inter-related processes: (1) habitat loss, (2) disruptions of habitat configuration (i.e. fragmentation). Understanding the relative effects of such processes is critical in designing effective management strategies to limit pollination and pollinator decline. We reviewed existing published work from 1989 to 2009 and found that only six of 303 studies considering the influence of landscape context on pollination separated the effects of habitat loss from fragmentation. We provide a synthesis of the current landscape, behavioural, and pollination ecology literature in order to present preliminary multiple working hypotheses explaining how these two landscape processes might independently influence pollination dynamics. Landscape disturbance primarily influences three components of pollination interactions: pollinator density, movement, and plant demography. We argue that effects of habitat loss on each of these components are likely to differ substantially from the effects of fragmentation, which is likely to be more complex and may influence each pollination component in contrasting ways. The interdependency between plants and animals inherent to pollination systems also has the possibility to drive cumulative effects of fragmentation, initiating negative feedback loops between animals and the plants they pollinate. Alternatively, due to their asymmetrical structure, pollination networks may be relatively robust to fragmentation. Despite the potential importance of independent effects of habitat fragmentation, its effects on pollination remain largely untested. We postulate that variation across studies in the effects of 'fragmentation' owes much to artifacts of the sampling regimes adopted, particularly (1

  1. Adaptive Landscape by Environment Interactions Dictate Evolutionary Dynamics in Models of Drug Resistance.

    PubMed

    Ogbunugafor, C Brandon; Wylie, C Scott; Diakite, Ibrahim; Weinreich, Daniel M; Hartl, Daniel L

    2016-01-01

    The adaptive landscape analogy has found practical use in recent years, as many have explored how their understanding can inform therapeutic strategies that subvert the evolution of drug resistance. A major barrier to applications of these concepts is a lack of detail concerning how the environment affects adaptive landscape topography, and consequently, the outcome of drug treatment. Here we combine empirical data, evolutionary theory, and computer simulations towards dissecting adaptive landscape by environment interactions for the evolution of drug resistance in two dimensions-drug concentration and drug type. We do so by studying the resistance mediated by Plasmodium falciparum dihydrofolate reductase (DHFR) to two related inhibitors-pyrimethamine and cycloguanil-across a breadth of drug concentrations. We first examine whether the adaptive landscapes for the two drugs are consistent with common definitions of cross-resistance. We then reconstruct all accessible pathways across the landscape, observing how their structure changes with drug environment. We offer a mechanism for non-linearity in the topography of accessible pathways by calculating of the interaction between mutation effects and drug environment, which reveals rampant patterns of epistasis. We then simulate evolution in several different drug environments to observe how these individual mutation effects (and patterns of epistasis) influence paths taken at evolutionary "forks in the road" that dictate adaptive dynamics in silico. In doing so, we reveal how classic metrics like the IC50 and minimal inhibitory concentration (MIC) are dubious proxies for understanding how evolution will occur across drug environments. We also consider how the findings reveal ambiguities in the cross-resistance concept, as subtle differences in adaptive landscape topography between otherwise equivalent drugs can drive drastically different evolutionary outcomes. Summarizing, we discuss the results with regards to their

  2. Adaptive Landscape by Environment Interactions Dictate Evolutionary Dynamics in Models of Drug Resistance

    PubMed Central

    Ogbunugafor, C. Brandon; Wylie, C. Scott; Diakite, Ibrahim; Weinreich, Daniel M.; Hartl, Daniel L.

    2016-01-01

    The adaptive landscape analogy has found practical use in recent years, as many have explored how their understanding can inform therapeutic strategies that subvert the evolution of drug resistance. A major barrier to applications of these concepts is a lack of detail concerning how the environment affects adaptive landscape topography, and consequently, the outcome of drug treatment. Here we combine empirical data, evolutionary theory, and computer simulations towards dissecting adaptive landscape by environment interactions for the evolution of drug resistance in two dimensions—drug concentration and drug type. We do so by studying the resistance mediated by Plasmodium falciparum dihydrofolate reductase (DHFR) to two related inhibitors—pyrimethamine and cycloguanil—across a breadth of drug concentrations. We first examine whether the adaptive landscapes for the two drugs are consistent with common definitions of cross-resistance. We then reconstruct all accessible pathways across the landscape, observing how their structure changes with drug environment. We offer a mechanism for non-linearity in the topography of accessible pathways by calculating of the interaction between mutation effects and drug environment, which reveals rampant patterns of epistasis. We then simulate evolution in several different drug environments to observe how these individual mutation effects (and patterns of epistasis) influence paths taken at evolutionary “forks in the road” that dictate adaptive dynamics in silico. In doing so, we reveal how classic metrics like the IC50 and minimal inhibitory concentration (MIC) are dubious proxies for understanding how evolution will occur across drug environments. We also consider how the findings reveal ambiguities in the cross-resistance concept, as subtle differences in adaptive landscape topography between otherwise equivalent drugs can drive drastically different evolutionary outcomes. Summarizing, we discuss the results with

  3. Exact dynamic stiffness matrix of non-symmetric thin-walled curved beams subjected to initial axial force

    NASA Astrophysics Data System (ADS)

    Nam-Il, Kim; Moon-Young, Kim

    2005-06-01

    An improved numerical method to exactly evaluate the dynamic element stiffness matrix is proposed for the spatially coupled free vibration analysis of non-symmetric thin-walled curved beams subjected to uniform axial force. For this purpose, firstly equations of motion, boundary conditions and force-deformation relations are rigorously derived from the total potential energy for a curved beam element. Next systems of linear algebraic equations with non-symmetric matrices are constructed by introducing 14 displacement parameters and transforming the fourth-order simultaneous differential equations into the first-order simultaneous equations. And then explicit expressions for displacement parameters are numerically evaluated via eigensolutions and the exact 14×14 element stiffness matrix is determined using force-deformation relations. In order to demonstrate the validity and the accuracy of this study, the spatially coupled natural frequencies of non-symmetric thin-walled curved beams subjected to uniform compressive and tensile forces are evaluated and compared with analytical and finite element solutions using Hermitian curved beam elements or ABAQUS's shell element. In addition, some results by the parametric study are reported.

  4. Dynamics, Fluxes, Stability, Succession and Landscape Formation in Cold Environments: The DYNAFLUX / DYNACOLD Network

    NASA Astrophysics Data System (ADS)

    Beylich, Achim A.

    2015-04-01

    Within Europe there is a wide array of high-latitude and high-altitude landscapes, covering a significant proportion of the total land area. These defined cold climate landscapes represent a variety of stages of deglaciation history and landscape formation. We find landscapes at different levels of postglacial stabilization, providing the unique opportunity to study the interactions between geo-, bio-, social and socio-economic systems at the land surface. The DYNAFLUX / DYNACOLD Network (2004 - ) bridges across the geo-, bio-, social and socio-economic sciences in order to investigate the complex dynamics of stabilization, succession and landscape formation during and after ice retreat and under human impact. The Network provides a multidisciplinary forum where research groups come together. It is linking and integrating a number of networks and programs and creates an umbrella program and a forum for sharing knowledge. The focus of this network is relevant for different end users, including risk and vulnerability assessment, sustainable land use, land management and conservation. Also questions closely related to Global Change like, e.g., hazards, permafrost degradation, loss of biodiversity are addressed.

  5. The DYNAFLUX / DYNACOLD Network: Dynamics, Fluxes, Stability, Succession and Landscape Formation in Cold Climate Environments

    NASA Astrophysics Data System (ADS)

    Beylich, Achim A.

    2016-04-01

    There is a wide range of high-latitude and high-altitude cold climate landscapes in Europe, covering a significant proportion of the total land surface area. This spectrum of defined cold climate landscapes represents a variety of stages of deglaciation history and landscape formation. We can find landscapes at different levels of postglacial stabilization which is providing the opportunity to study the interactions between geo-, bio-, social and socio-economic systems at the land surface. The DYNAFLUX / DYNACOLD Network (2004-) bridges across the geo-, bio-, social and socio-economic sciences in order to analyze the complex dynamics of stabilization, succession and landscape formation during and after ice retreat and under ongoing human influences. The network provides a multidisciplinary forum where researchers come together. In addition, it is linking a number of networks, working groups and programs and creates an umbrella network and a forum for sharing knowledge. The scientific focus of this network is also relevant for different end users, including risk and vulnerability assessment, sustainable land use, land management and conservation. In addition, key questions related to Global Change like, e.g., hazards, permafrost degradation and loss of biodiversity are discussed.

  6. Exact analysis of particle dynamics in combined field of finite duration laser pulse and static axial magnetic field

    SciTech Connect

    Sagar, Vikram; Sengupta, Sudip; Kaw, Predhiman

    2012-11-15

    Dynamics of a charged particle is studied in the field of a relativistically intense linearly polarized finite duration laser pulse in the presence of a static axial magnetic field. For a finite duration laser pulse whose temporal shape is defined by Gaussian profile, exact analytical expressions are derived for the particle trajectory, momentum, and energy as function of laser phase. From the solutions, it is shown that, unlike for the monochromatic plane wave case, resonant phase locking time between the particle and laser pulse is finite. The net energy transferred to the particle does not increase monotonically but tends to saturate. It is further shown that appropriate tuning of cyclotron frequency of the particle with the characteristic frequency in the pulse spectrum can lead to the generation of accelerated particles with variable energies in MeV-TeV range.

  7. Exact dynamic stiffness matrix of a three-dimensional shear beam with doubly asymmetric cross-section

    NASA Astrophysics Data System (ADS)

    Rafezy, B.; Howson, W. P.

    2006-02-01

    The dynamic member stiffness matrix of a three-dimensional shear beam with doubly asymmetric cross-section is derived exactly from the governing, sixth-order differential equation of motion. Such a formulation accounts for the uniform distribution of mass in the member and necessitates the solution of a transcendental eigenvalue problem. This is achieved using the Wittrick-Williams algorithm, where the necessary parameters are developed using a generalised procedure. An example is given to clarify the theory, together with a small parametric study that indicates when lateral-torsional coupling may safely be ignored. The work also holds considerable potential in its application to the approximate analysis of asymmetric, multi-storey, three-dimensional frame structures.

  8. [Assessing dynamic patterns of forest fragmentation based on a landscape mosaic indicator: a case study of Oregon State, USA].

    PubMed

    Ren, Xin-Yu; Lü, Ying-Ying; Li, Ming-Shi

    2014-08-01

    Effectively assessing landscape pattern characteristics and predicting their dynamics have been a basic prerequisite for more reasonably regulating and managing forest landscape, and maintaining landscape security patterns. In this study, based on three U. S. National Land Cover Databases (1992, 2001 and 2006), the landscape mosaic indicator in combination with the Markov model was adopted to analyze forest fragmentation patterns and changes in the characteristics of spatial interactions between forests and other land use types in Oregon State, USA. The results showed that conversion from the development-dominated type D to the single development type DD in landscape mosaic model had the highest transition probability 0.319, indicating that urbanization has been the major force responsible for the change of regional landscape patterns. In the forest security model, the highest rates of forest loss occurred in agriculture and the developed landscape mosaic type (ad), showing that in the development and agriculture dominated landscapes, encroaching upon forests was at the highest likelihood. The areal percentage of forest over the total study area was less than 50% when reaching a steady-state distribution, with an accelerating rate of forest fragmentation, and the landscape spatial distribution tended to be a mixed landscape pattern. The Kappa coefficient between the simulated values and the observed values from the 2006 landscape mosaic model was estimated at 0.82, indicating this model had a high precision. However, the accuracy of the forest security model was poor, with a Kappa coefficient of 0.21.

  9. A Spatial Landscape Model of Forest Patch Dynamics and Climate Change

    USGS Publications Warehouse

    Busing, Richard T.

    2007-01-01

    FOREL (a FOREst Landscape model) is an individual-based, multi-scale simulator of forest and climate dynamics. Rationale and design of the model are presented in relation to other forest patch models. Information on implementation of the model is also provided. Capabilities of the FOREL model are demonstrated for forest composition, structure and dynamics along climatic gradients. The model relies on a patch simulation approach that has been tested and developed by independent ecologists for more than three decades. Improvements made over the last decade to the simulation of climate effects on trees are incorporated in the landscape model. A single parameterization of the model is capable of simulating major shifts in forest composition and structure across broad climatic gradients. It is responsive along moisture gradients and temperature gradients. The landscape model is flexible and can be altered easily to test various assumptions about the effects of climate on trees, and the effects of spatial pattern on processes operating within and among forest stands. The spatial structure of the model makes interaction of patches possible. Interactions may include dispersal of propagules and competition for light. The model is a useful tool for projecting temporal climate change effects on forested sites, landscapes and regions.

  10. Exploration of Multi-State Conformational Dynamics and Underlying Global Functional Landscape of Maltose Binding Protein

    PubMed Central

    Wang, Yong; Tang, Chun; Wang, Erkang; Wang, Jin

    2012-01-01

    An increasing number of biological machines have been revealed to have more than two macroscopic states. Quantifying the underlying multiple-basin functional landscape is essential for understanding their functions. However, the present models seem to be insufficient to describe such multiple-state systems. To meet this challenge, we have developed a coarse grained triple-basin structure-based model with implicit ligand. Based on our model, the constructed functional landscape is sufficiently sampled by the brute-force molecular dynamics simulation. We explored maltose-binding protein (MBP) which undergoes large-scale domain motion between open, apo-closed (partially closed) and holo-closed (fully closed) states responding to ligand binding. We revealed an underlying mechanism whereby major induced fit and minor population shift pathways co-exist by quantitative flux analysis. We found that the hinge regions play an important role in the functional dynamics as well as that increases in its flexibility promote population shifts. This finding provides a theoretical explanation of the mechanistic discrepancies in PBP protein family. We also found a functional “backtracking” behavior that favors conformational change. We further explored the underlying folding landscape in response to ligand binding. Consistent with earlier experimental findings, the presence of ligand increases the cooperativity and stability of MBP. This work provides the first study to explore the folding dynamics and functional dynamics under the same theoretical framework using our triple-basin functional model. PMID:22532792

  11. Linking river management to species conservation using dynamic landscape scale models

    USGS Publications Warehouse

    Freeman, Mary C.; Buell, Gary R.; Hay, Lauren E.; Hughes, W. Brian; Jacobson, Robert B.; Jones, John W.; Jones, S.A.; LaFontaine, Jacob H.; Odom, Kenneth R.; Peterson, James T.; Riley, Jeffrey W.; Schindler, J. Stephen; Shea, C.; Weaver, J.D.

    2013-01-01

    Efforts to conserve stream and river biota could benefit from tools that allow managers to evaluate landscape-scale changes in species distributions in response to water management decisions. We present a framework and methods for integrating hydrology, geographic context and metapopulation processes to simulate effects of changes in streamflow on fish occupancy dynamics across a landscape of interconnected stream segments. We illustrate this approach using a 482 km2 catchment in the southeastern US supporting 50 or more stream fish species. A spatially distributed, deterministic and physically based hydrologic model is used to simulate daily streamflow for sub-basins composing the catchment. We use geographic data to characterize stream segments with respect to channel size, confinement, position and connectedness within the stream network. Simulated streamflow dynamics are then applied to model fish metapopulation dynamics in stream segments, using hypothesized effects of streamflow magnitude and variability on population processes, conditioned by channel characteristics. The resulting time series simulate spatially explicit, annual changes in species occurrences or assemblage metrics (e.g. species richness) across the catchment as outcomes of management scenarios. Sensitivity analyses using alternative, plausible links between streamflow components and metapopulation processes, or allowing for alternative modes of fish dispersal, demonstrate large effects of ecological uncertainty on model outcomes and highlight needed research and monitoring. Nonetheless, with uncertainties explicitly acknowledged, dynamic, landscape-scale simulations may prove useful for quantitatively comparing river management alternatives with respect to species conservation.

  12. An exact relationship between invasion probability and endemic prevalence for Markovian SIS dynamics on networks.

    PubMed

    Wilkinson, Robert R; Sharkey, Kieran J

    2013-01-01

    Understanding models which represent the invasion of network-based systems by infectious agents can give important insights into many real-world situations, including the prevention and control of infectious diseases and computer viruses. Here we consider Markovian susceptible-infectious-susceptible (SIS) dynamics on finite strongly connected networks, applicable to several sexually transmitted diseases and computer viruses. In this context, a theoretical definition of endemic prevalence is easily obtained via the quasi-stationary distribution (QSD). By representing the model as a percolation process and utilising the property of duality, we also provide a theoretical definition of invasion probability. We then show that, for undirected networks, the probability of invasion from any given individual is equal to the (probabilistic) endemic prevalence, following successful invasion, at the individual (we also provide a relationship for the directed case). The total (fractional) endemic prevalence in the population is thus equal to the average invasion probability (across all individuals). Consequently, for such systems, the regions or individuals already supporting a high level of infection are likely to be the source of a successful invasion by another infectious agent. This could be used to inform targeted interventions when there is a threat from an emerging infectious disease.

  13. The dynamic conformational landscape of γ-secretase

    PubMed Central

    Elad, Nadav; De Strooper, Bart; Lismont, Sam; Hagen, Wim; Veugelen, Sarah; Arimon, Muriel; Horré, Katrien; Berezovska, Oksana; Sachse, Carsten; Chávez-Gutiérrez, Lucía

    2015-01-01

    ABSTRACT The structure and function of the γ-secretase proteases are of great interest because of their crucial roles in cellular and disease processes. We established a novel purification protocol for the γ-secretase complex that involves a conformation- and complex-specific nanobody, yielding highly pure and active enzyme. Using single particle electron microscopy, we analyzed the γ-secretase structure and its conformational variability. Under steady-state conditions, the complex adopts three major conformations, which differ in overall compactness and relative position of the nicastrin ectodomain. Occupancy of the active or substrate-binding sites by inhibitors differentially stabilizes subpopulations of particles with compact conformations, whereas a mutation linked to familial Alzheimer disease results in enrichment of extended-conformation complexes with increased flexibility. Our study presents the γ-secretase complex as a dynamic population of interconverting conformations, involving rearrangements at the nanometer scale and a high level of structural interdependence between subunits. The fact that protease inhibition or clinical mutations, which affect amyloid β (Aβ) generation, enrich for particular subpopulations of conformers indicates the functional relevance of the observed dynamic changes, which are likely to be instrumental for highly allosteric behavior of the enzyme. PMID:25501811

  14. Landscape pattern dynamic change analysis based on eco-hydrological process in the lower reaches of Tarim River, China

    NASA Astrophysics Data System (ADS)

    Huang, Qing; Zhou, Qing-bo; Cheng, Xiao-qian; Wang, Wen; Zhang, Hong-bin

    2009-01-01

    Landscape pattern and eco-hydrological process had changed greatly after seven times emergency water transportation in the lower reaches of Tarim River, Xinjiang, China. After analyzing the changes of eco-hydrological process, ground water level, soil moisture and vegetation growth etc. of emergency water transportation, remote sensing images in 2000 and 2005 year which present the situation before and after the emergency water transportation were processed and dynamic change characteristics of landscape pattern were analyzed. The changes of landscape pattern were described as follows: The forest land, waters, farmland and construction landscape area increase, and forest land increases the biggest, which increased by 23.03% during last 5 years. Waters landscape change is only inferior to forest land, which increased by 16.04%. The lawn, sand and Gobi saline-alkali land landscape area reduced; lawn and farmland had made the biggest contribution to the increase of forest land by 6.46% and 4.79% in the year 2005. Landscape diversity index, evenness index, fractal dimension and general fragmentation increased, but dominance index reduced. The results indicate that RS plays the vital role in the macroscopic dynamic change analysis of landscape pattern and seven times emergency water transportation has greatly influenced eco-hydrology process and landscape pattern changes in the lower reaches of Tarim River.

  15. Modeling Fluvial Incision and Transient Landscape Evolution: Influence of Dynamic Channel Adjustment

    NASA Astrophysics Data System (ADS)

    Attal, M.; Tucker, G. E.; Cowie, P. A.; Whittaker, A. C.; Roberts, G. P.

    2007-12-01

    Channel geometry exerts a fundamental control on fluvial processes. Recent work has shown that bedrock channel width (W) depends on a number of parameters, including channel slope, and is not only a function of drainage area (A) as is commonly assumed. The present work represents the first attempt to investigate the consequences, for landscape evolution, of using a static expression of channel width (W ~ A0.5) versus a relationship that allows channels to dynamically adjust to changes in slope. We consider different models for the evolution of the channel geometry, including constant width-to-depth ratio (after Finnegan et al., Geology, v. 33, no. 3, 2005), and width-to-depth ratio varying as a function of slope (after Whittaker et al., Geology, v. 35, no. 2, 2007). We use the Channel-Hillslope Integrated Landscape Development (CHILD) model to analyze the response of a catchment to a given tectonic disturbance. The topography of a catchment in the footwall of an active normal fault in the Apennines (Italy) is used as a template for the study. We show that, for this catchment, the transient response can be fairly well reproduced using a simple detachment-limited fluvial incision law. We also show that, depending on the relationship used to express channel width, initial steady-state topographies differ, as do transient channel width, slope, and the response time of the fluvial system. These differences lead to contrasting landscape morphologies when integrated at the scale of a whole catchment. Our results emphasize the importance of channel width in controlling fluvial processes and landscape evolution. They stress the need for using a dynamic hydraulic scaling law when modeling landscape evolution, particularly when the uplift field is non-uniform.

  16. Dynamics of driven transitions between minima of a complex energy landscapes

    NASA Astrophysics Data System (ADS)

    Pusuluri, Sai Teja; Lang, Alex H.; Mehta, Pankaj; Castillo, Horacio E.

    We recently modeled cellular interconvertion dynamics by using an epigenetic landscape model inspired by neural network models. Given an arbitrary set of patterns, the model can be used to construct an energy landscape in which those patterns are the global minima. Here we study the transitions between stable states of the landscapes thus constructed, under the effect of an external driving force. We consider three different cases: i) choosing the patterns to be random and independendently distributed ii) choosing a set of patterns directly derived from the experimental cellular transcription factor expression data for a representative set of cell types in an organism and iii) choosing randomly generated trees of hierarchically correlated patterns, inspired by biology. For each of the three cases, we study the stability of the global minima against thermal fluctuations and external driving forces, and the dynamics of the driven transitions away from global minima. We compare the results obtained in the three cases defined above, and in particular we explore to what degree the correlations between patterns affect the transition dynamics.

  17. Energy landscape scheme for an intuitive understanding of complex domain dynamics in ferroelectric thin films

    PubMed Central

    Heon Kim, Tae; Yoon, Jong-Gul; Hyub Baek, Seung; Park, Woong-kyu; Mo Yang, Sang; Yup Jang, Seung; Min, Taeyuun; Chung, Jin-Seok; Eom, Chang-Beom; Won Noh, Tae

    2015-01-01

    Fundamental understanding of domain dynamics in ferroic materials has been a longstanding issue because of its relevance to many systems and to the design of nanoscale domain-wall devices. Despite many theoretical and experimental studies, a full understanding of domain dynamics still remains incomplete, partly due to complex interactions between domain-walls and disorder. We report domain-shape-preserving deterministic domain-wall motion, which directly confirms microscopic return point memory, by observing domain-wall breathing motion in ferroelectric BiFeO3 thin film using stroboscopic piezoresponse force microscopy. Spatial energy landscape that provides new insights into domain dynamics is also mapped based on the breathing motion of domain walls. The evolution of complex domain structure can be understood by the process of occupying the lowest available energy states of polarization in the energy landscape which is determined by defect-induced internal fields. Our result highlights a pathway for the novel design of ferroelectric domain-wall devices through the engineering of energy landscape using defect-induced internal fields such as flexoelectric fields. PMID:26130159

  18. Optimal control landscape for the generation of unitary transformations with constrained dynamics

    SciTech Connect

    Hsieh, Michael; Wu, Rebing; Rabitz, Herschel; Lidar, Daniel

    2010-06-15

    The reliable and precise generation of quantum unitary transformations is essential for the realization of a number of fundamental objectives, such as quantum control and quantum information processing. Prior work has explored the optimal control problem of generating such unitary transformations as a surface-optimization problem over the quantum control landscape, defined as a metric for realizing a desired unitary transformation as a function of the control variables. It was found that under the assumption of nondissipative and controllable dynamics, the landscape topology is trap free, which implies that any reasonable optimization heuristic should be able to identify globally optimal solutions. The present work is a control landscape analysis, which incorporates specific constraints in the Hamiltonian that correspond to certain dynamical symmetries in the underlying physical system. It is found that the presence of such symmetries does not destroy the trap-free topology. These findings expand the class of quantum dynamical systems on which control problems are intrinsically amenable to a solution by optimal control.

  19. From understanding the development landscape of the canonical fate-switch pair to constructing a dynamic landscape for two-step neural differentiation.

    PubMed

    Qiu, Xiaojie; Ding, Shanshan; Shi, Tieliu

    2012-12-20

    Recent progress in stem cell biology, notably cell fate conversion, calls for novel theoretical understanding for cell differentiation. The existing qualitative concept of Waddington's "epigenetic landscape" has attracted particular attention because it captures subsequent fate decision points, thus manifesting the hierarchical ("tree-like") nature of cell fate diversification. Here, we generalized a recent work and explored such a developmental landscape for a two-gene fate decision circuit by integrating the underlying probability landscapes with different parameters (corresponding to distinct developmental stages). The change of entropy production rate along the parameter changes indicates which parameter changes can represent a normal developmental process while other parameters' change can not. The transdifferentiation paths over the landscape under certain conditions reveal the possibility of a direct and reversible phenotypic conversion. As the intensity of noise increases, we found that the landscape becomes flatter and the dominant paths more straight, implying the importance of biological noise processing mechanism in development and reprogramming. We further extended the landscape of the one-step fate decision to that for two-step decisions in central nervous system (CNS) differentiation. A minimal network and dynamic model for CNS differentiation was firstly constructed where two three-gene motifs are coupled. We then implemented the SDEs (Stochastic Differentiation Equations) simulation for the validity of the network and model. By integrating the two landscapes for the two switch gene pairs, we constructed the two-step development landscape for CNS differentiation. Our work provides new insights into cellular differentiation and important clues for better reprogramming strategies.

  20. Neoantigen landscape dynamics during human melanoma-T cell interactions.

    PubMed

    Verdegaal, Els M E; de Miranda, Noel F C C; Visser, Marten; Harryvan, Tom; van Buuren, Marit M; Andersen, Rikke S; Hadrup, Sine R; van der Minne, Caroline E; Schotte, Remko; Spits, Hergen; Haanen, John B A G; Kapiteijn, Ellen H W; Schumacher, Ton N; van der Burg, Sjoerd H

    2016-08-01

    Recognition of neoantigens that are formed as a consequence of DNA damage is likely to form a major driving force behind the clinical activity of cancer immunotherapies such as T-cell checkpoint blockade and adoptive T-cell therapy. Therefore, strategies to selectively enhance T-cell reactivity against genetically defined neoantigens are currently under development. In mouse models, T-cell pressure can sculpt the antigenicity of tumours, resulting in the emergence of tumours that lack defined mutant antigens. However, whether the T-cell-recognized neoantigen repertoire in human cancers is constant over time is unclear. Here we analyse the stability of neoantigen-specific T-cell responses and the antigens they recognize in two patients with stage IV melanoma treated by adoptive T-cell transfer. The T-cell-recognized neoantigens can be selectively lost from the tumour cell population, either by overall reduced expression of the genes or loss of the mutant alleles. Notably, loss of expression of T-cell-recognized neoantigens was accompanied by development of neoantigen-specific T-cell reactivity in tumour-infiltrating lymphocytes. These data demonstrate the dynamic interactions between cancer cells and T cells, which suggest that T cells mediate neoantigen immunoediting, and indicate that the therapeutic induction of broad neoantigen-specific T-cell responses should be used to avoid tumour resistance. PMID:27350335

  1. A rhythm landscape approach to the developmental dynamics of birdsong

    PubMed Central

    Sasahara, Kazutoshi; Tchernichovski, Ofer; Takahasi, Miki; Suzuki, Kenta; Okanoya, Kazuo

    2015-01-01

    Unlike simple biological rhythms, the rhythm of the oscine bird song is a learned time series of diverse sounds that change dynamically during vocal ontogeny. How to quantify rhythm development is one of the most important challenges in behavioural biology. Here, we propose a simple method, called ‘rhythm landscape’, to visualize and quantify how rhythm structure, which is measured as durational patterns of sounds and silences, emerges and changes over development. Applying this method to the development of Bengalese finch songs, we show that the rhythm structure begins with a broadband rhythm that develops into diverse rhythms largely through branching from precursors. Furthermore, an information-theoretic measure, the Jensen–Shannon divergence, was used to characterize the crystallization process of birdsong rhythm, which started with a high rate of rhythm change and progressed to a stage of slow refinement. This simple method provides a useful description of rhythm development, thereby helping to reveal key temporal constraints on complex biological rhythms. PMID:26538559

  2. Dynamic landscape of tandem 3' UTRs during zebrafish development.

    PubMed

    Li, Yuxin; Sun, Yu; Fu, Yonggui; Li, Mengzhen; Huang, Guangrui; Zhang, Chenxu; Liang, Jiahui; Huang, Shengfeng; Shen, Gaoyang; Yuan, Shaochun; Chen, Liangfu; Chen, Shangwu; Xu, Anlong

    2012-10-01

    Tandem 3' untranslated regions (UTRs), produced by alternative polyadenylation (APA) in the terminal exon of a gene, could have critical roles in regulating gene networks. Here we profiled tandem poly(A) events on a genome-wide scale during the embryonic development of zebrafish (Danio rerio) using a recently developed SAPAS method. We showed that 43% of the expressed protein-coding genes have tandem 3' UTRs. The average 3' UTR length follows a V-shaped dynamic pattern during early embryogenesis, in which the 3' UTRs are first shortened at zygotic genome activation, and then quickly lengthened during gastrulation. Over 4000 genes are found to switch tandem APA sites, and the distinct functional roles of these genes are indicated by Gene Ontology analysis. Three families of cis-elements, including miR-430 seed, U-rich element, and canonical poly(A) signal, are enriched in 3' UTR-shortened/lengthened genes in a stage-specific manner, suggesting temporal regulation coordinated by APA and trans-acting factors. Our results highlight the regulatory role of tandem 3' UTR control in early embryogenesis and suggest that APA may represent a new epigenetic paradigm of physiological regulations.

  3. Ranking landscape development scenarios affecting natterjack toad (Bufo calamita) population dynamics in Central Poland.

    PubMed

    Franz, Kamila W; Romanowski, Jerzy; Johst, Karin; Grimm, Volker

    2013-01-01

    When data are limited it is difficult for conservation managers to assess alternative management scenarios and make decisions. The natterjack toad (Bufo calamita) is declining at the edges of its distribution range in Europe and little is known about its current distribution and abundance in Poland. Although different landscape management plans for central Poland exist, it is unclear to what extent they impact this species. Based on these plans, we investigated how four alternative landscape development scenarios would affect the total carrying capacity and population dynamics of the natterjack toad. To facilitate decision-making, we first ranked the scenarios according to their total carrying capacity. We used the software RAMAS GIS to determine the size and location of habitat patches in the landscape. The estimated carrying capacities were very similar for each scenario, and clear ranking was not possible. Only the reforestation scenario showed a marked loss in carrying capacity. We therefore simulated metapopulation dynamics with RAMAS taking into account dynamical processes such as reproduction and dispersal and ranked the scenarios according to the resulting species abundance. In this case, we could clearly rank the development scenarios. We identified road mortality of adults as a key process governing the dynamics and separating the different scenarios. The renaturalisation scenario clearly ranked highest due to its decreased road mortality. Taken together our results suggest that road infrastructure development might be much more important for natterjack toad conservation than changes in the amount of habitat in the semi-natural river valley. We gained these insights by considering both the resulting metapopulation structure and dynamics in the form of a PVA. We conclude that the consideration of dynamic processes in amphibian conservation management may be indispensable for ranking management scenarios.

  4. Ranking Landscape Development Scenarios Affecting Natterjack Toad (Bufo calamita) Population Dynamics in Central Poland

    PubMed Central

    Franz, Kamila W.; Romanowski, Jerzy; Johst, Karin; Grimm, Volker

    2013-01-01

    When data are limited it is difficult for conservation managers to assess alternative management scenarios and make decisions. The natterjack toad (Bufo calamita) is declining at the edges of its distribution range in Europe and little is known about its current distribution and abundance in Poland. Although different landscape management plans for central Poland exist, it is unclear to what extent they impact this species. Based on these plans, we investigated how four alternative landscape development scenarios would affect the total carrying capacity and population dynamics of the natterjack toad. To facilitate decision-making, we first ranked the scenarios according to their total carrying capacity. We used the software RAMAS GIS to determine the size and location of habitat patches in the landscape. The estimated carrying capacities were very similar for each scenario, and clear ranking was not possible. Only the reforestation scenario showed a marked loss in carrying capacity. We therefore simulated metapopulation dynamics with RAMAS taking into account dynamical processes such as reproduction and dispersal and ranked the scenarios according to the resulting species abundance. In this case, we could clearly rank the development scenarios. We identified road mortality of adults as a key process governing the dynamics and separating the different scenarios. The renaturalisation scenario clearly ranked highest due to its decreased road mortality. Taken together our results suggest that road infrastructure development might be much more important for natterjack toad conservation than changes in the amount of habitat in the semi-natural river valley. We gained these insights by considering both the resulting metapopulation structure and dynamics in the form of a PVA. We conclude that the consideration of dynamic processes in amphibian conservation management may be indispensable for ranking management scenarios. PMID:23734223

  5. Hominin-bearing caves and landscape dynamics in the Cradle of Humankind, South Africa

    NASA Astrophysics Data System (ADS)

    Dirks, Paul H. G. M.; Berger, Lee R.

    2013-02-01

    sediment traps on the landscape. Caves in the CoH are distributed along lithological boundaries and NNE and ESE fractures. Fossil-bearing caves have a distinct distribution pattern, with different directional controls, a high degree of clustering, a characteristic spacing of 1700 m or 3400 m, and a characteristic bi-model fractal distribution best explained by a combination of geological and biological controls. It is suggested that clustering of fossil-bearing caves reflects a Lévy flight patterns typical for foraging behavior in animals. The controlling element in this behavior could have been availability of water in or near groups of caves, resulting in preferential occupation of these caves with accumulation of diverse faunal fossil assemblages. The tectonic drivers shaping the dynamic landscape of the CoH did not involve large, seismically active fault lines, but complex interactions between multiple smaller fractures and joints activated in a far field stress controlled by uplift. The landscape of the CoH, with its caves and water sources and dissected landscape provided a setting favored by many animals including hominins. A modern day analog for what the CoH would have looked like 2 My ago is found 50 km east of Johannesburg, near the SE margin of the Johannesburg Dome.

  6. Coastal landscape dynamics in NE Sørkapp Land (SE Spitsbergen), 1900-2005.

    PubMed

    Ziaja, Wieslaw; Maciejowski, Wojciech; Ostafin, Krzysztof

    2009-06-01

    This report presents the current dynamics of the natural environment and landscape in a part of the mountainous southeastern Spitsbergen coast on the Barents Sea in 1900-2005. Its current state substantially varies from what is shown on recently published topographic maps actual for 1936. The physico-geographical mapping and GPS survey were the basic field methods of recognizing the area, supplemented by remote sensing. Each landscape component, except for the Pre-Quaternary bedrock, has been changed primarily as a direct or indirect result of the current warming. The most dramatic landscape transformation has been connected with the formation of a fjord, the abandoning of the lower parts of valleys by tidewater glaciers, and the alteration of the coastline. This transformation's pace has been increasing visibly over the last few decades. The landscape became more diversified. There is a positive feedback in the process of life expansion in the study area: the processes of animal colonization and plant succession stimulate each other. PMID:19739554

  7. [Dynamics of ecological landscape pattern and its affecting factors in desert-oasis in Fukang, Xinjiang].

    PubMed

    Liu, Xinchun; Zhang, Yuandong; Ren, Guangyao; Pan, Xiaoling; He, Qing

    2004-07-01

    The spatial pattern of ecological landscape during land utilization in Fukang is heavily influenced by natural difference and the scale of water and land resource development. Analyses on the spatial pattern based on different zones and indexes showed that from 1987 to 1998, the change of the spatial pattern of ecological landscape during land utilization in Fukang was mainly the increase of plantation area in pluvial fan and the decrease in alluvial plain. The case was on the contrary about badlands. The acreage of woodland decreased in lower mountains, uplands and alluvial plain, but no variety in alluvial plain. The acreage of grassland increased in lower mountains and uplands, while decreased in other fields. The acreage of town increased in each sample field, while that of water area remained uncharged. The landscape diversity and evenness was descending, the dominance was ascending in lower mountains and in pluvial fan, while it was reverse in alluvial plain. Accessorial fragmentation showed the increasing influence of human beings. The change of the spatial pattern of ecological landscape in Fukang focused on the acreage alteration of plantation and badlands in pluvial fan and alluvial plain. The key factor was the dynamic variation of water-salt in water and soil resource utilization. Terrain and land utilization were the key factors affecting water table, and the continuous changes of the water table worked on the spatial distribution of soil water-salt. PMID:15506098

  8. Soluble Model of Evolution and Extinction Dynamics in a Rugged Fitness Landscape

    NASA Astrophysics Data System (ADS)

    Sibani, Paolo

    1997-08-01

    We consider a continuum version of a previously introduced and numerically studied model of macroevolution [P. Sibani, M. R. Schimdt, and P. Alstrøm, Phys. Rev. Lett. 75, 2055 (1995)] in which agents evolve by an optimization process in a rugged fitness landscape and die due to their competitive interactions. We first formulate dynamical equations for the fitness distribution and the survival probability. Secondly, we analytically derive the t-2 law which characterizes the lifetime distribution of biological genera. Thirdly, we discuss other dynamical properties of the model as the rate of extinction and conclude with a brief discussion.

  9. Alternative future analysis for assessing the potential impact of climate change on urban landscape dynamics.

    PubMed

    He, Chunyang; Zhao, Yuanyuan; Huang, Qingxu; Zhang, Qiaofeng; Zhang, Da

    2015-11-01

    Assessing the impact of climate change on urban landscape dynamics (ULD) is the foundation for adapting to climate change and maintaining urban landscape sustainability. This paper demonstrates an alternative future analysis by coupling a system dynamics (SD) and a cellular automata (CA) model. The potential impact of different climate change scenarios on ULD from 2009 to 2030 was simulated and evaluated in the Beijing-Tianjin-Tangshan megalopolis cluster area (BTT-MCA). The results suggested that the integrated model, which combines the advantages of the SD and CA model, has the strengths of spatial quantification and flexibility. Meanwhile, the results showed that the influence of climate change would become more severe over time. In 2030, the potential urban area affected by climate change will be 343.60-1260.66 km(2) (5.55 -20.37 % of the total urban area, projected by the no-climate-change-effect scenario). Therefore, the effects of climate change should not be neglected when designing and managing urban landscape.

  10. Badlands: An open-source, flexible and parallel framework to study landscape dynamics

    NASA Astrophysics Data System (ADS)

    Salles, T.; Hardiman, L.

    2016-06-01

    In this paper, we propose a minimal numerical model which governing equations describe the following processes: erosion, sedimentation, diffusion and flexure. The model respects conservation laws for water and sediment. The implementation is based on a finite volume approach and the explicit solution stability is ensured by a CFL-like condition. This common core of accepted physical principles governing landscape evolution is ported into a distributed memory parallel environment. Badlands (acronym for BAsin anD LANdscape DynamicS) is an open-source, flexible, TIN-based landscape evolution model, built to simulate landform development and test source-to-sink concepts at regional to continental scale over thousands to millions of years. To illustrate the model capabilities, we first present an example of delta evolution under sea-level fluctuations. The model predicts the successive progradation and transgression phases, the development of depositional and erosional patterns as well as the associated stratigraphic formation. Then, we investigate the importance of climate, and in particular the spatial pattern of precipitation, on the topographic evolution of mountain belts. The simulation and associated quantitative analyses suggest that the main drainage divide migrates and asymmetric topography develops in response to orographic precipitation. This mechanism, documented in recent analogue and numerical experiments, results in a complex reorganisation of drainage networks that our model is able to reproduce.

  11. Encounter success of free-ranging marine predator movements across a dynamic prey landscape

    PubMed Central

    Sims, David W; Witt, Matthew J; Richardson, Anthony J; Southall, Emily J; Metcalfe, Julian D

    2006-01-01

    Movements of wide-ranging top predators can now be studied effectively using satellite and archival telemetry. However, the motivations underlying movements remain difficult to determine because trajectories are seldom related to key biological gradients, such as changing prey distributions. Here, we use a dynamic prey landscape of zooplankton biomass in the north-east Atlantic Ocean to examine active habitat selection in the plankton-feeding basking shark Cetorhinus maximus. The relative success of shark searches across this landscape was examined by comparing prey biomass encountered by sharks with encounters by random-walk simulations of ‘model’ sharks. Movements of transmitter-tagged sharks monitored for 964 days (16 754 km estimated minimum distance) were concentrated on the European continental shelf in areas characterized by high seasonal productivity and complex prey distributions. We show movements by adult and sub-adult sharks yielded consistently higher prey encounter rates than 90% of random-walk simulations. Behavioural patterns were consistent with basking sharks using search tactics structured across multiple scales to exploit the richest prey areas available in preferred habitats. Simple behavioural rules based on learned responses to previously encountered prey distributions may explain the high performances. This study highlights how dynamic prey landscapes enable active habitat selection in large predators to be investigated from a trophic perspective, an approach that may inform conservation by identifying critical habitat of vulnerable species. PMID:16720391

  12. Soil profile dynamics in an eroding soil landscape - a catena through a kettle hole

    NASA Astrophysics Data System (ADS)

    Gerke, Horst H.; Kaczorek, Danuta; Hierold, Wilfried; Deumlich, Detlef; Koszinski, Sylvia; Ellerbrock, Ruth H.; Sommer, Michael

    2015-04-01

    The arable hummocky ground moraine soil landscapes are characterized by a spatial continuum of more or less eroded soils at hilltops and slopes, and by colluviated soils in topographic depressions. After removal of forest in the middle ages, colluvium started covering the pre-existing Histosols and Gleysols within and Luvisols in the vicinity of kettle holes. A catena through originally peat-filled kettle-hole has hardly been described with respect to ongoing pedological modifications according to changes in landscape and hydrology. The objective was to derive the lateral continuum of soil horizons by identifying the location of the lateral boundaries between regions of clay mobilization/migration and gleisation (gleyic conditions), peat accumulation, and secondary carbonate accumulation. Data from an intensively-sampled field in northeastern Germany are presented. The start of colluviation could be dated by tree ring analyses of a buried stem. The location of the fossil topsoil A and peat horizons was determined from a dense grid of auger holes and geophysical explorations. In addition to older processes in the landscape, also younger redoximorphic processes were indicating changes in soil hydraulic properties and a modified hydrology of the arable soil landscape. We found in micromorphological analyses of soil thin sections that clay migration is an ongoing process; samples indicated vertical gradients in C-contents and secondary carbonate accumulation. The clay mobilization in the colluvium and the migration into the fossil horizons seemed to depend on the direction of soil water movement; anisotropic hydraulic conductivity indicated a potential for lateral water movement. The catena data suggest that the soil landscape development was relatively dynamic; the results may allow the reconstruction of former land surfaces, soil distributions, and erosion rates and may help predicting future developments.

  13. Visualization of topological landscape in shear-flow dynamics of amorphous solids

    NASA Astrophysics Data System (ADS)

    Fujita, Takeshi; Ohara, Koji; Miura, Keiji; Hirata, Akihiko; Kotani, Motoko; Nishiura, Yasumasa; Chen, Mingwei

    2015-05-01

    A potential energy landscape (PEL) gives rise to diverse non-equilibrium dynamics in complex systems. In this study, we visualize the topological landscape of a steady-state flow under shear deformation in a model metallic glass. We use the “state space network” as the best predictor of state transitions in terms of statistical model selection. The proposed scheme visualizes the underlying PEL regarding α transitions associated with irreversible cage-breaking events as the cooperative motion of clusters. By characterizing the topological property of the state space network, we observe characteristics of a small-world network. The proposed scheme has a significant potential to enable the understanding of the underlying mechanisms of glass physics, and is analogous to biological networks.

  14. Shallow groundwater dynamics across complex terrain: Influences of landscape position and climate

    NASA Astrophysics Data System (ADS)

    Jencso, K. G.; McGlynn, B. L.

    2014-12-01

    Prediction of hillslope and riparian water table dynamics across headwater catchments remains challenging. We suggest that this is partially due to the lack of spatially distributed, high frequency, long duration observations of shallow subsurface flows that connect hillsopes to riparian and stream landscape positions. Further, these observations are rarely considered in the context of both local and watershed scale structure and organization. Here, we provide a synthesis of shallow subsurface hydrologic connectivity duration and magnitude across 9 years of hourly stage recordings for 30 transects of shallow groundwater wells (hillslope size from 0.07 to 4.6 ha) in the Tenderfoot Creek Experimental Forest, MT. Key results include: 1) the annual average water table depth across all hillsope wells was exponentially related (r2 = 0.94) to upslope accumulated area (UAA). 2) K means analysis of the annual hilllsope water table stage duration curves indicated a transition across the continuum of wells from short duration hydrologic connectivity and low stage (UAA = 0.07 - 1ha, n= 90), sustained snowmelt hydrologic connectivity and moderate stage (UAA = 1.2 - 3ha, n = 20), and continuous hydrologic connectivity and highest stage (UAA = 3.1 - 4.6ha, n=11). 3) hillslopes with the largest UAA (n= 11; continuous connectivity and sustained groundwater stage) exhibited groundwater dynamics similar to those in riparian wells. The synthesis of the well water stage responses across space and time suggests strong emergent behavior according to landscape position and topography. These preliminary analyses provide insight into watershed behavior that is requisite for understanding where streamflow originates in the landscape, appropriate model structures for predicting streamflow, predicting landscape position sensitivity to climate variability, and informing land management decisions.

  15. Evaluating complementary networks of restoration plantings for landscape-scale occurrence of temporally dynamic species.

    PubMed

    Ikin, Karen; Tulloch, Ayesha; Gibbons, Philip; Ansell, Dean; Seddon, Julian; Lindenmayer, David

    2016-10-01

    Multibillion dollar investments in land restoration make it critical that conservation goals are achieved cost-effectively. Approaches developed for systematic conservation planning offer opportunities to evaluate landscape-scale, temporally dynamic biodiversity outcomes from restoration and improve on traditional approaches that focus on the most species-rich plantings. We investigated whether it is possible to apply a complementarity-based approach to evaluate the extent to which an existing network of restoration plantings meets representation targets. Using a case study of woodland birds of conservation concern in southeastern Australia, we compared complementarity-based selections of plantings based on temporally dynamic species occurrences with selections based on static species occurrences and selections based on ranking plantings by species richness. The dynamic complementarity approach, which incorporated species occurrences over 5 years, resulted in higher species occurrences and proportion of targets met compared with the static complementarity approach, in which species occurrences were taken at a single point in time. For equivalent cost, the dynamic complementarity approach also always resulted in higher average minimum percent occurrence of species maintained through time and a higher proportion of the bird community meeting representation targets compared with the species-richness approach. Plantings selected under the complementarity approaches represented the full range of planting attributes, whereas those selected under the species-richness approach were larger in size. Our results suggest that future restoration policy should not attempt to achieve all conservation goals within individual plantings, but should instead capitalize on restoration opportunities as they arise to achieve collective value of multiple plantings across the landscape. Networks of restoration plantings with complementary attributes of age, size, vegetation structure, and

  16. Ecosystem Function in Amazon Floodplain Wetlands: Climate Variability, Landscape Dynamics and Carbon Biogeochemistry.

    NASA Astrophysics Data System (ADS)

    Silva, T. S. F.; Melack, J. M.; Sousa, R. N. D.; Ferreira-Ferreira, J.; Streher, A. S.; Fragal, E. H.; Furtado, L. F.; Resende, A. F. D.; Luize, B. G.; Rudorff, C.; Queiroz, H. L.; Schongart, J.; Novo, E. M.

    2015-12-01

    Wetlands comprise 14% of the Amazon basin, and are a major component of the hydrological and biogeochemical cycles. Most of these areas correspond to floodplain ecosystems along the Amazon River and its major tributaries, hosting unique vegetation types that are strongly controlled by annual hydrological fluctuations. The combination of strong environmental filtering and active fluvial dynamics results in a highly heterogeneous landscape, and in physiological linkages between climate variability and ecosystem processes. We will show several years of results obtained within the framework of the LBA program, discussing the interplay between hydroclimatic variability, landscape dynamics, ecosystem functioning and carbon biogeochemistry in the Amazon floodplains. Using optical and microwave remote sensing, we assessed the distribution of major vegetation types and flooding regimes at several locations across the floodplain. Strong variability in vegetation distribution can be observed, with high and low várzea forests ranging from 30% and 34%, respectively, at the upper Solimões River, to 6% and 25% at the lower Solimões, while non-forested habitats and lakes increase from a percent cover of 8% and 10% to 28% and 27%, respectively. Strong variability in local flood regimes was also determined for each vegetation type, revealing a gradient of habitats within each floodplain. As tree growth, diversity and phenology are affected by flood duration, we expect local conditions to strongly impact carbon stocks and cycling at the landscape scale. Fluvial processes also disturb forest patches, ensuring a mixture of age distributions in the landscape, with varying species composition, carbon stocks, and carbon uptake rates. Herbaceous vegetation growth responds very rapidly to changes in hydrological conditions, and modeling based on microwave imagery and in situ observations showed expected changes of up to 50% in annual net primary production between regular and extreme

  17. Tropical forest landscape dynamics: Population consequences for neotropical lianas, genus Passiflora

    NASA Astrophysics Data System (ADS)

    Plowes, Robert Merrick

    Treefall gaps in rainforest landscapes play a crucial role in providing opportunities for establishment and growth of rare, light-demanding plants such as Passifora vines in Corcovado rainforests, Costa Rica. This study considers the interplay of landscape dynamics with plant life history traits and strategies in an ephemeral patch network. In Chapter One, I show how patch quality dynamics and propagule dispersal affect colonization of treefall gaps by Passifora vitifolia. Recruitment required high patch quality, exceeding 3 hours of sunlight and patches closed after about 6 years. Colonization by seed dispersal (80%) was constrained by patch quality and isolation, while clonal growth from dormant plants (20%) was limited to rare adjacent patches. Since patch turnover is critical in these systems, Chapter Two is focused on factors affecting canopy structure. I showed that prior landuse altered the dynamics of frequent, small-scale disturbances during succession following a single, large deforestation event. Here, I used Landsat subpixel analysis, aerial photographs and field surveys to demonstrate major changes in dynamics of regenerating canopies following release from agricultural activity in 1975. Little work has considered the role of life history traits in persistence of patchy populations, and so in Chapter Three I asked what life history strategies are used by 9 Passiflora species that occur in these transient forest gaps. Although Passiflora species exhibited differences in dormancy or dispersal strategies, abundance was not associated with any one strategy. Elasticities of vital rates (stasis, growth and fecundity) of P. vitifolia differed empirically in old growth and regenerating forests. To explore population responses to changes in landscape parameters or life history strategies, I created a spatially-explicit individual-based model. Simulations indicate that plant types with a dormancy phase have a greater suite of responses since they persist after

  18. Linking land cover dynamics with driving forces in mountain landscape of the Northwestern Iberian Peninsula

    NASA Astrophysics Data System (ADS)

    Regos, Adrián; Ninyerola, Miquel; Moré, Gerard; Pons, Xavier

    2015-06-01

    The mountainous areas of the northwestern Iberian Peninsula have undergone intense land abandonment. In this work, we wanted to determine if the abandonment of the rural areas was the main driver of landscape dynamics in Gerês-Xurés Transboundary Biosphere Reserve (NW Iberian Peninsula), or if other factors, such as wildfires and the land management were also directly affecting these spatio-temporal dynamics. For this purpose, we used earth observation data acquired from Landsat TM and ETM + satellite sensors, complemented by ancillary data and prior field knowledge, to evaluate the land use/land cover changes in our study region over a 10-year period (2000-2010). The images were radiometrically calibrated using a digital elevation model to avoid cast- and self-shadows and different illumination effects caused by the intense topographic variations in the study area. We applied a maximum likelihood classifier, as well as other five approaches that provided insights into the comparison of thematic maps. To describe the land cover changes we addressed the analysis from a multilevel approach in three areas with different regimes of environmental protection. The possible impact of wildfires was assessed from statistical and spatially explicit fire data. Our findings suggest that land abandonment and forestry activities are the main factors causing the changes in landscape patterns. Specifically, we found a strong decrease of the 'meadows and crops' and 'sparse vegetation areas' in favor of woodlands and scrublands. In addition, the huge impact of wildfires on the Portuguese side have generated new 'rocky areas', while on the Spanish side its impact does not seem to have been a decisive factor on the landscape dynamics in recent years. We conclude rural exodus of the last century, differences in land management and fire suppression policies between the two countries and the different protection schemes could partly explain the different patterns of changes recorded in

  19. Temporal dynamics influenced by global change: bee community phenology in urban, agricultural, and natural landscapes.

    PubMed

    Leong, Misha; Ponisio, Lauren C; Kremen, Claire; Thorp, Robbin W; Roderick, George K

    2016-03-01

    Urbanization and agricultural intensification of landscapes are important drivers of global change, which in turn have direct impacts on local ecological communities leading to shifts in species distributions and interactions. Here, we illustrate how human-altered landscapes, with novel ornamental and crop plant communities, result not only in changes to local community diversity of floral-dependent species, but also in shifts in seasonal abundance of bee pollinators. Three years of data on the spatio-temporal distributions of 91 bee species show that seasonal patterns of abundance and species richness in human-altered landscapes varied significantly less compared to natural habitats in which floral resources are relatively scarce in the dry summer months. These findings demonstrate that anthropogenic environmental changes in urban and agricultural systems, here mediated through changes in plant resources and water inputs, can alter the temporal dynamics of pollinators that depend on them. Changes in phenology of interactions can be an important, though frequently overlooked, mechanism of global change.

  20. Pervasive canopy dynamics produce short-term stability in a tropical rain forest landscape.

    PubMed

    Kellner, James R; Clark, David B; Hubbell, Stephen P

    2009-02-01

    A fundamental property of all forest landscapes is the size frequency distribution of canopy gap disturbances. But characterizing forest structure and changes at large spatial scales has been challenging and most of our understanding is from permanent inventory plots. Here we report the first application of light detection and ranging remote sensing to measurements of canopy disturbance and regeneration in an old-growth tropical rain forest landscape. Pervasive local height changes figure prominently in the dynamics of this forest. Although most canopy gaps recruited to higher positions during 8.5 years, size frequency distributions were similar at two points in time and well-predicted by power-laws. At larger spatial scales (hundreds of ha), height increases and decreases occurred with similar frequency and changes to canopy height that were analysed using a height transition matrix suggest that the distribution of canopy height at the beginning of the study was close to the projected steady-state equilibrium under the recent disturbance regime. Taken together, these findings show how widespread local height changes can produce short-term stability in a tropical rain forest landscape.

  1. The emergence of topographic steady state in a perpetually dynamic self-organized critical landscape

    NASA Astrophysics Data System (ADS)

    Reinhardt, Liam; Ellis, Michael A.

    2015-07-01

    We conducted a series of four physical modeling experiments of mountain growth at differing rates of uplift and three distinct climates ranging from relatively wet to relatively dry. The spatial and temporal pattern of landscape behavior is characterized by ˜f-1 scaling in sediment discharge and power law scaling in the magnitude and frequency of ridge movement in all four experiments. We find that internally generated self-organized critical (SOC) processes generate dynamically stable catchment geometries after ˜1 relief depths of erosion: these regularly spaced catchments have an average outlet-spacing ratio of 2.16, well within the range of values reported in field studies. Once formed, large catchment bounding ridges oscillate about a critically balanced mean location, with occasional large-scale changes in catchment size. Ridge movement appears to be driven by the competition for discharge as landslides push ridges back and forth. These dynamics lead to the emergence of a complex twofold scaling in catchment dynamics that is fully established by 1.8 relief depths of erosion; at this stage, a clear threshold has emerged separating two distinct scaling regimes, where large ridge mobility is insensitive to relief and small ridge mobility is relief dependent. Overall, we demonstrate that the development of dynamically stable large-scale landforms is related to the emergence of a complex-system hierarchy in topographic dynamics. Once formed, these landscapes do not evolve; statistical properties such as average topography and discharge become stationary while topography remains highly dynamic at smaller length scales.

  2. An extended patch-dynamic framework for food chains in fragmented landscapes.

    PubMed

    Liao, Jinbao; Chen, Jiehong; Ying, Zhixia; Hiebeler, David E; Nijs, Ivan

    2016-09-09

    Habitat destruction, a key determinant of species loss, can be characterized by two components, patch loss and patch fragmentation, where the former refers to the reduction in patch availability, and the latter to the division of the remaining patches. Classical metacommunity models have recently explored how food web dynamics respond to patch loss, but the effects of patch fragmentation have largely been overlooked. Here we develop an extended patch-dynamic model that tracks the patch occupancy of the various trophic links subject to colonization-extinction-predation dynamics by incorporating species dispersal with patch connectivity. We found that, in a simple food chain, species at higher trophic level become extinct sooner with increasing patch loss and fragmentation due to the constraint in resource availability, confirming the trophic rank hypothesis. Yet, effects of fragmentation on species occupancy are largely determined by patch loss, with maximal fragmentation effects occurring at intermediate patch loss. Compared to the spatially explicit simulations that we also performed, the current model with pair approximation generates similar community patterns especially in spatially clustered landscapes. Overall, our extended framework can be applied to model more complex food webs in fragmented landscapes, broadening the scope of existing metacommunity theory.

  3. An extended patch-dynamic framework for food chains in fragmented landscapes

    PubMed Central

    Liao, Jinbao; Chen, Jiehong; Ying, Zhixia; Hiebeler, David E.; Nijs, Ivan

    2016-01-01

    Habitat destruction, a key determinant of species loss, can be characterized by two components, patch loss and patch fragmentation, where the former refers to the reduction in patch availability, and the latter to the division of the remaining patches. Classical metacommunity models have recently explored how food web dynamics respond to patch loss, but the effects of patch fragmentation have largely been overlooked. Here we develop an extended patch-dynamic model that tracks the patch occupancy of the various trophic links subject to colonization-extinction-predation dynamics by incorporating species dispersal with patch connectivity. We found that, in a simple food chain, species at higher trophic level become extinct sooner with increasing patch loss and fragmentation due to the constraint in resource availability, confirming the trophic rank hypothesis. Yet, effects of fragmentation on species occupancy are largely determined by patch loss, with maximal fragmentation effects occurring at intermediate patch loss. Compared to the spatially explicit simulations that we also performed, the current model with pair approximation generates similar community patterns especially in spatially clustered landscapes. Overall, our extended framework can be applied to model more complex food webs in fragmented landscapes, broadening the scope of existing metacommunity theory. PMID:27608823

  4. How interactions between animal movement and landscape processes modify local range dynamics and extinction risk

    PubMed Central

    Fordham, Damien A.; Shoemaker, Kevin T.; Schumaker, Nathan H.; Akçakaya, H. Reşit; Clisby, Nathan; Brook, Barry W.

    2014-01-01

    Forecasts of range dynamics now incorporate many of the mechanisms and interactions that drive species distributions. However, connectivity continues to be simulated using overly simple distance-based dispersal models with little consideration of how the individual behaviour of dispersing organisms interacts with landscape structure (functional connectivity). Here, we link an individual-based model to a niche-population model to test the implications of this omission. We apply this novel approach to a turtle species inhabiting wetlands which are patchily distributed across a tropical savannah, and whose persistence is threatened by two important synergistic drivers of global change: predation by invasive species and overexploitation. We show that projections of local range dynamics in this study system change substantially when functional connectivity is modelled explicitly. Accounting for functional connectivity in model simulations causes the estimate of extinction risk to increase, and predictions of range contraction to slow. We conclude that models of range dynamics that simulate functional connectivity can reduce an important source of bias in predictions of shifts in species distributions and abundances, especially for organisms whose dispersal behaviours are strongly affected by landscape structure. PMID:24806426

  5. How interactions between animal movement and landscape processes modify local range dynamics and extinction risk.

    PubMed

    Fordham, Damien A; Shoemaker, Kevin T; Schumaker, Nathan H; Akçakaya, H Reşit; Clisby, Nathan; Brook, Barry W

    2014-05-01

    Forecasts of range dynamics now incorporate many of the mechanisms and interactions that drive species distributions. However, connectivity continues to be simulated using overly simple distance-based dispersal models with little consideration of how the individual behaviour of dispersing organisms interacts with landscape structure (functional connectivity). Here, we link an individual-based model to a niche-population model to test the implications of this omission. We apply this novel approach to a turtle species inhabiting wetlands which are patchily distributed across a tropical savannah, and whose persistence is threatened by two important synergistic drivers of global change: predation by invasive species and overexploitation. We show that projections of local range dynamics in this study system change substantially when functional connectivity is modelled explicitly. Accounting for functional connectivity in model simulations causes the estimate of extinction risk to increase, and predictions of range contraction to slow. We conclude that models of range dynamics that simulate functional connectivity can reduce an important source of bias in predictions of shifts in species distributions and abundances, especially for organisms whose dispersal behaviours are strongly affected by landscape structure. PMID:24806426

  6. An extended patch-dynamic framework for food chains in fragmented landscapes.

    PubMed

    Liao, Jinbao; Chen, Jiehong; Ying, Zhixia; Hiebeler, David E; Nijs, Ivan

    2016-01-01

    Habitat destruction, a key determinant of species loss, can be characterized by two components, patch loss and patch fragmentation, where the former refers to the reduction in patch availability, and the latter to the division of the remaining patches. Classical metacommunity models have recently explored how food web dynamics respond to patch loss, but the effects of patch fragmentation have largely been overlooked. Here we develop an extended patch-dynamic model that tracks the patch occupancy of the various trophic links subject to colonization-extinction-predation dynamics by incorporating species dispersal with patch connectivity. We found that, in a simple food chain, species at higher trophic level become extinct sooner with increasing patch loss and fragmentation due to the constraint in resource availability, confirming the trophic rank hypothesis. Yet, effects of fragmentation on species occupancy are largely determined by patch loss, with maximal fragmentation effects occurring at intermediate patch loss. Compared to the spatially explicit simulations that we also performed, the current model with pair approximation generates similar community patterns especially in spatially clustered landscapes. Overall, our extended framework can be applied to model more complex food webs in fragmented landscapes, broadening the scope of existing metacommunity theory. PMID:27608823

  7. Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape

    SciTech Connect

    Wales, D. J.

    2015-04-07

    This perspective focuses on conceptual and computational aspects of the potential energy landscape framework. It has two objectives: first to summarise some key developments of the approach and second to illustrate how such techniques can be applied using a specific example that exploits knowledge of pathways. Recent developments in theory and simulation within the landscape framework are first outlined, including methods for structure prediction, analysis of global thermodynamic properties, and treatment of rare event dynamics. We then develop a connection between the kinetic transition network treatment of dynamics and a potential of mean force defined by a reaction coordinate. The effect of projection from the full configuration space to low dimensionality is illustrated for an atomic cluster. In this example, where a relatively successful structural order parameter is available, the principal change in cluster morphology is reproduced, but some details are not faithfully represented. In contrast, a profile based on configurations that correspond to the discrete path defined geometrically retains all the barriers and minima. This comparison provides insight into the physical origins of “friction” effects in low-dimensionality descriptions of dynamics based upon a reaction coordinate.

  8. Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape

    NASA Astrophysics Data System (ADS)

    Wales, D. J.

    2015-04-01

    This perspective focuses on conceptual and computational aspects of the potential energy landscape framework. It has two objectives: first to summarise some key developments of the approach and second to illustrate how such techniques can be applied using a specific example that exploits knowledge of pathways. Recent developments in theory and simulation within the landscape framework are first outlined, including methods for structure prediction, analysis of global thermodynamic properties, and treatment of rare event dynamics. We then develop a connection between the kinetic transition network treatment of dynamics and a potential of mean force defined by a reaction coordinate. The effect of projection from the full configuration space to low dimensionality is illustrated for an atomic cluster. In this example, where a relatively successful structural order parameter is available, the principal change in cluster morphology is reproduced, but some details are not faithfully represented. In contrast, a profile based on configurations that correspond to the discrete path defined geometrically retains all the barriers and minima. This comparison provides insight into the physical origins of "friction" effects in low-dimensionality descriptions of dynamics based upon a reaction coordinate.

  9. Numerical Uncertainty Analysis for Computational Fluid Dynamics using Student T Distribution -- Application of CFD Uncertainty Analysis Compared to Exact Analytical Solution

    NASA Technical Reports Server (NTRS)

    Groves, Curtis E.; Ilie, marcel; Shallhorn, Paul A.

    2014-01-01

    Computational Fluid Dynamics (CFD) is the standard numerical tool used by Fluid Dynamists to estimate solutions to many problems in academia, government, and industry. CFD is known to have errors and uncertainties and there is no universally adopted method to estimate such quantities. This paper describes an approach to estimate CFD uncertainties strictly numerically using inputs and the Student-T distribution. The approach is compared to an exact analytical solution of fully developed, laminar flow between infinite, stationary plates. It is shown that treating all CFD input parameters as oscillatory uncertainty terms coupled with the Student-T distribution can encompass the exact solution.

  10. How Adequate are One- and Two-Dimensional Free Energy Landscapes for Protein Folding Dynamics?

    PubMed Central

    Maisuradze, Gia G.; Liwo, Adam; Scheraga, Harold A.

    2009-01-01

    The molecular dynamics trajectories of protein folding or unfolding, generated with the coarse-grained united-residue force field for the B domain of staphylococcal protein A, were analyzed by principal component analysis (PCA). The folding or unfolding process was examined by using free-energy landscapes (FELs) in PC space. By introducing a novel multidimensional FEL, it was shown that the low-dimensional FELs are not always sufficient for the description of folding or unfolding processes. Similarities between the topographies of FELs along low- and high-indexed principal components were observed. PMID:19658975

  11. Investigating protein conformational energy landscapes and atomic resolution dynamics from NMR dipolar couplings: a review.

    PubMed

    Salmon, Loïc; Blackledge, Martin

    2015-12-01

    Nuclear magnetic resonance spectroscopy is exquisitely sensitive to protein dynamics. In particular inter-nuclear dipolar couplings, that become measurable in solution when the protein is dissolved in a dilute liquid crystalline solution, report on all conformations sampled up to millisecond timescales. As such they provide the opportunity to describe the Boltzmann distribution present in solution at atomic resolution, and thereby to map the conformational energy landscape in unprecedented detail. The development of analytical methods and approaches based on numerical simulation and their application to numerous biologically important systems is presented. PMID:26517337

  12. Dynamic Landscapes and Sea Level Change in Human Evolution and Dispersal

    NASA Astrophysics Data System (ADS)

    King, G. C.; Devès, M. H.; Bailey, G.; Inglis, R.; Williams, M.

    2012-12-01

    Archaeological studies of human settlement in its wider landscape setting usually focus on climate change as the principal environmental driver of change in the physical features of the landscape, even on the long time scales of early human evolution. We emphasize that landscapes evolve dynamically due to an interplay of processes occurring over different timescales. Tectonic deformation, volcanism, sea level changes, by acting on the topography, the lithology and on the patterns of erosion-deposition in a given area, can moderate or amplify the influence of climate at the regional and local scale. These processes impose or alleviate physical barriers to movement, and modify the distribution and accessibility of plant and animal resources in ways critical to human ecological and evolutionary success (King and Bailey, JHE 2006; Bailey and King, Antiquity 2011). The DISPERSE project, an ERC-funded collaboration between the University of York and the Institut de Physique du Globe de Paris,are developing systematic methods for reconstructing landscapes associated with active tectonics, volcanism and sea level change at a variety of scales in order to study their potential impact on patterns of human evolution and dispersal. These approaches use remote sensing techniques combined with archaeological and tectonic field surveys on land and underwater. Examples are shown from Europe, the Middle East and Africa to illustrate the ways in which changes of significance to human settlement can occur at a range of geographical scales and on time scales that range from lifetimes to tens of millennia, creating and sustaining attractive conditions for human settlement and exercising powerful selective pressures on human development.

  13. Impact of forestry practices at a landscape scale on the dynamics of amphibian populations.

    PubMed

    Harper, Elizabeth B; Patrick, David A; Gibbs, James P

    2015-12-01

    Forest loss is a primary cause of worldwide amphibian decline. Timber harvesting in the United States has caused dramatic changes in quality and extent of forest ecosystems, and intensive forest management still occurs. Although numerous studies have documented substantial reductions in amphibian densities related to timber harvest, subsequent extinctions are rare. To better understand the population dynamics that have allowed so many amphibian species to persist in the face of widespread forest disturbance, we developed spatially explicit metapopulation models for four forest-dependent amphibian species (Lithobates sylvaticus, Ambystoma opacum, A. talpoideum, and A. maculatum) that incorporated demographic and habitat selection data derived from experiments conducted as part of the Land Use Effects on Amphibian Populations Project (LEAP). We projected local and landscape-scale population persistence under 108 different forestry practice scenarios, varying treatment (partial cut, clear-cut with coarse woody debris [CWD] removed, and clearcut with CWD retained), cut patch size (1, 10, or 50 ha), total area cut (10, 20, or 30%), and initial amphibian population size (5, 50, or 500 adult females per local breeding population). Under these scenarios, landscape-scale extinction was highly unlikely, occurring in < 1% of model runs and for only 2 of the 4 species, because landscape-scale populations were able to persist via dispersal even despite frequent local extinctions. Yet for all species, population sizes were reduced to -50% in all clear-cut scenarios, regardless of the size of harvested patches. These findings suggest that debate over timber harvesting on pool-breeding amphibian populations in the United States should focus not on questions of landscape-scale extinction but on the ecological consequences of dramatic reductions in amphibian biomass, including changes in trophic interactions, nutrient cycling, and energy transfer. Additionally, we conclude that

  14. Nutrient uptake dynamics across a gradient of nutrient concentrations and ratios at the landscape scale

    NASA Astrophysics Data System (ADS)

    Gibson, Catherine A.; O'Reilly, Catherine M.; Conine, Andrea L.; Lipshutz, Sondra M.

    2015-02-01

    Understanding interactions between nutrient cycles is essential for recognizing and remediating human impacts on water quality, yet multielemental approaches to studying nutrient cycling in streams are currently rare. Here we utilized a relatively new approach (tracer additions for spiraling curve characterization) to examine uptake dynamics for three essential nutrients across a landscape that varied in absolute and relative nutrient availability. We measured nutrient uptake for soluble reactive phosphorous, ammonium-nitrogen, and nitrate-nitrogen in 16 headwater streams in the Catskill Mountains, New York. Across the landscape, ammonium-nitrogen and soluble reactive phosphorus had shorter uptake lengths and higher uptake velocities than nitrate-nitrogen. Ammonium-nitrogen and soluble reactive phosphorus uptake velocities were tightly correlated, and the slope of the relationship did not differ from one, suggesting strong demand for both nutrients despite the high ambient water column dissolved inorganic nitrogen: soluble reactive phosphorus ratios. Ammonium-nitrogen appeared to be the preferred form of nitrogen despite much higher nitrate-nitrogen concentrations. The uptake rate of nitrate-nitrogen was positively correlated with ambient soluble reactive phosphorus concentration and soluble reactive phosphorus areal uptake rate, suggesting that higher soluble reactive phosphorus concentrations alleviate phosphorus limitation and facilitate nitrate-nitrogen uptake. In addition, these streams retained a large proportion of soluble reactive phosphorus, ammonium-nitrogen, and nitrate-nitrogen supplied by the watershed, demonstrating that these streams are important landscape filters for nutrients. Together, these results (1) indicated phosphorus limitation across the landscape but similarly high demand for ammonium-nitrogen and (2) suggested that nitrate-nitrogen uptake was influenced by variability in soluble reactive phosphorus availability and preference for

  15. Impact of forestry practices at a landscape scale on the dynamics of amphibian populations.

    PubMed

    Harper, Elizabeth B; Patrick, David A; Gibbs, James P

    2015-12-01

    Forest loss is a primary cause of worldwide amphibian decline. Timber harvesting in the United States has caused dramatic changes in quality and extent of forest ecosystems, and intensive forest management still occurs. Although numerous studies have documented substantial reductions in amphibian densities related to timber harvest, subsequent extinctions are rare. To better understand the population dynamics that have allowed so many amphibian species to persist in the face of widespread forest disturbance, we developed spatially explicit metapopulation models for four forest-dependent amphibian species (Lithobates sylvaticus, Ambystoma opacum, A. talpoideum, and A. maculatum) that incorporated demographic and habitat selection data derived from experiments conducted as part of the Land Use Effects on Amphibian Populations Project (LEAP). We projected local and landscape-scale population persistence under 108 different forestry practice scenarios, varying treatment (partial cut, clear-cut with coarse woody debris [CWD] removed, and clearcut with CWD retained), cut patch size (1, 10, or 50 ha), total area cut (10, 20, or 30%), and initial amphibian population size (5, 50, or 500 adult females per local breeding population). Under these scenarios, landscape-scale extinction was highly unlikely, occurring in < 1% of model runs and for only 2 of the 4 species, because landscape-scale populations were able to persist via dispersal even despite frequent local extinctions. Yet for all species, population sizes were reduced to -50% in all clear-cut scenarios, regardless of the size of harvested patches. These findings suggest that debate over timber harvesting on pool-breeding amphibian populations in the United States should focus not on questions of landscape-scale extinction but on the ecological consequences of dramatic reductions in amphibian biomass, including changes in trophic interactions, nutrient cycling, and energy transfer. Additionally, we conclude that

  16. Holocene landscape dynamics of the Ghaggar-Hakra floodplain, India: implications for the Indus Civilisation

    NASA Astrophysics Data System (ADS)

    Durcan, Julie; Thomas, David; Pawar, Vikas; Gupta, Sanjeev; Petrie, Cameron; Singh, Ravindra

    2016-04-01

    The area around the ephemeral Ghaggar-Hakra River system in India and Pakistan is associated with a dense concentration of Indus Civilisation archaeological sites. Giosan et al. (2012) have suggested that a decline, and ultimately cessation, of flow in this river system in response to the weakening of the Asian Monsoon was influential in the collapse of the Indus Civilisation around 4,000 years ago and palaeoclimatic studies in the region (e.g. Berkelhammer et al., 2012; Dixit et al., 2014; Leipe et al., 2014) have shown abrupt drying events during the mid-Holocene, which are superimposed onto a longer-term insolation driven decline in Asian Monsoon intensity. Further work is required to understand the dynamics of this river system during the Holocene and to assess the importance of changing landscape dynamics, as well as climatic variability, in the decline of the Indus Civilisation. This paper presents optically stimulated luminescence (OSL) dates from palaeochannel sediments and associated dune deposits in the Ghaggar-Hakra river system in Northwest India, with the aim of understanding late Quaternary geomorphological and palaeoenvironmental change. Reconstructing palaeoenvironmental variability will allow a comparison between the documented archaeological record of the Indus Civilisation and an absolute chronology of regional landscape dynamism. This comparison will also allow an insight into whether the mid-Holocene collapse and/or transformation of the Indus Civilisation can be correlated with geomorphological and/or climatic variability. Berkelhammer, M., Sinha, A., Stott, L., Cheng, H., Pausata, F.S.R., and Yoshimura, K., 2012, An abrupt shift in the Indian monsoon 4000 years ago, in Giosan, L., Fuller, D.Q., Nicoll, K., Flad, R.K. and Clift P.D. (eds.), Climates, landscapes, and civilizations. American Geophysical Union Geophysical Monograph, 198, 75-87. Dixit, Y., Hodell, D.A. and Petrie, C.A., 2012. Abrupt weakening of the summer monsoon in northwest

  17. Forest dynamics in Oregon landscapes: Evaluation and application of an individual-based model

    USGS Publications Warehouse

    Busing, R.T.; Solomon, A.M.; McKane, R.B.; Burdick, C.A.

    2007-01-01

    The FORCLIM model of forest dynamics was tested against field survey data for its ability to simulate basal area and composition of old forests across broad climatic gradients in western Oregon, USA. The model was also tested for its ability to capture successional trends in ecoregions of the west Cascade Range. It was then applied to simulate present and future (1990-2050) forest landscape dynamics of a watershed in the west Cascades. Various regimes of climate change and harvesting in the watershed were considered in the landscape application. The model was able to capture much of the variation in forest basal area and composition in western Oregon even though temperature and precipitation were the only inputs that were varied among simulated sites. The measured decline in total basal area from tall coastal forests eastward to interior steppe was matched by simulations. Changes in simulated forest dominants also approximated those in the actual data. Simulated abundances of a few minor species did not match actual abundances, however. Subsequent projections of climate change and harvest effects in a west Cascades landscape indicated no change in forest dominance as of 2050. Yet, climate-driven shifts in the distributions of some species were projected. The simulation of both stand-replacing and partial-stand disturbances across western Oregon improved agreement between simulated and actual data. Simulations with fire as an agent of partial disturbance suggested that frequent fires of low severity can alter forest composition and structure as much or more than severe fires at historic frequencies. ?? 2007 by the Ecological Society of America.

  18. Monitored landscape change of Lake Baiyangdian wetland with dynamic reed area based on remote sensing

    NASA Astrophysics Data System (ADS)

    Wang, Zhen; He, Lei; Zhang, Shengwei; Lei, Yuping

    2009-09-01

    Lake Baiyangdian, a largest wetland ecosystem in North China Plain, has dried up on seven occasions since the 1960s. In recent years, more than one billion of cubic meters of water from upstream reservoirs and Yellow river have been transported to the lake to rescue the shrinking wetlands. Since the Lake Baiyangdian was actually composed of 143 small lakes and more than 70 villages with large or small area of cropland, dynamic distribution of aquatic plants in wetland such as reed and associated growth condition of these allowed to monitor the changes of wetland landscape and water quality to support the policy applications of water conveyance and wetland environmental treatment and control. Assisted with ground survey analyses and Landsat TM image, the MODIS 250 m time series Normalized Difference Vegetation Index (NDVI), given its combination of medium spatial and high temporal resolution, were applied to detect the unique rapid growth stage of reed in the spring from adjacent crops such as winter wheat, cotton, and spring maize, of which has a similar phenology in development of leaf area index, and dynamic reed areas were mapped in recent decade. Landscape changes of the wetland were analyzed using maps of reed area and hydrological data.

  19. HIRA orchestrates a dynamic chromatin landscape in senescence and is required for suppression of neoplasia

    PubMed Central

    Cole, John J.; Nelson, David M.; Dikovskaya, Dina; Faller, William J.; Vizioli, Maria Grazia; Hewitt, Rachael N.; Anannya, Orchi; McBryan, Tony; Manoharan, Indrani; van Tuyn, John; Morrice, Nicholas; Pchelintsev, Nikolay A.; Ivanov, Andre; Brock, Claire; Drotar, Mark E.; Nixon, Colin; Clark, William; Sansom, Owen J.; Anderson, Kurt I.; King, Ayala; Blyth, Karen

    2014-01-01

    Cellular senescence is a stable proliferation arrest that suppresses tumorigenesis. Cellular senescence and associated tumor suppression depend on control of chromatin. Histone chaperone HIRA deposits variant histone H3.3 and histone H4 into chromatin in a DNA replication-independent manner. Appropriately for a DNA replication-independent chaperone, HIRA is involved in control of chromatin in nonproliferating senescent cells, although its role is poorly defined. Here, we show that nonproliferating senescent cells express and incorporate histone H3.3 and other canonical core histones into a dynamic chromatin landscape. Expression of canonical histones is linked to alternative mRNA splicing to eliminate signals that confer mRNA instability in nonproliferating cells. Deposition of newly synthesized histones H3.3 and H4 into chromatin of senescent cells depends on HIRA. HIRA and newly deposited H3.3 colocalize at promoters of expressed genes, partially redistributing between proliferating and senescent cells to parallel changes in expression. In senescent cells, but not proliferating cells, promoters of active genes are exceptionally enriched in H4K16ac, and HIRA is required for retention of H4K16ac. HIRA is also required for retention of H4K16ac in vivo and suppression of oncogene-induced neoplasia. These results show that HIRA controls a specialized, dynamic H4K16ac-decorated chromatin landscape in senescent cells and enforces tumor suppression. PMID:25512559

  20. Picosecond fluctuating protein energy landscape mapped by pressure temperature molecular dynamics simulation.

    SciTech Connect

    Meinhold, Lars; Smith, Jeremy C; Kitao, Akio; Zewail, Ahmed H.

    2007-10-01

    Microscopic statistical pressure fluctuations can, in principle, lead to corresponding fluctuations in the shape of a protein energy landscape. To examine this, nanosecond molecular dynamics simulations of lysozyme are performed covering a range of temperatures and pressures. The well known dynamical transition with temperature is found to be pressure-independent, indicating that the effective energy barriers separating conformational substates are not significantly influenced by pressure. In contrast, vibrations within substates stiffen with pressure, due to increased curvature of the local harmonic potential in which the atoms vibrate. The application of pressure is also shown to selectively increase the damping of the anharmonic, low-frequency collective modes in the protein, leaving the more local modes relatively unaffected. The critical damping frequency, i.e., the frequency at which energy is most efficiently dissipated, increases linearly with pressure. The results suggest that an invariant description of protein energy landscapes should be subsumed by a fluctuating picture and that this may have repercussions in, for example, mechanisms of energy dissipation accompanying functional, structural, and chemical relaxation.

  1. Picosecond Fluctuating Protein Energy Landscape Mapped by Pressure-Temperature Molecular Dynamics Simulation

    SciTech Connect

    Meinhold, Lars; Smith, Jeremy C; Kitao, Akio; Zewail, Ahmed H.

    2007-08-01

    Microscopic statistical pressure fluctuations can, in principle, lead to corresponding fluctuations in the shape of a protein energy landscape. To examine this, nanosecond molecular dynamics simulations of lysozyme are performed covering a range of temperatures and pressures. The well known dynamical transition with temperature is found to be pressure-independent, indicating that the effective energy barriers separating conformational substates are not significantly influenced by pressure. In contrast, vibrations within substates stiffen with pressure, due to increased curvature of the local harmonic potential in which the atoms vibrate. The application of pressure is also shown to selectively increase the damping of the anharmonic, low-frequency collective modes in the protein, leaving the more local modes relatively unaffected. The critical damping frequency, i.e., the frequency at which energy is most efficiently dissipated, increases linearly with pressure. The results suggest that an invariant description of protein energy landscapes should be subsumed by a fluctuating picture and that this may have repercussions in, for example, mechanisms of energy dissipation accompanying functional, structural, and chemical relaxation.

  2. The movement ecology and dynamics of plant communities in fragmented landscapes.

    PubMed

    Damschen, Ellen I; Brudvig, Lars A; Haddad, Nick M; Levey, Douglas J; Orrock, John L; Tewksbury, Joshua J

    2008-12-01

    A conceptual model of movement ecology has recently been advanced to explain all movement by considering the interaction of four elements: internal state, motion capacity, navigation capacities, and external factors. We modified this framework to generate predictions for species richness dynamics of fragmented plant communities and tested them in experimental landscapes across a 7-year time series. We found that two external factors, dispersal vectors and habitat features, affected species colonization and recolonization in habitat fragments and their effects varied and depended on motion capacity. Bird-dispersed species richness showed connectivity effects that reached an asymptote over time, but no edge effects, whereas wind-dispersed species richness showed steadily accumulating edge and connectivity effects, with no indication of an asymptote. Unassisted species also showed increasing differences caused by connectivity over time, whereas edges had no effect. Our limited use of proxies for movement ecology (e.g., dispersal mode as a proxy for motion capacity) resulted in moderate predictive power for communities and, in some cases, highlighted the importance of a more complete understanding of movement ecology for predicting how landscape conservation actions affect plant community dynamics.

  3. Landscape dynamics in aspen and western juniper woodlands on the Owyhee Plateau, Idaho

    NASA Astrophysics Data System (ADS)

    Strand, Eva K.

    A century of altered fire regimes has affected the landscape vegetation dynamics in the Intermountain West. Suppression of wildfires has resulted in increases in woody plant cover in these semi-arid ecosystems, which has resulted in land cover changes affecting biogeochemical cycling, landscape composition, and habitat diversity. Recent developments in remote sensing technology, computational power, and a rapid development of analysis techniques have enabled us to quantify such changes at the landscape scale. Wavelet analysis is a powerful image analysis technique that is here applied in a novel fashion to fine scale remote sensing imagery to automatically detect the location and crown diameter of individual western juniper plants (Juniperus occidentalis ssp. occidentalis) expanding into sagebrush (Artemisia spp.) steppe at multiple scales. The produced marked point pattern of historical and current spatial juniper distribution was compared regionally and changes in foliar cover and above ground biomass were estimated across a 330,000 ha area on the Owyhee Plateau, Idaho. The above ground carbon accumulation rate from 1946 to 1998 was estimate to be 3.3 gCm-2yr-1 and 10.0 gCm-2yr -1 employing the wavelet and conventional texture analysis methods, respectively, with an additional 25% rise in belowground carbon accumulation in root stock. This research further demonstrates that estimates of carbon accumulation rates as a result of woody encroachment are highly dependent on the spatial and temporal scales of analysis. Conifer species, western juniper and Douglas-fir (Pseudotsuga menziesii) on the Owyhee Plateau, have further expanded into the biologically important quaking aspen ( Populus tremuloides) habitats resulting in conifer dominance and occasional loss of aspen clones. Classification of remotely sensed imagery combined with spatially explicit modeling of aspen successional stages indicate that, in the absence of management activity, loss of seral aspen stands

  4. Mapping the Dynamics Landscape of Conformational Transitions in Enzyme: The Adenylate Kinase Case

    PubMed Central

    Li, Dechang; Liu, Ming S.; Ji, Baohua

    2015-01-01

    Conformational transition describes the essential dynamics and mechanism of enzymes in pursuing their various functions. The fundamental and practical challenge to researchers is to quantitatively describe the roles of large-scale dynamic transitions for regulating the catalytic processes. In this study, we tackled this challenge by exploring the pathways and free energy landscape of conformational changes in adenylate kinase (AdK), a key ubiquitous enzyme for cellular energy homeostasis. Using explicit long-timescale (up to microseconds) molecular dynamics and bias-exchange metadynamics simulations, we determined at the atomistic level the intermediate conformational states and mapped the transition pathways of AdK in the presence and absence of ligands. There is clearly chronological operation of the functional domains of AdK. Specifically in the ligand-free AdK, there is no significant energy barrier in the free energy landscape separating the open and closed states. Instead there are multiple intermediate conformational states, which facilitate the rapid transitions of AdK. In the ligand-bound AdK, the closed conformation is energetically most favored with a large energy barrier to open it up, and the conformational population prefers to shift to the closed form coupled with transitions. The results suggest a perspective for a hybrid of conformational selection and induced fit operations of ligand binding to AdK. These observations, depicted in the most comprehensive and quantitative way to date, to our knowledge, emphasize the underlying intrinsic dynamics of AdK and reveal the sophisticated conformational transitions of AdK in fulfilling its enzymatic functions. The developed methodology can also apply to other proteins and biomolecular systems. PMID:26244746

  5. Disturbance, life history traits, and dynamics in an old-growth forest landscape of southeastern Europe.

    PubMed

    Nagel, Thomas A; Svoboda, Miroslav; Kobal, Milan

    2014-06-01

    Much of our understanding of natural forest dynamics in the temperate region of Europe is based on observational studies in old-growth remnants that have emphasized small-scale gap dynamics and equilibrium stand structure and composition. Relatively little attention has been given to the role of infrequent disturbance events in forest dynamics. In this study, we analyzed dendroecological data from four stands and three windthrow patches in an old-growth landscape in the Dinaric Mountains of Bosnia and Herzegovina to examine disturbance history, tree life history traits, and compositional dynamics. Over all stands, most decades during the past 340 years experienced less than 10% canopy loss, yet each stand showed evidence of periodic intermediate-severity disturbances that removed > 40% of the canopy, some of which were synchronized over the study area landscape. Analysis of radial growth patterns indicated several life history differences among the dominant canopy trees; beech was markedly older than fir, while growth patterns of dead and dying trees suggested that fir was able to tolerate longer periods of suppressed growth in shade. Maple had the fastest radial growth and accessed the canopy primarily through rapid early growth in canopy gaps, whereas most beech and fir experienced a period of suppressed growth prior to canopy accession. Peaks in disturbance were roughly linked to increased recruitment, but mainly of shade-tolerant beech and fir; less tolerant species (i.e., maple, ash, and elm) recruited successfully on some of the windthown sites where advance regeneration of beech and fir was less abundant. The results challenge the traditional notions of stability in temperate old-growth forests of Europe and highlight the nonequilibrial nature of canopy composition due to unique histories of disturbance and tree life history differences. These findings provide valuable information for developing natural disturbance-based silvicultural systems, as well as

  6. [Dynamic changes of landscape pattern and eco-disturbance degree in Shuangtai estuary wetland of Liaoning Province, China].

    PubMed

    Chen, Ai-lian; Zhu, Bo-qin; Chen, Li-ding; Wu, Yan-hua; Sun, Ran-hao

    2010-05-01

    The main objective of establishing natural reserve is to protect its natural resources from human disturbances and maintain its critical ecological service values. This paper introduced the concept of hemeroby, and by using remote sensing technology, systematically assessed the dynamic changes of landscape pattern and eco-disturbance degree in Shuangtai estuary wetland of Liaoning Province, China. Firstly, a knowledge-based expert system was used to classify the landscape into three first-level types based on eco-disturbance degree, i.e., undisturbed, partially disturbed, or completely disturbed, which were further classified into 30 second-level categories. Secondly, questionnaire and experts knowledge were adopted to determine the hemeroby index for each landscape type and to formulate a landscape classification system. Finally, the landscape classification maps and hemeroby indices were derived by using the Landsat Thematic Mapper (TM)/Enhanced Thematic Mapper Plus (ETM+) data acquired on 30 April 1987, 7 June 1995, 12 June 2000, and 11 October 2006. The results indicated that from 1987 to 2006, the landscape patches in the study area became more fragmented, being most obvious for reed marsh. Undisturbed landscape type decreased in area, while partially and completely disturbed types were in adverse. The overall characteristics of the spatial distribution of hemeroby index were of most variable in the areas along the river and surrounding the estuary and being the highest in the areas surrounding the city, largely due to the rapid urbanization and the blooming fishery in the study area. PMID:20707090

  7. Effects of individual, community, and landscape drivers on the dynamics of a wildland forest epidemic.

    PubMed

    Haas, Sarah E; Cushman, J Hall; Dillon, Whalen W; Rank, Nathan E; Rizzo, David M; Meentemeyer, Ross K

    2016-03-01

    The challenges posed by observing host-pathogen-environment interactions across large geographic extents and over meaningful time scales limit our ability to understand and manage wildland epidemics. We conducted a landscape-scale, longitudinal study designed to analyze the dynamics of sudden oak death (an emerging forest disease caused by Phytophthora ramorum) across hierarchical levels of ecological interactions, from individual hosts up to the community and across the broader landscape. From 2004 to 2011, we annually assessed disease status of 732 coast live oak, 271 black oak, and 122 canyon live oak trees in 202 plots across a 275-km2 landscape in central California. The number of infected oak stems steadily increased during the eight-year study period. A survival analysis modeling framework was used to examine which level of ecological heterogeneity best predicted infection risk of susceptible oak species, considering variability at the level of individuals (species identity, stem size), the community (host density, inoculum load, and species richness), and the landscape (seasonal climate variability, habitat connectivity, and topographic gradients). After accounting for unobserved risk shared among oaks in the same plot, survival models incorporating heterogeneity across all three levels better predicted oak infection than did models focusing on only one level. We show that larger oak trees (especially coast live oak) were more susceptible, and that interannual variability in inoculum production by the highly infectious reservoir host, California bay laurel, more strongly influenced disease risk than simply the density of this important host. Concurrently, warmer and wetter rainy-season conditions in consecutive years intensified infection risk, presumably by creating a longer period of inoculum build-up and increased probability of pathogen spillover from bay laurel to oaks. Despite the presence of many alternate host species, we found evidence of pathogen

  8. Short and long-term controls of SOM dynamics in a South African Landscape

    NASA Astrophysics Data System (ADS)

    Khomo, L.; Chadwick, O. A.; Rogers, K.; Trumbore, S.

    2012-04-01

    We used the variations in parent material, climate and topography found in Kruger National Park, South Africa, to investigate the most important factors controlling carbon dynamics in savannah soils. Carbon dynamics were investigated using radiocarbon signatures of carbon in density-separated organic matter and in CO2 respired during incubation of surface soils. Carbon respired in incubations of 0-2cm and 2-8 cm depth intervals had a narrow range of 14C signatures regardless of the parent material, topographic position or climate conditions. The 14C values indicated that the C contributing to decomposition was fixed on average <1 to 5 years previously. Vegetation was apparently linked to these variations. The respired C with highest 14C signature also had the lowest 13C signatures, indicating more C3 (woody) plant influence. The 14C signatures of C in the low-density fraction (<1.7 or 1.9 g cm-3) had a larger range of 14C signatures than respired CO2, again with highest 14C signatures (indicating ages of up to a decade) in C that also had more C3-enriched 13C signatures. Charred material is found in the low density fraction which may explain why its 14C signature differs from that of respired CO2 in these fire-prone landscapes. The age of carbon in the dense fractions was considerably older (up to several thousand radiocarbon years) and strongly related to soil clay content, which in turn reflects a combination of parent material and landscape position. Overall, the age of all organic carbon in these soils was much less than the age of the soil itself, and also less than the age of pedogenic carbonates found in some of the soils. Parent material and landscape position both play a strong role in the storage of carbon across these landscapes over longer timescales. Indirectly, these factors control vegetation patterns, which in turn influence the age of faster cycling carbon in this savannah system.

  9. Effects of individual, community, and landscape drivers on the dynamics of a wildland forest epidemic.

    PubMed

    Haas, Sarah E; Cushman, J Hall; Dillon, Whalen W; Rank, Nathan E; Rizzo, David M; Meentemeyer, Ross K

    2016-03-01

    The challenges posed by observing host-pathogen-environment interactions across large geographic extents and over meaningful time scales limit our ability to understand and manage wildland epidemics. We conducted a landscape-scale, longitudinal study designed to analyze the dynamics of sudden oak death (an emerging forest disease caused by Phytophthora ramorum) across hierarchical levels of ecological interactions, from individual hosts up to the community and across the broader landscape. From 2004 to 2011, we annually assessed disease status of 732 coast live oak, 271 black oak, and 122 canyon live oak trees in 202 plots across a 275-km2 landscape in central California. The number of infected oak stems steadily increased during the eight-year study period. A survival analysis modeling framework was used to examine which level of ecological heterogeneity best predicted infection risk of susceptible oak species, considering variability at the level of individuals (species identity, stem size), the community (host density, inoculum load, and species richness), and the landscape (seasonal climate variability, habitat connectivity, and topographic gradients). After accounting for unobserved risk shared among oaks in the same plot, survival models incorporating heterogeneity across all three levels better predicted oak infection than did models focusing on only one level. We show that larger oak trees (especially coast live oak) were more susceptible, and that interannual variability in inoculum production by the highly infectious reservoir host, California bay laurel, more strongly influenced disease risk than simply the density of this important host. Concurrently, warmer and wetter rainy-season conditions in consecutive years intensified infection risk, presumably by creating a longer period of inoculum build-up and increased probability of pathogen spillover from bay laurel to oaks. Despite the presence of many alternate host species, we found evidence of pathogen

  10. [Dynamic changes of urban architecture landscape based on Barista: a case study in Tiexi District of Shenyang City].

    PubMed

    Zhang, Pei-feng; Hu, Yuan-man; He, Hong-shi; Xiong, Zai-ping; Liu, Miao

    2010-12-01

    In this paper, three-dimensional building information was extracted from high resolution satellite image based on Barista software. Combined with ArcGIS software, the dynamic changes of the building landscape in Tiexi District of Shenyang City during urban renewal process were analyzed from the conversion contribution rate, building density, average building height, and built-up area rate. It was found that during this urban renewal process, four dominant landscape types (vacant lot, residential building, industrial building, and road) were the main parts of the landscape changes. The areas of vacant lot, residential building, commercial building, and road increased, while that of industrial building decreased. The building density decreased, while the average building height increased. There was an obvious regional variation in building landscape. The building density in industrial district was higher than that in residential district, while the average building height was in adverse. The further from the city center, the lower the building density and building average height.

  11. Late Holocene landscape dynamics and ecosystem stability in the Upper Zambezi Valley

    NASA Astrophysics Data System (ADS)

    Burrough, Sallie; Thomas, David; Willis, Kathy; Orijemie, Emuobosa

    2014-05-01

    The summer rainfall zone in central southern Africa is critically vulnerable to changes in hydroclimate. The Intergovernmental Panel on Climate Change expects late 21st century subtropical temperatures to be on average at least 3-4°C warmer than a century earlier. Precipitation forecasts indicate substantial inter-model agreement for some African regions including significant drying in central southern Africa. The Zambezi basin has been identified as being particularly vulnerable to environmental change with down-the-line consequences being identified as potential political unrest, economic disturbances and food insecurity (Swain et al., 2012). Predicting the real environmental impact of changing climates, in terms of future landscape change and ecological response however, relies strongly on records of how these systems have responded to past climatic changes. To date, very few records exist for the Zambezi basin and very little is known about underlying stability or variability of both the landscape and the ecology. In western Zambia 'dambos' can be broadly described as shallow seasonally or interannually waterlogged depressions formed either at the headwaters of ephemeral drainage networks or within the disconnected drainage network itself where low relief facilitates infiltration and acts against channel formation and erosional processes. Sediments from these depressions which span a broad climate and ecological gradient from NW to SW Zambia preserve a palaeoecological record of late Holocene vegetation and fire dynamics and for the first time offer a long-term perspective on the ecological stability of this understudied region. In conjunction with new ages from optical dating of dune and plateau sands, we present new data that suggest the region is sensitive to rapid climate changes exemplified by multi-tiered threshold responses which include i) widespread sediment mobilisation ii) sufficient landscape stability to allow organic accumulation (and

  12. The energy landscape of glassy dynamics on the amorphous hafnium diboride surface.

    PubMed

    Nguyen, Duc; Mallek, Justin; Cloud, Andrew N; Abelson, John R; Girolami, Gregory S; Lyding, Joseph; Gruebele, Martin

    2014-11-28

    Direct visualization of the dynamics of structural glasses and amorphous solids on the sub-nanometer scale provides rich information unavailable from bulk or conventional single molecule techniques. We study the surface of hafnium diboride, a conductive ultrahigh temperature ceramic material that can be grown in amorphous films. Our scanning tunneling movies have a second-to-hour dynamic range and single-point current measurements extend that to the millisecond-to-minute time scale. On the a-HfB2 glass surface, two-state hopping of 1-2 nm diameter cooperatively rearranging regions or "clusters" occurs from sub-milliseconds to hours. We characterize individual clusters in detail through high-resolution (<0.5 nm) imaging, scanning tunneling spectroscopy and voltage modulation, ruling out individual atoms, diffusing adsorbates, or pinned charges as the origin of the observed two-state hopping. Smaller clusters are more likely to hop, larger ones are more likely to be immobile. HfB2 has a very high bulk glass transition temperature Tg, and we observe no three-state hopping or sequential two-state hopping previously seen on lower Tg glass surfaces. The electronic density of states of clusters does not change when they hop up or down, allowing us to calibrate an accurate relative z-axis scale. By directly measuring and histogramming single cluster vertical displacements, we can reconstruct the local free energy landscape of individual clusters, complete with activation barrier height, a reaction coordinate in nanometers, and the shape of the free energy landscape basins between which hopping occurs. The experimental images are consistent with the compact shape of α-relaxors predicted by random first order transition theory, whereas the rapid hopping rate, even taking less confined motion at the surface into account, is consistent with β-relaxations. We make a proposal of how "mixed" features can show up in surface dynamics of glasses.

  13. The energy landscape of glassy dynamics on the amorphous hafnium diboride surface.

    PubMed

    Nguyen, Duc; Mallek, Justin; Cloud, Andrew N; Abelson, John R; Girolami, Gregory S; Lyding, Joseph; Gruebele, Martin

    2014-11-28

    Direct visualization of the dynamics of structural glasses and amorphous solids on the sub-nanometer scale provides rich information unavailable from bulk or conventional single molecule techniques. We study the surface of hafnium diboride, a conductive ultrahigh temperature ceramic material that can be grown in amorphous films. Our scanning tunneling movies have a second-to-hour dynamic range and single-point current measurements extend that to the millisecond-to-minute time scale. On the a-HfB2 glass surface, two-state hopping of 1-2 nm diameter cooperatively rearranging regions or "clusters" occurs from sub-milliseconds to hours. We characterize individual clusters in detail through high-resolution (<0.5 nm) imaging, scanning tunneling spectroscopy and voltage modulation, ruling out individual atoms, diffusing adsorbates, or pinned charges as the origin of the observed two-state hopping. Smaller clusters are more likely to hop, larger ones are more likely to be immobile. HfB2 has a very high bulk glass transition temperature Tg, and we observe no three-state hopping or sequential two-state hopping previously seen on lower Tg glass surfaces. The electronic density of states of clusters does not change when they hop up or down, allowing us to calibrate an accurate relative z-axis scale. By directly measuring and histogramming single cluster vertical displacements, we can reconstruct the local free energy landscape of individual clusters, complete with activation barrier height, a reaction coordinate in nanometers, and the shape of the free energy landscape basins between which hopping occurs. The experimental images are consistent with the compact shape of α-relaxors predicted by random first order transition theory, whereas the rapid hopping rate, even taking less confined motion at the surface into account, is consistent with β-relaxations. We make a proposal of how "mixed" features can show up in surface dynamics of glasses. PMID:25429948

  14. The energy landscape of glassy dynamics on the amorphous hafnium diboride surface

    NASA Astrophysics Data System (ADS)

    Nguyen, Duc; Mallek, Justin; Cloud, Andrew N.; Abelson, John R.; Girolami, Gregory S.; Lyding, Joseph; Gruebele, Martin

    2014-11-01

    Direct visualization of the dynamics of structural glasses and amorphous solids on the sub-nanometer scale provides rich information unavailable from bulk or conventional single molecule techniques. We study the surface of hafnium diboride, a conductive ultrahigh temperature ceramic material that can be grown in amorphous films. Our scanning tunneling movies have a second-to-hour dynamic range and single-point current measurements extend that to the millisecond-to-minute time scale. On the a-HfB2 glass surface, two-state hopping of 1-2 nm diameter cooperatively rearranging regions or "clusters" occurs from sub-milliseconds to hours. We characterize individual clusters in detail through high-resolution (<0.5 nm) imaging, scanning tunneling spectroscopy and voltage modulation, ruling out individual atoms, diffusing adsorbates, or pinned charges as the origin of the observed two-state hopping. Smaller clusters are more likely to hop, larger ones are more likely to be immobile. HfB2 has a very high bulk glass transition temperature Tg, and we observe no three-state hopping or sequential two-state hopping previously seen on lower Tg glass surfaces. The electronic density of states of clusters does not change when they hop up or down, allowing us to calibrate an accurate relative z-axis scale. By directly measuring and histogramming single cluster vertical displacements, we can reconstruct the local free energy landscape of individual clusters, complete with activation barrier height, a reaction coordinate in nanometers, and the shape of the free energy landscape basins between which hopping occurs. The experimental images are consistent with the compact shape of α-relaxors predicted by random first order transition theory, whereas the rapid hopping rate, even taking less confined motion at the surface into account, is consistent with β-relaxations. We make a proposal of how "mixed" features can show up in surface dynamics of glasses.

  15. Comment on "Exact solution of the wave dynamics of a particle bouncing chaotically on a periodically oscillating wall"

    NASA Astrophysics Data System (ADS)

    Dembiński, S. T.; Makowski, A. J.; Pepłowski, P.; Wolniewicz, L.

    1996-04-01

    We attempt to show both analytically and numerically that a recent work by Willemsen

    [Phys. Rev. E 50, 3116 (1994)]
    is not correct and the proposed exact solution of the so-called bouncer model appears to be incorrect.

  16. A dynamic CTCF chromatin binding landscape promotes DNA hydroxymethylation and transcriptional induction of adipocyte differentiation

    PubMed Central

    Dubois-Chevalier, Julie; Oger, Frédérik; Dehondt, Hélène; Firmin, François F.; Gheeraert, Céline; Staels, Bart; Lefebvre, Philippe; Eeckhoute, Jérôme

    2014-01-01

    CCCTC-binding factor (CTCF) is a ubiquitously expressed multifunctional transcription factor characterized by chromatin binding patterns often described as largely invariant. In this context, how CTCF chromatin recruitment and functionalities are used to promote cell type-specific gene expression remains poorly defined. Here, we show that, in addition to constitutively bound CTCF binding sites (CTS), the CTCF cistrome comprises a large proportion of sites showing highly dynamic binding patterns during the course of adipogenesis. Interestingly, dynamic CTCF chromatin binding is positively linked with changes in expression of genes involved in biological functions defining the different stages of adipogenesis. Importantly, a subset of these dynamic CTS are gained at cell type-specific regulatory regions, in line with a requirement for CTCF in transcriptional induction of adipocyte differentiation. This relates to, at least in part, CTCF requirement for transcriptional activation of both the nuclear receptor peroxisome proliferator-activated receptor gamma (PPARG) and its target genes. Functionally, we show that CTCF interacts with TET methylcytosine dioxygenase (TET) enzymes and promotes adipogenic transcriptional enhancer DNA hydroxymethylation. Our study reveals a dynamic CTCF chromatin binding landscape required for epigenomic remodeling of enhancers and transcriptional activation driving cell differentiation. PMID:25183525

  17. Temporal bird community dynamics are strongly affected by landscape fragmentation in a Central American tropical forest region

    USGS Publications Warehouse

    Blandón, A.C.; Perelman, S.B.; Ramírez, M.; López, A.; Javier, O.; Robbins, Chandler S.

    2016-01-01

    Habitat loss and fragmentation are considered the main causes of species extinctions, particularly in tropical ecosystems. The objective of this work was to evaluate the temporal dynamics of tropical bird communities in landscapes with different levels of fragmentation in eastern Guatemala. We evaluated five bird community dynamic parameters for forest specialists and generalists: (1) species extinction, (2) species turnover, (3) number of colonizing species, (4) relative species richness, and (5) a homogeneity index. For each of 24 landscapes, community dynamic parameters were estimated from bird point count data, for the 1998–1999 and 2008–2009 periods, accounting for species’ detection probability. Forest specialists had higher extinction rates and a smaller number of colonizing species in landscapes with higher fragmentation, thus having lower species richness in both time periods. Alternatively, forest generalists elicited a completely different pattern, showing a curvilinear association to forest fragmentation for most parameters. Thus, greater community dynamism for forest generalists was shown in landscapes with intermediate levels of fragmentation. Our study supports general theory regarding the expected negative effects of habitat loss and fragmentation on the temporal dynamics of biotic communities, particularly for forest specialists, providing strong evidence from understudied tropical bird communities.

  18. Effects of dynamic landscape elements on fish dispersal: the example of creek chub (Semotilus atromaculatus).

    PubMed

    Boizard, J; Magnan, P; Angers, B

    2009-02-01

    Barriers along a watercourse and interconnections between drainage systems are dynamic landscape elements that are expected to play major roles in the dispersal and genetic structure of fish species. The objective of this study was to assess the role of these elements using creek chub (Semotilus atromaculatus) in the Mastigouche Wildlife Reserve (Québec, Canada) as model. Numerous impassable waterfalls and interconnections among drainage systems were inferred with geographic information systems and confirmed de visu. The analysis of 32 populations using seven nuclear microsatellites revealed the presence of three genetically distinct groups. Some groups were found upstream of impassable barriers and in adjacent portions of distinct drainage systems. Admixture among groups was also detected in some populations. Constraining phylogenetic procedures as well as Mantel correlation tests confirmed that the genetic structure is more likely to result from interconnections between the drainage systems than from the permanent network. This study indicates that landscape elements such as interconnections are of major importance for circumventing impassable barriers and colonizing lakes that are otherwise inaccessible. Such an approach could be relevant for determining the origins of fish species (i.e. native vs. introduced) in the context of conservation. PMID:19161466

  19. Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution.

    PubMed

    Adams, Richard H; Blackmon, Heath; Reyes-Velasco, Jacobo; Schield, Drew R; Card, Daren C; Andrew, Audra L; Waynewood, Nyimah; Castoe, Todd A

    2016-05-01

    The evolutionary dynamics of simple sequence repeats (SSRs or microsatellites) across the vertebrate tree of life remain largely undocumented and poorly understood. In this study, we analyzed patterns of genomic microsatellite abundance and evolution across 71 vertebrate genomes. The highest abundances of microsatellites exist in the genomes of ray-finned fishes, squamate reptiles, and mammals, while crocodilian, turtle, and avian genomes exhibit reduced microsatellite landscapes. We used comparative methods to infer evolutionary rates of change in microsatellite abundance across vertebrates and to highlight particular lineages that have experienced unusually high or low rates of change in genomic microsatellite abundance. Overall, most variation in microsatellite content, abundance, and evolutionary rate is observed among major lineages of reptiles, yet we found that several deeply divergent clades (i.e., squamate reptiles and mammals) contained relatively similar genomic microsatellite compositions. Archosauromorph reptiles (turtles, crocodilians, and birds) exhibit reduced genomic microsatellite content and the slowest rates of microsatellite evolution, in contrast to squamate reptile genomes that have among the highest rates of microsatellite evolution. Substantial branch-specific shifts in SSR content in primates, monotremes, rodents, snakes, and fish are also evident. Collectively, our results support multiple major shifts in microsatellite genomic landscapes among vertebrates. PMID:27064176

  20. Effects of dynamic landscape elements on fish dispersal: the example of creek chub (Semotilus atromaculatus).

    PubMed

    Boizard, J; Magnan, P; Angers, B

    2009-02-01

    Barriers along a watercourse and interconnections between drainage systems are dynamic landscape elements that are expected to play major roles in the dispersal and genetic structure of fish species. The objective of this study was to assess the role of these elements using creek chub (Semotilus atromaculatus) in the Mastigouche Wildlife Reserve (Québec, Canada) as model. Numerous impassable waterfalls and interconnections among drainage systems were inferred with geographic information systems and confirmed de visu. The analysis of 32 populations using seven nuclear microsatellites revealed the presence of three genetically distinct groups. Some groups were found upstream of impassable barriers and in adjacent portions of distinct drainage systems. Admixture among groups was also detected in some populations. Constraining phylogenetic procedures as well as Mantel correlation tests confirmed that the genetic structure is more likely to result from interconnections between the drainage systems than from the permanent network. This study indicates that landscape elements such as interconnections are of major importance for circumventing impassable barriers and colonizing lakes that are otherwise inaccessible. Such an approach could be relevant for determining the origins of fish species (i.e. native vs. introduced) in the context of conservation.

  1. [Dynamics and influence width of dry valley landscape boundary in upper reaches of Minjiang River].

    PubMed

    Yang, Zhao-Ping; Chang, Yu; Yang, Meng; Hu, Yuan-Man; Bu, Ren-Cang; He, Xing-Yuan

    2007-09-01

    Based on RS and GIS techniques, the distribution extent of the dry valley in upper reaches of Minjiang River was determined, with the dynamics and influence width of its landscape boundary analyzed. The results indicated that the dry valley had a gradually expanded distribution, and the total length of its boundary was increased. The boundary complexity increased from 1974 to 1995 but decreased from 1995 to 2000, and the upper boundary of the dry valley ascended rapidly along mountain slope. The uppermost elevation of the dry valley boundary was 3128 m in 1974, 3167 m in 1995, and 3181 m in 2000. In the last 26 years, the upper boundary of the dry valley ascended 53 m in total, being about 2 m per year. The influence width of the dry valley boundary was 800 m, which could be regarded as a buffer zone to disturbances. The area between 800-1200 m from the dry valley boundary to exterior was a transition zone intensely influenced by the dry valley and its surrounding landscape, which should be addressed in the restoration of the dry valley. PMID:18062298

  2. An Integrated Model of Market-Driven Dynamics of Carbon in Exurban Landscapes

    NASA Astrophysics Data System (ADS)

    Brown, D. G.; Sun, S.; Currie, W.; Nassauer, J. I.; Page, S. E.; Parker, D. C.; Riolo, R. L.; Robinson, D. T.

    2012-12-01

    As coupled human-environment system, exurban land-use systems and their ecological and social outcomes are driven by interactions between the human actors and natural processes at play. Carbon storage in exurban land-use systems is driven by interactions among market forces driving land-use change, developer and resident decisions about land cover and land management, and ecosystem processes affecting ecosystem function. Whether or not vegetation in these landscapes contribute to carbon sinks that mitigate global change, and their future trajectory, depends on dynamics in both human and biophysical processes. Understanding these interactions in a coupled human and natural system might best be advanced by iterating between data collection efforts on various aspects of the system (including the states and changes in the social and natural aspects of the system) and modeling in ways that explicitly represents social and natural processes and their interactions. A challenge is to build models that are both explicable based on existing process knowledge and supportable by existing or newly collected data. We coupled an agent-based model of developer and resident decision making about landscape structure and management with a biogeochemical model of carbon flux and storage to evaluate the drivers of and possible mechanisms to achieve increased carbon storage. Model-based experiments demonstrate the (a) effects of various residential land management strategies on carbon storage, suggesting that removals of litter have a larger effect on overall carbon storage than additions of fertilizer and irrigation; (b) effects of subsidies or payments for increased carbon storage paid to developers can result in choices about development types that result in increased carbon storage, but that the effects are highly sensitive to the price of carbon and the basis for calculating payments. The experiments highlight the need for integrated modeling, but also point to specific needs for

  3. Alpine treeline of western North America: Linking organism-to-landscape dynamics

    USGS Publications Warehouse

    Malanson, George P.; Butler, David R.; Fagre, Daniel B.; Walsh, Stephen J; Tomback, Diana F.; Daniels, Lori D.; Resler, Lynn M.; Smith, William K.; Weiss, Daniel J.; Peterson, David L.; Bunn, Andrew G.; Hiemstra, Christopher A.; Liptzin, Daniel; Bourgeron, Patrick S.; Shen, Zehao; Millar, Constance I.

    2007-01-01

    Although the ecological dynamics of the alpine treeline ecotone are influenced by climate, it is an imperfect indicator of climate change. Mechanistic processes that shape the ecotone—seed rain, seed germination, seedling establishment and subsequent tree growth form, or, conversely tree dieback—depend on microsite patterns. Growth forms affect wind and snow, and so develop positive and negative feedback loops that create these microsites. As a result, complex landscape patterns are generated at multiple spatial scales. Although these mechanistic processes are fundamentally the same for all forest-tundra ecotones across western North America, factors such as prior climate, underlying geology and geomorphology, and genetic constraints of dominant tree species lead to geographic differences in the responses of particular ecotones to climate change.

  4. Evaluating Effects of Localized Habitat Manipulations on Landscape-level Dynamics of White-footed Mouse Populations

    EPA Science Inventory

    Due to complex population dynamics and migration behaviors, the well-being of animal populations that host human diseases sometimes varies across landscapes in ways that cannot be deduced from geographic abundance patterns alone. In such cases, efficient management of ecological...

  5. The dynamic effects of sea level rise on low-gradient coastal landscapes: A review

    USGS Publications Warehouse

    Passeri, Davina; Hagen, Scott C.; Medeiros, Stephen C.; Bilskie, Matthew V.; Alizad, Karim; Wang, Dingbao

    2015-01-01

    Coastal responses to sea level rise (SLR) include inundation of wetlands, increased shoreline erosion, and increased flooding during storm events. Hydrodynamic parameters such as tidal ranges, tidal prisms, tidal asymmetries, increased flooding depths and inundation extents during storm events respond nonadditively to SLR. Coastal morphology continually adapts toward equilibrium as sea levels rise, inducing changes in the landscape. Marshes may struggle to keep pace with SLR and rely on sediment accumulation and the availability of suitable uplands for migration. Whether hydrodynamic, morphologic, or ecologic, the impacts of SLR are interrelated. To plan for changes under future sea levels, coastal managers need information and data regarding the potential effects of SLR to make informed decisions for managing human and natural communities. This review examines previous studies that have accounted for the dynamic, nonlinear responses of hydrodynamics, coastal morphology, and marsh ecology to SLR by implementing more complex approaches rather than the simplistic “bathtub” approach. These studies provide an improved understanding of the dynamic effects of SLR on coastal environments and contribute to an overall paradigm shift in how coastal scientists and engineers approach modeling the effects of SLR, transitioning away from implementing the “bathtub” approach. However, it is recommended that future studies implement a synergetic approach that integrates the dynamic interactions between physical and ecological environments to better predict the impacts of SLR on coastal systems.

  6. High Resolution Modeling of Tile-Drained Controls on Ecohydrologic Dynamics in Intensively Managed Landscapes.

    NASA Astrophysics Data System (ADS)

    Wagner, D.; Le, P. V.; Kumar, P.; Woo, D.

    2015-12-01

    Tile drains are widely used in the Midwestern United States to improve the productivity of poorly drained agricultural fields. Since tile drain reduces vadose zone soil moisture by lowering the water table, and its outlets feed directly into streams and ditches, tile flow can affect various hydrologic, biotic and biogeochemical processes in the watershed. However, the effects of tile flow on ecohydrologic and nutrient dynamics at scales dominated by microtopographic variability, such as depression and roadside ditches, remain poorly understood. Here we present an explicit model of tile flow and incorporate into the integrated ecohydrologic-flow model, MLCan-GCSFlow, to investigate the impacts of tile drain on ecohydrologic and nutrient dynamics in intensively managed agricultural fields at lidar-resolution scales. Explicit coupling between subsurface and tile flow is obtained by modifications of variably saturated Richards equation to capture the impacts of tile drain on soil moisture. The coupling between subsurface and overland flow is obtained by prescribing a boundary condition switching approach at the top surface of the computational domain. Model results for study sites in Critical Zone Observatory for Intensively Managed Landscapes (IMLCZO) show the significance of tile drain flow on the vertical and spatial soil moisture distribution and coupled surface - sub-surface flow dynamics.

  7. Self-organization in irregular landscapes: Detecting autogenic interactions from field data using descriptive statistics and dynamical systems theory

    NASA Astrophysics Data System (ADS)

    Larsen, L.; Watts, D.; Khurana, A.; Anderson, J. L.; Xu, C.; Merritts, D. J.

    2015-12-01

    The classic signal of self-organization in nature is pattern formation. However, the interactions and feedbacks that organize depositional landscapes do not always result in regular or fractal patterns. How might we detect their existence and effects in these "irregular" landscapes? Emergent landscapes such as newly forming deltaic marshes or some restoration sites provide opportunities to study the autogenic processes that organize landscapes and their physical signatures. Here we describe a quest to understand autogenic vs. allogenic controls on landscape evolution in Big Spring Run, PA, a landscape undergoing restoration from bare-soil conditions to a target wet meadow landscape. The contemporary motivation for asking questions about autogenic vs. allogenic controls is to evaluate how important initial conditions or environmental controls may be for the attainment of management objectives. However, these questions can also inform interpretation of the sedimentary record by enabling researchers to separate signals that may have arisen through self-organization processes from those resulting from environmental perturbations. Over three years at Big Spring Run, we mapped the dynamic evolution of floodplain vegetation communities and distributions of abiotic variables and topography. We used principal component analysis and transition probability analysis to detect associative interactions between vegetation and geomorphic variables and convergent cross-mapping on lidar data to detect causal interactions between biomass and topography. Exploratory statistics revealed that plant communities with distinct morphologies exerted control on landscape evolution through stress divergence (i.e., channel initiation) and promoting the accumulation of fine sediment in channels. Together, these communities participated in a negative feedback that maintains low energy and multiple channels. Because of the spatially explicit nature of this feedback, causal interactions could not

  8. Invasion Dynamics of a Fish-Free Landscape by Brown Trout (Salmo trutta)

    PubMed Central

    Labonne, Jacques; Vignon, Matthias; Prévost, Etienne; Lecomte, Frédéric; Dodson, Julian J.; Kaeuffer, Renaud; Aymes, Jean-Christophe; Jarry, Marc; Gaudin, Philippe; Davaine, Patrick; Beall, Edward

    2013-01-01

    Metapopulation dynamics over the course of an invasion are usually difficult to grasp because they require large and reliable data collection, often unavailable. The invasion of the fish-free freshwater ecosystems of the remote sub-Antarctic Kerguelen Islands following man-made introductions of brown trout (Salmo trutta) in the 1950's is an exception to this rule. Benefiting from a full long term environmental research monitoring of the invasion, we built a Bayesian dynamic metapopulation model to analyze the invasion dynamics of 85 river systems over 51 years. The model accounted for patch size (river length and connections to lakes), alternative dispersal pathways between rivers, temporal trends in dynamics, and uncertainty in colonization date. The results show that the model correctly represents the observed pattern of invasion, especially if we assume a coastal dispersal pathway between patches. Landscape attributes such as patch size influenced the colonization function, but had no effect on propagule pressure. Independently from patch size and distance between patches, propagule pressure and colonization function were not constant through time. Propagule pressure increased over the course of colonization, whereas the colonization function decreased, conditional on propagule pressure. The resulting pattern of this antagonistic interplay is an initial rapid invasion phase followed by a strong decrease in the invasion rate. These temporal trends may be due to either adaptive processes or environmental gradients encountered along the colonization front. It was not possible to distinguish these two hypotheses. Because invasibility of Kerguelen Is. freshwater ecosystems is very high due to the lack of a pre-existing fish fauna and minimal human interference, our estimates of invasion dynamics represent a blueprint for the potential of brown trout invasiveness in pristine environments. Our conclusions shed light on the future of polar regions where, because of

  9. Optimal dimensionality reduction of complex dynamics: The chess game as diffusion on a free-energy landscape

    NASA Astrophysics Data System (ADS)

    Krivov, Sergei V.

    2011-07-01

    Dimensionality reduction is ubiquitous in the analysis of complex dynamics. The conventional dimensionality reduction techniques, however, focus on reproducing the underlying configuration space, rather than the dynamics itself. The constructed low-dimensional space does not provide a complete and accurate description of the dynamics. Here I describe how to perform dimensionality reduction while preserving the essential properties of the dynamics. The approach is illustrated by analyzing the chess game—the archetype of complex dynamics. A variable that provides complete and accurate description of chess dynamics is constructed. The winning probability is predicted by describing the game as a random walk on the free-energy landscape associated with the variable. The approach suggests a possible way of obtaining a simple yet accurate description of many important complex phenomena. The analysis of the chess game shows that the approach can quantitatively describe the dynamics of processes where human decision-making plays a central role, e.g., financial and social dynamics.

  10. Where wolves kill moose: the influence of prey life history dynamics on the landscape ecology of predation.

    PubMed

    Montgomery, Robert A; Vucetich, John A; Roloff, Gary J; Bump, Joseph K; Peterson, Rolf O

    2014-01-01

    The landscape ecology of predation is well studied and known to be influenced by habitat heterogeneity. Little attention has been given to how the influence of habitat heterogeneity on the landscape ecology of predation might be modulated by life history dynamics of prey in mammalian systems. We demonstrate how life history dynamics of moose (Alces alces) contribute to landscape patterns in predation by wolves (Canis lupus) in Isle Royale National Park, Lake Superior, USA. We use pattern analysis and kernel density estimates of moose kill sites to demonstrate that moose in senescent condition and moose in prime condition tend to be wolf-killed in different regions of Isle Royale in winter. Predation on senescent moose was clustered in one kill zone in the northeast portion of the island, whereas predation on prime moose was clustered in 13 separate kill zones distributed throughout the full extent of the island. Moreover, the probability of kill occurrence for senescent moose, in comparison to prime moose, increased in high elevation habitat with patches of dense coniferous trees. These differences can be attributed, at least in part, to senescent moose being more vulnerable to predation and making different risk-sensitive habitat decisions than prime moose. Landscape patterns emerging from prey life history dynamics and habitat heterogeneity have been observed in the predation ecology of fish and insects, but this is the first mammalian system for which such observations have been made. PMID:24622241

  11. Where wolves kill moose: the influence of prey life history dynamics on the landscape ecology of predation.

    PubMed

    Montgomery, Robert A; Vucetich, John A; Roloff, Gary J; Bump, Joseph K; Peterson, Rolf O

    2014-01-01

    The landscape ecology of predation is well studied and known to be influenced by habitat heterogeneity. Little attention has been given to how the influence of habitat heterogeneity on the landscape ecology of predation might be modulated by life history dynamics of prey in mammalian systems. We demonstrate how life history dynamics of moose (Alces alces) contribute to landscape patterns in predation by wolves (Canis lupus) in Isle Royale National Park, Lake Superior, USA. We use pattern analysis and kernel density estimates of moose kill sites to demonstrate that moose in senescent condition and moose in prime condition tend to be wolf-killed in different regions of Isle Royale in winter. Predation on senescent moose was clustered in one kill zone in the northeast portion of the island, whereas predation on prime moose was clustered in 13 separate kill zones distributed throughout the full extent of the island. Moreover, the probability of kill occurrence for senescent moose, in comparison to prime moose, increased in high elevation habitat with patches of dense coniferous trees. These differences can be attributed, at least in part, to senescent moose being more vulnerable to predation and making different risk-sensitive habitat decisions than prime moose. Landscape patterns emerging from prey life history dynamics and habitat heterogeneity have been observed in the predation ecology of fish and insects, but this is the first mammalian system for which such observations have been made.

  12. Where Wolves Kill Moose: The Influence of Prey Life History Dynamics on the Landscape Ecology of Predation

    PubMed Central

    Montgomery, Robert A.; Vucetich, John A.; Roloff, Gary J.; Bump, Joseph K.; Peterson, Rolf O.

    2014-01-01

    The landscape ecology of predation is well studied and known to be influenced by habitat heterogeneity. Little attention has been given to how the influence of habitat heterogeneity on the landscape ecology of predation might be modulated by life history dynamics of prey in mammalian systems. We demonstrate how life history dynamics of moose (Alces alces) contribute to landscape patterns in predation by wolves (Canis lupus) in Isle Royale National Park, Lake Superior, USA. We use pattern analysis and kernel density estimates of moose kill sites to demonstrate that moose in senescent condition and moose in prime condition tend to be wolf-killed in different regions of Isle Royale in winter. Predation on senescent moose was clustered in one kill zone in the northeast portion of the island, whereas predation on prime moose was clustered in 13 separate kill zones distributed throughout the full extent of the island. Moreover, the probability of kill occurrence for senescent moose, in comparison to prime moose, increased in high elevation habitat with patches of dense coniferous trees. These differences can be attributed, at least in part, to senescent moose being more vulnerable to predation and making different risk-sensitive habitat decisions than prime moose. Landscape patterns emerging from prey life history dynamics and habitat heterogeneity have been observed in the predation ecology of fish and insects, but this is the first mammalian system for which such observations have been made. PMID:24622241

  13. Modeling range dynamics in heterogeneous landscapes: invasion of the hemlock woolly adelgid in eastern North America.

    PubMed

    Fitzpatrick, Matthew C; Preisser, Evan L; Porter, Adam; Elkinton, Joseph; Ellison, Aaron M

    2012-03-01

    Range expansion by native and exotic species will continue to be a major component of global change. Anticipating the potential effects of changes in species distributions requires models capable of forecasting population spread across realistic, heterogeneous landscapes and subject to spatiotemporal variability in habitat suitability. Several decades of theory and model development, as well as increased computing power and availability of fine-resolution GIS data, now make such models possible. Still unanswered, however, is the question of how well this new generation of dynamic models will anticipate range expansion. Here we develop a spatially explicit stochastic model that combines dynamic dispersal and population processes with fine-resolution maps characterizing spatiotemporal heterogeneity in climate and habitat to model range expansion of the hemlock woolly adelgid (HWA; Adelges tsugae). We parameterize this model using multiyear data sets describing population and dispersal dynamics of HWA and apply it to eastern North America over a 57-year period (1951-2008). To evaluate the model, the observed pattern of spread of HWA during this same period was compared to model predictions. Our model predicts considerable heterogeneity in the risk of HWA invasion across space and through time, and it suggests that spatiotemporal variation in winter temperature, rather than hemlock abundance, exerts a primary control on the spread of HWA. Although the simulations generally matched the observed current extent of the invasion of HWA and patterns of anisotropic spread, it did not correctly predict when HWA was observed to arrive in different geographic regions. We attribute differences between the modeled and observed dynamics to an inability to capture the timing and direction of long-distance dispersal events that substantially affected the ensuing pattern of spread.

  14. Landscape evolution in tidal embayments: modeling the interplay of erosion, sedimentation, and vegetation dynamics

    NASA Astrophysics Data System (ADS)

    D'Alpaos, A.; Lanzoni, S.; Marani, M.; Rinaldo, A.

    2006-12-01

    Modeling the long-term landscape evolution of tidal embayments requires a holistic eco-geomorphological approach to incorporate the description of the delicate balance and strong feedbacks characterizing hydrodinamic and sediment transport processes on the one hand, and ecological dynamics on the other. In order to address issues of conservation of these delicate systems and predict their future fate we have set up a process-based eco-morphodynamic model which conceptualizes the chief landforming processes operating on the intertwined, long-term evolution of marsh platforms and tidal networks cutting through them. Such a model is aimed at improving our understanding of the main processes shaping the geomorphological and biological characters of the tidal landscape. Based on observational evidence indicating the existence of different time scales governing the various landscape-forming processes, the model decouples the initial rapid network incision from its subsequent slower elaboration and from the eco-morphological evolution of intertidal areas, governed by sediment erosion and deposition and crucially affected by the presence of vegetation. This allows us to investigate the response of tidal morphologies to different scenarios of sediment supply, colonization by halophytes and changing sea level. Different morphological evolutionary regimes are shown to depend on marsh ecology. Marsh accretion rates, enhanced by vegetation growth, and the related platform elevations are found to decrease with distance from the creek, measured along suitably defined flow paths. The negative feedback between surface elevation and its inorganic accretion rate is reinforced by the relation between plant productivity and soil elevation in Spartina-dominated marshes, whereas counteracted by positive feedbacks in marshes populated by a variety of vegetation species. When evolving under constant sea level, unvegetated and Spartina-dominated marshes asymptotically tend to mean high

  15. The energy landscape of glassy dynamics on the amorphous hafnium diboride surface

    SciTech Connect

    Nguyen, Duc; Girolami, Gregory S.; Mallek, Justin; Cloud, Andrew N.; Abelson, John R.; Lyding, Joseph; Gruebele, Martin

    2014-11-28

    Direct visualization of the dynamics of structural glasses and amorphous solids on the sub-nanometer scale provides rich information unavailable from bulk or conventional single molecule techniques. We study the surface of hafnium diboride, a conductive ultrahigh temperature ceramic material that can be grown in amorphous films. Our scanning tunneling movies have a second-to-hour dynamic range and single-point current measurements extend that to the millisecond-to-minute time scale. On the a-HfB{sub 2} glass surface, two-state hopping of 1–2 nm diameter cooperatively rearranging regions or “clusters” occurs from sub-milliseconds to hours. We characterize individual clusters in detail through high-resolution (<0.5 nm) imaging, scanning tunneling spectroscopy and voltage modulation, ruling out individual atoms, diffusing adsorbates, or pinned charges as the origin of the observed two-state hopping. Smaller clusters are more likely to hop, larger ones are more likely to be immobile. HfB{sub 2} has a very high bulk glass transition temperature T{sub g}, and we observe no three-state hopping or sequential two-state hopping previously seen on lower T{sub g} glass surfaces. The electronic density of states of clusters does not change when they hop up or down, allowing us to calibrate an accurate relative z-axis scale. By directly measuring and histogramming single cluster vertical displacements, we can reconstruct the local free energy landscape of individual clusters, complete with activation barrier height, a reaction coordinate in nanometers, and the shape of the free energy landscape basins between which hopping occurs. The experimental images are consistent with the compact shape of α-relaxors predicted by random first order transition theory, whereas the rapid hopping rate, even taking less confined motion at the surface into account, is consistent with β-relaxations. We make a proposal of how “mixed” features can show up in surface dynamics of glasses.

  16. Mapping the temperature-dependent conformational landscapes of the dynamic enzymes cyclophilin A and urease

    NASA Astrophysics Data System (ADS)

    Thorne, Robert; Keedy, Daniel; Warkentin, Matthew; Fraser, James; Moreau, David; Atakisi, Hakan; Rau, Peter

    Proteins populate complex, temperature-dependent ensembles of conformations that enable their function. Yet in X-ray crystallographic studies, roughly 98% of structures have been determined at 100 K, and most refined to only a single conformation. A combination of experimental methods enabled by studies of ice formation and computational methods for mining low-density features in electron density maps have been applied to determine the evolution of the conformational landscapes of the enzymes cyclophilin A and urease between 300 K and 100 K. Minority conformations of most side chains depopulate on cooling from 300 to ~200 K, below which subsequent conformational evolution is quenched. The characteristic temperatures for this depopulation are highly heterogeneous throughout each enzyme. The temperature-dependent ensemble of the active site flap in urease has also been mapped. These all-atom, site-resolved measurements and analyses rule out one interpretation of the protein-solvent glass transition, and give an alternative interpretation of a dynamical transition identified in site-averaged experiments. They demonstrate a powerful approach to structural characterization of the dynamic underpinnings of protein function. Supported by NSF MCB-1330685.

  17. Unraveling Landscape Complexity: Land Use/Land Cover Changes and Landscape Pattern Dynamics (1954-2008) in Contrasting Peri-Urban and Agro-Forest Regions of Northern Italy.

    PubMed

    Smiraglia, D; Ceccarelli, T; Bajocco, S; Perini, L; Salvati, L

    2015-10-01

    This study implements an exploratory data analysis of landscape metrics and a change detection analysis of land use and population density to assess landscape dynamics (1954-2008) in two physiographic zones (plain and hilly-mountain area) of Emilia Romagna, northern Italy. The two areas are characterized by different landscape types: a mixed urban-rural landscape dominated by arable land and peri-urban settlements in the plain and a traditional agro-forest landscape in the hilly-mountain area with deciduous and conifer forests, scrublands, meadows, and crop mosaic. Urbanization and, to a lesser extent, agricultural intensification were identified as the processes underlying landscape change in the plain. Land abandonment determining natural forestation and re-forestation driven by man was identified as the process of change most representative of the hilly-mountain area. Trends in landscape metrics indicate a shift toward more fragmented and convoluted patterns in both areas. Number of patches, the interspersion and juxtaposition index, and the large patch index are the metrics discriminating the two areas in terms of landscape patterns in 1954. In 2008, mean patch size, edge density, interspersion and juxtaposition index, and mean Euclidean nearest neighbor distance were the metrics with the most different spatial patterns in the two areas. The exploratory data analysis of landscape metrics contributed to link changes over time in both landscape composition and configuration providing a comprehensive picture of landscape transformations in a wealthy European region. Evidence from this study are hoped to inform sustainable land management designed for homogeneous landscape units in similar socioeconomic contexts.

  18. Unraveling Landscape Complexity: Land Use/Land Cover Changes and Landscape Pattern Dynamics (1954-2008) in Contrasting Peri-Urban and Agro-Forest Regions of Northern Italy

    NASA Astrophysics Data System (ADS)

    Smiraglia, D.; Ceccarelli, T.; Bajocco, S.; Perini, L.; Salvati, L.

    2015-10-01

    This study implements an exploratory data analysis of landscape metrics and a change detection analysis of land use and population density to assess landscape dynamics (1954-2008) in two physiographic zones (plain and hilly-mountain area) of Emilia Romagna, northern Italy. The two areas are characterized by different landscape types: a mixed urban-rural landscape dominated by arable land and peri-urban settlements in the plain and a traditional agro-forest landscape in the hilly-mountain area with deciduous and conifer forests, scrublands, meadows, and crop mosaic. Urbanization and, to a lesser extent, agricultural intensification were identified as the processes underlying landscape change in the plain. Land abandonment determining natural forestation and re-forestation driven by man was identified as the process of change most representative of the hilly-mountain area. Trends in landscape metrics indicate a shift toward more fragmented and convoluted patterns in both areas. Number of patches, the interspersion and juxtaposition index, and the large patch index are the metrics discriminating the two areas in terms of landscape patterns in 1954. In 2008, mean patch size, edge density, interspersion and juxtaposition index, and mean Euclidean nearest neighbor distance were the metrics with the most different spatial patterns in the two areas. The exploratory data analysis of landscape metrics contributed to link changes over time in both landscape composition and configuration providing a comprehensive picture of landscape transformations in a wealthy European region. Evidence from this study are hoped to inform sustainable land management designed for homogeneous landscape units in similar socioeconomic contexts.

  19. How landscape dynamics link individual- to population-level movement patterns: A multispecies comparison of ungulate relocation data

    USGS Publications Warehouse

    Mueller, T.; Olson, K.A.; Dressler, G.; Leimgruber, P.; Fuller, T.K.; Nicolson, C.; Novaro, A.J.; Bolgeri, M.J.; Wattles, D.; DeStefano, S.; Calabrese, J.M.; Fagan, W.F.

    2011-01-01

    Aim To demonstrate how the interrelations of individual movements form large-scale population-level movement patterns and how these patterns are associated with the underlying landscape dynamics by comparing ungulate movements across species. Locations Arctic tundra in Alaska and Canada, temperate forests in Massachusetts, Patagonian Steppes in Argentina, Eastern Steppes in Mongolia. Methods We used relocation data from four ungulate species (barren-ground caribou, Mongolian gazelle, guanaco and moose) to examine individual movements and the interrelation of movements among individuals. We applied and developed a suite of spatial metrics that measure variation in movement among individuals as population dispersion, movement coordination and realized mobility. Taken together, these metrics allowed us to quantify and distinguish among different large-scale population-level movement patterns such as migration, range residency and nomadism. We then related the population-level movement patterns to the underlying landscape vegetation dynamics via long-term remote sensing measurements of the temporal variability, spatial variability and unpredictability of vegetation productivity. Results Moose, which remained in sedentary home ranges, and guanacos, which were partially migratory, exhibited relatively short annual movements associated with landscapes having very little broad-scale variability in vegetation. Caribou and gazelle performed extreme long-distance movements that were associated with broad-scale variability in vegetation productivity during the peak of the growing season. Caribou exhibited regular seasonal migration in which individuals were clustered for most of the year and exhibited coordinated movements. In contrast, gazelle were nomadic, as individuals were independently distributed and moved in an uncoordinated manner that relates to the comparatively unpredictable (yet broad-scale) vegetation dynamics of their landscape. Main conclusions We show how

  20. Climate-Induced Dynamics of Periglacial Landscapes in NE Siberia: The Western Edge of Beringia During the Late Quaternary

    NASA Astrophysics Data System (ADS)

    Grosse, G.; Schirrmeister, L.; Siegert, C.; Meyer, H.; Andreev, A. A.; Kunitsky, V. V.; Derevyagin, A. Y.; Hubberten, H.

    2006-12-01

    Periglacial landscape dynamics have direct impacts on energy and matter cycles as well as ecosystems in large parts of the Arctic. Over the last decade, modern processes and past environments of periglacial landscapes in the Laptev Sea coastal lowlands were intensively studied within Russian and joint German- Russian research projects. A variety of palaeo-environmental records exists now for assessing the Late Quaternary dynamics of permafrost-dominated landscapes of this westernmost edge of Beringia. The main focus of this presentation is on the spatial and temporal dimensions of regional landscape changes in the Laptev Sea region induced by climatic change, especially by Holocene climate warming. For this purpose, we combine a variety of palaeo-environmental studies with remote sensing, terrain modelling, and GIS-based analyses of the modern landscape composition. We assess the landscape dynamics at the study site level and then draw conclusions for the whole region. Due to the low global sea level during the Late Weichselian cold stage, the Laptev Sea lowlands extended far on the shelf forming part of the unique continental environment of Western Beringia. The special periglacial environmental conditions of this period are recorded in frozen sediment sequences with palaeo-proxies ranging from lithology, ground ice, plant and animal fossils, to geomorphology. The Late Weichselian depositional environment there was characterized by ice-rich permafrost deposits (so-called Yedoma or Ice Complex formation) with up to 75 wt% absolute ice content. The Yedoma accumulated in lowland plains with polygonal tundra surrounding bedrock hills and mountain ridges. Additionally, the tundra plains were segmented by large river systems depositing fluvial sandy sediments. Major environmental changes affecting hydrology, geocryology, accumulation, and ecosystems in the region took place during the climate warming at the Late-Glacial Holocene transition. Within a short period in the

  1. Quantitative modeling of virus evolutionary dynamics and adaptation in serial passages using empirically inferred fitness landscapes.

    PubMed

    Woo, Hyung Jun; Reifman, Jaques

    2014-01-01

    We describe a stochastic virus evolution model representing genomic diversification and within-host selection during experimental serial passages under cell culture or live-host conditions. The model incorporates realistic descriptions of the virus genotypes in nucleotide and amino acid sequence spaces, as well as their diversification from error-prone replications. It quantitatively considers factors such as target cell number, bottleneck size, passage period, infection and cell death rates, and the replication rate of different genotypes, allowing for systematic examinations of how their changes affect the evolutionary dynamics of viruses during passages. The relative probability for a viral population to achieve adaptation under a new host environment, quantified by the rate with which a target sequence frequency rises above 50%, was found to be most sensitive to factors related to sequence structure (distance from the wild type to the target) and selection strength (host cell number and bottleneck size). For parameter values representative of RNA viruses, the likelihood of observing adaptations during passages became negligible as the required number of mutations rose above two amino acid sites. We modeled the specific adaptation process of influenza A H5N1 viruses in mammalian hosts by simulating the evolutionary dynamics of H5 strains under the fitness landscape inferred from multiple sequence alignments of H3 proteins. In light of comparisons with experimental findings, we observed that the evolutionary dynamics of adaptation is strongly affected not only by the tendency toward increasing fitness values but also by the accessibility of pathways between genotypes constrained by the genetic code.

  2. Potential and flux field landscape theory. II. Non-equilibrium thermodynamics of spatially inhomogeneous stochastic dynamical systems

    SciTech Connect

    Wu, Wei; Wang, Jin

    2014-09-14

    We have established a general non-equilibrium thermodynamic formalism consistently applicable to both spatially homogeneous and, more importantly, spatially inhomogeneous systems, governed by the Langevin and Fokker-Planck stochastic dynamics with multiple state transition mechanisms, using the potential-flux landscape framework as a bridge connecting stochastic dynamics with non-equilibrium thermodynamics. A set of non-equilibrium thermodynamic equations, quantifying the relations of the non-equilibrium entropy, entropy flow, entropy production, and other thermodynamic quantities, together with their specific expressions, is constructed from a set of dynamical decomposition equations associated with the potential-flux landscape framework. The flux velocity plays a pivotal role on both the dynamic and thermodynamic levels. On the dynamic level, it represents a dynamic force breaking detailed balance, entailing the dynamical decomposition equations. On the thermodynamic level, it represents a thermodynamic force generating entropy production, manifested in the non-equilibrium thermodynamic equations. The Ornstein-Uhlenbeck process and more specific examples, the spatial stochastic neuronal model, in particular, are studied to test and illustrate the general theory. This theoretical framework is particularly suitable to study the non-equilibrium (thermo)dynamics of spatially inhomogeneous systems abundant in nature. This paper is the second of a series.

  3. Potential and flux field landscape theory. II. Non-equilibrium thermodynamics of spatially inhomogeneous stochastic dynamical systems

    NASA Astrophysics Data System (ADS)

    Wu, Wei; Wang, Jin

    2014-09-01

    We have established a general non-equilibrium thermodynamic formalism consistently applicable to both spatially homogeneous and, more importantly, spatially inhomogeneous systems, governed by the Langevin and Fokker-Planck stochastic dynamics with multiple state transition mechanisms, using the potential-flux landscape framework as a bridge connecting stochastic dynamics with non-equilibrium thermodynamics. A set of non-equilibrium thermodynamic equations, quantifying the relations of the non-equilibrium entropy, entropy flow, entropy production, and other thermodynamic quantities, together with their specific expressions, is constructed from a set of dynamical decomposition equations associated with the potential-flux landscape framework. The flux velocity plays a pivotal role on both the dynamic and thermodynamic levels. On the dynamic level, it represents a dynamic force breaking detailed balance, entailing the dynamical decomposition equations. On the thermodynamic level, it represents a thermodynamic force generating entropy production, manifested in the non-equilibrium thermodynamic equations. The Ornstein-Uhlenbeck process and more specific examples, the spatial stochastic neuronal model, in particular, are studied to test and illustrate the general theory. This theoretical framework is particularly suitable to study the non-equilibrium (thermo)dynamics of spatially inhomogeneous systems abundant in nature. This paper is the second of a series.

  4. Erosion-vegetation dynamics in the Lucciolabella biancane badland cultural landscape (Southern Tuscany, Italy)

    NASA Astrophysics Data System (ADS)

    Maccherini, Simona; Vergari, Francesca; Santi, Elisa; Marignani, Michela; Della Seta, Marta; Rossi, Mauro; Torri, Dino; Del Monte, Maurizio

    2014-05-01

    In this work we present the results of multidisciplinary and long-lasting investigations on the complex cause-effect relationship among water erosion processes and vegetation cover on the Lucciolabella Natural Reserve, located in Upper Orcia Valley (Southern Tuscany). The area is a Site of Community Importance, where the cultural landscape of biancane badlands - water erosion landforms generated on Plio-Pleistocene marine clay outcrops - is preserved. We explored the direction and rate of change in land use and natural habitats of the biancana badland landscapes over the last 50 years, evaluating the erosion-vegetation dynamics and examining the processes involved in the biancana badland area. Historical information, such as early cadastral documents and diachronically analyzed aerial photographs, has been used to construct a database of the natural trends of modifications relative to habitat and plant species distribution, with the analysis of the consequent variations on the frequency of instability events. Old and recent land use maps were compared by using the TWINSPAN classification. Soil erodibility evaluation on the eroded biancana surfaces, regosols and well-developed vertisols, was carried out together with a decadal erosion monitoring program and the investigation of the physico-chemical properties of parent material. We also considered the effects of a few roots on saturated soil shear strength to introduce direct links between plants and soil processes. Moreover we run the LANDPLANER model in order to deepen the effect of the fragmentation of the vegetation cover on water erosion processes affecting biancana badlands. Long-lasting geomorphological survey and field erosion monitoring highlighted that biancana stations experience a very strong surface lowering rate due to water erosion, attaining an average rate of 2.4 - 2.6 cm/a. Moreover, biancanas in a more juvenile development phase, such as the ones of Lucciolabella Natural Reserve, show the maximum

  5. The invasive species Ulex europaeus (Fabaceae) shows high dynamism in a fragmented landscape of south-central Chile.

    PubMed

    Altamirano, Adison; Cely, Jenny Paola; Etter, Andrés; Miranda, Alejandro; Fuentes-Ramirez, Andres; Acevedo, Patricio; Salas, Christian; Vargas, Rodrigo

    2016-08-01

    Ulex europaeus (gorse) is an invasive shrub deemed as one of the most invasive species in the world. U. europaeus is widely distributed in the south-central area of Chile, which is considered a world hotspot for biodiversity conservation. In addition to its negative effects on the biodiversity of natural ecosystems, U. europaeus is one of the most severe pests for agriculture and forestry. Despite its importance as an invasive species, U. europaeus has been little studied. Although information exists on the potential distribution of the species, the interaction of the invasion process with the spatial dynamic of the landscape and the landscape-scale factors that control the presence or absence of the species is still lacking. We studied the spatial and temporal dynamics of the landscape and how these relate to U. europaeus invasion in south-central Chile. We used supervised classification of satellite images to determine the spatial distribution of the species and other land covers for the years 1986 and 2003, analysing the transitions between the different land covers. We used logistic regression for modelling the increase, decrease and permanence of U. europaeus invasion considering landscape variables. Results showed that the species covers only around 1 % of the study area and showed a 42 % reduction in area for the studied period. However, U. europaeus was the cover type which presented the greatest dynamism in the landscape. We found a strong relationship between changes in land cover and the invasion process, especially connected with forest plantations of exotic species, which promotes the displacement of U. europaeus. The model of gorse cover increase presented the best performance, and the most important predictors were distance to seed source and landscape complexity index. Our model predicted high spread potential of U. europaeus in areas of high conservation value. We conclude that proper management for this invasive species must take into account

  6. The invasive species Ulex europaeus (Fabaceae) shows high dynamism in a fragmented landscape of south-central Chile.

    PubMed

    Altamirano, Adison; Cely, Jenny Paola; Etter, Andrés; Miranda, Alejandro; Fuentes-Ramirez, Andres; Acevedo, Patricio; Salas, Christian; Vargas, Rodrigo

    2016-08-01

    Ulex europaeus (gorse) is an invasive shrub deemed as one of the most invasive species in the world. U. europaeus is widely distributed in the south-central area of Chile, which is considered a world hotspot for biodiversity conservation. In addition to its negative effects on the biodiversity of natural ecosystems, U. europaeus is one of the most severe pests for agriculture and forestry. Despite its importance as an invasive species, U. europaeus has been little studied. Although information exists on the potential distribution of the species, the interaction of the invasion process with the spatial dynamic of the landscape and the landscape-scale factors that control the presence or absence of the species is still lacking. We studied the spatial and temporal dynamics of the landscape and how these relate to U. europaeus invasion in south-central Chile. We used supervised classification of satellite images to determine the spatial distribution of the species and other land covers for the years 1986 and 2003, analysing the transitions between the different land covers. We used logistic regression for modelling the increase, decrease and permanence of U. europaeus invasion considering landscape variables. Results showed that the species covers only around 1 % of the study area and showed a 42 % reduction in area for the studied period. However, U. europaeus was the cover type which presented the greatest dynamism in the landscape. We found a strong relationship between changes in land cover and the invasion process, especially connected with forest plantations of exotic species, which promotes the displacement of U. europaeus. The model of gorse cover increase presented the best performance, and the most important predictors were distance to seed source and landscape complexity index. Our model predicted high spread potential of U. europaeus in areas of high conservation value. We conclude that proper management for this invasive species must take into account

  7. Exact results in the large system size limit for the dynamics of the chemical master equation, a one dimensional chain of equations.

    PubMed

    Martirosyan, A; Saakian, David B

    2011-08-01

    We apply the Hamilton-Jacobi equation (HJE) formalism to solve the dynamics of the chemical master equation (CME). We found exact analytical expressions (in large system-size limit) for the probability distribution, including explicit expression for the dynamics of variance of distribution. We also give the solution for some simple cases of the model with time-dependent rates. We derived the results of the Van Kampen method from the HJE approach using a special ansatz. Using the Van Kampen method, we give a system of ordinary differential equations (ODEs) to define the variance in a two-dimensional case. We performed numerics for the CME with stationary noise. We give analytical criteria for the disappearance of bistability in the case of stationary noise in one-dimensional CMEs.

  8. Exact results in the large system size limit for the dynamics of the chemical master equation, a one dimensional chain of equations.

    PubMed

    Martirosyan, A; Saakian, David B

    2011-08-01

    We apply the Hamilton-Jacobi equation (HJE) formalism to solve the dynamics of the chemical master equation (CME). We found exact analytical expressions (in large system-size limit) for the probability distribution, including explicit expression for the dynamics of variance of distribution. We also give the solution for some simple cases of the model with time-dependent rates. We derived the results of the Van Kampen method from the HJE approach using a special ansatz. Using the Van Kampen method, we give a system of ordinary differential equations (ODEs) to define the variance in a two-dimensional case. We performed numerics for the CME with stationary noise. We give analytical criteria for the disappearance of bistability in the case of stationary noise in one-dimensional CMEs. PMID:21928964

  9. Potential and flux field landscape theory. I. Global stability and dynamics of spatially dependent non-equilibrium systems.

    PubMed

    Wu, Wei; Wang, Jin

    2013-09-28

    We established a potential and flux field landscape theory to quantify the global stability and dynamics of general spatially dependent non-equilibrium deterministic and stochastic systems. We extended our potential and flux landscape theory for spatially independent non-equilibrium stochastic systems described by Fokker-Planck equations to spatially dependent stochastic systems governed by general functional Fokker-Planck equations as well as functional Kramers-Moyal equations derived from master equations. Our general theory is applied to reaction-diffusion systems. For equilibrium spatially dependent systems with detailed balance, the potential field landscape alone, defined in terms of the steady state probability distribution functional, determines the global stability and dynamics of the system. The global stability of the system is closely related to the topography of the potential field landscape in terms of the basins of attraction and barrier heights in the field configuration state space. The effective driving force of the system is generated by the functional gradient of the potential field alone. For non-equilibrium spatially dependent systems, the curl probability flux field is indispensable in breaking detailed balance and creating non-equilibrium condition for the system. A complete characterization of the non-equilibrium dynamics of the spatially dependent system requires both the potential field and the curl probability flux field. While the non-equilibrium potential field landscape attracts the system down along the functional gradient similar to an electron moving in an electric field, the non-equilibrium flux field drives the system in a curly way similar to an electron moving in a magnetic field. In the small fluctuation limit, the intrinsic potential field as the small fluctuation limit of the potential field for spatially dependent non-equilibrium systems, which is closely related to the steady state probability distribution functional, is

  10. The nucleosome landscape of Plasmodium falciparum reveals chromatin architecture and dynamics of regulatory sequences

    PubMed Central

    Kensche, Philip Reiner; Hoeijmakers, Wieteke Anna Maria; Toenhake, Christa Geeke; Bras, Maaike; Chappell, Lia; Berriman, Matthew; Bártfai, Richárd

    2016-01-01

    In eukaryotes, the chromatin architecture has a pivotal role in regulating all DNA-associated processes and it is central to the control of gene expression. For Plasmodium falciparum, a causative agent of human malaria, the nucleosome positioning profile of regulatory regions deserves particular attention because of their extreme AT-content. With the aid of a highly controlled MNase-seq procedure we reveal how positioning of nucleosomes provides a structural and regulatory framework to the transcriptional unit by demarcating landmark sites (transcription/translation start and end sites). In addition, our analysis provides strong indications for the function of positioned nucleosomes in splice site recognition. Transcription start sites (TSSs) are bordered by a small nucleosome-depleted region, but lack the stereotypic downstream nucleosome arrays, highlighting a key difference in chromatin organization compared to model organisms. Furthermore, we observe transcription-coupled eviction of nucleosomes on strong TSSs during intraerythrocytic development and demonstrate that nucleosome positioning and dynamics can be predictive for the functionality of regulatory DNA elements. Collectively, the strong nucleosome positioning over splice sites and surrounding putative transcription factor binding sites highlights the regulatory capacity of the nucleosome landscape in this deadly human pathogen. PMID:26578577

  11. The nucleosome landscape of Plasmodium falciparum reveals chromatin architecture and dynamics of regulatory sequences.

    PubMed

    Kensche, Philip Reiner; Hoeijmakers, Wieteke Anna Maria; Toenhake, Christa Geeke; Bras, Maaike; Chappell, Lia; Berriman, Matthew; Bártfai, Richárd

    2016-03-18

    In eukaryotes, the chromatin architecture has a pivotal role in regulating all DNA-associated processes and it is central to the control of gene expression. For Plasmodium falciparum, a causative agent of human malaria, the nucleosome positioning profile of regulatory regions deserves particular attention because of their extreme AT-content. With the aid of a highly controlled MNase-seq procedure we reveal how positioning of nucleosomes provides a structural and regulatory framework to the transcriptional unit by demarcating landmark sites (transcription/translation start and end sites). In addition, our analysis provides strong indications for the function of positioned nucleosomes in splice site recognition. Transcription start sites (TSSs) are bordered by a small nucleosome-depleted region, but lack the stereotypic downstream nucleosome arrays, highlighting a key difference in chromatin organization compared to model organisms. Furthermore, we observe transcription-coupled eviction of nucleosomes on strong TSSs during intraerythrocytic development and demonstrate that nucleosome positioning and dynamics can be predictive for the functionality of regulatory DNA elements. Collectively, the strong nucleosome positioning over splice sites and surrounding putative transcription factor binding sites highlights the regulatory capacity of the nucleosome landscape in this deadly human pathogen.

  12. Disease in a dynamic landscape: host behavior and wildfire reduce amphibian chytrid infection

    USGS Publications Warehouse

    Hossack, Blake R.; Lowe, Winsor H.; Ware, Joy L.; Corn, Paul Stephen

    2013-01-01

    Disturbances are often expected to magnify effects of disease, but these effects may depend on the ecology, behavior, and life history of both hosts and pathogens. In many ecosystems, wildfire is the dominant natural disturbance and thus could directly or indirectly affect dynamics of many diseases. To determine how probability of infection by the aquatic fungus Batrachochytrium dendrobatidis (Bd) varies relative to habitat use by individuals, wildfire, and host characteristics, we sampled 404 boreal toads (Anaxyrus boreas boreas) across Glacier National Park, Montana (USA). Bd causes chytridiomycosis, an emerging infectious disease linked with widespread amphibian declines, including the boreal toad. Probability of infection was similar for females and the combined group of males and juveniles. However, only 9% of terrestrial toads were infected compared to >30% of aquatic toads, and toads captured in recently burned areas were half as likely to be infected as toads in unburned areas. We suspect these large differences in infection reflect habitat choices by individuals that affect pathogen exposure and persistence, especially in burned forests where warm, arid conditions could limit Bd growth. Our results show that natural disturbances such as wildfire and the resulting diverse habitats can influence infection across large landscapes, potentially maintaining local refuges and host behaviors that facilitate evolution of disease resistance.

  13. Modelling land cover dynamics: integration of fine-scale land cover data with landscape attributes

    NASA Astrophysics Data System (ADS)

    Mertens, Benoît; Lambin, Eric

    Land cover change detection based on remote sensing data allows the identification of major processes of change and, by inference, the characterization of land use dynamics. Empirical diagnostic models of land use/cover change can be developed from these observations. To grasp the complexity of landscape mosaics and changes in land use, fine-scale land cover and socio-economic data are required. Case studies need to be representative of conditions at a broader scale, and selected where sufficient knowledge on social and ecological processes leading to land use changes exists. For this reason, collaboration between remote sensing specialists and human ecologists conducting long-term field-based land use studies is extremely productive. Continental-scale analysis of Africa was conducted to detect land cover change "hot spots". Fine-scale analyses were performed for validation purposes and to understand better the land cover change processes. Spatial statistical models of land cover change can be developed in order to anticipate where changes are more likely to occur next. Such predictive information is essential to support the implementation of appropriate policy responses to, for example, land degradation that would lead to the depletion of essential resources. Results of a spatial model of deforestation in southern Cameroon are discussed.

  14. 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.

  15. Modelling Landscape Dynamics in a Highland Mediterranean Catchment: Establishing the impact of Climate Variation and Human Activity

    NASA Astrophysics Data System (ADS)

    van Beek, L. P. H.; Feiken, H.; van Asch, T. W. J.; Bierkens, M. F. P.

    2012-04-01

    The close link between human occupancy and the Mediterranean landscape has long been recognized. Through the exploitation of the various but fragmented resources that these landscapes have to offer, man has been able to secure a living. However, these activities are often marginal and small shifts in population pressure, corresponding land use patterns or climatic variability can have large consequences on the redistribution of water and sediment in these areas. The meso-scale landscape dynamics model, CALEROS, has been developed to simulate the interactions between climate, soil production and erosion, vegetation and land use on geomorphological to human time scales in Mediterranean environments. Starting from an initial landscape consisting of a DTM, soil distribution and underlying lithology, the landscape is free to develop in response to the imposed climate variability and seismicity. In addition to changes in soil distribution and bedrock lowering, this includes the establishment of vegetation as conditioned by a selection of plant functional types and, optionally, population and land use dynamics as conditioned by land use scenarios specifying technological and dietary constraints for different periods. As such CALEROS is well-suited to investigate the relative impacts of climate, land cover and human activities on the hydrological catchment response and the associated sediment fluxes due to soil erosion and mass movements. Within the context of a geo-archeological study on the conservation potential of settlement history in the Contrada Maddalena (~14km2, Calabria, Italy), we apply CALEROS to investigate the relative contributions of climate and man from Neolithic times onwards (5000 BP-present). Model results allow to establish when human impacts become significant over natural variations and to discern shifts in catchment functioning as a result of sudden or climatic variations (e.g., Little Ice Age) as reflected in vegetation patterns and water and

  16. Modeling seasonal dynamics of the small fish cohorts in fluctuating freshwater marsh landscapes

    USGS Publications Warehouse

    Jopp, Fred; DeAngelis, Donald L.; Trexler, Joel C.

    2010-01-01

    Small-bodied fishes constitute an important assemblage in many wetlands. In wetlands that dry periodically except for small permanent waterbodies, these fishes are quick to respond to change and can undergo large fluctuations in numbers and biomasses. An important aspect of landscapes that are mixtures of marsh and permanent waterbodies is that high rates of biomass production occur in the marshes during flooding phases, while the permanent waterbodies serve as refuges for many biotic components during the dry phases. The temporal and spatial dynamics of the small fishes are ecologically important, as these fishes provide a crucial food base for higher trophic levels, such as wading birds. We develop a simple model that is analytically tractable, describing the main processes of the spatio-temporal dynamics of a population of small-bodied fish in a seasonal wetland environment, consisting of marsh and permanent waterbodies. The population expands into newly flooded areas during the wet season and contracts during declining water levels in the dry season. If the marsh dries completely during these times (a drydown), the fish need refuge in permanent waterbodies. At least three new and general conclusions arise from the model: (1) there is an optimal rate at which fish should expand into a newly flooding area to maximize population production; (2) there is also a fluctuation amplitude of water level that maximizes fish production, and (3) there is an upper limit on the number of fish that can reach a permanent waterbody during a drydown, no matter how large the marsh surface area is that drains into the waterbody. Because water levels can be manipulated in many wetlands, it is useful to have an understanding of the role of these fluctuations.

  17. Spatial Patterns of Channel Steepness in the Central Rockies: Do River Profiles Record Landscape Evolution Forcing By Yellowstone Dynamic Topography?

    NASA Astrophysics Data System (ADS)

    Guerrero, E. F.; Meigs, A.; Kirby, E.; Gregg, P. M.

    2014-12-01

    Numerous investigations demonstrate that mantle convective processes affect the surface topography of the overriding plate. 'Positive dynamic topography' refers to the surface expression of mantle upwelling. An advecting wave of dynamic topographic surface uplift plate is thought to result from migration of North America relative to the Yellowstone hotspot. Advection of positive dynamic topography through an overriding plate disturbs the landscape by a combination of a change in surface uplift rate and tilting. Identification of dynamic topography's contribution to evolution of the greater Yellowstone region's landscape, however, is complicated by the polygenetic regional topography that results from glaciation, bimodal volcanism, Basin and Range extension, early Cenozoic arc volcanism, and Laramide contraction. Our model, which is parameterized to Yellowstone but doesn't include climate variations, suggests contribution of the dynamic topography erosional signal should decrease from 0.1mm/yr to 0.5 mm/yr at a 100km radius from the hotspot uplift source. The cosmogenic chronology that we are building to constrain spatial patterns of incision in the Bighorn Basin indicates that there is differential incision occurring in the Bighorn basin. Rates vary from 2.8mm/yr in the western basin, which is closer to Yellowstone to 1.1mm/yr in the eastern basin. Global cooling and its effects at the Plio-Pleistocene transition is thought to be the dominant control on the region's erosional regime. However, the magnitude of the contribution from Yellowstone dynamic topography to the regional landscape evolution is still unknown because published incision rates lack the resolution to differentiate between incision forcing mechanisms. Bedrock stream profile analysis is powerful tool for determining spatial patterns of surface deformation. We compare results for normalized channel steepness indices across various basins in the Central Rockies and Greater Yellowstone area with

  18. Towards understanding temporal and spatial dynamics of seagrass landscapes using time-series remote sensing

    NASA Astrophysics Data System (ADS)

    Lyons, Mitchell B.; Roelfsema, Chris M.; Phinn, Stuart R.

    2013-03-01

    The spatial and temporal dynamics of seagrasses have been well studied at the leaf to patch scales, however, the link to large spatial extent landscape and population dynamics is still unresolved in seagrass ecology. Traditional remote sensing approaches have lacked the temporal resolution and consistency to appropriately address this issue. This study uses two high temporal resolution time-series of thematic seagrass cover maps to examine the spatial and temporal dynamics of seagrass at both an inter- and intra-annual time scales, one of the first globally to do so at this scale. Previous work by the authors developed an object-based approach to map seagrass cover level distribution from a long term archive of Landsat TM and ETM+ images on the Eastern Banks (≈200 km2), Moreton Bay, Australia. In this work a range of trend and time-series analysis methods are demonstrated for a time-series of 23 annual maps from 1988 to 2010 and a time-series of 16 monthly maps during 2008-2010. Significant new insight was presented regarding the inter- and intra-annual dynamics of seagrass persistence over time, seagrass cover level variability, seagrass cover level trajectory, and change in area of seagrass and cover levels over time. Overall we found that there was no significant decline in total seagrass area on the Eastern Banks, but there was a significant decline in seagrass cover level condition. A case study of two smaller communities within the Eastern Banks that experienced a decline in both overall seagrass area and condition are examined in detail, highlighting possible differences in environmental and process drivers. We demonstrate how trend and time-series analysis enabled seagrass distribution to be appropriately assessed in context of its spatial and temporal history and provides the ability to not only quantify change, but also describe the type of change. We also demonstrate the potential use of time-series analysis products to investigate seagrass growth and

  19. Carbon and Nitrogen Cycling in Urban Landscapes: Global, Regional Dynamics and Case Studies.

    NASA Astrophysics Data System (ADS)

    Svirejeva-Hopkins, A.; Nardoto, G. B.; Schellnhuber, H.

    2008-12-01

    The urban population has been growing rapidly in the last decades and is predicted to continue its exponential trend, especially in the developing countries, which would create additional pressure on the environment by overpopulated unsustainable cities and will continue to substantially change the main Biogeochemical cycles. Such disturbances in the main driving cycle of the Biosphere (global carbon cycle) and the nitrogen cycle, induced by sprawling urban human activities, lead to global, regional and local environmental problems, i.e. global warming, photochemical smog, stratospheric ozone depletion, soil acidification, nitrate pollution of surface and ground water, coastal ecosystem disturbances. Since urban areas are expected to continue their rapid expansion in the 21st century, accompanied by growing energy production, increased food demand, expanding transportation and industrialization it becomes more and more important to be able to describe and forecast the dynamics of biogeochemical functioning of these landscapes (which have altered characteristics compared to the natural ecosystems). Moreover, from the environmental policy perspective, a high density of people makes cities focal points of vulnerability to global environmental change. The model based on the forecasting the dynamics of urban area growth, allows us to forecast the dynamics of Carbon and Nitrogen on the urban territories at different scales. However, nitrogen cycle is very complex and is closely interlinked with the other major biogeochemical cycles, such as oxygen and water. The system of water supply and liquid waste carried by water out of the system 'city' is investigated. In order to better understand the mechanisms of cycling, we consider the case studies, when we investigated the detailed fluxes of Carbon and Nitrogen in Sao Paolo (Brazil) and Paris (France). When we know the yearly amounts of carbon and nitrogen, produced by a city, we should be capable of coming up with what

  20. Site-level model intercomparison of high latitude and high altitude soil thermal dynamics in tundra and barren landscapes

    NASA Astrophysics Data System (ADS)

    Ekici, A.; Chadburn, S.; Chaudhary, N.; Hajdu, L. H.; Marmy, A.; Peng, S.; Boike, J.; Burke, E.; Friend, A. D.; Hauck, C.; Krinner, G.; Langer, M.; Miller, P. A.; Beer, C.

    2015-07-01

    Modeling soil thermal dynamics at high latitudes and altitudes requires representations of physical processes such as snow insulation, soil freezing and thawing and subsurface conditions like soil water/ice content and soil texture. We have compared six different land models: JSBACH, ORCHIDEE, JULES, COUP, HYBRID8 and LPJ-GUESS, at four different sites with distinct cold region landscape types, to identify the importance of physical processes in capturing observed temperature dynamics in soils. The sites include alpine, high Arctic, wet polygonal tundra and non-permafrost Arctic, thus showing how a range of models can represent distinct soil temperature regimes. For all sites, snow insulation is of major importance for estimating topsoil conditions. However, soil physics is essential for the subsoil temperature dynamics and thus the active layer thicknesses. This analysis shows that land models need more realistic surface processes, such as detailed snow dynamics and moss cover with changing thickness and wetness, along with better representations of subsoil thermal dynamics.

  1. Landscape epidemiology of plant diseases.

    PubMed

    Plantegenest, Manuel; Le May, Christophe; Fabre, Frédéric

    2007-10-22

    Many agricultural landscapes are characterized by a high degree of heterogeneity and fragmentation. Landscape ecology focuses on the influence of habitat heterogeneity in space and time on ecological processes. Landscape epidemiology aims at applying concepts and approaches originating from landscape ecology to the study of pathogen dynamics at the landscape scale. However, despite the strong influence that the landscape properties may have on the spread of plant diseases, landscape epidemiology has still received little attention from plant pathologists. Some recent methodological and technological progress provides new and powerful tools to describe and analyse the spatial patterns of host-pathogen interactions. Here, we review some important topics in plant pathology that may benefit from a landscape perspective. These include the influence of: landscape composition on the global inoculum pressure; landscape heterogeneity on pathogen dynamics; landscape structure on pathogen dispersal; and landscape properties on the emergence of pathogens and on their evolution.

  2. Linking demographic effects of habitat fragmentation across landscapes to continental source-sink dynamics

    USGS Publications Warehouse

    Lloyd, P.; Martin, T.E.; Redmond, R.L.; Langner, U.; Hart, M.M.

    2005-01-01

    Forest fragmentation may cause increased brood parasitism and nest predation of breeding birds. In North America, nest parasitism and predation are expected to increase closer to forest edges because the brood-parasitic Brown-headed Cowbird (Molothrus ater) and generalist nest predators often enter the forest from adjoining developed (largely agricultural) habitats. Yet the abundance of brood parasites and nest predators at the patch scale may be strongly constrained by the total area of developed habitat at landscape scales. The scale and extent of landscape effects are unclear, however, because past studies were mostly conducted within local landscapes rather than across independent landscapes. We report replicated studies from 30 independent landscapes across 17 states of the United States that show that nest parasitism is strongly affected by fragmentation at a 20 km radius scale, equivalent to the maximum foraging range of cowbirds. Nest predation is influenced by both edge and landscape effects, and increases with fragmentation at a 10 km radius scale. Predation is additive to parasitism mortality, and the two together yield decreased population growth potential with increasing forest fragmentation at a 10 km radius scale for 20 of 22 bird species. Mapping of population growth potential across continental landscapes displays broad impacts of fragmentation on population viability and allows geographic prioritization for conservation. ?? 2005 by the Ecological Society of America.

  3. Detecting the dynamic linkage between landscape characteristics and water quality in a subtropical coastal watershed, Southeast China.

    PubMed

    Huang, Jinliang; Li, Qingsheng; Pontius, Robert Gilmore; Klemas, Victor; Hong, Huasheng

    2013-01-01

    Geospatial analysis and statistical analysis are coupled in this study to determine the dynamic linkage between landscape characteristics and water quality for the years 1996, 2002, and 2007 in a subtropical coastal watershed of Southeast China. The landscape characteristics include Percent of Built (%BL), Percent of Agriculture, Percent of Natural, Patch Density and Shannon's Diversity Index (SHDI), with water quality expressed in terms of COD(Mn) and NH(4)(+)-N. The %BL was consistently positively correlated with NH(4)(+)-N and COD(Mn) at time three points. SHDI is significantly positively correlated with COD(Mn) in 2002. The relationship between NH(4)(+)-N, COD(Mn) and landscape variables in the wet precipitation year 2007 is stronger, with R(2) = 0.892, than that in the dry precipitation years 1996 and 2002, which had R(2) values of 0.712 and 0.455, respectively. Two empirical regression models constructed in this study proved more suitable for predicting COD(Mn) than for predicting NH(4)(+)-N concentration in the unmonitored watersheds that do not have wastewater treatment plants. The calibrated regression equations have a better predictive ability over space within the wet precipitation year of 2007 than over time during the dry precipitation years from 1996 to 2002. Results show clearly that climatic variability influences the linkage of water quality-landscape characteristics and the fit of empirical regression models.

  4. When the entire landscape is riparian: the challenges to understanding and modeling ecosystem dynamics in lowland headwaters

    NASA Astrophysics Data System (ADS)

    Bernhardt, E. S.; Poole, G.; Ardon, M.; Helton, A. M.; Morse, J. L.; Payn, R.; Burgin, A. J.

    2011-12-01

    In the low relief landscapes of the southeastern coastal plain, headwater ecosystems have ill defined channels and lack visible valleys. The links between rivers and their floodplains in such landscapes are so spatially extensive that many headwaters in this region are classified as stream swamps or riverine wetlands. Frequently flooded soils are highly organic and drain slowly so that the water table often rises above the ground surface. Hydrologic flowpaths through the riparian zone are thus quite different from upland systems and are often dominated by lateral surface water connections, while the vertical movement of the water table is a critical control over biogeochemical function within all landscape patches. Linking the variation in vertical hydrologic connectivity to biogeochemical function at the patch scale and setting patch dynamics into a landscape level hydrologic context are ultimately necessary steps towards building a mechanistic, ecosystem-level understanding of these extensive coastal habitats. In this talk I will discuss our progress in developing conceptual and empirical models of riverine wetland biogeochemistry based upon four years of intensive observational and experimental research in a large (440ha) restored coastal plain wetland in the North Carolina coastal plain.

  5. Detecting the Dynamic Linkage between Landscape Characteristics and Water Quality in a Subtropical Coastal Watershed, Southeast China

    NASA Astrophysics Data System (ADS)

    Huang, Jinliang; Li, Qingsheng; Pontius, Robert Gilmore; Klemas, Victor; Hong, Huasheng

    2013-01-01

    Geospatial analysis and statistical analysis are coupled in this study to determine the dynamic linkage between landscape characteristics and water quality for the years 1996, 2002, and 2007 in a subtropical coastal watershed of Southeast China. The landscape characteristics include Percent of Built (%BL), Percent of Agriculture, Percent of Natural, Patch Density and Shannon's Diversity Index (SHDI), with water quality expressed in terms of CODMn and NH4 +-N. The %BL was consistently positively correlated with NH4 +-N and CODMn at time three points. SHDI is significantly positively correlated with CODMn in 2002. The relationship between NH4 +-N, CODMn and landscape variables in the wet precipitation year 2007 is stronger, with R2 = 0.892, than that in the dry precipitation years 1996 and 2002, which had R2 values of 0.712 and 0.455, respectively. Two empirical regression models constructed in this study proved more suitable for predicting CODMn than for predicting NH4 +-N concentration in the unmonitored watersheds that do not have wastewater treatment plants. The calibrated regression equations have a better predictive ability over space within the wet precipitation year of 2007 than over time during the dry precipitation years from 1996 to 2002. Results show clearly that climatic variability influences the linkage of water quality-landscape characteristics and the fit of empirical regression models.

  6. Sediment Dynamics in Shallow Tidal Landscapes: The Role of Wind Waves and Tidal Currents

    NASA Astrophysics Data System (ADS)

    Carniello, L.; D'Alpaos, A.

    2014-12-01

    A precise description of sediment dynamics (resuspension and re-distribution of sediments) is crucial when investigating the long term evolution of the different morphological entities characterizing tidal landscapes. It has been demonstrated that wind waves are the main responsible for sediment resuspension in shallow micro-tidal lagoons where tidal currents, which produce shear stresses large enough to carry sediments into suspension only within the main channels, are mainly responsible for sediment redistribution. A mathematical model has been developed to describe sediment entrainment, transport and deposition due to the combined effect of tidal currents and wind waves in shallow lagoons considering both cohesive and non-cohesive sediments. The model was calibrated and tested using both in situ point observations and turbidity maps obtained analyzing satellite images. Once calibrated the model can integrate the high temporal resolution of point observations with the high spatial resolution of remote sensing, overcoming the intrinsic limitation of these two types of observations. The model was applied to the specific test case of the Venice lagoon simulating an entire year (2005) which was shown to be a "representative" year for wind and tide characteristics. The time evolution of the computed total bottom shear stresses (BSS) and suspended sediment concentration (SSC) was analyzed on the basis of a "Peaks Over Threshold" method once a critical value for shear stress and turbidity were chosen. The analyses of the numerical results enabled us to demonstrate that resuspension events can be modeled as marked Poisson processes: interarrival time, intensity of peak excesses and duration being exponentially distributed random variable. The probability distributions of the interarrival time of overthreshold exceedances in both BSS and SSC as well as their intensity and duration can be used in long-term morphodynamic studies to generate synthetic series statistically

  7. Storage Dynamics and Non-Linear Connectivity between Landscape Units Control Runoff Generation and Stream Water Age Distributions

    NASA Astrophysics Data System (ADS)

    Soulsby, C.; Birkel, C.; Geris, J.; Tetzlaff, D.

    2015-12-01

    We assess the influence of storage dynamics and non-linearities in hydrological connectivity on runoff generation and stream water ages, using a long-term record of daily isotopes in precipitation and stream flow. These were used to test a parsimonious tracer-aided runoff model for a Scottish catchment. The model tracks tracers and the ages of water fluxes through and between conceptual stores representing steeper hillslopes, dynamically saturated riparian peatlands and deeper groundwater (i.e. the main landscape units involved in runoff generation). Storage is largest in groundwater and on the steep hillslopes, though most dynamic mixing occurs in smaller stores in the riparian peat. The model also couples the ecohydrological effects of different vegetation communities in contrasting landscape units, by estimating evaporation, resulting moisture deficits and the ages of evaporated waters, which also affect the generation and age of runoff. Both stream flow and isotope variations are well-captured by the model, and the simulated storage and tracer dynamics in the main landscape units are consistent with independent measurements. The model predicts the mean age of runoff as ~1.8 years. On a daily basis, this varies from ~1 month in storm events, when younger waters draining the riparian peatland dominate, to around 4 years in dry periods, when groundwater sustains flow. Hydrological connectivity between the units varies non-linearly with storage which depends upon antecedent conditions and event characteristics. This, in turn, determines the spatial distribution of flow paths and the integration of their contrasting non-stationary ages. Improving the representation of storage dynamics and quantifying the ages of water fluxes in such models gives a more complete conceptualisation of the importance of the soil water fluxes in critical zone processes and a framework for tracking diffuse pollutants in water quality assessment.

  8. Effects of natural and human-assisted regeneration on landscape dynamics in a Korean pine forest in Northeast China.

    PubMed

    Zhao, Fuqiang; Yang, Jian; He, Hong S; Dai, Limin

    2013-01-01

    Improper forest harvesting can potentially degrade forest ecosystem functions and services. Human-assisted regeneration (e.g., planting) is often used to increase the rate of forest recovery and thereby reduce regeneration failure. Seed dispersal is a fundamental ecological process that can also influence spatio-temporal patterns of forest regeneration. In this study, we investigated the relative contribution of planting and seed dispersal on forest regeneration at landscape scales. Because such influences can be further complicated by timber harvest intensity and seed availability within and around harvested area, we also evaluated the effects of those factors on forest landscape dynamics. We used the forest landscape model LANDIS to simulate the dynamics of Korean pine-broadleaf mixed forests in Northeast China. We considered three factors: timber harvest intensity (3 levels), seed dispersal and whether or not planting was used. The results showed that planting was more important in maintaining the abundance of Korean pine (Pinus koraiensis), a climax keystone species in this region, under the high-intensity harvesting option during early succession. In contrast, seed dispersal was more important during late succession. Korean pine can be successfully regenerated through seed dispersal under low and medium harvest intensities. Our results also indicated that effective natural regeneration will require protecting seed-production trees (seed rain). This study results provide a basis for more effectively managing Chinese temperate forests and possibly other similar ecosystems.

  9. Effects of Natural and Human-Assisted Regeneration on Landscape Dynamics in a Korean Pine Forest in Northeast China

    PubMed Central

    Zhao, Fuqiang; Yang, Jian; He, Hong S.; Dai, Limin

    2013-01-01

    Improper forest harvesting can potentially degrade forest ecosystem functions and services. Human-assisted regeneration (e.g., planting) is often used to increase the rate of forest recovery and thereby reduce regeneration failure. Seed dispersal is a fundamental ecological process that can also influence spatio-temporal patterns of forest regeneration. In this study, we investigated the relative contribution of planting and seed dispersal on forest regeneration at landscape scales. Because such influences can be further complicated by timber harvest intensity and seed availability within and around harvested area, we also evaluated the effects of those factors on forest landscape dynamics. We used the forest landscape model LANDIS to simulate the dynamics of Korean pine-broadleaf mixed forests in Northeast China. We considered three factors: timber harvest intensity (3 levels), seed dispersal and whether or not planting was used. The results showed that planting was more important in maintaining the abundance of Korean pine (Pinus koraiensis), a climax keystone species in this region, under the high-intensity harvesting option during early succession. In contrast, seed dispersal was more important during late succession. Korean pine can be successfully regenerated through seed dispersal under low and medium harvest intensities. Our results also indicated that effective natural regeneration will require protecting seed-production trees (seed rain). This study results provide a basis for more effectively managing Chinese temperate forests and possibly other similar ecosystems. PMID:24324785

  10. Simulation of the Vortex Dynamics in a Real Pinning Landscape of YBa2 Cu3 O7 -δ Coated Conductors

    NASA Astrophysics Data System (ADS)

    Sadovskyy, I. A.; Koshelev, A. E.; Glatz, A.; Ortalan, V.; Rupich, M. W.; Leroux, M.

    2016-01-01

    The ability of high-temperature superconductors (HTSs) to carry very large currents with almost no dissipation makes them irreplaceable for high-power applications. The development and further improvement of HTS-based cables require an in-depth understanding of the superconducting vortex dynamics in the presence of complex pinning landscapes. We present a critical current analysis of a real HTS sample in a magnetic field by combining state-of-the-art large-scale Ginzburg-Landau simulations with reconstructive three-dimensional scanning-transmission-electron-microscopy tomography of the pinning landscape in Dy-doped YBa2 Cu3 O7 -δ . This methodology provides a unique look at the vortex dynamics in the presence of a complex pinning landscape responsible for the high-current-carrying-capacity characteristic of commercial HTS wires. Our method demonstrates very good functional and quantitative agreement of the critical current between simulation and experiment, providing a new predictive tool for HTS wire designs.

  11. Characterization of climate- and human-induced slope, soil and grassland dynamics in Bavarian landscapes under climate change

    NASA Astrophysics Data System (ADS)

    Waltl, Peter; Schwindt, Daniel; Völkel, Jörg

    2016-04-01

    Since the Neolithic Revolution the intensification of agriculture has been causing increased erosion in Bavarian landscapes. The correlated sediments often induce the formation of new colluvial and alluvial soils (WRB: Regic Anthrosol and Fluvisol i.a.). The soils themselves are able to absorb, bind, and store considerable amounts of C- and N-compounds. Therefore, they are important reactors regarding climate-relevant greenhouse-gas balances in the atmosphere. Learning about the exact spatial extent and thickness of these soils in representative landscapes, but also about their geneses and processes is essential. It allows for a detailed quantification and understanding of the current and potential properties and characteristics of these soils in their role of greenhouse-gas reactors. Two research locations were elected as representative Bavarian landscapes composed of different lithology and pedo-chemical environments (limestone versus crystalline setting): Rottenbuch is situated at the Ammer River in the Upper Bavarian pre-alpine forelands (Lkr. Weilheim-Schongau). The Otterbach Creek lies at the southwestern foothills of the Bavarian Forest at the Donaurandbruch tectonic line next to Donaustauf (Lkr. Regensburg). Detailed information on the soil horizons and layers within these research areas are accumulated by sounding or burrowing soil profiles and subsequently analyzing the soil samples in the lab. Geophysical methods, such as electrical resistivity tomography (ERT), seismic refraction tomography (SRT), and ground penetrating radar (GPR), allow for the extension of this point-source information into three dimensions. By repeatedly and regularly applying these methods, also temporal changes such as soil hydrology or freeze and thaw cycles can be monitored and their influence on fluxes and exchanges can be taken into account.

  12. Exact two-body quantum dynamics of an electron-hole pair in semiconductor coupled quantum wells: A time-dependent approach

    NASA Astrophysics Data System (ADS)

    Grasselli, Federico; Bertoni, Andrea; Goldoni, Guido

    2016-05-01

    We simulate the time-dependent coherent dynamics of a spatially indirect exciton—an electron-hole pair with the two particles confined in different layers—in a GaAs coupled quantum well system. We use a unitary wave-packet propagation method taking into account in full the four degrees of freedom of the two particles in a two-dimensional system, including both the long-range Coulomb attraction and arbitrary two-dimensional electrostatic potentials affecting the electron and/or the hole separately. The method has been implemented for massively parallel architectures to cope with the huge numerical problem, showing good scaling properties and allowing evolution for tens of picoseconds. We have investigated both transient time phenomena and asymptotic time transmission and reflection coefficients for potential profiles consisting of (i) extended barriers and wells and (ii) a single-slit geometry. We found clear signatures of the internal two-body dynamics, with transient phenomena in the picosecond time scale which might be revealed by optical spectroscopy. Exact results have been compared with mean-field approaches which, neglecting dynamical correlations by construction, turn out to be inadequate to describe the electron-hole pair evolution in realistic experimental conditions.

  13. Feedbacks between subglacial dynamics and long-term glacial landscape evolution (Invited)

    NASA Astrophysics Data System (ADS)

    Brædstrup, C. F.; Egholm, D. L.; Ugelvig, S. V.; Christensen, A. D.; Andersen, J. L.

    2013-12-01

    Several well-known glacial landforms (such as U-shaped troughs and cirques) are associated with characteristic length scales, indicating that the viscosity of the ice and the stress gradients associated with ice flow exert first-order controls on their formation. The evolution of these glacial landforms has so far mostly been explored using phenomenological models that simply link the subglacial erosion rate to sliding or ice discharge. In order to improve our understanding of the causal links between the glacial landforms and the physics of the subglacial environment, we have performed computational experiments with a higher-order ice sheet model (Egholm et al., 2009) capable of simulating the long-term evolution of subglacial dynamics at a high spatial resolution. The orientation and magnitude of subglacial stress components depend not only on ice thickness and ice surface gradients, but also on the details of the bed topography and the regional variations in ice flow velocity. As glaciers erode their beds and modify the morphology of glaciated valleys, the subglacial dynamics therefore change with important implications for the sliding patterns and the continued erosion rates. We focus this presentation on feedbacks between the evolving bed topography and the subglacial erosion patterns. We have performed our experiments with different sliding and erosion laws, including highly non-linear rules representing coulomb-type slip at the bed (Schoof, 2010) and a quarrying model associated to the level of cavitation (Iverson, 2012). The highly non-linear computational experiments are made possible by new and very efficient GPU-accelerated multigrid algorithms. The computational experiments show that higher-order stress effects associated with local changes to the bed gradient provide important stabilizing effects for example in overdeepenings and near topographic steps. The experiments also show how a narrow and meandering pre-glacial valley represents a much more

  14. Validation of computational fluid dynamics methods with anatomically exact, 3D printed MRI phantoms and 4D pcMRI.

    PubMed

    Anderson, Jeff R; Diaz, Orlando; Klucznik, Richard; Zhang, Y Jonathan; Britz, Gavin W; Grossman, Robert G; Lv, Nan; Huang, Qinghai; Karmonik, Christof

    2014-01-01

    A new concept of rapid 3D prototyping was implemented using cost-effective 3D printing for creating anatomically correct replica of cerebral aneurysms. With a dedicated flow loop set-up in a full body human MRI scanner, flow measurements were performed using 4D phase contrast magnetic resonance imaging to visualize and quantify intra-aneurysmal flow patterns. Ultrashort TE sequences were employed to obtain high-resolution 3D image data to visualize the lumen inside the plastic replica. In-vitro results were compared with retrospectively obtained in-vivo data and results from computational fluid dynamics simulations (CFD). Rapid prototyping of anatomically realistic 3D models may have future impact in treatment planning, design of image acquisition methods for MRI and angiographic systems and for the design and testing of advanced image post-processing technologies.

  15. Simulation of the vortex dynamics in a real pinning landscape of YBa2Cu3O7-δ coated conductors

    NASA Astrophysics Data System (ADS)

    Sadovskyy, Ivan; Koshelev, Alexei; Glatz, Andreas; Ortalan, Volkan; Rupich, Martin; Leroux, Maxime

    We present a critical current analysis of a real high-temperature superconducting (HTS) sample in a magnetic field by combining state-of-the-art large-scale Ginzburg-Landau simulations with reconstructive three-dimensional scanning transmission electron microscopy tomography of the pinning landscape in Dy-doped YBa2Cu3O7-δ. This methodology provides a unique look at the vortex dynamics in the presence of a complex pinning landscape, responsible for the high current-carrying capacity characteristic of commercial HTS wires. Our method demonstrates very good functional and quantitative agreement of the critical current between simulation and experiment, providing a new predictive tool for HTS wires design. Work was supported by the Scientific Discovery through Advanced Computing (SciDAC) program funded by U.S. Department of Energy, Office of Science, Advanced Scientific Computing Research and Basic Energy Sciences.

  16. Joint effects of habitat heterogeneity and species' life-history traits on population dynamics in spatially structured landscapes.

    PubMed

    Ye, Xinping; Skidmore, Andrew K; Wang, Tiejun

    2014-01-01

    Both habitat heterogeneity and species' life-history traits play important roles in driving population dynamics, yet there is little scientific consensus around the combined effect of these two factors on populations in complex landscapes. Using a spatially explicit agent-based model, we explored how interactions between habitat spatial structure (defined here as the scale of spatial autocorrelation in habitat quality) and species life-history strategies (defined here by species environmental tolerance and movement capacity) affect population dynamics in spatially heterogeneous landscapes. We compared the responses of four hypothetical species with different life-history traits to four landscape scenarios differing in the scale of spatial autocorrelation in habitat quality. The results showed that the population size of all hypothetical species exhibited a substantial increase as the scale of spatial autocorrelation in habitat quality increased, yet the pattern of population increase was shaped by species' movement capacity. The increasing scale of spatial autocorrelation in habitat quality promoted the resource share of individuals, but had little effect on the mean mortality rate of individuals. Species' movement capacity also determined the proportion of individuals in high-quality cells as well as the proportion of individuals experiencing competition in response to increased spatial autocorrelation in habitat quality. Positive correlations between the resource share of individuals and the proportion of individuals experiencing competition indicate that large-scale spatial autocorrelation in habitat quality may mask the density-dependent effect on populations through increasing the resource share of individuals, especially for species with low mobility. These findings suggest that low-mobility species may be more sensitive to habitat spatial heterogeneity in spatially structured landscapes. In addition, localized movement in combination with spatial

  17. Modelling Population Dynamics in Realistic Landscapes with Linear Elements: A Mechanistic-Statistical Reaction-Diffusion Approach

    PubMed Central

    2016-01-01

    We propose and develop a general approach based on reaction-diffusion equations for modelling a species dynamics in a realistic two-dimensional (2D) landscape crossed by linear one-dimensional (1D) corridors, such as roads, hedgerows or rivers. Our approach is based on a hybrid “2D/1D model”, i.e, a system of 2D and 1D reaction-diffusion equations with homogeneous coefficients, in which each equation describes the population dynamics in a given 2D or 1D element of the landscape. Using the example of the range expansion of the tiger mosquito Aedes albopictus in France and its main highways as 1D corridors, we show that the model can be fitted to realistic observation data. We develop a mechanistic-statistical approach, based on the coupling between a model of population dynamics and a probabilistic model of the observation process. This allows us to bridge the gap between the data (3 levels of infestation, at the scale of a French department) and the output of the model (population densities at each point of the landscape), and to estimate the model parameter values using a maximum-likelihood approach. Using classical model comparison criteria, we obtain a better fit and a better predictive power with the 2D/1D model than with a standard homogeneous reaction-diffusion model. This shows the potential importance of taking into account the effect of the corridors (highways in the present case) on species dynamics. With regard to the particular case of A. albopictus, the conclusion that highways played an important role in species range expansion in mainland France is consistent with recent findings from the literature. PMID:26986201

  18. Modelling Population Dynamics in Realistic Landscapes with Linear Elements: A Mechanistic-Statistical Reaction-Diffusion Approach.

    PubMed

    Roques, Lionel; Bonnefon, Olivier

    2016-01-01

    We propose and develop a general approach based on reaction-diffusion equations for modelling a species dynamics in a realistic two-dimensional (2D) landscape crossed by linear one-dimensional (1D) corridors, such as roads, hedgerows or rivers. Our approach is based on a hybrid "2D/1D model", i.e, a system of 2D and 1D reaction-diffusion equations with homogeneous coefficients, in which each equation describes the population dynamics in a given 2D or 1D element of the landscape. Using the example of the range expansion of the tiger mosquito Aedes albopictus in France and its main highways as 1D corridors, we show that the model can be fitted to realistic observation data. We develop a mechanistic-statistical approach, based on the coupling between a model of population dynamics and a probabilistic model of the observation process. This allows us to bridge the gap between the data (3 levels of infestation, at the scale of a French department) and the output of the model (population densities at each point of the landscape), and to estimate the model parameter values using a maximum-likelihood approach. Using classical model comparison criteria, we obtain a better fit and a better predictive power with the 2D/1D model than with a standard homogeneous reaction-diffusion model. This shows the potential importance of taking into account the effect of the corridors (highways in the present case) on species dynamics. With regard to the particular case of A. albopictus, the conclusion that highways played an important role in species range expansion in mainland France is consistent with recent findings from the literature. PMID:26986201

  19. Multistate electron transfer dynamics in the condensed phase: Exact calculations from the reduced hierarchy equations of motion approach

    SciTech Connect

    Tanaka, Midori; Tanimura, Yoshitaka

    2010-06-07

    Multiple displaced oscillators coupled to an Ohmic heat bath are used to describe electron transfer (ET) in a dissipative environment. By performing a canonical transformation, the model is reduced to a multilevel system coupled to a heat bath with the Brownian spectral distribution. A reduced hierarchy equations of motion approach is introduced for numerically rigorous simulation of the dynamics of the three-level system with various oscillator configurations, for different nonadiabatic coupling strengths and damping rates, and at different temperatures. The time evolution of the reduced density matrix elements illustrates the interplay of coherences between the electronic and vibrational states. The ET reaction rates, defined as a flux-flux correlation function, are calculated using the linear response of the system to an external perturbation as a function of activation energy. The results exhibit an asymmetric inverted parabolic profile in a small activation regime due to the presence of the intermediate state between the reactant and product states and a slowly decaying profile in a large activation energy regime, which arises from the quantum coherent transitions.

  20. A spatio-temporal analysis of landscape dynamics under changing environmental regimes in southern African savannas

    NASA Astrophysics Data System (ADS)

    Bunting, Erin L.

    The United Nations and Intergovernmental Panel on Climate Change (IPCC) deem many regions of southern Africa as vulnerable landscapes due to changing climatic regimes, ecological condition, and low adaptive capacity. The savanna ecosystems of southern Africa are of great ecological importance due to the high biodiversity they sustain, their high level of productivity, and the great role they play in the global carbon cycle. Given the dependence of humans on the lands it is essential to explore landscape level trends in patterns and processes in an effort to inform management practices. Even if climate change mitigation strategies were put in place, this is still a region heavily dependent on rain-fed agriculture and tourism of the biological diverse lands. Therefore analysis of climate variability, both interannual and intra-annual, and the changing role it plays on the landscape is critical. This body of research analyzes the role of climate variability and climate on environmental condition and socio-economic development via research on (1) spatial and temporal vegetation patterns, (2) the underlying processes that influence savanna ecosystem resilience, (3) local perception of risk to livelihood development, and (4) potential consequences of climate change on vegetation patterns. As a whole this demonstrates the key role that climate plays on savanna landscapes, which would be highly beneficial when developing conservation or mitigation strategies. Increased climate variability is occurring, but what is still open to debate is the resilience of savanna landscape and vulnerability of socio-economic development.

  1. Dynamics of a molecular glass former: Energy landscapes for diffusion in ortho-terphenyl

    NASA Astrophysics Data System (ADS)

    Niblett, S. P.; de Souza, V. K.; Stevenson, J. D.; Wales, D. J.

    2016-07-01

    Relaxation times and transport processes of many glass-forming supercooled liquids exhibit a super-Arrhenius temperature dependence. We examine this phenomenon by computer simulation of the Lewis-Wahnström model for ortho-terphenyl. We propose a microscopic definition for a single-molecule cage-breaking transition and show that, when correlation behaviour is taken into account, these rearrangements are sufficient to reproduce the correct translational diffusion constants over an intermediate temperature range in the supercooled regime. We show that super-Arrhenius behaviour can be attributed to increasing negative correlation in particle movement at lower temperatures and relate this to the cage-breaking description. Finally, we sample the potential energy landscape of the model and show that it displays hierarchical ordering. Substructures in the landscape, which may correspond to metabasins, have boundaries defined by cage-breaking transitions. The cage-breaking formulation provides a direct link between the potential energy landscape and macroscopic diffusion behaviour.

  2. Numerically Exact Dynamics of Functional Quantum Systems - Applications to GaAs Quantum Dot Qubits and 2-DIMENSIONAL Spectra of Very Large Photosyntheitc Complexes

    NASA Astrophysics Data System (ADS)

    Dattani, Nikesh S.

    2013-06-01

    Functional quantum systems is an emerging research field which includes quantum engineering (the design of technologies that make use of quantum mechanics to outperform their classical counterparts, such as quantum computers, quantum communication devices, quantum thermometers, quantum telescopes, etc.) and the study of natural processes where quantum mechanics provides some improvement that cannot be realized with classical mechanics (possible examples are photosynthesis, animal navigation, the sense of smell, etc.). Being able to predict how a quantum mechanical system changes (ie, how its density matrix changes), given its hamiltonian, is paramount in quantum engineering as one needs to know which hamiltonian will give the desired outcome. Likewise, being able to predict density matrix dynamics in natural systems can help in understanding the system's mechanism, in controlling the system's processes, and can be helpful if designing a technology which attempts to mimic a natural process. State of the art techniques for calculating density matrix dynamics of functional quantum systems in real-time, and with numerically exact accuracy, have been developed over the last year. These techniques will be presented, followed by applications for quantum dot based quantum computing, and for calculating the 2D spectra of large biological systems.

  3. Occupancy and abundance of wintering birds in a dynamic agricultural landscape

    USGS Publications Warehouse

    Miller, M.W.; Pearlstine, E.V.; Dorazio, R.M.; Mazzotti, F.J.

    2011-01-01

    Assessing wildlife management action requires monitoring populations, and abundance often is the parameter monitored. Recent methodological advances have enabled estimation of mean abundance within a habitat using presence-absence or count data obtained via repeated visits to a sample of sites. These methods assume populations are closed and intuitively assume habitats within sites change little during a field season. However, many habitats are highly variable over short periods. We developed a variation of existing occupancy and abundance models that allows for extreme spatio-temporal differences in habitat, and resulting changes in wildlife abundance, among sites and among visits to a site within a field season. We conducted our study in sugarcane habitat within the Everglades Agricultural Area southeast of Lake Okeechobee in south Florida. We counted wintering birds, primarily passerines, within 245 sites usually 5 times at each site during December 2006-March 2007. We estimated occupancy and mean abundance of birds in 6 vegetation states during the sugarcane harvest and allowed these parameters to vary temporally or spatially within a vegetation state. Occupancy and mean abundance of the common yellowthroat (Geothlypis trichas) was affected by structure of sugarcane and uncultivated edge vegetation (occupancy = 1.00 [95%C?? = 0.96-1.00] and mean abundance = 7.9 [95%C?? = 3.2-19.5] in tall sugarcane with tall edge vegetation versus 0.20 [95%C?? = 0.04-0.71] and 0.22 [95%C?? = 0.04-1.2], respectively, in short sugarcane with short edge vegetation in one half of the study area). Occupancy and mean abundance of palm warblers (Dendroica palmarum) were constant (occupancy = 1.00, 95%C?? = 0.69-1.00; mean abundance = 18, 95%C?? = 1-270). Our model may enable wildlife managers to assess rigorously effects of future edge habitat management on avian distribution and abundance within agricultural landscapes during winter or the breeding season. The model may also help

  4. Occupancy and abundance of wintering birds in a dynamic agricultural landscape

    USGS Publications Warehouse

    Miller, Mark W.; Pearlstine, Elise V.; Dorazio, Robert M.; Mazzotti, Frank J.

    2011-01-01

    Assessing wildlife management action requires monitoring populations, and abundance often is the parameter monitored. Recent methodological advances have enabled estimation of mean abundance within a habitat using presence–absence or count data obtained via repeated visits to a sample of sites. These methods assume populations are closed and intuitively assume habitats within sites change little during a field season. However, many habitats are highly variable over short periods. We developed a variation of existing occupancy and abundance models that allows for extreme spatio-temporal differences in habitat, and resulting changes in wildlife abundance, among sites and among visits to a site within a field season. We conducted our study in sugarcane habitat within the Everglades Agricultural Area southeast of Lake Okeechobee in south Florida. We counted wintering birds, primarily passerines, within 245 sites usually 5 times at each site during December 2006–March 2007. We estimated occupancy and mean abundance of birds in 6 vegetation states during the sugarcane harvest and allowed these parameters to vary temporally or spatially within a vegetation state. Occupancy and mean abundance of the common yellowthroat (Geothlypis trichas) was affected by structure of sugarcane and uncultivated edge vegetation (occupancy=1.00 [95%CĪ=0.96–1.00] and mean abundance=7.9 [95%CĪ=3.2–19.5] in tall sugarcane with tall edge vegetation versus 0.20 [95%CĪ=0.04–0.71] and 0.22 [95%CĪ=0.04–1.2], respectively, in short sugarcane with short edge vegetation in one half of the study area). Occupancy and mean abundance of palm warblers (Dendroica palmarum) were constant (occupancy=1.00, 95%CĪ=0.69–1.00; mean abundance=18, 95%CĪ=1–270). Our model may enable wildlife managers to assess rigorously effects of future edge habitat management on avian distribution and abundance within agricultural landscapes during winter or the breeding season. The model may also help

  5. Climatic effects of 30 years of landscape change over the Greater Phoenix, Arizona, region: 2. Dynamical and thermodynamical response

    NASA Astrophysics Data System (ADS)

    Georgescu, M.; Miguez-Macho, G.; Steyaert, L. T.; Weaver, C. P.

    2009-03-01

    This paper is part 2 of a two-part study evaluating the climatic effect of one of the nation's most rapidly expanding metropolitan complexes, the Greater Phoenix, Arizona, region. Part 1, using a set of sensitivity experiments, estimated the potential impact of observed landscape evolution, since the dawn of the Landsat satellite era on the near surface climate, with a primary focus on the alteration of the surface radiation and energy budgets and through use of high-resolution, 2km grid spacing, Regional Atmospheric Modeling System (RAMS) simulations with circa 1973, circa 1992, and circa 2001 landscape data sets. In this paper, part 2, we address the role of the previously discussed surface budget changes and subsequent repartitioning of energy on the mesoscale dynamics and thermodynamics of the region, the effect on convective rainfall, and their association with the large-scale North American Monsoon System (NAMS). Our results show that contrasts in surface heating resulting from landscape change are responsible for the development of preferentially located mesoscale circulations, on most days, which were stronger for the 2001 compared to the 1973 landscape, due to increased planetary boundary layer (PBL) heating via enhanced turbulent heat flux. The effect of these stronger circulations was to warm and dry the lower part of the PBL and moisten the upper part of the PBL for the 2001 relative to the 1973 landscape. The precise physical pathway(s) whereby precipitation enhancement is initiated with evolving landscape, since the early 1970s, reveals a complicated interplay among scales (from the turbulent to the synoptic scale) that warrants future research. Precipitation recycling, however, was found to be an important driver in the overall sustenance of rainfall enhancement. Although this study was not designed to investigate other radiative forcing factors such as greenhouse gas emissions and aerosols, the results of our sensitivity experiments do suggest that

  6. Exact approaches for scaffolding

    PubMed Central

    2015-01-01

    This paper presents new structural and algorithmic results around the scaffolding problem, which occurs prominently in next generation sequencing. The problem can be formalized as an optimization problem on a special graph, the "scaffold graph". We prove that the problem is polynomial if this graph is a tree by providing a dynamic programming algorithm for this case. This algorithm serves as a basis to deduce an exact algorithm for general graphs using a tree decomposition of the input. We explore other structural parameters, proving a linear-size problem kernel with respect to the size of a feedback-edge set on a restricted version of Scaffolding. Finally, we examine some parameters of scaffold graphs, which are based on real-world genomes, revealing that the feedback edge set is significantly smaller than the input size. PMID:26451725

  7. Evaluating the landscape of fear between apex predatory sharks and mobile sea turtles across a large dynamic seascape.

    PubMed

    Hammerschlag, Neil; Broderick, Annette C; Coker, John W; Coyne, Michael S; Dodd, Mark; Frick, Michael G; Godfrey, Matthew H; Godley, Brendan J; Griffin, DuBose B; Hartog, Kyra; Murphy, Sally R; Murphy, Thomas M; Nelson, Emily Rose; Williams, Kristina L; Witt, Matthew J; Hawkes, Lucy A

    2015-08-01

    The "landscape of fear" model has been proposed as a unifying concept in ecology, describing, in part, how animals behave and move about in their environment. The basic model predicts that as an animal's landscape changes from low to high risk of predation, prey species will alter their behavior to risk avoidance. However, studies investigating and evaluating the landscape of fear model across large spatial scales (tens to hundreds of thousands of square kilometers) in dynamic, open, aquatic systems involving apex predators and highly mobile prey are lacking. To address this knowledge gap, we investigated predator-prey relationships between. tiger sharks (Galeocerdo cuvier) and loggerhead turtles (Caretta caretta) in the North Atlantic Ocean. This included the use of satellite tracking to examine shark and turtle distributions as well as their surfacing behaviors under varying levels of home range overlap. Our findings revealed patterns that deviated from our a priori predictions based on the landscape of fear model. Specifically, turtles did not alter their surfacing behaviors to risk avoidance when overlap in shark-turtle core home range was high. However, in areas of high overlap with turtles, sharks exhibited modified surfacing behaviors that may enhance predation opportunity. We suggest that turtles may be an important factor in determining shark,distribution, whereas for turtles, other life history trade-offs may play a larger role in defining their habitat use. We propose that these findings are a result of both biotic and physically driven factors that independently or synergistically affect predator-prey interactions in this system. These results have implications for evolutionary biology, community ecology; and wildlife conservation. Further, given the difficulty in studying highly migratory marine species, our approach and conclusions may be applied to the study of other predator-prey systems. PMID:26405737

  8. Evaluating the landscape of fear between apex predatory sharks and mobile sea turtles across a large dynamic seascape.

    PubMed

    Hammerschlag, Neil; Broderick, Annette C; Coker, John W; Coyne, Michael S; Dodd, Mark; Frick, Michael G; Godfrey, Matthew H; Godley, Brendan J; Griffin, DuBose B; Hartog, Kyra; Murphy, Sally R; Murphy, Thomas M; Nelson, Emily Rose; Williams, Kristina L; Witt, Matthew J; Hawkes, Lucy A

    2015-08-01

    The "landscape of fear" model has been proposed as a unifying concept in ecology, describing, in part, how animals behave and move about in their environment. The basic model predicts that as an animal's landscape changes from low to high risk of predation, prey species will alter their behavior to risk avoidance. However, studies investigating and evaluating the landscape of fear model across large spatial scales (tens to hundreds of thousands of square kilometers) in dynamic, open, aquatic systems involving apex predators and highly mobile prey are lacking. To address this knowledge gap, we investigated predator-prey relationships between. tiger sharks (Galeocerdo cuvier) and loggerhead turtles (Caretta caretta) in the North Atlantic Ocean. This included the use of satellite tracking to examine shark and turtle distributions as well as their surfacing behaviors under varying levels of home range overlap. Our findings revealed patterns that deviated from our a priori predictions based on the landscape of fear model. Specifically, turtles did not alter their surfacing behaviors to risk avoidance when overlap in shark-turtle core home range was high. However, in areas of high overlap with turtles, sharks exhibited modified surfacing behaviors that may enhance predation opportunity. We suggest that turtles may be an important factor in determining shark,distribution, whereas for turtles, other life history trade-offs may play a larger role in defining their habitat use. We propose that these findings are a result of both biotic and physically driven factors that independently or synergistically affect predator-prey interactions in this system. These results have implications for evolutionary biology, community ecology; and wildlife conservation. Further, given the difficulty in studying highly migratory marine species, our approach and conclusions may be applied to the study of other predator-prey systems.

  9. River dynamics and landscape evolution in La Réunion Island: insights from luminescence dating

    NASA Astrophysics Data System (ADS)

    Farvacque, Manon; Valla, Pierre

    2016-04-01

    Tropical volcanic islands are natural laboratories to investigate the competition between volcanic construction (lava eruptions) and erosional destruction (extreme climatic events) in long-term landscape evolution. In La Réunion Island (Indian Ocean), the present day topography of the Piton des Neiges results from these competing processes. It presents three large-scale excavations called "cirques" that have been significantly eroded since the latest eruptive events but whose origin and formation time are still unclear. Indeed, the morphologic evolution of the Piton des Neiges is mostly known from K-Ar dating of lava flows and associated reconstructions of post-eruption eroded volumes. However, involved erosion processes and their rates through time remain poorly constrained, making it difficult to understand the geomorphic response to volcanic activity in this setting. Here, we focus on the "Bras de Cilaos" river that drains the "Cilaos cirque" (southern part of the Piton des Neiges). The Cilaos cirque has been first excavated between 140-180 ka [1], and it has been filled again during a late-stage eruptive event at ~145 ka [2] that also entirely filled the Bras de Cilaos valley. Alternatively, some studies have proposed that the Cilaos cirque and the Bras de Cilaos have been more recently filled by an eruption event at ~70 ka [3]. The Bras de Cilaos river is characterized by high relief (400-650 m) with no remaining evidence for these late eruptive events, showing significant incision and efficient fluvial erosion/transport processes after lava emplacement. In its downstream part, it presents thick alluvial deposits preserved along its riverbanks. The presence of such deposits may provide important constraints on the river dynamics and especially its response to the latest eruption events. However this requires establishing a tight temporal framework for these sediment archives. We thus sampled five different sedimentary sequences along the river to date their

  10. Dynamic landscapes and human dispersal patterns: tectonics, coastlines, and the reconstruction of human habitats

    NASA Astrophysics Data System (ADS)

    Bailey, Geoffrey N.; King, Geoffrey C. P.

    2011-06-01

    Studies of the impact of physical environment on human evolution usually focus on climate as the main external forcing agent of evolutionary and cultural change. In this paper we focus on changes in the physical character of the landscape driven by geophysical processes as an equally potent factor. Most of the landscapes where finds of early human fossils and artefacts are concentrated are ones that have been subjected to high levels of geological instability, either because of especially active tectonic processes associated with faulting and volcanic activity or because of proximity to coastlines subject to dramatic changes of geographical position and physical character by changes of relative sea level. These processes can have both beneficial effects, creating ecologically attractive conditions for human settlement, and deleterious or disruptive ones, creating barriers to movement, disruption of ecological conditions, or hazards to survival. Both positive and negative factors can have powerful selective effects on human behaviour and patterns of settlement and dispersal. We consider both these aspects of the interaction, develop a framework for the reconstruction and comparison of landscapes and landscape change at a variety of scales, and illustrate this with selected examples drawn from Africa and Arabia.

  11. Southeastern USA regional landscape patterns and population dynamics of the stink bug, Euchistus servus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Introduction: The brown stink bug, Euschistus servus is an economically important pest of many agronomic crops in the southern USA, motivating the study of factors influencing population build-up in agricultural regions and landscapes to facilitate management. Methods: ArcGIS was used to characteriz...

  12. Patterns of landscape dynamics and land use systems in the Southeastern Coastal Plain, USA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A variety of topics focused on research accomplished in the southeastern US were presented at this talk given on January 28, 2016, at the Brown Bag colloquium hosted by the University of Georgia Department of Geography. Topics covered included: a study analyzing road network and landscape change in ...

  13. Species differentiation on a dynamic landscape: shifts in metapopulation genetic structure using the chronology of the Hawaiian Archipelago

    USGS Publications Warehouse

    Roderick, George K.; Croucher, Peter J.P.; Vandergast, Amy G.; Gillespie, Rosemary G.

    2012-01-01

    Species formation during adaptive radiation often occurs in the context of a changing environment. The establishment and arrangement of populations, in space and time, sets up ecological and genetic processes that dictate the rate and pattern of differentiation. Here, we focus on how a dynamic habitat can affect genetic structure, and ultimately, differentiation among populations. We make use of the chronology and geographical history provided by the Hawaiian archipelago to examine the initial stages of population establishment and genetic divergence. We use data from a set of 6 spider lineages that differ in habitat affinities, some preferring low elevation habitats with a longer history of connection, others being more specialized for high elevation and/or wet forest, some with more general habitat affinities. We show that habitat preferences associated with lineages are important in ecological and genetic structuring. Lineages that have more restricted habitat preferences are subject to repeated episodes of isolation and fragmentation as a result of lava flows and vegetation succession. The initial dynamic set up by the landscape translates over time into discrete lineages. Further work is needed to understand how genetic changes interact with a changing set of ecological interactions amongst a shifting mosaic of landscapes to achieve species formation.

  14. Dynamical theory of scattering, exact unidirectional invisibility, and truncated {\\mathfrak{z}}\\,{{\\rm{e}}}^{-2{{\\rm{i}}{k}}_{0}x} potential

    NASA Astrophysics Data System (ADS)

    Mostafazadeh, Ali

    2016-11-01

    The dynamical formulation of time-independent scattering theory that is developed in (2014 Ann. Phys., NY 341 70–85) offers simple formulas for the reflection and transmission amplitudes of finite-range potentials in terms of the solution of an initial-value differential equation. We prove a theorem that simplifies the application of this result and use it to give a complete characterization of the invisible configurations of the truncated {z} {{{e}}}-2{{{i}{k}}0x} potential to a closed interval, [0,L], with k 0 being a positive integer multiple of π /L. This reveals a large class of exact unidirectionally and bidirectionally invisible configurations of this potential. The former arise for particular values of {z} that are given by certain zeros of Bessel functions. The latter occur when the wavenumber k is an integer multiple of π /L but not of k 0. We discuss the optical realizations of these configurations and explore spectral singularities of this potential.

  15. Channel and landscape dynamics in the alluvial forest mosaic of the Carmanah River valley, British Columbia, Canada

    NASA Astrophysics Data System (ADS)

    Little, Patrick J.; Richardson, John S.; Alila, Younes

    2013-11-01

    The highly diverse shifting-mosaic of forest patches of an alluvial forest within the Carmanah River valley on the west coast of Vancouver Island, British Columbia was studied to examine the hydrogeomorphic disturbance regime that structures it. We used a landscape-scale analysis to quantify historical channel migrations and changes in the extent of specific forest types. This GIS-based analysis using a 70-year aerial photographic record was complemented by field-based research. Thirty-eight plots containing 4509 trees were sampled for forest structure, age, and elevation above the contemporary channel. These data, including a vegetation chronosequence spanning over 500 years, were used to examine channel and landscape dynamics. Our findings support a general conceptual model that describes cycles of patch development and destruction in unconfined alluvial forests of the Pacific Coastal Ecoregion. Over the past century, Carmanah River has eroded nearly 30% of the alluvial forest in this study area, and approximately 65% over the past 500 years. At least 80% of the 2007 channel was forested area within the past 70 years. Younger landforms were disturbed more frequently than mature forest patches, which suggest that as biogeomorphic succession progresses the likelihood of future disturbance decreases. Estimated half lives of landforms ranged from 24 years for pioneer bars to over 1500 years for old growth terraces. Years of regional high magnitude floods resulted in a net loss of floodplain forest area indicating that disturbance was climate driven in this pluvial watershed, whereby rain events result in flood disturbance that converted forests to channel. These events initiate a subsequent course of vegetation succession and geomorphic development, and often result in the deposition of large wood that modifies the channel environment and contributes to channel avulsion and further hydrogeomorphic disturbance. The composition of the landscape is a reflection of the

  16. Chromatin landscape and circadian dynamics: Spatial and temporal organization of clock transcription

    PubMed Central

    Aguilar-Arnal, Lorena; Sassone-Corsi, Paolo

    2015-01-01

    Circadian rhythms drive the temporal organization of a wide variety of physiological and behavioral functions in ∼24-h cycles. This control is achieved through a complex program of gene expression. In mammals, the molecular clock machinery consists of interconnected transcriptional–translational feedback loops that ultimately ensure the proper oscillation of thousands of genes in a tissue-specific manner. To achieve circadian transcriptional control, chromatin remodelers serve the clock machinery by providing appropriate oscillations to the epigenome. Recent findings have revealed the presence of circadian interactomes, nuclear “hubs” of genome topology where coordinately expressed circadian genes physically interact in a spatial and temporal-specific manner. Thus, a circadian nuclear landscape seems to exist, whose interplay with metabolic pathways and clock regulators translates into specific transcriptional programs. Deciphering the molecular mechanisms that connect the circadian clock machinery with the nuclear landscape will reveal yet unexplored pathways that link cellular metabolism to epigenetic control. PMID:25378702

  17. Dark matter RNA: an intelligent scaffold for the dynamic regulation of the nuclear information landscape

    PubMed Central

    St. Laurent, Georges; Savva, Yiannis A.; Kapranov, Philipp

    2012-01-01

    Perhaps no other topic in contemporary genomics has inspired such diverse viewpoints as the 95+% of the genome, previously known as “junk DNA,” that does not code for proteins. Here, we present a theory in which dark matter RNA plays a role in the generation of a landscape of spatial micro-domains coupled to the information signaling matrix of the nuclear landscape. Within and between these micro-domains, dark matter RNAs additionally function to tether RNA interacting proteins and complexes of many different types, and by doing so, allow for a higher performance of the various processes requiring them at ultra-fast rates. This improves signal to noise characteristics of RNA processing, trafficking, and epigenetic signaling, where competition and differential RNA binding among proteins drives the computational decisions inherent in regulatory events. PMID:22539933

  18. Dark matter RNA: an intelligent scaffold for the dynamic regulation of the nuclear information landscape.

    PubMed

    St Laurent, Georges; Savva, Yiannis A; Kapranov, Philipp

    2012-01-01

    Perhaps no other topic in contemporary genomics has inspired such diverse viewpoints as the 95+% of the genome, previously known as "junk DNA," that does not code for proteins. Here, we present a theory in which dark matter RNA plays a role in the generation of a landscape of spatial micro-domains coupled to the information signaling matrix of the nuclear landscape. Within and between these micro-domains, dark matter RNAs additionally function to tether RNA interacting proteins and complexes of many different types, and by doing so, allow for a higher performance of the various processes requiring them at ultra-fast rates. This improves signal to noise characteristics of RNA processing, trafficking, and epigenetic signaling, where competition and differential RNA binding among proteins drives the computational decisions inherent in regulatory events.

  19. Landscape connectivity dynamics based on network analysis in the Xishuangbanna Nature Reserve, China

    NASA Astrophysics Data System (ADS)

    Liu, Shiliang; Deng, Li; Dong, Shikui; Zhao, Qinghe; Yang, Juejie; Wang, Cong

    2014-02-01

    Lack of landscape connectivity and habitat loss is major threats to biodiversity and ecosystem integrity in nature reserves aimed at conservation. In this study, we used structural pattern and functional connectivity metrics to analyze the spatial patterns and landscape connectivity of habitat patches for the Shangyong sub-reserve of the Xishuangbanna Nature Reserve from 1970, 1990, and 2000. On the basis of vegetation and land cover data, we applied the equivalent connected area ECA(PC) indicator to analyze the changes in forest connectivity. Four distance thresholds (2, 4, 8, 12 km) were considered to compare the patch importance of connectivity by dECA values. The results showed the declining trends of landscape connectivity measured by ECA(PC) index from 1970 to 2000. The importance of connectivity in each forest patch varied with the increment of dispersal distances at the patch level, and some important habitat patches, which exhibit a potential to enhance landscape connectivity, should be given more attention. The least-cost pathways based on network structure were displayed under four dispersal distances in three periods. The results showed that the number of paths among the fragments of forest patches exhibited radical increases for larger dispersal distances. Further correlation analyses of AWF, ECA (IIC), and ECA (PC) showed the weakest and least-frequent correlations with the structural pattern indices, while H presented more significant correlations with the PD fragmentation metric. Furthermore, Kendall's rank correlations between the forest patch area and functional connectivity indicators showed that dECA (PC) and dAWF indicators should provided the area-based prioritization of habitat patches. Moreover, the low-rank correlations showed that dF and dLCP can be considered as effective and appropriate indicators for the evaluation of habitat features and network patterns.

  20. Hypotheses testing of watershed/landscape dynamics in northern Alaska using digital analysis

    SciTech Connect

    Evans, B.M.; Petersen, G.W.; Connors, K.F.

    1989-09-01

    Since July of 1985, Penn State scientists have been cooperating with investigators from other universities in several ecosystem studies at an existing Department of Energy (DOE) study site on the North Slope of Alaska. The primary focus of the REFLEX program is to test new applications of remote sensing systems and allied digital database processing techniques for studying hydrologic/ecologic interactions. One of the goals of this particular REFLEX project was to complement ongoing R4D studies near Toolik Lake. Since their initial cooperative efforts with R4D investigators at the R4D study site in Phase I, scientists (primarily G. Petersen and B. Evans), have been intimately involved with the Landscape Ecology Working Group, one of several such groups established within the R4D program. As part of the R4D program, the Landscape Ecology Working Group is focusing on landscape-scale patterns and interactions that have applications to long slopes, watersheds, and large regions of the Alaskan North Slope.

  1. Site-level model intercomparison of high latitude and high altitude soil thermal dynamics in tundra and barren landscapes

    NASA Astrophysics Data System (ADS)

    Ekici, A.; Chadburn, S.; Chaudhary, N.; Hajdu, L. H.; Marmy, A.; Peng, S.; Boike, J.; Burke, E.; Friend, A. D.; Hauck, C.; Krinner, G.; Langer, M.; Miller, P. A.; Beer, C.

    2014-09-01

    Modelling soil thermal dynamics at high latitudes and altitudes requires representations of specific physical processes such as snow insulation, soil freezing/thawing, as well as subsurface conditions like soil water/ice content and soil texture type. We have compared six different land models (JSBACH, ORCHIDEE, JULES, COUP, HYBRID8, LPJ-GUESS) at four different sites with distinct cold region landscape types (i.e. Schilthorn-Alpine, Bayelva-high Arctic, Samoylov-wet polygonal tundra, Nuuk-non permafrost Arctic) to quantify the importance of physical processes in capturing observed temperature dynamics in soils. This work shows how a range of models can represent distinct soil temperature regimes in permafrost and non-permafrost soils. Snow insulation is of major importance for estimating topsoil conditions and must be combined with accurate subsoil temperature dynamics to correctly estimate active layer thicknesses. Analyses show that land models need more realistic surface processes (such as detailed snow dynamics and moss cover with changing thickness/wetness) as well as better representations of subsoil thermal dynamics (i.e. soil heat transfer mechanism and correct parameterization of heat conductivity/capacities).

  2. The effects of spatial and temporal heterogeneity on the population dynamics of four animal species in a Danish landscape

    PubMed Central

    Sibly, Richard M; Nabe-Nielsen, Jacob; Forchhammer, Mads C; Forbes, Valery E; Topping, Christopher J

    2009-01-01

    Background Variation in carrying capacity and population return rates is generally ignored in traditional studies of population dynamics. Variation is hard to study in the field because of difficulties controlling the environment in order to obtain statistical replicates, and because of the scale and expense of experimenting on populations. There may also be ethical issues. To circumvent these problems we used detailed simulations of the simultaneous behaviours of interacting animals in an accurate facsimile of a real Danish landscape. The models incorporate as much as possible of the behaviour and ecology of skylarks Alauda arvensis, voles Microtus agrestis, a ground beetle Bembidion lampros and a linyphiid spider Erigone atra. This allows us to quantify and evaluate the importance of spatial and temporal heterogeneity on the population dynamics of the four species. Results Both spatial and temporal heterogeneity affected the relationship between population growth rate and population density in all four species. Spatial heterogeneity accounted for 23–30% of the variance in population growth rate after accounting for the effects of density, reflecting big differences in local carrying capacity associated with the landscape features important to individual species. Temporal heterogeneity accounted for 3–13% of the variance in vole, skylark and spider, but 43% in beetles. The associated temporal variation in carrying capacity would be problematic in traditional analyses of density dependence. Return rates were less than one in all species and essentially invariant in skylarks, spiders and beetles. Return rates varied over the landscape in voles, being slower where there were larger fluctuations in local population sizes. Conclusion Our analyses estimated the traditional parameters of carrying capacities and return rates, but these are now seen as varying continuously over the landscape depending on habitat quality and the mechanisms of density dependence. The

  3. Determinants of extinction-colonization dynamics in Mediterranean butterflies: the role of landscape, climate and local habitat features.

    PubMed

    Fernández-Chacón, Albert; Stefanescu, Constantí; Genovart, Meritxell; Nichols, James D; Hines, James E; Páramo, Ferran; Turco, Marco; Oro, Daniel

    2014-01-01

    Many species are found today in the form of fragmented populations occupying patches of remnant habitat in human-altered landscapes. The persistence of these population networks requires a balance between extinction and colonization events assumed to be primarily related to patch area and isolation, but the contribution of factors such as the characteristics of patch and matrix habitats, the species' traits (habitat specialization and dispersal capabilities) and variation in climatic conditions have seldom been evaluated simultaneously. The identification of environmental variables associated with patch occupancy and turnover may be especially useful to enhance the persistence of multiple species under current global change. However, for robust inference on occupancy and related parameters, we must account for detection errors, a commonly overlooked problem that leads to biased estimates and misleading conclusions about population dynamics. Here, we provide direct empirical evidence of the effects of different environmental variables on the extinction and colonization rates of a rich butterfly community in the western Mediterranean. The analysis was based on a 17-year data set containing detection/nondetection data on 73 butterfly species for 26 sites in north-eastern Spain. Using multiseason occupancy models, which take into account species' detectability, we were able to obtain robust estimates of local extinction and colonization probabilities for each species and test the potential effects of site covariates such as the area of suitable habitat, topographic variability, landscape permeability around the site and climatic variability in aridity conditions. Results revealed a general pattern across species with local habitat composition and landscape features as stronger predictors of occupancy dynamics compared with topography and local aridity. Increasing area of suitable habitat in a site strongly decreased local extinction risks and, for a number of species

  4. Determinants of extinction-colonization dynamics in Mediterranean butterflies: the role of landscape, climate and local habitat features.

    PubMed

    Fernández-Chacón, Albert; Stefanescu, Constantí; Genovart, Meritxell; Nichols, James D; Hines, James E; Páramo, Ferran; Turco, Marco; Oro, Daniel

    2014-01-01

    Many species are found today in the form of fragmented populations occupying patches of remnant habitat in human-altered landscapes. The persistence of these population networks requires a balance between extinction and colonization events assumed to be primarily related to patch area and isolation, but the contribution of factors such as the characteristics of patch and matrix habitats, the species' traits (habitat specialization and dispersal capabilities) and variation in climatic conditions have seldom been evaluated simultaneously. The identification of environmental variables associated with patch occupancy and turnover may be especially useful to enhance the persistence of multiple species under current global change. However, for robust inference on occupancy and related parameters, we must account for detection errors, a commonly overlooked problem that leads to biased estimates and misleading conclusions about population dynamics. Here, we provide direct empirical evidence of the effects of different environmental variables on the extinction and colonization rates of a rich butterfly community in the western Mediterranean. The analysis was based on a 17-year data set containing detection/nondetection data on 73 butterfly species for 26 sites in north-eastern Spain. Using multiseason occupancy models, which take into account species' detectability, we were able to obtain robust estimates of local extinction and colonization probabilities for each species and test the potential effects of site covariates such as the area of suitable habitat, topographic variability, landscape permeability around the site and climatic variability in aridity conditions. Results revealed a general pattern across species with local habitat composition and landscape features as stronger predictors of occupancy dynamics compared with topography and local aridity. Increasing area of suitable habitat in a site strongly decreased local extinction risks and, for a number of species

  5. The relative importance of fertilization and soil erosion on C-dynamics in agricultural landscapes of NE Germany

    NASA Astrophysics Data System (ADS)

    Pohl, Madlen; Hoffmann, Mathias; Hagemann, Ulrike; Jurisch, Nicole; Remus, Rainer; Sommer, Michael; Augustin, Jürgen

    2016-04-01

    The hummocky ground moraine landscape of north-east Germany is characterized by distinct small-scale soil heterogeneity on the one hand, and intensive energy crop cultivation on the other. Both factors are assumed to significantly influence gaseous C exchange, and thus driving the dynamics of soil organic carbon stocks in terrestrial, agricultural ecosystems. However, it is not yet clear to which extent fertilization and soil erosional status influence soil C dynamics and whether one of these factors is more relevant than the other. We present seasonal and dynamic soil C balances of biogas maize for the growing season 2011, recorded at different sites located within the CarboZALF experimental area. The sites differ regarding soils (non-eroded Albic Luvisols (Cutanic), extremely eroded Calcaric Regosol and depositional Endogleyic Colluvic Regosol,) and applied fertilizer (100% mineral N fertilizer, 50% mineral and 50% N organic fertilizer, 100% organic N fertilizer). Fertilization treatments were established on the Albic Luvisol (Cutanic). Net-CO2-exchange (NEE) and ecosystem respiration (Reco) were measured every four weeks using a dynamic flow-through non-steady-state closed manual chamber system. Gap filling was performed based on empirical temperature and PAR dependency functions to derive daily NEE values. At the same time, daily above-ground biomass production (NPP) was estimated based on biomass samples and final harvest, using a sigmoidal growth function. In a next step, dynamic soil C balances were generated as the balance of daily NEE and NPP considering the initial C input due to N fertilizers. The resulted seasonal soil C balances varied from strong C losses at the Endogleyic Colluvic Regosol (602 g C m-2) to C gains at the Calcaric Regosol (-132 g C m-2). In general, soils exerted a stronger impact on seasonal and dynamic C balances compared to differences in applied N fertilizer. There are indications that inter-annual variations in climate conditions

  6. Landscape dynamics in northwestern Amazonia: an assessment of pastures, fire and illicit crops as drivers of tropical deforestation.

    PubMed

    Armenteras, Dolors; Rodríguez, Nelly; Retana, Javier

    2013-01-01

    Many studies have identified drivers of deforestation throughout the tropics and, in most cases, have recognised differences in the level of threat. However, only a few have also looked at the temporal and spatial dynamics by which those drivers act, which is critical for assessing the conservation of biodiversity as well as for landscape planning. In this study, we analyse land cover change between 2000 and 2009 in north-western Colombian Amazonia to identify the interactions between the use of fire, cultivation of illicit crops and establishment of pastures, and their impacts on the loss of forest in the region. Yearly analyses were undertaken at randomly selected sample areas to quantify the average areas of transition of land cover types under different landscape compositions: forest-dominated mosaics, pasture mosaics, fire mosaics, and illicit crop mosaics. Our results indicate that despite the fact that forest areas were well-preserved, deforestation occurred at a low annual rate (0.06%). Conversion to pasture was the main factor responsible for forest loss (the area of pastures tripled within forest mosaics over 8 years), and this process was independent of the landscape matrix in which the forests were located. In fire mosaics, burning is a common tool for forest clearing and conversion to pasture. Thus, forests in fire mosaics were highly disturbed and frequently transformed from primary to secondary forests. The use of fire for illicit cropping was not detected, partly due to the small size of common illicit crops. Forest regeneration from pastures and secondary vegetation was observed in areas with large amounts of natural forest. Overall, assuming the continuation of the observed pasture conversion trend and the use of forest fire, we suggest that our results should be incorporated into a spatially explicit and integrated decision support tool to target and focus land-planning activities and policies.

  7. Landscape dynamics in northwestern Amazonia: an assessment of pastures, fire and illicit crops as drivers of tropical deforestation.

    PubMed

    Armenteras, Dolors; Rodríguez, Nelly; Retana, Javier

    2013-01-01

    Many studies have identified drivers of deforestation throughout the tropics and, in most cases, have recognised differences in the level of threat. However, only a few have also looked at the temporal and spatial dynamics by which those drivers act, which is critical for assessing the conservation of biodiversity as well as for landscape planning. In this study, we analyse land cover change between 2000 and 2009 in north-western Colombian Amazonia to identify the interactions between the use of fire, cultivation of illicit crops and establishment of pastures, and their impacts on the loss of forest in the region. Yearly analyses were undertaken at randomly selected sample areas to quantify the average areas of transition of land cover types under different landscape compositions: forest-dominated mosaics, pasture mosaics, fire mosaics, and illicit crop mosaics. Our results indicate that despite the fact that forest areas were well-preserved, deforestation occurred at a low annual rate (0.06%). Conversion to pasture was the main factor responsible for forest loss (the area of pastures tripled within forest mosaics over 8 years), and this process was independent of the landscape matrix in which the forests were located. In fire mosaics, burning is a common tool for forest clearing and conversion to pasture. Thus, forests in fire mosaics were highly disturbed and frequently transformed from primary to secondary forests. The use of fire for illicit cropping was not detected, partly due to the small size of common illicit crops. Forest regeneration from pastures and secondary vegetation was observed in areas with large amounts of natural forest. Overall, assuming the continuation of the observed pasture conversion trend and the use of forest fire, we suggest that our results should be incorporated into a spatially explicit and integrated decision support tool to target and focus land-planning activities and policies. PMID:23382890

  8. Landscape Dynamics in Northwestern Amazonia: An Assessment of Pastures, Fire and Illicit Crops as Drivers of Tropical Deforestation

    PubMed Central

    Armenteras, Dolors; Rodríguez, Nelly; Retana, Javier

    2013-01-01

    Many studies have identified drivers of deforestation throughout the tropics and, in most cases, have recognised differences in the level of threat. However, only a few have also looked at the temporal and spatial dynamics by which those drivers act, which is critical for assessing the conservation of biodiversity as well as for landscape planning. In this study, we analyse land cover change between 2000 and 2009 in north-western Colombian Amazonia to identify the interactions between the use of fire, cultivation of illicit crops and establishment of pastures, and their impacts on the loss of forest in the region. Yearly analyses were undertaken at randomly selected sample areas to quantify the average areas of transition of land cover types under different landscape compositions: forest-dominated mosaics, pasture mosaics, fire mosaics, and illicit crop mosaics. Our results indicate that despite the fact that forest areas were well-preserved, deforestation occurred at a low annual rate (0.06%). Conversion to pasture was the main factor responsible for forest loss (the area of pastures tripled within forest mosaics over 8 years), and this process was independent of the landscape matrix in which the forests were located. In fire mosaics, burning is a common tool for forest clearing and conversion to pasture. Thus, forests in fire mosaics were highly disturbed and frequently transformed from primary to secondary forests. The use of fire for illicit cropping was not detected, partly due to the small size of common illicit crops. Forest regeneration from pastures and secondary vegetation was observed in areas with large amounts of natural forest. Overall, assuming the continuation of the observed pasture conversion trend and the use of forest fire, we suggest that our results should be incorporated into a spatially explicit and integrated decision support tool to target and focus land-planning activities and policies. PMID:23382890

  9. From Particles and Point Clouds to Voxel Models: High Resolution Modeling of Dynamic Landscapes in Open Source GIS

    NASA Astrophysics Data System (ADS)

    Mitasova, H.; Hardin, E. J.; Kratochvilova, A.; Landa, M.

    2012-12-01

    Multitemporal data acquired by modern mapping technologies provide unique insights into processes driving land surface dynamics. These high resolution data also offer an opportunity to improve the theoretical foundations and accuracy of process-based simulations of evolving landforms. We discuss development of new generation of visualization and analytics tools for GRASS GIS designed for 3D multitemporal data from repeated lidar surveys and from landscape process simulations. We focus on data and simulation methods that are based on point sampling of continuous fields and lead to representation of evolving surfaces as series of raster map layers or voxel models. For multitemporal lidar data we present workflows that combine open source point cloud processing tools with GRASS GIS and custom python scripts to model and analyze dynamics of coastal topography (Figure 1) and we outline development of coastal analysis toolbox. The simulations focus on particle sampling method for solving continuity equations and its application for geospatial modeling of landscape processes. In addition to water and sediment transport models, already implemented in GIS, the new capabilities under development combine OpenFOAM for wind shear stress simulation with a new module for aeolian sand transport and dune evolution simulations. Comparison of observed dynamics with the results of simulations is supported by a new, integrated 2D and 3D visualization interface that provides highly interactive and intuitive access to the redesigned and enhanced visualization tools. Several case studies will be used to illustrate the presented methods and tools and demonstrate the power of workflows built with FOSS and highlight their interoperability.Figure 1. Isosurfaces representing evolution of shoreline and a z=4.5m contour between the years 1997-2011at Cape Hatteras, NC extracted from a voxel model derived from series of lidar-based DEMs.

  10. Evaluating the Impact of Abrupt Changes in Forest Policy and Management Practices on Landscape Dynamics: Analysis of a Landsat Image Time Series in the Atlantic Northern Forest

    PubMed Central

    Legaard, Kasey R.; Sader, Steven A.; Simons-Legaard, Erin M.

    2015-01-01

    Sustainable forest management is based on functional relationships between management actions, landscape conditions, and forest values. Changes in management practices make it fundamentally more difficult to study these relationships because the impacts of current practices are difficult to disentangle from the persistent influences of past practices. Within the Atlantic Northern Forest of Maine, U.S.A., forest policy and management practices changed abruptly in the early 1990s. During the 1970s-1980s, a severe insect outbreak stimulated salvage clearcutting of large contiguous tracts of spruce-fir forest. Following clearcut regulation in 1991, management practices shifted abruptly to near complete dependence on partial harvesting. Using a time series of Landsat satellite imagery (1973-2010) we assessed cumulative landscape change caused by these very different management regimes. We modeled predominant temporal patterns of harvesting and segmented a large study area into groups of landscape units with similar harvest histories. Time series of landscape composition and configuration metrics averaged within groups revealed differences in landscape dynamics caused by differences in management history. In some groups (24% of landscape units), salvage caused rapid loss and subdivision of intact mature forest. Persistent landscape change was created by large salvage clearcuts (often averaging > 100 ha) and conversion of spruce-fir to deciduous and mixed forest. In groups that were little affected by salvage (56% of landscape units), contemporary partial harvesting caused loss and subdivision of intact mature forest at even greater rates. Patch shape complexity and edge density reached high levels even where cumulative harvest area was relatively low. Contemporary practices introduced more numerous and much smaller patches of stand-replacing disturbance (typically averaging <15 ha) and a correspondingly large amount of edge. Management regimes impacted different areas to

  11. Evaluating the impact of abrupt changes in forest policy and management practices on landscape dynamics: analysis of a Landsat image time series in the Atlantic Northern Forest.

    PubMed

    Legaard, Kasey R; Sader, Steven A; Simons-Legaard, Erin M

    2015-01-01

    Sustainable forest management is based on functional relationships between management actions, landscape conditions, and forest values. Changes in management practices make it fundamentally more difficult to study these relationships because the impacts of current practices are difficult to disentangle from the persistent influences of past practices. Within the Atlantic Northern Forest of Maine, U.S.A., forest policy and management practices changed abruptly in the early 1990s. During the 1970s-1980s, a severe insect outbreak stimulated salvage clearcutting of large contiguous tracts of spruce-fir forest. Following clearcut regulation in 1991, management practices shifted abruptly to near complete dependence on partial harvesting. Using a time series of Landsat satellite imagery (1973-2010) we assessed cumulative landscape change caused by these very different management regimes. We modeled predominant temporal patterns of harvesting and segmented a large study area into groups of landscape units with similar harvest histories. Time series of landscape composition and configuration metrics averaged within groups revealed differences in landscape dynamics caused by differences in management history. In some groups (24% of landscape units), salvage caused rapid loss and subdivision of intact mature forest. Persistent landscape change was created by large salvage clearcuts (often averaging > 100 ha) and conversion of spruce-fir to deciduous and mixed forest. In groups that were little affected by salvage (56% of landscape units), contemporary partial harvesting caused loss and subdivision of intact mature forest at even greater rates. Patch shape complexity and edge density reached high levels even where cumulative harvest area was relatively low. Contemporary practices introduced more numerous and much smaller patches of stand-replacing disturbance (typically averaging <15 ha) and a correspondingly large amount of edge. Management regimes impacted different areas to

  12. Evaluating the impact of abrupt changes in forest policy and management practices on landscape dynamics: analysis of a Landsat image time series in the Atlantic Northern Forest.

    PubMed

    Legaard, Kasey R; Sader, Steven A; Simons-Legaard, Erin M

    2015-01-01

    Sustainable forest management is based on functional relationships between management actions, landscape conditions, and forest values. Changes in management practices make it fundamentally more difficult to study these relationships because the impacts of current practices are difficult to disentangle from the persistent influences of past practices. Within the Atlantic Northern Forest of Maine, U.S.A., forest policy and management practices changed abruptly in the early 1990s. During the 1970s-1980s, a severe insect outbreak stimulated salvage clearcutting of large contiguous tracts of spruce-fir forest. Following clearcut regulation in 1991, management practices shifted abruptly to near complete dependence on partial harvesting. Using a time series of Landsat satellite imagery (1973-2010) we assessed cumulative landscape change caused by these very different management regimes. We modeled predominant temporal patterns of harvesting and segmented a large study area into groups of landscape units with similar harvest histories. Time series of landscape composition and configuration metrics averaged within groups revealed differences in landscape dynamics caused by differences in management history. In some groups (24% of landscape units), salvage caused rapid loss and subdivision of intact mature forest. Persistent landscape change was created by large salvage clearcuts (often averaging > 100 ha) and conversion of spruce-fir to deciduous and mixed forest. In groups that were little affected by salvage (56% of landscape units), contemporary partial harvesting caused loss and subdivision of intact mature forest at even greater rates. Patch shape complexity and edge density reached high levels even where cumulative harvest area was relatively low. Contemporary practices introduced more numerous and much smaller patches of stand-replacing disturbance (typically averaging <15 ha) and a correspondingly large amount of edge. Management regimes impacted different areas to

  13. A dynamic early East Antarctic Ice Sheet suggested by ice-covered fjord landscapes.

    PubMed

    Young, Duncan A; Wright, Andrew P; Roberts, Jason L; Warner, Roland C; Young, Neal W; Greenbaum, Jamin S; Schroeder, Dustin M; Holt, John W; Sugden, David E; Blankenship, Donald D; van Ommen, Tas D; Siegert, Martin J

    2011-06-01

    The first Cenozoic ice sheets initiated in Antarctica from the Gamburtsev Subglacial Mountains and other highlands as a result of rapid global cooling ∼34 million years ago. In the subsequent 20 million years, at a time of declining atmospheric carbon dioxide concentrations and an evolving Antarctic circumpolar current, sedimentary sequence interpretation and numerical modelling suggest that cyclical periods of ice-sheet expansion to the continental margin, followed by retreat to the subglacial highlands, occurred up to thirty times. These fluctuations were paced by orbital changes and were a major influence on global sea levels. Ice-sheet models show that the nature of such oscillations is critically dependent on the pattern and extent of Antarctic topographic lowlands. Here we show that the basal topography of the Aurora Subglacial Basin of East Antarctica, at present overlain by 2-4.5 km of ice, is characterized by a series of well-defined topographic channels within a mountain block landscape. The identification of this fjord landscape, based on new data from ice-penetrating radar, provides an improved understanding of the topography of the Aurora Subglacial Basin and its surroundings, and reveals a complex surface sculpted by a succession of ice-sheet configurations substantially different from today's. At different stages during its fluctuations, the edge of the East Antarctic Ice Sheet lay pinned along the margins of the Aurora Subglacial Basin, the upland boundaries of which are currently above sea level and the deepest parts of which are more than 1 km below sea level. Although the timing of the channel incision remains uncertain, our results suggest that the fjord landscape was carved by at least two iceflow regimes of different scales and directions, each of which would have over-deepened existing topographic depressions, reversing valley floor slopes. PMID:21637255

  14. Dynamics and pattern of a managed coniferous forest landscape in Oregon

    NASA Technical Reports Server (NTRS)

    Spies, Thomas A.; Ripple, William J.; Bradshaw, G. A.

    1995-01-01

    We examined the process of fragmentation in a managed forest landscape by comparing rates and patterns of disturbance (primarily clear-cutting) and regrowth between 1972 and 1988 using Landsat imagery. A 2589-km(exp 2) managed forest landscape in western Oregon was classified into two forest types, closed-canopy conifer forest (CF) (typically, greater than 60% conifer cover) and other forest and nonforest types (OT) (typically, less than 40 yr old or deciduous forest). The percentage of CF declined from 71 to 58% between 1972 and 1988. Declines were greatest on private land, least in wilderness, and intermediate in public nonwilderness. High elevations (greater than 914 m) maintained a greater percentage of CF than lower elevations (less than 914 m). The percentage of the area at the edge of the two cover types increased on all ownerships and in both elevational zones, whereas the amount of interior habitat (defined as CF at least 100 m from OT) decreased on all ownerships and elevational zones. By 1988 public lands contained approximately 45% interior habitat while private lands had 12% interior habitat. Mean interior patch area declined from 160 to 62 ha. The annual rate of disturbance (primarily clear-cutting) for the entire area including the wilderness was 1.19%, which corresponds to a cutting rotation of 84 yr. The forest landscape was not in a steady state or regulated condition which is not projected to occur for at least 40 yr under current forest plans. Variability in cutting rates within ownerships was higher on private land than on nonreserve public land. However, despite the use of dispersed cutting patterns on public land, spatial patterns of cutting and remnant forest patches were nonuniform across the entire public ownership. Large remaining patches (less than 5000 ha) of contiguous interior forest were restricted to public lands designated for uses other than timber production such as wilderness areas and research natural areas.

  15. Drainage and leaching dynamics in a cropped hummocky soil landscape with erosion-affected pedogenesis

    NASA Astrophysics Data System (ADS)

    Gerke, Horst H.; Rieckh, Helene; Sommer, Michael

    2016-04-01

    Hummocky soil landscapes are characterized by 3D spatial patterns of soil types that result from erosion-affected pedogenesis. Due to tillage and water erosion, truncated profiles have been formed at steep and mid slopes and colluvial soils at hollows. Pedogenetic variations in soil horizons at the different hillslope positions suggested feedback effects between erosion affected soil properties, the water balances, and the crop growth and leaching rates. Water balance simulations compared uniform with hillslope position-specific crop and root growths for soils at plateau, flat mid slope, steep slope, and hollow using the Hydrus-1D program. The boundary condition data were monitored at the CarboZALF-D experimental field site, which was cropped with perennial lucerne (Medicago sativa L.) in 2013 and 2014. Crop and root growth was assumed proportional to observed leaf area index (LAI). Fluxes of dissolved organic and inorganic carbon (DOC, DIC) were obtained from simulated water fluxes and measured DOC and DIC concentrations. For the colluvic soil, the predominately upward flow led to a net input in DIC and DOC. For the truncated soils at steep slopes, a reduced crop growth caused an relative increase in drainage, suggesting an accelerated leaching, which in the long term could accelerate the soil development and more soil variations along eroding hillslopes in arable soil landscapes.

  16. Past landscape dynamics in mountain territories: historical trajectory of vulnerability in the Vars catchment (French Alps)

    NASA Astrophysics Data System (ADS)

    Puissant, Anne; Cioloboc, Florin; Schlosser, Arnaud; Gazo, Aurelien; Martin, Brice; Malet, Jean-Philippe

    2016-04-01

    Over the last decades and centuries, mountain landscapes have experiment natural and man-made landcover/use changes with mainly the development of tourism activities and the reduction of agro-pastoral activities. These transformations have directly influenced the spatial organization of mountain landscapes. To better anticipate the future exposure of the territory to natural hazards, decision-makers need retrospective analyses of the past changes. In the frame of the SAMCO project, whose objective is to propose mountain risk assessment methodologies in the context of global changes, this research presents a retrospective analysis of land cover/use changes (from 1948 to 2013) in the Vars catchment (French South Alps) submitted to several natural hazards (rockfall, landslide, and flood). Database of elements at risk has been built for five dates and evolution of vulnerability is performed through a versatile GIS-based analysis tool developed for the estimation of vulnerability indicators (physical, economical, social) at a fine scale (1:5000). Results allow identifying several areas with different trajectories of vulnerability which can be use as input data for risk analysis and define future trends.

  17. Biodiversity and agriculture in dynamic landscapes: Integrating ground and remotely-sensed baseline surveys.

    PubMed

    Gillison, Andrew N; Asner, Gregory P; Fernandes, Erick C M; Mafalacusser, Jacinto; Banze, Aurélio; Izidine, Samira; da Fonseca, Ambrósio R; Pacate, Hermenegildo

    2016-07-15

    Sustainable biodiversity and land management require a cost-effective means of forecasting landscape response to environmental change. Conventional species-based, regional biodiversity assessments are rarely adequate for policy planning and decision making. We show how new ground and remotely-sensed survey methods can be coordinated to help elucidate and predict relationships between biodiversity, land use and soil properties along complex biophysical gradients that typify many similar landscapes worldwide. In the lower Zambezi valley, Mozambique we used environmental, gradient-directed transects (gradsects) to sample vascular plant species, plant functional types, vegetation structure, soil properties and land-use characteristics. Soil fertility indices were derived using novel multidimensional scaling of soil properties. To facilitate spatial analysis, we applied a probabilistic remote sensing approach, analyzing Landsat 7 satellite imagery to map photosynthetically active and inactive vegetation and bare soil along each gradsect. Despite the relatively low sample number, we found highly significant correlations between single and combined sets of specific plant, soil and remotely sensed variables that permitted testable spatial projections of biodiversity and soil fertility across the regional land-use mosaic. This integrative and rapid approach provides a low-cost, high-return and readily transferable methodology that permits the ready identification of testable biodiversity indicators for adaptive management of biodiversity and potential agricultural productivity. PMID:27064732

  18. Modeling the Impact of Landscape Variability on Nutrient and Pesticide Dynamics in CEAP Watersheds

    NASA Astrophysics Data System (ADS)

    Saia, S. M.; Steenhuis, T. S.; Easton, Z. M.; Boll, J.; Brooks, E. S.

    2010-12-01

    Keywords: water quality, best management practices, runoff The effectiveness of agricultural conservation strategies for reducing soil, nutrient, and pesticide transport varies among landscape type and climate. For instance, a riparian buffer may reduce phosphorous loading to a Northeastern stream but fail to have the same impact on a stream in the Midwest. We propose a model based on readily available input data that can be used to prioritize the implementation of agricultural practices across a range of landscapes. Because areas generating overland flow are more prone to nutrient and pesticide transport, new management tools must accurately predict surface and subsurface flows. A modified version of the process-based Water Erosion Prediction Project (WEPP) model was developed to more accurately estimate surface and subsurface flows as well as sediment, nutrient, and pesticide transport from saturated and unsaturated hill slopes. We compare model results to available nutrient transport data from 13 USDA funded Conservation Effects Assessment Project (CEAP) watersheds. Core objectives of the CEAP initiative include the quantitative evaluation of agricultural conservation practices through enhanced data collection and model development in selected watersheds. Once available online, this modified WEPP model will be a valuable tool for water resource managers to make scientifically informed decisions concerning the impact on and selection of conservation practices for improved stream water quality.

  19. Biodiversity and agriculture in dynamic landscapes: Integrating ground and remotely-sensed baseline surveys.

    PubMed

    Gillison, Andrew N; Asner, Gregory P; Fernandes, Erick C M; Mafalacusser, Jacinto; Banze, Aurélio; Izidine, Samira; da Fonseca, Ambrósio R; Pacate, Hermenegildo

    2016-07-15

    Sustainable biodiversity and land management require a cost-effective means of forecasting landscape response to environmental change. Conventional species-based, regional biodiversity assessments are rarely adequate for policy planning and decision making. We show how new ground and remotely-sensed survey methods can be coordinated to help elucidate and predict relationships between biodiversity, land use and soil properties along complex biophysical gradients that typify many similar landscapes worldwide. In the lower Zambezi valley, Mozambique we used environmental, gradient-directed transects (gradsects) to sample vascular plant species, plant functional types, vegetation structure, soil properties and land-use characteristics. Soil fertility indices were derived using novel multidimensional scaling of soil properties. To facilitate spatial analysis, we applied a probabilistic remote sensing approach, analyzing Landsat 7 satellite imagery to map photosynthetically active and inactive vegetation and bare soil along each gradsect. Despite the relatively low sample number, we found highly significant correlations between single and combined sets of specific plant, soil and remotely sensed variables that permitted testable spatial projections of biodiversity and soil fertility across the regional land-use mosaic. This integrative and rapid approach provides a low-cost, high-return and readily transferable methodology that permits the ready identification of testable biodiversity indicators for adaptive management of biodiversity and potential agricultural productivity.

  20. Quantitative functional assessment of SOM dynamics in changing land-use and landscape conditions at the Central region of Russia

    NASA Astrophysics Data System (ADS)

    Vasenev, I. I.; Valentini, R.

    2012-12-01

    Terrestrial ecosystems are a major player in the global and regional carbon cycles acting as carbon stocks and carbon sources. Soil organic matter (SOM) is the largest carbon stock in the most of terrestrial ecosystems.Soil CO2 emission is a predominant terrestrial carbon outflow, including autotrophic respiration of plant roots and heterotrophic microbial respiration. The capacity for carbon sequestration is widely accepted as a principal soil ecological function. Soil respiration is assumed as an important carbon source, included in the studies, assessing carbon budget in changing land-use and landscape conditions. The Central region of the European territory of Russia is especially interested for this kind of researches due to essential original spatial heterogeneity of its forest and forest-steppe soils and landscapes that has been further complicated by a specific land-use history and different-direction soil successions as a results of past century environmental changes and human impacts. SOM stocks and especially CO2 emission demonstrates a very high spatial and temporal variability here, which is mutual feature for most regional natural and man-changed ecosystems and may have a strong influence on land-use and farming change strategy and climate change. However quite a few studies focus on this problem here with application of modern field tools and quantitative functional assessment of SOM dynamics variability at the level of changing elementary soil cover patterns (ESCP) that includes in the key issues of our project. Development the zonal-regional set of criteria for logically formalized distinguishing of the most "stable" & "hot" areas in soil cover patterns make it possible for quantitative assessment of dominating in them elementary landscape, soil-forming and degradation processes. The received data essentially expand known ranges of the soil forming processes (SFP) rate «in situ». In case of mature southern taiga ecosystems mutual for them the

  1. Fort Collins Science Center Ecosystem Dynamics branch--interdisciplinary research for addressing complex natural resource issues across landscapes and time

    USGS Publications Warehouse

    Bowen, Zachary H.; Melcher, Cynthia P.; Wilson, Juliette T.

    2013-01-01

    The Ecosystem Dynamics Branch of the Fort Collins Science Center offers an interdisciplinary team of talented and creative scientists with expertise in biology, botany, ecology, geology, biogeochemistry, physical sciences, geographic information systems, and remote-sensing, for tackling complex questions about natural resources. As demand for natural resources increases, the issues facing natural resource managers, planners, policy makers, industry, and private landowners are increasing in spatial and temporal scope, often involving entire regions, multiple jurisdictions, and long timeframes. Needs for addressing these issues include (1) a better understanding of biotic and abiotic ecosystem components and their complex interactions; (2) the ability to easily monitor, assess, and visualize the spatially complex movements of animals, plants, water, and elements across highly variable landscapes; and (3) the techniques for accurately predicting both immediate and long-term responses of system components to natural and human-caused change. The overall objectives of our research are to provide the knowledge, tools, and techniques needed by the U.S. Department of the Interior, state agencies, and other stakeholders in their endeavors to meet the demand for natural resources while conserving biodiversity and ecosystem services. Ecosystem Dynamics scientists use field and laboratory research, data assimilation, and ecological modeling to understand ecosystem patterns, trends, and mechanistic processes. This information is used to predict the outcomes of changes imposed on species, habitats, landscapes, and climate across spatiotemporal scales. The products we develop include conceptual models to illustrate system structure and processes; regional baseline and integrated assessments; predictive spatial and mathematical models; literature syntheses; and frameworks or protocols for improved ecosystem monitoring, adaptive management, and program evaluation. The descriptions

  2. Patch quality and context, but not patch number, drive multi-scale colonization dynamics in experimental aquatic landscapes.

    PubMed

    Resetarits, William J; Binckley, Christopher A

    2013-11-01

    Colonization and extinction are primary drivers of local population dynamics, community structure, and spatial patterns of biological diversity. Existing paradigms of island biogeography, metapopulation biology, and metacommunity ecology, as well as habitat management and conservation biology based on those paradigms, emphasize patch size, number, and isolation as primary characteristics influencing colonization and extinction. Habitat selection theory suggests that patch quality could rival size, number, and isolation in determining rates of colonization and resulting community structure. We used naturally colonized experimental landscapes to address four issues: (a) how do colonizing aquatic beetles respond to variation in patch number, (b) how do they respond to variation in patch quality, (c) does patch context affect colonization dynamics, and (d) at what spatial scales do beetles respond to habitat variation? Increasing patch number had no effect on per patch colonization rates, while patch quality and context were critical in determining colonization rates and resulting patterns of abundance and species richness at multiple spatial scales. We graphically illustrate how variation in immigration rates driven by perceived predation risk (habitat quality) can further modify dynamics of the equilibrium theory of island biogeography beyond predator-driven effects on extinction rates. Our data support the importance of patch quality and context as primary determinants of colonization rate, occupancy, abundance, and resulting patterns of species richness, and reinforce the idea that management of metapopulations for species preservation, and metacommunities for local and regional diversity, should incorporate habitat quality into the predictive equation. PMID:23609801

  3. Patch quality and context, but not patch number, drive multi-scale colonization dynamics in experimental aquatic landscapes.

    PubMed

    Resetarits, William J; Binckley, Christopher A

    2013-11-01

    Colonization and extinction are primary drivers of local population dynamics, community structure, and spatial patterns of biological diversity. Existing paradigms of island biogeography, metapopulation biology, and metacommunity ecology, as well as habitat management and conservation biology based on those paradigms, emphasize patch size, number, and isolation as primary characteristics influencing colonization and extinction. Habitat selection theory suggests that patch quality could rival size, number, and isolation in determining rates of colonization and resulting community structure. We used naturally colonized experimental landscapes to address four issues: (a) how do colonizing aquatic beetles respond to variation in patch number, (b) how do they respond to variation in patch quality, (c) does patch context affect colonization dynamics, and (d) at what spatial scales do beetles respond to habitat variation? Increasing patch number had no effect on per patch colonization rates, while patch quality and context were critical in determining colonization rates and resulting patterns of abundance and species richness at multiple spatial scales. We graphically illustrate how variation in immigration rates driven by perceived predation risk (habitat quality) can further modify dynamics of the equilibrium theory of island biogeography beyond predator-driven effects on extinction rates. Our data support the importance of patch quality and context as primary determinants of colonization rate, occupancy, abundance, and resulting patterns of species richness, and reinforce the idea that management of metapopulations for species preservation, and metacommunities for local and regional diversity, should incorporate habitat quality into the predictive equation.

  4. Navigating Membrane Protein Structure, Dynamics, and Energy Landscapes Using Spin Labeling and EPR Spectroscopy.

    PubMed

    Claxton, Derek P; Kazmier, Kelli; Mishra, Smriti; Mchaourab, Hassane S

    2015-01-01

    A detailed understanding of the functional mechanism of a protein entails the characterization of its energy landscape. Achieving this ambitious goal requires the integration of multiple approaches including determination of high-resolution crystal structures, uncovering conformational sampling under distinct biochemical conditions, characterizing the kinetics and thermodynamics of transitions between functional intermediates using spectroscopic techniques, and interpreting and harmonizing the data into novel computational models. With increasing sophistication in solution-based and ensemble-oriented biophysical approaches such as electron paramagnetic resonance (EPR) spectroscopy, atomic resolution structural information can be directly linked to conformational sampling in solution. Here, we detail how recent methodological and technological advances in EPR spectroscopy have contributed to the elucidation of membrane protein mechanisms. Furthermore, we aim to assist investigators interested in pursuing EPR studies by providing an introduction to the technique, a primer on experimental design, and a description of the practical considerations of the method toward generating high quality data.

  5. Nitrogen dynamics among cropland and riparian buffers: soil-landscape influences.

    PubMed

    Young, Eric O; Briggs, Russell D

    2007-01-01

    Nitrate (NO3-) leaching to ground water poses water quality concerns in some settings. Riparian buffers have been advocated to reduce excess ground water NO3- concentrations. We characterized inorganic N in soil solution and shallow ground water for 16 paired cropland-riparian plots from 2003 to 2005. The sites were located at two private dairy farms in Central New York on silt and gravelly silt loam soils (Aeric Endoaqualfs, Fluvaquentic Endoaquepts, Fluvaquentic Eutrudepts, Glossaquic Hapludalfs, and Glossic Hapludalfs). It was hypothesized that cropland N inputs and soil-landscape variability would jointly affect NO3- leaching and transformations in ground water. Results showed that well and moderately well drained fields had consistently higher ground water NO3- compared to more imperfectly drained fields receiving comparable N inputs. Average 50-cm depth soil solution NO3- and ground water dissolved oxygen (DO) explained 64% of average cropland ground water NO3- variability. Cropland ground water with an average DO of <3 mg L(-1) tended to have <4 mg L(-1) of NO3- with a water table depth (WTD) of landscape factors strongly influenced NO3- behavior and suggest the importance of accurately characterizing soil variability along cropland-riparian zones.

  6. An enhanced Bayesian fingerprinting framework for studying sediment source dynamics in intensively managed landscapes

    NASA Astrophysics Data System (ADS)

    Abban, B.; (Thanos) Papanicolaou, A. N.; Cowles, M. K.; Wilson, C. G.; Abaci, O.; Wacha, K.; Schilling, K.; Schnoebelen, D.

    2016-06-01

    An enhanced revision of the Fox and Papanicolaou (hereafter referred to as "F-P") (2008a) Bayesian, Markov Chain Monte Carlo fingerprinting framework for estimating sediment source contributions and their associated uncertainties is presented. The F-P framework included two key deterministic parameters, α and β, that, respectively, reflected the spatial origin attributes of sources and the time history of eroded material delivered to and collected at the watershed outlet. However, the deterministic treatment of α and β is limited to cases with well-defined spatial partitioning of sources, high sediment delivery, and relatively short travel times with little variability in transport within the watershed. For event-based studies in intensively managed landscapes, this may be inadequate since landscape heterogeneity results in variabilities in source contributions, their pathways, delivery times, and storage within the watershed. Thus, probabilistic treatments of α and β are implemented in the enhanced framework to account for these variabilities. To evaluate the effects of the treatments of α and β on source partitioning, both frameworks are applied to the South Amana Subwatershed (SASW) in the U.S. midwest. The enhanced framework is found to estimate mean source contributions that are in good agreement with estimates from other studies in SASW. The enhanced framework is also able to produce expected trends in uncertainty during the study period, unlike the F-P framework, which does not perform as expected. Overall, the enhanced framework is found to be less sensitive to changes in α and β than the F-P framework, and, therefore, is more robust and desirable from a management standpoint.

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

    EPA Science Inventory

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

  8. Luminous Landscapes.

    ERIC Educational Resources Information Center

    Okrent, Inez

    2000-01-01

    Describes an activity for third-grade students in which they learn about early American landscape painters, specifically Frederick Church, Thomas Moran, and Albert Bierstadt. Students create natural landscapes, using the basic elements of landscape compositions. Discusses the process. (CMK)

  9. Temperature and solvent dependence of the dynamical landscape of tau protein conformations.

    PubMed

    Bianconi, Antonio; Ciasca, Gabriele; Tenenbaum, Alexander; Battisti, Anna; Campi, Gaetano

    2012-01-01

    We report the variation with temperature of the ensemble distribution of conformations spanned by the tau protein in its dynamical states measured by small-angle X-ray scattering (SAXS) using synchrotron radiation. The SAXS data show a clear temperature variation of the distribution of occupied protein conformations from 293 to 318 K. More conformations with a smaller radius of gyration are occupied at higher temperature. The protein-solvent interactions are shown by computer simulation to be essential for controlling the dynamics of protein conformations, providing evidence for the key role of water solvent in the protein dynamics, as proposed by Giorgio Careri. PMID:23277677

  10. Dynamics of the 2001 UK Foot and Mouth Epidemic: Stochastic Dispersal in a Heterogeneous Landscape

    NASA Astrophysics Data System (ADS)

    Keeling, Matt J.; Woolhouse, Mark E. J.; Shaw, Darren J.; Matthews, Louise; Chase-Topping, Margo; Haydon, Dan T.; Cornell, Stephen J.; Kappey, Jens; Wilesmith, John; Grenfell, Bryan T.

    2001-10-01

    Foot-and-mouth is one of the world's most economically important livestock diseases. We developed an individual farm-based stochastic model of the current UK epidemic. The fine grain of the epidemiological data reveals the infection dynamics at an unusually high spatiotemporal resolution. We show that the spatial distribution, size, and species composition of farms all influence the observed pattern and regional variability of outbreaks. The other key dynamical component is long-tailed stochastic dispersal of infection, combining frequent local movements with occasional long jumps. We assess the history and possible duration of the epidemic, the performance of control strategies, and general implications for disease dynamics in space and time.

  11. Dynamics of the 2001 UK foot and mouth epidemic: stochastic dispersal in a heterogeneous landscape.

    PubMed

    Keeling, M J; Woolhouse, M E; Shaw, D J; Matthews, L; Chase-Topping, M; Haydon, D T; Cornell, S J; Kappey, J; Wilesmith, J; Grenfell, B T

    2001-10-26

    Foot-and-mouth is one of the world's most economically important livestock diseases. We developed an individual farm-based stochastic model of the current UK epidemic. The fine grain of the epidemiological data reveals the infection dynamics at an unusually high spatiotemporal resolution. We show that the spatial distribution, size, and species composition of farms all influence the observed pattern and regional variability of outbreaks. The other key dynamical component is long-tailed stochastic dispersal of infection, combining frequent local movements with occasional long jumps. We assess the history and possible duration of the epidemic, the performance of control strategies, and general implications for disease dynamics in space and time.

  12. How interactions between animal movement and landscape processes modify range dynamics and extinction risk

    EPA Science Inventory

    Range dynamics models now incorporate many of the mechanisms and interactions that drive species distributions. However, connectivity continues to be studied using overly simple distance-based dispersal models with little consideration of how the individual behavior of dispersin...

  13. Landscape and plant physiological controls on water dynamics within a watershed

    NASA Astrophysics Data System (ADS)

    Hu, J.; Looker, N. T.; Martin, J. T.; Hoylman, Z. H.; Jencso, K. G.

    2014-12-01

    Across the Western U.S., declining snowpacks have resulted in increased water limitation, leading to reduced productivity in high elevation forests. While our current understanding of how forests respond to climate change is typically focused on measuring/modeling the physiological responses and climate feedbacks, our study aims to combine physiology with hydrology to examine how landscape topography modulates the sensitivity of forests to climate. In a forested watershed in Western Montana, we linked climate variability to the physical watershed characteristics and the physiological response of vegetation to examine forest transpiration and productivity rates. Across the entire watershed, we found a strong relationship between productivity and the topographic wetness index, a proxy for soil moisture storage. However, this relationship was highly dependent on the intensity of solar radiation, suggesting that at high elevations productivity was limited by temperature, while at low elevations productivity was limited by moisture. In order to identify the mechanisms responsible for this relationship, we then examined how different coniferous species respond to changing environmental and hydrologic regimes. We first examined transpiration and productivity rates at the hillslope scale at four plots, ranging in elevation and aspect across the watershed. We found trees growing in the hollows had higher transpiration and productivity rates than trees growing in the side slope, but that these differences were more pronounced at lower elevations. We then used oxygen isotope to examine water source use by different species across the watershed. We found that trees growing in the hollows used snowmelt for a longer period. This was most likely due to upslope subsidies of snowmelt water to the hollow areas. However, we found that trees growing at lower elevations used proportionally more snowmelt than trees at the higher elevations. This was most likely due to the trees at lower

  14. Landscape and plant physiological controls on water dynamics and forest productivity within a watershed

    NASA Astrophysics Data System (ADS)

    Hu, Jia; Jencso, Kelsey; Looker, Nathaniel; Martin, Justin; Hoylman, Zachary

    2015-04-01

    Across the Western U.S., declining snowpacks have resulted in increased water limitation, leading to reduced productivity in high elevation forests. While our current understanding of how forests respond to climate change is typically focused on measuring/modeling the physiological responses and climate feedbacks, our study aims to combine physiology with hydrology to examine how landscape topography modulates the sensitivity of forests to climate. In a forested watershed in Western Montana, we linked climate variability to the physical watershed characteristics and the physiological response of vegetation to examine forest transpiration and productivity rates. Across the entire watershed, we found a strong relationship between productivity and the topographic wetness index, a proxy for soil moisture storage. However, this relationship was highly dependent on the intensity of solar radiation, suggesting that at high elevations productivity was limited by temperature, while at low elevations productivity was limited by moisture. In order to identify the mechanisms responsible for this relationship, we then examined how different coniferous species respond to changing environmental and hydrologic regimes. We first examined transpiration and productivity rates at the hillslope scale at four plots, ranging in elevation and aspect across the watershed. We found trees growing in the hollows had higher transpiration and productivity rates than trees growing in the side slope, but that these differences were more pronounced at lower elevations. We then used oxygen isotope to examine water source use by different species across the watershed. We found that trees growing in the hollows used snowmelt for a longer period. This was most likely due to upslope subsidies of snowmelt water to the hollow areas. However, we found that trees growing at lower elevations used proportionally more snowmelt than trees at the higher elevations. This was most likely due to the trees at lower

  15. ELECTROMAGNETISM, OPTICS, ACOUSTICS, HEAT TRANSFER, CLASSICAL MECHANICS, AND FLUID DYNAMICS: Exact Soliton Solutions to a Generalized Nonlinear Schrödinger Equation

    NASA Astrophysics Data System (ADS)

    Xu, Si-Liu; Liang, Jian-Chu; Yi, Lin

    2010-01-01

    The (1+1)-dimensional F-expansion technique and the homogeneous nonlinear balance principle have been generalized and applied for solving exact solutions to a general (3+1)-dimensional nonlinear Schrödinger equation (NLSE) with varying coefficients and a harmonica potential. We found that there exist two kinds of soliton solutions. The evolution features of exact solutions have been numerically studied. The (3+1)D soliton solutions may help us to understand the nonlinear wave propagation in the nonlinear media such as classical optical waves and the matter waves of the Bose-Einstein condensates.

  16. Energy landscapes of dynamic ensembles of rolling triplet repeat bulge loops: implications for DNA expansion associated with disease states.

    PubMed

    Völker, Jens; Gindikin, Vera; Klump, Horst H; Plum, G Eric; Breslauer, Kenneth J

    2012-04-01

    DNA repeat domains can form ensembles of canonical and noncanonical states, including stable and metastable DNA secondary structures. Such sequence-induced structural diversity creates complex conformational landscapes for DNA processing pathways, including those triplet expansion events that accompany replication, recombination, and/or repair. Here we demonstrate further levels of conformational complexity within repeat domains. Specifically, we show that bulge loop structures within an extended repeat domain can form dynamic ensembles containing a distribution of loop positions, thereby yielding families of positional loop isomers, which we designate as "rollamers". Our fluorescence, absorbance, and calorimetric data are consistent with loop migration/translocation between sites within the repeat domain ("rollamerization"). We demonstrate that such "rollameric" migration of bulge loops within repeat sequences can invade and disrupt previously formed base-paired domains via an isoenthalpic, entropy-driven process. We further demonstrate that destabilizing abasic lesions alter the loop distributions so as to favor "rollamers" with the lesion positioned at the duplex/loop junction, sites where the flexibility of the abasic "universal hinge" relaxes unfavorable interactions and/or facilitates topological accommodation. Another strategic siting of an abasic site induces directed loop migration toward denaturing domains, a phenomenon that merges destabilizing domains. In the aggregate, our data reveal that dynamic ensembles within repeat domains profoundly impact the overall energetics of such DNA constructs as well as the distribution of states by which they denature/renature. These static and dynamic influences within triplet repeat domains expand the conformational space available for selection and targeting by the DNA processing machinery. We propose that such dynamic ensembles and their associated impact on DNA properties influence pathways that lead to DNA

  17. Advances in global sensitivity analyses of demographic-based species distribution models to address uncertainties in dynamic landscapes.

    PubMed

    Naujokaitis-Lewis, Ilona; Curtis, Janelle M R

    2016-01-01

    Developing a rigorous understanding of multiple global threats to species persistence requires the use of integrated modeling methods that capture processes which influence species distributions. Species distribution models (SDMs) coupled with population dynamics models can incorporate relationships between changing environments and demographics and are increasingly used to quantify relative extinction risks associated with climate and land-use changes. Despite their appeal, uncertainties associated with complex models can undermine their usefulness for advancing predictive ecology and informing conservation management decisions. We developed a computationally-efficient and freely available tool (GRIP 2.0) that implements and automates a global sensitivity analysis of coupled SDM-population dynamics models for comparing the relative influence of demographic parameters and habitat attributes on predicted extinction risk. Advances over previous global sensitivity analyses include the ability to vary habitat suitability across gradients, as well as habitat amount and configuration of spatially-explicit suitability maps of real and simulated landscapes. Using GRIP 2.0, we carried out a multi-model global sensitivity analysis of a coupled SDM-population dynamics model of whitebark pine (Pinus albicaulis) in Mount Rainier National Park as a case study and quantified the relative influence of input parameters and their interactions on model predictions. Our results differed from the one-at-time analyses used in the original study, and we found that the most influential parameters included the total amount of suitable habitat within the landscape, survival rates, and effects of a prevalent disease, white pine blister rust. Strong interactions between habitat amount and survival rates of older trees suggests the importance of habitat in mediating the negative influences of white pine blister rust. Our results underscore the importance of considering habitat attributes along

  18. Advances in global sensitivity analyses of demographic-based species distribution models to address uncertainties in dynamic landscapes.

    PubMed

    Naujokaitis-Lewis, Ilona; Curtis, Janelle M R

    2016-01-01

    Developing a rigorous understanding of multiple global threats to species persistence requires the use of integrated modeling methods that capture processes which influence species distributions. Species distribution models (SDMs) coupled with population dynamics models can incorporate relationships between changing environments and demographics and are increasingly used to quantify relative extinction risks associated with climate and land-use changes. Despite their appeal, uncertainties associated with complex models can undermine their usefulness for advancing predictive ecology and informing conservation management decisions. We developed a computationally-efficient and freely available tool (GRIP 2.0) that implements and automates a global sensitivity analysis of coupled SDM-population dynamics models for comparing the relative influence of demographic parameters and habitat attributes on predicted extinction risk. Advances over previous global sensitivity analyses include the ability to vary habitat suitability across gradients, as well as habitat amount and configuration of spatially-explicit suitability maps of real and simulated landscapes. Using GRIP 2.0, we carried out a multi-model global sensitivity analysis of a coupled SDM-population dynamics model of whitebark pine (Pinus albicaulis) in Mount Rainier National Park as a case study and quantified the relative influence of input parameters and their interactions on model predictions. Our results differed from the one-at-time analyses used in the original study, and we found that the most influential parameters included the total amount of suitable habitat within the landscape, survival rates, and effects of a prevalent disease, white pine blister rust. Strong interactions between habitat amount and survival rates of older trees suggests the importance of habitat in mediating the negative influences of white pine blister rust. Our results underscore the importance of considering habitat attributes along

  19. Advances in global sensitivity analyses of demographic-based species distribution models to address uncertainties in dynamic landscapes

    PubMed Central

    Curtis, Janelle M.R.

    2016-01-01

    Developing a rigorous understanding of multiple global threats to species persistence requires the use of integrated modeling methods that capture processes which influence species distributions. Species distribution models (SDMs) coupled with population dynamics models can incorporate relationships between changing environments and demographics and are increasingly used to quantify relative extinction risks associated with climate and land-use changes. Despite their appeal, uncertainties associated with complex models can undermine their usefulness for advancing predictive ecology and informing conservation management decisions. We developed a computationally-efficient and freely available tool (GRIP 2.0) that implements and automates a global sensitivity analysis of coupled SDM-population dynamics models for comparing the relative influence of demographic parameters and habitat attributes on predicted extinction risk. Advances over previous global sensitivity analyses include the ability to vary habitat suitability across gradients, as well as habitat amount and configuration of spatially-explicit suitability maps of real and simulated landscapes. Using GRIP 2.0, we carried out a multi-model global sensitivity analysis of a coupled SDM-population dynamics model of whitebark pine (Pinus albicaulis) in Mount Rainier National Park as a case study and quantified the relative influence of input parameters and their interactions on model predictions. Our results differed from the one-at-time analyses used in the original study, and we found that the most influential parameters included the total amount of suitable habitat within the landscape, survival rates, and effects of a prevalent disease, white pine blister rust. Strong interactions between habitat amount and survival rates of older trees suggests the importance of habitat in mediating the negative influences of white pine blister rust. Our results underscore the importance of considering habitat attributes along

  20. Variation and Trends of Landscape Dynamics, Land Surface Phenology and Net Primary Production of the Appalachian Mountains

    SciTech Connect

    Wang, Yeqiao; Zhao, Jianjun; Zhou, Yuyu; Zhang, Hongyan

    2012-12-15

    The gradients of the Appalachian Mountains in elevations and latitudes provide a unique regional perspective of landscape variations in the eastern United States and a section of the southeastern Canada. This study reveals patterns and trends of landscape dynamics, land surface phenology and ecosystem production along the Appalachian Mountains using time series data from Global Inventory Modeling and Mapping Studies (GIMMS) and AVHRR Global Production Efficiency Model (GloPEM) datasets. We analyzed the spatial and temporal patterns of Normalized Difference Vegetation Index (NDVI), length of growing season (LOS) and net primary production (NPP) of selected ecoregions along the Appalachian Mountains regions. We compared the results out of the Appalachian Mountains regions in different spatial contexts including the North America and the Appalachian Trail corridor area. To reveal latitudinal variations we analyzed data and compared the results between 30°N-40°N and 40°N-50°N latitudes. The result revealed significant decreases in annual peak NDVI in the Appalachian Mountains regions. The trend for the Appalachian Mountains regions was -0.0018 (R2=0.55, P<0.0001) NDVI unit decrease per year during 25 years between 1982 and 2006. The LOS had prolonged 0.3 day yr-1 during 25 years over the Appalachian Mountains regions. The NPP increased by 2.68 gC m-2yr-2 in Appalachian Mountains regions from 1981 to 2000. The comparison with the North America reveals the effects of topography and ecosystem compositions of the Appalachian Mountains. The comparison with the Appalachian Trail corridor area provides a regional mega-transect view of the measured variables.

  1. Species and Media Effects on Soil Carbon Dynamics in the Landscape.

    PubMed

    Marble, S Christopher; Prior, Stephen A; Runion, G Brett; Torbert, H Allen; Gilliam, Charles H; Fain, Glenn B; Sibley, Jeff L; Knight, Patricia R

    2016-01-01

    Three woody shrub species [cleyera (Ternstroemia gymnanthera Thunb. 'Conthery'), Indian hawthorn (Rhaphiolepis indica L.) and loropetalum (Loropetalum chinensis Oliv.'Ruby')] were container-grown for one growing season in 2008 using either pinebark (industry standard), clean chip residual or WholeTree (derived by-products from the forestry industry) as potting substrates and then transplanted into the landscape in 2008. An Automated Carbon Efflux System was used to continually monitor soil CO2 efflux from December 2010 through November 2011 in each species and substrate combination. Changes in soil carbon (C) levels as a result of potting substrate were assessed through soil sampling in 2009 and 2011 and plant biomass was determined at study conclusion. Results showed that soil CO2-C efflux was similar among all species and substrates, with few main effects of species or substrate observed throughout the study. Soil analysis showed that plots with pinebark contained higher levels of soil C in both 2009 and 2011, suggesting that pinebark decomposes slower than clean chip residual or WholeTree and consequently has greater C storage potential than the two alternative substrates. Results showed a net C gain for all species and substrate combinations; however, plants grown in pinebark had greater C sequestration potential. PMID:27140321

  2. Species and Media Effects on Soil Carbon Dynamics in the Landscape.

    PubMed

    Marble, S Christopher; Prior, Stephen A; Runion, G Brett; Torbert, H Allen; Gilliam, Charles H; Fain, Glenn B; Sibley, Jeff L; Knight, Patricia R

    2016-05-03

    Three woody shrub species [cleyera (Ternstroemia gymnanthera Thunb. 'Conthery'), Indian hawthorn (Rhaphiolepis indica L.) and loropetalum (Loropetalum chinensis Oliv.'Ruby')] were container-grown for one growing season in 2008 using either pinebark (industry standard), clean chip residual or WholeTree (derived by-products from the forestry industry) as potting substrates and then transplanted into the landscape in 2008. An Automated Carbon Efflux System was used to continually monitor soil CO2 efflux from December 2010 through November 2011 in each species and substrate combination. Changes in soil carbon (C) levels as a result of potting substrate were assessed through soil sampling in 2009 and 2011 and plant biomass was determined at study conclusion. Results showed that soil CO2-C efflux was similar among all species and substrates, with few main effects of species or substrate observed throughout the study. Soil analysis showed that plots with pinebark contained higher levels of soil C in both 2009 and 2011, suggesting that pinebark decomposes slower than clean chip residual or WholeTree and consequently has greater C storage potential than the two alternative substrates. Results showed a net C gain for all species and substrate combinations; however, plants grown in pinebark had greater C sequestration potential.

  3. Complex spatial dynamics maintain northern leopard frog (Lithobates pipiens) genetic diversity in a temporally varying landscape

    USGS Publications Warehouse

    Mushet, David M.; Euliss, Ned H.; Chen, Yongjiu; Stockwell, Craig A.

    2013-01-01

    In contrast to most local amphibian populations, northeastern populations of the Northern Leopard Frog (Lithobates pipiens) have displayed uncharacteristically high levels of genetic diversity that have been attributed to large, stable populations. However, this widely distributed species also occurs in areas known for great climatic fluctuations that should be reflected in corresponding fluctuations in population sizes and reduced genetic diversity. To test our hypothesis that Northern Leopard Frog genetic diversity would be reduced in areas subjected to significant climate variability, we examined the genetic diversity of L. pipiens collected from 12 sites within the Prairie Pothole Region of North Dakota. Despite the region's fluctuating climate that includes periods of recurring drought and deluge, we found unexpectedly high levels of genetic diversity approaching that of northeastern populations. Further, genetic structure at a landscape scale was strikingly homogeneous; genetic differentiation estimates (Dest) averaged 0.10 (SD = 0.036) across the six microsatellite loci we studied, and two Bayesian assignment tests (STRUCTURE and BAPS) failed to reveal the development of significant population structure across the 68 km breadth of our study area. These results suggest that L. pipiens in the Prairie Pothole Region consists of a large, panmictic population capable of maintaining high genetic diversity in the face of marked climate variability.

  4. The dynamics of land cover change pattern and landscape fragmentation in Jiuzhaigou Nature Reserve, China

    NASA Astrophysics Data System (ADS)

    Hao, Yunqing; Wang, Jinxi; Jiang, Hong

    2009-10-01

    Nature reserves are facing a very challenging conflict between conservation and development today. The protection effect of Jiuzhaigou Nature Reserve has received considerable attention, especially in view of its stimulating tourism after the 1990s. Remote sensing data from 1974, 1994 and 2002 were chosen for the analysis of this reserve, since they closely represented the vegetation situation before and after felling, as well as the disturbance from the flush of tourism. We find that the quality and quantity of the forest in Jiuzhaigou Nature Reserve continues to decline, owing to the conifer area and whole forest area constantly shrinking, as well as the landscape fragmentation increasing. The rate of loss of forest in the second period (1994-2002) had showed down much than that in the first period (1974-1994), due to nature protection. Shrubland area continued to increase throughout the two periods, with an increased speed in the second period which was about 3.5 times that in the first period. The treeline was consistently retreating, contributing a total of 467.96 ha of conifer forest lost. However, the causes involved in tree mortality and the resulting regression of the treeline are not clear. In any case, under the general background of global warming, human impact undoubtedly should have direct or indirect cause dramatic consequences for the forest in this very sensitive zone, while there are many uncertainties in the behaviour of high mountain ecosystems. Keywords: Jiuzhaigou Nature Reserve, Vegetation, Habitats fragment,

  5. Species and Media Effects on Soil Carbon Dynamics in the Landscape

    PubMed Central

    Marble, S. Christopher; Prior, Stephen A.; Runion, G. Brett; Torbert, H. Allen; Gilliam, Charles H.; Fain, Glenn B.; Sibley, Jeff L.; Knight, Patricia R.

    2016-01-01

    Three woody shrub species [cleyera (Ternstroemia gymnanthera Thunb. ‘Conthery’), Indian hawthorn (Rhaphiolepis indica L.) and loropetalum (Loropetalum chinensis Oliv.‘Ruby’)] were container-grown for one growing season in 2008 using either pinebark (industry standard), clean chip residual or WholeTree (derived by-products from the forestry industry) as potting substrates and then transplanted into the landscape in 2008. An Automated Carbon Efflux System was used to continually monitor soil CO2 efflux from December 2010 through November 2011 in each species and substrate combination. Changes in soil carbon (C) levels as a result of potting substrate were assessed through soil sampling in 2009 and 2011 and plant biomass was determined at study conclusion. Results showed that soil CO2-C efflux was similar among all species and substrates, with few main effects of species or substrate observed throughout the study. Soil analysis showed that plots with pinebark contained higher levels of soil C in both 2009 and 2011, suggesting that pinebark decomposes slower than clean chip residual or WholeTree and consequently has greater C storage potential than the two alternative substrates. Results showed a net C gain for all species and substrate combinations; however, plants grown in pinebark had greater C sequestration potential. PMID:27140321

  6. The dynamics of social-ecological systems in urban landscapes: Stockholm and the National Urban Park, Sweden.

    PubMed

    Elmqvist, T; Colding, J; Barthel, S; Borgstrom, S; Duit, A; Lundberg, J; Andersson, E; Ahrné, K; Ernstson, H; Folke, C; Bengtsson, J

    2004-06-01

    This study addresses social-ecological dynamics in the greater metropolitan area of Stockholm County, Sweden, with special focus on the National Urban Park (NUP). It is part of the Millennium Ecosystem Assessment (MA) and has the following specific objectives: (1) to provide scientific information on biodiversity patterns, ecosystem dynamics, and ecosystem services generated; (2) to map interplay between actors and institutions involved in management of ecosystem services; and (3) to identify strategies for strengthening social-ecological resilience. The green areas in Stockholm County deliver numerous ecosystem services, for example, air filtration, regulation of microclimate, noise reduction, surface water drainage, recreational and cultural values, nutrient retention, and pollination and seed dispersal. Recreation is among the most important services and NUP, for example, has more than 15 million visitors per year. More than 65 organizations representing 175,000 members are involved in management of ecosystem services. However, because of population increase and urban growth during the last three decades, the region displays a quite dramatic loss of green areas and biodiversity. An important future focus is how management may reduce increasing isolation of urban green areas and enhance connectivity. Comanagement should be considered where locally managed green space may function as buffer zones and for management of weak links that connect larger green areas; for example, there are three such areas around NUP identified. Preliminary results indicate that areas of informal management represent centers on which to base adaptive comanagement, with the potential to strengthen biodiversity management and resilience in the landscape.

  7. A dynamic, non-steady state approach for paritioning of soil evaporation and plant water use at landscape scales

    NASA Astrophysics Data System (ADS)

    Caylor, K. K.; Wayland, H.; Scanlon, T. M.

    2015-12-01

    Seperate characterization of plant water use and soil evaporation are critical to understanding ecohydrological dynamics of dryland ecosystems and for efficiently managing water in dryland agriculture. The application of stable isotopes as a tracer of these individual fluxes has been constrained by obtaining robust measurements of the isotopic composition of plant water use (δT) that may be scaled up to the ecosystem level. Of particular concern is the fact that the isotopic composition of plant transpiration is usually assumed to be equal to the isotopic composition of xylem water; the so-called steady-state assumption. However, our results and the findings of other published studies strongly suggest that steady state conditions are unrealistic for vegetation in dynamic natural environments. This talk focuses on the development of a simple framework for using relationships between plant transpiration and δT to partition ET at the landscape level. Our method uses a newly-derived empirical relationship between leaf conductance and isotopic fractionation during transpiration to solve a system of equations that can provide solutions to the fraction of total ET composed of bare soil evaporation and transpiration. We apply our method to a time series of evapotranspiration fluxes and near-surface water vapor isotopic composition at a field station in central Kenya and compare the results with partitioning obtained from both steady-state approaches and non-isotopic approaches for partitioning.

  8. Measure of Landscape Heterogeneity by Agent-Based Methodology

    NASA Astrophysics Data System (ADS)

    Wirth, E.; Szabó, Gy.; Czinkóczky, A.

    2016-06-01

    With the rapid increase of the world's population, the efficient food production is one of the key factors of the human survival. Since biodiversity and heterogeneity is the basis of the sustainable agriculture, the authors tried to measure the heterogeneity of a chosen landscape. The EU farming and subsidizing policies (EEA, 2014) support landscape heterogeneity and diversity, nevertheless exact measurements and calculations apart from statistical parameters (standard deviation, mean), do not really exist. In the present paper the authors' goal is to find an objective, dynamic method that measures landscape heterogeneity. It is achieved with the so called agent-based modelling, where randomly dispatched dynamic scouts record the observed land cover parameters and sum up the features of a new type of land. During the simulation the agents collect a Monte Carlo integral as a diversity landscape potential which can be considered as the unit of the `greening' measure. As a final product of the ABM method, a landscape potential map is obtained that can serve as a tool for objective decision making to support agricultural diversity.

  9. Dynamics in Protected Areas and Domesticated Landscapes Caused by Climate Change and Anthropogenic Use

    NASA Astrophysics Data System (ADS)

    Hartter, J.; Ryan, S.; Stampone, M.; Chapman, C.

    2009-12-01

    Climate change, a key factor of concern for conservation, has important biological and social implications. Africa’s Albertine Rift is an area of extremely high endemic biodiversity and is classed as a world conservation priority. However, natural areas are represented by a chain of protected forest areas in a matrix of intensive smallholder agriculture and dense human settlements. Kibale National Park in western Uganda has become an island of forest surrounded by intensive small-scale agriculture and is the only remaining large area of mid-altitude forest remaining in Albertine Rift Region and East Africa. Increased temperature and precipitation over recent decades has been observed by scientists and local farmers, however, to date, rigorous analysis of local climate data and the impact of climate change on local resources does not exist. Moreover, local farmers report that some crops die or ripen too early because of increased precipitation. Conservation biologists and park managers are concerned that changes in tree phenology and primary productivity will alter wildlife feeding preferences and ranges leading to more human-wildlife conflict. Understanding the impact of local and regional climate change and variation within the social, conservation, and geographic context is necessary to construct informed management plans and to maintain positive park-people relationships. This paper describes our first attempt to fully integrate multiple temporal and spatial datasets, and our progress in developing an interdisciplinary framework to study social and ecological relationships in the Kibale landscape. We examine historical in situ climate data and proxy climate information derived from remotely sensed satellite-borne imagery in our preliminary analyses. Our goal is to link these data with both pre-existing imagery analyses and tree community composition and phenology data from 39 years of ongoing research to identify the pattern, trajectory, and drivers of local

  10. The chromatin landscape of the moss Physcomitrella patens and its dynamics during development and drought stress.

    PubMed

    Widiez, Thomas; Symeonidi, Aikaterini; Luo, Chongyuan; Lam, Eric; Lawton, Michael; Rensing, Stefan A

    2014-07-01

    The moss Physcomitrella patens is an important model organism for evo-devo studies. Here, we determined the genome-wide chromatin landscape of five important histone three (H3) modifications (H3K4me3, H3K27me3, H3K27Ac, H3K9Ac and H3K9me2) and describe the changes to these histone marks in two contrasted situations, developmental transition and abiotic (drought) stress. Integrative analysis of these histone H3 modifications revealed their preferential association into 15 chromatin states (CS) in genic regions of the P. patens genome. Synergistic relationships that influence expression levels were revealed for the three activating marks H3K4me3, H3K27Ac and H3K9Ac, while an antagonistic relationship was found between CS containing the H3K27me3 and H3K27Ac marks, suggesting that H3K27 is a key indexing residue regarding transcriptional output. Concerning the alteration of histone marks in response to developmental transition (juvenile to adult) and drought stress, the three activating marks H3K4me3, H3K27Ac and H3K9Ac show significant changes in both situations. However, changes to H3K27me3 are central only for genes differentially expressed during development. Interestingly, genes induced during drought stress show significant histone mark toggling during developmental transition. This situation suggests that drought induced adult (gametophore expressed) genes are primed to respond to this stress during the juvenile to adult transition.

  11. Thermokarst and thaw-related landscape dynamics -- an annotated bibliography with an emphasis on potential effects on habitat and wildlife

    USGS Publications Warehouse

    Jones, Benjamin M.; Amundson, Courtney L.; Koch, Joshua C.; Grosse, Guido

    2013-01-01

    Permafrost has warmed throughout much of the Northern Hemisphere since the 1980s, with colder permafrost sites warming more rapidly (Romanovsky and others, 2010; Smith and others, 2010). Warming of the near-surface permafrost may lead to widespread terrain instability in ice-rich permafrost in the Arctic and the Subarctic, and may result in thermokarst development and other thaw-related landscape features (Jorgenson and others, 2006; Gooseff and others, 2009). Thermokarst and other thaw-related landscape features result from varying modes and scales of permafrost thaw, subsidence, and removal of material. An increase in active-layer depth, water accumulation on the soil surface, permafrost degradation and associated retreat of the permafrost table, and changes to lake shores and coastal bluffs act and interact to create thermokarst and other thaw-related landscape features (Shur and Osterkamp, 2007). There is increasing interest in the spatial and temporal dynamics of thermokarst and other thaw-related features from diverse disciplines including landscape ecology, hydrology, engineering, and biogeochemistry. Therefore, there is a need to synthesize and disseminate knowledge on the current state of near-surface permafrost terrain. The term "thermokarst" originated in the Russian literature, and its scientific use has varied substantially over time (Shur and Osterkamp, 2007). The modern definition of thermokarst refers to the process by which characteristic landforms result from the thawing of ice-rich permafrost or the melting of massive ice (van Everdingen, 1998), or, more specifically, the thawing of ice-rich permafrost and (or) melting of massive ice that result in consolidation and deformation of the soil surface and formation of specific forms of relief (Shur, 1988). Jorgenson (2013) identifies 23 distinct thermokarst and other thaw-related features in the Arctic, Subarctic, and Antarctic based primarily on differences in terrain condition, ground-ice volume

  12. Exploring water cycle dynamics by sampling multiple stable water isotope pools in a developed landscape in Germany

    NASA Astrophysics Data System (ADS)

    Orlowski, Natalie; Kraft, Philipp; Pferdmenges, Jakob; Breuer, Lutz

    2016-09-01

    A dual stable water isotope (δ2H and δ18O) study was conducted in the developed (managed) landscape of the Schwingbach catchment (Germany). The 2-year weekly to biweekly measurements of precipitation, stream, and groundwater isotopes revealed that surface and groundwater are isotopically disconnected from the annual precipitation cycle but showed bidirectional interactions between each other. Apparently, snowmelt played a fundamental role for groundwater recharge explaining the observed differences to precipitation δ values. A spatially distributed snapshot sampling of soil water isotopes at two soil depths at 52 sampling points across different land uses (arable land, forest, and grassland) revealed that topsoil isotopic signatures were similar to the precipitation input signal. Preferential water flow paths occurred under forested soils, explaining the isotopic similarities between top- and subsoil isotopic signatures. Due to human-impacted agricultural land use (tilling and compression) of arable and grassland soils, water delivery to the deeper soil layers was reduced, resulting in significant different isotopic signatures. However, the land use influence became less pronounced with depth and soil water approached groundwater δ values. Seasonally tracing stable water isotopes through soil profiles showed that the influence of new percolating soil water decreased with depth as no remarkable seasonality in soil isotopic signatures was obvious at depths > 0.9 m and constant values were observed through space and time. Since classic isotope evaluation methods such as transfer-function-based mean transit time calculations did not provide a good fit between the observed and calculated data, we established a hydrological model to estimate spatially distributed groundwater ages and flow directions within the Vollnkirchener Bach subcatchment. Our model revealed that complex age dynamics exist within the subcatchment and that much of the runoff must has been stored

  13. Modeling infectious disease dynamics in the complex landscape of global health

    PubMed Central

    Heesterbeek, Hans; Anderson, Roy; Andreasen, Viggo; Bansal, Shweta; De Angelis, Daniela; Dye, Chris; Eames, Ken; Edmunds, John; Frost, Simon; Funk, Sebastian; Hollingsworth, Deirdre; House, Thomas; Isham, Valerie; Klepac, Petra; Lessler, Justin; Lloyd-Smith, James; Metcalf, Jessica; Mollison, Denis; Pellis, Lorenzo; Pulliam, Juliet; Roberts, Mick; Viboud, Cecile

    2015-01-01

    Despite some notable successes in the control of infectious diseases, transmissible pathogens still pose an enormous threat to human and animal health. The ecological and evolutionary dynamics of infections play out on a wide range of interconnected temporal, organizational and spatial scales, which even within a single pathogen often span hours to months, cellular to ecosystem levels, and local to pandemic spread. Some pathogens are directly transmitted between individuals of a single species, while others circulate among multiple hosts, need arthropod vectors, or can survive in environmental reservoirs. Many factors, including increasing antimicrobial resistance, increased human connectivity, and dynamic human behavior, raise prevention and control from formerly national to international issues. In the face of this complexity, mathematical models offer essential tools for synthesizing information to understand epidemiological patterns, and for developing the quantitative evidence base for decision-making in global health. PMID:25766240

  14. Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography

    DOE PAGES

    Keedy, Daniel A.; Kenner, Lillian R.; Warkentin, Matthew; Woldeyes, Rahel A.; Hopkins, Jesse B.; Thompson, Michael C.; Brewster, Aaron S.; Van Benschoten, Andrew H.; Baxter, Elizabeth L.; Uervirojnangkoorn, Monarin; et al

    2015-09-30

    Determining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity in the active site of the dynamic enzyme cyclophilin A (CypA) has been previously linked to its catalytic function, but the extent to which the different conformations of these residues are correlated is unclear. Here we compare the conformational ensembles of CypA by multitemperature synchrotron crystallography and fixed-target X-ray free-electron laser (XFEL) crystallography. The diffraction-before-destruction nature of XFEL experiments provides a radiation-damage-free view of the functionally important alternative conformations of CypA, confirming earlier synchrotron-based results. We monitored the temperature dependences ofmore » these alternative conformations with eight synchrotron datasets spanning 100-310 K. Multiconformer models show that many alternative conformations in CypA are populated only at 240 K and above, yet others remain populated or become populated at 180 K and below. These results point to a complex evolution of conformational heterogeneity between 180-–240 K that involves both thermal deactivation and solvent-driven arrest of protein motions in the crystal. The lack of a single shared conformational response to temperature within the dynamic active-site network provides evidence for a conformation shuffling model, in which exchange between rotamer states of a large aromatic ring in the middle of the network shifts the conformational ensemble for the other residues in the network. Together, our multitemperature analyses and XFEL data motivate a new generation of temperature- and time-resolved experiments to structurally characterize the dynamic underpinnings of protein function.« less

  15. Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography.

    PubMed

    Keedy, Daniel A; Kenner, Lillian R; Warkentin, Matthew; Woldeyes, Rahel A; Hopkins, Jesse B; Thompson, Michael C; Brewster, Aaron S; Van Benschoten, Andrew H; Baxter, Elizabeth L; Uervirojnangkoorn, Monarin; McPhillips, Scott E; Song, Jinhu; Alonso-Mori, Roberto; Holton, James M; Weis, William I; Brunger, Axel T; Soltis, S Michael; Lemke, Henrik; Gonzalez, Ana; Sauter, Nicholas K; Cohen, Aina E; van den Bedem, Henry; Thorne, Robert E; Fraser, James S

    2015-01-01

    Determining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity in the active site of the dynamic enzyme cyclophilin A (CypA) has been previously linked to its catalytic function, but the extent to which the different conformations of these residues are correlated is unclear. Here we compare the conformational ensembles of CypA by multitemperature synchrotron crystallography and fixed-target X-ray free-electron laser (XFEL) crystallography. The diffraction-before-destruction nature of XFEL experiments provides a radiation-damage-free view of the functionally important alternative conformations of CypA, confirming earlier synchrotron-based results. We monitored the temperature dependences of these alternative conformations with eight synchrotron datasets spanning 100-310 K. Multiconformer models show that many alternative conformations in CypA are populated only at 240 K and above, yet others remain populated or become populated at 180 K and below. These results point to a complex evolution of conformational heterogeneity between 180--240 K that involves both thermal deactivation and solvent-driven arrest of protein motions in the crystal. The lack of a single shared conformational response to temperature within the dynamic active-site network provides evidence for a conformation shuffling model, in which exchange between rotamer states of a large aromatic ring in the middle of the network shifts the conformational ensemble for the other residues in the network. Together, our multitemperature analyses and XFEL data motivate a new generation of temperature- and time-resolved experiments to structurally characterize the dynamic underpinnings of protein function. PMID:26422513

  16. Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography

    SciTech Connect

    Keedy, Daniel A.; Kenner, Lillian R.; Warkentin, Matthew; Woldeyes, Rahel A.; Hopkins, Jesse B.; Thompson, Michael C.; Brewster, Aaron S.; Van Benschoten, Andrew H.; Baxter, Elizabeth L.; Uervirojnangkoorn, Monarin; McPhillips, Scott E.; Song, Jinhu; Alonso-Mori, Roberto; Holton, James M.; Weis, William I.; Brunger, Axel T.; Soltis, S. Michael; Lemke, Henrik; Gonzalez, Ana; Sauter, Nicholas K.; Cohen, Aina E.; van den Bedem, Henry; Thorne, Robert E.; Fraser, James S.

    2015-09-30

    Determining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity in the active site of the dynamic enzyme cyclophilin A (CypA) has been previously linked to its catalytic function, but the extent to which the different conformations of these residues are correlated is unclear. Here we compare the conformational ensembles of CypA by multitemperature synchrotron crystallography and fixed-target X-ray free-electron laser (XFEL) crystallography. The diffraction-before-destruction nature of XFEL experiments provides a radiation-damage-free view of the functionally important alternative conformations of CypA, confirming earlier synchrotron-based results. We monitored the temperature dependences of these alternative conformations with eight synchrotron datasets spanning 100-310 K. Multiconformer models show that many alternative conformations in CypA are populated only at 240 K and above, yet others remain populated or become populated at 180 K and below. These results point to a complex evolution of conformational heterogeneity between 180-–240 K that involves both thermal deactivation and solvent-driven arrest of protein motions in the crystal. The lack of a single shared conformational response to temperature within the dynamic active-site network provides evidence for a conformation shuffling model, in which exchange between rotamer states of a large aromatic ring in the middle of the network shifts the conformational ensemble for the other residues in the network. Together, our multitemperature analyses and XFEL data motivate a new generation of temperature- and time-resolved experiments to structurally characterize the dynamic underpinnings of protein function.

  17. Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

    PubMed Central

    Nepal, Chirag; Hadzhiev, Yavor; Previti, Christopher; Haberle, Vanja; Li, Nan; Takahashi, Hazuki; Suzuki, Ana Maria M.; Sheng, Ying; Abdelhamid, Rehab F.; Anand, Santosh; Gehrig, Jochen; Akalin, Altuna; Kockx, Christel E.M.; van der Sloot, Antoine A.J.; van IJcken, Wilfred F.J.; Armant, Olivier; Rastegar, Sepand; Watson, Craig; Strähle, Uwe; Stupka, Elia; Carninci, Piero; Lenhard, Boris; Müller, Ferenc

    2013-01-01

    Spatiotemporal control of gene expression is central to animal development. Core promoters represent a previously unanticipated regulatory level by interacting with cis-regulatory elements and transcription initiation in different physiological and developmental contexts. Here, we provide a first and comprehensive description of the core promoter repertoire and its dynamic use during the development of a vertebrate embryo. By using cap analysis of gene expression (CAGE), we mapped transcription initiation events at single nucleotide resolution across 12 stages of zebrafish development. These CAGE-based transcriptome maps reveal genome-wide rules of core promoter usage, structure, and dynamics, key to understanding the control of gene regulation during vertebrate ontogeny. They revealed the existence of multiple classes of pervasive intra- and intergenic post-transcriptionally processed RNA products and their developmental dynamics. Among these RNAs, we report splice donor site-associated intronic RNA (sRNA) to be specific to genes of the splicing machinery. For the identification of conserved features, we compared the zebrafish data sets to the first CAGE promoter map of Tetraodon and the existing human CAGE data. We show that a number of features, such as promoter type, newly discovered promoter properties such as a specialized purine-rich initiator motif, as well as sRNAs and the genes in which they are detected, are conserved in mammalian and Tetraodon CAGE-defined promoter maps. The zebrafish developmental promoterome represents a powerful resource for studying developmental gene regulation and revealing promoter features shared across vertebrates. PMID:24002785

  18. The analytical landscape of static and temporal dynamics in transcriptome data

    PubMed Central

    Oh, Sunghee; Song, Seongho; Dasgupta, Nupur; Grabowski, Gregory

    2014-01-01

    Interpreting gene expression profiles often involves statistical analysis of large numbers of differentially expressed genes, isoforms, and alternative splicing events at either static or dynamic spectrums. Reduced sequencing costs have made feasible dense time-series analysis of gene expression using RNA-seq; however, statistical methods in the context of temporal RNA-seq data are poorly developed. Here we will review current methods for identifying temporal changes in gene expression using RNA-seq, which are limited to static pairwise comparisons of time points and which fail to account for temporal dependencies in gene expression patterns. We also review recently developed very few number of temporal dynamic RNA-seq specific methods. Application and development of RNA-specific temporal dynamic methods have been continuously under the development, yet, it is still in infancy. We fully cover microarray specific temporal methods and transcriptome studies in initial digital technology (e.g., SAGE) between traditional microarray and new RNA-seq. PMID:24600473

  19. Biophysical approach for studying the MinD protein dynamics and energy landscape: a novel use of the spot tracking technique

    NASA Astrophysics Data System (ADS)

    Kanthang, P.; Ngamsaad, W.; Nuttavut, N.; Triampo, W.; Triampo, D.; Krittanai, C.

    2011-07-01

    The dynamics of MinD proteins have been acknowledged as playing a central role in accurate cell division. In our study, a spot tracking technique (STT) was applied to track motion and quantitatively characterize the dynamic behavior of MinD proteins on the level of particle cluster in Escherichia coli. We focused on the time and spatial distribution of MinD proteins. With the STT technique, the main quantitative results are twofold: (i) dynamic local and global pattern formations and (ii) energy landscape. The overall MinD cluster motion is governed by two dynamical time scales, namely the (slow) trapping time (~26 s) that appears at the cell poles, and the (fast) switching time (~1-2 s) which emerges between the cell poles. MinD cluster motion at the polar zones performs subdiffusion. The energy landscape is found to be two wells and one barrier. These energy landscape results are to relate with the memory effect of GFP-MinD cluster motion, measuring the PSD exponent approximately 1.57 (α ~ 0.57) corresponding to the estimated potential depth U0 ~ 1.75kBT.

  20. The binding landscape of plasmepsin V and the implications for flap dynamics.

    PubMed

    L, McGillewie; Soliman, Mahmoud E

    2016-04-26

    Plasmepsin V belongs to the plasmepsin family of aspartic proteases. PlmV is unique compared to other plasmepsins, as this membrane bound aspartic protease resides in the endoplasmic reticulum and is responsible for the cleavage of PEXEL tagged proteins destined for export outside of the host red blood cell. Plasmepsin V is highly conserved throughout the Plasmodium species, and is essential to the survival of the parasite. Recently, two potent inhibitors of Plmv have been identified, WEHI-916 and WEHI-842. Of these inhibitors, WEHI-842 has a higher binding affinity for P. vivax PlmV, and a crystal structure of PlmV in complex with WEHI-842 has recently been resolved (). The structure of PlmV is unique compared to other plasmepsins; it is stabilised internally by seven disulfide bonds, a NAP1 insert/fold is associated with the movement of the flap covering the active site and a highly conserved helix-turn-helix is situated towards the C-terminus. Flap motion and dynamics play an important role in enzyme selectivity and function. To better understand the impact of ligand binding on the flap dynamics, molecular dynamic simulations and post-dynamic analysis were employed in the present study on PlmV in complex with WEHI-842. Previously defined parameters, which accurately accounted for the opening and closing of the active site, were used to assess the conformational changes induced in the absence and presence of WEHI-842. From the simulations it can be seen that inhibitor binding significantly reduces the flexibility and mobility of not only the flap and flexible loop but areas outside of the active site. Ligand binding leads to the formation of a more stable compact structure. This being said, there is a possibility of reducing the flexibility even further with potentially more lethal effects on the plasmodium parasite. We believe that results presented herein would assist researchers in the discovery of potent PlmV inhibitors as potential antimalarial therapies

  1. Late Quaternary environmental and landscape dynamics revealed by a pingo sequence on the northern Seward Peninsula, Alaska

    NASA Astrophysics Data System (ADS)

    Wetterich, Sebastian; Grosse, Guido; Schirrmeister, Lutz; Andreev, Andrei A.; Bobrov, Anatoly A.; Kienast, Frank; Bigelow, Nancy H.; Edwards, Mary E.

    2012-04-01

    A terrestrial sediment sequence exposed in an eroding pingo provides insights into the late-Quaternary environmental history of the northern Seward Peninsula, Alaska. We have obtained the first radiocarbon-dated evidence for a mid-Wisconsin thermokarst lake, demonstrating that complex landscape dynamics involving cyclic permafrost aggradation and thermokarst lake formation occurred over stadial-interstadial as well as glacial-interglacial time periods. High values of Picea pollen and the presence of Larix pollen in sediments dated to 50-40 ka BP strongly suggest the presence of forest or woodland early in MIS 3; the trees grew within a vegetation matrix dominated by grass and sedge, and there is indirect evidence of grazing animals. Thus the interstadial ecosystem was different in structure and composition from the Holocene or from the preceding Last Interglacial period. An early Holocene warm period is indicated by renewed thermokarst lake formation and a range of fossil taxa. Multiple extralimital plant taxa suggest mean July temperatures above modern values. The local presence of spruce during the early Holocene warm interval is evident from a radiocarbon-dated spruce macrofossil remain and indicates significant range extension far beyond the modern tree line. The first direct evidence of spruce in Northwest Alaska during the early Holocene has implications for the presence of forest refugia in Central Beringia and previously assumed routes and timing of post-glacial forest expansion in Alaska.

  2. Groundwater dynamics in wetland soils control the production and transfer mechanisms of dissolved reactive phosphorus in an agricultural landscape

    NASA Astrophysics Data System (ADS)

    Dupas, Rémi; Gu, Sen; Gruau, Gérard; Gascuel-Odoux, Chantal

    2015-04-01

    Because of its high sorption affinity on soils solid phase, mitigation options to reduce diffuse P transfer usually focus on trapping particulate P forms delivered via surface flowpaths. Therefore, vegetated buffer zones placed between croplands and watercourses have been promoted worldwide, sometimes in wetland areas. To investigate the risk of such P trapping riparian wetlands (RWs) releasing dissolved P to rivers, we monitored molybdate reactive P (MRP) in the free soil solution of two RWs in an intensively farmed catchment. Two main mechanisms causing MRP release were identified in light of the geochemical and hydrological conditions in the RWs, controlled by groundwater dynamics. First, soil rewetting after the dry summer was associated with the presence of a pool of mobile P, limited in size. Its mobilization started under conditions of water saturation caused by groundwater uprise in RW organo-mineral soil horizons. Second, the establishment of anoxic conditions in the end of the winter caused reductive solubilization of Fe oxide-hydroxide, along with release of P. Comparison between sites revealed that the first MRP release occurred only in a RW with P enriched soils, whereas the second was recorded even in a RW with a low soil P status. Seasonal variations in MRP concentrations in the stream were synchronized with those in RW soils. Hence, enriched and/or periodically anoxic RWs can act as a key component of the P transfer continuum in agricultural landscapes by converting particulate P from croplands into MRP released to rivers.

  3. Asymmetric inflation: Exact solutions

    SciTech Connect

    Buniy, Roman V.; Berera, Arjun; Kephart, Thomas W.

    2006-03-15

    We provide exact solutions to the Einstein equations when the universe contains vacuum energy plus a uniform arrangement of magnetic fields, strings, or domain walls. Such a universe has planar symmetry; i.e., it is homogeneous but not isotropic. Further exact solutions are obtained when dust is included and approximate solutions are found for w{ne}0 matter. These cosmologies also have planar symmetry. These results may eventually be used to explain some features in the Wilkinson Microwave Anisotropy Probe data. The magnetic field case is the easiest to motivate and has the highest possibility of yielding reliable constraints on observational cosmology.

  4. Influence of magnetic domain landscape on the flux dynamics in superconductor/ferromagnet bilayers

    NASA Astrophysics Data System (ADS)

    Adamus, Z.; Cieplak, Marta Z.; Kończykowski, M.; Zhu, L. Y.; Chien, C. L.

    2016-02-01

    We use a line of miniature Hall sensors to study the influence of the magnetic domain distribution on the flux dynamics in superconductor/ferromagnet bilayers. Two bilayers are built of a ferromagnetic Co/Pt multilayer with perpendicular magnetic anisotropy and a superconducting Nb layer, with the insulating layer in-between to avoid proximity effect. The magnetic domain patterns of various geometries are reversibly predefined in the Co/Pt multilayers using the appropriate magnetization procedure. The Pt thickness is different in the two bilayers, resulting in different width and length of the domains, which profoundly affects vortex dynamics. We show that narrow short domains lead to strong confinement of vortices at the sample edge, while narrow elongated domains of uniform width induce smaller confinement and easy vortex entry. Large enhancement of flux pinning and critical current density, by a factor of more than 7, is observed in the last case, while the former results in smaller enhancement. When domains are wide, the disorder in the domain widths becomes beneficial for larger enhancement of pinning, while more uniform distribution of domain widths results in a precipitous drop of the enhancement. The analysis of these results suggests that with increasing domain width, a transition occurs from vortex chains pinned by narrow domains to disordered triangular vortex lattice pinned by a maze of multiply interconnected magnetic domains.

  5. Actin-binding proteins: the long road to understanding the dynamic landscape of cellular actin networks.

    PubMed

    Lappalainen, Pekka

    2016-08-15

    The actin cytoskeleton supports a vast number of cellular processes in nonmuscle cells. It is well established that the organization and dynamics of the actin cytoskeleton are controlled by a large array of actin-binding proteins. However, it was only 40 years ago that the first nonmuscle actin-binding protein, filamin, was identified and characterized. Filamin was shown to bind and cross-link actin filaments into higher-order structures and contribute to phagocytosis in macrophages. Subsequently many other nonmuscle actin-binding proteins were identified and characterized. These proteins regulate almost all steps of the actin filament assembly and disassembly cycles, as well as the arrangement of actin filaments into diverse three-dimensional structures. Although the individual biochemical activities of most actin-regulatory proteins are relatively well understood, knowledge of how these proteins function together in a common cytoplasm to control actin dynamics and architecture is only beginning to emerge. Furthermore, understanding how signaling pathways and mechanical cues control the activities of various actin-binding proteins in different cellular, developmental, and pathological processes will keep researchers busy for decades. PMID:27528696

  6. Exploring the free-energy landscapes of biological systems with steered molecular dynamics.

    PubMed

    Chen, L Y

    2011-04-01

    We perform steered molecular dynamics (SMD) simulations and use the Brownian dynamics fluctuation-dissipation-theorem (BD-FDT) to accurately compute the free-energy profiles for several biophysical processes of fundamental importance: hydration of methane and cations, binding of benzene to T4-lysozyme L99A mutant, and permeation of water through aquaglyceroporin. For each system, the center-of-mass of the small molecule (methane, ion, benzene, and water, respectively) is steered (pulled) at a given speed over a period of time, during which the system transitions from one macroscopic state/conformation (State A) to another one (State B). The mechanical work of pulling the system is measured during the process, sampling a forward pulling path. Then the reverse pulling is conducted to sample a reverse path from B back to A. Sampling a small number of forward and reverse paths, we are able to accurately compute the free-energy profiles for all the afore-listed systems that represent various important aspects of biological physics. The numerical results are in excellent agreement with the experimental data and/or other computational studies available in the literature.

  7. The influence of hydrogeomorphic dynamics on fish habitat: A case study using the ooCAESAR landscape evolution model

    NASA Astrophysics Data System (ADS)

    Wheaton, J. M.; Sear, D. A.; Darby, S. E.; Booker, D. E.; Acreman, M.

    2005-12-01

    The sediments, morphological features and riverflows that define the hydrogeomorphology of natural river channels provide physical habitat diversity that sustains the aquatic biodiversity of river ecosystems. This simple concept underpins the large number of contemporary ecohydraulic models that are available in the literature. Such models have been widely used to predict how morphological diversity (taken here to encompass channel sediments, topography and flow velocity) influences habitat quality for target species at the reach scale. The accuracy of these predictions is a matter of considerable practical importance, as the results are frequently used as the basis for restoration or rehabilitation. However, such models are limited in that they do not account for dynamic changes in river morphology, which themselves are triggered by changes in the flows of water and sediment delivered from the watershed upstream and stimulated by climatic, tectonic or land cover perturbations across a wide range of temporal scales. Accordingly there is an urgent need to combine the outputs of catchment-based geomorphological models with ecohydraulic models, so that predictions of habitat quality focused on specific reaches can be placed into their appropriate (i.e., the watershed) spatial context. To address these issues we herein present preliminary simulations from a case study of the Sulphur Creek watershed, a 24.2 sq. km., third-order catchment draining one of 47 tributaries to the Napa River, which empties southerly into the San Francisco Bay of northern California. Therein, the influence of catchment-scale geomorphic dynamics on reach-scale fish habitat is investigated using the ooCAESAR landscape evolution model. This cellular automaton model, based on its predecessor CAESAR, was chosen because it can be run at spatial resolutions (1 to 5 m.) that are ecologically meaningful and at temporal resolutions that capture both individual event dynamics and long-term evolutionary

  8. Modeling infectious disease dynamics in the complex landscape of global health.

    PubMed

    Heesterbeek, Hans; Anderson, Roy M; Andreasen, Viggo; Bansal, Shweta; De Angelis, Daniela; Dye, Chris; Eames, Ken T D; Edmunds, W John; Frost, Simon D W; Funk, Sebastian; Hollingsworth, T Deirdre; House, Thomas; Isham, Valerie; Klepac, Petra; Lessler, Justin; Lloyd-Smith, James O; Metcalf, C Jessica E; Mollison, Denis; Pellis, Lorenzo; Pulliam, Juliet R C; Roberts, Mick G; Viboud, Cecile

    2015-03-13

    Despite some notable successes in the control of infectious diseases, transmissible pathogens still pose an enormous threat to human and animal health. The ecological and evolutionary dynamics of infections play out on a wide range of interconnected temporal, organizational, and spatial scales, which span hours to months, cells to ecosystems, and local to global spread. Moreover, some pathogens are directly transmitted between individuals of a single species, whereas others circulate among multiple hosts, need arthropod vectors, or can survive in environmental reservoirs. Many factors, including increasing antimicrobial resistance, increased human connectivity and changeable human behavior, elevate prevention and control from matters of national policy to international challenge. In the face of this complexity, mathematical models offer valuable tools for synthesizing information to understand epidemiological patterns, and for developing quantitative evidence for decision-making in global health.

  9. Modeling infectious disease dynamics in the complex landscape of global health.

    PubMed

    Heesterbeek, Hans; Anderson, Roy M; Andreasen, Viggo; Bansal, Shweta; De Angelis, Daniela; Dye, Chris; Eames, Ken T D; Edmunds, W John; Frost, Simon D W; Funk, Sebastian; Hollingsworth, T Deirdre; House, Thomas; Isham, Valerie; Klepac, Petra; Lessler, Justin; Lloyd-Smith, James O; Metcalf, C Jessica E; Mollison, Denis; Pellis, Lorenzo; Pulliam, Juliet R C; Roberts, Mick G; Viboud, Cecile

    2015-03-13

    Despite some notable successes in the control of infectious diseases, transmissible pathogens still pose an enormous threat to human and animal health. The ecological and evolutionary dynamics of infections play out on a wide range of interconnected temporal, organizational, and spatial scales, which span hours to months, cells to ecosystems, and local to global spread. Moreover, some pathogens are directly transmitted between individuals of a single species, whereas others circulate among multiple hosts, need arthropod vectors, or can survive in environmental reservoirs. Many factors, including increasing antimicrobial resistance, increased human connectivity and changeable human behavior, elevate prevention and control from matters of national policy to international challenge. In the face of this complexity, mathematical models offer valuable tools for synthesizing information to understand epidemiological patterns, and for developing quantitative evidence for decision-making in global health. PMID:25766240

  10. Exploring the Dynamics and Mutational Landscape of Riboregulation with a Minimal Synthetic Circuit in Living Cells

    PubMed Central

    Rodrigo, Guillermo; Majer, Eszter; Prakash, Satya; Daròs, José-Antonio; Jaramillo, Alfonso; Poyatos, Juan F.

    2015-01-01

    The regulation of gene expression, triggered by conformational changes in RNA molecules, is widely observed in cellular systems. Here, we examine this mode of control by means of a model-based design and construction of a fully synthetic riboregulatory device. We present a theoretical framework that rests on a simple energy model to predict the dynamic response of such a system. Following an equilibrium description, our framework integrates thermodynamic properties—anticipated with an RNA physicochemical model—with a detailed description of the intermolecular interaction. The theoretical calculations are confirmed with an experimental characterization of the action of the riboregulatory device within living cells. This illustrates, more broadly, the predictability of genetic robustness on synthetic systems, and the faculty to engineer gene expression programs from a minimal set of first principles. PMID:26331264

  11. Conservation of species in dynamic landscapes: divergent fates of Silene tatarica populations in riparian habitats.

    PubMed

    Jäkäläniemi, Anne; Tuomi, Juha; Siikamäki, Pirkko

    2006-06-01

    In transient environments, where local extinctions occur as a result of destruction or deterioration of the local habitat, the long-term persistence of a species requires successful colonizations at new, suitable sites. This kind of habitat tracking should be associated with the asynchronous dynamics of local populations, and it can be especially important for the conservation of rare plant species in riparian habitats. We determined spatiotemporal variation in the demography of the perennial Silene tatarica (L.) Pers. in 15 populations (1998-2003) located in periodically disturbed riparian habitats. The habitats differed according to their morphology (flat shores, slopes) and the amount of bare ground (open, intermediate, closed) along a successional gradient. We used elasticity and life-table response analyses and stochastic simulations to study the variation in population demography. Finite population growth rate was higher in intermediate habitats than in open and closed habitats. In stochastic simulations population size increased in most cases, but four populations were projected to become extinct within 12-70 years. The viability of local populations depended most on the survival and growth of juvenile individuals and on the fecundity of large fertile individuals. On a regional scale, the persistence of this species will require a viable network of local populations as protection against local extinctions caused by natural disturbances and succession. Accordingly, the long-term persistence of riparian species may depend on habitat changes; thus, their conservation requires maintenance of natural disturbance dynamics. Along regulated rivers, management activities such as the creation of open habitats for new colonization should be implemented. Similarly, these activities can be rather general requirements for the conservation of endangered species dependent on transient habitats along successional gradients.

  12. Exploring the structure and conformational landscape of human leptin. A molecular dynamics approach.

    PubMed

    Chimal-Vega, Brenda; Paniagua-Castro, Norma; Carrillo Vazquez, Jonathan; Rosas-Trigueros, Jorge L; Zamorano-Carrillo, Absalom; Benítez-Cardoza, Claudia G

    2015-11-21

    Leptin is a hormone that regulates energy homeostasis, inflammation, hematopoiesis and immune response, among other functions (Houseknecht et al., 1998; Zhang et al., 1995; Paz-Filho et al., 2010). To obtain its crystallographic structure, it was necessary to substitute a tryptophan for a glutamic acid at position 100, thus creating a mutant leptin that has been reported to have biological activity comparable to the activity of the wild type but that crystallizes more readily. Here, we report a comparative study of the conformational space of WT and W100E leptin using molecular dynamics simulations performed at 300, 400, and 500 K. We detected differences between the interactions of the two proteins with local and distal effects, resulting in changes in the conformation, accessible surface area, compactness, electrostatic potential and dynamic behavior. Additionally, the series of unfolding events that occur when leptin is subjected to high temperature differs for the two constructs. We observed that both proteins are mostly unstructured after 20 ns of MD simulation at 500 K. However, WT leptin maintains a significant amount of secondary structure in helix α2, while the most stable region of W100E leptin is helix α3. Furthermore, we found that the region between residues 25 and 42 might adopt interconverting secondary structures ranging from α-helices and random coils to β-strand structures. Thus, this region can be considered an intrinsically disordered region. This atomistic description supports our understanding of leptin signaling and consequently might facilitate the use of leptin in treatments for the pathophysiologies in which it is implicated.

  13. Human-caused mortality influences spatial population dynamics: pumas in landscapes with varying mortality risks

    USGS Publications Warehouse

    Newby, Jesse R.; Mills, L. Scott; Ruth, Toni K.; Pletscher, Daniel H.; Mitchell, Michael S.; Quigley, Howard B.; Murphy, Kerry M.; DeSimone, Rich

    2013-01-01

    An understanding of how stressors affect dispersal attributes and the contribution of local populations to multi-population dynamics are of immediate value to basic and applied ecology. Puma (Puma concolor) populations are expected to be influenced by inter-population movements and susceptible to human-induced source–sink dynamics. Using long-term datasets we quantified the contribution of two puma populations to operationally define them as sources or sinks. The puma population in the Northern Greater Yellowstone Ecosystem (NGYE) was largely insulated from human-induced mortality by Yellowstone National Park. Pumas in the western Montana Garnet Mountain system were exposed to greater human-induced mortality, which changed over the study due to the closure of a 915 km2 area to hunting. The NGYE’s population growth depended on inter-population movements, as did its ability to act as a source to the larger region. The heavily hunted Garnet area was a sink with a declining population until the hunting closure, after which it became a source with positive intrinsic growth and a 16× increase in emigration. We also examined the spatial and temporal characteristics of individual dispersal attributes (emigration, dispersal distance, establishment success) of subadult pumas (N = 126). Human-caused mortality was found to negatively impact all three dispersal components. Our results demonstrate the influence of human-induced mortality on not only within population vital rates, but also inter-population vital rates, affecting the magnitude and mechanisms of local population’s contribution to the larger metapopulation.

  14. Linking the terrestrial and aquatic system across scales: The role of connectivity, landscape organization and catchment size for the dynamics of DOC

    NASA Astrophysics Data System (ADS)

    Laudon, Hjalmar

    2014-05-01

    While the production and export of DOC - dissolved organic carbon - from the terrestrial landscape has been extensively studied during the past decades, mechanistic understanding of processes that control stream water quality at the soil/water interface, across different spatial scales, are still at its infancy. To improve the process description of DOC regulation, I use data and understanding from three decades of research that has been conducted within the interdisciplinary, multi-scale Krycklan Catchment Study (KCS) in northern Sweden (www.slu.se/Krycklan). KCS consists of 17 intensively long-term monitored catchments ranging over three orders of magnitude in size, from 3 ha to over 6780 ha, to elucidate the dominate hydrobiogeophysical processes regulating the concentration and export of nutrients, metals and organic pollutants. By combining the use of detailed catchment information with natural isotopes and the dynamics of stream biogeochemistry we can directly link variability in hydrological flow pathways, catchment characteristics and scale with the spatial and temporal dynamics of DOC. Our results suggest that the contrasting spatial variability in the flow pathways among the different landscape types has a first order control on the DOC. As a result, large variations in the dynamics of DOC and its quality are observed that varies with changes in hydrological connectivity, landscape organization and catchment size.

  15. The Roles of Groundwater Flowpaths and Stream Network Expansion in Landscape Connectivity and Resulting Runoff and Solute Dynamics in an Ephemeral Piedmont Catchment

    NASA Astrophysics Data System (ADS)

    Zimmer, M. A.; McGlynn, B. L.

    2014-12-01

    Much catchment hydrology has been conducted in steep, perennial stream watersheds with shallow soil. In contrast, we investigated an ephemeral stream watershed with deep, highly weathered soils, gentle relief, and the dynamic hydro-climatology of the Piedmont region of the United States. We seek to gain new understanding about increasingly recognized challenges in the hydrological sciences, including influences of shallow and deep flowpath connectivity and the role of ephemeral streams in hydrologically connecting distal portions of landscapes. We investigated how overland, shallow soil, and deep subsurface flow across landscape positions and antecedent conditions manifest in observed baseflow and stormflow generation and the dynamics of dissolved organic carbon, electrical conductivity, and a suite of cations and anions. Extensive channel expansion and contraction coupled with spatially and temporally variable shallow and deep groundwater flowpaths led to both clockwise and counter-clockwise hysteresis in the relationship between runoff and solute concentrations as a function of antecedent moisture conditions. This suggests that vertical and horizontal hillslope connectivity to the aquatic system is variable across seasons and storms and influences biogeochemical expression at the watershed scale. Our research in Duke Forest, North Carolina has begun to elucidate the interrelationships between the space-time dynamics of runoff generation processes and observed biogeochemical behavior in this deeply weathered, low relief landscape, to provide new insight into processes widely active but less easily identified and quantified elsewhere.

  16. On exactly conservative integrators

    SciTech Connect

    Bowman, J.C.; Shadwick, B.A.; Morrison, P.J.

    1997-06-01

    Traditional explicit numerical discretizations of conservative systems generically predict artificial secular drifts of nonlinear invariants. These algorithms are based on polynomial functions of the time step. The authors discuss a general approach for developing explicit algorithms that conserve such invariants exactly. They illustrate the method by applying it to the truncated two-dimensional Euler equations.

  17. Quasispecies on Fitness Landscapes.

    PubMed

    Schuster, Peter

    2016-01-01

    Selection-mutation dynamics is studied as adaptation and neutral drift on abstract fitness landscapes. Various models of fitness landscapes are introduced and analyzed with respect to the stationary mutant distributions adopted by populations upon them. The concept of quasispecies is introduced, and the error threshold phenomenon is analyzed. Complex fitness landscapes with large scatter of fitness values are shown to sustain error thresholds. The phenomenological theory of the quasispecies introduced in 1971 by Eigen is compared to approximation-free numerical computations. The concept of strong quasispecies understood as mutant distributions, which are especially stable against changes in mutations rates, is presented. The role of fitness neutral genotypes in quasispecies is discussed.

  18. Population dynamics of hispid cotton rats (Sigmodon hispidus) across a nitrogen-amended landscape

    USGS Publications Warehouse

    Clark, J.E.; Hellgren, E.C.; Jorgensen, E.E.; Tunnell, S.J.; Engle, David M.; Leslie, David M.

    2003-01-01

    We conducted a mark-recapture experiment to examine the population dynamics of hispid cotton rats (Sigmodon hispidus) in response to low-level nitrogen amendments (16.4 kg nitrogen/ha per year) and exclosure fencing in an old-field grassland. The experimental design consisted of sixteen 0.16-ha plots with 4 replicates of each treatment combination. We predicted that densities, reproductive success, movement probabilities, and survival rates of cotton rats would be greater on nitrogen-amended plots because of greater aboveground biomass and canopy cover. Population densities of cotton rats tended to be highest on fenced nitrogen plots, but densities on unfenced nitrogen plots were similar to those on control and fenced plots. We observed no distinct patterns in survival rates, reproductive success, or movement probabilities with regard to nitrogen treatments. However, survival rates and reproductive success tended to be higher for cotton rats on fenced plots than for those on unfenced plots and this was likely attributable to decreased predation on fenced plots. As low-level nitrogen amendments continue to be applied, we predict that survival, reproduction, and population-growth rates of cotton rats on control plots, especially fenced plots with no nitrogen amendment, will eventually exceed those on nitrogen-amended plots as a result of higher plant-species diversity, greater food availability, and better quality cover.

  19. Deciphering the energy landscape of the interaction uranyl-DCP with antibodies using dynamic force spectroscopy.

    PubMed

    Teulon, Jean-Marie; Parot, Pierre; Odorico, Michael; Pellequer, Jean-Luc

    2008-11-15

    Previous studies on molecular recognition of uranyl-DCP (dicarboxy-phenanthroline chelator) compound by two distinct monoclonal antibodies (Mabs U04S and U08S) clearly showed the presence of a biphasic shape in Bell-Evans' plots and an accentuated difference in slopes at the high loading rates. To further explore the basis in the slope difference, we have performed complementary experiments using antibody PHE03S, raised against uranyl-DCP but, presenting a strong cross-reactivity toward the DCP chelator. This work allowed us to obtain a reallocation of the respective contributions of the metal ion itself and that of the chelator. Results led us to propose a 2D schematic model representing two energy barriers observed in the systems Mabs U04S- and U08S-[UO(2)-DCP] where the outer barrier characterizes the interaction between UO(2) and Mab whereas the inner barrier characterizes the interaction between DCP and Mab. Using dynamic force spectroscopy, it is thus possible to dissect molecular interactions during the unbinding between proteins and ligands.

  20. The Dynamic Architectural and Epigenetic Nuclear Landscape: Developing the Genomic Almanac of Biology and Disease

    PubMed Central

    Tai, Phillip W. L.; Zaidi, Sayyed K.; Wu, Hai; Grandy, Rodrigo A.; Montecino, Martin M.; van Wijnen, André J.; Lian, Jane B.; Stein, Gary S.; Stein, Janet L.

    2014-01-01

    Compaction of the eukaryotic genome into the confined space of the cell nucleus must occur faithfully throughout each cell cycle to retain gene expression fidelity. For decades, experimental limitations to study the structural organization of the interphase nucleus restricted our understanding of its contributions towards gene regulation and disease. However, within the past few years, our capability to visualize chromosomes in vivo with sophisticated fluorescence microscopy, and to characterize chromosomal regulatory environments via massively-parallel sequencing methodologies have drastically changed how we currently understand epigenetic gene control within the context of three-dimensional nuclear structure. The rapid rate at which information on nuclear structure is unfolding brings challenges to compare and contrast recent observations with historic findings. In this review, we discuss experimental breakthroughs that have influenced how we understand and explore the dynamic structure and function of the nucleus, and how we can incorporate historical perspectives with insights acquired from the ever-evolving advances in molecular biology and pathology. PMID:24242872

  1. Linking runoff and erosion dynamics to nutrient fluxes in a degrading dryland landscape

    NASA Astrophysics Data System (ADS)

    Michaelides, Katerina; Lister, Debbie; Wainwright, John; Parsons, Anthony J.

    2012-12-01

    Current theories of land degradation assume that shifts in vegetation communities result in changes to the rates and patterns of water and sediment movement, which are vectors of nutrient redistribution. This nutrient redistribution is hypothesized to reinforce, through positive feedbacks, progressive vegetation changes toward a more degraded ecosystem. A key component of this theory, which is currently poorly resolved, is the relative role of runoff and erosion in driving nutrient fluxes from different vegetation types. We address this gap through a series of field-based, rainfall-simulation experiments designed to explore plant-level dynamics of runoff- and erosion-driven nutrient fluxes of N, P and K species. Our results highlight important linkages between physical and biogeochemical processes that are controlled by plant structure. We found that: 1) the magnitude of sediment-bound nutrient export is determined by the grain-size distribution of the eroded sediment and the total sediment yield; 2) the partitioning of nutrients in dissolved and sediment-bound form is determined by the availability and concentration of different nutrient species in the soil or rainfall; 3) these processes varied according to vegetation type and resulted in stark differences between degrading and invading plant communities. Specifically, we observed that grassland areas consistently exported the highest yields of sediment-bound N, P and K despite producing similar erosion rates to shrub and intershrub areas. Our results have implications for better understanding how grassland areas are being replaced by shrubs and provide insights into the mechanisms of continuing land degradation in drylands.

  2. Landscape evolution in tidal embayments: Modeling the interplay of erosion, sedimentation, and vegetation dynamics

    NASA Astrophysics Data System (ADS)

    D'Alpaos, Andrea; Lanzoni, Stefano; Marani, Marco; Rinaldo, Andrea

    2007-03-01

    We propose an ecomorphodynamic model which conceptualizes the chief land-forming processes operating on the intertwined, long-term evolution of marsh platforms and embedded tidal networks. The rapid network incision (previously addressed by the authors) is decoupled from the geomorphological dynamics of intertidal areas, governed by sediment erosion and deposition and crucially affected by the presence of vegetation. This allows us to investigate the response of tidal morphologies to different scenarios of sediment supply, colonization by halophytes, and changing sea level. Different morphological evolutionary regimes are shown to depend on marsh ecology. Marsh accretion rates, enhanced by vegetation growth, and the related platform elevations tend to decrease with distance from the creek, measured along suitably defined flow paths. The negative feedback between surface elevation and its inorganic accretion rate is reinforced by the relation between plant productivity and soil elevation in Spartina-dominated marshes and counteracted by positive feedbacks in multispecies-vegetated marshes. When evolving under constant sea level, unvegetated and Spartina-dominated marshes asymptotically tend to mean high water level (MHWL), different from multiple vegetation species marshes, which can make the evolutionary transition to upland. Equilibrium configurations below MHWL can be reached under constant rates of sea level rise, depending on sediment supply and vegetation productivity. Our analyses on marine regressions and transgressions show that when the system is in a supply-limited regime, network retreat and expansion (associated with regressions and transgressions, respectively) tend to be cyclic. Conversely, in a transport-limited regime, network reexpansion following a regression tends to take on a new configuration, showing a hysteretic behavior.

  3. Urban expansion dynamics and natural habitat loss in China: a multiscale landscape perspective.

    PubMed

    He, Chunyang; Liu, Zhifeng; Tian, Jie; Ma, Qun

    2014-09-01

    China's extensive urbanization has resulted in a massive loss of natural habitat, which is threatening the nation's biodiversity and socioeconomic sustainability. A timely and accurate understanding of natural habitat loss caused by urban expansion will allow more informed and effective measures to be taken for the conservation of biodiversity. However, the impact of urban expansion on natural habitats is not well-understood, primarily due to the lack of accurate spatial information regarding urban expansion across China. In this study, we proposed an approach that can be used to accurately summarize the dynamics of urban expansion in China over two recent decades (1992-2012), by integrating data on nighttime light levels, a vegetation index, and land surface temperature. The natural habitat loss during the time period was evaluated at the national, ecoregional, and local scales. The results revealed that China had experienced extremely rapid urban growth from 1992 to 2012 with an average annual growth rate of 8.74%, in contrast with the global average of 3.20%. The massive urban expansion has resulted in significant natural habitat loss in some areas in China. Special attention needs to be paid to the Pearl River Delta, where 25.79% or 1518 km(2) of the natural habitat and 41.99% or 760 km(2) of the local wetlands were lost during 1992-2012. This raises serious concerns about species viability and biodiversity. Effective policies and regulations must be implemented and enforced to sustain regional and national development in the context of rapid urbanization.

  4. Hydrogeologic Controls on Water Dynamics in a Discontinuous Permafrost, Lake-Rich Landscape

    NASA Astrophysics Data System (ADS)

    Walvoord, M. A.; Briggs, M. A.; Day-Lewis, F. D.; Jepsen, S. M.; Lane, J. W., Jr.; McKenzie, J. M.; Minsley, B. J.; Striegl, R. G.; Voss, C. I.; Wellman, T. P.

    2014-12-01

    Glacier sliding plays a central role in ice dynamics. A number of remote sensing and deep drilling initiatives have therefore focused on the ice-bed interface. Although these techniques have provided valuable insights into bed properties, they do not supply theorists with data of sufficient temporal and spatial resolution to rigorously test mathematical sliding laws. As an alternative, passive seismic techniques have gained popularity in glacier monitoring. Analysis of glacier-related seismic sources ('icequakes') has become a useful technique to study inaccessible regions of the cryosphere, including the ice-bed interface. Seismic monitoring networks on the polar ice sheets have shown that ice sliding is not only a smooth process involving viscous deformation and regelation of basal ice layers. Instead, ice streams exhibit sudden slip episodes over their beds and intermittent phases of partial or complete stagnation. Here we discuss new and recently published discoveries of basal seismic sources beneath various glacial bodies. We revisit basal seismicity of hard-bedded Alpine glaciers, which is not the result of pure stick-slip motion. Sudden changes in seismicity suggest that the local configuration of the subglacial drainage system undergoes changes on sub daily time scales. Accordingly, such observations place constraints on basal resistance and sliding of hard-bedded glaciers. In contrast, certain clusters of stick-slip dislocations associated with micro seismicity beneath the Greenland ice sheet undergo diurnal variations in magnitudes and inter event times. This is best explained with a soft till bed, which hosts the shear dislocations and whose strength varies in response to changes in subglacial water pressure. These results suggest that analysis of basal icequakes is well suited for characterizing glacier and ice sheet beds. Future studies should address the relative importance between "smooth" and seismogenic sliding in different glacial environments.

  5. Geomorpho-Landscapes

    NASA Astrophysics Data System (ADS)

    Farabollini, Piero; Lugeri, Francesca; Amadio, Vittorio

    2014-05-01

    Landscape is the object of human perceptions, being the image of spatial organization of elements and structures: mankind lives the first approach with the environment, viewing and feeling the landscape. Many definitions of landscape have been given over time: in this case we refer to the Landscape defined as the result of interaction among physical, biotic and anthropic phenomena acting in a different spatial-temporal scale (Foreman & Godron) Following an Aristotelic approach in studying nature, we can assert that " Shape is synthesis": so it is possible to read the land features as the expression of the endogenous and exogenous processes that mould earth surfaces; moreover, Landscape is the result of the interaction of natural and cultural components, and conditions the spatial-temporal development of a region. The study of the Landscape offers results useful in order to promote sustainable development, ecotourism, enhancement of natural and cultural heritage, popularization of the scientific knowledge. In Italy, a very important GIS-based tool to represent the territory is the "Carta della Natura" ("Map of Nature", presently coordinated by the ISPRA) that aims at assessing the state of the whole Italian territory, analyzing Landscape. The methodology follows a holistic approach, taking into consideration all the components of a landscape and then integrating the information. Each individual landscape, studied at different scales, shows distinctive elements: structural, which depend on physical form and specific spatial organization; functional, which depend on relationships created between biotic and abiotic elements, and dynamic, which depend on the successive evolution of the structure. The identification of the landscape units, recognized at different scales of analysis, allows an evaluation of the state of the land, referring to the dual risk/resource which characterizes the Italian country. An interesting opportunity is to discover those areas of unusual

  6. Linking recent landscape changes in thawed permafrost with sediment dynamics in thermokarst ponds of subarctic Quebec (Canada)

    NASA Astrophysics Data System (ADS)

    Bouchard, F.; Pienitz, R.; Francus, P.

    2012-12-01

    Thermokarst (thaw) ponds and lakes are a major feature in arctic and subarctic permafrost regions. These ecosystems receive growing attention due to their potential contribution to global carbon budgets as greenhouse gas emitters. However, the geomorphological changes in their catchment and the impact on sediment dynamics and composition remain largely unexplored. Here we present a study that synthesizes recent landscape evolution and modern sedimentology of limnologically diverse thermokarst ponds at the southern limit of the discontinuous permafrost zone in southeastern Hudson Bay, Canada. Spatio-temporal analysis (remote sensing) of permafrost mounds, thermokarst ponds and vegetation surface areas over the last five decades revealed that recent sharp decreases of permafrost-affected areas (> 95 %) were not primarily compensated by thermokarst pond development, but rather by a remarkable increase (> 300 %) in vegetation cover. These changes appeared to follow the topographical/hydrological gradient in the area, which is associated with the eastward increasing thickness of postglacial marine deposits. Moreover, these impermeable silts and clays likely prevented the drainage of ponds related to permafrost disappearance, in contrast to what has been reported from other circumpolar permafrost areas. In fact, thermokarst pond total surface area remained relatively stable (~ 2.5 % decrease) between the late 1950s and late 2000s, whereas their absolute number decreased significantly (> 25 %), resulting in generally larger ponds (> 30 % increase in mean pond area). Additionally, physico-chemical measurements made on sedimenting materials (sediment traps) and freshly deposited lacustrine sediments of thermokarst ponds revealed striking differences between the oxic epilimnion and the oxygen-depleted hypolimnion, underscoring the major influence of oxycline development on pond sedimentology and geochemistry (e.g., transport of detritic particles, concentration of organic

  7. Exact Relativistic `Antigravity' Propulsion

    NASA Astrophysics Data System (ADS)

    Felber, Franklin S.

    2006-01-01

    The Schwarzschild solution is used to find the exact relativistic motion of a payload in the gravitational field of a mass moving with constant velocity. At radial approach or recession speeds faster than 3-1/2 times the speed of light, even a small mass gravitationally repels a payload. At relativistic speeds, a suitable mass can quickly propel a heavy payload from rest nearly to the speed of light with negligible stresses on the payload.

  8. Assessment of present day geomorphological dynamics to decipher landscape evolution around the Paleolithic sites of Melka Kunture, Ethiopia

    NASA Astrophysics Data System (ADS)

    Maerker, Michael; Schillaci, Calogero; Melis, Rita; Mussi, Margherita

    2014-05-01

    The area of Melka Kunture (central Ethiopia) is one of the most important clusters of Paleolithic sites in Eastern Africa. The archaeological record spans from c. 1.7 Ma onwards, with a number of stratified occurrences of Oldowan, Acheulean, Middle Stone Age and Late Stone Age industries, together with faunal remains and human fossils. However, the archaeological sites are endangered by flooding and soil erosion. The main excavation area lies close to the convergence of the Awash river with the Atabella river, one of the main tributaries of the upper Awash catchment. In the semi-arid Ethiopian highlands, gully networks develop especially in the vicinity of the active and inactive river meanders. Various erosion processes are linked to specific driving factors such as the rainfall regime, the land use/cover changes and vertic soils with a specific hydrological behaviour. It was documented in the field and by previous research that the origin of most of the man made erosion channels is due to animal pathways and car tracks. However, paleolandscape features increase the general erosion risk. Former wetland areas and deposition zones are particularly affected by soil erosion processes. Hence, the spatial distribution and characteristics of present day geomorphic processes also reveal information on the paleolandscape. In order to assess landscape evolution and present day geomorphologic dynamics, we mapped the geomorphology describing in detail the present-day slope processes at a 10.000 scale. We performed a detailed terrain analysis based on high resolution DEMs such as SRTM-X with 25m resolution and ALOS/PRISM with 10m resolution to characterize the main erosion processes and surface runoff dynamics. The latter ones are simulated using a Soil Conservation Service Curve Number method. Landuse was delineated for a larger area using ASTER 25m multispectral data. Finally, using calibrated topographic indices and a simple hydrological model we were able to detect and

  9. Dynamic ancient ice caps in the sub-Antarctic suggested by new mapping of submarine ice-formed landscapes

    NASA Astrophysics Data System (ADS)

    Graham, Alastair; Hodgson, Dominic; Cofaigh, Colm Ó.; Hillenbrand, Claus-Dieter; Kuhn, Gerhard

    2014-05-01

    Recent bathymetric investigations have provided hints of significant past glaciations on several Southern Ocean sub-polar islands. The extent and behaviour of ice cover in these regions is important because it provides critical limits on the evolution of refugia and marine benthic organisms, as well as unique far-field constraints for improving polar ice-sheet model sensitivity. However, despite improvements in regional mapping, sea-floor acoustic data from key shelf areas have still not been of sufficient quality, or broad enough in their coverage, to resolve the number, form or flow of past glacial episodes. Hence the history and style of sub-Antarctic glaciation remains poorly known. Here we use a compilation of multibeam bathymetry and fisheries echo-sounding data to provide evidence for dynamic, widespread ice caps on sub-Antarctic South Georgia during past glacial periods. We present a hitherto unmapped record of sea-bed glacigenic structures, including end moraines and subglacial landforms, from which the flow and form of at least three major, entirely marine-terminating configurations is resolved. The largest glaciation covered the majority of the continental shelf, and included fast-flowing outlets, possible switching of internal flow, meltwater activity, warm-based ice erosion, and substantial marginal deposition during retreat: all features of dynamic ice-cap behaviour. Existing biological evidence suggests the largest glaciation likely pre-dated the Last Glacial Maximum, which may have been restricted in extent reaching to the island's fjord mouths, while a third mid-shelf limit appears partially recorded. Work on dating the relict landscape of ancient ice cap advance and retreat is ongoing, but our preliminary age model suggests that South Georgia's history is unique from the Antarctic polar glacial record, and may be more similar to that of past ice caps on Patagonia. The glacial configurations revealed by these data will provide the basis of new

  10. Landscape-seascape dynamics in the isthmus between Sørkapp Land and the rest of Spitsbergen: Will a new big Arctic island form?

    PubMed

    Ziaja, Wieslaw; Ostafin, Krzysztof

    2015-05-01

    Transformation of the glaciated isthmus between Sørkapp Land and the rest of Spitsbergen since 1900 is described. The landscape-seascape dynamics depends on the glacial recession determined by climate warming after the Little Ice Age (i.e., since the beginning of the twentieth century, and especially since the 1980s). The isthmus has been narrowed from 28 km in 1899-1900 to 6.2 km in 2013, and lowered by 60-200 m from 1936 to 2005. Two isthmus' glaciers will have melted, given the current thermic conditions, by 2030-2035. It cannot be ruled out that Sørkapp Land will become an island after that period, because the altitude of the glaciers' bedrock is close to the sea level. The disappearance of this huge ice mass, even without origin of a sound and island, will lead to a great transformation of the landscape and the ecosystem.

  11. Dynamics and the free-energy landscape of proteins, explored with the Mössbauer effect and quasi-elastic neutron scattering.

    PubMed

    Frauenfelder, Hans; Young, Robert D; Fenimore, Paul W

    2013-10-24

    The Mössbauer effect and quasi-elastic neutron scattering (QENS) from hydrated proteins yield sharp elastic lines that are accompanied by broad wings. Conventionally, the elastic line and the broad wings are treated as separate phenomena. We show that there is no separation; the entire spectrum consists of Lorentzians with the natural line width. In protein crystals, the shifts of the individual lines from the elastic center above about 150 K are caused by beta fluctuations in the hydration shell. Vibrations cause shifts in the entire temperature range but are best seen below about 150 K. We construct a microscopic model for the dynamics that is based on a random walk of the proteins in their free-energy landscape. The model yields approximate values for the steps in the energy landscape. Remarkably, the quantum electrodynamic concept of gamma rays is needed to justify the model. PMID:23962200

  12. Satellite remote sensing of landscape freeze/thaw state dynamics for complex Topography and Fire Disturbance Areas Using multi-sensor radar and SRTM digital elevation models

    NASA Technical Reports Server (NTRS)

    Podest, Erika; McDonald, Kyle; Kimball, John; Randerson, James

    2003-01-01

    We characterize differences in radar-derived freeze/thaw state, examining transitions over complex terrain and landscape disturbance regimes. In areas of complex terrain, we explore freezekhaw dynamics related to elevation, slope aspect and varying landcover. In the burned regions, we explore the timing of seasonal freeze/thaw transition as related to the recovering landscape, relative to that of a nearby control site. We apply in situ biophysical measurements, including flux tower measurements to validate and interpret the remotely sensed parameters. A multi-scale analysis is performed relating high-resolution SAR backscatter and moderate resolution scatterometer measurements to assess trade-offs in spatial and temporal resolution in the remotely sensed fields.

  13. [Dynamics of salinization land based on EVI series data and landscape pattern analysis in Songnen Plain: a case study in Da'an City].

    PubMed

    Liu, Shi-Liang; Dong, Yu-Hong; An, Nan-Nan; Wang, Jun; Zhao, Hai-Di

    2014-11-01

    The west part of Jilin Province is one of the most salinization regions in China and much attention has been paid to the dynamics and monitoring of the salinization land. Based on the land use data derived from TM images in 2000, 2005 and 2010 and the enhanced vegetation index (EVI) series data from 2000 to 2012 of Da'an City as a typical salinization region, we used landscape pattern analysis to elucidate the dynamics of salinization land, and used gray incidence method to analyze the main driving factors for the dynamics of land salinization. The results showed that the dominant land use types in Da'an City were cultivated land, grassland and salinization land. From 2000 to 2010, the area of salinization land and construction land showed an increasing trend, while that of grassland tended to decrease. Salinization land, which showed increased connectivity and integrity, was mainly transformed from grassland, swamp land and water area. Annual EVI values in Da'an City showed an overall increasing trend while the average values showed obvious spatial differences with the lowest EVI level in salinization land. From 2000 to 2012, the increment of vegetation cover area was larger than that of the degraded area. Landscape transformation affected the changing trends of EVI. Both natural factors and human activities affected the dynamics of salinization land, and human activities showed a greater impact on land salinization than climate factors.

  14. Age and dynamics of the Namib Sand Sea: A review of chronological evidence and possible landscape development models

    NASA Astrophysics Data System (ADS)

    Stone, A. E. C.

    2013-06-01

    The Namib Sand Sea constitutes a major physiographic feature of the Namib Desert on the west of Namibia, covering a 50-160 km wide region of the coast between Lüderitz and Walvis Bay. It is widely considered to be one of the oldest desert regions, with a Tertiary-aged fossil desert underlying the modern sand sea. The sand sea has been well studied, benefiting from the presence of the Gobabeb Training and Research Centre during the past 50 years. Whilst much is understood about its sediments and geomorphology, it is only recently that new chronological information, using cosmogenic-nuclide burial dating and optically stimulated luminescence dating have offered new insights, and this calls for an updated review of the age and landscape development of the sand sea. This assessment of the geomorphological and Quaternary dynamics of the region is complemented by developments in the description and analysis of sediment composition. New age control from cosmogenic dating indicates that the sand sea is in excess of a million years old. Initial data from luminescence dating yields depositional ages for dune sediments from three broad areas of the sand sea that include MIS 5, later in the Pleistocene around the Last Glacial Maximum and the Holocene, although it is not expected that these will be the only, or discrete age groupings. Detailed dating and application of ground penetrating radar in the far northern reaches reveals extensive dune migration and deposition during the Holocene. It is important to stress that the upper limit of luminescence dating here is about ˜200 ka (depending on the environmental dose rate of the site) and that migration and reworking of dunes resets the luminescence signal (so what is recorded is(are) the last phase(s) of preserved sediment accumulation). Whilst there are three potential sources of material for the Namib Sand Sea (reworked Tsondab Sandstone (TSS), material from the Great Escarpment derived by rivers and water and wind

  15. Exact Lattice Supersymmetry

    SciTech Connect

    Catterall, Simon; Kaplan, David B.; Unsal, Mithat

    2009-03-31

    We provide an introduction to recent lattice formulations of supersymmetric theories which are invariant under one or more real supersymmetries at nonzero lattice spacing. These include the especially interesting case of N = 4 SYM in four dimensions. We discuss approaches based both on twisted supersymmetry and orbifold-deconstruction techniques and show their equivalence in the case of gauge theories. The presence of an exact supersymmetry reduces and in some cases eliminates the need for fine tuning to achieve a continuum limit invariant under the full supersymmetry of the target theory. We discuss open problems.

  16. Exactly conservation integrators

    SciTech Connect

    Shadwick, B.A.; Bowman, J.C.; Morrison, P.J.

    1999-03-01

    Traditional explicit numerical discretizations of conservative systems generically predict artificial secular drifts of any nonlinear invariants. In this work the authors present a general approach for developing explicit nontraditional algorithms that conserve such invariants exactly. They illustrate the method by applying it to the three-wave truncation of the Euler equations, the Lotka-Volterra predator-prey model, and the Kepler problem. The ideas are discussed in the context of symplectic (phase-space-conserving) integration methods as well as nonsymplectic conservative methods. They comment on the application of the method to general conservative systems.

  17. Exactly conservative integrators

    SciTech Connect

    Shadwick, B.A.; Bowman, J.C.; Morrison, P.J.

    1995-07-19

    Traditional numerical discretizations of conservative systems generically yield an artificial secular drift of any nonlinear invariants. In this work we present an explicit nontraditional algorithm that exactly conserves invariants. We illustrate the general method by applying it to the Three-Wave truncation of the Euler equations, the Volterra-Lotka predator-prey model, and the Kepler problem. We discuss our method in the context of symplectic (phase space conserving) integration methods as well as nonsymplectic conservative methods. We comment on the application of our method to general conservative systems.

  18. Exact folded-band chaotic oscillator

    NASA Astrophysics Data System (ADS)

    Corron, Ned J.; Blakely, Jonathan N.

    2012-06-01

    An exactly solvable chaotic oscillator with folded-band dynamics is shown. The oscillator is a hybrid dynamical system containing a linear ordinary differential equation and a nonlinear switching condition. Bounded oscillations are provably chaotic, and successive waveform maxima yield a one-dimensional piecewise-linear return map with segments of both positive and negative slopes. Continuous-time dynamics exhibit a folded-band topology similar to Rössler's oscillator. An exact solution is written as a linear convolution of a fixed basis pulse and a discrete binary sequence, from which an equivalent symbolic dynamics is obtained. The folded-band topology is shown to be dependent on the symbol grammar.

  19. Tracking Fine-Grain Phenological Dynamics at a Landscape Extent Using a Network of Near-Surface Digital Repeat Photography Stations in West Greenland

    NASA Astrophysics Data System (ADS)

    Kerby, J.; Post, E.

    2014-12-01

    The phenology of vegetation emergence in the Arctic is highly sensitive to climatic fluctuations. Spring phenology drives ecological processes across local, population, and ecosystem scales. Traditional approaches to capturing spatio-temporal variation in the annual timing and pace of Arctic green-up, like satellite-derived and plot-level records, are limited by trade-offs in the grain and extent of monitoring through both space and time. Recent studies demonstrate the utility of tracking canopy phenology using near-surface digital repeat photography (phenocams) to overcome spatial and temporal grain limitations at the extent of individual plants or vegetation stands. However, our understanding of how fine-grain phenological dynamics scale to landscape extents is incomplete. Here we report on the fine-grain green-up dynamics of a low-Arctic tundra system in West Greenland at the extent of a caribou calving range (40 km2) using three years (2012-2014) of phenological records derived from a network of 50 phenocams, field observations, and high-resolution satellite imagery. Using geostatistics and multiple-regression models, we characterize spatiotemporal patterns of plant phenology, landscape controls on the timing of emergence of common shrub and graminoid species, and assess scale-dependency in patterns of vegetation green-up. We link these results with coarse-grained satellite records of plant phenology to clarify how fine-grained dynamics contribute to the widely reported broad-scale patterns of phenological and ecological change in the Arctic.

  20. Vulnerability and Resilience of Temperate Forest Landscapes to Broad-Scale Deforestation in Response to Changing Fire Regimes and Altered Post-Fire Vegetation Dynamics

    NASA Astrophysics Data System (ADS)

    Tepley, A. J.; Veblen, T. T.; Perry, G.; Anderson-Teixeira, K. J.

    2015-12-01

    In the face of on-going climatic warming and land-use change, there is growing concern that temperate forest landscapes could be near a tipping point where relatively small changes to the fire regime or altered post-fire vegetation dynamics could lead to extensive conversion to shrublands or savannas. To evaluate vulnerability and resilience to such conversion, we develop a simple model based on three factors we hypothesize to be key in predicting temperate forest responses to changing fire regimes: (1) the hazard rate (i.e., the probability of burning in the next year given the time since the last fire) in closed-canopy forests, (2) the hazard rate for recently-burned, open-canopy vegetation, and (3) the time to redevelop canopy closure following fire. We generate a response surface representing the proportions of the landscape potentially supporting closed-canopy forest and non-forest vegetation under nearly all combinations of these three factors. We then place real landscapes on this response surface to assess the type and magnitude of changes to the fire regime that would drive extensive forest loss. We show that the deforestation of much of New Zealand that followed initial human colonization and the introduction of a new ignition source ca. 750 years ago was essentially inevitable due to the slow rate of forest recovery after fire and the high flammability of post-fire vegetation. In North America's Pacific Northwest, by contrast, a predominantly forested landscape persisted despite two periods of widespread burning in the recent past due in large part to faster post-fire forest recovery and less pronounced differences in flammability between forests and the post-fire vegetation. We also assess the factors that could drive extensive deforestation in other regions to identify where management could reduce this potential and to guide field and modeling work to better understand the responses and ecological feedbacks to changing fire regimes.

  1. Satellite Remote Sensing of Landscape Freeze/Thaw State Dynamics for Complex Topography and Fire Disturbance Areas Using Multi-Sensor Radar and SRTM Digital Elevation Models

    NASA Astrophysics Data System (ADS)

    Podest, E.; McDonald, K.; Kimball, J.; Randerson, J. T.

    2003-12-01

    The annual freeze/thaw cycle drives the length of the growing season in the boreal forest, and is a major factor determining annual productivity and associated exchange of CO2 with the atmosphere. Variations in freeze/thaw processes are spatially and temporally complex in boreal environments, particularly in areas of complex topography and in fire disturbance regimes. We investigate the spatial and temporal characteristics of seasonal freeze/thaw dynamics in complex boreal landscapes, as derived from radar backscatter measured with ERS (C-band, VV polarization, 200m resolution) and JERS-1 (L-band, HH polarization, 100m resolution) Synthetic Aperture Radars (SARs), and with the SeaWinds scatterometer (Ku-band, 25km resolution). C- and L-band backscatter are applied to characterize freeze/thaw transitions for a chronosequence of recovering burn sites near Delta Junction, Alaska, and for a region of complex topography on the Kenai Peninsula, Alaska. We characterize differences in radar-derived freeze/thaw state, examining transitions over complex terrain and landscape disturbance regimes. In areas of complex terrain, we explore freeze/thaw dynamics related to elevation, slope aspect and varying landcover. In the burned regions, we explore the timing of seasonal freeze/thaw transition as related to the recovering landscape, relative to that of a nearby control site. We apply in situ biophysical measurements, including flux tower measurements to validate and interpret the remotely sensed parameters. A multi-scale analysis is performed relating high-resolution SAR backscatter and moderate resolution scatterometer measurements to assess trade-offs in spatial and temporal resolution in the remotely sensed fields. A temporal change discriminator is applied to classify time series radar imagery to classify the landscape freeze-thaw state. We apply a 30m-resolution digital elevation model (DEM) derived from Shuttle Radar Topography Mission (SRTM) data to orthorectify the time

  2. Exact solution of the robust knapsack problem☆

    PubMed Central

    Monaci, Michele; Pferschy, Ulrich; Serafini, Paolo

    2013-01-01

    We consider an uncertain variant of the knapsack problem in which the weight of the items is not exactly known in advance, but belongs to a given interval, and an upper bound is imposed on the number of items whose weight differs from the expected one. For this problem, we provide a dynamic programming algorithm and present techniques aimed at reducing its space and time complexities. Finally, we computationally compare the performances of the proposed algorithm with those of different exact algorithms presented so far in the literature for robust optimization problems. PMID:24187428

  3. Laccoliths as a probe for bedrock landscape transient dynamics: Numerical modeling and application to erosion history of the Colorado Plateau

    NASA Astrophysics Data System (ADS)

    Karlstrom, L.; O'Hara, D.

    2015-12-01

    The response of bedrock landscapes to localized perturbations that uplift the land surface remains an important and unsolved problem in geomorphology. Laccoliths, shallow plutonic structures relatively common in magmatic environments that dome overlying crustal rocks, represent a simple and near-axisymmetric perturbation on the landscape. The structures are commonly smaller than typical drainage basins, allowing their erosional response to be used as a proxy for relative uplift rates and position in pre-existing drainage networks. Using a landscape evolution model, we analyze the coupling between pre-intrusion drainage conditions and laccolith uplift. We study the effects of laccolith uplift rate, geometry, and basin position on drainage development on both the laccolith and surrounding landscape. We use a Monte Carlo scheme to sample the large parameter space and develop a series of metrics based on channel network and landform geometries to characterize the results. In particular, we develop two dimensionless numbers to quantify the importance of uplift versus erosion, and initial condition (position of laccolith in pre-existing landscape). We then apply our results to Oligocene-age laccoliths on the Colorado Plateau, USA. The age of the Plateau's present drainage network is debated, with some arguing for a long-lived drainage network active since 60-70 Ma, and others arguing for a much younger pulse of incision at <6 Ma to integrate the modern drainage system. The laccoliths (i.e. the Henry, La Sal, and Ute Mountains, and Navajo Mountain), emplaced at 25-28 Ma, are potentially well suited to inform this debate. Laccolith erosion patterns on the Colorado Plateau are highly asymmetric, with long-axis orientations paralleling present directions of the Colorado River and its tributaries. Thus, the current drainage pattern is strongly imprinted on the laccoliths, suggesting we can characterize controls on laccolith erosion to invert for timing and rates of erosion.

  4. Conformational dynamics of cancer-associated MyD88-TIR domain mutant L252P (L265P) allosterically tilts the landscape toward homo-dimerization.

    PubMed

    Zhan, Chendi; Qi, Ruxi; Wei, Guanghong; Guven-Maiorov, Emine; Nussinov, Ruth; Ma, Buyong

    2016-09-01

    MyD88 is an essential adaptor protein, which mediates the signaling of the toll-like and interleukin-1 receptors' superfamily. The MyD88 L252P (L265P) mutation has been identified in diffuse large B-cell lymphoma. The identification of this mutation has been a major advance in the diagnosis of patients with aldenstrom macroglobulinemia and related lymphoid neoplasms. Here we used computational methods to characterize the conformational effects of the mutation. Our molecular dynamics simulations revealed that the mutation allosterically quenched the global conformational dynamics of the toll/IL-1R (TIR) domain, and readjusted its salt bridges and dynamic community network. Specifically, the mutation changed the orientation and reduced the fluctuation of α-helix 3, possibly through eliminating/weakening ~8 salt bridges and enhancing the salt bridge D225-K258. Using the energy landscape of the TIR domains of MyD88, we identified two dynamic conformational basins, which correspond to the binding sites used in homo- and hetero-oligomerization, respectively. Our results indicate that the mutation stabilizes the core of the homo-dimer interface of the MyD88-TIR domain, and increases the population of homo-dimer-compatible conformational states in MyD88 family proteins. However, the dampened motion restricts its ability to heterodimerize with other TIR domains, thereby curtailing physiological signaling. In conclusion, the L252P both shifts the landscape toward homo-dimerization and restrains the dynamics of the MyD88-TIR domain, which disfavors its hetero-dimerization with other TIR domains. We further put these observations within the framework of MyD88-mediated cell signaling. PMID:27503954

  5. Landscape evolution (A Review)

    PubMed Central

    Sharp, Robert P.

    1982-01-01

    Landscapes are created by exogenic and endogenic processes acting along the interface between the lithosphere and the atmosphere and hydrosphere. Various landforms result from the attack of weathering and erosion upon the highly heterogeneous lithospheric surface. Landscapes are dynamic, acutely sensitive to natural and artificial perturbation. Undisturbed, they can evolve through a succession of stages to a plain of low relief. Often, the progression of an erosion cycle is interrupted by tectonic or environmental changes; thus, many landscapes preserve vestiges of earlier cycles useful in reconstructing the recent history of Earth's surface. Landforms are bounded by slopes, so their evolution is best understood through study of slopes and the complex of factors controlling slope character and development. The substrate, biosphere, climatic environment, and erosive processes are principal factors. Creep of the disintegrated substrate and surface wash by water are preeminent. Some slopes attain a quasisteady form and recede parallel to themselves (backwearing); others become ever gentler with time (downwearing). The lovely convex/rectilinear/concave profile of many debris-mantled slopes reflects an interplay between creep and surface wash. Landscapes of greatest scenic attraction are usually those in which one or two genetic factors have strongly dominated or those perturbed by special events. Nature has been perturbing landscapes for billions of years, so mankind can learn about landscape perturbation from natural examples. Images

  6. Rivers and landscape

    SciTech Connect

    Petts, G.; Foster, I.

    1985-01-01

    This book provides readers with a knowledge of river systems, emphasising functional relationships between forms and processes, and the historical change of fluvial landscapes including evidence from valley fills and lake sediments. In explaining the properties and dynamics of river systems, the authors focus on new approaches, ideas and interpretations.

  7. [Quantitative Evaluation of Intracardiac Blood Flow by Left Ventricle Dynamic Anatovy Based On Exact Solutions of Non-Stationary Navier-Stocks Equations for Selforganized tornado-Like Flows of Viscous Incompresssible Fluid].

    PubMed

    Talygin, E A; Zazybo, N A; Zhorzholiany, S T; Krestinich, I M; Mironov, A A; Kiknadze, G I; Bokerya, L A; Gorodkov, A Y; Makarenko, V N; Alexandrova, S A

    2016-01-01

    New approach to intracardiac blood flow condition analysis based on geometric parameters of left ventricle flow channel has been suggested. Parameters, that used in this method, follow from exact solutions of nonstationary Navier-Stocks equations for selforganized tornado-like flows of viscous incompressible fluid. The main advantage of this method is considering dynamic anatomy of intracardiac cavity and trabeculae relief of left ventricle streamlined surface, both registered in a common mri-process, as flow condition indicator. Calculated quantity options that characterizes blood flow condition can be use as diagnostic criterias for estimation of violation in blood circulation function which entails heart ejection reduction. Developed approach allows to clarify heart jet organization mechanism and estimate the share of the tornado-like flow self-organization in heart ejection structure. PMID:27149823

  8. [Quantitative Evaluation of Intracardiac Blood Flow by Left Ventricle Dynamic Anatovy Based On Exact Solutions of Non-Stationary Navier-Stocks Equations for Selforganized tornado-Like Flows of Viscous Incompresssible Fluid].

    PubMed

    Talygin, E A; Zazybo, N A; Zhorzholiany, S T; Krestinich, I M; Mironov, A A; Kiknadze, G I; Bokerya, L A; Gorodkov, A Y; Makarenko, V N; Alexandrova, S A

    2016-01-01

    New approach to intracardiac blood flow condition analysis based on geometric parameters of left ventricle flow channel has been suggested. Parameters, that used in this method, follow from exact solutions of nonstationary Navier-Stocks equations for selforganized tornado-like flows of viscous incompressible fluid. The main advantage of this method is considering dynamic anatomy of intracardiac cavity and trabeculae relief of left ventricle streamlined surface, both registered in a common mri-process, as flow condition indicator. Calculated quantity options that characterizes blood flow condition can be use as diagnostic criterias for estimation of violation in blood circulation function which entails heart ejection reduction. Developed approach allows to clarify heart jet organization mechanism and estimate the share of the tornado-like flow self-organization in heart ejection structure.

  9. Changes of ecosystem service values in response to land use/land cover dynamics in Munessa-Shashemene landscape of the Ethiopian highlands.

    PubMed

    Kindu, Mengistie; Schneider, Thomas; Teketay, Demel; Knoke, Thomas

    2016-03-15

    Land use/land cover (LULC) dynamics alter ecosystem services values (ESVs), yet quantitative evaluations of changes in ESVs are seldom attempted. Using Munessa-Shashemene landscape of the Ethiopian highlands as an example, we showed estimate of changes in ESVs in response to LULC dynamics over the past four decades (1973-2012). Estimation and change analyses of ESVs were conducted, mainly, by employing GIS using LULC datasets of the year 1973, 1986, 2000 and 2012 with their corresponding global value coefficients developed earlier and our own modified conservative value coefficients for the studied landscape. The results between periods revealed a decrease of total ESVs from US$ 130.5 million in 1973, to US$ 118.5, 114.8 and 111.1 million in 1986, 2000 and 2012, respectively. While using global value coefficients, the total ESVs declined from US$ 164.6 million in 1973, to US$ 135.8, 127.2 and 118.7 million in 1986, 2000 and 2012, respectively. The results from the analyses of changes in the four decades revealed a total loss of ESVs ranging from US$ 19.3 million when using our own modified value coefficients to US$ 45.9 million when employing global value coefficients. Changes have also occurred in values of individual ecosystem service functions, such as erosion control, nutrient cycling, climate regulation and water treatment, which were among the highest contributors of the total ESVs. However, the value of food production service function consistently increased during the study periods although not drastically. All in all, it must be considered a minimum estimate of ESV changes due to uncertainties in the value coefficients used in this study. We conclude that the decline of ESVs reflected the effects of ecological degradation in the studied landscape and suggest further studies to explore future options and formulate intervention strategies. PMID:26780139

  10. Mid-Wisconsin to Holocene permafrost and landscape dynamics based on a drained lake basin core from the northern Seward Peninsula, northwest Alaska

    USGS Publications Warehouse

    Lenz, Josefine; Grosse, Guido; Jones, Benjamin M.; Anthony, Katey M. Walter; Bobrov, Anatoly; Wulf, Sabine; Wetterich, Sebastian

    2016-01-01

    Permafrost-related processes drive regional landscape dynamics in the Arctic terrestrial system. A better understanding of past periods indicative of permafrost degradation and aggradation is important for predicting the future response of Arctic landscapes to climate change. Here, we used a multi-proxy approach to analyse a ~ 4 m long sediment core from a drained thermokarst lake basin on the northern Seward Peninsula in western Arctic Alaska (USA). Sedimentological, biogeochemical, geochronological, micropalaeontological (ostracoda, testate amoebae) and tephra analyses were used to determine the long-term environmental Early-Wisconsin to Holocene history preserved in our core for central Beringia. Yedoma accumulation dominated throughout the Early to Late-Wisconsin but was interrupted by wetland formation from 44.5 to 41.5 ka BP. The latter was terminated by the deposition of 1 m of volcanic tephra, most likely originating from the South Killeak Maar eruption at about 42 ka BP. Yedoma deposition continued until 22.5 ka BP and was followed by a depositional hiatus in the sediment core between 22.5 and 0.23 ka BP. We interpret this hiatus as due to intense thermokarst activity in the areas surrounding the site, which served as a sediment source during the Late-Wisconsin to Holocene climate transition. The lake forming the modern basin on the upland initiated around 0.23 ka BP and drained catastrophically in spring 2005. The present study emphasises that Arctic lake systems and periglacial landscapes are highly dynamic and that permafrost formation as well as degradation in central Beringia was controlled by regional to global climate patterns as well as by local disturbances.

  11. Changes of ecosystem service values in response to land use/land cover dynamics in Munessa-Shashemene landscape of the Ethiopian highlands.

    PubMed

    Kindu, Mengistie; Schneider, Thomas; Teketay, Demel; Knoke, Thomas

    2016-03-15

    Land use/land cover (LULC) dynamics alter ecosystem services values (ESVs), yet quantitative evaluations of changes in ESVs are seldom attempted. Using Munessa-Shashemene landscape of the Ethiopian highlands as an example, we showed estimate of changes in ESVs in response to LULC dynamics over the past four decades (1973-2012). Estimation and change analyses of ESVs were conducted, mainly, by employing GIS using LULC datasets of the year 1973, 1986, 2000 and 2012 with their corresponding global value coefficients developed earlier and our own modified conservative value coefficients for the studied landscape. The results between periods revealed a decrease of total ESVs from US$ 130.5 million in 1973, to US$ 118.5, 114.8 and 111.1 million in 1986, 2000 and 2012, respectively. While using global value coefficients, the total ESVs declined from US$ 164.6 million in 1973, to US$ 135.8, 127.2 and 118.7 million in 1986, 2000 and 2012, respectively. The results from the analyses of changes in the four decades revealed a total loss of ESVs ranging from US$ 19.3 million when using our own modified value coefficients to US$ 45.9 million when employing global value coefficients. Changes have also occurred in values of individual ecosystem service functions, such as erosion control, nutrient cycling, climate regulation and water treatment, which were among the highest contributors of the total ESVs. However, the value of food production service function consistently increased during the study periods although not drastically. All in all, it must be considered a minimum estimate of ESV changes due to uncertainties in the value coefficients used in this study. We conclude that the decline of ESVs reflected the effects of ecological degradation in the studied landscape and suggest further studies to explore future options and formulate intervention strategies.

  12. Landscape dynamics and fire activity since 6740 cal yr BP in the Cantabrian region (La Molina peat bog, Puente Viesgo, Spain)

    NASA Astrophysics Data System (ADS)

    Pérez-Obiol, R.; García-Codron, J. C.; Pèlachs, A.; Pérez-Haase, A.; Soriano, J. M.

    2016-03-01

    A lack of paleobotanic studies with adequate resolution and multiproxy approaches has limited proper discussion of vegetation dynamics in Cantabria and of the role of fires in the configuration of the plant landscape during the Holocene in the northwest part of the Iberian peninsula. The pollen diagram of La Molina peat bog in Puente Viesgo (43°15‧38″ N-3°58‧37″ W; ETRS89), located at 484 m.a.s.l., and the study of its sedimentary charcoals allowed the acquisition of a continuous and thorough fire sequence for the last 6700 cal yr BP and an understanding of its relationship to the forest. The results show the importance of human influence on the incidence and characteristics of fire activity during the different phases studied: the Neolithic, Bronze Age, Iron Age, Roman period, and Middle Ages. A synergy seems to exist between dry climate periods (especially during Bond events 3 and 4) and a greater presence of biomass. As the Holocene advances, vegetation coverage clearly tends to decrease. This study provides key elements for understanding the role of fire activity in the forest dynamics of deciduous and evergreen Quercus, Corylus, Pinus, Fagus, and Alnus and demonstrates the strongly artificialized character of the present landscape.

  13. Holocene Landscape Dynamics in the Ammer Rv. Catchment (Bavarian Alps) - Influence of extreme weather events and land use on soil erosion using peat bogs as geoarchives

    NASA Astrophysics Data System (ADS)

    Schwindt, Daniel; Manthe, Pierre; Völkel, Jörg

    2016-04-01

    Soil degradation and the loss of soil organic carbon (SOC) induced by erosion events significantly influence soils and fertility as parts of the ecosystem services and play an important role with regard to global carbon dynamics. Soil erosion is strongly correlated with anthropogenic land use since the Neolithic Revolution around 8.000 BP. Likewise the effect of extreme weather events on soil erosion is of great interest with regard to the recent climate change debate, predicting a strong increase of extreme weather events. Aim of this study is the reconstruction of the Holocene landscape dynamic as influenced by land use and climate conditions. In this study peat bogs containing layers of colluvial sediments directly correlated to soil erosion were used as geoarchives for landscape dynamics. A temporal classification of extreme erosion events was established by dating organic material via 14C within both, colluvial layers as well as their direct peat surroundings. Detection and characterization of peat bogs containing colluvial sediments was based on geomorphological mapping, the application of geophysical methods (ERT - electrical resistivity tomography, GPR - ground penetrating radar) and core soundings. Laboratory analysis included the analysis of particle sizes and the content of organic material. We investigated 16 peat bogs following the altitudinal gradient of the Ammer River from alpine and subalpine towards lowland environments. A deposition of colluvial material could be detected in 4 peat bogs, all situated in the lower parts of the catchment. The minerogenic entry into peat bogs occurred throughout the Holocene as revealed by radiocarbon dating. A distinct cluster of erosional events e.g. during the little ice age could not be detected. Therefore, soil erosion dynamics and the appearance of colluvial sediments within peat bogs must rather be regarded as an effect of land use, actually farming and crop cultivation, or small-scale morphodynamic like

  14. Molecular Dynamics Simulations and Classical Multidimensional Scaling Unveil New Metastable States in the Conformational Landscape of CDK2

    PubMed Central

    Pisani, Pasquale; Rastelli, Giulio

    2016-01-01

    Protein kinases are key regulatory nodes in cellular networks and their function has been shown to be intimately coupled with their structural flexibility. However, understanding the key structural mechanisms of large conformational transitions remains a difficult task. CDK2 is a crucial regulator of cell cycle. Its activity is finely tuned by Cyclin E/A and the catalytic segment phosphorylation, whereas its deregulation occurs in many types of cancer. ATP competitive inhibitors have failed to be approved for clinical use due to toxicity issues raised by a lack of selectivity. However, in the last few years type III allosteric inhibitors have emerged as an alternative strategy to selectively modulate CDK2 activity. In this study we have investigated the conformational variability of CDK2. A low dimensional conformational landscape of CDK2 was modeled using classical multidimensional scaling on a set of 255 crystal structures. Microsecond-scale plain and accelerated MD simulations were used to populate this landscape by using an out-of-sample extension of multidimensional scaling. CDK2 was simulated in the apo-form and in complex with the allosteric inhibitor 8-anilino-1-napthalenesulfonic acid (ANS). The apo-CDK2 landscape analysis showed a conformational equilibrium between an Src-like inactive conformation and an active-like form. These two states are separated by different metastable states that share hybrid structural features with both forms of the kinase. In contrast, the CDK2/ANS complex landscape is compatible with a conformational selection picture where the binding of ANS in proximity of the αC helix causes a population shift toward the inactive conformation. Interestingly, the new metastable states could enlarge the pool of candidate structures for the development of selective allosteric CDK2 inhibitors. The method here presented should not be limited to the CDK2 case but could be used to systematically unmask similar mechanisms throughout the human

  15. Molecular Dynamics Simulations and Classical Multidimensional Scaling Unveil New Metastable States in the Conformational Landscape of CDK2.

    PubMed

    Pisani, Pasquale; Caporuscio, Fabiana; Carlino, Luca; Rastelli, Giulio

    2016-01-01

    Protein kinases are key regulatory nodes in cellular networks and their function has been shown to be intimately coupled with their structural flexibility. However, understanding the key structural mechanisms of large conformational transitions remains a difficult task. CDK2 is a crucial regulator of cell cycle. Its activity is finely tuned by Cyclin E/A and the catalytic segment phosphorylation, whereas its deregulation occurs in many types of cancer. ATP competitive inhibitors have failed to be approved for clinical use due to toxicity issues raised by a lack of selectivity. However, in the last few years type III allosteric inhibitors have emerged as an alternative strategy to selectively modulate CDK2 activity. In this study we have investigated the conformational variability of CDK2. A low dimensional conformational landscape of CDK2 was modeled using classical multidimensional scaling on a set of 255 crystal structures. Microsecond-scale plain and accelerated MD simulations were used to populate this landscape by using an out-of-sample extension of multidimensional scaling. CDK2 was simulated in the apo-form and in complex with the allosteric inhibitor 8-anilino-1-napthalenesulfonic acid (ANS). The apo-CDK2 landscape analysis showed a conformational equilibrium between an Src-like inactive conformation and an active-like form. These two states are separated by different metastable states that share hybrid structural features with both forms of the kinase. In contrast, the CDK2/ANS complex landscape is compatible with a conformational selection picture where the binding of ANS in proximity of the αC helix causes a population shift toward the inactive conformation. Interestingly, the new metastable states could enlarge the pool of candidate structures for the development of selective allosteric CDK2 inhibitors. The method here presented should not be limited to the CDK2 case but could be used to systematically unmask similar mechanisms throughout the human

  16. Labyrinthine granular landscapes.

    PubMed

    Caps, H; Vandewalle, N

    2001-11-01

    We have numerically studied a model of granular landscape eroded by wind. We show the appearance of labyrinthic patterns when the wind orientation turns by 90 degrees. The occurrence of such structures is discussed. Moreover, we introduce the density n(k) of "defects" as the dynamic parameter governing the landscape evolution. A power-law behavior of n(k) is found as a function of time. In the case of wind variations, the exponent (drastically) shifts from two to one. The presence of two asymptotic values of n(k) implies the irreversibility of the labyrinthic formation process.

  17. Landscape Architecture.

    ERIC Educational Resources Information Center

    American School and University, 1985

    1985-01-01

    Members of the American Society of Landscape Architects shape open spaces on the campuses of Georgetown University, District of Columbia; the University of Missouri; Auraria Higher Education Center, Colorado; and the University of Michigan. (MLF)

  18. Mars Landscapes

    NASA Video Gallery

    Spacecraft have studied the Martian surface for decades, giving Earthlings insights into the history, climate and geology of our nearest neighbor, Mars. These images are from "Mars Landscapes," a v...

  19. The Neglected Exactness

    NASA Astrophysics Data System (ADS)

    Endom, Joerg

    2014-05-01

    negligible any more. Locating for example the exact position of joints, rebars on site, getting correct calibration information or overlaying measurements of independent methods requires high accuracy positioning for all data. Different technologies of synchronizing and stabilizing are discussed in this presentation. Furthermore a scale problem for interdisciplinary work between the geotechnical engineer, the civil engineer, the surveyor and the geophysicist is presented. Manufacturers as well as users are addressed to work on a unified methodology that could be implemented in future. This presentation is a contribution to COST Action TU1208.

  20. Assessing Potential Future Carbon Dynamics with Climate Change and Fire Management in a Mountainous Landscape on the Olympic Peninsula, Washington, USA

    NASA Astrophysics Data System (ADS)

    Kennedy, R. S.

    2010-12-01

    Forests of the mountainous landscapes of the maritime Pacific Northwestern USA may have high carbon sequestration potential via their high productivity and moderate to infrequent fire regimes. With climate change, there may be shifts in incidence and severity of fire, especially in the drier areas of the region, via changes to forest productivity and hydrology, and consequent effects to C sequestration and forest structure. To explore this issue, I assessed potential effects of fire management (little fire suppression/wildland fire management/highly effective fire suppression) under two climate change scenarios on future C sequestration dynamics (amounts and spatial pattern) in Olympic National Park, WA, over a 500-year simulation period. I used the simulation platform FireBGCv2, which contains a mechanistic, individual tree succession model, a spatially explicit climate-based biophysical model that uses daily weather data, and a spatially explicit fire model incorporating ignition, spread, and effects on ecosystem components. C sequestration patterns varied over time and spatial and temporal patterns differed somewhat depending on the climate change scenario applied and the fire management methods employed. Under the more extreme climate change scenario with little fire suppression, fires were most frequent and severe and C sequestration decreased. General trends were similar under the more moderate climate change scenario, as compared to current climate, but spatial patterns differed. Both climate change scenarios under highly effective fire suppression showed about 50% of starting total C after the initial transition phase, whereas with 10% fire suppression both scenarios exhibited about 10% of starting amounts. Areas of the landscape that served as refugia for older forest under increasing frequency of high severity fire were also hotspots for C sequestration in a landscape experiencing increasing frequency of disturbance with climate change.

  1. Exact law of live nature

    NASA Astrophysics Data System (ADS)

    Azbel, Mark Ya.

    2005-07-01

    Exact law of mortality dynamics in changing populations and environment is derived. It includes no explicit characteristics of animal- environment interactions (metabolism etc) which are a must for life; it is universal for all animals, from single cell yeast to humans, with their drastically different biology, evolutionary history, and complexity; it is rapidly (within few percent of life span) reversible. Such law is unique for live systems with their homeostatic self-adjustment to environment (cf. thermodynamics of liquids and glasses). The law which is valid for all live, and only live, systems is their specific natural law. Mortality is an instrument of natural selection and biological diversity. Its law, which is preserved in evolution of all species, is a conservation law of mortality, selection, evolution, biology. The law implies new kind of intrinsic mortality and adaptation which dominate in evolutionary unprecedented protected populations and, in contrast to species specific natural selection, proceed via universal stepwise rungs and reduce to universal cellular mechanism. The law demonstrates that intrinsic mortality and at least certain aspects of aging are disposable evolutionary byproducts, and directed genetic and/or biological changes may yield healthy and vital Methuselah lifespan. This is consistent with experiments. Universality implies that single cell yeast may provide a master key to the cellular mechanism of universal mortality, aging, selection, evolution, and its regulation in all animals. One may look for its manifestations in animal cells also, e.g., in their replicative senescence and cancer. Evolutionary origin and genetic nature of universality are suggested.

  2. Quantum-control-landscape structure viewed along straight paths through the space of control fields

    NASA Astrophysics Data System (ADS)

    Nanduri, Arun; Ho, Tak-San; Rabitz, Herschel

    2016-02-01

    The dynamics of closed quantum systems may be manipulated by using an applied field to achieve a control objective value for a physical goal. The functional relationship between the applied field and the objective value forms a quantum control landscape, and the optimization process consists of a guided climb up the landscape from the bottom to the top. Two classes of landscape features are important for understanding the ease of finding an optimal control field. The first class of topological landscape features has been proven to be especially simple in that no suboptimal local maxima exist (upon satisfaction of certain assumptions), which partially accounts for the ease of finding optimal fields. Complementary to the topology, the second class of features entails the landscape structure, characterizing the sinuous nature of the paths leading to an optimal control field. Previous work found that the landscape structure is also particularly simple, as excursions up the landscape guided by a gradient algorithm correspond to nearly straight paths through the space of control fields. In this paper we take an alternative approach to examining landscape structure by constructing, and then following, exactly straight trajectories in control space. Each trajectory starts at a corresponding point on the bottom of the landscape and ends at an associated point on the top, with the observable values taken either as the state-to-state transition probability, the expectation value of a general observable, or the distance from a desired unitary transformation. In some cases the starting point is at a suboptimal critical-point saddle, with the goal, again, of following a straight field path to the optimal objective yield or another suboptimal critical point. We find that the objective value almost always rises monotonically upon following a straight control path from one critical point to another, which shows that landscape structure is very simple, being devoid of rough bumps

  3. What exactly do numbers mean?

    PubMed Central

    Huang, Yi Ting; Spelke, Elizabeth; Snedeker, Jesse

    2014-01-01

    Number words are generally used to refer to the exact cardinal value of a set, but cognitive scientists disagree about their meanings. Although most psychological analyses presuppose that numbers have exact semantics (two means EXACTLY TWO), many linguistic accounts propose that numbers have lower-bounded semantics (AT LEAST TWO), and that speakers restrict their reference through a pragmatic inference (scalar implicature). We address this debate through studies of children who are in the process of acquiring the meanings of numbers. Adults and 2- and 3-year-olds were tested in a novel paradigm that teases apart semantic and pragmatic aspects of interpretation (the covered box task). Our findings establish that when scalar implicatures are cancelled in the critical trials of this task, both adults and children consistently give exact interpretations for number words. These results, in concert with recent work on real-time processing, provide the first unambiguous evidence that number words have exact semantics. PMID:25285053

  4. Geomorpho-Landscapes

    NASA Astrophysics Data System (ADS)

    Farabollini, Piero; Lugeri, Francesca; Amadio, Vittorio

    2014-05-01

    Landscape is the object of human perceptions, being the image of spatial organization of elements and structures: mankind lives the first approach with the environment, viewing and feeling the landscape. Many definitions of landscape have been given over time: in this case we refer to the Landscape defined as the result of interaction among physical, biotic and anthropic phenomena acting in a different spatial-temporal scale (Foreman & Godron) Following an Aristotelic approach in studying nature, we can assert that " Shape is synthesis": so it is possible to read the land features as the expression of the endogenous and exogenous processes that mould earth surfaces; moreover, Landscape is the result of the interaction of natural and cultural components, and conditions the spatial-temporal development of a region. The study of the Landscape offers results useful in order to promote sustainable development, ecotourism, enhancement of natural and cultural heritage, popularization of the scientific knowledge. In Italy, a very important GIS-based tool to represent the territory is the "Carta della Natura" ("Map of Nature", presently coordinated by the ISPRA) that aims at assessing the state of the whole Italian territory, analyzing Landscape. The methodology follows a holistic approach, taking into consideration all the components of a landscape and then integrating the information. Each individual landscape, studied at different scales, shows distinctive elements: structural, which depend on physical form and specific spatial organization; functional, which depend on relationships created between biotic and abiotic elements, and dynamic, which depend on the successive evolution of the structure. The identification of the landscape units, recognized at different scales of analysis, allows an evaluation of the state of the land, referring to the dual risk/resource which characterizes the Italian country. An interesting opportunity is to discover those areas of unusual

  5. Dynamical Collective Potential Energy Landscape: Its Impact on the Competition Between Fusion and Quasi-fission in a Heavy Fusing System

    SciTech Connect

    Diaz-Torres, Alexis

    2006-08-14

    A realistic microscopically-based quantum approach to the competition between fusion and quasi-fission in a heavy fusing system is applied to several reactions leading to 256No. Fusion and quasi-fission are described in terms of a diffusion process of nuclear shapes through a dynamical collective potential energy landscape which is initially diabatic and gradually becomes adiabatic. The microscopic ingredients of the theory are obtained with a realistic two-center shell model based on Woods-Saxon potentials. The results indicate that (i) the diabatic effects play a very important role in the onset of fusion hindrance for heavy systems, and (ii) very asymmetric reactions induced by closed shell nuclei seem to be the best suited to synthesize the heaviest compound nuclei.

  6. The interaction between land use change, sediment fluxes and carbon dynamics: evaluating an integrated soil-landscape model at the millennial time-scale.

    NASA Astrophysics Data System (ADS)

    Bouchoms, Samuel; Van Oost, Kristof; Vanacker, Veerle

    2015-04-01

    Soil-landscape modelling has received growing attention as it allows us to evaluate the interaction between earth surface and soil bio-physical processes. At the landscape scale, human-induced land use change has altered the balance between soil erosion and production, and largely modified sediment fluxes. Intensification in soil redistribution rates affects the interaction between soil chemical, physical and biological processes at the landscape scale. Here, we evaluate the SPEROS-LT model, a spatially explicit 3D model combining a dynamic representation of land use, soil erosion and deposition and the soil carbon cycle. We assess the impact of millennial-scale human-induced land use change on sediment fluxes and carbon dynamics in the Dijle catchement (central Belgium). The watershed has undergone a 3000 years continuous human-induced alteration of the vegetation covers for agricultural characterized by Our study is based on land use reconstructions for the last 3000 years, including massive deforestation for agriculture in Roman Times and the Middle Ages followed by urbanization in the last 150 years. Land use reconstructions rely on simple land use allocation rules based on slope gradients. SPEROS-LT is parametrized for erosion rates against available figures in the literature by changing the transport capacity and the transfer coefficient which defines the amount of flux transferred between different land uses. Carbon content profiles at steady state (i.e. without influence of erosion or deposition) are calibrated for each land use and for the first upper meter of soil by comparing modeled profiles to an averaged observed profiles in stable areas of the pedologic region. We present a model sensitivity analysis and a full validation of the predicted soil carbon storage (horizontally, i.e. in space, and vertically, i.e. with depth) using a large database of observational data. The results indicate (i) a good agreement of the erosion rates. Speros LT modeled

  7. A graphical method for fluvial network analysis: a case study of the dynamic landscapes in the eastern Central Range of Taiwan

    NASA Astrophysics Data System (ADS)

    Chen, Chia-Yu; Willett, Sean D.; Giuditta Fellin, Maria

    2014-05-01

    We construct a graphical method to analyze dynamic reorganization of river basins and infer the tectonic forcing encoded in the landscapes of Taiwan. The island of Taiwan is built by ongoing arc-continent collision of the Luzon Arc and the Asian continental margin. The high tectonic convergence and uplift rates together with the sub-tropical climates and frequent typhoons result in high exhumation rates, and well-developed detachment-limited river networks. To analyze these rivers, we propose a new graphical method similar to a χ-plot, in which distance along channel is rescaled by drainage area so as to make an equilibrium river profile linear. We generate the equivalent plot for an entire river basin, but rather than collapsing all tributaries onto a single set of Cartesian axes, we map the basin into polar coordinates in which the radial dimension is chi. The angular coordinate is arbitrary, but we assign each channel head a unique value by numbering them topologically clockwise so to spread the basin over an azimuth of 90-180 degrees depending on the size of drainage basin. The elevations are then contoured on this mapping. Channel steepness (scaled uplift rate) is estimated by fitting a conical surface to the elevations. This can be plotted on the radial plot as a series of concentric circles. The advantage of this graph is it maintains a shape comparable to the original drainage basin, which simplifies comparison of χ and elevation among different channels to aid in interpretation of differences. The misfits between the predicted and observed elevations in radial plots highlight transient signals of landscapes. If the uplift rate and erodibility are spatially uniform, the misfits can be interpreted in terms of changes in drainage area. We identify many examples indicating migration of divides and discrete river captures, which must be taken into account when estimating the channel steepness. The estimated channel steepnesses of basins in eastern Taiwan

  8. Timescales of sediment dynamics, climate and topographic change in mountain landscapes (SedyMONT) - Erdalen and Bodalen site project

    NASA Astrophysics Data System (ADS)

    Beylich, A. A.

    2009-04-01

    The focus of this Norwegian Individual Project (2008-2012) within the European Science Foundation (ESF) EUROCORES TOPO-EUROPE programme is on the Erdalen and Bodalen catchments (glacier-fed tributary streams) in Nordfjord, western Norway. The innovative approach of this new project is the integrated quantitative study of longer-term (Holocene), sub-recent and contemporary sedimentary fluxes, budgets and process rates using a novel combination of advanced methods and techniques. With respect to the main aims and objectives of ESF SedyMONT, the following key aims of the Erdalen and Bodalen site project can be stressed: (1) Analyse how the inheritance of the landscape due to the influence of the Last Glacial Maximum (LGM) has affected process rates over time (paraglacial system), (2) Document changes in process rates over different timescales by combining existing quantitative knowledge on Holocene process rates with newly generated data on sub-recent and contemporary process rates. Monitoring programmes in Erdalen and Bodalen, in combination with repeated analyses of surface water chemistry, atmospheric solute inputs and granulometric analyses of suspended sediments provide high-resolution data to analyse and quantify present-day sedimentary and solute fluxes as well as sediment sources, denudation rates, and meteorological and topographic / landscape morphometric controls of denudative processes. In addition to standard methods for monitoring bedload transport, innovative techniques like shock sensor tracers and biofilm analyses are applied to analyse channel stability / mobility and bedload transport rates in both valleys. The volume and composition of lake sediments are investigated using echo-sounder, georadar and coring. Studies on volumes and architecture of storage elements (valley infills, talus cones) using different geophysical methods like georadar and seismic refraction surveys are carried out to further improve the quantitative knowledge on Holocene

  9. Temporal and spatial variation in landscape connectivity for a freshwater turtle in a temporally dynamic wetland system.

    PubMed

    Roe, John H; Brinton, Alicia C; Georges, Arthur

    2009-07-01

    Inter-wetland connectivity, defined here as the movement of biota among discrete water bodies, can have important population- and community-level consequences in aquatic systems. We examined inter-wetland connectivity in a southeastern Australian national park by intensively monitoring the movements of freshwater turtles (Chelodina longicollis) via capture-mark-recapture over a three-year period, and more sporadically for 25 years. A high percentage (33%) of turtles moved between wetlands, suggesting that single wetlands should not represent the minimum habitat unit harboring a C. longicollis population. Distance was the only structural landscape metric correlated with inter-patch transition probability, with probability declining as inter-wetland distance increased. Movements also appear to be strongly influenced by shifting resource quality gradients between temporary wetlands and permanent lakes according to drought and flood cycles, a pattern more consistent with migration between critical resource patches than occasional interpopulational dispersal. Rare dispersal events of up to 5.2 km were known to occur. Captures at a terrestrial drift fence suggest that small and immature turtles moved between wetlands more frequently than our aquatic sampling indicated. We caution that measures of actual (or functional) connectivity can be biased by sampling methods and the temporal scale of sampling and must also be interpreted in the context of factors that motivate animal movements. This requires some understanding of spatial and temporal variation in intra-patch processes (e.g., quality and extent) and the expected movement responses of animals (e.g., habitat selection) over extended time frames, information that can potentially yield more important insight on connectivity than measures of landscape structural features alone. PMID:19688935

  10. Singularities of quantum control landscapes

    NASA Astrophysics Data System (ADS)

    Wu, Re-Bing; Long, Ruixing; Dominy, Jason; Ho, Tak-San; Rabitz, Herschel

    2012-07-01

    Quantum control landscape theory was formulated to assess the ease of finding optimal control fields in simulations and in the laboratory. The landscape is the observable as a function of the controls, and a primary goal of the theory is the analysis of landscape features. In what is referred to as the kinematic picture of the landscape, prior work showed that the landscapes are generally free of traps that could halt the search for an optimal control at a suboptimal observable value. The present paper considers the dynamical picture of the landscape, seeking the existence of singular controls, especially of a nonkinematic nature along with an assessment of whether they correspond to traps. We analyze the necessary and sufficient conditions for singular controls to be kinematic or nonkinematic critical solutions and the likelihood of their being encountered while maximizing an observable. An algorithm is introduced to seek singular controls on the landscape in simulations along with an associated Hessian landscape analysis. Simulations are performed for a large number of model finite-level quantum systems, showing that all the numerically identified kinematic and nonkinematic singular critical controls are not traps, in support of the prior empirical observations on the ease of finding high-quality optimal control fields.

  11. Exact law of live nature

    NASA Astrophysics Data System (ADS)

    Azbel‧, Mark Ya.

    2005-08-01

    The exact law of mortality dynamics in changing populations and environment is derived. It includes no explicit characteristics of animal-environment interactions (metabolism, etc.) which are a must for life; it is universal for all animals, from single-cell yeast to humans, with their drastically different biology, evolutionary history, and complexity; it is rapidly (within few percent of life span) reversible. Such a law is unique for live systems with their homeostatic self-adjustment to environment (cf. thermodynamics of liquids and glasses). The law which is valid for all live, and only live, systems is their specific natural law. Mortality is an instrument of natural selection and biological diversity. Its law, which is preserved in evolution of all species, is a conservation law of mortality, selection, evolution, biology. The law implies new kinds of intrinsic mortality and adaptation which dominate in evolutionary unprecedented protected populations and, in contrast to species-specific natural selection, proceed via universal stepwise rungs and reduce to universal cellular mechanism. The law demonstrates that intrinsic mortality and at least certain aspects of aging are disposable evolutionary byproducts, and directed genetic and/or biological changes may yield healthy and vital Methuselah lifespan. This is consistent with experiments. Universality implies that single-cell yeast may provide a master key to the cellular mechanism of universal mortality, aging, selection, evolution, and its regulation in all animals. One may look for its manifestations in animal cells also, e.g., in their replicative senescence and cancer. Evolutionary origin and genetic nature of universality are suggested.

  12. Learning Landscapes

    ERIC Educational Resources Information Center

    Noyes, Andrew

    2004-01-01

    This article explores the metaphor of learning landscapes, a tool developed in order to map children's experiences of, and attitudes to, learning (mathematics) before and after the transfer from primary to secondary school. Firstly, the continuing problems surrounding school transfer and why a re-examination of this is required are considered.…

  13. Dynamic topography of the western Great Plains: landscape evidence for mantle-driven uplift associated with the Jemez lineament of NE New Mexico and SE Colorado

    NASA Astrophysics Data System (ADS)

    Nereson, A. L.; Karlstrom, K. E.; McIntosh, W. C.; Heizler, M. T.; Kelley, S. A.; Brown, S. W.

    2011-12-01

    Dynamic topography results when viscous stresses created by flow within the mantle are transmitted through the lithosphere and interact with, and deform, the Earth's surface. Because dynamic topography is characterized by low amplitudes and long wavelengths, its subtle effects may be best recorded in low-relief areas such as the Great Plains of the USA where they can be readily observed and measured. We apply this concept to a unique region of the western Great Plains in New Mexico and Colorado where basalt flows of the Jemez lineament (Raton-Clayton and Ocate fields) form mesas (inverted topography) that record the evolution of the Great Plains surface through time. This study uses multiple datasets to evaluate the mechanisms which have driven the evolution of this landscape. Normalized channel steepness index (ksn) analysis identifies anomalously steep river gradients across broad (50-100 km) convexities within a NE- trending zone of differential river incision where higher downstream incision rates in the last 1.5 Ma suggest headwater uplift. At 2-8 Ma timescales, 40Ar/39Ar ages of basalt-capped paleosurfaces in the Raton-Clayton and Ocate volcanic fields indicate that rates of denudation increase systematically towards the NW from a NE-trending zone of approximately zero denudation (that approximately coincides with the high ksn zone), also suggestive of regional warping above the Jemez lineament. Onset of more rapid denudation is observed in the Raton-Clayton field beginning at ca. 3.6 Ma. Furthermore, two 300-400-m-high NE-trending erosional escarpments impart a staircase-like topographic profile to the region. Tomographic images from the EarthScope experiment show that NE-trending topographic features of this region correspond to an ~8 % P-wave velocity gradient of similar trend at the margin of the low-velocity Jemez mantle anomaly. We propose that the erosional landscapes of this unique area are, in large part, the surface expression of dynamic mantle

  14. Modeling the effects of fire severity and climate warming on active layer and soil carbon dynamics of black spruce forests across the landscape in interior Alaska

    USGS Publications Warehouse

    Genet, H.; McGuire, Anthony David; Barrett, K.; Breen, A.; Euskirchen, E.S.; Johnstone, J.F.; Kasischke, E.S.; Melvin, A.M.; Bennett, A.; Mack, M.C.; Rupp, T.S.; Schuur, A.E.G.; Turetsky, M.R.; Yuan, F.

    2013-01-01

    There is a substantial amount of carbon stored in the permafrost soils of boreal forest ecosystems, where it is currently protected from decomposition. The surface organic horizons insulate the deeper soil from variations in atmospheric temperature. The removal of these insulating horizons through consumption by fire increases the vulnerability of permafrost to thaw, and the carbon stored in permafrost to decomposition. In this study we ask how warming and fire regime may influence spatial and temporal changes in active layer and carbon dynamics across a boreal forest landscape in interior Alaska. To address this question, we (1) developed and tested a predictive model of the effect of fire severity on soil organic horizons that depends on landscape-level conditions and (2) used this model to evaluate the long-term consequences of warming and changes in fire regime on active layer and soil carbon dynamics of black spruce forests across interior Alaska. The predictive model of fire severity, designed from the analysis of field observations, reproduces the effect of local topography (landform category, the slope angle and aspect and flow accumulation), weather conditions (drought index, soil moisture) and fire characteristics (day of year and size of the fire) on the reduction of the organic layer caused by fire. The integration of the fire severity model into an ecosystem process-based model allowed us to document the relative importance and interactions among local topography, fire regime and climate warming on active layer and soil carbon dynamics. Lowlands were more resistant to severe fires and climate warming, showing smaller increases in active layer thickness and soil carbon loss compared to drier flat uplands and slopes. In simulations that included the effects of both warming and fire at the regional scale, fire was primarily responsible for a reduction in organic layer thickness of 0.06 m on average by 2100 that led to an increase in active layer thickness

  15. Free-Energy Landscape of Reverse tRNA Translocation through the Ribosome Analyzed by Electron Microscopy Density Maps and Molecular Dynamics Simulations

    PubMed Central

    Ishida, Hisashi; Matsumoto, Atsushi

    2014-01-01

    To understand the mechanism of reverse tRNA translocation in the ribosome, all-atom molecular dynamics simulations of the ribosome-tRNAs-mRNA-EFG complex were performed. The complex at the post-translocational state was directed towards the translocational and pre-translocational states by fitting the complex into cryo-EM density maps. Between a series of the fitting simulations, umbrella sampling simulations were performed to obtain the free-energy landscape. Multistep structural changes, such as a ratchet-like motion and rotation of the head of the small subunit were observed. The free-energy landscape showed that there were two main free-energy barriers: one between the post-translocational and intermediate states, and the other between the pre-translocational and intermediate states. The former corresponded to a clockwise rotation, which was coupled to the movement of P-tRNA over the P/E-gate made of G1338, A1339 and A790 in the small subunit. The latter corresponded to an anticlockwise rotation of the head, which was coupled to the location of the two tRNAs in the hybrid state. This indicates that the coupled motion of the head rotation and tRNA translocation plays an important role in opening and closing of the P/E-gate during the ratchet-like movement in the ribosome. Conformational change of EF-G was interpreted to be the result of the combination of the external motion by L12 around an axis passing near the sarcin-ricin loop, and internal hinge-bending motion. These motions contributed to the movement of domain IV of EF-G to maintain its interaction with A/P-tRNA. PMID:24999999

  16. A reduced order modeling approach to represent subgrid-scale hydrological dynamics for regional- and climate-scale land-surface simulations: application in a polygonal tundra landscape

    NASA Astrophysics Data System (ADS)

    Pau, G. S. H.; Bisht, G.; Riley, W. J.

    2014-04-01

    Existing land surface models (LSMs) describe physical and biological processes that occur over a wide range of spatial and temporal scales. For example, biogeochemical and hydrological processes responsible for carbon (CO2, CH4) exchanges with the atmosphere range from molecular scale (pore-scale O2 consumption) to tens of kilometer scale (vegetation distribution, river networks). Additionally, many processes within LSMs are nonlinearly coupled (e.g., methane production and soil moisture dynamics), and therefore simple linear upscaling techniques can result in large prediction error. In this paper we applied a particular reduced-order modeling (ROM) technique known as "Proper Orthogonal Decomposition mapping method" that reconstructs temporally-resolved fine-resolution solutions based on coarse-resolution solutions. We applied this technique to four study sites in a polygonal tundra landscape near Barrow, Alaska. Coupled surface-subsurface isothermal simulations were performed for summer months (June-September) at fine (0.25 m) and coarse (8 m) horizontal resolutions. We used simulation results from three summer seasons (1998-2000) to build ROMs of the 4-D soil moisture field for the four study sites individually (single-site) and aggregated (multi-site). The results indicate that the ROM produced a significant computational speedup (> 103) with very small relative approximation error (< 0.1%) for two validation years not used in training the ROM. We also demonstrated that our approach: (1) efficiently corrects for coarse-resolution model bias and (2) can be used for polygonal tundra sites not included in the training dataset with relatively good accuracy (< 1.5% relative error), thereby allowing for the possibility of applying these ROMs across a much larger landscape. This method has the potential to efficiently increase the resolution of land models for coupled climate simulations, allowing LSMs to be used at spatial scales consistent with mechanistic physical

  17. A reduced-order modeling approach to represent subgrid-scale hydrological dynamics for land-surface simulations: application in a polygonal tundra landscape

    NASA Astrophysics Data System (ADS)

    Pau, G. S. H.; Bisht, G.; Riley, W. J.

    2014-09-01

    Existing land surface models (LSMs) describe physical and biological processes that occur over a wide range of spatial and temporal scales. For example, biogeochemical and hydrological processes responsible for carbon (CO2, CH4) exchanges with the atmosphere range from the molecular scale (pore-scale O2 consumption) to tens of kilometers (vegetation distribution, river networks). Additionally, many processes within LSMs are nonlinearly coupled (e.g., methane production and soil moisture dynamics), and therefore simple linear upscaling techniques can result in large prediction error. In this paper we applied a reduced-order modeling (ROM) technique known as "proper orthogonal decomposition mapping method" that reconstructs temporally resolved fine-resolution solutions based on coarse-resolution solutions. We developed four different methods and applied them to four study sites in a polygonal tundra landscape near Barrow, Alaska. Coupled surface-subsurface isothermal simulations were performed for summer months (June-September) at fine (0.25 m) and coarse (8 m) horizontal resolutions. We used simulation results from three summer seasons (1998-2000) to build ROMs of the 4-D soil moisture field for the study sites individually (single-site) and aggregated (multi-site). The results indicate that the ROM produced a significant computational speedup (> 103) with very small relative approximation error (< 0.1%) for 2 validation years not used in training the ROM. We also demonstrate that our approach: (1) efficiently corrects for coarse-resolution model bias and (2) can be used for polygonal tundra sites not included in the training data set with relatively good accuracy (< 1.7% relative error), thereby allowing for the possibility of applying these ROMs across a much larger landscape. By coupling the ROMs constructed at different scales together hierarchically, this method has the potential to efficiently increase the resolution of land models for coupled climate

  18. A reduced-order modeling approach to represent subgrid-scale hydrological dynamics for land-surface simulations: application in a polygonal tundra landscape

    DOE PAGES

    Pau, G. S. H.; Bisht, G.; Riley, W. J.

    2014-09-17

    Existing land surface models (LSMs) describe physical and biological processes that occur over a wide range of spatial and temporal scales. For example, biogeochemical and hydrological processes responsible for carbon (CO2, CH4) exchanges with the atmosphere range from the molecular scale (pore-scale O2 consumption) to tens of kilometers (vegetation distribution, river networks). Additionally, many processes within LSMs are nonlinearly coupled (e.g., methane production and soil moisture dynamics), and therefore simple linear upscaling techniques can result in large prediction error. In this paper we applied a reduced-order modeling (ROM) technique known as "proper orthogonal decomposition mapping method" that reconstructs temporally resolvedmore » fine-resolution solutions based on coarse-resolution solutions. We developed four different methods and applied them to four study sites in a polygonal tundra landscape near Barrow, Alaska. Coupled surface–subsurface isothermal simulations were performed for summer months (June–September) at fine (0.25 m) and coarse (8 m) horizontal resolutions. We used simulation results from three summer seasons (1998–2000) to build ROMs of the 4-D soil moisture field for the study sites individually (single-site) and aggregated (multi-site). The results indicate that the ROM produced a significant computational speedup (> 103) with very small relative approximation error (< 0.1%) for 2 validation years not used in training the ROM. We also demonstrate that our approach: (1) efficiently corrects for coarse-resolution model bias and (2) can be used for polygonal tundra sites not included in the training data set with relatively good accuracy (< 1.7% relative error), thereby allowing for the possibility of applying these ROMs across a much larger landscape. By coupling the ROMs constructed at different scales together hierarchically, this method has the potential to efficiently increase the resolution of land models for coupled

  19. A reduced order modeling approach to represent subgrid-scale hydrological dynamics for regional- and climate-scale land-surface simulations: application in a polygonal tundra landscape

    DOE PAGES

    Pau, G. S. H.; Bisht, G.; Riley, W. J.

    2014-04-04

    Existing land surface models (LSMs) describe physical and biological processes that occur over a wide range of spatial and temporal scales. For example, biogeochemical and hydrological processes responsible for carbon (CO2, CH4) exchanges with the atmosphere range from molecular scale (pore-scale O2 consumption) to tens of kilometer scale (vegetation distribution, river networks). Additionally, many processes within LSMs are nonlinearly coupled (e.g., methane production and soil moisture dynamics), and therefore simple linear upscaling techniques can result in large prediction error. In this paper we applied a particular reduced-order modeling (ROM) technique known as "Proper Orthogonal Decomposition mapping method" that reconstructs temporally-resolvedmore » fine-resolution solutions based on coarse-resolution solutions. We applied this technique to four study sites in a polygonal tundra landscape near Barrow, Alaska. Coupled surface-subsurface isothermal simulations were performed for summer months (June–September) at fine (0.25 m) and coarse (8 m) horizontal resolutions. We used simulation results from three summer seasons (1998–2000) to build ROMs of the 4-D soil moisture field for the four study sites individually (single-site) and aggregated (multi-site). The results indicate that the ROM produced a significant computational speedup (> 103) with very small relative approximation error (< 0.1%) for two validation years not used in training the ROM. We also demonstrated that our approach: (1) efficiently corrects for coarse-resolution model bias and (2) can be used for polygonal tundra sites not included in the training dataset with relatively good accuracy (< 1.5% relative error), thereby allowing for the possibility of applying these ROMs across a much larger landscape. This method has the potential to efficiently increase the resolution of land models for coupled climate simulations, allowing LSMs to be used at spatial scales consistent with

  20. Landscape Factors Facilitating the Invasive Dynamics and Distribution of the Brown Marmorated Stink Bug, Halyomorpha halys (Hemiptera: Pentatomidae), after Arrival in the United States

    PubMed Central

    Wallner, Adam M.; Hamilton, George C.; Nielsen, Anne L.; Hahn, Noel; Green, Edwin J.; Rodriguez-Saona, Cesar R.

    2014-01-01

    The brown marmorated stink bug, Halyomorpha halys, a native of Asia, has become a serious invasive pest in the USA. H. halys was first detected in the USA in the mid 1990s, dispersing to over 41 other states. Since 1998, H. halys has spread throughout New Jersey, becoming an important pest of agriculture, and a major nuisance in urban developments. In this study, we used spatial analysis, geostatistics, and Bayesian linear regression to investigate the invasion dynamics and colonization processes of this pest in New Jersey. We present the results of monitoring H. halys from 51 to 71 black light traps that were placed on farms throughout New Jersey from 2004 to 2011 and examined relationships between total yearly densities of H. halys and square hectares of 48 landscape/land use variables derived from urban, wetland, forest, and agriculture metadata, as well as distances to nearest highways. From these analyses we propose the following hypotheses: (1) H. halys density is strongly associated with urban developments and railroads during its initial establishment and dispersal from 2004 to 2006; (2) H. halys overwintering in multiple habitats and feeding on a variety of plants may have reduced the Allee effect, thus facilitating movement into the southernmost regions of the state by railroads from 2005 to 2008; (3) density of H. halys contracted in 2009 possibly from invading wetlands or sampling artifact; (4) subsequent invasion of H. halys from the northwest to the south in 2010 may conform to a stratified-dispersal model marked by rapid long-distance movement, from railroads and wetland rights-of-way; and (5) high densities of H. halys may be associated with agriculture in southern New Jersey in 2011. These landscape features associated with the invasion of H. halys in New Jersey may predict its potential rate of invasion across the USA and worldwide. PMID:24787576

  1. Conformational landscape of an amyloid intra-cellular domain and Landau-Ginzburg-Wilson paradigm in protein dynamics

    NASA Astrophysics Data System (ADS)

    Dai, Jin; Niemi, Antti J.; He, Jianfeng

    2016-07-01

    The Landau-Ginzburg-Wilson paradigm is proposed as a framework, to investigate the conformational landscape of intrinsically unstructured proteins. A universal Cα-trace Landau free energy is deduced from general symmetry considerations, with the ensuing all-atom structure modeled using publicly available reconstruction programs Pulchra and Scwrl. As an example, the conformational stability of an amyloid precursor protein intra-cellular domain (AICD) is inspected; the reference conformation is the crystallographic structure with code 3DXC in Protein Data Bank (PDB) that describes a heterodimer of AICD and a nuclear multi-domain adaptor protein Fe65. Those conformations of AICD that correspond to local or near-local minima of the Landau free energy are identified. For this, the response of the original 3DXC conformation to variations in the ambient temperature is investigated, using the Glauber algorithm. The conclusion is that in isolation the AICD conformation in 3DXC must be unstable. A family of degenerate conformations that minimise the Landau free energy is identified, and it is proposed that the native state of an isolated AICD is a superposition of these conformations. The results are fully in line with the presumed intrinsically unstructured character of isolated AICD and should provide a basis for a systematic analysis of AICD structure in future NMR experiments.

  2. Conformational landscape of an amyloid intra-cellular domain and Landau-Ginzburg-Wilson paradigm in protein dynamics.

    PubMed

    Dai, Jin; Niemi, Antti J; He, Jianfeng

    2016-07-28

    The Landau-Ginzburg-Wilson paradigm is proposed as a framework, to investigate the conformational landscape of intrinsically unstructured proteins. A universal Cα-trace Landau free energy is deduced from general symmetry considerations, with the ensuing all-atom structure modeled using publicly available reconstruction programs Pulchra and Scwrl. As an example, the conformational stability of an amyloid precursor protein intra-cellular domain (AICD) is inspected; the reference conformation is the crystallographic structure with code 3DXC in Protein Data Bank (PDB) that describes a heterodimer of AICD and a nuclear multi-domain adaptor protein Fe65. Those conformations of AICD that correspond to local or near-local minima of the Landau free energy are identified. For this, the response of the original 3DXC conformation to variations in the ambient temperature is investigated, using the Glauber algorithm. The conclusion is that in isolation the AICD conformation in 3DXC must be unstable. A family of degenerate conformations that minimise the Landau free energy is identified, and it is proposed that the native state of an isolated AICD is a superposition of these conformations. The results are fully in line with the presumed intrinsically unstructured character of isolated AICD and should provide a basis for a systematic analysis of AICD structure in future NMR experiments.

  3. Conformational landscape of an amyloid intra-cellular domain and Landau-Ginzburg-Wilson paradigm in protein dynamics.

    PubMed

    Dai, Jin; Niemi, Antti J; He, Jianfeng

    2016-07-28

    The Landau-Ginzburg-Wilson paradigm is proposed as a framework, to investigate the conformational landscape of intrinsically unstructured proteins. A universal Cα-trace Landau free energy is deduced from general symmetry considerations, with the ensuing all-atom structure modeled using publicly available reconstruction programs Pulchra and Scwrl. As an example, the conformational stability of an amyloid precursor protein intra-cellular domain (AICD) is inspected; the reference conformation is the crystallographic structure with code 3DXC in Protein Data Bank (PDB) that describes a heterodimer of AICD and a nuclear multi-domain adaptor protein Fe65. Those conformations of AICD that correspond to local or near-local minima of the Landau free energy are identified. For this, the response of the original 3DXC conformation to variations in the ambient temperature is investigated, using the Glauber algorithm. The conclusion is that in isolation the AICD conformation in 3DXC must be unstable. A family of degenerate conformations that minimise the Landau free energy is identified, and it is proposed that the native state of an isolated AICD is a superposition of these conformations. The results are fully in line with the presumed intrinsically unstructured character of isolated AICD and should provide a basis for a systematic analysis of AICD structure in future NMR experiments. PMID:27475398

  4. Preferential solvation dynamics in liquids: How geodesic pathways through the potential energy landscape reveal mechanistic details about solute relaxation in liquids

    NASA Astrophysics Data System (ADS)

    Nguyen, Crystal N.; Stratt, Richard M.

    2010-09-01

    It is not obvious that many-body phenomena as collective as solute energy relaxation in liquid solution should ever have identifiable molecular mechanisms, at least not in the sense of the well-defined sequence of molecular events one often attributes to chemical reactions. What can define such mechanisms, though, are the most efficient relaxation paths that solutions take through their potential energy landscapes. When liquid dynamics is dominated by slow diffusive processes, there are mathematically precise and computationally accessible routes to searching for such paths. We apply this observation to the dynamics of preferential solvation, the relaxation around a newly excited solute by a solvent composed of different components with different solvating abilities. The slow solvation seen experimentally in these mixtures stems from the dual needs to compress the solvent and to do solvent-solvent exchanges near the solute. By studying the geodesic (most efficient) paths for this combined process in a simple atomic liquid mixture, we show that the mechanism for preferential solvation features a reasonably sharp onset for slow diffusion, and that this diffusion involves a sequential, rather than concerted, series of solvent exchanges.