Science.gov

Sample records for landscapes exact dynamics

  1. Energy landscape and dynamics of proteins: An exact analysis of a simplified lattice model

    NASA Astrophysics Data System (ADS)

    Cieplak, Marek; Banavar, Jayanth R.

    2013-10-01

    We present the results of exact numerical studies of the energy landscape and the dynamics of a 12-monomer chain with contact interactions encoding the ground state on a square lattice. In spite of its simplicity, the model is shown to exhibit behavior at odds with the standard picture of proteins.

  2. Energy landscape and dynamics of proteins: an exact analysis of a simplified lattice model.

    PubMed

    Cieplak, Marek; Banavar, Jayanth R

    2013-10-01

    We present the results of exact numerical studies of the energy landscape and the dynamics of a 12-monomer chain with contact interactions encoding the ground state on a square lattice. In spite of its simplicity, the model is shown to exhibit behavior at odds with the standard picture of proteins. PMID:24229101

  3. Landscape of an exact energy functional

    NASA Astrophysics Data System (ADS)

    Cohen, Aron J.; Mori-Sánchez, Paula

    2016-04-01

    One of the great challenges of electronic structure theory is the quest for the exact functional of density functional theory. Its existence is proven, but it is a complicated multivariable functional that is almost impossible to conceptualize. In this paper the asymmetric two-site Hubbard model is studied, which has a two-dimensional universe of density matrices. The exact functional becomes a simple function of two variables whose three-dimensional energy landscape can be visualized and explored. A walk on this unique landscape, tilted to an angle defined by the one-electron Hamiltonian, gives a valley whose minimum is the exact total energy. This is contrasted with the landscape of some approximate functionals, explaining their failure for electron transfer in the strongly correlated limit. We show concrete examples of pure-state density matrices that are not v representable due to the underlying nonconvex nature of the energy landscape. The exact functional is calculated for all numbers of electrons, including fractional, allowing the derivative discontinuity to be visualized and understood. The fundamental gap for all possible systems is obtained solely from the derivatives of the exact functional.

  4. 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.

  5. Boundary dynamics in landscapes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Landscapes consist of a mosaic of distinct vegetation types and their intervening boundaries with distinct characteristics. Boundaries can exist along abrupt environmental gradients or along gradual changes that are reinforced by feedback mechanisms between plants and soil properties. Boundaries can...

  6. Landscape dynamics of northeastern forests

    NASA Technical Reports Server (NTRS)

    Canham, Charles D.; Silander, John A., Jr.; Civco, Daniel L.

    1994-01-01

    This project involves collaborative research with Stephen W. Pacala and Simon A. Levin of Princeton University to calibrate, test, and analyze models of heterogeneous forested landscapes containing a diverse array of habitats. The project is an extension of previous, NASA-supported research to develop a spatially-explicit model of forest dynamics at the scale of an individual forest stand (hectares to square kilometer spatial scales). That model (SORTIE) has been thoroughly parameterized from field studies in the modal upland environment of western Connecticut. Under our current funding, we are scaling-up the model and parameterizing it for the broad range of upland environments in the region. Our most basic goal is to understand the linkages between stand-level dynamics (as revealed in our previous research) and landscape-level dynamics of forest composition and structure.

  7. 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

  8. Applications of an exact counting formula in the Bousso-Polchinski landscape

    NASA Astrophysics Data System (ADS)

    Asensio, César; Seguí, Antonio

    2010-12-01

    The Bousso-Polchinski landscape is a proposal for solving the cosmological constant problem. The solution requires counting the states in a very thin shell in flux space. We find an exact formula for this counting problem which has two simple asymptotic regimes, one of them being the method of counting low Λ states given originally by Bousso and Polchinski. We finally give some applications of the extended formula: a robust property of the landscape which can be identified with an effective occupation number, an estimator for the minimum cosmological constant, and a possible influence on the Kachru-Kallosh-Linde-Trivedi stabilization mechanism.

  9. Landscape response to changes in dynamic topography

    NASA Astrophysics Data System (ADS)

    Ruetenik, Gregory A.; Moucha, Robert; Hoke, Gregory D.

    2015-04-01

    Dynamic topography is characterized by broad wavelength, low amplitude undulations of the Earth's surface maintained by stresses arising from mantle convection. Earth's topography is thus an aggregate of both dynamic and isostatic topography that is modulated by surface processes and changes in topography and/or the climate can be recorded in the offshore sedimentary record. However, it is generally difficult to deconvolve this record into contributions from changes in climate, isostatic topography, and dynamic topography. Herein, we use a landscape evolution model that is capable of producing simulations at the necessary scale and resolution for quantifying landscape response to moderate changes in dynamic topography in the presence of flexural unloading and loading due to erosion and deposition. We demonstrate that moderate changes in dynamic topography coupled with flexural response imposed on a landscape with pre-existing relief and drainage divide, disequilibrates the landscape resulting in a measurable increase in erosion rates and corresponding sedimentary flux to the margin. The magnitude and timing of this erosional response to dynamic topography is dependent on several key landscape evolution parameters, most notably the erosion (advection) coefficient and effective elastic thickness. Moreover, to maximize this response, we find that changes in dynamic topography must be slow enough and long-lived for given rates of erosion otherwise the landscape will not have sufficient time to generate a response. Lastly, this anomalous flux can persist for a significant amount of time beyond the influence of dynamic topography change as the landscape strives to re-equilibrate.

  10. 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

  11. DYNAMIC LANDSCAPES, STABILITY AND ECOLOGICAL MODELING

    EPA Science Inventory

    The image of a ball rolling along a series of hills and valleys is an effective heuristic by which to communicate stability concepts in ecology. However, the dynamics of this landscape model have little to do with ecological systems. Other landscape representations, however, are ...

  12. 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.

  13. 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

  14. 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.

  15. Exact dynamic properties of molecular motors.

    PubMed

    Boon, N J; Hoyle, R B

    2012-08-28

    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)] 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. PMID:22938213

  16. Electron transfer dynamics: Zusman equation versus exact theory.

    PubMed

    Shi, Qiang; Chen, Liping; Nan, Guangjun; Xu, Ruixue; Yan, YiJing

    2009-04-28

    The Zusman equation has been widely used to study the effect of solvent dynamics on electron transfer reactions. However, application of this equation is limited by the classical treatment of the nuclear degrees of freedom. In this paper, we revisit the Zusman equation in the framework of the exact hierarchical equations of motion formalism, and show that a high temperature approximation of the hierarchical theory is equivalent to the Zusman equation in describing electron transfer dynamics. Thus the exact hierarchical formalism naturally extends the Zusman equation to include quantum nuclear dynamics at low temperatures. This new finding has also inspired us to rescale the original hierarchical equations and incorporate a filtering algorithm to efficiently propagate the hierarchical equations. Numerical exact results are also presented for the electron transfer reaction dynamics and rate constant calculations. PMID:19405605

  17. 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.

  18. Exact Computation of Probability Landscape of Stochastic Networks of Single Input and Coupled Toggle Switch Modules

    PubMed Central

    Terebus, Anna; Cao, Youfang; Liang, Jie

    2016-01-01

    Gene regulatory networks depict the interactions between genes, proteins, and other components of the cell. These interactions often are stochastic that can influence behavior of the cells. Discrete Chemical Master Equation (dCME) provides a general framework for understanding the stochastic nature of these networks. However solving dCME is challenging due to the enormous state space, one effective approach is to study the behavior of individual modules of the stochastic network. Here we used the finite buffer dCME method and directly calculated the exact steady state probability landscape for the two stochastic networks of Single Input and Coupled Toggle Switch Modules. The first example is a switch network consisting of three genes, and the second example is a double switching network consisting of four coupled genes. Our results show complex switching behavior of these networks can be quantified. PMID:25571172

  19. Dynamics of coupled human-landscape systems

    NASA Astrophysics Data System (ADS)

    Werner, B. T.; McNamara, D. E.

    2007-11-01

    A preliminary dynamical analysis of landscapes and humans as hierarchical complex systems suggests that strong coupling between the two that spreads to become regionally or globally pervasive should be focused at multi-year to decadal time scales. At these scales, landscape dynamics is dominated by water, sediment and biological routing mediated by fluvial, oceanic, atmospheric processes and human dynamics is dominated by simplifying, profit-maximizing market forces and political action based on projection of economic effect. Also at these scales, landscapes impact humans through patterns of natural disasters and trends such as sea level rise; humans impact landscapes by the effect of economic activity and changes meant to mitigate natural disasters and longer term trends. Based on this analysis, human-landscape coupled systems can be modeled using heterogeneous agents employing prediction models to determine actions to represent the nonlinear behavior of economic and political systems and rule-based routing algorithms to represent landscape processes. A cellular model for the development of New Orleans illustrates this approach, with routing algorithms for river and hurricane-storm surge determining flood extent, five markets (home, labor, hotel, tourism and port services) connecting seven types of economic agents (home buyers/laborers, home developers, hotel owners/ employers, hotel developers, tourists, port services developer and port services owners/employers), building of levees or a river spillway by political agents and damage to homes, hotels or port services within cells determined by the passage or depth of flood waters. The model reproduces historical aspects of New Orleans economic development and levee construction and the filtering of frequent small-scale floods at the expense of large disasters.

  20. Exact dynamics of finite Glauber-Fock photonic lattices

    SciTech Connect

    Rodriguez-Lara, B. M.

    2011-11-15

    The dynamics of Glauber-Fock lattice of size N is given through exact diagonalization of the corresponding Hamiltonian; the spectra {l_brace}{lambda}{sub k}{r_brace} is given as the roots of the Nth Hermite polynomial, H{sub N}({lambda}{sub k}/{radical}(2))=0, and the eigenstates are given in terms of Hermite polynomials evaluated at these roots. The exact dynamics is used to study coherent phenomena in discrete lattices. Due to the symmetry and spacing of the eigenvalues {l_brace}{lambda}{sub k}{r_brace}, oscillatory behavior is predicted with highly localized spectra, that is, near complete revivals of the photon number and partial recovery of the initial state at given waveguides.

  1. Archetypal energy landscapes: Dynamical diagnosis

    NASA Astrophysics Data System (ADS)

    Despa, Florin; Wales, David J.; Berry, R. Stephen

    2005-01-01

    Recent studies have identified several motifs for potential energy surfaces corresponding to distinct dynamic and thermodynamic properties. The corresponding disconnectivity graphs were identified as "palm tree," "willow tree," and "banyan tree" patterns. In the present contribution we present a quantitative analysis of the relation between the topography and dynamics for each of these motifs. For the palm tree and willow tree forms we find that the arrangement of the stationary points in the monotonic sequences with respect to the global minimum is the most important factor in establishing the kinetic properties. However, the results are somewhat different for motifs involving a rough surface with several deep basins (banyan tree motif), with large barriers relative to the energy differences between minima. Here it is the size of the barrier for escape from the region relative to the barriers at the bottom that is most important. The present results may be helpful in distinguishing between the dynamics of "structure seeking" and "glass forming" systems.

  2. Archetypal energy landscapes: dynamical diagnosis.

    PubMed

    Despa, Florin; Wales, David J; Berry, R Stephen

    2005-01-01

    Recent studies have identified several motifs for potential energy surfaces corresponding to distinct dynamic and thermodynamic properties. The corresponding disconnectivity graphs were identified as "palm tree," "willow tree," and "banyan tree" patterns. In the present contribution we present a quantitative analysis of the relation between the topography and dynamics for each of these motifs. For the palm tree and willow tree forms we find that the arrangement of the stationary points in the monotonic sequences with respect to the global minimum is the most important factor in establishing the kinetic properties. However, the results are somewhat different for motifs involving a rough surface with several deep basins (banyan tree motif), with large barriers relative to the energy differences between minima. Here it is the size of the barrier for escape from the region relative to the barriers at the bottom that is most important. The present results may be helpful in distinguishing between the dynamics of "structure seeking" and "glass forming" systems. PMID:15638568

  3. 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.

  4. 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.

  5. Exact mapping between different dynamics of isotropically trapped quantum gases

    NASA Astrophysics Data System (ADS)

    Wamba, Etienne; Pelster, Axel; Anglin, James R.

    2016-05-01

    Experiments on trapped quantum gases can probe challenging regimes of quantum many-body dynamics, where strong interactions or non-equilibrium states prevent exact theoretical treatment. In this talk, we present a class of exact mappings between all the observables of different experiments, under the experimentally attainable conditions that the gas particles interact via a homogeneously scaling two-body potential which is in general time-dependent, and are confined in an isotropic harmonic trap. We express our result through an identity relating second-quantized field operators in the Heisenberg picture of quantum mechanics which makes it general. It applies to arbitrary measurements on possibly multi-component Bose or Fermi gases in arbitrary initial quantum states, no matter how highly excited or far from equilibrium. We use an example to show how the results of two different and currently feasible experiments can be mapped onto each other by our spacetime transformation. DAMOP sorting category: 6.11 Nonlinear dynamics and out-of-equilibrium trapped gases EW acknowledge the financial support from the Alexander von Humboldt foundation.

  6. AN INDICATOR OF FOREST DYNAMICS USING A SHIFTING LANDSCAPE MOSAIC

    EPA Science Inventory

    The composition of a landscape is a fundamental indicator in land-cover pattern assessments. The objective of this paper was to evaluate a landscape composition indicator called ‘landscape mosaic’ as a framework for interpreting land-cover dynamics over a 9-year period in a 360,...

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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. PMID:25837918

  14. 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).

  15. 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.

  16. Energy landscape and dynamics of an HP lattice model of proteins —The role of anisotropy

    NASA Astrophysics Data System (ADS)

    Cieplak, Marek; Banavar, Jayanth R.

    2013-12-01

    We present the results of exact numerical studies of the energy landscape and the dynamics of a 12-monomer chain comprised of two types of amino acids called the HP model. We benchmark our findings against the corresponding results of previous studies of a Go model, which encodes the native state conformation. We also show how the energy landscape gets modified dramatically and improves the folding properties on incorporating the inherent anisotropy of a chain, albeit in a simplified manner.

  17. 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.

  18. Exact milestoning

    PubMed Central

    Bello-Rivas, Juan M.; Elber, Ron

    2015-01-01

    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. PMID:25747056

  19. 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.

  20. Exact milestoning.

    PubMed

    Bello-Rivas, Juan M; Elber, Ron

    2015-03-01

    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. PMID:25747056

  1. Biodiversity and ecosystem functioning in dynamic landscapes.

    PubMed

    Brose, Ulrich; Hillebrand, Helmut

    2016-05-19

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

  2. 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

  3. 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.

  4. 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. PMID:26865299

  5. 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...

  6. 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}.

  7. Integrating Landscape Ecology and Geoinformatics to Decipher Landscape Dynamics for Regional Planning

    NASA Astrophysics Data System (ADS)

    Dikou, Angela; Papapanagiotou, Evangelos; Troumbis, Andreas

    2011-09-01

    We used remote sensing and GIS in conjunction with multivariate statistical methods to: (i) quantify landscape composition (land cover types) and configuration (patch density, diversity, fractal dimension, contagion) for five coastal watersheds of Kalloni gulf, Lesvos Island, Greece, in 1945, 1960, 1971, 1990 and 2002/2003, (ii) evaluate the relative importance of physical (slope, geologic substrate, stream order) and human (road network, population density) variables on landscape composition and configuration, and (iii) characterize processes that led to land cover changes through land cover transitions between these five successive periods in time. Distributions of land cover types did not differ among the five time periods at the five watersheds studied because the largest cumulative changes between 1945 and 2002/2003 did not take place at dominant land cover types. Landscape composition related primarily to the physical attributes of the landscape. Nevertheless, increase in population density and the road network were found to increase heterogeneity of the landscape mosaic (patchiness), complexity of patch shape (fractal dimension), and patch disaggregation (contagion). Increase in road network was also found to increase landscape diversity due to the creation of new patches. The main processes involved in land cover changes were plough-land abandonment and ecological succession. Landscape dynamics during the last 50 years corroborate the ecotouristic-agrotouristic model for regional development to reverse trends in agricultural land abandonment and human population decline and when combined with hypothetical regulatory approaches could predict how this landscape could develop in the future, thus, providing a valuable tool to regional planning.

  8. 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.

  9. Calculation of exact vibration modes for plane grillages by the dynamic stiffness method

    NASA Technical Reports Server (NTRS)

    Hallauer, W. L., Jr.; Liu, R. Y. L.

    1982-01-01

    A dynamic stiffness method is developed for the calculation of the exact modal parameters for plane grillages which consist of straight and uniform beams with coincident elastic and inertial axes. Elementary bending-torsion beam theory is utilized, and bending translation is restricted to one direction. The exact bending-torsion dynamic stiffness matrix is obtained for a straight and uniform beam element with coincident elastic and inertial axes. The element stiffness matrices are assembled using the standard procedure of the static stiffness method to form the dynamic stiffness matrix of the complete grillage. The exact natural frequencies, mode shapes, and generalized masses of the grillage are then calculated by solving a nonlinear eigenvalue problem based on the dynamic stiffness matrix. The exact modal solutions for an example grillage are calculated and compared with the approximate solutions obtained by using the finite element method.

  10. 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.

  11. Integrating landscape ecology and geoinformatics to decipher landscape dynamics for regional planning.

    PubMed

    Dikou, Angela; Papapanagiotou, Evangelos; Troumbis, Andreas

    2011-09-01

    We used remote sensing and GIS in conjunction with multivariate statistical methods to: (i) quantify landscape composition (land cover types) and configuration (patch density, diversity, fractal dimension, contagion) for five coastal watersheds of Kalloni gulf, Lesvos Island, Greece, in 1945, 1960, 1971, 1990 and 2002/2003, (ii) evaluate the relative importance of physical (slope, geologic substrate, stream order) and human (road network, population density) variables on landscape composition and configuration, and (iii) characterize processes that led to land cover changes through land cover transitions between these five successive periods in time. Distributions of land cover types did not differ among the five time periods at the five watersheds studied because the largest cumulative changes between 1945 and 2002/2003 did not take place at dominant land cover types. Landscape composition related primarily to the physical attributes of the landscape. Nevertheless, increase in population density and the road network were found to increase heterogeneity of the landscape mosaic (patchiness), complexity of patch shape (fractal dimension), and patch disaggregation (contagion). Increase in road network was also found to increase landscape diversity due to the creation of new patches. The main processes involved in land cover changes were plough-land abandonment and ecological succession. Landscape dynamics during the last 50 years corroborate the ecotouristic-agrotouristic model for regional development to reverse trends in agricultural land abandonment and human population decline and when combined with hypothetical regulatory approaches could predict how this landscape could develop in the future, thus, providing a valuable tool to regional planning. PMID:21744152

  12. 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.

  13. 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…

  14. 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.

  15. 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.

  16. 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.

  17. Exact Potential Driving the Electron Dynamics in Enhanced Ionization of H2+

    NASA Astrophysics Data System (ADS)

    Khosravi, Elham; Abedi, Ali; Maitra, Neepa T.

    2015-12-01

    It was recently shown that the exact factorization of the electron-nuclear wave function allows the construction of a Schrödinger equation for the electronic system, in which the potential contains exactly the effect of coupling to the nuclear degrees of freedom and any external fields. Here we study the exact potential acting on the electron in charge-resonance enhanced ionization in a model one-dimensional H2+ molecule. We show there can be significant differences between the exact potential and that used in the traditional quasistatic analyses, arising from nonadiabatic coupling to the nuclear system, and that these are crucial to include for accurate simulations of time-resolved ionization dynamics and predictions of the ionization yield.

  18. 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.

  19. Asymptotically exact analysis of stochastic metapopulation dynamics with explicit spatial structure.

    PubMed

    Ovaskainen, Otso; Cornell, Stephen J

    2006-02-01

    We describe a mathematically exact method for the analysis of spatially structured Markov processes. The method is based on a systematic perturbation expansion around the deterministic, non-spatial mean-field theory, using the theory of distributions to account for space and the underlying stochastic differential equations to account for stochasticity. As an example, we consider a spatial version of the Levins metapopulation model, in which the habitat patches are distributed in the d-dimensional landscape Rd in a random (but possibly correlated) manner. Assuming that the dispersal kernel is characterized by a length scale L, we examine how the behavior of the metapopulation deviates from the mean-field model for a finite but large L. For example, we show that the equilibrium fraction of occupied patches is given by p(0)+c/L(d)+O(L(-3d/2)), where p(0) is the equilibrium state of the Levins model and the constant c depends on p(0), the dispersal kernel, and the structure of the landscape. We show that patch occupancy can be increased or decreased by spatial structure, but is always decreased by stochasticity. Comparison with simulations show that the analytical results are not only asymptotically exact (as L-->infinity), but a good approximation also when L is relatively small. PMID:16246386

  20. 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.

  1. 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. PMID:22612355

  2. 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

  3. 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.

  4. Exact spin dynamics of inhomogeneous 1-d systems at high temperature

    NASA Astrophysics Data System (ADS)

    Danieli, E. P.; Pastawski, H. M.; Levstein, P. R.

    2002-07-01

    The evaluation of spin excitation dynamics in finite 1-d systems of spins {1}/{2} with XY exchange interaction J acquired new interest because NMR experiments at high temperature ( kBT≫ J) confirmed the predicted spin wave behavior of mesoscopic echoes. In this work, we use the Jordan-Wigner transformation to obtain the exact dynamics of inhomogeneous chains and rings where the evolution is reduced to one-body dynamics. For higher dimensions, the spin excitations manifest many-body effects that can be interpreted as a simple dynamics of non-interacting fermions plus a decoherent process.

  5. Elongation dynamics of amyloid fibrils: A rugged energy landscape picture

    NASA Astrophysics Data System (ADS)

    Lee, Chiu Fan; Loken, James; Jean, Létitia; Vaux, David J.

    2009-10-01

    Protein amyloid fibrils are a form of linear protein aggregates that are implicated in many neurodegenerative diseases. Here, we study the dynamics of amyloid fibril elongation by performing Langevin dynamic simulations on a coarse-grained model of peptides. Our simulation results suggest that the elongation process is dominated by a series of local minimum due to frustration in monomer-fibril interactions. This rugged energy landscape picture indicates that the amount of recycling of monomers at the fibrils’ ends before being fibrilized is substantially reduced in comparison to the conventional two-step elongation model. This picture, along with other predictions discussed, can be tested with current experimental techniques.

  6. 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

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

    NASA Astrophysics Data System (ADS)

    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.

  8. 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.

  9. 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

  10. Protein dynamics, thermal stability, and free-energy landscapes: a molecular dynamics investigation.

    PubMed

    Tavernelli, Ivano; Cotesta, Simona; Di Iorio, Ernesto E

    2003-10-01

    Proteins have a complex free-energy landscape because of their rich topology and the nature of their nonbonded interaction potential. This has important consequences because the roughness of the landscape affects the ease with which a chain folds and also determines the dynamic behavior of the folded structure, thus influencing its functional and stability properties. A detailed description of the free-energy landscape is therefore of paramount importance for a quantitative understanding of the relationships between structure, dynamics, stability, and functional behavior of proteins. The free-energy landscape of a protein is a high-dimensional hypersurface, difficult to rationalize. Therefore, achieving its detailed graphical representation in a way that goes beyond the familiar funnel-like free-energy model is still a big challenge. We describe here an approach based on global structural parameters that allows a two-dimensional representation of the free-energy landscape from simulated atomic trajectories. As shown in this and in the accompanying article, our representation of the landscape, combined with other conformational analyses, provides valuable information on its roughness and on how atomic trajectories evolve with time. PMID:14507727

  11. 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

  12. 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.

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

    PubMed

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

    2011-06-01

    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. PMID:21774412

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. Multiple coupled landscapes and non-adiabatic dynamics with applications to self-activating genes.

    PubMed

    Chen, Cong; Zhang, Kun; Feng, Haidong; Sasai, Masaki; Wang, Jin

    2015-11-21

    Many physical, chemical and biochemical systems (e.g. electronic dynamics and gene regulatory networks) are governed by continuous stochastic processes (e.g. electron dynamics on a particular electronic energy surface and protein (gene product) synthesis) coupled with discrete processes (e.g. hopping among different electronic energy surfaces and on and off switching of genes). One can also think of the underlying dynamics as the continuous motion on a particular landscape and discrete hoppings among different landscapes. The main difference of such systems from the intra-landscape dynamics alone is the emergence of the timescale involved in transitions among different landscapes in addition to the timescale involved in a particular landscape. The adiabatic limit when inter-landscape hoppings are fast compared to continuous intra-landscape dynamics has been studied both analytically and numerically, but the analytical treatment of the non-adiabatic regime where the inter-landscape hoppings are slow or comparable to continuous intra-landscape dynamics remains challenging. In this study, we show that there exists mathematical mapping of the dynamics on 2(N) discretely coupled N continuous dimensional landscapes onto one single landscape in 2N dimensional extended continuous space. On this 2N dimensional landscape, eddy current emerges as a sign of non-equilibrium non-adiabatic dynamics and plays an important role in system evolution. Many interesting physical effects such as the enhancement of fluctuations, irreversibility, dissipation and optimal kinetics emerge due to non-adiabaticity manifested by the eddy current illustrated for an N = 1 self-activator. We further generalize our theory to the N-gene network with multiple binding sites and multiple synthesis rates for discretely coupled non-equilibrium stochastic physical and biological systems. PMID:26455835

  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. 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

  2. Biomolecular dynamics: order-disorder transitions and energy landscapes.

    PubMed

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

    2012-07-01

    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 toward 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 have provided 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 provides 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

  3. 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

  4. 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.

  5. 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

  6. 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. PMID:26303925

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. Exact dynamic and static stiffness matrices of shear deformable thin-walled beam-columns

    NASA Astrophysics Data System (ADS)

    Moon-Young, Kim; Nam, Kim; Hee-Taek, Yun

    2003-10-01

    Total potential energy of non-symmetric thin-walled beam-columns in the general form is presented by introducing the displacement field based on semitangential rotations and deriving transformation equations between displacement and force parameters defined at the arbitrary axis and the centroid-shear center axis, respectively. Next, governing equations and force-deformation relations are derived from the total potential energy for a shear-deformable, uniform beam element and a system of linear eigenproblem with non-symmetric matrices is constructed based on 14 displacement parameters. And then explicit expressions for displacement parameters are derived and exact dynamic stiffness matrices are determined using force-deformatin relationships. In addition, the modified numerical method to eliminate multiple zero eigenvalues and to evaluate the exact static stiffness matrix is developed for spatial stability analysis. Finally, in order to demonstrate the validity and the accuracy of this study, the spatially coupled natural frequencies and buckling loads are evaluated and compared with analytical solutions or results analyzed by thin-walled beam elements and ABAQUS's shell elements.

  13. How Predation and Landscape Fragmentation Affect Vole Population Dynamics

    PubMed Central

    Dalkvist, Trine; Sibly, Richard M.; Topping, Chris J.

    2011-01-01

    importance of landscape fragmentation for population cycling and we recommend that the degree of fragmentation be more fully considered in future analyses of vole dynamics. PMID:21829528

  14. 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.

  15. An exact conserving algorithm for nonlinear dynamics with rotational DOFs and general hyperelasticity. Part 2: shells

    NASA Astrophysics Data System (ADS)

    Campello, E. M. B.; Pimenta, P. M.; Wriggers, P.

    2011-08-01

    Following the approach developed for rods in Part 1 of this paper (Pimenta et al. in Comput. Mech. 42:715-732, 2008), this work presents a fully conserving algorithm for the integration of the equations of motion in nonlinear shell dynamics. We begin with a re-parameterization of the rotation field in terms of the so-called Rodrigues rotation vector, allowing for an extremely simple update of the rotational variables within the scheme. The weak form is constructed via non-orthogonal projection, the time-collocation of which ensures exact conservation of momentum and total energy in the absence of external forces. Appealing is the fact that general hyperelastic materials (and not only materials with quadratic potentials) are permitted in a totally consistent way. Spatial discretization is performed using the finite element method and the robust performance of the scheme is demonstrated by means of numerical examples.

  16. 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.

  17. Nonequilibrium dynamics of arbitrary-range Ising models with decoherence: An exact analytic solution

    NASA Astrophysics Data System (ADS)

    Foss-Feig, Michael; Hazzard, Kaden R. A.; Bollinger, John J.; Rey, Ana Maria

    2013-04-01

    The interplay between interactions and decoherence in many-body systems is of fundamental importance in quantum physics. In a step toward understanding this interplay, we obtain an exact analytic solution for the nonequilibrium dynamics of Ising models with arbitrary couplings (and therefore in arbitrary dimension) and subject to local Markovian decoherence. Our solution shows that decoherence significantly degrades the nonclassical correlations developed during coherent Ising spin dynamics, which relax much faster than predicted by treating decoherence and interactions separately. We also show that the competition of decoherence and interactions induces a transition from oscillatory to overdamped dynamics that is absent at the single-particle or mean-field level. These calculations are applicable to ongoing quantum information and emulation efforts using a variety of atomic, molecular, optical, and solid-state systems. In particular, we apply our results to the NIST Penning trapped-ion experiment and show that the current experiment is capable of producing entanglement amongst hundreds of quantum spins.

  18. 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...

  19. Effects of local and landscape factors on population dynamics of a cotton pest

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Local diversification of vegetation is used extensively to reduce pest pressure in crops, but little is known about effects of landscape diversity on pest metapopulation dynamics. Many polyphagous pests sequentially use crops and uncultivated habitats in landscapes dominated by annual crops. As the...

  20. 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.

  1. 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.

  2. 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. PMID:26160664

  3. 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.

  4. 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.

  5. 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

  6. Particle dynamics in two-dimensional random-energy landscapes: Experiments and simulations

    NASA Astrophysics Data System (ADS)

    Evers, Florian; Zunke, Christoph; Hanes, Richard D. L.; Bewerunge, Jörg; Ladadwa, Imad; Heuer, Andreas; Egelhaaf, Stefan U.

    2013-08-01

    The dynamics of individual colloidal particles in random potential energy landscapes was investigated experimentally and by Monte Carlo simulations. The value of the potential at each point in the two-dimensional energy landscape follows a Gaussian distribution. The width of the distribution, and hence the degree of roughness of the energy landscape, was varied and its effect on the particle dynamics studied. This situation represents an example of Brownian dynamics in the presence of disorder. In the experiments, the energy landscapes were generated optically using a holographic setup with a spatial light modulator, and the particle trajectories were followed by video microscopy. The dynamics is characterized using, e.g., the time-dependent diffusion coefficient, the mean squared displacement, the van Hove function, and the non-Gaussian parameter. In both experiments and simulations the dynamics is initially diffusive, showing an extended subdiffusive regime at intermediate times before diffusive motion is recovered at very long times. The dependence of the long-time diffusion coefficient on the width of the Gaussian distribution agrees with theoretical predictions. Compared to the dynamics in a one-dimensional potential energy landscape, the localization at intermediate times is weaker and the diffusive regime at long times reached earlier, which is due to the possibility to avoid local maxima in two-dimensional energy landscapes.

  7. 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

  8. Exact solutions to the governing dynamic equations of plasma armature electromagnetic railguns

    SciTech Connect

    Shahinpoor, M.; Hawke, R.S.

    1987-08-01

    General governing nonlinear differential equations pertaining to the dynamic behavior of a plasma armature electromagnetic railgun are first derived. Three different cases are then considered and the corresponding governing equations are then solved exactly by means of a set of nonlinear transformations. These cases correspond to (1) no-ablation, (2) continuous-ablation, and (3) partial-ablation for which an ablation threshold velocity nu/sub t/ plays a fundamental role. Corresponding to each case, a nonlinear transformation is employed to reduce the nonlinear differential equations to their equivalent linear ones and subsequently allow solution of the pertinent linear differential equations, which are second order, by means of the transition matrix technique. It is concluded that in order to achieve very high projectile velocities the projectile should be injected into the railgun at velocities higher than the ablation threshold velocity. Thus, the ablation may be completely alleviated and the ensuing turbulent drag may be significantly diminished. It is shown that under these conditions one may typically accelerate projectiles up to 30 km/s or more while without hypervelocity injection, for the same railgun and typical operating conditions, one might severely limit the maximum projectile velocity.

  9. A multi-scale modelling approach for analysing landscape service dynamics.

    PubMed

    Willemen, L; Veldkamp, A; Verburg, P H; Hein, L; Leemans, R

    2012-06-15

    Shifting societal needs drive and shape landscapes and the provision of their services. This paper presents a modelling approach to visualize the regional spatial and temporal dynamics in landscape service supply as a function of changing landscapes and societal demand. This changing demand can result from different policy targets. In this paper we conceptualise the system in which these dynamics take place by explicitly addressing (i) the multifunctional character of a landscape, (ii) the different spatial levels at which interactions between landscape service supply, demand, and land management occur, and (iii) trade-offs in service supply as a result of land management actions. Next, we translate the resulting conceptual framework into an operational model. As a demonstration, this model is applied to simulate changes in landscape service supply driven by regional policies in a rural region of the Netherlands. This application demonstrates potential trade-offs, which emerge in a spatially explicit way in the region over time. It illustrates the potential relevance of modelling landscape service dynamics for environmental management and decision making. PMID:22366361

  10. 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.

  11. Flood Regime Dynamics with Slow-Fast Landscape-Climate Feedbacks

    NASA Astrophysics Data System (ADS)

    Perdigão, Rui A. P.; Blöschl, Günter

    2015-04-01

    The dynamical evolution of flood regimes is evaluated in the general case whereby floods interact nonlinearly with coevolving climate and landscape factors at different scales. For that purpose, a spatiotemporal analysis of the dynamic flood response to precipitation changes is conducted and a slow-fast nonlinear dynamical model is built linking flood regime dynamics with climate, landscape and their feedbacks. These involve nonlinear scale interactions, with landform evolution processes taking place at the millennial scale (slow dynamics), and climate adjusting in years to decades (fast dynamics). A dynamic coevolution index is introduced relating spatiotemporal symmetry with relative characteristic celerities, which need to be taken into account in hydrological space-time trading. Coevolution is expressed here by the scale interaction between slow and fast dynamics, represented respectively by spatial and temporal characteristics of the hydroclimate dynamics. The spatiotemporal analysis shows that in general floods are more responsive to spatial (regional) than to temporal (decadal) variability in its dominant controls, except in stable hydroclimatic regions. In fact, on one hand catchments from stable dry lowlands and high wetlands exhibit similarity between spatial and temporal relative rates of change (spatiotemporal symmetry) and low landscape-climate codependence, suggesting they are not coevolving significantly. On the other hand, intermediate, dynamically evolving regions show differences between those sensitivities (symmetry breaks) and higher landscape-climate codependence, in line with undergoing coevolution. The break of symmetry is an emerging behaviour from nonlinear dynamic feedbacks within the hydroclimate system. The dynamical model captures emerging features of the flood regime dynamics and nonlinear landscape-climate feedbacks, supporting the assessment of spatiotemporally asymmetric flood change. Moreover, it informs on the precipitation and

  12. 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

  13. 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)

  14. The effect of heterogeneous landscape dynamics on ecotone types at two convergent semi-arid biomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Landscapes in biome transition zones consist of a mosaic of patches dominated or codominated by species from adjacent biomes. Shifts in the vegetation composition and dynamics of a biome transition zone depend upon the underlying patch dynamics of the ecotones between these dominant species. Landsca...

  15. 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.

  16. 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

  17. A half-century analysis of landscape dynamics in southern Québec, Canada.

    PubMed

    Jobin, Benoît; Latendresse, Claudie; Baril, Alain; Maisonneuve, Charles; Boutin, Céline; Côté, Dominique

    2014-04-01

    We studied landscape dynamics for three time periods (<1950, 1965, and 1997) along a gradient of agricultural intensity from highly intensive agriculture to forested areas in southern Québec. Air photos were analyzed to obtain long-term information on land cover (crop and habitat types) and linear habitats (hedgerows and riparian habitats) and landscape metrics were calculated to quantify changes in habitat configuration. Anthropogenic areas increased in all types of landscapes but mostly occurred in the highly disturbed cash crop dominated landscape. Perennial crops (pasture and hayfields) were largely converted into annual crops (corn and soybean) between 1965 and 1997. The coalescence of annual crop fields resulted in a more homogeneous agricultural landscape. Old fields and forest cover was consistently low and forest fragmentation remained stable through time in the intensive agriculture landscapes. However, forest cover increased and forest fragmentation receded in the forest-dominated landscapes following farm abandonment and the transition of old fields into forests. Tree-dominated hedgerows and riparian habitats increased in areas with intensive agriculture. Observed changes in land cover classes are related to proximate factors, such as surficial deposits and topography. Agriculture intensification occurred in areas highly suitable for agriculture whereas farm abandonment was observed in poor-quality agriculture terrains. Large-scale conversion of perennial crops into annual crops along with continued urbanization exerts strong pressures on residual natural habitats and their inhabiting wildlife. The afforestation process occurring in the more forested landscapes along with the addition of tree-dominated hedgerows and riparian habitats in the agriculture-dominated landscapes should improve landscape ecological value. PMID:24287717

  18. 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

  19. 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

  20. Stochastic time-dependent Hartree-Fock methods for fermions: Quasiprobability distributions, master equations, and convergence towards exact quantum dynamics

    NASA Astrophysics Data System (ADS)

    Polyakov, Evgeny A.

    2016-02-01

    The time-dependent fermionic Hartree-Fock equations can be stochastically extended in such a way as to become the exact representation of quantum dynamics. This fact was first observed in the work of Juillet and Chomaz [Phys. Rev. Lett. 88, 142503 (2002), 10.1103/PhysRevLett.88.142503]. During the past decade, this observation has led to the emergence of a whole family of stochastic wave-function methods for fermions. The common feature of all these methods is that they are based on the expansion of the density operator over the dyadic product of the two fermionic Slater determinant states. In this work, we develop a unified and rigorous foundation for this family of methods. We find a general form of stochastic equations and describe the sufficient conditions under which these methods converge towards exact quantum dynamics. To achieve these goals, we employ the representation of quantum dynamics in generalized phase space. In particular, we consider the quasiprobability distributions which emerge in these stochastic methods and their master equations. It is shown that the convergence towards exact quantum dynamics is controlled by the problem of boundary terms. We provide an example of stochastic Hartree-Fock method which is well-defined and free from this problem.

  1. 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.

  2. Exactly computing the parsimony scores on phylogenetic networks using dynamic programming.

    PubMed

    Kannan, Lavanya; Wheeler, Ward C

    2014-04-01

    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(m(p)k) 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(nm(p)k(2)) 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

  3. 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

  4. 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

  5. Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework.

    PubMed

    Zhuravlev, Pavel I; Papoian, Garegin A

    2010-08-01

    Energy landscape theories have provided a common ground for understanding the protein folding problem, which once seemed to be overwhelmingly complicated. At the same time, the native state was found to be an ensemble of interconverting states with frustration playing a more important role compared to the folding problem. The landscape of the folded protein - the native landscape - is glassier than the folding landscape; hence, a general description analogous to the folding theories is difficult to achieve. On the other hand, the native basin phase volume is much smaller, allowing a protein to fully sample its native energy landscape on the biological timescales. Current computational resources may also be used to perform this sampling for smaller proteins, to build a 'topographical map' of the native landscape that can be used for subsequent analysis. Several major approaches to representing this topographical map are highlighted in this review, including the construction of kinetic networks, hierarchical trees and free energy surfaces with subsequent structural and kinetic analyses. In this review, we extensively discuss the important question of choosing proper collective coordinates characterizing functional motions. In many cases, the substates on the native energy landscape, which represent different functional states, can be used to obtain variables that are well suited for building free energy surfaces and analyzing the protein's functional dynamics. Normal mode analysis can provide such variables in cases where functional motions are dictated by the molecule's architecture. Principal component analysis is a more expensive way of inferring the essential variables from the protein's motions, one that requires a long molecular dynamics simulation. Finally, the two popular models for the allosteric switching mechanism, 'preexisting equilibrium' and 'induced fit', are interpreted within the energy landscape paradigm as extreme points of a continuum of

  6. 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.

  7. 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.

  8. 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.

  9. Colloids in light fields: Particle dynamics in random and periodic energy landscapes

    NASA Astrophysics Data System (ADS)

    Evers, F.; Hanes, R. D. L.; Zunke, C.; Capellmann, R. F.; Bewerunge, J.; Dalle-Ferrier, C.; Jenkins, M. C.; Ladadwa, I.; Heuer, A.; Castañeda-Priego, R.; Egelhaaf, S. U.

    2013-11-01

    The dynamics of colloidal particles in potential energy landscapes have mainly been investigated theoretically. In contrast, here we discuss the experimental realization of potential energy landscapes with the help of laser light fields and the observation of the particle dynamics by video microscopy. The experimentally observed dynamics in periodic and random potentials are compared to simulation and theoretical results in terms of, e.g. the mean-squared displacement, the time-dependent diffusion coefficient or the non-Gaussian parameter. The dynamics are initially diffusive followed by intermediate subdiffusive behaviour which again becomes diffusive at long times. How pronounced and extended the different regimes are, depends on the specific conditions, in particular the shape of the potential as well as its roughness or amplitude but also the particle concentration. Here we focus on dilute systems, but the dynamics of interacting systems in external potentials, and thus the interplay between particle-particle and particle-potential interactions, are also mentioned briefly. Furthermore, the observed dynamics of dilute systems resemble the dynamics of concentrated systems close to their glass transition, with which it is compared. The effect of certain potential energy landscapes on the dynamics of individual particles appears similar to the effect of interparticle interactions in the absence of an external potential.

  10. Fixation, transient landscape, and diffusion dilemma in stochastic evolutionary game dynamics

    NASA Astrophysics Data System (ADS)

    Zhou, Da; Qian, Hong

    2011-09-01

    Agent-based stochastic models for finite populations have recently received much attention in the game theory of evolutionary dynamics. Both the ultimate fixation and the pre-fixation transient behavior are important to a full understanding of the dynamics. In this paper, we study the transient dynamics of the well-mixed Moran process through constructing a landscape function. It is shown that the landscape playing a central theoretical “device” that integrates several lines of inquiries: the stable behavior of the replicator dynamics, the long-time fixation, and continuous diffusion approximation associated with asymptotically large population. Several issues relating to the transient dynamics are discussed: (i) multiple time scales phenomenon associated with intra- and inter-attractoral dynamics; (ii) discontinuous transition in stochastically stationary process akin to Maxwell construction in equilibrium statistical physics; and (iii) the dilemma diffusion approximation facing as a continuous approximation of the discrete evolutionary dynamics. It is found that rare events with exponentially small probabilities, corresponding to the uphill movements and barrier crossing in the landscape with multiple wells that are made possible by strong nonlinear dynamics, plays an important role in understanding the origin of the complexity in evolutionary, nonlinear biological systems.

  11. Disturbance and landscape dynamics in a changing world.

    PubMed

    Turner, Monica G

    2010-10-01

    Disturbance regimes are changing rapidly, and the consequences of such changes for ecosystems and linked social-ecological systems will be profound. This paper synthesizes current understanding of disturbance with an emphasis on fundamental contributions to contemporary landscape and ecosystem ecology, then identifies future research priorities. Studies of disturbance led to insights about heterogeneity, scale, and thresholds in space and time and catalyzed new paradigms in ecology. Because they create vegetation patterns, disturbances also establish spatial patterns of many ecosystem processes on the landscape. Drivers of global change will produce new spatial patterns, altered disturbance regimes, novel trajectories of change, and surprises. Future disturbances will continue to provide valuable opportunities for studying pattern-process interactions. Changing disturbance regimes will produce acute changes in ecosystems and ecosystem services over the short (years to decades) and long-term (centuries and beyond). Future research should address questions related to (1) disturbances as catalysts of rapid ecological change, (2) interactions among disturbances, (3) relationships between disturbance and society, especially the intersection of land use and disturbance, and (4) feedbacks from disturbance to other global drivers. Ecologists should make a renewed and concerted effort to understand and anticipate the causes and consequences of changing disturbance regimes. PMID:21058545

  12. 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.

  13. 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.

  14. 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 ...

  15. 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...

  16. 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

  17. Exact result vs. dynamic renormalization group analysis for the non-local Kardar-Parisi-Zhang equation

    NASA Astrophysics Data System (ADS)

    Katzav, Eytan

    2002-06-01

    In this paper I discuss a generalization of the well-known Kardar-Parisi-Zhang (KPZ) equation that includes long-range interactions. This Non-local Kardar-Parisi-Zhang (NKPZ) equation has been suggested in the past to describe physical phenomena such as burning paper or deposition of colloids. I show that the steady state strong coupling solution for a subfamily of the NKPZ models can be solved exactly in one dimension, using the Fokker-Planck form of the equation, and yields a Gaussian distribution. This exact result does not agree with a previous result obtained by dynamic renormalization group (DRG) analysis. The reasons for this disagreement are not yet clear.

  18. 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.).

  19. Free energy landscapes of short peptide chains using adaptively biased molecular dynamics

    NASA Astrophysics Data System (ADS)

    Karpusenka, Vadzim; Babin, Volodymyr; Roland, Christopher; Sagui, Celeste

    2009-03-01

    We present the results of a computational study of the free energy landscapes of short polypeptide chains, as a function of several reaction coordinates meant to distinguish between several known types of helices. The free energy landscapes were calculated using the recently developed adaptively biased molecular dynamics method followed up with equilibrium ``umbrella correction'' runs. Specific polypeptides investigated include small chains of pure and mixed alanine, glutamate, leucine, lysine and methionine (all amino acids with strong helix-forming propensities), as well as glycine, proline(having a low helix forming propensities), tyrosine, serine and arginine. Our results are consistent with the existing experimental and other theoretical evidence.

  20. 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

  1. 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.

  2. [Dynamic characteristics of forest landscape in Chengdu City in last 20 years].

    PubMed

    Gu, Lin; Liu, Bo; Gong, Gu-tang; Chen, Jun-hua; Zhu, Zhi-fang; Zhang, Hai-ou; Mu, Chang-long

    2010-05-01

    Based on the remote sensing data of Landsat TM (1985, 1995, and 2000) and CBERS (2006), and by using landscape pattern method and index model of regional land use change in combining with eco-function regionalization, this paper analyzed the dynamic characteristics of forest landscape in Chengdu City in 1985-2006. In the study period, over 17,000 hm2 of forest land lost, and the number and area of small- and medium-size patches changed significantly, indicating the apparent conversion and fragmentation of forest land. Forest land was mainly distributed in mountainous area, accounting for 70% of the total. In contrast, more number of patches was found in plain region, amounting to 70% of the total. The most rapid change of forest land area occurred in 1985-1995, especially in mountainous region. The relative change rate of forest land area in different eco-function regions also varied in different periods. Forest land, converted to or converted from, was mainly related to cropland and grassland. In 2000-2006, forest land was quite stable. Survival-oriented economic welfare, environmental security, and fast urbanization process were the main driving forces of the temporal dynamic change of forest landscape, whereas geographical division and socio-economic layout were the main constraints to the spatial dynamic change of forest landscape. PMID:20707085

  3. Improving approximate-optimized effective potentials by imposing exact conditions: Theory and applications to electronic statics and dynamics

    NASA Astrophysics Data System (ADS)

    Kurzweil, Yair; Head-Gordon, Martin

    2009-07-01

    We develop a method that can constrain any local exchange-correlation potential to preserve basic exact conditions. Using the method of Lagrange multipliers, we calculate for each set of given Kohn-Sham orbitals a constraint-preserving potential which is closest to the given exchange-correlation potential. The method is applicable to both the time-dependent (TD) and independent cases. The exact conditions that are enforced for the time-independent case are Galilean covariance, zero net force and torque, and Levy-Perdew virial theorem. For the time-dependent case we enforce translational covariance, zero net force, Levy-Perdew virial theorem, and energy balance. We test our method on the exchange (only) Krieger-Li-Iafrate (xKLI) approximate-optimized effective potential for both cases. For the time-independent case, we calculated the ground state properties of some hydrogen chains and small sodium clusters for some constrained xKLI potentials and Hartree-Fock (HF) exchange. The results (total energy, Kohn-Sham eigenvalues, polarizability, and hyperpolarizability) indicate that enforcing the exact conditions is not important for these cases. On the other hand, in the time-dependent case, constraining both energy balance and zero net force yields improved results relative to TDHF calculations. We explored the electron dynamics in small sodium clusters driven by cw laser pulses. For each laser pulse we compared calculations from TD constrained xKLI, TD partially constrained xKLI, and TDHF. We found that electron dynamics such as electron ionization and moment of inertia dynamics for the constrained xKLI are most similar to the TDHF results. Also, energy conservation is better by at least one order of magnitude with respect to the unconstrained xKLI. We also discuss the problems that arise in satisfying constraints in the TD case with a non-cw driving force.

  4. Improving approximate-optimized effective potentials by imposing exact conditions: Theory and applications to electronic statics and dynamics

    SciTech Connect

    Kurzweil, Yair; Head-Gordon, Martin

    2009-07-15

    We develop a method that can constrain any local exchange-correlation potential to preserve basic exact conditions. Using the method of Lagrange multipliers, we calculate for each set of given Kohn-Sham orbitals a constraint-preserving potential which is closest to the given exchange-correlation potential. The method is applicable to both the time-dependent (TD) and independent cases. The exact conditions that are enforced for the time-independent case are Galilean covariance, zero net force and torque, and Levy-Perdew virial theorem. For the time-dependent case we enforce translational covariance, zero net force, Levy-Perdew virial theorem, and energy balance. We test our method on the exchange (only) Krieger-Li-Iafrate (xKLI) approximate-optimized effective potential for both cases. For the time-independent case, we calculated the ground state properties of some hydrogen chains and small sodium clusters for some constrained xKLI potentials and Hartree-Fock (HF) exchange. The results (total energy, Kohn-Sham eigenvalues, polarizability, and hyperpolarizability) indicate that enforcing the exact conditions is not important for these cases. On the other hand, in the time-dependent case, constraining both energy balance and zero net force yields improved results relative to TDHF calculations. We explored the electron dynamics in small sodium clusters driven by cw laser pulses. For each laser pulse we compared calculations from TD constrained xKLI, TD partially constrained xKLI, and TDHF. We found that electron dynamics such as electron ionization and moment of inertia dynamics for the constrained xKLI are most similar to the TDHF results. Also, energy conservation is better by at least one order of magnitude with respect to the unconstrained xKLI. We also discuss the problems that arise in satisfying constraints in the TD case with a non-cw driving force.

  5. 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.

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

    DOE PAGESBeta

    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

  7. 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.

  8. Landscape-Scale Disturbances Modified Bird Community Dynamics in Successional Forest Environment

    PubMed Central

    Zhao, Qing; Azeria, Ermias T.; Le Blanc, Mélanie-Louise; Lemaître, Jérôme; Fortin, Daniel

    2013-01-01

    Ecosystem-based forest management strives to develop silvicultural practices that best emulate natural disturbances such as wildfire to conserve biodiversity representative of natural forest ecosystems. Yet, current logging practices alter forest structure and reduce the proportion of old-growth forest and, consequently, can exert long-term effects on the dynamics of forest biota. The stand- and landscape-scale factors driving bird community dynamics in post-disturbance environment remain poorly understood. In this study, we examined bird community dynamics along successional gradients in boreal ecosystems originating from fire and logging in landscapes dominated by old-growth forest. We tested if bird species richness and community compositions in clear-cutting stands became comparable to those in natural stands after 70 years, and identified the relative contributions of stand- and landscape-scale forest attributes in bird community dynamics. Based on records of bird occurrences at 185 field sites in natural and clearcutting stands, we demonstrate that (1) both forest structures and bird communities underwent evident changes along successional gradients in post-clearcutting environment; (2) bird species richness and community composition in 60- to 70-years-old clearcutting stands still differed from those in 50- to 79-years-old natural stands, in spite of the fact that most forest attributes of clearcutting stands became comparable to those of natural stands after 40 years; and (3) landscape disturbances contributed more than stand characteristics in explaining the lack of convergence of mature forest species, residents, and short-distance migrants in post-clearcutting environment. Our study points out that more regards should be paid to improve the landscape configuration of the managed forests, and implies that old-growth forest retention within logged areas, combined with selection cutting and prolonged logging rotations, can better emulate fire and alleviate

  9. 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.

  10. 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

  11. 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

  12. 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.

  13. 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.

  14. Dynamic power balance for nonlinear waves in unbalanced gain and loss landscapes

    NASA Astrophysics Data System (ADS)

    Kominis, Yannis

    2015-12-01

    The presence of losses in nonlinear photonic structures necessitates the introduction of active parts for wave power compensation resulting in unbalanced gain and loss landscapes where localized beam propagation is, in general, dynamically unstable. Here we provide generic sufficient conditions for the relation between the gain-loss and the refractive index profiles in order to ensure efficient wave trapping and stable propagation for a wide range of beam launching conditions such as initial power, angle of incidence, and position. The stability is a consequence of an underlying dynamic power balance mechanism related to a conserved quantity of wave dynamics.

  15. 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.

  16. Anomalous diffusion in folding dynamics of minimalist protein landscape.

    PubMed

    Matsunaga, Yasuhiro; Li, Chun-Biu; Komatsuzaki, Tamiki

    2007-12-01

    A novel method is proposed to quantify collectivity at different space and time scales in multiscale dynamics of proteins. This is based on the combination of the principal component (PC) and the concept recently developed for multiscale dynamical systems called the finite size Lyapunov exponent. The method can differentiate the well-known apparent correlation along the low-indexed PCs in multidimensional Brownian systems from the correlated motion inherent to the system. As an illustration, we apply the method to a model protein of 46 amino beads with three different types of residues. We show how the motion of the model protein changes depending on the space scales and the choices of degrees of freedom. In particular, anomalous superdiffusion is revealed along the low-indexed PC in the unfolded state. The implication of superdiffusion in the process of folding is also discussed. PMID:18233416

  17. Quantifying slow evolutionary dynamics in RNA fitness landscapes.

    PubMed

    Sulc, Petr; Wagner, Andreas; Martin, Olivier C

    2010-12-01

    We re-examine the evolutionary dynamics of RNA secondary structures under directional selection towards an optimum RNA structure. We find that the punctuated equilibria lead to a very slow approach to the optimum, following on average an inverse power of the evolutionary time. In addition, our study of the trajectories shows that the out-of-equilibrium effects due to the evolutionary process are very weak. In particular, the distribution of genotypes is close to that arising during equilibrium stabilizing selection. As a consequence, the evolutionary dynamics leave almost no measurable out-of-equilibrium trace, only the transition genotypes (close to the border between different periods of stasis) have atypical mutational properties. PMID:21121025

  18. Assessing the Impact of Landscape Evolution on Carbon Dynamics: A Coupled Physically-Based Modelling Approach

    NASA Astrophysics Data System (ADS)

    Dialynas, Y. G.; Bastola, S.; Billings, S. A.; Bras, R. L.

    2014-12-01

    Soil erosion and deposition play an important role in the global carbon (C) cycle, constituting an important driver of atmospheric CO2. Clarification of the net effect of landscape evolution on the C cycle may be achieved using coupled fully-distributed modelling of hydro-geomorphic and biogeochemical processes. We developed a distributed model of soil organic C (SOC) dynamics within an existing coupled physically-based hydro-geomorphic model (tRIBS - Erosion) to simulate the effects of soil erosion and deposition on C dynamics at basin scale. The SOC mass balance is analytically formulated at each cell using temporally variant, continuous vertical profiles of SOC content and SOC production and oxidation rate constants derived from SOC turnover characteristics. Landscape evolution feedbacks on C dynamics include the redistribution of eroded SOC, and the alteration of the SOC production and oxidation throughout the corresponding vertical profiles due to geomorphic perturbations. At each time step, model outputs include lateral and vertical C fluxes, and SOC content, at each soil column. We applied the model to the Calhoun Experimental Forest in South Carolina, which constitutes a forest recovering from agricultural land degradation prior to the mid-20th century. To test performance we carried out a point comparison against a spreadsheet-based model, SOrCERO (Soil Organic Carbon, Erosion, Replacement, and Oxidation) of SOC dynamics, which estimates effects of SOC erosion and altered SOC production and oxidation on CO2 release at an eroding profile. At a point, time integrated results from the two models were comparable. The proposed model has the additional advantage of being able to quantify C sinks and sources across the landscape in a spatially explicit manner, by systematically accounting for topographic controls on C dynamics. Sensitivity analysis suggested that the alteration of SOC production and oxidation due to landscape evolution and management practices

  19. Dynamical universality class of Brownian motion and exact results for a single-impurity s=1/2 XY chain

    NASA Astrophysics Data System (ADS)

    Sen, Surajit

    1996-03-01

    Relaxation phenomena in a class of nondissipative systems with two highly disparate time scales (i.e., Brownian systems) have unique commonalities quantifiable via two scalars. It is shown that the exactly solvable problem of the dynamics of a weakly linked impurity spin in a s=1/2 XY chain belongs to this dynamical universality class and so does that of a heavy mass in an infinite harmonic oscillator chain and a spinless quasi two-dimensional attractive Fermi gas in the long-wavelength limit. The case of the strongly linked impurity in the XY chain is also discussed along with the corresponding limits in the harmonic oscillator chain and the electron-gas problems.

  20. Human myoglobin recognition of oxygen: dynamics of the energy landscape.

    PubMed

    Wang, Yuhong; Baskin, J Spencer; Xia, Tianbing; Zewail, Ahmed H

    2004-12-28

    Femtosecond to nanosecond dynamics of O(2) rebinding to human WT myoglobin and its mutants, V68F and I107F, have been studied by using transient absorption. The results are compared with NO rebinding. Even though the immediate environment around the heme binding site is changed by the mutations, the picosecond geminate rebinding of oxygen is at most minimally affected. On the other hand, the V68F (E11) mutation causes drastic differences in rebinding on the nanosecond time scale, whereas the effect of the I107F (G8) mutation remains relatively small within our 10-ns time window. Unlike traditional homogeneous kinetics and molecular dynamics collisional simulations, we propose a "bifurcation model" for populations of directed and undirected dynamics on the ultrafast time scale, reflecting the distribution of initial protein conformations. The major mutation effect occurs on the time scale on which global protein conformational change is possible, consistent with transitions between the conformations of directed and undirected population playing a role in the O(2) binding. We discuss the relevance of these findings to the bimolecular function of the protein. PMID:15601759

  1. Changing landscapes: monitoring ecologically sensitive ecosystems in a dynamic semi-arid landscape using satellite imagery: a case study in Ejin Oasis, western China

    NASA Astrophysics Data System (ADS)

    Lin, Meng-Lung; Cao, Yu; Tao, Yi-Huang; Shih, Jyh-yi; Yan, Guo-Jing; Lee, Yung-Tan; Xiao, Du-Ning; Wang, Shin; Chiu, Hsien-Hao

    2006-12-01

    Land degradation has become an important issue in western China recently. Oasis ecosystem is sensitive to environmental disturbances, such as abnormal /extreme events of precipitations, water supply from upper watersheds, fluctuations of temperatures, etc. Satellite remote sensing of terrestrial ecosystems provides temporal dynamics and spatial distributions of landscape green covers over large areas. Seasonal green cover data are normally important in assessing landscape health (ex. desertification, rate of urban sprawl, natural disturbances) in arid and semi-arid regions. In this study, green cover data is derived from vegetation indices retrieved from MODIS sensors onboard Terra. The satellite images during the period April 2000 to December 2005 are analyzed to quantify the spatial distribution and temporal changes of Ejin Oasis. The results will help improving monitoring techniques to evaluate land degradation and to estimate the newest tendency of landscape green cover dynamics in the Ejin Oasis.

  2. Driven colloidal fluids: construction of dynamical density functional theories from exactly solvable limits.

    PubMed

    Scacchi, Alberto; Krüger, Matthias; Brader, Joseph M

    2016-06-22

    The classical dynamical density functional theory (DDFT) provides an approximate extension of equilibrium DFT to treat nonequilibrium systems subject to Brownian dynamics. However, the method fails when applied to driven systems, such as sheared colloidal dispersions. The breakdown of DDFT can be traced back to an inadequate treatment of the flow-induced distortion of the pair correlation functions. By considering the distortion of the pair correlations to second order in the flow-rate we show how to systematically correct the DDFT for driven systems. As an application of our approach we consider Poiseuille flow. The theory predicts that the particles will accumulate in spatial regions where the local shear rate is small, an effect known as shear-induced migration. We compare these predictions to Brownian dynamics simulations with generally good agreement. PMID:27115521

  3. Driven colloidal fluids: construction of dynamical density functional theories from exactly solvable limits

    NASA Astrophysics Data System (ADS)

    Scacchi, Alberto; Krüger, Matthias; Brader, Joseph M.

    2016-06-01

    The classical dynamical density functional theory (DDFT) provides an approximate extension of equilibrium DFT to treat nonequilibrium systems subject to Brownian dynamics. However, the method fails when applied to driven systems, such as sheared colloidal dispersions. The breakdown of DDFT can be traced back to an inadequate treatment of the flow-induced distortion of the pair correlation functions. By considering the distortion of the pair correlations to second order in the flow-rate we show how to systematically correct the DDFT for driven systems. As an application of our approach we consider Poiseuille flow. The theory predicts that the particles will accumulate in spatial regions where the local shear rate is small, an effect known as shear-induced migration. We compare these predictions to Brownian dynamics simulations with generally good agreement.

  4. 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.

  5. Landscape pattern dynamic change analysis based on ecohydrological process in the lower reaches of Tarim River, China

    NASA Astrophysics Data System (ADS)

    Huang, Q.; Wang, R. H.; Cheng, Q.; Wu, S. X.

    2006-12-01

    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.

  6. 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.

  7. 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.

  8. 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

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

    NASA Astrophysics Data System (ADS)

    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

    2015-07-01

    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.

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

    PubMed

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

    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

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. Landscape Response to Changes in Dynamic Topography on the U.S. Atlantic Passive Margin

    NASA Astrophysics Data System (ADS)

    Ruetenik, G.; Moucha, R.; Hoke, G. D.

    2014-12-01

    Recent global backwards-in time models of mantle convection have resulted in vastly different interpretations of the transient state of dynamic topography on the U.S. Atlantic passive margin over the past 30 Myr (Moucha et al., 2008; Spacejovic et al., 2008; Rowley et al., 2013; Liu, 2014) . A promising way of benchmarking these geodynamic models is by reconciling them with the observed offshore sedimentary record. However, it is difficult to deconvolve the erosional response produced by changes in dynamic topography from other sources of landscape change because the erosional response is a convolution of dynamic topography changes, tectonic uplift/subsidence, flexural response to erosional unloading and depositional loading, rock properties, and climate. Herein, we present results from a new landscape evolution model that is capable of producing simulations that are required at the scale and resolution necessary to quantify the landscape response to various models of dynamic topographic change on the U.S. Atlantic passive margin in the presence of flexural unloading and loading due to erosion and deposition. We perform a sensitivity study on the effects of geodynamic modeling parameters including effective elastic thickness, climate and rock properties. We find that, while models of dynamic topography are difficult to discern from the available sedimentary record at the scale of the continent in part due to induced topologic (stream geometry) change, at the catchment scale deposition rates are vastly different through time with differing dynamic topography models. At this scale, all models show distinct peaks in deposition rates, and varying elastic thickness has a significant effect on altering the timing of peak deposition.

  16. 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.

  17. 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

  18. Dynamic transcriptome landscape of maize embryo and endosperm development.

    PubMed

    Chen, Jian; Zeng, Biao; Zhang, Mei; Xie, Shaojun; Wang, Gaokui; Hauck, Andrew; Lai, Jinsheng

    2014-09-01

    Maize (Zea mays) is an excellent cereal model for research on seed development because of its relatively large size for both embryo and endosperm. Despite the importance of seed in agriculture, the genome-wide transcriptome pattern throughout seed development has not been well characterized. Using high-throughput RNA sequencing, we developed a spatiotemporal transcriptome atlas of B73 maize seed development based on 53 samples from fertilization to maturity for embryo, endosperm, and whole seed tissues. A total of 26,105 genes were found to be involved in programming seed development, including 1,614 transcription factors. Global comparisons of gene expression highlighted the fundamental transcriptomic reprogramming and the phases of development. Coexpression analysis provided further insight into the dynamic reprogramming of the transcriptome by revealing functional transitions during maturation. Combined with the published nonseed high-throughput RNA sequencing data, we identified 91 transcription factors and 1,167 other seed-specific genes, which should help elucidate key mechanisms and regulatory networks that underlie seed development. In addition, correlation of gene expression with the pattern of DNA methylation revealed that hypomethylation of the gene body region should be an important factor for the expressional activation of seed-specific genes, especially for extremely highly expressed genes such as zeins. This study provides a valuable resource for understanding the genetic control of seed development of monocotyledon plants. PMID:25037214

  19. 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.

  20. 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.

  1. Object-based "dynamic cover types" - a new framework for monitoring landscape-level ecosystem change

    NASA Astrophysics Data System (ADS)

    Dronova, I.; Wang, L.; Gong, P.; Zhong, L.

    2012-12-01

    Traditional analyses of ecosystem change with remote sensing data often focus on transitions between 'static' landscape cover types. However, in dynamic landscapes with frequent disturbance long-term surface trends may be obscured by intermediate shorter-term variation. Availability of high-quality remote sensing data is often inconsistent among change periods, which contributes to the uncertainty in change detection among 'static' classes. Alternatively, we propose Dynamic Cover Types (DCTs) to characterize highly variable areas based on their nested change regimes shaped by climate, phenology and disturbance. We define DCTs as sequences of surface transformations that have distinct temporal trajectories observable across landscapes within a given change period. To illustrate and test this concept, we combined multispectral and microwave satellite imagery to classify DCTs for a large complex seasonally inundated freshwater wetland in China in 2007-2008. Instead of using pixels, we mapped DCTs using object-based image analysis and supervised machine-learning algorithms to characterize common change types based on their spatial and temporal context. Spatial distributions of mapped DCTs simultaneously reflected several key drivers of wetland change, including broad-scale changes in submersion times, vegetation phenology and prevalence of plant cover and localized fine-scale disturbance. We further examined DCT response to a hypothetical scenario of a warmer wetter early spring by substituting spring 2008 images with 2007 ones. In this comparison, the strongest response was detected from DCTs that were closely associated with the water body and represented critical habitat for wintering migratory waterbirds in this area. Results indicate that object-based dynamic class boundaries may provide useful spatial units to highlight characteristic types of landscape change for environmental research, ecosystem monitoring and management considerations.

  2. Linking populations to landscapes: richness scenarios resulting from changes in the dynamics of an ecosystem engineer.

    PubMed

    Wright, Justin P

    2009-12-01

    Predicting the effects of the loss of individual species on diversity represents one of the primary challenges facing community ecology. One pathway by which organisms of one species affect the distribution of species is ecosystem engineering. Changes in the dynamics of ecosystem engineers that lead to changes in the distribution of the patches of altered habitat are likely to lead to changes in diversity. I link data on the distribution of plant species found in the riparian zone of the Adirondacks (New York, USA) in patches modified by beaver and in unmodified forest patches to a model connecting the dynamics of ecosystem engineers to the dynamics of the patches that they create. These analyses demonstrate that changes in key parameters of the model, such as decreases in beaver colonization rates and rate of patch abandonment, lead to changes in species richness of up to 45% at the landscape scale, and that these changes are likely to occur over long time scales. This general approach of linking the population dynamics or behavior of a single species to changes in species richness at the landscape scale provides a means for both testing the importance of ecosystem engineering in different systems and developing scenarios to predict how changes in the dynamics of a single species are likely to affect species richness. PMID:20120810

  3. The Marsden-Weinstein Reduction Structure of Integrable Dynamical Systems and a Generalized Exactly Solvable Quantum Superradiance Model

    NASA Astrophysics Data System (ADS)

    Bogolubov, N. N.; Prykarpatsky, Y. A.

    2013-03-01

    An approach to describing nonlinear Lax type integrable dynamical systems of modern mathematical and theoretical physics, based on the Marsden-Weinstein reduction method on canonically symplectic manifolds with group symmetry, is proposed. Its natural relationship with the well-known Adler-Kostant-Souriau-Berezin-Kirillov method and the associated R-matrix approach is analyzed. A new generalized exactly solvable spatially one-dimensional quantum superradiance model, describing a charged fermionic medium interacting with external electromagnetic field, is suggested. The Lax type operator spectral problem is presented, the related R-structure is calculated. The Hamilton operator renormalization procedure subject to a physically stable vacuum is described, the quantum excitations and quantum solitons, related with the thermodynamical equilibrity of the model, are discussed.

  4. Solvation force induced by short range, exact dissipative particle dynamics effective surfaces on a simple fluid and on polymer brushes.

    PubMed

    Goicochea, Armando Gama; Alarcón, Francisco

    2011-01-01

    The thermodynamic properties of a simple fluid confined by effective wall forces are calculated using Monte Carlo simulations in the grand canonical ensemble. The solvation force produced by polymer brushes of two different lengths is obtained also. For the particular type of model interactions used, known as the dissipative particle dynamics method, we find that it is possible to obtain an exact, simple expression for the effective force induced by a planar wall composed of identical particles that interact with those in the fluid. We show that despite the short range of all forces in the model, the solvation force can be finite at relatively large distances and therefore does not depend only on the range of the interparticle or solvent-surface forces. As for the polymer brushes, we find that the shape of the solvation force profiles is in fair agreement with scaling and self-consistent field theories. The applications and possible extensions of this work are discussed. PMID:21219016

  5. 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.

  6. 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. PMID:26057724

  7. 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.

  8. 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.

  9. Gene expression dynamics with stochastic bursts: Construction and exact results for a coarse-grained model

    NASA Astrophysics Data System (ADS)

    Lin, Yen Ting; Doering, Charles R.

    2016-02-01

    We present a theoretical framework to analyze the dynamics of gene expression with stochastic bursts. Beginning with an individual-based model which fully accounts for the messenger RNA (mRNA) and protein populations, we propose an expansion of the master equation for the joint process. The resulting coarse-grained model reduces the dimensionality of the system, describing only the protein population while fully accounting for the effects of discrete and fluctuating mRNA population. Closed form expressions for the stationary distribution of the protein population and mean first-passage times of the coarse-grained model are derived and large-scale Monte Carlo simulations show that the analysis accurately describes the individual-based process accounting for mRNA population, in contrast to the failure of commonly proposed diffusion-type models.

  10. Free-energy calculation via mean-force dynamics using a logarithmic energy landscape.

    PubMed

    Morishita, Tetsuya; Itoh, Satoru G; Okumura, Hisashi; Mikami, Masuhiro

    2012-06-01

    A method for free-energy calculation based on mean-force dynamics (fictitious dynamics on a potential of mean force) is presented. The method utilizes a logarithmic form of free energy to enhance crossing barriers on a free-energy landscape, which results in efficient sampling of "rare" events. Invoking a conserved quantity in mean-force dynamics, free energy can be estimated on-the-fly without postprocessing. This means that an estimate of the free-energy profile can be locally made in contrast to the other methods based on mean-force dynamics such as metadynamics. The method is benchmarked against conventional methods and its high efficiency is demonstrated in the free-energy calculation for a glycine dipeptide molecule. PMID:23005238

  11. Dynamical phase transitions reveal amyloid-like states on protein folding landscapes.

    PubMed

    Weber, Jeffrey K; Jack, Robert L; Schwantes, Christian R; Pande, Vijay S

    2014-08-19

    Developing an understanding of protein misfolding processes presents a crucial challenge for unlocking the mysteries of human disease. In this article, we present our observations of β-sheet-rich misfolded states on a number of protein dynamical landscapes investigated through molecular dynamics simulation and Markov state models. We employ a nonequilibrium statistical mechanical theory to identify the glassy states in a protein's dynamics, and we discuss the nonnative, β-sheet-rich states that play a distinct role in the slowest dynamics within seven protein folding systems. We highlight the fundamental similarity between these states and the amyloid structures responsible for many neurodegenerative diseases, and we discuss potential consequences for mechanisms of protein aggregation and intermolecular amyloid formation. PMID:25140433

  12. From Understanding the Development Landscape of the Canonical Fate-Switch Pair to Constructing a Dynamic Landscape for Two-Step Neural Differentiation

    PubMed Central

    2012-01-01

    Abstract 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. PMID:23300518

  13. Dynamic Landscape Connectivity, Threshold Behavior, and Scaling Frameworks for Hydrologic and Bio-geochemical Fluxes

    NASA Astrophysics Data System (ADS)

    Foufoula, E.; Zanardo, S.; Danesh-Yazdi, M.; Zaliapin, I.; Power, M.; Dietrich, W.

    2012-12-01

    The hydrologic connectivity of landscapes (the surface fluvial and non-fluvial flowpaths and the flowpaths in the sub-surface) is temporally and spatially changing as dictated by landscape features and precipitation. Developing simple conceptual frameworks for quantifying the response of a basin (hydrologic, sedimentologic, and bio-geochemical) based on theories of network dynamics is still an open problem with slow progress. In this talk two issues will be addressed: (1) scaling of peak flows in response to space-time variable rainfall of duration smaller than the time of concentration of the basin, and (2) predictive modeling and scaling of bio-geochemical fluxes using a spatially explicit model of light and nutrient availability, streamflow, and temperature on the connected network. Data from the Walnut Gulch watershed and the Eel river at Angelo Coast Range Reserve are used for model development and testing.

  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. 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. PMID:23935916

  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. PMID:26663622

  20. 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

  1. 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

  2. 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.

  3. 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

  4. 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

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

    NASA Astrophysics Data System (ADS)

    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.

  6. Impacts of Climate Change on Landscape Dynamics in the US Southeast

    NASA Astrophysics Data System (ADS)

    Costanza, J. K.; Earnhardt, T.; Terando, A. J.; Hulcr, J.; McKerrow, A.

    2010-12-01

    Predicting the potential impacts of climate change on ecosystems is increasingly important for developing mitigation and adaptation strategies. In particular, climate change is likely to significantly affect disturbance dynamics, which have consequences for ecosystems. In forested ecosystems of the Southeast US, two important types of disturbances are wildfires and insect outbreaks. As part of the USGS’s Southeast Regional Assessment Project (SERAP), we examined those disturbances in the context of climate change through 2060 on the landscape of the Ichawaynochaway watershed on the coastal plain of Georgia. In the Ichawaynochaway, we asked: (1) How do wildfires and Southern Pine Beetle (SPB) outbreaks impact the landscape? and (2) How will climate change modify these impacts in the future? To project landscape dynamics, we used TELSA, a spatially-explicit model of ecological succession and disturbance. We measured changes in the landscape in terms of the vegetation state, which is a combination of successional stage (early-, mid-, or late-succession) and vegetation structure (open or closed canopy) for each ecosystem. We based wildfire and SPB outbreak probabilities on recent empirical data from the Ichawaynochaway area. To examine the effect of climate, for both wildfire and SPB outbreaks, we developed an empirical relationship between past climate and each of the disturbances. We projected those relationships to 2060 under current climate, as well as under the Intergovernmental Panel on Climate Change (IPCC) A1FI emission scenario using an ensemble of downscaled Global Climate Model (GCM) output. Our results show that under current climate, wildfire activity and SPB outbreaks have less of an impact on the landscape than they likely will under climate change. In particular, these results suggest that open, mature stands of longleaf pine, a fire-dependent habitat that is less susceptible to SPB outbreaks, is likely to be favored under future change. In contrast

  7. 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

  8. 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.

  9. 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

  10. Effects of Local and Landscape Factors on Population Dynamics of a Cotton Pest

    PubMed Central

    Carrière, Yves; Goodell, Peter B.; Ellers-Kirk, Christa; Larocque, Guillaume; Dutilleul, Pierre; Naranjo, Steven E.; Ellsworth, Peter C.

    2012-01-01

    Background Many polyphagous pests sequentially use crops and uncultivated habitats in landscapes dominated by annual crops. As these habitats may contribute in increasing or decreasing pest density in fields of a specific crop, understanding the scale and temporal variability of source and sink effects is critical for managing landscapes to enhance pest control. Methodology/Principal Findings We evaluated how local and landscape characteristics affect population density of the western tarnished plant bug, Lygus hesperus (Knight), in cotton fields of the San Joaquin Valley in California. During two periods covering the main window of cotton vulnerability to Lygus attack over three years, we examined the associations between abundance of six common Lygus crops, uncultivated habitats and Lygus population density in these cotton fields. We also investigated impacts of insecticide applications in cotton fields and cotton flowering date. Consistent associations observed across periods and years involved abundances of cotton and uncultivated habitats that were negatively associated with Lygus density, and abundance of seed alfalfa and cotton flowering date that were positively associated with Lygus density. Safflower and forage alfalfa had variable effects, possibly reflecting among-year variation in crop management practices, and tomato, sugar beet and insecticide applications were rarely associated with Lygus density. Using data from the first two years, a multiple regression model including the four consistent factors successfully predicted Lygus density across cotton fields in the last year of the study. Conclusions/Significance Our results show that the approach developed here is appropriate to characterize and test the source and sink effects of various habitats on pest dynamics and improve the design of landscape-level pest management strategies. PMID:22768147

  11. 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

  12. ES4LUCC: A GIS-tool for remotely monitoring landscape dynamics

    NASA Astrophysics Data System (ADS)

    Forzieri, Giovanni; Battistini, Alessandro; Catani, Filippo

    2012-12-01

    Given the potential impacts of land cover changes on surface processes, accurate mapping of landscape dynamics is a crucial task in environmental monitoring. The use of commercial software for remote sensing of landscape changes requires appropriate expertise in sensor technology and computing resources that are not always available to decision makers. This paper presents the development of an experimental prototype of a lightweight and user-friendly GIS tool - ES4LUCC - a semiautomatic software for change detection and classification of land use/cover. The tool is based on image processing techniques applied on multi-temporal remotely sensed spectral and surface model data. The GIS-based tiling approach allows to non-specialists of remote sensing to manage high-dimensional data even from low performance computing platforms. The paper synthesizes the implemented digital image processing that form the basis of ES4LUCC, including data correction, classification and change detection, map refinements. It also describes the software architecture, the main IDL modules and the integration with GIS through a tight coupling approach and.dll calling functions. The main modelling process is controlled through a powerful GUI developed as part of the ArcMap component of ESRI ArcGIS. The software is tested by using bi-temporal color-infrared ADS40 and Light detection and ranging data acquired on a 80-km transect of the Marecchia river (Italy). The outputs of ES4LUCC give an understanding of the natural- and human-induced surface processes, such as urban planning, agricultural and forest practices, fluvial dynamics and slope instability. The model provides reliable maps (90.77% overall classification accuracy) that represent useful layers for environmental landscape management.

  13. 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.

  14. 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

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

    PubMed

    Rai, Taranjit Singh; 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; Adams, Peter D

    2014-12-15

    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

  16. 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.

  17. 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

  18. [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

  19. 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.

  20. 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

  1. Exploration of the Energy Landscape of Acetylcholinesterase by Molecular Dynamics Simulation.

    NASA Astrophysics Data System (ADS)

    McCammon, J. Andrew

    2002-03-01

    Proteins have rough energy landscapes. Often more states than just the ground state are occupied and have biological functions. It is essential to study these conformational substates and the dynamical transitions among them. Acetylcholinesterase (AChE) is an important enzyme that has biological functions including the termination of synaptic transmission signals. X-ray structures show that it has an active site that is accessible only via a long and narrow channel from its surface. Therefore the fact that acetylcholine and larger ligands can reach the active site is believed to reflect the protein's structural fluctuation. We carried out long molecular dynamics simulations to investigate the dynamics of AChE and its relation to biological function, and compared our results with experiments. The results reveal several "doors" that open intermittantly between the active site and the surface. Instead of having simple exponential decay correlation functions, the time series of these channels reveal complex, fractal gating between conformations. We also compared the AChE dynamics data with those from an AchE-fasciculin complex. (Fasciculin is a small protein that is a natural inhibitor of AChE.) The results show remarkable effects of the protein-protein interaction, including allosteric and dynamical inhibition by fasciculin besides direct steric blocking. More information and images can be found at http://mccammon.ucsd.edu

  2. Detecting and comparing static and dynamic gaps in a western Amazonian tropical forest landscape

    NASA Astrophysics Data System (ADS)

    Marvin, D.; Asner, G. P.; Anderson, C. B.; Knapp, D. E.; Martin, R.; Vaughn, N.

    2014-12-01

    Spatial and temporal variation in forest structure is a central aspect of tropical forest carbon dynamics. A major determinant of forest structure is the size and frequency of natural forest disturbance events. The resulting forest gaps are direct expressions of tree mortality, damage, and regrowth, and play integral roles in community structure and forest carbon storage. Static forest gaps, or those found at a single timeframe, express the time-integrated pattern of both past disturbance and forest regrowth. Dynamic gaps, or those appearing between two measurement periods, reflect committed carbon losses to the atmosphere. Studies of tropical forest disturbance often examine only static gaps to make inferences about annual carbon dynamics. Our goal was to determine whether the use of static gaps rather than dynamic gaps is appropriate for quantifying annual carbon flux. Using airborne LiDAR data collected by the Carnegie Airborne Observatory at two time periods (2011 and 2012) and a new gap detection technique, we compared static and dynamic gaps over a 9000 ha lowland tropical forest in southeastern Colombia. We find static gaps are present across the landscape at 1.6 gaps ha-1, while dynamic gaps are present at 0.5 gaps ha-1. Moreover, 60% of these dynamic gaps are connected to pre-existing gaps (i.e., gap edge expansion), with new isolated gaps making up just 0.2 gaps ha-1. The lower density of dynamic gaps suggests studies using static gaps may overestimate the amount of tropical forest carbon lost annually to natural disturbance.

  3. 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.

  4. 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

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

    PubMed

    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

  6. 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

  7. 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.

  8. Directed Magnetic Particle Transport above Artificial Magnetic Domains Due to Dynamic Magnetic Potential Energy Landscape Transformation.

    PubMed

    Holzinger, Dennis; Koch, Iris; Burgard, Stefan; Ehresmann, Arno

    2015-07-28

    An approach for a remotely controllable transport of magnetic micro- and/or nanoparticles above a topographically flat exchange-bias (EB) thin film system, magnetically patterned into parallel stripe domains, is presented where the particle manipulation is achieved by sub-mT external magnetic field pulses. Superparamagnetic core-shell particles are moved stepwise by the dynamic transformation of the particles' magnetic potential energy landscape due to the external magnetic field pulses without affecting the magnetic state of the thin film system. The magnetic particle velocity is adjustable in the range of 1-100 μm/s by the design of the substrate's magnetic field landscape (MFL), the particle-substrate distance, and the magnitude of the applied external magnetic field pulses. The agglomeration of magnetic particles is avoided by the intrinsic magnetostatic repulsion of particles due to the parallel alignment of the particles' magnetic moments perpendicular to the transport direction and parallel to the surface normal of the substrate during the particle motion. The transport mechanism is modeled by a quantitative theory based on the precise knowledge of the sample's MFL and the particle-substrate distance. PMID:26134922

  9. 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

  10. Embedding reach-scale fluvial dynamics within the CAESAR cellular automaton landscape evolution model

    NASA Astrophysics Data System (ADS)

    Van De Wiel, Marco J.; Coulthard, Tom J.; Macklin, Mark G.; Lewin, John

    2007-10-01

    We introduce a new computational model designed to simulate and investigate reach-scale alluvial dynamics within a landscape evolution model. The model is based on the cellular automaton concept, whereby the continued iteration of a series of local process 'rules' governs the behaviour of the entire system. The model is a modified version of the CAESAR landscape evolution model, which applies a suite of physically based rules to simulate the entrainment, transport and deposition of sediments. The CAESAR model has been altered to improve the representation of hydraulic and geomorphic processes in an alluvial environment. In-channel and overbank flow, sediment entrainment and deposition, suspended load and bed load transport, lateral erosion and bank failure have all been represented as local cellular automaton rules. Although these rules are relatively simple and straightforward, their combined and repeatedly iterated effect is such that complex, non-linear geomorphological response can be simulated within the model. Examples of such larger-scale, emergent responses include channel incision and aggradation, terrace formation, channel migration and river meandering, formation of meander cutoffs, and transitions between braided and single-thread channel patterns. In the current study, the model is illustrated on a reach of the River Teifi, near Lampeter, Wales, UK.

  11. [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

  12. 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

  13. 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

  14. 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.

  15. Emergent Behavior in Slow-Fast Landscape-Climate Dynamics: Evidence from Spatiotemporal Flood Statistics and a Nonlinear Dynamical Model of Coevolution.

    NASA Astrophysics Data System (ADS)

    Perdigão, R. A. P.; Bloeschl, G.

    2014-12-01

    Emergent features of landscape-climate coevolution are evaluated on the basis of the sensitivity of floods to annual precipitation in space and time. For that purpose, a spatiotemporal sensitivity analysis is performed at regional scale using data from 804 catchments in Austria from 1976 to 2008. Results show that flood peaks are more responsive to spatial (regional) than to temporal (decadal) variability. Space-wise a 10% increase in precipitation leads to a 23% increase in flood peaks in Austria, whereas timewise a 10% increase in precipitation leads to an increase of just 6% in flood peaks. Catchments from dry lowlands and high wetlands exhibit similarity between the spatial and temporal sensitivities (spatiotemporal symmetry) and low landscape-climate codependence. This suggests that such regions are not coevolving significantly. However, intermediate regions show differences between those sensitivities (symmetry breaks) and higher landscape-climate codependence, suggesting undergoing coevolution. The break of symmetry is considered an emergent behavior of the coupled system. A new coevolution index is then proposed relating spatiotemporal symmetry with relative characteristic celerities. The descriptive assessment of coevolution is complemented by a simple nonlinear dynamical model of landscape-climate coevolution, in which landform evolution processes take place at the millennial scale (slow dynamics), and climate adjusts in years to decades (fast dynamics). Coevolution is expressed by the interplay between slow and fast dynamics, represented, respectively, by spatial and temporal characteristics. The model captures key features of the joint landscape-climate distribution, supporting the descriptive assessment. This paper ultimately brings to light signatures of coevolution that arise from the nonlinear coupling of the landscape-climate system at slow and fast time scales. The presented work builds on Perdigão and Blöschl (2014). Perdigão, R. A. P., and G

  16. 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...

  17. 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

  18. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    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.

  20. 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

  1. Determination of the Dynamic Stresses in an Infinite Plate on the Basis of an Exact Analytical Solution of the Hyperbolic Heat-Conduction Equation for It

    NASA Astrophysics Data System (ADS)

    Kudinov, I. V.; Kudinov, V. A.

    2015-03-01

    With the use of an exact analytical solution of the classical hyperbolic heat-conduction equation, derived on the basis of the Maxwell-Cattaneo-Luikov relaxation formula, an exact analytical solution of the problem on the dynamic thermoelasticity of an infinite plate was obtained for the case where the outer surfaces of this plate are free of mechanical loads. It is shown that the undamped thermoelastic stresses in this plate vary spasmodically in time with periodic change in their sign. The stress jumps arising near the opposite outer surfaces of the indicated plate move along the spatial variable to its center where they superimpose, with the result that the dynamic thermal stresses in the plate double.

  2. Human-induced landscape dynamics in South Brandenburg - findings from different geoarchives

    NASA Astrophysics Data System (ADS)

    Raab, Thomas; Raab, Alexandra; Nicolay, Alexander; Takla, Melanie; Hirsch, Florian; Schneider, Anna; Rösler, Horst; Bönisch, Eberhard

    2014-05-01

    South Brandenburg is the central part of the North European Lowland (NEL) extending as a plain landscape from the North and Baltic Sea to the foothills of the Central European Highlands and reaching from the Netherlands to Poland. Since many decades lignite opencast mines have been operating in this region which is known as the Lusatian mining district. The total land demand in Lusatia is about 852 square kilometres and mining will continue for many more years or even decades. Large-scale outcrops resulting from these mining activities are excellent archives to study the younger Earth's history. The scope of our research in open cast mines is to reconstruct the Late Quaternary landscape development and to distinguishing natural from anthropogenic forcing and processes. In more detail, the aims are to identify and to quantify the impact of past land uses, i.e. changes of vegetation, landforms and soils induced by agriculture and/or forestry. Here, we are presenting latest results from our research and review important findings giving novel insights into man-induced environmental changes in Lusatia within the past thousands years and thus improving the general understanding of Late Quaternary landscape dynamics. Direct legacies of historical farming can be found in form of hook ploughs as well as ridge and furrow systems. Several sites have been documented within the last decades giving us nowadays a quite solid picture of the type and of the spatio-temporal dimension the former agricultural system. During years Airborne Laser Scanning (ALS) data help us to identify ridge and furrow systems under forest canopy and thus to support these findings. Sometimes hook ploughs and ridge and furrow systems are found buried under aeolian sediments proving a causal connection between farming and wind erosion. Obviously the well-drained, sandy and humus-poor soils are prone to dry out easily by agricultural overuse and thus can be eroded by wind. The flat landscape and missing

  3. 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.

  4. 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

  5. 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

  6. Dynamic metropolitan landscapes: Residential development and vegetation change in the U.S

    NASA Astrophysics Data System (ADS)

    Jantz, Patrick Arthur

    Residential development is now a major contributor to land surface change in the U.S. From 1990 - 2000, over thirteen million housing units were added to the nation's housing stock which stood at 102.3 million in 1990. Another 15.8 million housing units were added from 2000 - 2010. Of particular concern is the ongoing increase in low-density residential development because of its large resource footprint and biodiversity impacts. In this dissertation I pose three broad questions 1) What were the trends in residential development in the U.S. from 1990 - 2000? 2) What were the trends in rural conversion to low-density residential use from 1990 - 2000 in the Mid-Atlantic and the Pacific Northwest and what social and environmental factors help explain these trends? 3) What were the effects of rural conversion to residential use on vegetation productivity in the Mid-Atlantic and the Pacific Northwest from 2000 - 2010? To answer these questions I created a database derived from U.S. Census blocks that allows for interdecadal comparison of recent housing density change in support of spatial demographic research. In a series of GIS based analyses I used the database to map changes in metropolitan housing density distributions in the Mid-Atlantic and western Washington regions and used a satellite derived index of vegetation productivity to assess the impacts of housing growth on vegetation carbon uptake. Results indicate that residential housing growth is more dynamic than previously thought and established approaches for mapping housing density tend to underestimate the local intensity of residential change. In the Mid-Atlantic and western Washington, low-density residential development is affecting large fractions of rural landscapes in metropolitan areas. The strongest correlates of low-density conversion of rural landscapes were population growth and extent of protected lands, suggesting future directions for modeling the drivers of rural conversion. Residential

  7. 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

  8. 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.

  9. 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.

  10. Study on the Dynamics of Influenza Hemagglutinin Based on Energy Landscape Theory

    NASA Astrophysics Data System (ADS)

    Lin, Xingcheng; Eddy, Nathanial; Noel, Jeffrey; Whitford, Paul; Ma, Jianpeng; Onuchic, Jose

    2014-03-01

    Hemagglutinin (HA2), a homotrimeric influenza surface protein crucial for membrane fusion, undergoes an drastic structural rearrangement during viral invasion of the host. X-ray crystallography shows that the pre- and post-fusion configurations have largely disparate secondary, tertiary and quaternary structures. Simulations allow us to explore the time-dependent high resolution structural information and function of HA2 dynamics. Here we use an approach based on energy landscape theory that combines the native information from both the starting and end points. Our simulation shows two key events in the conformational transition of HA2: The extension of its fusion peptides away from the viral membrane and the melting of its globular C-terminal portion. The similar timescale and a kinetic competition between these two events lead to two main pathways and generic kinetic intermediates during this transition. Through considering the biological context of HA, we test perturbations of the baseline model that are useful in understanding the robustness of our predictions and how they translate into the function of HA. The all-atom explicit solvent simulation is performed and convince the cracking phenomenon at the start of this protein dynamics. Center for Theoretical Biological Physics.