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. 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

  7. 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.

  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. 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.

  15. 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).

  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

    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.

  19. 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

  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

    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.

  3. 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

  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. 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.

  15. 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.

  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.

    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

  4. 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.

  5. 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.

  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

    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

  16. 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.

  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. 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

  19. 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

  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. 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...

  15. 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 ...

  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. 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

  4. 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.

  5. 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.

  6. 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.

  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. 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

  20. 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.

  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. 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.

  8. 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

  9. 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

  10. 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.

  11. 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.

  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. 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.

  20. 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.

  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. 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

  4. 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.

  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. 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

  11. 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

  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. 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

  1. 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

  2. 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

  3. 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.

  4. 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

  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. 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

  8. 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

  9. 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.

  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. 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.

  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. 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

  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. 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

  20. 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.

  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. [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

  9. 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

  10. 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

  11. 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

  12. 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.

  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 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

  5. 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

  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.

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

    NASA Astrophysics Data System (ADS)

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

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

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

    USGS Publications Warehouse

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

    2011-01-01

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

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

    PubMed

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

    2016-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  15. Landscape-scale Dynamics of Wood in Stream Networks of the Western Cascades, Oregon

    NASA Astrophysics Data System (ADS)

    Czarnomski, N. M.; Dreher, D. M.; Jones, J. A.; Swanson, F. J.

    2006-12-01

    This study develops a network and patchwork dynamics approach to predict wood in a stream network in order to understand wood dynamics in river networks and address riparian reserve design for managed forest landscapes. We examined the effect of four factors on wood sources and transport: (1) forest harvest, removal of wood from streams, and creation of young forest plantations; (2) roads adjacent to or crossing the stream; (3) debris flows in tributary channels; and (4) capacity of the stream to transport wood by fluvial processes (i.e. floods). Wood volumes and numbers of pieces were surveyed along 25 km of 3^{rd}- through 5^{th}-order stream reaches in summer 2002 in a steep forested basin in western Oregon, and related to land use (forest harvest and roads) and fluvial geomorphic processes (debris flows and floods) recorded over the period 1948- 2002. Overall 20,299 pieces of wood with a total volume of 17,688 m3 were measured (averaging 70 m3 per 100m or 80 pieces per 100 m of stream length). Large wood pieces anchored 85% of accumulations, accounting for only 8% of pieces (1468 pieces), but 66% of wood volume (9818 m3). Wood patterns reflect 50-year legacies of land use practices, especially the conversion of old-growth forest to young forest near the stream, and the construction of roads alongside, or crossing, streams. Controlling for stream order, stream segments with adjacent roads had 56%, stream segments with young forest plantations on one side had 34 to 56%, and stream segments with young forest plantations on both sides had 12% of the wood volume found in stream segments adjacent to mature or old-growth forest (150 to 500 yrs). In channels with low fluvial transport wood depletion was localized adjacent to harvest patches, but wood reductions were extensive in channels with high fluvial transport, or where debris flows have entered the mainstem. The configuration of harvest patches, road networks, and stream networks provide a landscape- scale basis

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

    SciTech Connect

    Wu, Wei; Wang, Jin

    2014-09-14

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

  17. Overshooting thunderstorm cloud top dynamics as approximated by a linear Lagrangian parcel model with analytic exact solutions

    NASA Technical Reports Server (NTRS)

    Schlesinger, Robert E.

    1990-01-01

    Results are presented from a linear Lagrangian entraining parcel model of an overshooting thunderstorm cloud top. The model, which is similar to that of Adler and Mack (1986), gives analytic exact solutions for vertical velocity and temperature by representing mixing with Rayleigh damping instead of nonlinearly. Model results are presented for various combinations of stratospheric lapse rate, drag intensity, and mixing strength. The results are compared to those of Adler and Mack.

  18. Quantifying nutrient export and deposition with a dynamic landscape evolution model for the lake Bolsena watershed, Italy

    NASA Astrophysics Data System (ADS)

    Pelorosso, Raffaele; Temme, Arnoud; Gobattoni, Federica; Leone, Antonio

    2010-05-01

    other hand, recent researches have been improving landscape evolution simulation models.. One such model, LAPSUS (LandscApe ProcesS modelling at mUlti-dimensions and Scales, Schoorl et al.,2002; Temme et al., 2009) has been applied to the Lake Bolsena watershed in Lazio, Italy. LAPSUS takes into account erosion as a naturally occurring process in landscape evolution and shapes landscapes by both erosion and deposition allowing interactions at different spatial and temporal resolutions and extents. An integrated approach to quantify nutrient export and deposition at catchment scale is presented and discussed here coupling such a dynamic landscape evolution model (LAPSUS) with the characteristic transport equations for nutrients.

  19. A dynamic landscape model for fish in the Everglades and its application to restoration

    USGS Publications Warehouse

    Gaff, H.D.; DeAngelis, D.L.; Gross, L.J.; Salinas, R.; Shorrosh, M.

    2000-01-01

    A model (ALFISH) for fish functional groups in freshwater marshes of the greater Everglades area of southern Florida has been developed. Its main objective is to assess the spatial pattern of fish densities through time across freshwater marshes. This model has the capability of providing a dynamic measure of the spatially-explicit food resources available to wading birds. ALFISH simulates two functional groups, large and small fish, where the larger ones can prey on the small fish type. Both functional groups are size-structured. The marsh landscape is modeled as 500×500 m spatial cells on a grid across southern Florida. A hydrology model predicts water levels in the spatial cells on 5-day time steps. Fish populations spread across the marsh during flooded conditions and either retreat into refugia (alligator ponds), move to other spatial cells, or die if their cell dries out. ALFISH has been applied to the evaluation of alternative water regulation scenarios under the Central and South Florida Comprehensive Project Review Study. The objective of this Review Study is to compare alternative methods for restoring historical ecological conditions in southern Florida. ALFISH has provided information on which plans are most are likely to increase fish biomass and its availability to wading bird populations.

  20. Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq

    PubMed Central

    Shepard, Peter J.; Choi, Eun-A; Lu, Jente; Flanagan, Lisa A.; Hertel, Klemens J.; Shi, Yongsheng

    2011-01-01

    Alternative polyadenylation (APA) of mRNAs has emerged as an important mechanism for post-transcriptional gene regulation in higher eukaryotes. Although microarrays have recently been used to characterize APA globally, they have a number of serious limitations that prevents comprehensive and highly quantitative analysis. To better characterize APA and its regulation, we have developed a deep sequencing-based method called Poly(A) Site Sequencing (PAS-Seq) for quantitatively profiling RNA polyadenylation at the transcriptome level. PAS-Seq not only accurately and comprehensively identifies poly(A) junctions in mRNAs and noncoding RNAs, but also provides quantitative information on the relative abundance of polyadenylated RNAs. PAS-Seq analyses of human and mouse transcriptomes showed that 40%–50% of all expressed genes produce alternatively polyadenylated mRNAs. Furthermore, our study detected evolutionarily conserved polyadenylation of histone mRNAs and revealed novel features of mitochondrial RNA polyadenylation. Finally, PAS-Seq analyses of mouse embryonic stem (ES) cells, neural stem/progenitor (NSP) cells, and neurons not only identified more poly(A) sites than what was found in the entire mouse EST database, but also detected significant changes in the global APA profile that lead to lengthening of 3′ untranslated regions (UTR) in many mRNAs during stem cell differentiation. Together, our PAS-Seq analyses revealed a complex landscape of RNA polyadenylation in mammalian cells and the dynamic regulation of APA during stem cell differentiation. PMID:21343387

  1. Orientational landscapes of peptides in membranes: prediction of (2)H NMR couplings in a dynamic context.

    PubMed

    Esteban-Martín, Santi; Giménez, Diana; Fuertes, Gustavo; Salgado, Jesús

    2009-12-01

    Unlike soluble proteins, membrane polypeptides face an anisotropic milieu. This imposes restraints on their orientation and provides a reference that makes structure prediction tractable by minimalistic thermodynamic models. Here we use this framework to build orientational distributions of monomeric membrane-bound peptides and to predict their expected solid-state (2)H NMR quadrupolar couplings when labeled at specific side chain positions. Using a complete rigid-body sampling of configurations relative to an implicit lipid membrane, peptide free energy landscapes are calculated. This allows us to obtain probability distributions of the peptide tilt, azimuthal rotation, and depth of membrane insertion. The orientational distributions are broad and originate from an interplay among the three relevant rigid-body degrees of freedom, which allows population of multiple states in shallow free energy minima. Remarkably, only when the orientational distributions are taken into account do we obtain a close correlation between predicted (2)H NMR splittings and values measured in experiments. Such a good correlation is not seen with splittings calculated from single configurations, being either the averaged or the lowest free energy state, showing there are distributions, rather than single structures, that best define the peptide-membrane systems. Moreover, we propose that these distributions contribute to the understanding of the rigid-body dynamics of the system. PMID:19860438

  2. Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer.

    PubMed

    Bindea, Gabriela; Mlecnik, Bernhard; Tosolini, Marie; Kirilovsky, Amos; Waldner, Maximilian; Obenauf, Anna C; Angell, Helen; Fredriksen, Tessa; Lafontaine, Lucie; Berger, Anne; Bruneval, Patrick; Fridman, Wolf Herman; Becker, Christoph; Pagès, Franck; Speicher, Michael R; Trajanoski, Zlatko; Galon, Jérôme

    2013-10-17

    The complex interactions between tumors and their microenvironment remain to be elucidated. Combining large-scale approaches, we examined the spatio-temporal dynamics of 28 different immune cell types (immunome) infiltrating tumors. We found that the immune infiltrate composition changed at each tumor stage and that particular cells had a major impact on survival. Densities of T follicular helper (Tfh) cells and innate cells increased, whereas most T cell densities decreased along with tumor progression. The number of B cells, which are key players in the core immune network and are associated with prolonged survival, increased at a late stage and showed a dual effect on recurrence and tumor progression. The immune control relevance was demonstrated in three endoscopic orthotopic colon-cancer mouse models. Genomic instability of the chemokine CXCL13 was a mechanism associated with Tfh and B cell infiltration. CXCL13 and IL21 were pivotal factors for the Tfh/B cell axis correlating with survival. This integrative study reveals the immune landscape in human colorectal cancer and the major hallmarks of the microenvironment associated with tumor progression and recurrence. PMID:24138885

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

    USGS Publications Warehouse

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Mertens, Benoît; Lambin, Eric

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

  5. Dynamic transition of transcription and chromatin landscape during fission yeast adaptation to glucose starvation.

    PubMed

    Oda, Arisa; Takemata, Naomichi; Hirata, Yoshito; Miyoshi, Tomoichiro; Suzuki, Yutaka; Sugano, Sumio; Ohta, Kunihiro

    2015-05-01

    Shortage of glucose, the primary energy source for all organisms, is one of the most critical stresses influencing cell viability. Glucose starvation promptly induces changes in mRNA and noncoding RNA (ncRNA) transcription. We previously reported that glucose starvation induces long ncRNA (lncRNA) transcription in the 5' segment of a fission yeast gluconeogenesis gene (fbp1+), which leads to stepwise chromatin alteration around the fbp1+ promoter and to subsequent robust gene activation. Here, we analyzed genomewide transcription by strand-specific RNA sequencing, together with chromatin landscape by immunoprecipitation sequencing (ChIP-seq). Clustering analysis showed that distinct mRNAs and ncRNAs are induced at the early, middle and later stages of cellular response to glucose starvation. The starvation-induced transcription depends substantially on the stress-responsive transcription factor Atf1. Using a new computer program that examines dynamic changes in expression patterns, we identified ncRNAs with similar behavior to the fbp1+ lncRNA. We confirmed that there are continuous lncRNAs associated with local reduction of histone density. Overlapping with the regions for transcription of these lncRNAs, antisense RNAs are antagonistically transcribed under glucose-rich conditions. These results suggest that Atf1-dependent integrated networks of mRNA and lncRNA govern drastic changes in cell physiology in response to glucose starvation. PMID:25728061

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

    PubMed Central

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

    2016-01-01

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

  7. Exploring the String Landscape: The Dynamics, Statistics, and Cosmology of Parallel Worlds

    NASA Astrophysics Data System (ADS)

    Ahlqvist, Stein Pontus

    This dissertation explores various facets of the low-energy solutions in string theory known as the string landscape. Three separate questions are addressed - the tunneling dynamics between these vacua, the statistics of their location in moduli space, and the potential realization of slow-roll inflation in the flux potentials generated in string theory. We find that the tunneling transitions that occur between a certain class of supersymmetric vacua related to each other via monodromies around the conifold point are sensitive to the details of warping in the near-conifold regime. We also study the impact of warping on the distribution of vacua near the conifold and determine that while previous work has concluded that the conifold point acts as an accumulation point for vacua, warping highly dilutes the distribution in precisely this regime. Finally we investigate a novel form of inflation dubbed spiral inflation to see if it can be realized near the conifold point. We conclude that for our particular models, spiral inflation seems to rely on a de Sitter-like vacuum energy. As a result, whenever spiral inflation is realized, the inflation is actually driven by a vacuum energy.

  8. Belowground Water Dynamics Under Contrasting Annual and Perennial Plant Communities in an Agriculturally-Dominated Landscape

    NASA Astrophysics Data System (ADS)

    Mora, G.; Asbjornsen, H.; Helmers, M. J.; Shepherd, G. W.

    2005-12-01

    The conversion from grasslands and forests to row-crops in the Midwest has affected soil water cycling because plant characteristics are one of the main parameters determining soil storage capacity, infiltration rates, and surface runoff. Little is known, however, about the extent of modification of soil water dynamics under different plant communities. To address this important issue, we are documenting soil water dynamics under contrasting perennial and annual plant communities in an agriculturally-dominated landscape. Measurements of soil moisture and depths of uptake of source water were obtained for six vegetative cover types (corn and soybean field, brome pasture, degraded savanna, restored savanna, and restored prairie) at the Neal Smith National Wildlife Refuge in Prairie City, Iowa. The depths of uptake of soil water were determined on the basis of oxygen isotope composition of soil water and stem water. Measurements were performed once a month during an entire growing season. Preliminary results indicate that soil water present under the different vegetation types show similar profiles with depth during the dry months. Soil water in the upper 5 cm is enriched in oxygen-18 by about 5 per mil relative to soil water at 100 cm. Our preliminary results also indicate that the isotopic composition of stem water from annual plants is typically higher by about 2 per mil relative to that of stem water from perennial plants during the dry period. Whereas the oxygen isotopic composition for corn stem water is -5.49 per mil, that for elm and oak stem water is -7.62 and -7.51 per mil, respectively. The higher isotope values for corn suggest that annual crop plants are withdrawing water from shallower soil horizons relative to perennial plants. Moreover, our preliminary data suggest lower moisture content in soil under annual plant cover. We propose that the presence of deeper roots in the perennial vegetation allows these plants to tap into deeper water sources when

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

    USGS Publications Warehouse

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

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  13. Closed-form exact solution to H(infinity) optimization of dynamic vibration absorbers: II. Application to different performance indexes for vibration isolation

    NASA Astrophysics Data System (ADS)

    Asami, Toshihiko; Nishihara, Osamu

    2000-04-01

    Recently, Nishihara and Matsuhisa have proposed a new theory for attaining the H(infinity) optimization of a dynamic vibration absorber (DVA) in the linear vibratory systems. The H(infinity) optimization of DVA is a classical optimization problem, and already solved more than 50 years ago. All of us know the solution through the textbook written by Den Hartog. The new theory proposed them gives us the exact algebraic solution of the problem. In the first report, we have expounded the theory and showed the procedure of finding the algebraic solution to a typical performance index (compliance transfer function) of the viscous damped system. In this paper, we will apply this theory to another performance indexes: mobility and accelerance transfer functions for force excitation system, and the absolute and relative displacement responses to acceleration, velocity or displacement input to foundation for motion excitation system. We apply this theory not only the viscous damped system but also the hysteretic damped system. As a result, we found the closed-form exact solutions in every performance indexes when the primary system has no damping. The solutions obtained here are compared with the classical ones solved by the fixed-points theory. We further apply this theory to design of DVAs attached to damped primary systems, and found the closed-form exact solutions to some performance indexes of the hysteretic damped system.

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

    PubMed

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

    2010-12-01

    In this paper, three-dimensional building information was extracted from high resolution satellite image based on Barista software. Combined with ArcGIS software, the dynamic changes of the building landscape in Tiexi District of Shenyang City during urban renewal process were analyzed from the conversion contribution rate, building density, average building height, and built-up area rate. It was found that during this urban renewal process, four dominant landscape types (vacant lot, residential building, industrial building, and road) were the main parts of the landscape changes. The areas of vacant lot, residential building, commercial building, and road increased, while that of industrial building decreased. The building density decreased, while the average building height increased. There was an obvious regional variation in building landscape. The building density in industrial district was higher than that in residential district, while the average building height was in adverse. The further from the city center, the lower the building density and building average height. PMID:21442996

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

    NASA Astrophysics Data System (ADS)

    Carniello, L.; D'Alpaos, A.

    2014-12-01

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

  16. Energy Landscape of Chelated Uranyl: Antibody Interactions by Dynamic Force Spectroscopy

    PubMed Central

    Odorico, Michael; Teulon, Jean-Marie; Bessou, Thérèse; Vidaud, Claude; Bellanger, Laurent; Chen, Shu-wen W.; Quéméneur, Éric; Parot, Pierre; Pellequer, Jean-Luc

    2007-01-01

    We used dynamic force spectroscopy (DFS) to explore the energy landscape of interactions between a chelated uranyl compound and a monoclonal antibody raised against the uranyl-dicarboxy-phenanthroline complex. We estimated the potential energy barrier widths and the relevant thermodynamic rate constants along the dissociation coordinate. Using atomic force microscopy, four different experimental setups with or without the uranyl ion in the chelate ligand, we have distinguished specific and nonspecific binding in the binding affinity of the uranyl compound to the antibody. The force loading rates for our system were measured from 15 to 26,400 pN/s. The results showed two regimes in the plot of the most probable unbinding force versus the logarithm of the loading rate, revealing the presence of two (at least) activation barriers. Analyses of DFS suggest parallel multivalent binding present in either regime. We have also built a molecular model for the variable fragment of the antibody and used computational graphics to dock the chelated uranyl ion into the binding pocket. The structural analysis led us to hypothesize that the two regimes originate from two interaction modes: the first one corresponds to an energy barrier with a very narrow width of 0.5 ± 0.2 Å, inferring dissociation of the uranyl ion from its first coordination shell (Asp residue); the second one with a broader energy barrier width (3.9 ± 0.3 Å) infers the entire chelate compound dissociated from the antibody. Our study highlights the sensitivity of DFS experiments to dissect protein-metal compound interactions. PMID:17449661

  17. Dynamics and functions of wetlands in different hydrological basins and landscapes

    NASA Astrophysics Data System (ADS)

    Destouni, G.

    2012-12-01

    This paper presents and synthesizes regional investigations of wetlands, and their change dynamics and ecosystem services as elements of hydrological basins in different types of landscapes. Starting from the Arctic, thermokarst lakes and wetlands represent here primary change responders to permafrost degradation caused by recent warming. To assess such change responses, in terms of the presence and distribution of thermokarst lakes and wetlands, we have used remotely sensed imagery in conjunction with long-term, catchment-wise water balance analysis of the Nadym and Pur river basins in Western Siberia, identifying hydrological change indicators of thermokarst lake-wetland responses to permafrost thawing. With regard to lake size and size distribution, we found that lakes-wetlands of or smaller than ~50 ha have decreased more than larger lakes over the period 1987-2010. Continuing further south to Swedish hydrological basins with major contributions to water quality changes in the Baltic Sea, wetland and lake systems represent here potential regulators of such changes, providing opportunities for basin-scale nutrient and pollutant load abatement. To assess these opportunities, we have investigated nutrient loads from the main Norrström basin and surrounding smaller catchments within the Swedish water management district Northern Baltic Proper, and heavy metal loading from the Dalälven River basin and its major mining areas. Results quantify wetland potential for reducing expected basin-scale loads, as well as reducing uncertainty in and cost of load abatement, and emphasize some main research questions for further investigation regarding this potential and the possibilities to realize it in different hydrological catchments.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

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

    PubMed

    Martirosyan, A; Saakian, David B

    2011-08-01

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

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

    NASA Astrophysics Data System (ADS)

    Waltl, Peter; Schwindt, Daniel; Völkel, Jörg

    2016-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

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

  5. Land use, water and Mediterranean landscapes: modelling long-term dynamics of complex socio-ecological systems.

    PubMed

    Barton, C Michael; Ullah, Isaac I; Bergin, Sean

    2010-11-28

    The evolution of Mediterranean landscapes during the Holocene has been increasingly governed by the complex interactions of water and human land use. Different land-use practices change the amount of water flowing across the surface and infiltrating the soil, and change water's ability to move surface sediments. Conversely, water amplifies the impacts of human land use and extends the ecological footprint of human activities far beyond the borders of towns and fields. Advances in computational modelling offer new tools to study the complex feedbacks between land use, land cover, topography and surface water. The Mediterranean Landscape Dynamics project (MedLand) is building a modelling laboratory where experiments can be carried out on the long-term impacts of agropastoral land use, and whose results can be tested against the archaeological record. These computational experiments are providing new insights into the socio-ecological consequences of human decisions at varying temporal and spatial scales. PMID:20956371

  6. Erosion, Weathering and Stepped Topography in the Sierra Nevada, California; Quantifying the Dynamics of Hybrid (Soil-Bedrock) Landscapes

    NASA Astrophysics Data System (ADS)

    Jessup, B. S.; Miller, S. N.; Kirchner, J. W.; Riebe, C. S.

    2010-12-01

    The dynamics of granitic landscapes are regulated, in part, by bimodal weathering, which produces granular soils and expanses of bare rock ranging from meter-scale boulders to mountain-scale domes. Conceptual models for the evolution of granitic landscapes date back to Gilbert and Penck. Yet few studies have been able to realistically predict the co-occurrence of bedrock and granular soil and its implications for mountain-scale topography -- despite marked advances in quantitative landscape evolution modeling over the last few decades. Here we use terrain analysis, together with cosmogenic-nuclide measurements of erosion and weathering, to quantitatively explore Wahrhaftig's decades-old hypothesis for the development of “stepped topography” by differential weathering of bare and soil-mantled granite. According to this hypothesis, soil-mantled granite weathers much faster than bare granite; thus random erosional exposure of bare rock leads to an alternating sequence of steep, slowly weathering bedrock “steps” and gently sloped, but rapidly weathering, soil-mantled “treads”. Such treads and steps are purported to collectively account for ~2000 m of relief in the southern Sierra Nevada, California, implying that the mechanisms behind the formation of stepped topography may also account for development of mountain-scale relief in granitic landscapes. Our preliminary analysis of granitic terrain in the Sierra Nevada range suggests that steep steps often grade into gentle treads, consistent with the stepped topography hypothesis. Our data and analysis further corroborate the hypothesis with indications that bare granitic rocks erode much more slowly than their soil-mantled counterparts. This suggests that the coupling between soil production and denudation in granitic landscapes harbors a crucial tipping point; if soils are stripped to bedrock, erosion slows and soil formation is restrained to the point that bare rock can persist and rise in relief relative

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

    PubMed

    Roques, Lionel; Bonnefon, Olivier

    2016-01-01

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

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

    PubMed Central

    2016-01-01

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

  9. Resolution of sub-element length scales in Brownian dynamics simulations of biopolymer networks with geometrically exact beam finite elements

    NASA Astrophysics Data System (ADS)

    Müller, Kei W.; Meier, Christoph; Wall, Wolfgang A.

    2015-12-01

    Networks of crosslinked biopolymer filaments such as the cytoskeleton are the subject of intense research. Oftentimes, mechanics on the scale of single monomers (∼ 5 nm) govern the mechanics of the entire network (∼ 10 μm). Until now, one either resolved the small scales and lost the big (network) picture or focused on mechanics above the single-filament scale and neglected the molecular architecture. Therefore, the study of network mechanics influenced by the entire spectrum of relevant length scales has been infeasible so far. We propose a method that reconciles both small and large length scales without the otherwise inevitable loss in either numerical efficiency or geometrical (molecular) detail. Both explicitly modeled species, filaments and their crosslinkers, are discretized with geometrically exact beam finite elements of Simo-Reissner type. Through specific coupling conditions between the elements of the two species, mechanical joints can be established anywhere along a beam's centerline, enabling arbitrary densities of chemical binding sites. These binding sites can be oriented to model the monomeric architecture of polymers. First, we carefully discuss the method and then demonstrate its capabilities by means of a series of numerical examples.

  10. The hills are alive: Earth surface dynamics in the University of Arizona Landscape Evolution Observatory

    NASA Astrophysics Data System (ADS)

    DeLong, S.; Troch, P. A.; Barron-Gafford, G. A.; Huxman, T. E.; Pelletier, J. D.; Dontsova, K.; Niu, G.; Chorover, J.; Zeng, X.

    2012-12-01

    To meet the challenge of predicting landscape-scale changes in Earth system behavior, the University of Arizona has designed and constructed a new large-scale and community-oriented scientific facility - the Landscape Evolution Observatory (LEO). The primary scientific objectives are to quantify interactions among hydrologic partitioning, geochemical weathering, ecology, microbiology, atmospheric processes, and geomorphic change associated with incipient hillslope development. LEO consists of three identical, sloping, 333 m2 convergent landscapes inside a 5,000 m2 environmentally controlled facility. These engineered landscapes contain 1 meter of basaltic tephra ground to homogenous loamy sand and contains a spatially dense sensor and sampler network capable of resolving meter-scale lateral heterogeneity and sub-meter scale vertical heterogeneity in moisture, energy and carbon states and fluxes. Each ~1000 metric ton landscape has load cells embedded into the structure to measure changes in total system mass with 0.05% full-scale repeatability (equivalent to less than 1 cm of precipitation), to facilitate better quantification of evapotraspiration. Each landscape has an engineered rain system that allows application of precipitation at rates between3 and 45 mm/hr. These landscapes are being studied in replicate as "bare soil" for an initial period of several years. After this initial phase, heat- and drought-tolerant vascular plant communities will be introduced. Introduction of vascular plants is expected to change how water, carbon, and energy cycle through the landscapes, with potentially dramatic effects on co-evolution of the physical and biological systems. LEO also provides a physical comparison to computer models that are designed to predict interactions among hydrological, geochemical, atmospheric, ecological and geomorphic processes in changing climates. These computer models will be improved by comparing their predictions to physical measurements made in

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

    NASA Astrophysics Data System (ADS)

    Bunting, Erin L.

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

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

    USGS Publications Warehouse

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

    2011-01-01

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

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

    USGS Publications Warehouse

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

    2011-01-01

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

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

    PubMed

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

    2015-08-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  17. Soil Microbial Community Dynamics as Influenced by Soil Properties and Landscape Position

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Factors that affect plant growth, whether it is manure addition, season, or soil-type and landscape variability may provide insight on how to better manage agricultural fields through the evaluation of soil microbial activity, biomass and community structure. Thus, an in situ study was conducted to ...

  18. Soil microbial community dynamics as influenced by composted dairy manure, soil properties and landscape position

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Understanding factors that affect plant growth, whether it is manure addition, season, or soil-type and landscape variability may also impact soil microbial activity, biomass and community structure. Thus an in situ study was conducted to evaluate microbiological properties of three different soil t...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    NASA Astrophysics Data System (ADS)

    Farvacque, Manon; Valla, Pierre

    2016-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Grasselli, Federico; Bertoni, Andrea; Goldoni, Guido

    2016-05-01

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

  2. Spatial distributions of forest aboveground biomass and landscape dynamics associated with conservation status and ownership in New England, USA

    NASA Astrophysics Data System (ADS)

    Zheng, D.; Heath, L. S.; Ducey, M. J.

    2009-05-01

    We combined remote sensing derived forest aboveground biomass (AGB) estimation and the Conservation Biology Institute/World Wildlife Fund Protected Area Database using GIS techniques and spatial pattern analysis to illustrate how different conservation status and ownership could affect the landscape dynamics and spatial distributions of AGB in New England states, USA. The AGB means between all pairs of protection status and ownership categories were significantly different (P < 0.05). The highest mean AGB was observed in the protected public lands (156 Mg/ha), 44% higher than the lowest AGB mean (108 Mg/ha) observed in private regulated lands (privately owned but under the regulatory control by a state agency), or 30% higher than that in privately owned lands on average (120 Mg/ha). Seventy-seven percent of the regional forests with AGB > 200 Mg/ha, totaling about 9,300 km2, were located outside protected areas and were concentrated in western MA, southern VT, southwestern NH, and northwestern CT. The fragmentation rate in protected public lands between 1992 and 2001 was the least with greater rates were observed in privately regulated and non-regulated lands. Changing rates for the 4 representative fragmentation indices (patch density (PD), edge density (ED), landscape shape index (LSI), and mean patch size (MPS)) ranged from 1% in MPS to 6% in PD in protected public lands during the 9-year period whereas the mean changing rates ranged from 21% in LSI to 32% in PD in private lands. Thus, ownership and conservation status appears to have a strong impact on the dynamic changes of landscape structures in the region. These results indicate that if maintenance and enhancement of relatively unfragmented, high-AGB forest is a goal, expansion of protected areas appears to be an important management strategy.

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

    USGS Publications Warehouse

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

    2012-01-01

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

  4. The inherent dynamics of a molecular liquid: Geodesic pathways through the potential energy landscape of a liquid of linear molecules

    NASA Astrophysics Data System (ADS)

    Jacobson, Daniel; Stratt, Richard M.

    2014-05-01

    Because the geodesic pathways that a liquid follows through its potential energy landscape govern its slow, diffusive motion, we suggest that these pathways are logical candidates for the title of a liquid's "inherent dynamics." Like their namesake "inherent structures," these objects are simply features of the system's potential energy surface and thus provide views of the system's structural evolution unobstructed by thermal kinetic energy. This paper shows how these geodesic pathways can be computed for a liquid of linear molecules, allowing us to see precisely how such molecular liquids mix rotational and translational degrees of freedom into their dynamics. The ratio of translational to rotational components of the geodesic path lengths, for example, is significantly larger than would be expected on equipartition grounds, with a value that scales with the molecular aspect ratio. These and other features of the geodesics are consistent with a picture in which molecular reorientation adiabatically follows translation—molecules largely thread their way through narrow channels available in the potential energy landscape.

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

    SciTech Connect

    Tanaka, Midori; Tanimura, Yoshitaka

    2010-06-07

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

  6. Brownian motion in time-dependent logarithmic potential: Exact results for dynamics and first-passage properties.

    PubMed

    Ryabov, Artem; Berestneva, Ekaterina; Holubec, Viktor

    2015-09-21

    The paper addresses Brownian motion in the logarithmic potential with time-dependent strength, U(x, t) = g(t)log(x), subject to the absorbing boundary at the origin of coordinates. Such model can represent kinetics of diffusion-controlled reactions of charged molecules or escape of Brownian particles over a time-dependent entropic barrier at the end of a biological pore. We present a simple asymptotic theory which yields the long-time behavior of both the survival probability (first-passage properties) and the moments of the particle position (dynamics). The asymptotic survival probability, i.e., the probability that the particle will not hit the origin before a given time, is a functional of the potential strength. As such, it exhibits a rather varied behavior for different functions g(t). The latter can be grouped into three classes according to the regime of the asymptotic decay of the survival probability. We distinguish 1. the regular (power-law decay), 2. the marginal (power law times a slow function of time), and 3. the regime of enhanced absorption (decay faster than the power law, e.g., exponential). Results of the asymptotic theory show good agreement with numerical simulations. PMID:26395697

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

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

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

    PubMed Central

    Aguilar-Arnal, Lorena; Sassone-Corsi, Paolo

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

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

  10. Dynamic selective environments and evolutionary traps in human-dominated landscapes.

    PubMed

    Rodewald, Amanda D; Shustack, Daniel P; Jones, Todd M

    2011-09-01

    Human activities can alter selective environments in ways that can reduce the usefulness of certain ornamental traits as honest signals of individual quality and, in some cases, may create evolutionary traps, where rapid changes in selective environments result in maladaptive behavioral decisions. Using the sexually dichromatic, socially monogamous Northern Cardinal (Cardinalis cardinalis) as a model, we hypothesized that urbanization would erode the relationship between plumage coloration and reproductive success. Because the exotic Amur honeysuckle (Lonicera maackii) provides carotenoids, is a preferred habitat attribute, and increases vulnerability to nest predation, we predicted the presence of an evolutionary trap, whereby the brightest males would achieve the lowest reproductive success. Working at 14 forests in Ohio, USA, 2006-2008, we measured plumage color, monitored reproduction, and quantified habitat within territories. In rural landscapes, the brightest males bred earliest in the season and secured more preferred territories; however, annual reproduction declined with plumage brightness. Coloration of urban males was not associated with territory attributes or reproduction. Female redness across all landscapes was negatively related to reproduction. Poor reproductive performance of otherwise higher-quality males probably resulted from preferences for honeysuckle, which reduces annual reproduction when used as a nesting substrate early in the season. In this way, exotic shrubs prompted an evolutionary trap that was avoided in urban forests where anthropogenic resources disassociated male color and reproductive phenology and success. Our study illustrates how modified selective environments in human-dominated landscapes might shape microevolutionary processes in wild bird populations. PMID:21939074

  11. Land use dynamics and landscape change pattern in Hetao irrigation district, Inner Mongolia, China

    NASA Astrophysics Data System (ADS)

    Zhang, Yinhui; Luo, Yi; Zhao, Wenwu

    2010-11-01

    This study analyzed spatial and temporal changes in land use in an irrigation district covering an area of 1.7 million ha in Northern China by GIS analyses and also investigated changes in landscape pattern using the landscape structure analysis program FRAGSTATS over the study period from 1986 to 2000. The decreases in farmland and the increases in grassland area mainly resulted from the policy of grain for green and converting slope farmland into pasture from China government. In spite of the efforts to conserve the fragile ecosystem, the land degradation, including soil salinization and grassland degradation, was spreading rapidly. The area of alkali-saline land increased by 22493 ha and about 50555 ha of dense grassland degraded into mid-density grassland. In terms of landscape fragmentation, both farmland and dense grassland showed the tendency of increased fragmentation. Both adverse natural conditions and human activities are responsible for the land degradation expansion in Hetao irrigation district, but the root causes are increasing population pressure and irrational human activities, such as flooding irrigation method and over-grazing. To prevent land degradation from spreading, population control and improvement of the management are prerequisite approaches.

  12. Land use dynamics and landscape change pattern in Hetao irrigation district, Inner Mongolia, China

    NASA Astrophysics Data System (ADS)

    Zhang, Yinhui; Luo, Yi; Zhao, Wenwu

    2009-09-01

    This study analyzed spatial and temporal changes in land use in an irrigation district covering an area of 1.7 million ha in Northern China by GIS analyses and also investigated changes in landscape pattern using the landscape structure analysis program FRAGSTATS over the study period from 1986 to 2000. The decreases in farmland and the increases in grassland area mainly resulted from the policy of grain for green and converting slope farmland into pasture from China government. In spite of the efforts to conserve the fragile ecosystem, the land degradation, including soil salinization and grassland degradation, was spreading rapidly. The area of alkali-saline land increased by 22493 ha and about 50555 ha of dense grassland degraded into mid-density grassland. In terms of landscape fragmentation, both farmland and dense grassland showed the tendency of increased fragmentation. Both adverse natural conditions and human activities are responsible for the land degradation expansion in Hetao irrigation district, but the root causes are increasing population pressure and irrational human activities, such as flooding irrigation method and over-grazing. To prevent land degradation from spreading, population control and improvement of the management are prerequisite approaches.

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

    SciTech Connect

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

    1989-09-01

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

  14. The potential and flux landscape, Lyapunov function and non-equilibrium thermodynamics for dynamic systems and networks with an application to signal-induced Ca2+ oscillation

    NASA Astrophysics Data System (ADS)

    Xu, Li; Zhang, Feng; Wang, Erkang; Wang, Jin

    2013-02-01

    In this review, we summarize our recent efforts in exploring the non-equilibrium potential and flux landscape for dynamical systems and networks. The driving force of non-equilibrium dynamics can be decomposed into the gradient of the non-equilibrium potential and the divergent free probability flux divided by the steady-state probability distribution. The potential landscape is linked to the probability distribution of the steady state. We found that the intrinsic potential landscape in the zero noise limit is a Lyapunov function. We have defined and quantified the entropy, energy and free energy of the non-equilibrium systems. These can be used for formulating the first law of non-equilibrium thermodynamics. The free energy of the non-equilibrium system is also a Lyapunov function. Therefore, we can use both the intrinsic potential landscape and the free energy to quantify the robustness and global stability of the system. The Lyapunov property provides the formulation for the second law of non-equilibrium thermodynamics. The non-zero probability flux breaks the detailed balance. The two driving forces from the gradient of intrinsic potential landscape and the probability flux are perpendicular to each other under the zero noise limit. We investigate the dynamics of a new biological example of signal-induced Ca2+ oscillation. We explored the underlying potential landscape which shows a Mexican hat shape attracting the system down to the oscillation ring and the flux which provides the driving force on the ring for coherent and stable oscillation. We explored how the landscape and flux topography change with respect to the system parameters and the relationship to the period of oscillations and how the non-equilibrium free energy changes with respect to different dynamic phases and phase transitions when the system parameters vary. These explain how the system becomes robust and stable under different conditions and can help guide the experiment.

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

    PubMed

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

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

    NASA Astrophysics Data System (ADS)

    Dattani, Nikesh S.

    2013-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

    The hummocky ground moraine landscape of north-east Germany is characterized by distinct small-scale soil heterogeneity on the one hand, and intensive energy crop cultivation on the other. Both factors are assumed to significantly influence gaseous C exchange, and thus driving the dynamics of soil organic carbon stocks in terrestrial, agricultural ecosystems. However, it is not yet clear to which extent fertilization and soil erosional status influence soil C dynamics and whether one of these factors is more relevant than the other. We present seasonal and dynamic soil C balances of biogas maize for the growing season 2011, recorded at different sites located within the CarboZALF experimental area. The sites differ regarding soils (non-eroded Albic Luvisols (Cutanic), extremely eroded Calcaric Regosol and depositional Endogleyic Colluvic Regosol,) and applied fertilizer (100% mineral N fertilizer, 50% mineral and 50% N organic fertilizer, 100% organic N fertilizer). Fertilization treatments were established on the Albic Luvisol (Cutanic). Net-CO2-exchange (NEE) and ecosystem respiration (Reco) were measured every four weeks using a dynamic flow-through non-steady-state closed manual chamber system. Gap filling was performed based on empirical temperature and PAR dependency functions to derive daily NEE values. At the same time, daily above-ground biomass production (NPP) was estimated based on biomass samples and final harvest, using a sigmoidal growth function. In a next step, dynamic soil C balances were generated as the balance of daily NEE and NPP considering the initial C input due to N fertilizers. The resulted seasonal soil C balances varied from strong C losses at the Endogleyic Colluvic Regosol (602 g C m-2) to C gains at the Calcaric Regosol (-132 g C m-2). In general, soils exerted a stronger impact on seasonal and dynamic C balances compared to differences in applied N fertilizer. There are indications that inter-annual variations in climate conditions

  19. Evaluating the Impact of Abrupt Changes in Forest Policy and Management Practices on Landscape Dynamics: Analysis of a Landsat Image Time Series in the Atlantic Northern Forest

    PubMed Central

    Legaard, Kasey R.; Sader, Steven A.; Simons-Legaard, Erin M.

    2015-01-01

    Sustainable forest management is based on functional relationships between management actions, landscape conditions, and forest values. Changes in management practices make it fundamentally more difficult to study these relationships because the impacts of current practices are difficult to disentangle from the persistent influences of past practices. Within the Atlantic Northern Forest of Maine, U.S.A., forest policy and management practices changed abruptly in the early 1990s. During the 1970s-1980s, a severe insect outbreak stimulated salvage clearcutting of large contiguous tracts of spruce-fir forest. Following clearcut regulation in 1991, management practices shifted abruptly to near complete dependence on partial harvesting. Using a time series of Landsat satellite imagery (1973-2010) we assessed cumulative landscape change caused by these very different management regimes. We modeled predominant temporal patterns of harvesting and segmented a large study area into groups of landscape units with similar harvest histories. Time series of landscape composition and configuration metrics averaged within groups revealed differences in landscape dynamics caused by differences in management history. In some groups (24% of landscape units), salvage caused rapid loss and subdivision of intact mature forest. Persistent landscape change was created by large salvage clearcuts (often averaging > 100 ha) and conversion of spruce-fir to deciduous and mixed forest. In groups that were little affected by salvage (56% of landscape units), contemporary partial harvesting caused loss and subdivision of intact mature forest at even greater rates. Patch shape complexity and edge density reached high levels even where cumulative harvest area was relatively low. Contemporary practices introduced more numerous and much smaller patches of stand-replacing disturbance (typically averaging <15 ha) and a correspondingly large amount of edge. Management regimes impacted different areas to

  20. Evaluating the impact of abrupt changes in forest policy and management practices on landscape dynamics: analysis of a Landsat image time series in the Atlantic Northern Forest.

    PubMed

    Legaard, Kasey R; Sader, Steven A; Simons-Legaard, Erin M

    2015-01-01

    Sustainable forest management is based on functional relationships between management actions, landscape conditions, and forest values. Changes in management practices make it fundamentally more difficult to study these relationships because the impacts of current practices are difficult to disentangle from the persistent influences of past practices. Within the Atlantic Northern Forest of Maine, U.S.A., forest policy and management practices changed abruptly in the early 1990s. During the 1970s-1980s, a severe insect outbreak stimulated salvage clearcutting of large contiguous tracts of spruce-fir forest. Following clearcut regulation in 1991, management practices shifted abruptly to near complete dependence on partial harvesting. Using a time series of Landsat satellite imagery (1973-2010) we assessed cumulative landscape change caused by these very different management regimes. We modeled predominant temporal patterns of harvesting and segmented a large study area into groups of landscape units with similar harvest histories. Time series of landscape composition and configuration metrics averaged within groups revealed differences in landscape dynamics caused by differences in management history. In some groups (24% of landscape units), salvage caused rapid loss and subdivision of intact mature forest. Persistent landscape change was created by large salvage clearcuts (often averaging > 100 ha) and conversion of spruce-fir to deciduous and mixed forest. In groups that were little affected by salvage (56% of landscape units), contemporary partial harvesting caused loss and subdivision of intact mature forest at even greater rates. Patch shape complexity and edge density reached high levels even where cumulative harvest area was relatively low. Contemporary practices introduced more numerous and much smaller patches of stand-replacing disturbance (typically averaging <15 ha) and a correspondingly large amount of edge. Management regimes impacted different areas to

  1. Landscape dynamics in northwestern Amazonia: an assessment of pastures, fire and illicit crops as drivers of tropical deforestation.

    PubMed

    Armenteras, Dolors; Rodríguez, Nelly; Retana, Javier

    2013-01-01

    Many studies have identified drivers of deforestation throughout the tropics and, in most cases, have recognised differences in the level of threat. However, only a few have also looked at the temporal and spatial dynamics by which those drivers act, which is critical for assessing the conservation of biodiversity as well as for landscape planning. In this study, we analyse land cover change between 2000 and 2009 in north-western Colombian Amazonia to identify the interactions between the use of fire, cultivation of illicit crops and establishment of pastures, and their impacts on the loss of forest in the region. Yearly analyses were undertaken at randomly selected sample areas to quantify the average areas of transition of land cover types under different landscape compositions: forest-dominated mosaics, pasture mosaics, fire mosaics, and illicit crop mosaics. Our results indicate that despite the fact that forest areas were well-preserved, deforestation occurred at a low annual rate (0.06%). Conversion to pasture was the main factor responsible for forest loss (the area of pastures tripled within forest mosaics over 8 years), and this process was independent of the landscape matrix in which the forests were located. In fire mosaics, burning is a common tool for forest clearing and conversion to pasture. Thus, forests in fire mosaics were highly disturbed and frequently transformed from primary to secondary forests. The use of fire for illicit cropping was not detected, partly due to the small size of common illicit crops. Forest regeneration from pastures and secondary vegetation was observed in areas with large amounts of natural forest. Overall, assuming the continuation of the observed pasture conversion trend and the use of forest fire, we suggest that our results should be incorporated into a spatially explicit and integrated decision support tool to target and focus land-planning activities and policies. PMID:23382890

  2. Landscape Dynamics in Northwestern Amazonia: An Assessment of Pastures, Fire and Illicit Crops as Drivers of Tropical Deforestation

    PubMed Central

    Armenteras, Dolors; Rodríguez, Nelly; Retana, Javier

    2013-01-01

    Many studies have identified drivers of deforestation throughout the tropics and, in most cases, have recognised differences in the level of threat. However, only a few have also looked at the temporal and spatial dynamics by which those drivers act, which is critical for assessing the conservation of biodiversity as well as for landscape planning. In this study, we analyse land cover change between 2000 and 2009 in north-western Colombian Amazonia to identify the interactions between the use of fire, cultivation of illicit crops and establishment of pastures, and their impacts on the loss of forest in the region. Yearly analyses were undertaken at randomly selected sample areas to quantify the average areas of transition of land cover types under different landscape compositions: forest-dominated mosaics, pasture mosaics, fire mosaics, and illicit crop mosaics. Our results indicate that despite the fact that forest areas were well-preserved, deforestation occurred at a low annual rate (0.06%). Conversion to pasture was the main factor responsible for forest loss (the area of pastures tripled within forest mosaics over 8 years), and this process was independent of the landscape matrix in which the forests were located. In fire mosaics, burning is a common tool for forest clearing and conversion to pasture. Thus, forests in fire mosaics were highly disturbed and frequently transformed from primary to secondary forests. The use of fire for illicit cropping was not detected, partly due to the small size of common illicit crops. Forest regeneration from pastures and secondary vegetation was observed in areas with large amounts of natural forest. Overall, assuming the continuation of the observed pasture conversion trend and the use of forest fire, we suggest that our results should be incorporated into a spatially explicit and integrated decision support tool to target and focus land-planning activities and policies. PMID:23382890

  3. Exact approaches for scaffolding

    PubMed Central

    2015-01-01

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

  4. Dynamics and pattern of a managed coniferous forest landscape in Oregon

    NASA Technical Reports Server (NTRS)

    Spies, Thomas A.; Ripple, William J.; Bradshaw, G. A.

    1995-01-01

    We examined the process of fragmentation in a managed forest landscape by comparing rates and patterns of disturbance (primarily clear-cutting) and regrowth between 1972 and 1988 using Landsat imagery. A 2589-km(exp 2) managed forest landscape in western Oregon was classified into two forest types, closed-canopy conifer forest (CF) (typically, greater than 60% conifer cover) and other forest and nonforest types (OT) (typically, less than 40 yr old or deciduous forest). The percentage of CF declined from 71 to 58% between 1972 and 1988. Declines were greatest on private land, least in wilderness, and intermediate in public nonwilderness. High elevations (greater than 914 m) maintained a greater percentage of CF than lower elevations (less than 914 m). The percentage of the area at the edge of the two cover types increased on all ownerships and in both elevational zones, whereas the amount of interior habitat (defined as CF at least 100 m from OT) decreased on all ownerships and elevational zones. By 1988 public lands contained approximately 45% interior habitat while private lands had 12% interior habitat. Mean interior patch area declined from 160 to 62 ha. The annual rate of disturbance (primarily clear-cutting) for the entire area including the wilderness was 1.19%, which corresponds to a cutting rotation of 84 yr. The forest landscape was not in a steady state or regulated condition which is not projected to occur for at least 40 yr under current forest plans. Variability in cutting rates within ownerships was higher on private land than on nonreserve public land. However, despite the use of dispersed cutting patterns on public land, spatial patterns of cutting and remnant forest patches were nonuniform across the entire public ownership. Large remaining patches (less than 5000 ha) of contiguous interior forest were restricted to public lands designated for uses other than timber production such as wilderness areas and research natural areas.

  5. Noise-induced bistable switching dynamics through a potential energy landscape

    NASA Astrophysics Data System (ADS)

    Bi, Yuanhong; Yang, Zhuoqin; Meng, Xiangying; Lu, Qishao

    2015-04-01

    Interlinked positive feedback loops, an important building block of biochemical systems, can induce bistable switching, leading to long-lasting state changes by brief stimuli. In this work, prevalent mutual activation between two species as another positive feedback is added to a generic interlinked positive-feedback-loop model originating from many realistic biological circuits. A stochastic fluctuation of the positive feedback strength is introduced in a bistable interval of the feedback strength, and bistability appears for the moderate feedback strength at a certain noise level. Stability analysis based on the potential energy landscape is further utilized to explore the noise-induced switching behavior of two stable steady states.

  6. Validating a Satellite Microwave Remote Sensing Based Global Record of Daily Landscape Freeze-Thaw Dynamics

    NASA Astrophysics Data System (ADS)

    Kimball, J. S.; Kim, Y.; McDonald, K. C.

    2012-12-01

    The freeze-thaw (FT) parameter from satellite microwave remote sensing quantifies the predominant landscape frozen or thawed state and is closely linked to surface energy budget and hydrologic activity, vegetation growth, terrestrial carbon budgets and land-atmosphere trace gas exchange. A global Earth System Data Record of daily landscape FT status (FT-ESDR) was developed using a temporal change classification of overlapping 37 GHz brightness temperature (Tb) series from the Scanning Multichannel Microwave Radiometer (SMMR) and Special Sensor Microwave Imager (SSM/I), and encompassing land areas where seasonal frozen temperatures influence ecosystem processes. A temporally consistent, long-term (>30 yr) FT record was created by ensuring cross-sensor consistency through pixel-wise adjustment of the SMMR Tb record based on empirical analyses of overlapping SMMR and SSM/I measurements. The FT-ESDR is designed to determine the FT status of the composite landscape vegetation-snow-soil medium with sufficient accuracy to characterize frozen temperature constraints to surface water mobility, vegetation productivity and land-atmosphere CO2 fluxes. A multi-tier validation scheme was applied using in situ temperature measurements, other satellite FT retrievals and synergistic biophysical data. These results are incorporated into the product metadata structure, including mean daily spatial classification accuracies and annual quality assessment (QA) maps accounting for landscape heterogeneity, algorithm limitations and sensor retrieval gaps. The resulting FT-ESDR shows mean annual spatial classification accuracies of 91 (+/-8.6) and 84 (+/-9.3) percent for PM and AM overpass retrievals. Accuracy is reduced during seasonal transition periods when FT heterogeneity is maximized within the relatively coarse (~25-km) satellite footprint. The QA rankings range from low (estimated accuracy <70%) to best (>90%) categories; mean annual QA results for the 1979-2011 period show relative

  7. Variation and trends of landscape dynamics, land surface phenology and net primary production of the Appalachian Mountains

    NASA Astrophysics Data System (ADS)

    Wang, Yeqiao; Zhao, Jianjun; Zhou, Yuyu; Zhang, Hongyan

    2012-01-01

    The gradients of elevations and latitudes in the Appalachian Mountains provide a unique regional perspective on landscape variations in the eastern United States and southeastern Canada. We reveal patterns and trends of landscape dynamics, land surface phenology, and ecosystem production along the Appalachian Mountains using time series data from Global Inventory Modeling and Mapping Studies and Advanced Very High Resolution Radiometer Global Production Efficiency Model datasets. We analyze the spatial and temporal patterns of the normalized difference vegetation index (NDVI), length of growing season (LOS), and net primary production (NPP) of selected ecoregions along the Appalachian Mountains regions. We compare the results in different spatial contexts, including North America and the Appalachian Trail corridor area. To reveal latitudinal variations, we analyze data and compare the results between the 30°-to-40°N and the 40°-to-50°N latitudes. The result reveal significant decreases in annual peak NDVI in the Appalachian Mountains regions. The trend for the Appalachian Mountains regions was a -0.0018 (R2=0.55, P<0.0001) NDVI unit decrease per year during 25 years from 1982 to 2006. The LOS was prolonged by 0.3 days per year-1 during the 25-year percent. The NPP increased by 2.68 g Cm-2 yr-2 from 1981 to 2000.

  8. Drainage and leaching dynamics in a cropped hummocky soil landscape with erosion-affected pedogenesis

    NASA Astrophysics Data System (ADS)

    Gerke, Horst H.; Rieckh, Helene; Sommer, Michael

    2016-04-01

    Hummocky soil landscapes are characterized by 3D spatial patterns of soil types that result from erosion-affected pedogenesis. Due to tillage and water erosion, truncated profiles have been formed at steep and mid slopes and colluvial soils at hollows. Pedogenetic variations in soil horizons at the different hillslope positions suggested feedback effects between erosion affected soil properties, the water balances, and the crop growth and leaching rates. Water balance simulations compared uniform with hillslope position-specific crop and root growths for soils at plateau, flat mid slope, steep slope, and hollow using the Hydrus-1D program. The boundary condition data were monitored at the CarboZALF-D experimental field site, which was cropped with perennial lucerne (Medicago sativa L.) in 2013 and 2014. Crop and root growth was assumed proportional to observed leaf area index (LAI). Fluxes of dissolved organic and inorganic carbon (DOC, DIC) were obtained from simulated water fluxes and measured DOC and DIC concentrations. For the colluvic soil, the predominately upward flow led to a net input in DIC and DOC. For the truncated soils at steep slopes, a reduced crop growth caused an relative increase in drainage, suggesting an accelerated leaching, which in the long term could accelerate the soil development and more soil variations along eroding hillslopes in arable soil landscapes.

  9. Biodiversity and agriculture in dynamic landscapes: Integrating ground and remotely-sensed baseline surveys.

    PubMed

    Gillison, Andrew N; Asner, Gregory P; Fernandes, Erick C M; Mafalacusser, Jacinto; Banze, Aurélio; Izidine, Samira; da Fonseca, Ambrósio R; Pacate, Hermenegildo

    2016-07-15

    Sustainable biodiversity and land management require a cost-effective means of forecasting landscape response to environmental change. Conventional species-based, regional biodiversity assessments are rarely adequate for policy planning and decision making. We show how new ground and remotely-sensed survey methods can be coordinated to help elucidate and predict relationships between biodiversity, land use and soil properties along complex biophysical gradients that typify many similar landscapes worldwide. In the lower Zambezi valley, Mozambique we used environmental, gradient-directed transects (gradsects) to sample vascular plant species, plant functional types, vegetation structure, soil properties and land-use characteristics. Soil fertility indices were derived using novel multidimensional scaling of soil properties. To facilitate spatial analysis, we applied a probabilistic remote sensing approach, analyzing Landsat 7 satellite imagery to map photosynthetically active and inactive vegetation and bare soil along each gradsect. Despite the relatively low sample number, we found highly significant correlations between single and combined sets of specific plant, soil and remotely sensed variables that permitted testable spatial projections of biodiversity and soil fertility across the regional land-use mosaic. This integrative and rapid approach provides a low-cost, high-return and readily transferable methodology that permits the ready identification of testable biodiversity indicators for adaptive management of biodiversity and potential agricultural productivity. PMID:27064732

  10. Past landscape dynamics in mountain territories: historical trajectory of vulnerability in the Vars catchment (French Alps)

    NASA Astrophysics Data System (ADS)

    Puissant, Anne; Cioloboc, Florin; Schlosser, Arnaud; Gazo, Aurelien; Martin, Brice; Malet, Jean-Philippe

    2016-04-01

    Over the last decades and centuries, mountain landscapes have experiment natural and man-made landcover/use changes with mainly the development of tourism activities and the reduction of agro-pastoral activities. These transformations have directly influenced the spatial organization of mountain landscapes. To better anticipate the future exposure of the territory to natural hazards, decision-makers need retrospective analyses of the past changes. In the frame of the SAMCO project, whose objective is to propose mountain risk assessment methodologies in the context of global changes, this research presents a retrospective analysis of land cover/use changes (from 1948 to 2013) in the Vars catchment (French South Alps) submitted to several natural hazards (rockfall, landslide, and flood). Database of elements at risk has been built for five dates and evolution of vulnerability is performed through a versatile GIS-based analysis tool developed for the estimation of vulnerability indicators (physical, economical, social) at a fine scale (1:5000). Results allow identifying several areas with different trajectories of vulnerability which can be use as input data for risk analysis and define future trends.

  11. Thermodynamical interpretation of evolutionary dynamics on a fitness landscape in a evolution reactor, I.

    PubMed

    Aita, Takuyo; Morinaga, Shunichi; Husimi, Yuzuru

    2004-09-01

    A theory for describing evolution as adaptive walks by a finite population with M walkers (M > or = 1) on an anisotropic Mt. Fuji-type fitness landscape is presented, from a thermodynamical point of view. Introducing the 'free fitness' as the sum of a fitness term and an entropy term and 'evolutionary force' as the gradient of free fitness on a fitness coordinate, we demonstrate that the behavior of these theoretical walkers is almost consistent with the thermodynamical schemes. The major conclusions are as follows: (1) an adaptive walk (=evolution) is driven by an evolutionary force in the direction in which free fitness increases; (2) the expectation of the climbing rate obeys an equation analogous to the Einstein relation in Brownian motion; (3) the standard deviation of the climbing rate is a quantity analogous to the mean thermal energy of a particle, kT (x constant). In addition, on the interpretation that the walkers climb the landscape by absorbing 'fitness information' from the surroundings, we succeeded in quantifying the fitness information and formulating a macroscopic scheme from an informational point of view. PMID:15294429

  12. Modeling the Impact of Landscape Variability on Nutrient and Pesticide Dynamics in CEAP Watersheds

    NASA Astrophysics Data System (ADS)

    Saia, S. M.; Steenhuis, T. S.; Easton, Z. M.; Boll, J.; Brooks, E. S.

    2010-12-01

    Keywords: water quality, best management practices, runoff The effectiveness of agricultural conservation strategies for reducing soil, nutrient, and pesticide transport varies among landscape type and climate. For instance, a riparian buffer may reduce phosphorous loading to a Northeastern stream but fail to have the same impact on a stream in the Midwest. We propose a model based on readily available input data that can be used to prioritize the implementation of agricultural practices across a range of landscapes. Because areas generating overland flow are more prone to nutrient and pesticide transport, new management tools must accurately predict surface and subsurface flows. A modified version of the process-based Water Erosion Prediction Project (WEPP) model was developed to more accurately estimate surface and subsurface flows as well as sediment, nutrient, and pesticide transport from saturated and unsaturated hill slopes. We compare model results to available nutrient transport data from 13 USDA funded Conservation Effects Assessment Project (CEAP) watersheds. Core objectives of the CEAP initiative include the quantitative evaluation of agricultural conservation practices through enhanced data collection and model development in selected watersheds. Once available online, this modified WEPP model will be a valuable tool for water resource managers to make scientifically informed decisions concerning the impact on and selection of conservation practices for improved stream water quality.

  13. Quantitative functional assessment of SOM dynamics in changing land-use and landscape conditions at the Central region of Russia

    NASA Astrophysics Data System (ADS)

    Vasenev, I. I.; Valentini, R.

    2012-12-01

    Terrestrial ecosystems are a major player in the global and regional carbon cycles acting as carbon stocks and carbon sources. Soil organic matter (SOM) is the largest carbon stock in the most of terrestrial ecosystems.Soil CO2 emission is a predominant terrestrial carbon outflow, including autotrophic respiration of plant roots and heterotrophic microbial respiration. The capacity for carbon sequestration is widely accepted as a principal soil ecological function. Soil respiration is assumed as an important carbon source, included in the studies, assessing carbon budget in changing land-use and landscape conditions. The Central region of the European territory of Russia is especially interested for this kind of researches due to essential original spatial heterogeneity of its forest and forest-steppe soils and landscapes that has been further complicated by a specific land-use history and different-direction soil successions as a results of past century environmental changes and human impacts. SOM stocks and especially CO2 emission demonstrates a very high spatial and temporal variability here, which is mutual feature for most regional natural and man-changed ecosystems and may have a strong influence on land-use and farming change strategy and climate change. However quite a few studies focus on this problem here with application of modern field tools and quantitative functional assessment of SOM dynamics variability at the level of changing elementary soil cover patterns (ESCP) that includes in the key issues of our project. Development the zonal-regional set of criteria for logically formalized distinguishing of the most "stable" & "hot" areas in soil cover patterns make it possible for quantitative assessment of dominating in them elementary landscape, soil-forming and degradation processes. The received data essentially expand known ranges of the soil forming processes (SFP) rate «in situ». In case of mature southern taiga ecosystems mutual for them the

  14. Fort Collins Science Center Ecosystem Dynamics branch--interdisciplinary research for addressing complex natural resource issues across landscapes and time

    USGS Publications Warehouse

    Bowen, Zachary H.; Melcher, Cynthia P.; Wilson, Juliette T.

    2013-01-01

    The Ecosystem Dynamics Branch of the Fort Collins Science Center offers an interdisciplinary team of talented and creative scientists with expertise in biology, botany, ecology, geology, biogeochemistry, physical sciences, geographic information systems, and remote-sensing, for tackling complex questions about natural resources. As demand for natural resources increases, the issues facing natural resource managers, planners, policy makers, industry, and private landowners are increasing in spatial and temporal scope, often involving entire regions, multiple jurisdictions, and long timeframes. Needs for addressing these issues include (1) a better understanding of biotic and abiotic ecosystem components and their complex interactions; (2) the ability to easily monitor, assess, and visualize the spatially complex movements of animals, plants, water, and elements across highly variable landscapes; and (3) the techniques for accurately predicting both immediate and long-term responses of system components to natural and human-caused change. The overall objectives of our research are to provide the knowledge, tools, and techniques needed by the U.S. Department of the Interior, state agencies, and other stakeholders in their endeavors to meet the demand for natural resources while conserving biodiversity and ecosystem services. Ecosystem Dynamics scientists use field and laboratory research, data assimilation, and ecological modeling to understand ecosystem patterns, trends, and mechanistic processes. This information is used to predict the outcomes of changes imposed on species, habitats, landscapes, and climate across spatiotemporal scales. The products we develop include conceptual models to illustrate system structure and processes; regional baseline and integrated assessments; predictive spatial and mathematical models; literature syntheses; and frameworks or protocols for improved ecosystem monitoring, adaptive management, and program evaluation. The descriptions

  15. An alternative to current psychiatric classifications: a psychological landscape hypothesis based on an integrative, dynamical and multidimensional approach

    PubMed Central

    2014-01-01

    Background Mental disorders as defined by current classifications are not fully supported by scientific evidence. It is unclear whether main disorders should be broken down into separate categories or disposed along a continuous spectrum. In the near future, new classes of mental disorders could be defined through associations of so-called abnormalities observed at the genetic, molecular and neuronal circuitry levels. Methods We propose an alternative hypothesis to these classifications based on an integrative, dynamical and multidimensional approach. Results We suggest that observed data collected in the general population can be used to build a psychological landscape. Innovative techniques issued from information processing and system dynamics can prove helpful in this task. Information preserving techniques can reduce the high dimensional data collected and provide an intrinsic map for psychological characteristics or behaviors. Dynamical patterns called attractors, which are linked to each other through continuous pathways, can be identified. Specific attractors can define mental disorders. Their causal structure can be investigated with causal networks. Conclusions Powerful and reliable tools are available so that an alternative to current psychiatric classifications can be built based on a genuine biopsychosocial model. The proposed model is ready to be tested on real data. PMID:25033795

  16. Characterizing the Free-Energy Landscape of MDM2 Protein-Ligand Interactions by Steered Molecular Dynamics Simulations.

    PubMed

    Hu, Guodong; Xu, Shicai; Wang, Jihua

    2015-12-01

    Inhibition of p53-MDM2 interaction by small molecules is considered to be a promising approach to re-activate wild-type p53 for tumor suppression. Several inhibitors of the MDM2-p53 interaction were designed and studied by the experimental methods and the molecular dynamics simulation. However, the unbinding mechanism was still unclear. The steered molecular dynamics simulations combined with Brownian dynamics fluctuation-dissipation theorem were employed to obtain the free-energy landscape of unbinding between MDM2 and their four ligands. It was shown that compounds 4 and 8 dissociate faster than compounds 5 and 7. The absolute binding free energies for these four ligands are in close agreement with experimental results. The open movement of helix II and helix IV in the MDM2 protein-binding pocket upon unbinding is also consistent with experimental MDM2-unbound conformation. We further found that different binding mechanisms among different ligands are associated with H-bond with Lys51 and Glu25. These mechanistic results may be useful for improving ligand design. PMID:26032728

  17. Patch quality and context, but not patch number, drive multi-scale colonization dynamics in experimental aquatic landscapes.

    PubMed

    Resetarits, William J; Binckley, Christopher A

    2013-11-01

    Colonization and extinction are primary drivers of local population dynamics, community structure, and spatial patterns of biological diversity. Existing paradigms of island biogeography, metapopulation biology, and metacommunity ecology, as well as habitat management and conservation biology based on those paradigms, emphasize patch size, number, and isolation as primary characteristics influencing colonization and extinction. Habitat selection theory suggests that patch quality could rival size, number, and isolation in determining rates of colonization and resulting community structure. We used naturally colonized experimental landscapes to address four issues: (a) how do colonizing aquatic beetles respond to variation in patch number, (b) how do they respond to variation in patch quality, (c) does patch context affect colonization dynamics, and (d) at what spatial scales do beetles respond to habitat variation? Increasing patch number had no effect on per patch colonization rates, while patch quality and context were critical in determining colonization rates and resulting patterns of abundance and species richness at multiple spatial scales. We graphically illustrate how variation in immigration rates driven by perceived predation risk (habitat quality) can further modify dynamics of the equilibrium theory of island biogeography beyond predator-driven effects on extinction rates. Our data support the importance of patch quality and context as primary determinants of colonization rate, occupancy, abundance, and resulting patterns of species richness, and reinforce the idea that management of metapopulations for species preservation, and metacommunities for local and regional diversity, should incorporate habitat quality into the predictive equation. PMID:23609801

  18. Nitrogen dynamics among cropland and riparian buffers: soil-landscape influences.

    PubMed

    Young, Eric O; Briggs, Russell D

    2007-01-01

    Nitrate (NO3-) leaching to ground water poses water quality concerns in some settings. Riparian buffers have been advocated to reduce excess ground water NO3- concentrations. We characterized inorganic N in soil solution and shallow ground water for 16 paired cropland-riparian plots from 2003 to 2005. The sites were located at two private dairy farms in Central New York on silt and gravelly silt loam soils (Aeric Endoaqualfs, Fluvaquentic Endoaquepts, Fluvaquentic Eutrudepts, Glossaquic Hapludalfs, and Glossic Hapludalfs). It was hypothesized that cropland N inputs and soil-landscape variability would jointly affect NO3- leaching and transformations in ground water. Results showed that well and moderately well drained fields had consistently higher ground water NO3- compared to more imperfectly drained fields receiving comparable N inputs. Average 50-cm depth soil solution NO3- and ground water dissolved oxygen (DO) explained 64% of average cropland ground water NO3- variability. Cropland ground water with an average DO of <3 mg L(-1) tended to have <4 mg L(-1) of NO3- with a water table depth (WTD) of landscape factors strongly influenced NO3- behavior and suggest the importance of accurately characterizing soil variability along cropland-riparian zones. PMID:17485712

  19. An enhanced Bayesian fingerprinting framework for studying sediment source dynamics in intensively managed landscapes

    NASA Astrophysics Data System (ADS)

    Abban, B.; (Thanos) Papanicolaou, A. N.; Cowles, M. K.; Wilson, C. G.; Abaci, O.; Wacha, K.; Schilling, K.; Schnoebelen, D.

    2016-06-01

    An enhanced revision of the Fox and Papanicolaou (hereafter referred to as "F-P") (2008a) Bayesian, Markov Chain Monte Carlo fingerprinting framework for estimating sediment source contributions and their associated uncertainties is presented. The F-P framework included two key deterministic parameters, α and β, that, respectively, reflected the spatial origin attributes of sources and the time history of eroded material delivered to and collected at the watershed outlet. However, the deterministic treatment of α and β is limited to cases with well-defined spatial partitioning of sources, high sediment delivery, and relatively short travel times with little variability in transport within the watershed. For event-based studies in intensively managed landscapes, this may be inadequate since landscape heterogeneity results in variabilities in source contributions, their pathways, delivery times, and storage within the watershed. Thus, probabilistic treatments of α and β are implemented in the enhanced framework to account for these variabilities. To evaluate the effects of the treatments of α and β on source partitioning, both frameworks are applied to the South Amana Subwatershed (SASW) in the U.S. midwest. The enhanced framework is found to estimate mean source contributions that are in good agreement with estimates from other studies in SASW. The enhanced framework is also able to produce expected trends in uncertainty during the study period, unlike the F-P framework, which does not perform as expected. Overall, the enhanced framework is found to be less sensitive to changes in α and β than the F-P framework, and, therefore, is more robust and desirable from a management standpoint.

  20. POPULATION DYNAMICS OF HISPID COTTON RATS (SIGMODON HISPIDUS) ACROSS A NITROGEN AMENDED LANDSCAPE

    EPA Science Inventory

    Population dynamics of some small-mammal species appear to be regulated by plant-community structure, vegetative cover, plant diversity, and food quality. Thus, plant community changes associated with nitrogen additions would likely impact dynamics and structure of small-mammal ...

  1. DISENTANGLING COMPLEX LANDSCAPES: NEW INSIGHTS INTO ARID AND SEMIARID SYSTEM DYNAMICS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although desertification is a global phenomenon and numerous studies have provided information on dynamics at specific sites, spatial and temporal variation in response to desertification have led to alternative, and often controversial, hypotheses about the key factors that determine these dynamics...

  2. Dynamics of the 2001 UK Foot and Mouth Epidemic: Stochastic Dispersal in a Heterogeneous Landscape

    NASA Astrophysics Data System (ADS)

    Keeling, Matt J.; Woolhouse, Mark E. J.; Shaw, Darren J.; Matthews, Louise; Chase-Topping, Margo; Haydon, Dan T.; Cornell, Stephen J.; Kappey, Jens; Wilesmith, John; Grenfell, Bryan T.

    2001-10-01

    Foot-and-mouth is one of the world's most economically important livestock diseases. We developed an individual farm-based stochastic model of the current UK epidemic. The fine grain of the epidemiological data reveals the infection dynamics at an unusually high spatiotemporal resolution. We show that the spatial distribution, size, and species composition of farms all influence the observed pattern and regional variability of outbreaks. The other key dynamical component is long-tailed stochastic dispersal of infection, combining frequent local movements with occasional long jumps. We assess the history and possible duration of the epidemic, the performance of control strategies, and general implications for disease dynamics in space and time.

  3. Temperature and solvent dependence of the dynamical landscape of tau protein conformations.

    PubMed

    Bianconi, Antonio; Ciasca, Gabriele; Tenenbaum, Alexander; Battisti, Anna; Campi, Gaetano

    2012-01-01

    We report the variation with temperature of the ensemble distribution of conformations spanned by the tau protein in its dynamical states measured by small-angle X-ray scattering (SAXS) using synchrotron radiation. The SAXS data show a clear temperature variation of the distribution of occupied protein conformations from 293 to 318 K. More conformations with a smaller radius of gyration are occupied at higher temperature. The protein-solvent interactions are shown by computer simulation to be essential for controlling the dynamics of protein conformations, providing evidence for the key role of water solvent in the protein dynamics, as proposed by Giorgio Careri. PMID:23277677

  4. Landscape and plant physiological controls on water dynamics and forest productivity within a watershed

    NASA Astrophysics Data System (ADS)

    Hu, Jia; Jencso, Kelsey; Looker, Nathaniel; Martin, Justin; Hoylman, Zachary

    2015-04-01

    Across the Western U.S., declining snowpacks have resulted in increased water limitation, leading to reduced productivity in high elevation forests. While our current understanding of how forests respond to climate change is typically focused on measuring/modeling the physiological responses and climate feedbacks, our study aims to combine physiology with hydrology to examine how landscape topography modulates the sensitivity of forests to climate. In a forested watershed in Western Montana, we linked climate variability to the physical watershed characteristics and the physiological response of vegetation to examine forest transpiration and productivity rates. Across the entire watershed, we found a strong relationship between productivity and the topographic wetness index, a proxy for soil moisture storage. However, this relationship was highly dependent on the intensity of solar radiation, suggesting that at high elevations productivity was limited by temperature, while at low elevations productivity was limited by moisture. In order to identify the mechanisms responsible for this relationship, we then examined how different coniferous species respond to changing environmental and hydrologic regimes. We first examined transpiration and productivity rates at the hillslope scale at four plots, ranging in elevation and aspect across the watershed. We found trees growing in the hollows had higher transpiration and productivity rates than trees growing in the side slope, but that these differences were more pronounced at lower elevations. We then used oxygen isotope to examine water source use by different species across the watershed. We found that trees growing in the hollows used snowmelt for a longer period. This was most likely due to upslope subsidies of snowmelt water to the hollow areas. However, we found that trees growing at lower elevations used proportionally more snowmelt than trees at the higher elevations. This was most likely due to the trees at lower

  5. Landscape and plant physiological controls on water dynamics within a watershed

    NASA Astrophysics Data System (ADS)

    Hu, J.; Looker, N. T.; Martin, J. T.; Hoylman, Z. H.; Jencso, K. G.

    2014-12-01

    Across the Western U.S., declining snowpacks have resulted in increased water limitation, leading to reduced productivity in high elevation forests. While our current understanding of how forests respond to climate change is typically focused on measuring/modeling the physiological responses and climate feedbacks, our study aims to combine physiology with hydrology to examine how landscape topography modulates the sensitivity of forests to climate. In a forested watershed in Western Montana, we linked climate variability to the physical watershed characteristics and the physiological response of vegetation to examine forest transpiration and productivity rates. Across the entire watershed, we found a strong relationship between productivity and the topographic wetness index, a proxy for soil moisture storage. However, this relationship was highly dependent on the intensity of solar radiation, suggesting that at high elevations productivity was limited by temperature, while at low elevations productivity was limited by moisture. In order to identify the mechanisms responsible for this relationship, we then examined how different coniferous species respond to changing environmental and hydrologic regimes. We first examined transpiration and productivity rates at the hillslope scale at four plots, ranging in elevation and aspect across the watershed. We found trees growing in the hollows had higher transpiration and productivity rates than trees growing in the side slope, but that these differences were more pronounced at lower elevations. We then used oxygen isotope to examine water source use by different species across the watershed. We found that trees growing in the hollows used snowmelt for a longer period. This was most likely due to upslope subsidies of snowmelt water to the hollow areas. However, we found that trees growing at lower elevations used proportionally more snowmelt than trees at the higher elevations. This was most likely due to the trees at lower

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

    EPA Science Inventory

    Range dynamics models now incorporate many of the mechanisms and interactions that drive species distributions. However, connectivity continues to be studied using overly simple distance-based dispersal models with little consideration of how the individual behavior of dispersin...

  7. Advances in global sensitivity analyses of demographic-based species distribution models to address uncertainties in dynamic landscapes

    PubMed Central

    Curtis, Janelle M.R.

    2016-01-01

    Developing a rigorous understanding of multiple global threats to species persistence requires the use of integrated modeling methods that capture processes which influence species distributions. Species distribution models (SDMs) coupled with population dynamics models can incorporate relationships between changing environments and demographics and are increasingly used to quantify relative extinction risks associated with climate and land-use changes. Despite their appeal, uncertainties associated with complex models can undermine their usefulness for advancing predictive ecology and informing conservation management decisions. We developed a computationally-efficient and freely available tool (GRIP 2.0) that implements and automates a global sensitivity analysis of coupled SDM-population dynamics models for comparing the relative influence of demographic parameters and habitat attributes on predicted extinction risk. Advances over previous global sensitivity analyses include the ability to vary habitat suitability across gradients, as well as habitat amount and configuration of spatially-explicit suitability maps of real and simulated landscapes. Using GRIP 2.0, we carried out a multi-model global sensitivity analysis of a coupled SDM-population dynamics model of whitebark pine (Pinus albicaulis) in Mount Rainier National Park as a case study and quantified the relative influence of input parameters and their interactions on model predictions. Our results differed from the one-at-time analyses used in the original study, and we found that the most influential parameters included the total amount of suitable habitat within the landscape, survival rates, and effects of a prevalent disease, white pine blister rust. Strong interactions between habitat amount and survival rates of older trees suggests the importance of habitat in mediating the negative influences of white pine blister rust. Our results underscore the importance of considering habitat attributes along

  8. Advances in global sensitivity analyses of demographic-based species distribution models to address uncertainties in dynamic landscapes.

    PubMed

    Naujokaitis-Lewis, Ilona; Curtis, Janelle M R

    2016-01-01

    Developing a rigorous understanding of multiple global threats to species persistence requires the use of integrated modeling methods that capture processes which influence species distributions. Species distribution models (SDMs) coupled with population dynamics models can incorporate relationships between changing environments and demographics and are increasingly used to quantify relative extinction risks associated with climate and land-use changes. Despite their appeal, uncertainties associated with complex models can undermine their usefulness for advancing predictive ecology and informing conservation management decisions. We developed a computationally-efficient and freely available tool (GRIP 2.0) that implements and automates a global sensitivity analysis of coupled SDM-population dynamics models for comparing the relative influence of demographic parameters and habitat attributes on predicted extinction risk. Advances over previous global sensitivity analyses include the ability to vary habitat suitability across gradients, as well as habitat amount and configuration of spatially-explicit suitability maps of real and simulated landscapes. Using GRIP 2.0, we carried out a multi-model global sensitivity analysis of a coupled SDM-population dynamics model of whitebark pine (Pinus albicaulis) in Mount Rainier National Park as a case study and quantified the relative influence of input parameters and their interactions on model predictions. Our results differed from the one-at-time analyses used in the original study, and we found that the most influential parameters included the total amount of suitable habitat within the landscape, survival rates, and effects of a prevalent disease, white pine blister rust. Strong interactions between habitat amount and survival rates of older trees suggests the importance of habitat in mediating the negative influences of white pine blister rust. Our results underscore the importance of considering habitat attributes along

  9. Variation and Trends of Landscape Dynamics, Land Surface Phenology and Net Primary Production of the Appalachian Mountains

    SciTech Connect

    Wang, Yeqiao; Zhao, Jianjun; Zhou, Yuyu; Zhang, Hongyan

    2012-12-15

    The gradients of the Appalachian Mountains in elevations and latitudes provide a unique regional perspective of landscape variations in the eastern United States and a section of the southeastern Canada. This study reveals patterns and trends of landscape dynamics, land surface phenology and ecosystem production along the Appalachian Mountains using time series data from Global Inventory Modeling and Mapping Studies (GIMMS) and AVHRR Global Production Efficiency Model (GloPEM) datasets. We analyzed the spatial and temporal patterns of Normalized Difference Vegetation Index (NDVI), length of growing season (LOS) and net primary production (NPP) of selected ecoregions along the Appalachian Mountains regions. We compared the results out of the Appalachian Mountains regions in different spatial contexts including the North America and the Appalachian Trail corridor area. To reveal latitudinal variations we analyzed data and compared the results between 30°N-40°N and 40°N-50°N latitudes. The result revealed significant decreases in annual peak NDVI in the Appalachian Mountains regions. The trend for the Appalachian Mountains regions was -0.0018 (R2=0.55, P<0.0001) NDVI unit decrease per year during 25 years between 1982 and 2006. The LOS had prolonged 0.3 day yr-1 during 25 years over the Appalachian Mountains regions. The NPP increased by 2.68 gC m-2yr-2 in Appalachian Mountains regions from 1981 to 2000. The comparison with the North America reveals the effects of topography and ecosystem compositions of the Appalachian Mountains. The comparison with the Appalachian Trail corridor area provides a regional mega-transect view of the measured variables.

  10. Species and Media Effects on Soil Carbon Dynamics in the Landscape.

    PubMed

    Marble, S Christopher; Prior, Stephen A; Runion, G Brett; Torbert, H Allen; Gilliam, Charles H; Fain, Glenn B; Sibley, Jeff L; Knight, Patricia R

    2016-01-01

    Three woody shrub species [cleyera (Ternstroemia gymnanthera Thunb. 'Conthery'), Indian hawthorn (Rhaphiolepis indica L.) and loropetalum (Loropetalum chinensis Oliv.'Ruby')] were container-grown for one growing season in 2008 using either pinebark (industry standard), clean chip residual or WholeTree (derived by-products from the forestry industry) as potting substrates and then transplanted into the landscape in 2008. An Automated Carbon Efflux System was used to continually monitor soil CO2 efflux from December 2010 through November 2011 in each species and substrate combination. Changes in soil carbon (C) levels as a result of potting substrate were assessed through soil sampling in 2009 and 2011 and plant biomass was determined at study conclusion. Results showed that soil CO2-C efflux was similar among all species and substrates, with few main effects of species or substrate observed throughout the study. Soil analysis showed that plots with pinebark contained higher levels of soil C in both 2009 and 2011, suggesting that pinebark decomposes slower than clean chip residual or WholeTree and consequently has greater C storage potential than the two alternative substrates. Results showed a net C gain for all species and substrate combinations; however, plants grown in pinebark had greater C sequestration potential. PMID:27140321

  11. Complex spatial dynamics maintain northern leopard frog (Lithobates pipiens) genetic diversity in a temporally varying landscape

    USGS Publications Warehouse

    Mushet, David M.; Euliss, Ned H.; Chen, Yongjiu; Stockwell, Craig A.

    2013-01-01

    In contrast to most local amphibian populations, northeastern populations of the Northern Leopard Frog (Lithobates pipiens) have displayed uncharacteristically high levels of genetic diversity that have been attributed to large, stable populations. However, this widely distributed species also occurs in areas known for great climatic fluctuations that should be reflected in corresponding fluctuations in population sizes and reduced genetic diversity. To test our hypothesis that Northern Leopard Frog genetic diversity would be reduced in areas subjected to significant climate variability, we examined the genetic diversity of L. pipiens collected from 12 sites within the Prairie Pothole Region of North Dakota. Despite the region's fluctuating climate that includes periods of recurring drought and deluge, we found unexpectedly high levels of genetic diversity approaching that of northeastern populations. Further, genetic structure at a landscape scale was strikingly homogeneous; genetic differentiation estimates (Dest) averaged 0.10 (SD = 0.036) across the six microsatellite loci we studied, and two Bayesian assignment tests (STRUCTURE and BAPS) failed to reveal the development of significant population structure across the 68 km breadth of our study area. These results suggest that L. pipiens in the Prairie Pothole Region consists of a large, panmictic population capable of maintaining high genetic diversity in the face of marked climate variability.

  12. The dynamics of land cover change pattern and landscape fragmentation in Jiuzhaigou Nature Reserve, China

    NASA Astrophysics Data System (ADS)

    Hao, Yunqing; Wang, Jinxi; Jiang, Hong

    2009-10-01

    Nature reserves are facing a very challenging conflict between conservation and development today. The protection effect of Jiuzhaigou Nature Reserve has received considerable attention, especially in view of its stimulating tourism after the 1990s. Remote sensing data from 1974, 1994 and 2002 were chosen for the analysis of this reserve, since they closely represented the vegetation situation before and after felling, as well as the disturbance from the flush of tourism. We find that the quality and quantity of the forest in Jiuzhaigou Nature Reserve continues to decline, owing to the conifer area and whole forest area constantly shrinking, as well as the landscape fragmentation increasing. The rate of loss of forest in the second period (1994-2002) had showed down much than that in the first period (1974-1994), due to nature protection. Shrubland area continued to increase throughout the two periods, with an increased speed in the second period which was about 3.5 times that in the first period. The treeline was consistently retreating, contributing a total of 467.96 ha of conifer forest lost. However, the causes involved in tree mortality and the resulting regression of the treeline are not clear. In any case, under the general background of global warming, human impact undoubtedly should have direct or indirect cause dramatic consequences for the forest in this very sensitive zone, while there are many uncertainties in the behaviour of high mountain ecosystems. Keywords: Jiuzhaigou Nature Reserve, Vegetation, Habitats fragment,

  13. Energy landscape view of phase transitions and slow dynamics in thermotropic liquid crystals

    PubMed Central

    Chakrabarti, Dwaipayan; Bagchi, Biman

    2006-01-01

    Thermotropic liquid crystals are known to display rich phase behavior on temperature variation. Although the nematic phase is orientationally ordered but translationally disordered, a smectic phase is characterized by the appearance of a partial translational order in addition to a further increase in orientational order. In an attempt to understand the interplay between orientational and translational order in the mesophases that thermotropic liquid crystals typically exhibit upon cooling from the high-temperature isotropic phase, we investigate the potential energy landscapes of a family of model liquid crystalline systems. The configurations of the system corresponding to the local potential energy minima, known as the inherent structures, are determined from computer simulations across the mesophases. We find that the depth of the potential energy minima explored by the system along an isochor grows through the nematic phase as temperature drops in contrast to its insensitivity to temperature in the isotropic and smectic phases. The onset of the growth of the orientational order in the parent phase is found to induce a translational order, resulting in a smectic-like layer in the underlying inherent structures; the inherent structures, surprisingly, never seem to sustain orientational order alone if the parent nematic phase is sandwiched between the high-temperature isotropic phase and the low-temperature smectic phase. The Arrhenius temperature dependence of the orientational relaxation time breaks down near the isotropic–nematic transition. We find that this breakdown occurs at a temperature below which the system explores increasingly deeper potential energy minima. PMID:16648269

  14. Beyond words: evidence for automatic language-gesture integration of symbolic gestures but not dynamic landscapes.

    PubMed

    Vainiger, Dana; Labruna, Ludovica; Ivry, Richard B; Lavidor, Michal

    2014-01-01

    Understanding actions based on either language or action observation is presumed to involve the motor system, reflecting the engagement of an embodied conceptual network. We examined how linguistic and gestural information were integrated in a series of cross-domain priming studies. We varied the task demands across three experiments in which symbolic gestures served as primes for verbal targets. Primes were clips of symbolic gestures taken from a rich set of emblems. Participants responded by making a lexical decision to the target (Experiment 1), naming the target (Experiment 2), or performing a semantic relatedness judgment (Experiment 3). The magnitude of semantic priming was larger in the relatedness judgment and lexical decision tasks compared to the naming task. Priming was also observed in a control task in which the primes were pictures of landscapes with conceptually related verbal targets. However, for these stimuli, the amount of priming was similar across the three tasks. We propose that action observation triggers an automatic, pre-lexical spread of activation, consistent with the idea that language-gesture integration occurs in an obligatory and automatic fashion. PMID:23307151

  15. Species and Media Effects on Soil Carbon Dynamics in the Landscape

    PubMed Central

    Marble, S. Christopher; Prior, Stephen A.; Runion, G. Brett; Torbert, H. Allen; Gilliam, Charles H.; Fain, Glenn B.; Sibley, Jeff L.; Knight, Patricia R.

    2016-01-01

    Three woody shrub species [cleyera (Ternstroemia gymnanthera Thunb. ‘Conthery’), Indian hawthorn (Rhaphiolepis indica L.) and loropetalum (Loropetalum chinensis Oliv.‘Ruby’)] were container-grown for one growing season in 2008 using either pinebark (industry standard), clean chip residual or WholeTree (derived by-products from the forestry industry) as potting substrates and then transplanted into the landscape in 2008. An Automated Carbon Efflux System was used to continually monitor soil CO2 efflux from December 2010 through November 2011 in each species and substrate combination. Changes in soil carbon (C) levels as a result of potting substrate were assessed through soil sampling in 2009 and 2011 and plant biomass was determined at study conclusion. Results showed that soil CO2-C efflux was similar among all species and substrates, with few main effects of species or substrate observed throughout the study. Soil analysis showed that plots with pinebark contained higher levels of soil C in both 2009 and 2011, suggesting that pinebark decomposes slower than clean chip residual or WholeTree and consequently has greater C storage potential than the two alternative substrates. Results showed a net C gain for all species and substrate combinations; however, plants grown in pinebark had greater C sequestration potential. PMID:27140321

  16. A dynamic, non-steady state approach for paritioning of soil evaporation and plant water use at landscape scales

    NASA Astrophysics Data System (ADS)

    Caylor, K. K.; Wayland, H.; Scanlon, T. M.

    2015-12-01

    Seperate characterization of plant water use and soil evaporation are critical to understanding ecohydrological dynamics of dryland ecosystems and for efficiently managing water in dryland agriculture. The application of stable isotopes as a tracer of these individual fluxes has been constrained by obtaining robust measurements of the isotopic composition of plant water use (δT) that may be scaled up to the ecosystem level. Of particular concern is the fact that the isotopic composition of plant transpiration is usually assumed to be equal to the isotopic composition of xylem water; the so-called steady-state assumption. However, our results and the findings of other published studies strongly suggest that steady state conditions are unrealistic for vegetation in dynamic natural environments. This talk focuses on the development of a simple framework for using relationships between plant transpiration and δT to partition ET at the landscape level. Our method uses a newly-derived empirical relationship between leaf conductance and isotopic fractionation during transpiration to solve a system of equations that can provide solutions to the fraction of total ET composed of bare soil evaporation and transpiration. We apply our method to a time series of evapotranspiration fluxes and near-surface water vapor isotopic composition at a field station in central Kenya and compare the results with partitioning obtained from both steady-state approaches and non-isotopic approaches for partitioning.

  17. Measure of Landscape Heterogeneity by Agent-Based Methodology

    NASA Astrophysics Data System (ADS)

    Wirth, E.; Szabó, Gy.; Czinkóczky, A.

    2016-06-01

    With the rapid increase of the world's population, the efficient food production is one of the key factors of the human survival. Since biodiversity and heterogeneity is the basis of the sustainable agriculture, the authors tried to measure the heterogeneity of a chosen landscape. The EU farming and subsidizing policies (EEA, 2014) support landscape heterogeneity and diversity, nevertheless exact measurements and calculations apart from statistical parameters (standard deviation, mean), do not really exist. In the present paper the authors' goal is to find an objective, dynamic method that measures landscape heterogeneity. It is achieved with the so called agent-based modelling, where randomly dispatched dynamic scouts record the observed land cover parameters and sum up the features of a new type of land. During the simulation the agents collect a Monte Carlo integral as a diversity landscape potential which can be considered as the unit of the `greening' measure. As a final product of the ABM method, a landscape potential map is obtained that can serve as a tool for objective decision making to support agricultural diversity.

  18. Dynamics in Protected Areas and Domesticated Landscapes Caused by Climate Change and Anthropogenic Use

    NASA Astrophysics Data System (ADS)

    Hartter, J.; Ryan, S.; Stampone, M.; Chapman, C.

    2009-12-01

    Climate change, a key factor of concern for conservation, has important biological and social implications. Africa’s Albertine Rift is an area of extremely high endemic biodiversity and is classed as a world conservation priority. However, natural areas are represented by a chain of protected forest areas in a matrix of intensive smallholder agriculture and dense human settlements. Kibale National Park in western Uganda has become an island of forest surrounded by intensive small-scale agriculture and is the only remaining large area of mid-altitude forest remaining in Albertine Rift Region and East Africa. Increased temperature and precipitation over recent decades has been observed by scientists and local farmers, however, to date, rigorous analysis of local climate data and the impact of climate change on local resources does not exist. Moreover, local farmers report that some crops die or ripen too early because of increased precipitation. Conservation biologists and park managers are concerned that changes in tree phenology and primary productivity will alter wildlife feeding preferences and ranges leading to more human-wildlife conflict. Understanding the impact of local and regional climate change and variation within the social, conservation, and geographic context is necessary to construct informed management plans and to maintain positive park-people relationships. This paper describes our first attempt to fully integrate multiple temporal and spatial datasets, and our progress in developing an interdisciplinary framework to study social and ecological relationships in the Kibale landscape. We examine historical in situ climate data and proxy climate information derived from remotely sensed satellite-borne imagery in our preliminary analyses. Our goal is to link these data with both pre-existing imagery analyses and tree community composition and phenology data from 39 years of ongoing research to identify the pattern, trajectory, and drivers of local

  19. EPIC Simulation of Landscape and Management Effects on Soil Organic Carbon Dynamics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Simulation models integrate our understanding of soil organic C (SOC) dynamics and are useful tools for evaluating impacts of crop management on soil C sequestration. Our objectives were to calibrate the Environmental Policy Integrated Climate (EPIC) model and evaluate its performance for simulating...

  20. Energy landscape and dynamics of brain activity during human bistable perception

    PubMed Central

    Watanabe, Takamitsu; Masuda, Naoki; Megumi, Fukuda; Kanai, Ryota; Rees, Geraint

    2014-01-01

    Individual differences in the structure of parietal and prefrontal cortex predict the stability of bistable visual perception. However, the mechanisms linking such individual differences in brain structures to behaviour remain elusive. Here we demonstrate a systematic relationship between the dynamics of brain activity, cortical structure and behaviour underpinning bistable perception. Using fMRI in humans, we find that the activity dynamics during bistable perception are well described as fluctuating between three spatially distributed energy minimums: visual-area-dominant, frontal-area-dominant and intermediate states. Transitions between these energy minimums predicted behaviour, with participants whose brain activity tend to reflect the visual-area-dominant state exhibiting more stable perception and those whose activity transits to frontal-area-dominant states reporting more frequent perceptual switches. Critically, these brain activity dynamics are correlated with individual differences in grey matter volume of the corresponding brain areas. Thus, individual differences in the large-scale dynamics of brain activity link focal brain structure with bistable perception. PMID:25163855

  1. The Landscape of Evolution: Reconciling Structural and Dynamic Properties of Metabolic Networks in Adaptive Diversifications.

    PubMed

    Morrison, Erin S; Badyaev, Alexander V

    2016-08-01

    The network of the interactions among genes, proteins, and metabolites delineates a range of potential phenotypic diversifications in a lineage, and realized phenotypic changes are the result of differences in the dynamics of the expression of the elements and interactions in this deterministic network. Regulatory mechanisms, such as hormones, mediate the relationship between the structural and dynamic properties of networks by determining how and when the elements are expressed and form a functional unit or state. Changes in regulatory mechanisms lead to variable expression of functional states of a network within and among generations. Functional properties of network elements, and the magnitude and direction of evolutionary change they determine, depend on their location within a network. Here, we examine the relationship between network structure and the dynamic mechanisms that regulate flux through a metabolic network. We review the mechanisms that control metabolic flux in enzymatic reactions and examine structural properties of the network locations that are targets of flux control. We aim to establish a predictive framework to test the contributions of structural and dynamic properties of deterministic networks to evolutionary diversifications. PMID:27252203

  2. Thermokarst and thaw-related landscape dynamics -- an annotated bibliography with an emphasis on potential effects on habitat and wildlife

    USGS Publications Warehouse

    Jones, Benjamin M.; Amundson, Courtney L.; Koch, Joshua C.; Grosse, Guido

    2013-01-01

    Permafrost has warmed throughout much of the Northern Hemisphere since the 1980s, with colder permafrost sites warming more rapidly (Romanovsky and others, 2010; Smith and others, 2010). Warming of the near-surface permafrost may lead to widespread terrain instability in ice-rich permafrost in the Arctic and the Subarctic, and may result in thermokarst development and other thaw-related landscape features (Jorgenson and others, 2006; Gooseff and others, 2009). Thermokarst and other thaw-related landscape features result from varying modes and scales of permafrost thaw, subsidence, and removal of material. An increase in active-layer depth, water accumulation on the soil surface, permafrost degradation and associated retreat of the permafrost table, and changes to lake shores and coastal bluffs act and interact to create thermokarst and other thaw-related landscape features (Shur and Osterkamp, 2007). There is increasing interest in the spatial and temporal dynamics of thermokarst and other thaw-related features from diverse disciplines including landscape ecology, hydrology, engineering, and biogeochemistry. Therefore, there is a need to synthesize and disseminate knowledge on the current state of near-surface permafrost terrain. The term "thermokarst" originated in the Russian literature, and its scientific use has varied substantially over time (Shur and Osterkamp, 2007). The modern definition of thermokarst refers to the process by which characteristic landforms result from the thawing of ice-rich permafrost or the melting of massive ice (van Everdingen, 1998), or, more specifically, the thawing of ice-rich permafrost and (or) melting of massive ice that result in consolidation and deformation of the soil surface and formation of specific forms of relief (Shur, 1988). Jorgenson (2013) identifies 23 distinct thermokarst and other thaw-related features in the Arctic, Subarctic, and Antarctic based primarily on differences in terrain condition, ground-ice volume

  3. Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts

    PubMed Central

    Sikosek, Tobias; Bornberg-Bauer, Erich; Chan, Hue Sun

    2012-01-01

    Experimental studies have shown that some proteins exist in two alternative native-state conformations. It has been proposed that such bi-stable proteins can potentially function as evolutionary bridges at the interface between two neutral networks of protein sequences that fold uniquely into the two different native conformations. Under adaptive conflict scenarios, bi-stable proteins may be of particular advantage if they simultaneously provide two beneficial biological functions. However, computational models that simulate protein structure evolution do not yet recognize the importance of bi-stability. Here we use a biophysical model to analyze sequence space to identify bi-stable or multi-stable proteins with two or more equally stable native-state structures. The inclusion of such proteins enhances phenotype connectivity between neutral networks in sequence space. Consideration of the sequence space neighborhood of bridge proteins revealed that bi-stability decreases gradually with each mutation that takes the sequence further away from an exactly bi-stable protein. With relaxed selection pressures, we found that bi-stable proteins in our model are highly successful under simulated adaptive conflict. Inspired by these model predictions, we developed a method to identify real proteins in the PDB with bridge-like properties, and have verified a clear bi-stability gradient for a series of mutants studied by Alexander et al. (Proc Nat Acad Sci USA 2009, 106:21149–21154) that connect two sequences that fold uniquely into two different native structures via a bridge-like intermediate mutant sequence. Based on these findings, new testable predictions for future studies on protein bi-stability and evolution are discussed. PMID:23028272

  4. Modeling infectious disease dynamics in the complex landscape of global health

    PubMed Central

    Heesterbeek, Hans; Anderson, Roy; Andreasen, Viggo; Bansal, Shweta; De Angelis, Daniela; Dye, Chris; Eames, Ken; Edmunds, John; Frost, Simon; Funk, Sebastian; Hollingsworth, Deirdre; House, Thomas; Isham, Valerie; Klepac, Petra; Lessler, Justin; Lloyd-Smith, James; Metcalf, Jessica; Mollison, Denis; Pellis, Lorenzo; Pulliam, Juliet; Roberts, Mick; Viboud, Cecile

    2015-01-01

    Despite some notable successes in the control of infectious diseases, transmissible pathogens still pose an enormous threat to human and animal health. The ecological and evolutionary dynamics of infections play out on a wide range of interconnected temporal, organizational and spatial scales, which even within a single pathogen often span hours to months, cellular to ecosystem levels, and local to pandemic spread. Some pathogens are directly transmitted between individuals of a single species, while others circulate among multiple hosts, need arthropod vectors, or can survive in environmental reservoirs. Many factors, including increasing antimicrobial resistance, increased human connectivity, and dynamic human behavior, raise prevention and control from formerly national to international issues. In the face of this complexity, mathematical models offer essential tools for synthesizing information to understand epidemiological patterns, and for developing the quantitative evidence base for decision-making in global health. PMID:25766240

  5. Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography.

    PubMed

    Keedy, Daniel A; Kenner, Lillian R; Warkentin, Matthew; Woldeyes, Rahel A; Hopkins, Jesse B; Thompson, Michael C; Brewster, Aaron S; Van Benschoten, Andrew H; Baxter, Elizabeth L; Uervirojnangkoorn, Monarin; McPhillips, Scott E; Song, Jinhu; Alonso-Mori, Roberto; Holton, James M; Weis, William I; Brunger, Axel T; Soltis, S Michael; Lemke, Henrik; Gonzalez, Ana; Sauter, Nicholas K; Cohen, Aina E; van den Bedem, Henry; Thorne, Robert E; Fraser, James S

    2015-01-01

    Determining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity in the active site of the dynamic enzyme cyclophilin A (CypA) has been previously linked to its catalytic function, but the extent to which the different conformations of these residues are correlated is unclear. Here we compare the conformational ensembles of CypA by multitemperature synchrotron crystallography and fixed-target X-ray free-electron laser (XFEL) crystallography. The diffraction-before-destruction nature of XFEL experiments provides a radiation-damage-free view of the functionally important alternative conformations of CypA, confirming earlier synchrotron-based results. We monitored the temperature dependences of these alternative conformations with eight synchrotron datasets spanning 100-310 K. Multiconformer models show that many alternative conformations in CypA are populated only at 240 K and above, yet others remain populated or become populated at 180 K and below. These results point to a complex evolution of conformational heterogeneity between 180--240 K that involves both thermal deactivation and solvent-driven arrest of protein motions in the crystal. The lack of a single shared conformational response to temperature within the dynamic active-site network provides evidence for a conformation shuffling model, in which exchange between rotamer states of a large aromatic ring in the middle of the network shifts the conformational ensemble for the other residues in the network. Together, our multitemperature analyses and XFEL data motivate a new generation of temperature- and time-resolved experiments to structurally characterize the dynamic underpinnings of protein function. PMID:26422513

  6. Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography

    DOE PAGESBeta

    Keedy, Daniel A.; Kenner, Lillian R.; Warkentin, Matthew; Woldeyes, Rahel A.; Hopkins, Jesse B.; Thompson, Michael C.; Brewster, Aaron S.; Van Benschoten, Andrew H.; Baxter, Elizabeth L.; Uervirojnangkoorn, Monarin; et al

    2015-09-30

    Determining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity in the active site of the dynamic enzyme cyclophilin A (CypA) has been previously linked to its catalytic function, but the extent to which the different conformations of these residues are correlated is unclear. Here we compare the conformational ensembles of CypA by multitemperature synchrotron crystallography and fixed-target X-ray free-electron laser (XFEL) crystallography. The diffraction-before-destruction nature of XFEL experiments provides a radiation-damage-free view of the functionally important alternative conformations of CypA, confirming earlier synchrotron-based results. We monitored the temperature dependences ofmore » these alternative conformations with eight synchrotron datasets spanning 100-310 K. Multiconformer models show that many alternative conformations in CypA are populated only at 240 K and above, yet others remain populated or become populated at 180 K and below. These results point to a complex evolution of conformational heterogeneity between 180-–240 K that involves both thermal deactivation and solvent-driven arrest of protein motions in the crystal. The lack of a single shared conformational response to temperature within the dynamic active-site network provides evidence for a conformation shuffling model, in which exchange between rotamer states of a large aromatic ring in the middle of the network shifts the conformational ensemble for the other residues in the network. Together, our multitemperature analyses and XFEL data motivate a new generation of temperature- and time-resolved experiments to structurally characterize the dynamic underpinnings of protein function.« less

  7. Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography

    PubMed Central

    Keedy, Daniel A; Kenner, Lillian R; Warkentin, Matthew; Woldeyes, Rahel A; Hopkins, Jesse B; Thompson, Michael C; Brewster, Aaron S; Van Benschoten, Andrew H; Baxter, Elizabeth L; Uervirojnangkoorn, Monarin; McPhillips, Scott E; Song, Jinhu; Alonso-Mori, Roberto; Holton, James M; Weis, William I; Brunger, Axel T; Soltis, S Michael; Lemke, Henrik; Gonzalez, Ana; Sauter, Nicholas K; Cohen, Aina E; van den Bedem, Henry; Thorne, Robert E; Fraser, James S

    2015-01-01

    Determining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity in the active site of the dynamic enzyme cyclophilin A (CypA) has been previously linked to its catalytic function, but the extent to which the different conformations of these residues are correlated is unclear. Here we compare the conformational ensembles of CypA by multitemperature synchrotron crystallography and fixed-target X-ray free-electron laser (XFEL) crystallography. The diffraction-before-destruction nature of XFEL experiments provides a radiation-damage-free view of the functionally important alternative conformations of CypA, confirming earlier synchrotron-based results. We monitored the temperature dependences of these alternative conformations with eight synchrotron datasets spanning 100-310 K. Multiconformer models show that many alternative conformations in CypA are populated only at 240 K and above, yet others remain populated or become populated at 180 K and below. These results point to a complex evolution of conformational heterogeneity between 180-–240 K that involves both thermal deactivation and solvent-driven arrest of protein motions in the crystal. The lack of a single shared conformational response to temperature within the dynamic active-site network provides evidence for a conformation shuffling model, in which exchange between rotamer states of a large aromatic ring in the middle of the network shifts the conformational ensemble for the other residues in the network. Together, our multitemperature analyses and XFEL data motivate a new generation of temperature- and time-resolved experiments to structurally characterize the dynamic underpinnings of protein function. DOI: http://dx.doi.org/10.7554/eLife.07574.001 PMID:26422513

  8. Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography

    SciTech Connect

    Keedy, Daniel A.; Kenner, Lillian R.; Warkentin, Matthew; Woldeyes, Rahel A.; Hopkins, Jesse B.; Thompson, Michael C.; Brewster, Aaron S.; Van Benschoten, Andrew H.; Baxter, Elizabeth L.; Uervirojnangkoorn, Monarin; McPhillips, Scott E.; Song, Jinhu; Alonso-Mori, Roberto; Holton, James M.; Weis, William I.; Brunger, Axel T.; Soltis, S. Michael; Lemke, Henrik; Gonzalez, Ana; Sauter, Nicholas K.; Cohen, Aina E.; van den Bedem, Henry; Thorne, Robert E.; Fraser, James S.

    2015-09-30

    Determining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity in the active site of the dynamic enzyme cyclophilin A (CypA) has been previously linked to its catalytic function, but the extent to which the different conformations of these residues are correlated is unclear. Here we compare the conformational ensembles of CypA by multitemperature synchrotron crystallography and fixed-target X-ray free-electron laser (XFEL) crystallography. The diffraction-before-destruction nature of XFEL experiments provides a radiation-damage-free view of the functionally important alternative conformations of CypA, confirming earlier synchrotron-based results. We monitored the temperature dependences of these alternative conformations with eight synchrotron datasets spanning 100-310 K. Multiconformer models show that many alternative conformations in CypA are populated only at 240 K and above, yet others remain populated or become populated at 180 K and below. These results point to a complex evolution of conformational heterogeneity between 180-–240 K that involves both thermal deactivation and solvent-driven arrest of protein motions in the crystal. The lack of a single shared conformational response to temperature within the dynamic active-site network provides evidence for a conformation shuffling model, in which exchange between rotamer states of a large aromatic ring in the middle of the network shifts the conformational ensemble for the other residues in the network. Together, our multitemperature analyses and XFEL data motivate a new generation of temperature- and time-resolved experiments to structurally characterize the dynamic underpinnings of protein function.

  9. The analytical landscape of static and temporal dynamics in transcriptome data

    PubMed Central

    Oh, Sunghee; Song, Seongho; Dasgupta, Nupur; Grabowski, Gregory

    2014-01-01

    Interpreting gene expression profiles often involves statistical analysis of large numbers of differentially expressed genes, isoforms, and alternative splicing events at either static or dynamic spectrums. Reduced sequencing costs have made feasible dense time-series analysis of gene expression using RNA-seq; however, statistical methods in the context of temporal RNA-seq data are poorly developed. Here we will review current methods for identifying temporal changes in gene expression using RNA-seq, which are limited to static pairwise comparisons of time points and which fail to account for temporal dependencies in gene expression patterns. We also review recently developed very few number of temporal dynamic RNA-seq specific methods. Application and development of RNA-specific temporal dynamic methods have been continuously under the development, yet, it is still in infancy. We fully cover microarray specific temporal methods and transcriptome studies in initial digital technology (e.g., SAGE) between traditional microarray and new RNA-seq. PMID:24600473

  10. Response of rotation-translation blocked proteins using Langevin dynamics on a locally harmonic landscape.

    PubMed

    Manson, Anthony C; Coalson, Rob D

    2012-10-11

    Langevin dynamics is used to compute the time evolution of the nonequilibrium motion of the atomic coordinates of a protein in response to ligand dissociation. The protein potential energy surface (PES) is approximated by a harmonic basin about the minimum of the unliganded state. Upon ligand dissociation, the protein undergoes relaxation from the bound to the unbound state. A coarse graining scheme based on rotation translation blocks (RTB) is applied to the relaxation of the two domain iron transport protein, ferric binding protein. This scheme provides a natural and efficient way to freeze out the small amplitude, high frequency motions within each rigid fragment, thereby allowing for the number of dynamical degrees of freedom to be reduced. The results obtained from all flexible atom (constraint free) dynamics are compared to those obtained using RTB-Langevin dynamics. To assess the impact of the assumed rigid fragment clustering on the temporal relaxation dynamics of the protein molecule, three distinct rigid block decompositions were generated and their responses compared. Each of the decompositions was a variant of the one-block-per-residue grouping, with their force and friction matrices being derived from their fully flexible counterpart. Monitoring the time evolution of the distance separating a selected pair of amino acids, the response curves of the blocked decompositions were similar in shape to each other and to the control system in which all atomic degrees of freedom are fully independent. The similar shape of the blocked responses showed that the variations in grouping had only a minor impact on the kinematics. Compared with the all atom responses, however, the blocked responses were faster as a result of the instantaneous transmission of force throughout each rigid block. This occurred because rigid blocking does not permit any intrablock deformation that could store or divert energy. It was found, however, that this accelerated response could be

  11. Groundwater dynamics in wetland soils control the production and transfer mechanisms of dissolved reactive phosphorus in an agricultural landscape

    NASA Astrophysics Data System (ADS)

    Dupas, Rémi; Gu, Sen; Gruau, Gérard; Gascuel-Odoux, Chantal

    2015-04-01

    Because of its high sorption affinity on soils solid phase, mitigation options to reduce diffuse P transfer usually focus on trapping particulate P forms delivered via surface flowpaths. Therefore, vegetated buffer zones placed between croplands and watercourses have been promoted worldwide, sometimes in wetland areas. To investigate the risk of such P trapping riparian wetlands (RWs) releasing dissolved P to rivers, we monitored molybdate reactive P (MRP) in the free soil solution of two RWs in an intensively farmed catchment. Two main mechanisms causing MRP release were identified in light of the geochemical and hydrological conditions in the RWs, controlled by groundwater dynamics. First, soil rewetting after the dry summer was associated with the presence of a pool of mobile P, limited in size. Its mobilization started under conditions of water saturation caused by groundwater uprise in RW organo-mineral soil horizons. Second, the establishment of anoxic conditions in the end of the winter caused reductive solubilization of Fe oxide-hydroxide, along with release of P. Comparison between sites revealed that the first MRP release occurred only in a RW with P enriched soils, whereas the second was recorded even in a RW with a low soil P status. Seasonal variations in MRP concentrations in the stream were synchronized with those in RW soils. Hence, enriched and/or periodically anoxic RWs can act as a key component of the P transfer continuum in agricultural landscapes by converting particulate P from croplands into MRP released to rivers.

  12. Late Quaternary environmental and landscape dynamics revealed by a pingo sequence on the northern Seward Peninsula, Alaska

    NASA Astrophysics Data System (ADS)

    Wetterich, Sebastian; Grosse, Guido; Schirrmeister, Lutz; Andreev, Andrei A.; Bobrov, Anatoly A.; Kienast, Frank; Bigelow, Nancy H.; Edwards, Mary E.

    2012-04-01

    A terrestrial sediment sequence exposed in an eroding pingo provides insights into the late-Quaternary environmental history of the northern Seward Peninsula, Alaska. We have obtained the first radiocarbon-dated evidence for a mid-Wisconsin thermokarst lake, demonstrating that complex landscape dynamics involving cyclic permafrost aggradation and thermokarst lake formation occurred over stadial-interstadial as well as glacial-interglacial time periods. High values of Picea pollen and the presence of Larix pollen in sediments dated to 50-40 ka BP strongly suggest the presence of forest or woodland early in MIS 3; the trees grew within a vegetation matrix dominated by grass and sedge, and there is indirect evidence of grazing animals. Thus the interstadial ecosystem was different in structure and composition from the Holocene or from the preceding Last Interglacial period. An early Holocene warm period is indicated by renewed thermokarst lake formation and a range of fossil taxa. Multiple extralimital plant taxa suggest mean July temperatures above modern values. The local presence of spruce during the early Holocene warm interval is evident from a radiocarbon-dated spruce macrofossil remain and indicates significant range extension far beyond the modern tree line. The first direct evidence of spruce in Northwest Alaska during the early Holocene has implications for the presence of forest refugia in Central Beringia and previously assumed routes and timing of post-glacial forest expansion in Alaska.

  13. The binding landscape of plasmepsin V and the implications for flap dynamics.

    PubMed

    L, McGillewie; Soliman, Mahmoud E

    2016-04-26

    Plasmepsin V belongs to the plasmepsin family of aspartic proteases. PlmV is unique compared to other plasmepsins, as this membrane bound aspartic protease resides in the endoplasmic reticulum and is responsible for the cleavage of PEXEL tagged proteins destined for export outside of the host red blood cell. Plasmepsin V is highly conserved throughout the Plasmodium species, and is essential to the survival of the parasite. Recently, two potent inhibitors of Plmv have been identified, WEHI-916 and WEHI-842. Of these inhibitors, WEHI-842 has a higher binding affinity for P. vivax PlmV, and a crystal structure of PlmV in complex with WEHI-842 has recently been resolved (). The structure of PlmV is unique compared to other plasmepsins; it is stabilised internally by seven disulfide bonds, a NAP1 insert/fold is associated with the movement of the flap covering the active site and a highly conserved helix-turn-helix is situated towards the C-terminus. Flap motion and dynamics play an important role in enzyme selectivity and function. To better understand the impact of ligand binding on the flap dynamics, molecular dynamic simulations and post-dynamic analysis were employed in the present study on PlmV in complex with WEHI-842. Previously defined parameters, which accurately accounted for the opening and closing of the active site, were used to assess the conformational changes induced in the absence and presence of WEHI-842. From the simulations it can be seen that inhibitor binding significantly reduces the flexibility and mobility of not only the flap and flexible loop but areas outside of the active site. Ligand binding leads to the formation of a more stable compact structure. This being said, there is a possibility of reducing the flexibility even further with potentially more lethal effects on the plasmodium parasite. We believe that results presented herein would assist researchers in the discovery of potent PlmV inhibitors as potential antimalarial therapies

  14. Actin-binding proteins: the long road to understanding the dynamic landscape of cellular actin networks.

    PubMed

    Lappalainen, Pekka

    2016-08-15

    The actin cytoskeleton supports a vast number of cellular processes in nonmuscle cells. It is well established that the organization and dynamics of the actin cytoskeleton are controlled by a large array of actin-binding proteins. However, it was only 40 years ago that the first nonmuscle actin-binding protein, filamin, was identified and characterized. Filamin was shown to bind and cross-link actin filaments into higher-order structures and contribute to phagocytosis in macrophages. Subsequently many other nonmuscle actin-binding proteins were identified and characterized. These proteins regulate almost all steps of the actin filament assembly and disassembly cycles, as well as the arrangement of actin filaments into diverse three-dimensional structures. Although the individual biochemical activities of most actin-regulatory proteins are relatively well understood, knowledge of how these proteins function together in a common cytoplasm to control actin dynamics and architecture is only beginning to emerge. Furthermore, understanding how signaling pathways and mechanical cues control the activities of various actin-binding proteins in different cellular, developmental, and pathological processes will keep researchers busy for decades. PMID:27528696

  15. Integrated Stochastic Evaluation of Flood and Vegetation Dynamics in Riverine Landscapes

    NASA Astrophysics Data System (ADS)

    Miyamoto, H.; Kimura, R.

    2014-12-01

    Areal expansion of trees on gravel beds and sand bars has been a serious problem for river management in Japan. From the viewpoints of ecological restoration and flood control, it would be necessary to accurately predict the vegetation dynamics for a long period of time. This presentation tries to evaluate both vegetation overgrowth tendency and flood protection safety in an integrated manner for several vegetated channels in Kako River, Japan. The predominant tree species in Kako River are willows and bamboos. The evaluation employs a stochastic process model, which has been developed for statistically evaluating flow and vegetation status in a river course through the Monte Carlo simulation. The model for vegetation dynamics includes the effects of tree growth, mortality by flood impacts, and infant tree invasion. Through the Monte Carlo simulation for several cross sections in Kako River, responses of the vegetated channels are stochastically evaluated in terms of the changes of discharge magnitude and channel geomorphology. The result shows that the river channels with high flood protection priority are extracted from the several channel sections with the corresponding vegetation status. The present investigation suggests that the stochastic analysis could be one of the powerful diagnostic methods for river management.

  16. Dynamic and Combinatorial Landscape of Histone Modifications during the Intraerythrocytic Developmental Cycle of the Malaria Parasite.

    PubMed

    Saraf, Anita; Cervantes, Serena; Bunnik, Evelien M; Ponts, Nadia; Sardiu, Mihaela E; Chung, Duk-Won D; Prudhomme, Jacques; Varberg, Joseph M; Wen, Zhihui; Washburn, Michael P; Florens, Laurence; Le Roch, Karine G

    2016-08-01

    A major obstacle in understanding the complex biology of the malaria parasite remains to discover how gene transcription is controlled during its life cycle. Accumulating evidence indicates that the parasite's epigenetic state plays a fundamental role in gene expression and virulence. Using a comprehensive and quantitative mass spectrometry approach, we determined the global and dynamic abundance of histones and their covalent post-transcriptional modifications throughout the intraerythrocytic developmental cycle of Plasmodium falciparum. We detected a total of 232 distinct modifications, of which 160 had never been detected in Plasmodium and 88 had never been identified in any other species. We further validated over 10% of the detected modifications and their expression patterns by multiple reaction monitoring assays. In addition, we uncovered an unusual chromatin organization with parasite-specific histone modifications and combinatorial dynamics that may be directly related to transcriptional activity, DNA replication, and cell cycle progression. Overall, our data suggest that the malaria parasite has a unique histone modification signature that correlates with parasite virulence. PMID:27291344

  17. Influence of magnetic domain landscape on the flux dynamics in superconductor/ferromagnet bilayers

    NASA Astrophysics Data System (ADS)

    Adamus, Z.; Cieplak, Marta Z.; Kończykowski, M.; Zhu, L. Y.; Chien, C. L.

    2016-02-01

    We use a line of miniature Hall sensors to study the influence of the magnetic domain distribution on the flux dynamics in superconductor/ferromagnet bilayers. Two bilayers are built of a ferromagnetic Co/Pt multilayer with perpendicular magnetic anisotropy and a superconducting Nb layer, with the insulating layer in-between to avoid proximity effect. The magnetic domain patterns of various geometries are reversibly predefined in the Co/Pt multilayers using the appropriate magnetization procedure. The Pt thickness is different in the two bilayers, resulting in different width and length of the domains, which profoundly affects vortex dynamics. We show that narrow short domains lead to strong confinement of vortices at the sample edge, while narrow elongated domains of uniform width induce smaller confinement and easy vortex entry. Large enhancement of flux pinning and critical current density, by a factor of more than 7, is observed in the last case, while the former results in smaller enhancement. When domains are wide, the disorder in the domain widths becomes beneficial for larger enhancement of pinning, while more uniform distribution of domain widths results in a precipitous drop of the enhancement. The analysis of these results suggests that with increasing domain width, a transition occurs from vortex chains pinned by narrow domains to disordered triangular vortex lattice pinned by a maze of multiply interconnected magnetic domains.

  18. Vegetal Optimality and Macro-Scale Dynamic Vegetation - Scaling from Leaf to Landscape

    NASA Astrophysics Data System (ADS)

    Quebbeman, J.; Ramirez, J. A.

    2014-12-01

    Macro-scale spatially distributed hydrologic models require extensive parameterization of both soil and vegetal properties. Proper parameterization of vegetation is critical for understanding vegetal response to hydro-climatic variability, as vegetation provides a key feedback to climate. A common practice for Dynamic Global Vegetation Models is to use plant functional types (PFTs), which limit vegetation to discrete classes. We present a physically based long-term macro-scale coupled vegetation and hydrology model capable of responding dynamically to climate variability, and parameterize it assuming vegetal optimality hypotheses. We hypothesize that canopy scale vegetation will adopt a strategy that maximizes the expected net assimilation, minus photosynthetic system construction and maintenance costs, over an annual basis. We perform stochastic multi-decadal simulations to estimate the expected fitness for a unique vegetal parameterization and water use strategy. As a result, optimal parameter sets are defined, which can be used instead of a PFT characterization of land cover. Estimates of evaporation, transpiration and gross primary production obtained using the optimal parameter sets over a range of climates are then compared against FLUXNET data.

  19. Dynamics of Plains Cottonwood ( Populus deltoides) Forests and Historical Landscape Change along Unchannelized Segments of the Missouri River, USA

    NASA Astrophysics Data System (ADS)

    Dixon, Mark D.; Johnson, W. Carter; Scott, Michael L.; Bowen, Daniel E.; Rabbe, Lisa A.

    2012-05-01

    Construction of six large dams and reservoirs on the Missouri River over the last 50-75 years has resulted in major landscape changes and alterations in flow patterns, with implications for riparian forests dominated by plains cottonwood ( Populus deltoides). We quantified changes in land cover from 1892-1950s and the 1950s-2006 and the current extent and age structure of cottonwood forests on seven segments (two reservoir and five remnant floodplain) comprising 1127 km (53 %) of the unchannelized upper two-thirds of the Missouri River. Riparian forest area declined by 49 %; grassland 61 %; shrubland 52 %; and sandbar habitat 96 %; while agricultural cropland increased six-fold and river/reservoir surface area doubled from 1892 to 2006. Net rates of erosion and accretion declined between the 1892-1950s and 1950s-2006 periods. Accretion exceeded erosion on remnant floodplain segments, resulting in declines in active channel width, particularly in 1950s-2006. Across all study segments in 2006, most cottonwood stands (67 %) were >50 years old, 22 % were 25-50 years old, and only 10 % were <25 years old. Among stands <50 years old, the higher proportion of 25-50 year old stands represents recruitment that accompanied initial post-dam channel narrowing; while declines in sandbar and shrubland area and the low proportion of stands <25 years old suggest declines in geomorphic dynamism and limited recruitment under recent river management. Future conservation and restoration efforts should focus both on limiting further loss of remnant cottonwood stands and developing approaches to restore river dynamics and cottonwood recruitment processes.

  20. Dynamics of plains cottonwood (Populus deltoides) forests and historical landscape change along unchannelized segments of the Missouri River, USA.

    PubMed

    Dixon, Mark D; Johnson, W Carter; Scott, Michael L; Bowen, Daniel E; Rabbe, Lisa A

    2012-05-01

    Construction of six large dams and reservoirs on the Missouri River over the last 50-75 years has resulted in major landscape changes and alterations in flow patterns, with implications for riparian forests dominated by plains cottonwood (Populus deltoides). We quantified changes in land cover from 1892-1950s and the 1950s-2006 and the current extent and age structure of cottonwood forests on seven segments (two reservoir and five remnant floodplain) comprising 1127 km (53 %) of the unchannelized upper two-thirds of the Missouri River. Riparian forest area declined by 49 %; grassland 61 %; shrubland 52 %; and sandbar habitat 96 %; while agricultural cropland increased six-fold and river/reservoir surface area doubled from 1892 to 2006. Net rates of erosion and accretion declined between the 1892-1950s and 1950s-2006 periods. Accretion exceeded erosion on remnant floodplain segments, resulting in declines in active channel width, particularly in 1950s-2006. Across all study segments in 2006, most cottonwood stands (67 %) were >50 years old, 22 % were 25-50 years old, and only 10 % were <25 years old. Among stands <50 years old, the higher proportion of 25-50 year old stands represents recruitment that accompanied initial post-dam channel narrowing; while declines in sandbar and shrubland area and the low proportion of stands <25 years old suggest declines in geomorphic dynamism and limited recruitment under recent river management. Future conservation and restoration efforts should focus both on limiting further loss of remnant cottonwood stands and developing approaches to restore river dynamics and cottonwood recruitment processes. PMID:22476667

  1. ELECTROMAGNETISM, OPTICS, ACOUSTICS, HEAT TRANSFER, CLASSICAL MECHANICS, AND FLUID DYNAMICS: Exact Soliton Solutions to a Generalized Nonlinear Schrödinger Equation

    NASA Astrophysics Data System (ADS)

    Xu, Si-Liu; Liang, Jian-Chu; Yi, Lin

    2010-01-01

    The (1+1)-dimensional F-expansion technique and the homogeneous nonlinear balance principle have been generalized and applied for solving exact solutions to a general (3+1)-dimensional nonlinear Schrödinger equation (NLSE) with varying coefficients and a harmonica potential. We found that there exist two kinds of soliton solutions. The evolution features of exact solutions have been numerically studied. The (3+1)D soliton solutions may help us to understand the nonlinear wave propagation in the nonlinear media such as classical optical waves and the matter waves of the Bose-Einstein condensates.

  2. The influence of hydrogeomorphic dynamics on fish habitat: A case study using the ooCAESAR landscape evolution model

    NASA Astrophysics Data System (ADS)

    Wheaton, J. M.; Sear, D. A.; Darby, S. E.; Booker, D. E.; Acreman, M.

    2005-12-01

    The sediments, morphological features and riverflows that define the hydrogeomorphology of natural river channels provide physical habitat diversity that sustains the aquatic biodiversity of river ecosystems. This simple concept underpins the large number of contemporary ecohydraulic models that are available in the literature. Such models have been widely used to predict how morphological diversity (taken here to encompass channel sediments, topography and flow velocity) influences habitat quality for target species at the reach scale. The accuracy of these predictions is a matter of considerable practical importance, as the results are frequently used as the basis for restoration or rehabilitation. However, such models are limited in that they do not account for dynamic changes in river morphology, which themselves are triggered by changes in the flows of water and sediment delivered from the watershed upstream and stimulated by climatic, tectonic or land cover perturbations across a wide range of temporal scales. Accordingly there is an urgent need to combine the outputs of catchment-based geomorphological models with ecohydraulic models, so that predictions of habitat quality focused on specific reaches can be placed into their appropriate (i.e., the watershed) spatial context. To address these issues we herein present preliminary simulations from a case study of the Sulphur Creek watershed, a 24.2 sq. km., third-order catchment draining one of 47 tributaries to the Napa River, which empties southerly into the San Francisco Bay of northern California. Therein, the influence of catchment-scale geomorphic dynamics on reach-scale fish habitat is investigated using the ooCAESAR landscape evolution model. This cellular automaton model, based on its predecessor CAESAR, was chosen because it can be run at spatial resolutions (1 to 5 m.) that are ecologically meaningful and at temporal resolutions that capture both individual event dynamics and long-term evolutionary

  3. Exploring the Dynamics and Mutational Landscape of Riboregulation with a Minimal Synthetic Circuit in Living Cells.

    PubMed

    Rodrigo, Guillermo; Majer, Eszter; Prakash, Satya; Daròs, José-Antonio; Jaramillo, Alfonso; Poyatos, Juan F

    2015-09-01

    The regulation of gene expression, triggered by conformational changes in RNA molecules, is widely observed in cellular systems. Here, we examine this mode of control by means of a model-based design and construction of a fully synthetic riboregulatory device. We present a theoretical framework that rests on a simple energy model to predict the dynamic response of such a system. Following an equilibrium description, our framework integrates thermodynamic properties—anticipated with an RNA physicochemical model—with a detailed description of the intermolecular interaction. The theoretical calculations are confirmed with an experimental characterization of the action of the riboregulatory device within living cells. This illustrates, more broadly, the predictability of genetic robustness on synthetic systems, and the faculty to engineer gene expression programs from a minimal set of first principles. PMID:26331264

  4. Modeling infectious disease dynamics in the complex landscape of global health.

    PubMed

    Heesterbeek, Hans; Anderson, Roy M; Andreasen, Viggo; Bansal, Shweta; De Angelis, Daniela; Dye, Chris; Eames, Ken T D; Edmunds, W John; Frost, Simon D W; Funk, Sebastian; Hollingsworth, T Deirdre; House, Thomas; Isham, Valerie; Klepac, Petra; Lessler, Justin; Lloyd-Smith, James O; Metcalf, C Jessica E; Mollison, Denis; Pellis, Lorenzo; Pulliam, Juliet R C; Roberts, Mick G; Viboud, Cecile

    2015-03-13

    Despite some notable successes in the control of infectious diseases, transmissible pathogens still pose an enormous threat to human and animal health. The ecological and evolutionary dynamics of infections play out on a wide range of interconnected temporal, organizational, and spatial scales, which span hours to months, cells to ecosystems, and local to global spread. Moreover, some pathogens are directly transmitted between individuals of a single species, whereas others circulate among multiple hosts, need arthropod vectors, or can survive in environmental reservoirs. Many factors, including increasing antimicrobial resistance, increased human connectivity and changeable human behavior, elevate prevention and control from matters of national policy to international challenge. In the face of this complexity, mathematical models offer valuable tools for synthesizing information to understand epidemiological patterns, and for developing quantitative evidence for decision-making in global health. PMID:25766240

  5. Human-caused mortality influences spatial population dynamics: pumas in landscapes with varying mortality risks

    USGS Publications Warehouse

    Newby, Jesse R.; Mills, L. Scott; Ruth, Toni K.; Pletscher, Daniel H.; Mitchell, Michael S.; Quigley, Howard B.; Murphy, Kerry M.; DeSimone, Rich

    2013-01-01

    An understanding of how stressors affect dispersal attributes and the contribution of local populations to multi-population dynamics are of immediate value to basic and applied ecology. Puma (Puma concolor) populations are expected to be influenced by inter-population movements and susceptible to human-induced source–sink dynamics. Using long-term datasets we quantified the contribution of two puma populations to operationally define them as sources or sinks. The puma population in the Northern Greater Yellowstone Ecosystem (NGYE) was largely insulated from human-induced mortality by Yellowstone National Park. Pumas in the western Montana Garnet Mountain system were exposed to greater human-induced mortality, which changed over the study due to the closure of a 915 km2 area to hunting. The NGYE’s population growth depended on inter-population movements, as did its ability to act as a source to the larger region. The heavily hunted Garnet area was a sink with a declining population until the hunting closure, after which it became a source with positive intrinsic growth and a 16× increase in emigration. We also examined the spatial and temporal characteristics of individual dispersal attributes (emigration, dispersal distance, establishment success) of subadult pumas (N = 126). Human-caused mortality was found to negatively impact all three dispersal components. Our results demonstrate the influence of human-induced mortality on not only within population vital rates, but also inter-population vital rates, affecting the magnitude and mechanisms of local population’s contribution to the larger metapopulation.

  6. Exploring the structure and conformational landscape of human leptin. A molecular dynamics approach.

    PubMed

    Chimal-Vega, Brenda; Paniagua-Castro, Norma; Carrillo Vazquez, Jonathan; Rosas-Trigueros, Jorge L; Zamorano-Carrillo, Absalom; Benítez-Cardoza, Claudia G

    2015-11-21

    Leptin is a hormone that regulates energy homeostasis, inflammation, hematopoiesis and immune response, among other functions (Houseknecht et al., 1998; Zhang et al., 1995; Paz-Filho et al., 2010). To obtain its crystallographic structure, it was necessary to substitute a tryptophan for a glutamic acid at position 100, thus creating a mutant leptin that has been reported to have biological activity comparable to the activity of the wild type but that crystallizes more readily. Here, we report a comparative study of the conformational space of WT and W100E leptin using molecular dynamics simulations performed at 300, 400, and 500 K. We detected differences between the interactions of the two proteins with local and distal effects, resulting in changes in the conformation, accessible surface area, compactness, electrostatic potential and dynamic behavior. Additionally, the series of unfolding events that occur when leptin is subjected to high temperature differs for the two constructs. We observed that both proteins are mostly unstructured after 20 ns of MD simulation at 500 K. However, WT leptin maintains a significant amount of secondary structure in helix α2, while the most stable region of W100E leptin is helix α3. Furthermore, we found that the region between residues 25 and 42 might adopt interconverting secondary structures ranging from α-helices and random coils to β-strand structures. Thus, this region can be considered an intrinsically disordered region. This atomistic description supports our understanding of leptin signaling and consequently might facilitate the use of leptin in treatments for the pathophysiologies in which it is implicated. PMID:26342543

  7. Hydrogeologic Controls on Water Dynamics in a Discontinuous Permafrost, Lake-Rich Landscape

    NASA Astrophysics Data System (ADS)

    Walvoord, M. A.; Briggs, M. A.; Day-Lewis, F. D.; Jepsen, S. M.; Lane, J. W., Jr.; McKenzie, J. M.; Minsley, B. J.; Striegl, R. G.; Voss, C. I.; Wellman, T. P.

    2014-12-01

    Understanding permafrost distribution, rate of change, and influence on groundwater movement are critical for assessing climate change impacts in northern ecosystems. Lake-rich lowlands in interior Alaska provide important habitat for migratory waterfowl, ungulates, and other wildlife. Despite low annual precipitation, the Yukon Flats area in the north central Yukon River Basin of Alaska (USA) supports over 20,000 lakes, due in part to the presence of permafrost. The fate of this lake-rich lowland and, by proxy, similar circumboreal lowland systems under projected climate warming is the focus of a series of recent studies highlighted here. Lake water chemistry analyses of over 200 lakes in the Yukon Flats reveal a large degree of spatial heterogeneity suggestive of a hydrologically disconnected system, a conclusion also supported by abrupt spatial changes in lake elevation. Airborne geophysical characterization shows a laterally continuous shallow gravel layer (~25-m thick) that would offer good hydraulic connectivity throughout the lowlands. However, the gravel layer is generally frozen (as permafrost) except beneath surface water bodies; thus inhibiting lateral pathways of groundwater flow under current conditions. Ground-based geophysical characterization provides a high resolution of permafrost distribution and relevant hydrogeologic features at several lake study sites. Relatively recent thaw in the gravel layer appears to be associated with lakes that have experienced change in size (area) over the past several decades, whereas lakes with taliks (unfrozen conduits) that fully penetrate the permafrost layer are more likely to be stable. Multi-scale permafrost characterization provides the basis for numerical models that simulate permafrost dynamics, lake-talik evolution, supra-, intra-, and sub-permafrost groundwater flow, lake-groundwater exchange, active layer dynamics, and permafrost aggradation response to lake recession. Collective field and simulation

  8. Geomorpho-Landscapes

    NASA Astrophysics Data System (ADS)

    Farabollini, Piero; Lugeri, Francesca; Amadio, Vittorio

    2014-05-01

    Landscape is the object of human perceptions, being the image of spatial organization of elements and structures: mankind lives the first approach with the environment, viewing and feeling the landscape. Many definitions of landscape have been given over time: in this case we refer to the Landscape defined as the result of interaction among physical, biotic and anthropic phenomena acting in a different spatial-temporal scale (Foreman & Godron) Following an Aristotelic approach in studying nature, we can assert that " Shape is synthesis": so it is possible to read the land features as the expression of the endogenous and exogenous processes that mould earth surfaces; moreover, Landscape is the result of the interaction of natural and cultural components, and conditions the spatial-temporal development of a region. The study of the Landscape offers results useful in order to promote sustainable development, ecotourism, enhancement of natural and cultural heritage, popularization of the scientific knowledge. In Italy, a very important GIS-based tool to represent the territory is the "Carta della Natura" ("Map of Nature", presently coordinated by the ISPRA) that aims at assessing the state of the whole Italian territory, analyzing Landscape. The methodology follows a holistic approach, taking into consideration all the components of a landscape and then integrating the information. Each individual landscape, studied at different scales, shows distinctive elements: structural, which depend on physical form and specific spatial organization; functional, which depend on relationships created between biotic and abiotic elements, and dynamic, which depend on the successive evolution of the structure. The identification of the landscape units, recognized at different scales of analysis, allows an evaluation of the state of the land, referring to the dual risk/resource which characterizes the Italian country. An interesting opportunity is to discover those areas of unusual

  9. The Dynamic Architectural and Epigenetic Nuclear Landscape: Developing the Genomic Almanac of Biology and Disease

    PubMed Central

    Tai, Phillip W. L.; Zaidi, Sayyed K.; Wu, Hai; Grandy, Rodrigo A.; Montecino, Martin M.; van Wijnen, André J.; Lian, Jane B.; Stein, Gary S.; Stein, Janet L.

    2014-01-01

    Compaction of the eukaryotic genome into the confined space of the cell nucleus must occur faithfully throughout each cell cycle to retain gene expression fidelity. For decades, experimental limitations to study the structural organization of the interphase nucleus restricted our understanding of its contributions towards gene regulation and disease. However, within the past few years, our capability to visualize chromosomes in vivo with sophisticated fluorescence microscopy, and to characterize chromosomal regulatory environments via massively-parallel sequencing methodologies have drastically changed how we currently understand epigenetic gene control within the context of three-dimensional nuclear structure. The rapid rate at which information on nuclear structure is unfolding brings challenges to compare and contrast recent observations with historic findings. In this review, we discuss experimental breakthroughs that have influenced how we understand and explore the dynamic structure and function of the nucleus, and how we can incorporate historical perspectives with insights acquired from the ever-evolving advances in molecular biology and pathology. PMID:24242872

  10. Deciphering the energy landscape of the interaction uranyl-DCP with antibodies using dynamic force spectroscopy.

    PubMed

    Teulon, Jean-Marie; Parot, Pierre; Odorico, Michael; Pellequer, Jean-Luc

    2008-11-15

    Previous studies on molecular recognition of uranyl-DCP (dicarboxy-phenanthroline chelator) compound by two distinct monoclonal antibodies (Mabs U04S and U08S) clearly showed the presence of a biphasic shape in Bell-Evans' plots and an accentuated difference in slopes at the high loading rates. To further explore the basis in the slope difference, we have performed complementary experiments using antibody PHE03S, raised against uranyl-DCP but, presenting a strong cross-reactivity toward the DCP chelator. This work allowed us to obtain a reallocation of the respective contributions of the metal ion itself and that of the chelator. Results led us to propose a 2D schematic model representing two energy barriers observed in the systems Mabs U04S- and U08S-[UO(2)-DCP] where the outer barrier characterizes the interaction between UO(2) and Mab whereas the inner barrier characterizes the interaction between DCP and Mab. Using dynamic force spectroscopy, it is thus possible to dissect molecular interactions during the unbinding between proteins and ligands. PMID:18790844

  11. Deciphering the Energy Landscape of the Interaction Uranyl-DCP with Antibodies Using Dynamic Force Spectroscopy

    PubMed Central

    Teulon, Jean-Marie; Parot, Pierre; Odorico, Michael; Pellequer, Jean-Luc

    2008-01-01

    Previous studies on molecular recognition of uranyl-DCP (dicarboxy-phenanthroline chelator) compound by two distinct monoclonal antibodies (Mabs U04S and U08S) clearly showed the presence of a biphasic shape in Bell-Evans' plots and an accentuated difference in slopes at the high loading rates. To further explore the basis in the slope difference, we have performed complementary experiments using antibody PHE03S, raised against uranyl-DCP but, presenting a strong cross-reactivity toward the DCP chelator. This work allowed us to obtain a reallocation of the respective contributions of the metal ion itself and that of the chelator. Results led us to propose a 2D schematic model representing two energy barriers observed in the systems Mabs U04S- and U08S-[UO2-DCP] where the outer barrier characterizes the interaction between UO2 and Mab whereas the inner barrier characterizes the interaction between DCP and Mab. Using dynamic force spectroscopy, it is thus possible to dissect molecular interactions during the unbinding between proteins and ligands. PMID:18790844

  12. Dynamic Transcriptome Landscape of Maize Embryo and Endosperm Development1[W][OPEN

    PubMed Central

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

    2014-01-01

    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

  13. Tropolone Complexes Formed with Amphoteric Ligands: Structure and Dynamics as Viewed across the Vibronic Landscape

    NASA Astrophysics Data System (ADS)

    Nemchick, Deacon J.; Chew, Kathryn; Vaccaro, Patrick H.

    2013-06-01

    Owing to the presence of a finite potential barrier that adjoins hydroxylic (proton-donating) and ketonic (proton-accepting) oxygen atom centers, tropolone (TrOH) long has served as a model system for the investigation of coherent (symmetrical) proton-transfer events. Hydrogen-bound complexes formed by docking amphoteric species onto the TrOH substrate, such as those involving formic acid [TrOH-(FA)_n] and other simultaneous donor-acceptor ligands, have been generated under supersonic free-jet expansion conditions. For binary adducts (n=1), quantum-chemical calculations predict two nearly degenerate isomers that can be labeled as external (ligand attached to the seven-membered aromatic ring) and internal (ligand bound to the O-H \\cdot\\cdot\\cdot O reaction site), where the latter cleft-bound form offers the tantalizing possibility of undergoing a double proton-transfer process. A variety of spectroscopic probes build around the intense ˜{A}^{1}{B}_{2}-˜{X}^{1}{A}_{1} (π ^{*}←π) near-ultraviolet absorption feature of bare tropolone have been enlisted to elucidate the binding motifs and reaction pathways in complexes containing one or more amphoteric ligands, including vibrationally resolved schemes based upon laser-induced fluorescence (LIF), dispersed fluorescence (DF), and fluorescence hole-burning (FHB) methods. Structural and dynamical information gleaned from these experiments will be discussed in light of complementary ab initio calculations.

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

    NASA Astrophysics Data System (ADS)

    D'Alpaos, Andrea; Lanzoni, Stefano; Marani, Marco; Rinaldo, Andrea

    2007-03-01

    We propose an ecomorphodynamic model which conceptualizes the chief land-forming processes operating on the intertwined, long-term evolution of marsh platforms and embedded tidal networks. The rapid network incision (previously addressed by the authors) is decoupled from the geomorphological dynamics of intertidal areas, governed by sediment erosion and deposition and crucially affected by the presence of vegetation. This allows us to investigate the response of tidal morphologies to different scenarios of sediment supply, colonization by halophytes, and changing sea level. Different morphological evolutionary regimes are shown to depend on marsh ecology. Marsh accretion rates, enhanced by vegetation growth, and the related platform elevations tend to decrease with distance from the creek, measured along suitably defined flow paths. The negative feedback between surface elevation and its inorganic accretion rate is reinforced by the relation between plant productivity and soil elevation in Spartina-dominated marshes and counteracted by positive feedbacks in multispecies-vegetated marshes. When evolving under constant sea level, unvegetated and Spartina-dominated marshes asymptotically tend to mean high water level (MHWL), different from multiple vegetation species marshes, which can make the evolutionary transition to upland. Equilibrium configurations below MHWL can be reached under constant rates of sea level rise, depending on sediment supply and vegetation productivity. Our analyses on marine regressions and transgressions show that when the system is in a supply-limited regime, network retreat and expansion (associated with regressions and transgressions, respectively) tend to be cyclic. Conversely, in a transport-limited regime, network reexpansion following a regression tends to take on a new configuration, showing a hysteretic behavior.

  15. Disorder on the landscape

    SciTech Connect

    Podolsky, Dmitry; Jokela, Niko; Majumder, Jaydeep E-mail: majumder@mnnit.ac.in

    2008-05-15

    Disorder on the string theory landscape may significantly affect dynamics of eternal inflation leading to the possibility for some vacua on the landscape to become dynamically preferable over others. We systematically study effects of a generic disorder on the landscape, starting by identifying a sector with built-in disorder-a set of de Sitter vacua corresponding to compactifications of the type IIB string theory on Calabi-Yau manifolds with a number of warped Klebanov-Strassler throats attached randomly to the bulk part of the Calabi-Yau. Further, we derive a continuum limit of the vacuum dynamics equations on the landscape. Using methods of the dynamical renormalization group we determine the late-time behavior of the probability distribution for an observer to measure a given value of the cosmological constant. We find the diffusion of the probability distribution to significantly slow down in sectors of the landscape where the number of nearest-neighboring vacua for any given vacuum is small. We discuss the relation of this slowdown with the phenomenon of Anderson localization in disordered media.

  16. Assessment of present day geomorphological dynamics to decipher landscape evolution around the Paleolithic sites of Melka Kunture, Ethiopia

    NASA Astrophysics Data System (ADS)

    Maerker, Michael; Schillaci, Calogero; Melis, Rita; Mussi, Margherita

    2014-05-01

    The area of Melka Kunture (central Ethiopia) is one of the most important clusters of Paleolithic sites in Eastern Africa. The archaeological record spans from c. 1.7 Ma onwards, with a number of stratified occurrences of Oldowan, Acheulean, Middle Stone Age and Late Stone Age industries, together with faunal remains and human fossils. However, the archaeological sites are endangered by flooding and soil erosion. The main excavation area lies close to the convergence of the Awash river with the Atabella river, one of the main tributaries of the upper Awash catchment. In the semi-arid Ethiopian highlands, gully networks develop especially in the vicinity of the active and inactive river meanders. Various erosion processes are linked to specific driving factors such as the rainfall regime, the land use/cover changes and vertic soils with a specific hydrological behaviour. It was documented in the field and by previous research that the origin of most of the man made erosion channels is due to animal pathways and car tracks. However, paleolandscape features increase the general erosion risk. Former wetland areas and deposition zones are particularly affected by soil erosion processes. Hence, the spatial distribution and characteristics of present day geomorphic processes also reveal information on the paleolandscape. In order to assess landscape evolution and present day geomorphologic dynamics, we mapped the geomorphology describing in detail the present-day slope processes at a 10.000 scale. We performed a detailed terrain analysis based on high resolution DEMs such as SRTM-X with 25m resolution and ALOS/PRISM with 10m resolution to characterize the main erosion processes and surface runoff dynamics. The latter ones are simulated using a Soil Conservation Service Curve Number method. Landuse was delineated for a larger area using ASTER 25m multispectral data. Finally, using calibrated topographic indices and a simple hydrological model we were able to detect and

  17. Satellite remote sensing of landscape freeze/thaw state dynamics for complex Topography and Fire Disturbance Areas Using multi-sensor radar and SRTM digital elevation models

    NASA Technical Reports Server (NTRS)

    Podest, Erika; McDonald, Kyle; Kimball, John; Randerson, James

    2003-01-01

    We characterize differences in radar-derived freeze/thaw state, examining transitions over complex terrain and landscape disturbance regimes. In areas of complex terrain, we explore freezekhaw dynamics related to elevation, slope aspect and varying landcover. In the burned regions, we explore the timing of seasonal freeze/thaw transition as related to the recovering landscape, relative to that of a nearby control site. We apply in situ biophysical measurements, including flux tower measurements to validate and interpret the remotely sensed parameters. A multi-scale analysis is performed relating high-resolution SAR backscatter and moderate resolution scatterometer measurements to assess trade-offs in spatial and temporal resolution in the remotely sensed fields.

  18. Age and dynamics of the Namib Sand Sea: A review of chronological evidence and possible landscape development models

    NASA Astrophysics Data System (ADS)

    Stone, A. E. C.

    2013-06-01

    The Namib Sand Sea constitutes a major physiographic feature of the Namib Desert on the west of Namibia, covering a 50-160 km wide region of the coast between Lüderitz and Walvis Bay. It is widely considered to be one of the oldest desert regions, with a Tertiary-aged fossil desert underlying the modern sand sea. The sand sea has been well studied, benefiting from the presence of the Gobabeb Training and Research Centre during the past 50 years. Whilst much is understood about its sediments and geomorphology, it is only recently that new chronological information, using cosmogenic-nuclide burial dating and optically stimulated luminescence dating have offered new insights, and this calls for an updated review of the age and landscape development of the sand sea. This assessment of the geomorphological and Quaternary dynamics of the region is complemented by developments in the description and analysis of sediment composition. New age control from cosmogenic dating indicates that the sand sea is in excess of a million years old. Initial data from luminescence dating yields depositional ages for dune sediments from three broad areas of the sand sea that include MIS 5, later in the Pleistocene around the Last Glacial Maximum and the Holocene, although it is not expected that these will be the only, or discrete age groupings. Detailed dating and application of ground penetrating radar in the far northern reaches reveals extensive dune migration and deposition during the Holocene. It is important to stress that the upper limit of luminescence dating here is about ˜200 ka (depending on the environmental dose rate of the site) and that migration and reworking of dunes resets the luminescence signal (so what is recorded is(are) the last phase(s) of preserved sediment accumulation). Whilst there are three potential sources of material for the Namib Sand Sea (reworked Tsondab Sandstone (TSS), material from the Great Escarpment derived by rivers and water and wind

  19. On exactly conservative integrators

    SciTech Connect

    Bowman, J.C.; Shadwick, B.A.; Morrison, P.J.

    1997-06-01

    Traditional explicit numerical discretizations of conservative systems generically predict artificial secular drifts of nonlinear invariants. These algorithms are based on polynomial functions of the time step. The authors discuss a general approach for developing explicit algorithms that conserve such invariants exactly. They illustrate the method by applying it to the truncated two-dimensional Euler equations.

  20. Local relativistic exact decoupling.

    PubMed

    Peng, Daoling; Reiher, Markus

    2012-06-28

    We present a systematic hierarchy of approximations for local exact decoupling of four-component quantum chemical Hamiltonians based on the Dirac equation. Our ansatz reaches beyond the trivial local approximation that is based on a unitary transformation of only the atomic block-diagonal part of the Hamiltonian. Systematically, off-diagonal Hamiltonian matrix blocks can be subjected to a unitary transformation to yield relativistically corrected matrix elements. The full hierarchy is investigated with respect to the accuracy reached for the electronic energy and for selected molecular properties on a balanced test molecule set that comprises molecules with heavy elements in different bonding situations. Our atomic (local) assembly of the unitary exact-decoupling transformation--called local approximation to the unitary decoupling transformation (DLU)--provides an excellent local approximation for any relativistic exact-decoupling approach. Its order-N(2) scaling can be further reduced to linear scaling by employing a neighboring-atomic-blocks approximation. Therefore, DLU is an efficient relativistic method well suited for relativistic calculations on large molecules. If a large molecule contains many light atoms (typically hydrogen atoms), the computational costs can be further reduced by employing a well-defined nonrelativistic approximation for these light atoms without significant loss of accuracy. We also demonstrate that the standard and straightforward transformation of only the atomic block-diagonal entries in the Hamiltonian--denoted diagonal local approximation to the Hamiltonian (DLH) in this paper--introduces an error that is on the order of the error of second-order Douglas-Kroll-Hess (i.e., DKH2) when compared with exact-decoupling results. Hence, the local DLH approximation would be pointless in an exact-decoupling framework, but can be efficiently employed in combination with the fast to evaluate DKH2 Hamiltonian in order to speed up calculations

  1. Tracking Fine-Grain Phenological Dynamics at a Landscape Extent Using a Network of Near-Surface Digital Repeat Photography Stations in West Greenland

    NASA Astrophysics Data System (ADS)

    Kerby, J.; Post, E.

    2014-12-01

    The phenology of vegetation emergence in the Arctic is highly sensitive to climatic fluctuations. Spring phenology drives ecological processes across local, population, and ecosystem scales. Traditional approaches to capturing spatio-temporal variation in the annual timing and pace of Arctic green-up, like satellite-derived and plot-level records, are limited by trade-offs in the grain and extent of monitoring through both space and time. Recent studies demonstrate the utility of tracking canopy phenology using near-surface digital repeat photography (phenocams) to overcome spatial and temporal grain limitations at the extent of individual plants or vegetation stands. However, our understanding of how fine-grain phenological dynamics scale to landscape extents is incomplete. Here we report on the fine-grain green-up dynamics of a low-Arctic tundra system in West Greenland at the extent of a caribou calving range (40 km2) using three years (2012-2014) of phenological records derived from a network of 50 phenocams, field observations, and high-resolution satellite imagery. Using geostatistics and multiple-regression models, we characterize spatiotemporal patterns of plant phenology, landscape controls on the timing of emergence of common shrub and graminoid species, and assess scale-dependency in patterns of vegetation green-up. We link these results with coarse-grained satellite records of plant phenology to clarify how fine-grained dynamics contribute to the widely reported broad-scale patterns of phenological and ecological change in the Arctic.

  2. Landscape evolution (A Review)

    PubMed Central

    Sharp, Robert P.

    1982-01-01

    Landscapes are created by exogenic and endogenic processes acting along the interface between the lithosphere and the atmosphere and hydrosphere. Various landforms result from the attack of weathering and erosion upon the highly heterogeneous lithospheric surface. Landscapes are dynamic, acutely sensitive to natural and artificial perturbation. Undisturbed, they can evolve through a succession of stages to a plain of low relief. Often, the progression of an erosion cycle is interrupted by tectonic or environmental changes; thus, many landscapes preserve vestiges of earlier cycles useful in reconstructing the recent history of Earth's surface. Landforms are bounded by slopes, so their evolution is best understood through study of slopes and the complex of factors controlling slope character and development. The substrate, biosphere, climatic environment, and erosive processes are principal factors. Creep of the disintegrated substrate and surface wash by water are preeminent. Some slopes attain a quasisteady form and recede parallel to themselves (backwearing); others become ever gentler with time (downwearing). The lovely convex/rectilinear/concave profile of many debris-mantled slopes reflects an interplay between creep and surface wash. Landscapes of greatest scenic attraction are usually those in which one or two genetic factors have strongly dominated or those perturbed by special events. Nature has been perturbing landscapes for billions of years, so mankind can learn about landscape perturbation from natural examples. Images

  3. Vulnerability and Resilience of Temperate Forest Landscapes to Broad-Scale Deforestation in Response to Changing Fire Regimes and Altered Post-Fire Vegetation Dynamics

    NASA Astrophysics Data System (ADS)

    Tepley, A. J.; Veblen, T. T.; Perry, G.; Anderson-Teixeira, K. J.

    2015-12-01

    In the face of on-going climatic warming and land-use change, there is growing concern that temperate forest landscapes could be near a tipping point where relatively small changes to the fire regime or altered post-fire vegetation dynamics could lead to extensive conversion to shrublands or savannas. To evaluate vulnerability and resilience to such conversion, we develop a simple model based on three factors we hypothesize to be key in predicting temperate forest responses to changing fire regimes: (1) the hazard rate (i.e., the probability of burning in the next year given the time since the last fire) in closed-canopy forests, (2) the hazard rate for recently-burned, open-canopy vegetation, and (3) the time to redevelop canopy closure following fire. We generate a response surface representing the proportions of the landscape potentially supporting closed-canopy forest and non-forest vegetation under nearly all combinations of these three factors. We then place real landscapes on this response surface to assess the type and magnitude of changes to the fire regime that would drive extensive forest loss. We show that the deforestation of much of New Zealand that followed initial human colonization and the introduction of a new ignition source ca. 750 years ago was essentially inevitable due to the slow rate of forest recovery after fire and the high flammability of post-fire vegetation. In North America's Pacific Northwest, by contrast, a predominantly forested landscape persisted despite two periods of widespread burning in the recent past due in large part to faster post-fire forest recovery and less pronounced differences in flammability between forests and the post-fire vegetation. We also assess the factors that could drive extensive deforestation in other regions to identify where management could reduce this potential and to guide field and modeling work to better understand the responses and ecological feedbacks to changing fire regimes.

  4. Satellite Remote Sensing of Landscape Freeze/Thaw State Dynamics for Complex Topography and Fire Disturbance Areas Using Multi-Sensor Radar and SRTM Digital Elevation Models

    NASA Astrophysics Data System (ADS)

    Podest, E.; McDonald, K.; Kimball, J.; Randerson, J. T.

    2003-12-01

    The annual freeze/thaw cycle drives the length of the growing season in the boreal forest, and is a major factor determining annual productivity and associated exchange of CO2 with the atmosphere. Variations in freeze/thaw processes are spatially and temporally complex in boreal environments, particularly in areas of complex topography and in fire disturbance regimes. We investigate the spatial and temporal characteristics of seasonal freeze/thaw dynamics in complex boreal landscapes, as derived from radar backscatter measured with ERS (C-band, VV polarization, 200m resolution) and JERS-1 (L-band, HH polarization, 100m resolution) Synthetic Aperture Radars (SARs), and with the SeaWinds scatterometer (Ku-band, 25km resolution). C- and L-band backscatter are applied to characterize freeze/thaw transitions for a chronosequence of recovering burn sites near Delta Junction, Alaska, and for a region of complex topography on the Kenai Peninsula, Alaska. We characterize differences in radar-derived freeze/thaw state, examining transitions over complex terrain and landscape disturbance regimes. In areas of complex terrain, we explore freeze/thaw dynamics related to elevation, slope aspect and varying landcover. In the burned regions, we explore the timing of seasonal freeze/thaw transition as related to the recovering landscape, relative to that of a nearby control site. We apply in situ biophysical measurements, including flux tower measurements to validate and interpret the remotely sensed parameters. A multi-scale analysis is performed relating high-resolution SAR backscatter and moderate resolution scatterometer measurements to assess trade-offs in spatial and temporal resolution in the remotely sensed fields. A temporal change discriminator is applied to classify time series radar imagery to classify the landscape freeze-thaw state. We apply a 30m-resolution digital elevation model (DEM) derived from Shuttle Radar Topography Mission (SRTM) data to orthorectify the time

  5. Constructing a field-scale dynamic landscape model of soil hydrology using data from a distributed wireless sensor network

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil scientists interested in landscape processes are faced with a trade-off when it comes to data collection: spatial vs. temporal resolution. We can infrequently measure static soil properties at many locations and interpolate spatially using external variables (e.g. terrain) or geostatistics. ...

  6. Surface water and groundwater nitrogen dynamics in a well drained riparian forest within a poorly drainged agricultural landscape

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Riparian ecosystems, through their unique position in the agricultural landscape and ability to influence nutrient cycles, can potentially reduce nutrient loading to surface and ground waters. The primary purpose of this study was to determine the efficacy of a well-drained, mixed-deciduous riparia...

  7. Exact Relativistic `Antigravity' Propulsion

    NASA Astrophysics Data System (ADS)

    Felber, Franklin S.

    2006-01-01

    The Schwarzschild solution is used to find the exact relativistic motion of a payload in the gravitational field of a mass moving with constant velocity. At radial approach or recession speeds faster than 3-1/2 times the speed of light, even a small mass gravitationally repels a payload. At relativistic speeds, a suitable mass can quickly propel a heavy payload from rest nearly to the speed of light with negligible stresses on the payload.

  8. Laccoliths as a probe for bedrock landscape transient dynamics: Numerical modeling and application to erosion history of the Colorado Plateau

    NASA Astrophysics Data System (ADS)

    Karlstrom, L.; O'Hara, D.

    2015-12-01

    The response of bedrock landscapes to localized perturbations that uplift the land surface remains an important and unsolved problem in geomorphology. Laccoliths, shallow plutonic structures relatively common in magmatic environments that dome overlying crustal rocks, represent a simple and near-axisymmetric perturbation on the landscape. The structures are commonly smaller than typical drainage basins, allowing their erosional response to be used as a proxy for relative uplift rates and position in pre-existing drainage networks. Using a landscape evolution model, we analyze the coupling between pre-intrusion drainage conditions and laccolith uplift. We study the effects of laccolith uplift rate, geometry, and basin position on drainage development on both the laccolith and surrounding landscape. We use a Monte Carlo scheme to sample the large parameter space and develop a series of metrics based on channel network and landform geometries to characterize the results. In particular, we develop two dimensionless numbers to quantify the importance of uplift versus erosion, and initial condition (position of laccolith in pre-existing landscape). We then apply our results to Oligocene-age laccoliths on the Colorado Plateau, USA. The age of the Plateau's present drainage network is debated, with some arguing for a long-lived drainage network active since 60-70 Ma, and others arguing for a much younger pulse of incision at <6 Ma to integrate the modern drainage system. The laccoliths (i.e. the Henry, La Sal, and Ute Mountains, and Navajo Mountain), emplaced at 25-28 Ma, are potentially well suited to inform this debate. Laccolith erosion patterns on the Colorado Plateau are highly asymmetric, with long-axis orientations paralleling present directions of the Colorado River and its tributaries. Thus, the current drainage pattern is strongly imprinted on the laccoliths, suggesting we can characterize controls on laccolith erosion to invert for timing and rates of erosion.

  9. Towards a true protein movie: a perspective on the potential impact of the ensemble-based structure determination using exact NOEs.

    PubMed

    Vögeli, Beat; Orts, Julien; Strotz, Dean; Chi, Celestine; Minges, Martina; Wälti, Marielle Aulikki; Güntert, Peter; Riek, Roland

    2014-04-01

    Confined by the Boltzmann distribution of the energies of the states, a multitude of structural states are inherent to biomolecules. For a detailed understanding of a protein's function, its entire structural landscape at atomic resolution and insight into the interconversion between all the structural states (i.e. dynamics) are required. Whereas dedicated trickery with NMR relaxation provides aspects of local dynamics, and 3D structure determination by NMR is well established, only recently have several attempts been made to formulate a more comprehensive description of the dynamics and the structural landscape of a protein. Here, a perspective is given on the use of exact NOEs (eNOEs) for the elucidation of structural ensembles of a protein describing the covered conformational space. PMID:24656080

  10. Conformational dynamics of cancer-associated MyD88-TIR domain mutant L252P (L265P) allosterically tilts the landscape toward homo-dimerization.

    PubMed

    Zhan, Chendi; Qi, Ruxi; Wei, Guanghong; Guven-Maiorov, Emine; Nussinov, Ruth; Ma, Buyong

    2016-09-01

    MyD88 is an essential adaptor protein, which mediates the signaling of the toll-like and interleukin-1 receptors' superfamily. The MyD88 L252P (L265P) mutation has been identified in diffuse large B-cell lymphoma. The identification of this mutation has been a major advance in the diagnosis of patients with aldenstrom macroglobulinemia and related lymphoid neoplasms. Here we used computational methods to characterize the conformational effects of the mutation. Our molecular dynamics simulations revealed that the mutation allosterically quenched the global conformational dynamics of the toll/IL-1R (TIR) domain, and readjusted its salt bridges and dynamic community network. Specifically, the mutation changed the orientation and reduced the fluctuation of α-helix 3, possibly through eliminating/weakening ~8 salt bridges and enhancing the salt bridge D225-K258. Using the energy landscape of the TIR domains of MyD88, we identified two dynamic conformational basins, which correspond to the binding sites used in homo- and hetero-oligomerization, respectively. Our results indicate that the mutation stabilizes the core of the homo-dimer interface of the MyD88-TIR domain, and increases the population of homo-dimer-compatible conformational states in MyD88 family proteins. However, the dampened motion restricts its ability to heterodimerize with other TIR domains, thereby curtailing physiological signaling. In conclusion, the L252P both shifts the landscape toward homo-dimerization and restrains the dynamics of the MyD88-TIR domain, which disfavors its hetero-dimerization with other TIR domains. We further put these observations within the framework of MyD88-mediated cell signaling. PMID:27503954

  11. Mid-Wisconsin to Holocene permafrost and landscape dynamics based on a drained lake basin core from the northern Seward Peninsula, northwest Alaska

    USGS Publications Warehouse

    Lenz, Josefine; Grosse, Guido; Jones, Benjamin M.; Anthony, Katey M. Walter; Bobrov, Anatoly; Wulf, Sabine; Wetterich, Sebastian

    2016-01-01

    Permafrost-related processes drive regional landscape dynamics in the Arctic terrestrial system. A better understanding of past periods indicative of permafrost degradation and aggradation is important for predicting the future response of Arctic landscapes to climate change. Here, we used a multi-proxy approach to analyse a ~ 4 m long sediment core from a drained thermokarst lake basin on the northern Seward Peninsula in western Arctic Alaska (USA). Sedimentological, biogeochemical, geochronological, micropalaeontological (ostracoda, testate amoebae) and tephra analyses were used to determine the long-term environmental Early-Wisconsin to Holocene history preserved in our core for central Beringia. Yedoma accumulation dominated throughout the Early to Late-Wisconsin but was interrupted by wetland formation from 44.5 to 41.5 ka BP. The latter was terminated by the deposition of 1 m of volcanic tephra, most likely originating from the South Killeak Maar eruption at about 42 ka BP. Yedoma deposition continued until 22.5 ka BP and was followed by a depositional hiatus in the sediment core between 22.5 and 0.23 ka BP. We interpret this hiatus as due to intense thermokarst activity in the areas surrounding the site, which served as a sediment source during the Late-Wisconsin to Holocene climate transition. The lake forming the modern basin on the upland initiated around 0.23 ka BP and drained catastrophically in spring 2005. The present study emphasises that Arctic lake systems and periglacial landscapes are highly dynamic and that permafrost formation as well as degradation in central Beringia was controlled by regional to global climate patterns as well as by local disturbances.

  12. Changes of ecosystem service values in response to land use/land cover dynamics in Munessa-Shashemene landscape of the Ethiopian highlands.

    PubMed

    Kindu, Mengistie; Schneider, Thomas; Teketay, Demel; Knoke, Thomas

    2016-03-15

    Land use/land cover (LULC) dynamics alter ecosystem services values (ESVs), yet quantitative evaluations of changes in ESVs are seldom attempted. Using Munessa-Shashemene landscape of the Ethiopian highlands as an example, we showed estimate of changes in ESVs in response to LULC dynamics over the past four decades (1973-2012). Estimation and change analyses of ESVs were conducted, mainly, by employing GIS using LULC datasets of the year 1973, 1986, 2000 and 2012 with their corresponding global value coefficients developed earlier and our own modified conservative value coefficients for the studied landscape. The results between periods revealed a decrease of total ESVs from US$ 130.5 million in 1973, to US$ 118.5, 114.8 and 111.1 million in 1986, 2000 and 2012, respectively. While using global value coefficients, the total ESVs declined from US$ 164.6 million in 1973, to US$ 135.8, 127.2 and 118.7 million in 1986, 2000 and 2012, respectively. The results from the analyses of changes in the four decades revealed a total loss of ESVs ranging from US$ 19.3 million when using our own modified value coefficients to US$ 45.9 million when employing global value coefficients. Changes have also occurred in values of individual ecosystem service functions, such as erosion control, nutrient cycling, climate regulation and water treatment, which were among the highest contributors of the total ESVs. However, the value of food production service function consistently increased during the study periods although not drastically. All in all, it must be considered a minimum estimate of ESV changes due to uncertainties in the value coefficients used in this study. We conclude that the decline of ESVs reflected the effects of ecological degradation in the studied landscape and suggest further studies to explore future options and formulate intervention strategies. PMID:26780139

  13. Landscape dynamics and fire activity since 6740 cal yr BP in the Cantabrian region (La Molina peat bog, Puente Viesgo, Spain)

    NASA Astrophysics Data System (ADS)

    Pérez-Obiol, R.; García-Codron, J. C.; Pèlachs, A.; Pérez-Haase, A.; Soriano, J. M.

    2016-03-01

    A lack of paleobotanic studies with adequate resolution and multiproxy approaches has limited proper discussion of vegetation dynamics in Cantabria and of the role of fires in the configuration of the plant landscape during the Holocene in the northwest part of the Iberian peninsula. The pollen diagram of La Molina peat bog in Puente Viesgo (43°15‧38″ N-3°58‧37″ W; ETRS89), located at 484 m.a.s.l., and the study of its sedimentary charcoals allowed the acquisition of a continuous and thorough fire sequence for the last 6700 cal yr BP and an understanding of its relationship to the forest. The results show the importance of human influence on the incidence and characteristics of fire activity during the different phases studied: the Neolithic, Bronze Age, Iron Age, Roman period, and Middle Ages. A synergy seems to exist between dry climate periods (especially during Bond events 3 and 4) and a greater presence of biomass. As the Holocene advances, vegetation coverage clearly tends to decrease. This study provides key elements for understanding the role of fire activity in the forest dynamics of deciduous and evergreen Quercus, Corylus, Pinus, Fagus, and Alnus and demonstrates the strongly artificialized character of the present landscape.

  14. Non-equilibrium hillslope dynamics and irreversible landscape changes at a shifting pinyon-juniper woodland ecotone

    NASA Astrophysics Data System (ADS)

    McAuliffe, Joseph R.; McFadden, Leslie D.; Roberts, Leah M.; Wawrzyniec, Tim F.; Scuderi, Louis A.; Meyer, Grant A.; King, Matthew P.

    2014-11-01

    Pinyon-juniper woodlands of the western United States frequently exist within topographically complex landscapes where varied slope aspect yields substantial, local microclimate variation. Vegetation composition and cover typically change markedly along the gradient of relatively mesic northern aspects to more xeric southern aspects. Ecohydrological processes including precipitation runoff, soil moisture storage, and erosion are strongly influenced by vegetation. In certain cases, reduction of plant cover may set self-enhancing feedbacks in motion that lead to further declines of both vegetation and soils, and in some cases, replacement of woodlands with more xerophytic vegetation. The first place such change is likely to occur is in the ecotone between the drier southern aspects and moister north aspects. We studied vegetation, soils, and soil erosion in two small (1-2 ha) drainage basins in northeastern Arizona where pinyon-juniper woodlands occupy northern aspects, grading to shrub-dominated vegetation on more xeric southern aspects. Mapping of soil thickness, use of tree-root exposure to measure long-term soil erosion rates, and data on tree mortality and establishment indicate that the ecotone between woodland and more xerophytic vegetation has apparently been shifting for centuries, with a reduction in woodland vegetation. Erosion rates on xeric aspects ranged from 14 to 23 cm per century in one basin and as much as 60 cm per century in the other basin. In contrast, mesic aspects showed either no net soil losses over the last several centuries or rates significantly less than on the xeric aspects. Exposure of small roots (< 5 mm diameter) of cliff rose (Purshia stansburiana) directly overlying bare bedrock surfaces indicates that the process of denudation is ongoing and probably expanding in ecotonal areas. Mesic and xeric aspects exemplify "conserving" vs. "non-conserving" ecohydrologic systems in terms of their capacities to retain water and soils. The

  15. Exactly conservative integrators

    SciTech Connect

    Shadwick, B.A.; Bowman, J.C.; Morrison, P.J.

    1995-07-19

    Traditional numerical discretizations of conservative systems generically yield an artificial secular drift of any nonlinear invariants. In this work we present an explicit nontraditional algorithm that exactly conserves invariants. We illustrate the general method by applying it to the Three-Wave truncation of the Euler equations, the Volterra-Lotka predator-prey model, and the Kepler problem. We discuss our method in the context of symplectic (phase space conserving) integration methods as well as nonsymplectic conservative methods. We comment on the application of our method to general conservative systems.

  16. Exact Lattice Supersymmetry

    SciTech Connect

    Catterall, Simon; Kaplan, David B.; Unsal, Mithat

    2009-03-31

    We provide an introduction to recent lattice formulations of supersymmetric theories which are invariant under one or more real supersymmetries at nonzero lattice spacing. These include the especially interesting case of N = 4 SYM in four dimensions. We discuss approaches based both on twisted supersymmetry and orbifold-deconstruction techniques and show their equivalence in the case of gauge theories. The presence of an exact supersymmetry reduces and in some cases eliminates the need for fine tuning to achieve a continuum limit invariant under the full supersymmetry of the target theory. We discuss open problems.

  17. Exact folded-band chaotic oscillator.

    PubMed

    Corron, Ned J; Blakely, Jonathan N

    2012-06-01

    An exactly solvable chaotic oscillator with folded-band dynamics is shown. The oscillator is a hybrid dynamical system containing a linear ordinary differential equation and a nonlinear switching condition. Bounded oscillations are provably chaotic, and successive waveform maxima yield a one-dimensional piecewise-linear return map with segments of both positive and negative slopes. Continuous-time dynamics exhibit a folded-band topology similar to Rössler's oscillator. An exact solution is written as a linear convolution of a fixed basis pulse and a discrete binary sequence, from which an equivalent symbolic dynamics is obtained. The folded-band topology is shown to be dependent on the symbol grammar. PMID:22757520

  18. Molecular Dynamics Simulations and Classical Multidimensional Scaling Unveil New Metastable States in the Conformational Landscape of CDK2

    PubMed Central

    Pisani, Pasquale; Rastelli, Giulio

    2016-01-01

    Protein kinases are key regulatory nodes in cellular networks and their function has been shown to be intimately coupled with their structural flexibility. However, understanding the key structural mechanisms of large conformational transitions remains a difficult task. CDK2 is a crucial regulator of cell cycle. Its activity is finely tuned by Cyclin E/A and the catalytic segment phosphorylation, whereas its deregulation occurs in many types of cancer. ATP competitive inhibitors have failed to be approved for clinical use due to toxicity issues raised by a lack of selectivity. However, in the last few years type III allosteric inhibitors have emerged as an alternative strategy to selectively modulate CDK2 activity. In this study we have investigated the conformational variability of CDK2. A low dimensional conformational landscape of CDK2 was modeled using classical multidimensional scaling on a set of 255 crystal structures. Microsecond-scale plain and accelerated MD simulations were used to populate this landscape by using an out-of-sample extension of multidimensional scaling. CDK2 was simulated in the apo-form and in complex with the allosteric inhibitor 8-anilino-1-napthalenesulfonic acid (ANS). The apo-CDK2 landscape analysis showed a conformational equilibrium between an Src-like inactive conformation and an active-like form. These two states are separated by different metastable states that share hybrid structural features with both forms of the kinase. In contrast, the CDK2/ANS complex landscape is compatible with a conformational selection picture where the binding of ANS in proximity of the αC helix causes a population shift toward the inactive conformation. Interestingly, the new metastable states could enlarge the pool of candidate structures for the development of selective allosteric CDK2 inhibitors. The method here presented should not be limited to the CDK2 case but could be used to systematically unmask similar mechanisms throughout the human

  19. Molecular Dynamics Simulations and Classical Multidimensional Scaling Unveil New Metastable States in the Conformational Landscape of CDK2.

    PubMed

    Pisani, Pasquale; Caporuscio, Fabiana; Carlino, Luca; Rastelli, Giulio

    2016-01-01

    Protein kinases are key regulatory nodes in cellular networks and their function has been shown to be intimately coupled with their structural flexibility. However, understanding the key structural mechanisms of large conformational transitions remains a difficult task. CDK2 is a crucial regulator of cell cycle. Its activity is finely tuned by Cyclin E/A and the catalytic segment phosphorylation, whereas its deregulation occurs in many types of cancer. ATP competitive inhibitors have failed to be approved for clinical use due to toxicity issues raised by a lack of selectivity. However, in the last few years type III allosteric inhibitors have emerged as an alternative strategy to selectively modulate CDK2 activity. In this study we have investigated the conformational variability of CDK2. A low dimensional conformational landscape of CDK2 was modeled using classical multidimensional scaling on a set of 255 crystal structures. Microsecond-scale plain and accelerated MD simulations were used to populate this landscape by using an out-of-sample extension of multidimensional scaling. CDK2 was simulated in the apo-form and in complex with the allosteric inhibitor 8-anilino-1-napthalenesulfonic acid (ANS). The apo-CDK2 landscape analysis showed a conformational equilibrium between an Src-like inactive conformation and an active-like form. These two states are separated by different metastable states that share hybrid structural features with both forms of the kinase. In contrast, the CDK2/ANS complex landscape is compatible with a conformational selection picture where the binding of ANS in proximity of the αC helix causes a population shift toward the inactive conformation. Interestingly, the new metastable states could enlarge the pool of candidate structures for the development of selective allosteric CDK2 inhibitors. The method here presented should not be limited to the CDK2 case but could be used to systematically unmask similar mechanisms throughout the human

  20. Holocene Landscape Dynamics in the Ammer Rv. Catchment (Bavarian Alps) - Influence of extreme weather events and land use on soil erosion using peat bogs as geoarchives

    NASA Astrophysics Data System (ADS)

    Schwindt, Daniel; Manthe, Pierre; Völkel, Jörg

    2016-04-01

    Soil degradation and the loss of soil organic carbon (SOC) induced by erosion events significantly influence soils and fertility as parts of the ecosystem services and play an important role with regard to global carbon dynamics. Soil erosion is strongly correlated with anthropogenic land use since the Neolithic Revolution around 8.000 BP. Likewise the effect of extreme weather events on soil erosion is of great interest with regard to the recent climate change debate, predicting a strong increase of extreme weather events. Aim of this study is the reconstruction of the Holocene landscape dynamic as influenced by land use and climate conditions. In this study peat bogs containing layers of colluvial sediments directly correlated to soil erosion were used as geoarchives for landscape dynamics. A temporal classification of extreme erosion events was established by dating organic material via 14C within both, colluvial layers as well as their direct peat surroundings. Detection and characterization of peat bogs containing colluvial sediments was based on geomorphological mapping, the application of geophysical methods (ERT - electrical resistivity tomography, GPR - ground penetrating radar) and core soundings. Laboratory analysis included the analysis of particle sizes and the content of organic material. We investigated 16 peat bogs following the altitudinal gradient of the Ammer River from alpine and subalpine towards lowland environments. A deposition of colluvial material could be detected in 4 peat bogs, all situated in the lower parts of the catchment. The minerogenic entry into peat bogs occurred throughout the Holocene as revealed by radiocarbon dating. A distinct cluster of erosional events e.g. during the little ice age could not be detected. Therefore, soil erosion dynamics and the appearance of colluvial sediments within peat bogs must rather be regarded as an effect of land use, actually farming and crop cultivation, or small-scale morphodynamic like

  1. Mars Landscapes

    NASA Video Gallery

    Spacecraft have studied the Martian surface for decades, giving Earthlings insights into the history, climate and geology of our nearest neighbor, Mars. These images are from "Mars Landscapes," a v...

  2. Landscape Architecture.

    ERIC Educational Resources Information Center

    American School and University, 1985

    1985-01-01

    Members of the American Society of Landscape Architects shape open spaces on the campuses of Georgetown University, District of Columbia; the University of Missouri; Auraria Higher Education Center, Colorado; and the University of Michigan. (MLF)

  3. Efficient exact motif discovery

    PubMed Central

    Marschall, Tobias; Rahmann, Sven

    2009-01-01

    Motivation: The motif discovery problem consists of finding over-represented patterns in a collection of biosequences. It is one of the classical sequence analysis problems, but still has not been satisfactorily solved in an exact and efficient manner. This is partly due to the large number of possibilities of defining the motif search space and the notion of over-representation. Even for well-defined formalizations, the problem is frequently solved in an ad hoc manner with heuristics that do not guarantee to find the best motif. Results: We show how to solve the motif discovery problem (almost) exactly on a practically relevant space of IUPAC generalized string patterns, using the p-value with respect to an i.i.d. model or a Markov model as the measure of over-representation. In particular, (i) we use a highly accurate compound Poisson approximation for the null distribution of the number of motif occurrences. We show how to compute the exact clump size distribution using a recently introduced device called probabilistic arithmetic automaton (PAA). (ii) We define two p-value scores for over-representation, the first one based on the total number of motif occurrences, the second one based on the number of sequences in a collection with at least one occurrence. (iii) We describe an algorithm to discover the optimal pattern with respect to either of the scores. The method exploits monotonicity properties of the compound Poisson approximation and is by orders of magnitude faster than exhaustive enumeration of IUPAC strings (11.8 h compared with an extrapolated runtime of 4.8 years). (iv) We justify the use of the proposed scores for motif discovery by showing our method to outperform other motif discovery algorithms (e.g. MEME, Weeder) on benchmark datasets. We also propose new motifs on Mycobacterium tuberculosis. Availability and Implementation: The method has been implemented in Java. It can be obtained from http://ls11-www

  4. What Exactly Do Numbers Mean?

    ERIC Educational Resources Information Center

    Huang, Yi Ting; Spelke, Elizabeth; Snedeker, Jesse

    2013-01-01

    Number words are generally used to refer to the exact cardinal value of a set, but cognitive scientists disagree about their meanings. Although most psychological analyses presuppose that numbers have exact semantics ("two" means exactly two), many linguistic accounts propose that numbers have lower-bounded semantics (at least two), and…

  5. Assessing Potential Future Carbon Dynamics with Climate Change and Fire Management in a Mountainous Landscape on the Olympic Peninsula, Washington, USA

    NASA Astrophysics Data System (ADS)

    Kennedy, R. S.

    2010-12-01

    Forests of the mountainous landscapes of the maritime Pacific Northwestern USA may have high carbon sequestration potential via their high productivity and moderate to infrequent fire regimes. With climate change, there may be shifts in incidence and severity of fire, especially in the drier areas of the region, via changes to forest productivity and hydrology, and consequent effects to C sequestration and forest structure. To explore this issue, I assessed potential effects of fire management (little fire suppression/wildland fire management/highly effective fire suppression) under two climate change scenarios on future C sequestration dynamics (amounts and spatial pattern) in Olympic National Park, WA, over a 500-year simulation period. I used the simulation platform FireBGCv2, which contains a mechanistic, individual tree succession model, a spatially explicit climate-based biophysical model that uses daily weather data, and a spatially explicit fire model incorporating ignition, spread, and effects on ecosystem components. C sequestration patterns varied over time and spatial and temporal patterns differed somewhat depending on the climate change scenario applied and the fire management methods employed. Under the more extreme climate change scenario with little fire suppression, fires were most frequent and severe and C sequestration decreased. General trends were similar under the more moderate climate change scenario, as compared to current climate, but spatial patterns differed. Both climate change scenarios under highly effective fire suppression showed about 50% of starting total C after the initial transition phase, whereas with 10% fire suppression both scenarios exhibited about 10% of starting amounts. Areas of the landscape that served as refugia for older forest under increasing frequency of high severity fire were also hotspots for C sequestration in a landscape experiencing increasing frequency of disturbance with climate change.

  6. Quantum-control-landscape structure viewed along straight paths through the space of control fields

    NASA Astrophysics Data System (ADS)

    Nanduri, Arun; Ho, Tak-San; Rabitz, Herschel

    2016-02-01

    The dynamics of closed quantum systems may be manipulated by using an applied field to achieve a control objective value for a physical goal. The functional relationship between the applied field and the objective value forms a quantum control landscape, and the optimization process consists of a guided climb up the landscape from the bottom to the top. Two classes of landscape features are important for understanding the ease of finding an optimal control field. The first class of topological landscape features has been proven to be especially simple in that no suboptimal local maxima exist (upon satisfaction of certain assumptions), which partially accounts for the ease of finding optimal fields. Complementary to the topology, the second class of features entails the landscape structure, characterizing the sinuous nature of the paths leading to an optimal control field. Previous work found that the landscape structure is also particularly simple, as excursions up the landscape guided by a gradient algorithm correspond to nearly straight paths through the space of control fields. In this paper we take an alternative approach to examining landscape structure by constructing, and then following, exactly straight trajectories in control space. Each trajectory starts at a corresponding point on the bottom of the landscape and ends at an associated point on the top, with the observable values taken either as the state-to-state transition probability, the expectation value of a general observable, or the distance from a desired unitary transformation. In some cases the starting point is at a suboptimal critical-point saddle, with the goal, again, of following a straight field path to the optimal objective yield or another suboptimal critical point. We find that the objective value almost always rises monotonically upon following a straight control path from one critical point to another, which shows that landscape structure is very simple, being devoid of rough bumps

  7. Geomorpho-Landscapes

    NASA Astrophysics Data System (ADS)

    Farabollini, Piero; Lugeri, Francesca; Amadio, Vittorio

    2014-05-01

    Landscape is the object of human perceptions, being the image of spatial organization of elements and structures: mankind lives the first approach with the environment, viewing and feeling the landscape. Many definitions of landscape have been given over time: in this case we refer to the Landscape defined as the result of interaction among physical, biotic and anthropic phenomena acting in a different spatial-temporal scale (Foreman & Godron) Following an Aristotelic approach in studying nature, we can assert that " Shape is synthesis": so it is possible to read the land features as the expression of the endogenous and exogenous processes that mould earth surfaces; moreover, Landscape is the result of the interaction of natural and cultural components, and conditions the spatial-temporal development of a region. The study of the Landscape offers results useful in order to promote sustainable development, ecotourism, enhancement of natural and cultural heritage, popularization of the scientific knowledge. In Italy, a very important GIS-based tool to represent the territory is the "Carta della Natura" ("Map of Nature", presently coordinated by the ISPRA) that aims at assessing the state of the whole Italian territory, analyzing Landscape. The methodology follows a holistic approach, taking into consideration all the components of a landscape and then integrating the information. Each individual landscape, studied at different scales, shows distinctive elements: structural, which depend on physical form and specific spatial organization; functional, which depend on relationships created between biotic and abiotic elements, and dynamic, which depend on the successive evolution of the structure. The identification of the landscape units, recognized at different scales of analysis, allows an evaluation of the state of the land, referring to the dual risk/resource which characterizes the Italian country. An interesting opportunity is to discover those areas of unusual

  8. Exact cumulant Kramers-Moyal-like expansion

    NASA Astrophysics Data System (ADS)

    Morgado, W. A. M.

    2015-11-01

    We derive an exact equation, a Cumulant Kramers-Moyal Equation (CKME), quite similar to the Kramers-Moyal Equation (KME), for the probability distribution of a Markovian dynamical system. It can be applied to any well behaved (converging cumulants) continuous time systems, such as Langevin equations or other models. An interesting but significant difference with respect to the KME is that their jump-moments are proportional to cumulants of the dynamical variables, but not proportional to central moments, as is the case for the KME. In fact, they still obey a weaker version of Pawula's theorem, namely Marcinkiewicz's theorem. We compare the results derived from the equations herein with the ones obtained by computing via Gaussian and biased, and unbiased, Poisson Langevin dynamics and a Poisson non-Langevin model. We obtain the exact CKME time-evolution equation for the systems, and in several cases, those are distinct from the Fokker-Planck equation or the KME.

  9. [Quantitative Evaluation of Intracardiac Blood Flow by Left Ventricle Dynamic Anatovy Based On Exact Solutions of Non-Stationary Navier-Stocks Equations for Selforganized tornado-Like Flows of Viscous Incompresssible Fluid].

    PubMed

    Talygin, E A; Zazybo, N A; Zhorzholiany, S T; Krestinich, I M; Mironov, A A; Kiknadze, G I; Bokerya, L A; Gorodkov, A Y; Makarenko, V N; Alexandrova, S A

    2016-01-01

    New approach to intracardiac blood flow condition analysis based on geometric parameters of left ventricle flow channel has been suggested. Parameters, that used in this method, follow from exact solutions of nonstationary Navier-Stocks equations for selforganized tornado-like flows of viscous incompressible fluid. The main advantage of this method is considering dynamic anatomy of intracardiac cavity and trabeculae relief of left ventricle streamlined surface, both registered in a common mri-process, as flow condition indicator. Calculated quantity options that characterizes blood flow condition can be use as diagnostic criterias for estimation of violation in blood circulation function which entails heart ejection reduction. Developed approach allows to clarify heart jet organization mechanism and estimate the share of the tornado-like flow self-organization in heart ejection structure. PMID:27149823

  10. Exactly solvable chaos in an electromechanical oscillator.

    PubMed

    Owens, Benjamin A M; Stahl, Mark T; Corron, Ned J; Blakely, Jonathan N; Illing, Lucas

    2013-09-01

    A novel electromechanical chaotic oscillator is described that admits an exact analytic solution. The oscillator is a hybrid dynamical system with governing equations that include a linear second order ordinary differential equation with negative damping and a discrete switching condition that controls the oscillatory fixed point. The system produces provably chaotic oscillations with a topological structure similar to either the Lorenz butterfly or Rössler's folded-band oscillator depending on the configuration. Exact solutions are written as a linear convolution of a fixed basis pulse and a sequence of discrete symbols. We find close agreement between the exact analytical solutions and the physical oscillations. Waveform return maps for both configurations show equivalence to either a shift map or tent map, proving the chaotic nature of the oscillations. PMID:24089945

  11. Exactly solvable chaos in an electromechanical oscillator

    NASA Astrophysics Data System (ADS)

    Owens, Benjamin A. M.; Stahl, Mark T.; Corron, Ned J.; Blakely, Jonathan N.; Illing, Lucas

    2013-09-01

    A novel electromechanical chaotic oscillator is described that admits an exact analytic solution. The oscillator is a hybrid dynamical system with governing equations that include a linear second order ordinary differential equation with negative damping and a discrete switching condition that controls the oscillatory fixed point. The system produces provably chaotic oscillations with a topological structure similar to either the Lorenz butterfly or Rössler's folded-band oscillator depending on the configuration. Exact solutions are written as a linear convolution of a fixed basis pulse and a sequence of discrete symbols. We find close agreement between the exact analytical solutions and the physical oscillations. Waveform return maps for both configurations show equivalence to either a shift map or tent map, proving the chaotic nature of the oscillations.

  12. Characterizing spatiotemporal dynamics of wetted soils across a polar desert landscape, McMurdo Dry Valleys Antarctica

    NASA Astrophysics Data System (ADS)

    Langford, Z. L.; Gooseff, M. N.; Lampkin, D. J.

    2012-12-01

    The McMurdo Dry Valleys is a landscape characterized by open expanses of bare soils, alpine and piedmont glaciers, and ice-covered lakes on the valley floors, all underlain by permafrost. There is contemporary evidence of changes to the near-surface hydrology of the Dry Valleys as extensive wet soil patches are being observed extensively throughout the valleys. The availability and movement of water across this landscape may drive important shifts in the interactions among meteorology, hydrology and biogeochemical processes. Wetted soils are generally found adjacent to streams and lakes, but have also been observed far from lake shorelines and channels. The relative contributions of water to the development of wetted zones from glaciers, ablated snow patches and melted permafrost has not been established. We evaluate the spatio-temporal variability of retrieved near surface soil moisture using high resolution optical data from Quickbird and Wordview satellites to document the occurrence, dimensions, and growth of wet spots during the 2009-10 and 2010-11 austral summers over Taylor Valley. The patterns on the distributed estimates of soil moisture are extracted from the satellite imagery based on an artificial neural network (ANN). The ANN utilizes a spectral library of representative surface types and states. The library was derived from measurements of in situ reflectance of soil moisture during the 2011 austral season, using a portable radiometer.

  13. The interaction between land use change, sediment fluxes and carbon dynamics: evaluating an integrated soil-landscape model at the millennial time-scale.

    NASA Astrophysics Data System (ADS)

    Bouchoms, Samuel; Van Oost, Kristof; Vanacker, Veerle

    2015-04-01

    Soil-landscape modelling has received growing attention as it allows us to evaluate the interaction between earth surface and soil bio-physical processes. At the landscape scale, human-induced land use change has altered the balance between soil erosion and production, and largely modified sediment fluxes. Intensification in soil redistribution rates affects the interaction between soil chemical, physical and biological processes at the landscape scale. Here, we evaluate the SPEROS-LT model, a spatially explicit 3D model combining a dynamic representation of land use, soil erosion and deposition and the soil carbon cycle. We assess the impact of millennial-scale human-induced land use change on sediment fluxes and carbon dynamics in the Dijle catchement (central Belgium). The watershed has undergone a 3000 years continuous human-induced alteration of the vegetation covers for agricultural characterized by Our study is based on land use reconstructions for the last 3000 years, including massive deforestation for agriculture in Roman Times and the Middle Ages followed by urbanization in the last 150 years. Land use reconstructions rely on simple land use allocation rules based on slope gradients. SPEROS-LT is parametrized for erosion rates against available figures in the literature by changing the transport capacity and the transfer coefficient which defines the amount of flux transferred between different land uses. Carbon content profiles at steady state (i.e. without influence of erosion or deposition) are calibrated for each land use and for the first upper meter of soil by comparing modeled profiles to an averaged observed profiles in stable areas of the pedologic region. We present a model sensitivity analysis and a full validation of the predicted soil carbon storage (horizontally, i.e. in space, and vertically, i.e. with depth) using a large database of observational data. The results indicate (i) a good agreement of the erosion rates. Speros LT modeled

  14. Integrating the impact of bioturbation to landscape-scale modeling of soil carbon dynamics: a case study of chernozems in Central Saskatchewan

    NASA Astrophysics Data System (ADS)

    Viaud, V.; Pennock, D.

    2010-12-01

    Plant-soil interactions and the addition of organic matter from grass have long been the only processes identified to explain soil organic carbon (SOC) distribution and the origin of the A-horizon of chernozemic soils (Dokutchaiev, 1967). But recent studies have suggested that the role of burrowing animals in soil mixing and its consequences on SOC distribution in chernozemic soils have been underestimated (Wilkinson et al., 2009). This work aims at modelling the spatio-temporal evolution of SOC stocks across a catena in a hummocky landscape of Central Saskatchewan. The catena was represented as a 2-dimensional system, divided into 1-m cells in the lateral dimension, and into 6 increments in the vertical dimension (0-to-10, 10-to-20, 20-to-30, 30-to-60, 60-to-90, and 90-to-120 cm). The carbon module of the CENTURY model was used to simulate SOC dynamics in each soil horizon, and the effect of bioturbation on soil vertical mixing in the top soil layers was explicitly modeled. The model also included a simulation of the water budget and water fluxes in soils that partly control SOC dynamics across a catena. The study was based on a detailed dataset from St Denis Wildlife Area (SK, Canada), including climate data, above- and belowground biomass measurements, soil survey, topography, and quantitative data on soil properties and C input in several landscape locations. The model was run over 10000 years. Precipitation and temperature were simulated stochastically. Simulation results, with and without bioturbation, were compared to the current values of SOC stocks.

  15. Landscape diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    While biodiversity is usually considered at the species level, maintenance of biodiversity requires management at higher levels of organization, particularly at the landscape scale. It is difficult to manage for each threatened species individually. Alternatively, management can focus on the ecosyst...

  16. Exploring water cycle dynamics through sampling multitude stable water isotope pools in a small developed landscape of Germany

    NASA Astrophysics Data System (ADS)

    Orlowski, N.; Kraft, P.; Breuer, L.

    2015-02-01

    Conducting a dual stable water isotope (δ2H and δ18O) study in the developed landscape of the Schwingbach catchment (Germany) helped to unravel connectivity and disconnectivity between the different water cycle components. The two-year weekly to biweekly measurements of precipitation, stream, and groundwater isotopes revealed that surface and groundwater are decoupled from the annual precipitation cycle but showed bidirectional interactions between each other. Seasonal variations based on temperature effects were observed in the precipitation signal but neither reflected in stream nor in groundwater isotopic signatures. Apparently, snowmelt played a fundamental role for groundwater recharge explaining the observed differences to precipitation δ-values. A spatially distributed snapshot sampling of soil water isotopes in two soil depths at 52 sampling points across different land uses (arable land, forest, and grassland) revealed that top soil isotopic signatures were similar to the precipitation input signal. Preferential water flow paths occurred under forested soils explaining the isotopic similarities between top and subsoil isotopic signatures. Due to human-impacted agricultural land use (tilling and compression) of arable and grassland soils, water delivery to the deeper soil layers was reduced, resulting in significant different isotopic signatures. However, the land use influence smoothed out with depth and soil water approached groundwater δ-values. Seasonally tracing stable water isotopes through soil profiles showed that the influence of new percolating soil water decreased with depth as no remarkable seasonality in soil isotopic signatures was obvious at depth > 0.9 m and constant values were observed through space and time. Little variation in individual isotope time series of stream and groundwater restricted the use of classical isotope hydrology techniques e.g. mean transit time estimation or hydrograph separation. Still, tracing stable water

  17. LANDSCAPE ECOLOGY AND THE CONSERVATION AND MANAGEMENT OF NEOTROPICAL MIGRATORY BIRDS

    EPA Science Inventory

    The conservation and management of neotropical migratory birds needs to include a landscape perspective. andscape ecology represents a renewed interest in the development and dynamics of landscape mosaics, the effects of landscape patterns on species, biotic interactions and ecol...

  18. The Neglected Exactness

    NASA Astrophysics Data System (ADS)

    Endom, Joerg

    2014-05-01

    negligible any more. Locating for example the exact position of joints, rebars on site, getting correct calibration information or overlaying measurements of independent methods requires high accuracy positioning for all data. Different technologies of synchronizing and stabilizing are discussed in this presentation. Furthermore a scale problem for interdisciplinary work between the geotechnical engineer, the civil engineer, the surveyor and the geophysicist is presented. Manufacturers as well as users are addressed to work on a unified methodology that could be implemented in future. This presentation is a contribution to COST Action TU1208.

  19. Adaptation and extinction in experimentally fragmented landscapes.

    PubMed

    Fakheran, Sima; Paul-Victor, Cloé; Heichinger, Christian; Schmid, Bernhard; Grossniklaus, Ueli; Turnbull, Lindsay A

    2010-11-01

    Competition and disturbance are potent ecological forces that shape evolutionary trajectories. These forces typically work in opposition: when disturbance is infrequent, densities are high and competition is intense. In contrast, frequent disturbance creates a low-density environment in which competition is weak and good dispersal essential. We exploited recent advances in genomic research to quantify the response to selection by these powerful ecological forces at the phenotypic and molecular genetic level in experimental landscapes. We grew the annual plant Arabidopsis thaliana in discrete patches embedded in a hostile matrix and varied the number and size of patches and the intensity of disturbance, by creating both static and dynamic landscapes. In static landscapes all patches were undisturbed, whereas in dynamic landscapes all patches were destroyed in each generation, forcing seeds to disperse to new locations. We measured the resulting changes in phenotypic, genetic, and genotypic diversity after five generations of selection. Simulations revealed that the observed loss of genetic diversity dwarfed that expected under drift, with dramatic diversity loss, particularly from dynamic landscapes. In line with ecological theory, static landscapes favored good competitors; however, competitive ability was linked to growth rate and not, as expected, to seed mass. In dynamic landscapes, there was strong selection for increased dispersal ability in the form of increased inflorescence height and reduced seed mass. The most competitive genotypes were almost eliminated from highly disturbed landscapes, raising concern over the impact of increased levels of human-induced disturbance in natural landscapes. PMID:20956303

  20. Effects of Landscape History and Forest Management on Landslide-Driven Sediment Dynamics in Mountain Drainage Basins of Coastal British Columbia

    NASA Astrophysics Data System (ADS)

    Brardinoni, F.

    2006-12-01

    Landslide magnitude-frequency (LMF) and yield-area relations are examined for evaluating landslide-driven sediment dynamics in the Tsitika and Eve Rivers (612 km{2}), British Columbia. Research methods couple field work and air photo interpretation (API) in a GIS environment. API covers a seventy year time window. Results show that the long history of glacial erosion and the more recent forest management affect contemporary landslide activity in many respects. First, the nature and distribution of Quaternary-derived surficial deposits confounds primary lithologic effects; therefore, topographies underlain by less resistant geology are not typically associated with higher rates of landsliding. Second, the stratifications of LMF by landslide and terrain attributes have allowed detecting for the first time characteristic landslide length scales dependent on (i) movement style (i.e., slide, avalanche, and flow); (ii) type of material mobilized (i.e., bedrock and debris); and (iii) land use (i.e., forest clearing). As a conclusion, landscape bio-morphometric controls override the theoretical self-organized criticality of LMF relations. Third, slope-area analysis of landslide initiation and deposition zones reveals that bedrock landslides dominate the landscape on mountain summits and ridges; these processes deliver material to colluvial channels, in which debris is temporarily stored until remobilization occurs via full-scale debris flows. In undisturbed forest, during the seventy years examined, colluvial activity across geomorphic process domains (seen as sediment reservoirs) has generated net volume accumulation in unchannelled valleys, sink colluvial, and fluvially-dominated channels; in contrast, planar slopes and gullies have been degrading. Logging operations have accentuated aggradation in gullies and in unchannelled topographies. Finally, the area-based scaling relation of landslide sediment yield appears to match the spatial organization of geomorphic process

  1. Water quality within biofuel production landscape: Integrating flow paths, residence time distribution and mixing dynamics in the stream side management zone

    NASA Astrophysics Data System (ADS)

    Blake, J. I.; Jackson, C. R.; Griffiths, N. A.; Klaus, J.; Du, E.; Vache, K. B.; McDonnell, J. J.

    2012-12-01

    Best Management Practices designed to protect water quality are largely based on empirical studies of runoff from various cropping practices and associated mitigation strategies. Application of the resulting mitigation strategies has resulted in significant improvements in water quality, particularly reductions in sediment yields. Watershed modeling can extend the observations to other crops, landscapes and climates, but extrapolation is often compromised by too many model parameters and assumptions. The sheer number of potential dedicated biofuel-biochemical crop species, crop practices and hydrologic landscapes makes it difficult to comprehensively test various alternatives when the final configurations are largely unknown. We argue that a dominant hydrologic process framework for evaluating and mitigating potential water quality impacts can be constructed from basic hydrologic principles coupled to the crop fertilizer uptake efficiency and pesticide properties. We illustrate the approach in the southeastern U.S. on an old-field landscape with zero and first order streams suitable for cellulosic biofuel crops. In this region nitrogen additions are essential to sustain and enhance production and herbicides are frequently required for establishment. If overland flow is effectively managed, the primary flow path transmits water to groundwater and contaminates are subject to dispersion, sorption, and biochemical reaction. Average residence times in headwater basins typically ranges from3-12 years. However, the array of flow paths and distribution of residence times may lead to undesirable transport of contaminates. For example, significant lateral interflow may occur within 25-50 meters of the stream interface. Transmissions of these materials through the biological active riparian zones can substantially reduce contaminate concentrations as long as flux rates do not exceed uptake rates. To the extent that subsurface interflow and groundwater dynamics can be

  2. Modeling the effects of fire severity and climate warming on active layer and soil carbon dynamics of black spruce forests across the landscape in interior Alaska

    USGS Publications Warehouse

    Genet, H.; McGuire, Anthony David; Barrett, K.; Breen, A.; Euskirchen, E.S.; Johnstone, J.F.; Kasischke, E.S.; Melvin, A.M.; Bennett, A.; Mack, M.C.; Rupp, T.S.; Schuur, A.E.G.; Turetsky, M.R.; Yuan, F.

    2013-01-01

    There is a substantial amount of carbon stored in the permafrost soils of boreal forest ecosystems, where it is currently protected from decomposition. The surface organic horizons insulate the deeper soil from variations in atmospheric temperature. The removal of these insulating horizons through consumption by fire increases the vulnerability of permafrost to thaw, and the carbon stored in permafrost to decomposition. In this study we ask how warming and fire regime may influence spatial and temporal changes in active layer and carbon dynamics across a boreal forest landscape in interior Alaska. To address this question, we (1) developed and tested a predictive model of the effect of fire severity on soil organic horizons that depends on landscape-level conditions and (2) used this model to evaluate the long-term consequences of warming and changes in fire regime on active layer and soil carbon dynamics of black spruce forests across interior Alaska. The predictive model of fire severity, designed from the analysis of field observations, reproduces the effect of local topography (landform category, the slope angle and aspect and flow accumulation), weather conditions (drought index, soil moisture) and fire characteristics (day of year and size of the fire) on the reduction of the organic layer caused by fire. The integration of the fire severity model into an ecosystem process-based model allowed us to document the relative importance and interactions among local topography, fire regime and climate warming on active layer and soil carbon dynamics. Lowlands were more resistant to severe fires and climate warming, showing smaller increases in active layer thickness and soil carbon loss compared to drier flat uplands and slopes. In simulations that included the effects of both warming and fire at the regional scale, fire was primarily responsible for a reduction in organic layer thickness of 0.06 m on average by 2100 that led to an increase in active layer thickness

  3. Dynamic topography of the western Great Plains: landscape evidence for mantle-driven uplift associated with the Jemez lineament of NE New Mexico and SE Colorado

    NASA Astrophysics Data System (ADS)

    Nereson, A. L.; Karlstrom, K. E.; McIntosh, W. C.; Heizler, M. T.; Kelley, S. A.; Brown, S. W.

    2011-12-01

    Dynamic topography results when viscous stresses created by flow within the mantle are transmitted through the lithosphere and interact with, and deform, the Earth's surface. Because dynamic topography is characterized by low amplitudes and long wavelengths, its subtle effects may be best recorded in low-relief areas such as the Great Plains of the USA where they can be readily observed and measured. We apply this concept to a unique region of the western Great Plains in New Mexico and Colorado where basalt flows of the Jemez lineament (Raton-Clayton and Ocate fields) form mesas (inverted topography) that record the evolution of the Great Plains surface through time. This study uses multiple datasets to evaluate the mechanisms which have driven the evolution of this landscape. Normalized channel steepness index (ksn) analysis identifies anomalously steep river gradients across broad (50-100 km) convexities within a NE- trending zone of differential river incision where higher downstream incision rates in the last 1.5 Ma suggest headwater uplift. At 2-8 Ma timescales, 40Ar/39Ar ages of basalt-capped paleosurfaces in the Raton-Clayton and Ocate volcanic fields indicate that rates of denudation increase systematically towards the NW from a NE-trending zone of approximately zero denudation (that approximately coincides with the high ksn zone), also suggestive of regional warping above the Jemez lineament. Onset of more rapid denudation is observed in the Raton-Clayton field beginning at ca. 3.6 Ma. Furthermore, two 300-400-m-high NE-trending erosional escarpments impart a staircase-like topographic profile to the region. Tomographic images from the EarthScope experiment show that NE-trending topographic features of this region correspond to an ~8 % P-wave velocity gradient of similar trend at the margin of the low-velocity Jemez mantle anomaly. We propose that the erosional landscapes of this unique area are, in large part, the surface expression of dynamic mantle

  4. Free-Energy Landscape of Reverse tRNA Translocation through the Ribosome Analyzed by Electron Microscopy Density Maps and Molecular Dynamics Simulations

    PubMed Central

    Ishida, Hisashi; Matsumoto, Atsushi

    2014-01-01

    To understand the mechanism of reverse tRNA translocation in the ribosome, all-atom molecular dynamics simulations of the ribosome-tRNAs-mRNA-EFG complex were performed. The complex at the post-translocational state was directed towards the translocational and pre-translocational states by fitting the complex into cryo-EM density maps. Between a series of the fitting simulations, umbrella sampling simulations were performed to obtain the free-energy landscape. Multistep structural changes, such as a ratchet-like motion and rotation of the head of the small subunit were observed. The free-energy landscape showed that there were two main free-energy barriers: one between the post-translocational and intermediate states, and the other between the pre-translocational and intermediate states. The former corresponded to a clockwise rotation, which was coupled to the movement of P-tRNA over the P/E-gate made of G1338, A1339 and A790 in the small subunit. The latter corresponded to an anticlockwise rotation of the head, which was coupled to the location of the two tRNAs in the hybrid state. This indicates that the coupled motion of the head rotation and tRNA translocation plays an important role in opening and closing of the P/E-gate during the ratchet-like movement in the ribosome. Conformational change of EF-G was interpreted to be the result of the combination of the external motion by L12 around an axis passing near the sarcin-ricin loop, and internal hinge-bending motion. These motions contributed to the movement of domain IV of EF-G to maintain its interaction with A/P-tRNA. PMID:24999999

  5. Landscape Factors Facilitating the Invasive Dynamics and Distribution of the Brown Marmorated Stink Bug, Halyomorpha halys (Hemiptera: Pentatomidae), after Arrival in the United States

    PubMed Central

    Wallner, Adam M.; Hamilton, George C.; Nielsen, Anne L.; Hahn, Noel; Green, Edwin J.; Rodriguez-Saona, Cesar R.

    2014-01-01

    The brown marmorated stink bug, Halyomorpha halys, a native of Asia, has become a serious invasive pest in the USA. H. halys was first detected in the USA in the mid 1990s, dispersing to over 41 other states. Since 1998, H. halys has spread throughout New Jersey, becoming an important pest of agriculture, and a major nuisance in urban developments. In this study, we used spatial analysis, geostatistics, and Bayesian linear regression to investigate the invasion dynamics and colonization processes of this pest in New Jersey. We present the results of monitoring H. halys from 51 to 71 black light traps that were placed on farms throughout New Jersey from 2004 to 2011 and examined relationships between total yearly densities of H. halys and square hectares of 48 landscape/land use variables derived from urban, wetland, forest, and agriculture metadata, as well as distances to nearest highways. From these analyses we propose the following hypotheses: (1) H. halys density is strongly associated with urban developments and railroads during its initial establishment and dispersal from 2004 to 2006; (2) H. halys overwintering in multiple habitats and feeding on a variety of plants may have reduced the Allee effect, thus facilitating movement into the southernmost regions of the state by railroads from 2005 to 2008; (3) density of H. halys contracted in 2009 possibly from invading wetlands or sampling artifact; (4) subsequent invasion of H. halys from the northwest to the south in 2010 may conform to a stratified-dispersal model marked by rapid long-distance movement, from railroads and wetland rights-of-way; and (5) high densities of H. halys may be associated with agriculture in southern New Jersey in 2011. These landscape features associated with the invasion of H. halys in New Jersey may predict its potential rate of invasion across the USA and worldwide. PMID:24787576

  6. A reduced-order modeling approach to represent subgrid-scale hydrological dynamics for land-surface simulations: application in a polygonal tundra landscape

    DOE PAGESBeta

    Pau, G. S. H.; Bisht, G.; Riley, W. J.

    2014-09-17

    Existing land surface models (LSMs) describe physical and biological processes that occur over a wide range of spatial and temporal scales. For example, biogeochemical and hydrological processes responsible for carbon (CO2, CH4) exchanges with the atmosphere range from the molecular scale (pore-scale O2 consumption) to tens of kilometers (vegetation distribution, river networks). Additionally, many processes within LSMs are nonlinearly coupled (e.g., methane production and soil moisture dynamics), and therefore simple linear upscaling techniques can result in large prediction error. In this paper we applied a reduced-order modeling (ROM) technique known as "proper orthogonal decomposition mapping method" that reconstructs temporally resolvedmore » fine-resolution solutions based on coarse-resolution solutions. We developed four different methods and applied them to four study sites in a polygonal tundra landscape near Barrow, Alaska. Coupled surface–subsurface isothermal simulations were performed for summer months (June–September) at fine (0.25 m) and coarse (8 m) horizontal resolutions. We used simulation results from three summer seasons (1998–2000) to build ROMs of the 4-D soil moisture field for the study sites individually (single-site) and aggregated (multi-site). The results indicate that the ROM produced a significant computational speedup (> 103) with very small relative approximation error (< 0.1%) for 2 validation years not used in training the ROM. We also demonstrate that our approach: (1) efficiently corrects for coarse-resolution model bias and (2) can be used for polygonal tundra sites not included in the training data set with relatively good accuracy (< 1.7% relative error), thereby allowing for the possibility of applying these ROMs across a much larger landscape. By coupling the ROMs constructed at different scales together hierarchically, this method has the potential to efficiently increase the resolution of land models for coupled

  7. A reduced order modeling approach to represent subgrid-scale hydrological dynamics for regional- and climate-scale land-surface simulations: application in a polygonal tundra landscape

    DOE PAGESBeta

    Pau, G. S. H.; Bisht, G.; Riley, W. J.

    2014-04-04

    Existing land surface models (LSMs) describe physical and biological processes that occur over a wide range of spatial and temporal scales. For example, biogeochemical and hydrological processes responsible for carbon (CO2, CH4) exchanges with the atmosphere range from molecular scale (pore-scale O2 consumption) to tens of kilometer scale (vegetation distribution, river networks). Additionally, many processes within LSMs are nonlinearly coupled (e.g., methane production and soil moisture dynamics), and therefore simple linear upscaling techniques can result in large prediction error. In this paper we applied a particular reduced-order modeling (ROM) technique known as "Proper Orthogonal Decomposition mapping method" that reconstructs temporally-resolvedmore » fine-resolution solutions based on coarse-resolution solutions. We applied this technique to four study sites in a polygonal tundra landscape near Barrow, Alaska. Coupled surface-subsurface isothermal simulations were performed for summer months (June–September) at fine (0.25 m) and coarse (8 m) horizontal resolutions. We used simulation results from three summer seasons (1998–2000) to build ROMs of the 4-D soil moisture field for the four study sites individually (single-site) and aggregated (multi-site). The results indicate that the ROM produced a significant computational speedup (> 103) with very small relative approximation error (< 0.1%) for two validation years not used in training the ROM. We also demonstrated that our approach: (1) efficiently corrects for coarse-resolution model bias and (2) can be used for polygonal tundra sites not included in the training dataset with relatively good accuracy (< 1.5% relative error), thereby allowing for the possibility of applying these ROMs across a much larger landscape. This method has the potential to efficiently increase the resolution of land models for coupled climate simulations, allowing LSMs to be used at spatial scales consistent with

  8. Conformational landscape of an amyloid intra-cellular domain and Landau-Ginzburg-Wilson paradigm in protein dynamics.

    PubMed

    Dai, Jin; Niemi, Antti J; He, Jianfeng

    2016-07-28

    The Landau-Ginzburg-Wilson paradigm is proposed as a framework, to investigate the conformational landscape of intrinsically unstructured proteins. A universal Cα-trace Landau free energy is deduced from general symmetry considerations, with the ensuing all-atom structure modeled using publicly available reconstruction programs Pulchra and Scwrl. As an example, the conformational stability of an amyloid precursor protein intra-cellular domain (AICD) is inspected; the reference conformation is the crystallographic structure with code 3DXC in Protein Data Bank (PDB) that describes a heterodimer of AICD and a nuclear multi-domain adaptor protein Fe65. Those conformations of AICD that correspond to local or near-local minima of the Landau free energy are identified. For this, the response of the original 3DXC conformation to variations in the ambient temperature is investigated, using the Glauber algorithm. The conclusion is that in isolation the AICD conformation in 3DXC must be unstable. A family of degenerate conformations that minimise the Landau free energy is identified, and it is proposed that the native state of an isolated AICD is a superposition of these conformations. The results are fully in line with the presumed intrinsically unstructured character of isolated AICD and should provide a basis for a systematic analysis of AICD structure in future NMR experiments. PMID:27475398

  9. Conformational landscape of an amyloid intra-cellular domain and Landau-Ginzburg-Wilson paradigm in protein dynamics

    NASA Astrophysics Data System (ADS)

    Dai, Jin; Niemi, Antti J.; He, Jianfeng

    2016-07-01

    The Landau-Ginzburg-Wilson paradigm is proposed as a framework, to investigate the conformational landscape of intrinsically unstructured proteins. A universal Cα-trace Landau free energy is deduced from general symmetry considerations, with the ensuing all-atom structure modeled using publicly available reconstruction programs Pulchra and Scwrl. As an example, the conformational stability of an amyloid precursor protein intra-cellular domain (AICD) is inspected; the reference conformation is the crystallographic structure with code 3DXC in Protein Data Bank (PDB) that describes a heterodimer of AICD and a nuclear multi-domain adaptor protein Fe65. Those conformations of AICD that correspond to local or near-local minima of the Landau free energy are identified. For this, the response of the original 3DXC conformation to variations in the ambient temperature is investigated, using the Glauber algorithm. The conclusion is that in isolation the AICD conformation in 3DXC must be unstable. A family of degenerate conformations that minimise the Landau free energy is identified, and it is proposed that the native state of an isolated AICD is a superposition of these conformations. The results are fully in line with the presumed intrinsically unstructured character of isolated AICD and should provide a basis for a systematic analysis of AICD structure in future NMR experiments.

  10. Exact Vlasov Solutions of Kinetic Flux Ropes

    NASA Astrophysics Data System (ADS)

    Ng, C. S.

    2014-12-01

    Small-scale magnetic flux ropes have been observed to form within the diffusion region in three-dimensional (3D) kinetic simulations of magnetic reconnection. Such 3D structures and the 2D version of them (plasmoids, secondary islands) could have important dynamical effects on the reconnection physics itself. Small-scale flux ropes have also been observed within the interplanetary space. We have found exact time-steady solutions of kinetic flux ropes by generalizing exact solutions of 2D Bernstein-Greene-Kruskal (BGK) modes in a magnetized plasma with finite magnetic field strength [Ng, Bhattacharjee, and Skiff, Phys. Plasmas 13, 055903 (2006)] to cases with azimuthal magnetic fields so that these structures carry electric current as well as steady electric and magnetic fields. Such fully nonlinear solutions now satisfy exactly the Vlasov-Poisson-Ampere system of equations. Solutions like these could describe small-scale flux ropes observed in reconnection diffusion regions or in the interplanetary space. They are also exact nonlinear solutions that can be used to validate numerical schemes for kinetic simulations. This work is supported by a National Science Foundation grant PHY-1004357.

  11. IMPACTS OF LANDSCAPE CHANGE ON WOLF RESTORATION SUCCESS: PLANNING A REINTRODUCTION PROGRAM USING STATIC AND DYNAMIC SPATIAL MODELS

    EPA Science Inventory

    Mammalian carnivores are increasingly the focus of reintroduction attempts in areas from which
    they have been extirpated by historic persecution. We used static and dynamic spatial models to evaluate whether a proposed wolf reintroduction to the southern Rocky Mountain region ...

  12. Spatial modeling of personalized exposure dynamics: the case of pesticide use in small-scale agricultural production landscapes of the developing world

    PubMed Central

    Leyk, Stefan; Binder, Claudia R; Nuckols, John R

    2009-01-01

    Background Pesticide poisoning is a global health issue with the largest impacts in the developing countries where residential and small-scale agricultural areas are often integrated and pesticides sprayed manually. To reduce health risks from pesticide exposure approaches for personalized exposure assessment (PEA) are needed. We present a conceptual framework to develop a spatial individual-based model (IBM) prototype for assessing potential exposure of farm-workers conducting small-scale agricultural production, which accounts for a considerable portion of global food crop production. Our approach accounts for dynamics in the contaminant distributions in the environment, as well as patterns of movement and activities performed on an individual level under different safety scenarios. We demonstrate a first prototype using data from a study area in a rural part of Colombia, South America. Results Different safety scenarios of PEA were run by including weighting schemes for activities performed under different safety conditions. We examined the sensitivity of individual exposure estimates to varying patterns of pesticide application and varying individual patterns of movement. This resulted in a considerable variation in estimates of magnitude, frequency and duration of exposure over the model runs for each individual as well as between individuals. These findings indicate the influence of patterns of pesticide application, individual spatial patterns of movement as well as safety conditions on personalized exposure in the agricultural production landscape that is the focus of our research. Conclusion This approach represents a conceptual framework for developing individual based models to carry out PEA in small-scale agricultural settings in the developing world based on individual patterns of movement, safety conditions, and dynamic contaminant distributions. The results of our analysis indicate our prototype model is sufficiently sensitive to differentiate and

  13. Glacial landscape evolution on Hall Peninsula, Baffin Island, since the Last Glacial Maximum: insights into switching glacial dynamics and thermo-mechanical conditions

    NASA Astrophysics Data System (ADS)

    Johnson, C. L.; Ross, M.

    2012-12-01

    Ice cover in north central Hall Peninsula, Baffin Island has evolved from full Laurentide Ice Sheet (LIS) cover during the Last Glacial Maximum (LGM) to a thin ice cap that now covers about 800 km2 in the northeast sector. The exposed subglacial landscape consists of contrasting geomorphological zones which allude to complex spatial and temporal changes in basal ice dynamics and thermal regime since LGM. We used satellite imagery, field observations, a large till geochemical database, and terrestrial cosmogenic isotopes to get new insights into subglacial erosion intensity, ice flow dynamics, and glacial history. Fields of streamlined bedrock-cored ridges (e.g. drumlins) have been mapped and their elongation ratios calculated. The density of bedrock-controlled lakes, which has traditionally been used as a proxy for subglacial erosion intensity on Baffin Island, has been re-examined using modern GIS techniques. This work has revealed a mosaic of glacial terrain zones each consisting of characteristics that are distinct from the other zones. Five glacial terrain zones (GTZ) have been recognized. One zone (GTZ 1) is characterized by a broad flowset of northeast trending streamlined hills and parallel paleo-flow indicators. It also has the highest streamlined hill density, longest elongation ratios, and the highest lake density of the study area. This northeast flowset is crosscut locally by ice flow indicators that converge into troughs that now form a series of fjords. Landforms and ice flow indicators of this younger system (GTZ 2) are traced inland showing propagation of the channelized system into this portion of the LIS. The central area of the peninsula contains a zone of thicker till and rolling topography (GTZ 3) as well as a zone consisting of southeast trending features and associated perpendicular moraines (GTZ 4). The modern ice cap and its past extension form the last zone (GTZ 5). The preservation of the northeast system (GTZ 1) outside of the

  14. Exact holographic mapping in free fermion systems

    NASA Astrophysics Data System (ADS)

    Lee, Ching Hua; Qi, Xiao-Liang

    2016-01-01

    In this paper, we perform a detailed analysis of the exact holographic mapping first introduced in arXiv:1309.6282, which was proposed as an explicit example of holographic duality between quantum many-body systems and gravitational theories. We obtain analytic results for free fermion systems that not only confirm previous numerical results, but also elucidate the exact relationships between the various physical properties of the bulk and boundary systems. These analytic results allow us to study the asymptotic properties that are difficult to probe numerically, such as the near-horizon regime of the black-hole geometry. We shall also explore a few interesting but hitherto unexplored bulk geometries, such as that corresponding to a boundary critical fermion with a nontrivial dynamical critical exponent. Our analytic framework also allows us to study the holographic mapping of some of these boundary theories in dimensions 2+1 or higher.

  15. Correlated Lloyd model: Exact solution

    NASA Astrophysics Data System (ADS)

    Kozlov, G. G.

    2014-11-01

    We describe an exactly solvable model of a disordered system that is a generalized Lloyd model; it differs from the classical model because the random potential is not a δ-correlated random process. We show that the exact average Green's function in this case is independent of the correlation radius of the random potential and, as in the classical Lloyd model, is a crystal Green's function whose energy argument acquires an imaginary part dependent on the disorder degree.

  16. Molecular dynamics characterization of the conformational landscape of small peptides: A series of hands-on collaborative practical sessions for undergraduate students.

    PubMed

    Rodrigues, João P G L M; Melquiond, Adrien S J; Bonvin, Alexandre M J J

    2016-01-01

    Molecular modelling and simulations are nowadays an integral part of research in areas ranging from physics to chemistry to structural biology, as well as pharmaceutical drug design. This popularity is due to the development of high-performance hardware and of accurate and efficient molecular mechanics algorithms by the scientific community. These improvements are also benefitting scientific education. Molecular simulations, their underlying theory, and their applications are particularly difficult to grasp for undergraduate students. Having hands-on experience with the methods contributes to a better understanding and solidification of the concepts taught during the lectures. To this end, we have created a computer practical class, which has been running for the past five years, composed of several sessions where students characterize the conformational landscape of small peptides using molecular dynamics simulations in order to gain insights on their binding to protein receptors. In this report, we detail the ingredients and recipe necessary to establish and carry out this practical, as well as some of the questions posed to the students and their expected results. Further, we cite some examples of the students' written reports, provide statistics, and share their feedbacks on the structure and execution of the sessions. These sessions were implemented alongside a theoretical molecular modelling course but have also been used successfully as a standalone tutorial during specialized workshops. The availability of the material on our web page also facilitates this integration and dissemination and lends strength to the thesis of open-source science and education. PMID:26751257

  17. "Dynamic Geodiversity" of glacial environments: new techniques for monitoring landscape variations on Alpine areas. Examples from the Gran Paradiso National Park

    NASA Astrophysics Data System (ADS)

    Bertotto, Stefania; Giardino, Marco; Perotti, Luigi; Mortara, Giovanni; Baroni, Carlo

    2014-05-01

    fans, torrents, falls, lakes; being "starting points" for studying geodiversity of the Park, they have been mapped in detail. Updates of historical geomorphological maps, monitoring of glacier outline evolution and detailed digital field surveys have been conducted through Geomatics techniques within this area thanks to the support of several research programs: 1) seasonal activities of the Italian Glaciological Committee; 2) the MIUR-PRIN 2011 Project "Response of morphoclimatic system dynamics to global changes and related geomorphological hazards"; 3) the planning program of the National Park; 4) activities in the framework of GlaRiskAlp project n.56 Alcotra 2007-2013. At a local scale, detailed analysis have been performed by using integrated geomatics techniques such as in the Capra Glacier site, in the Orco Valley, near Serrù Lake (Piemonte Region). Results have been obtained in tracing changes of "dynamic geodiversity" features that can trigger natural processes (e.g. moraines, lakes, debris). These are useful features for preventing natural hazards in touristic or anthropized areas, by means of proper planning of access of the area and geodiversity exploitation measures. Results demonstrated that knowledge on dynamic geodiversity of glacial environments is crucial for understanding how these high altitude dynamic landscapes are changing, not only for their external appearance, but also for their complex internal mechanisms and values.

  18. The temporal dynamics of a scaling relationship between soil grading and landscape geomorphology using a pedogenesis model

    NASA Astrophysics Data System (ADS)

    Welivitiya, Dimuth; Willgoose, Garry; Hancock, Greg

    2015-04-01

    Using the mARM3D pedogenesis model (which simulated armouring and weathering processes on a hillslope) previous work by Cohen and the coauthors of this abstract found a strong log-log linear relationship between the particle size distribution of the soil (e.g. d50), the contributing area and the local slope. In recent work using our SSSPAM pedogenesis model (a generalisation of mARM3D) we have confirmed this relationship is robust against changes in climate and geology and is also true for more general grading properties of the soil at the surface (e.g. d10, d90). However, this previous work was for equilibrium soils and time invariant landforms. In this presentation we will extend this work to show the effect of temporal dynamics in the pedogenesis model by exploring the spatial organisation of the time varying behaviour of soil grading. We will show how the within-profile weathering processes change the variation with depth of the soil grading, and how the spatial variation of the soil surface and depth averaged grading properties change with the temporal dynamics. These results strengthen our confidence in the generality of the log-log linear scaling relationship between area, slope and soil grading. The paper will present the results of our simulations and will highlight the potential uses of the relationship for digital soil mapping and better characterization of soils in environmental models.

  19. Exploring complex dynamics in multi agent-based intelligent systems: Theoretical and experimental approaches using the Multi Agent-based Behavioral Economic Landscape (MABEL) model

    NASA Astrophysics Data System (ADS)

    Alexandridis, Konstantinos T.

    This dissertation adopts a holistic and detailed approach to modeling spatially explicit agent-based artificial intelligent systems, using the Multi Agent-based Behavioral Economic Landscape (MABEL) model. The research questions that addresses stem from the need to understand and analyze the real-world patterns and dynamics of land use change from a coupled human-environmental systems perspective. Describes the systemic, mathematical, statistical, socio-economic and spatial dynamics of the MABEL modeling framework, and provides a wide array of cross-disciplinary modeling applications within the research, decision-making and policy domains. Establishes the symbolic properties of the MABEL model as a Markov decision process, analyzes the decision-theoretic utility and optimization attributes of agents towards comprising statistically and spatially optimal policies and actions, and explores the probabilogic character of the agents' decision-making and inference mechanisms via the use of Bayesian belief and decision networks. Develops and describes a Monte Carlo methodology for experimental replications of agent's decisions regarding complex spatial parcel acquisition and learning. Recognizes the gap on spatially-explicit accuracy assessment techniques for complex spatial models, and proposes an ensemble of statistical tools designed to address this problem. Advanced information assessment techniques such as the Receiver-Operator Characteristic curve, the impurity entropy and Gini functions, and the Bayesian classification functions are proposed. The theoretical foundation for modular Bayesian inference in spatially-explicit multi-agent artificial intelligent systems, and the ensembles of cognitive and scenario assessment modular tools build for the MABEL model are provided. Emphasizes the modularity and robustness as valuable qualitative modeling attributes, and examines the role of robust intelligent modeling as a tool for improving policy-decisions related to land

  20. Driving the Landscape

    NASA Astrophysics Data System (ADS)

    Haff, P. K.

    2012-12-01

    Technological modification of the earth's surface (e.g., agriculture, urbanization) is an old story in human history, but what about the future? The future of landscape in an accelerating technological world, beyond a relatively short time horizon, lies hidden behind an impenetrable veil of complexity. Sufficiently complex dynamics generates not only the trajectory of a variable of interest (e.g., vegetation cover) but also the environment in which that variable evolves (e.g., background climate). There is no way to anticipate what variables will define that environment—the dynamics creates its own variables. We are always open to surprise by a change of conditions we thought or assumed were fixed or by the appearance of new phenomena of whose possible existence we had been unaware or thought unlikely. This is especially true under the influence of technology, where novelty is the rule. Lack of direct long-term predictability of landscape change does not, however, mean we cannot say anything about its future. The presence of persistence (finite time scales) in a system means that prediction by a calibrated numerical model should be good for a limited period of time barring bad luck or faulty implementation. Short-term prediction, despite its limitations, provides an option for dealing with the longer-term future. If a computer-controlled car tries to drive itself from New York to Los Angeles, no conceivable (or possible) stand-alone software can be constructed to predict a priori the space-time trajectory of the vehicle. Yet the drive is normally completed easily by most drivers. The trip is successfully completed because each in a series of very short (linear) steps can be "corrected" on the fly by the driver, who takes her cues from the environment to keep the car on the road and headed toward its destination. This metaphor differs in a fundamental way from the usual notion of predicting geomorphic change, because it involves a goal—to reach a desired

  1. Simulations of thermodynamics and kinetics on rough energy landscapes with milestoning.

    PubMed

    Bello-Rivas, Juan M; Elber, Ron

    2016-03-01

    We investigated by computational means the kinetics and stationary behavior of stochastic dynamics on an ensemble of rough two-dimensional energy landscapes. There are no obvious separations of temporal scales in these systems, which constitute a simple model for the behavior of glasses and some biomaterials. Even though there are significant computational challenges present in these systems due to the large number of metastable states, the Milestoning method is able to compute their kinetic and thermodynamic properties exactly. We observe two clearly distinguished regimes in the overall kinetics: one in which diffusive behavior dominates and another that follows an Arrhenius law (despite the absence of a dominant barrier). We compare our results with those obtained with an exactly-solvable one-dimensional model, and with the results from the rough one-dimensional energy model introduced by Zwanzig. © 2015 Wiley Periodicals, Inc. PMID:26265358

  2. Seasonal dynamics of the land surface energy balance of a boreal forest-peatland landscape affected by degrading permafrost in the Taiga Plains, Canada

    NASA Astrophysics Data System (ADS)

    Helbig, M.; Wischnewski, K.; Chasmer, L.; Quinton, W. L.; Kljun, N.; Detto, M.; Sonnentag, O.

    2014-12-01

    Northern boreal ecosystems along the southern limit of permafrost comprise a mosaic of forests with permafrost, and permafrost-free peatland and lake ecosystems. The proportion of permafrost-free areas has rapidly increased over the last decades due to increasingly warmer air temperatures. This change in land cover causes changes in vegetation composition and structure affecting land surface characteristics such as albedo and surface roughness with important implications for the land surface energy balance and thus regional climate. For example, a decrease in sensible heat flux potentially cools the atmosphere and thus constitutes a negative feedback to the climate system. Changes in latent heat fluxes alter regional water vapour dynamics and thus may affect precipitation patterns. To better understand the land surface energy balance under the influence of degrading permafrost, we measured sensible and latent heat fluxes with two eddy covariance systems, one at 15 m and one at 2 m above the ground surface, along with net radiation and soil heat flux at Scotty Creek, a watershed in the discontinuous permafrost zone in the southern part of the Northwest Territories, Canada. The flux footprint of the 15 m-eddy covariance system covers an area equally covered by black spruce forests and permafrost-free, treeless peatlands whereas the flux footprint of the adjacent 2 m-eddy covariance system covers a single bog within the footprint of the 15 m system. Peak sensible heat fluxes at the bog were up to 200 W m-2 smaller than the landscape-scale fluxes between April and July 2014. During the snow free period, peak latent heat fluxes at the wet bog were about 50 W m-2 higher than the landscape-scale fluxes. Albedo of the forest was generally smaller compared to the bog except for the immediate post-melt period when the bog was affected by widespread surface flooding. This difference in albedo leads to higher net radiation at the forest site, particularly during the snow cover

  3. Multiproxy Analysis of Droughts, Landscape Changes, Sediment Dynamics, and Human Disturbances in Hudson River Marsh Peat, using Pollen, Spores, Macrofossils, LOI, and X- Ray Fluorescence Spectroscopy

    NASA Astrophysics Data System (ADS)

    Sritrairat, S.; Kenna, T. C.; Peteet, D. M.; Pederson, D.

    2008-12-01

    Marsh peat is an excellent archive for local and regional paleoecological and paleoclimate studies because of high preservation and low disturbance. Under climatic and anthropogenic changes, sediment composition and sedimentation patterns can be altered. Using this principle, we have implemented the use of field portable X-Ray Fluoresecence Spectroscopy (Innov-X, USA) to rapidly quantify stratigraphic sediment elemental composition changes. We will discuss findings from two marshes of the lower Hudson Estuary, NY. More than 250 cm depth of Piermont Marsh sediment (41.00N, 73.91W) and 100 cm depth of Iona Island Marsh sediment (41.30N, 73.97W) were analyzed. Dry and homogenized samples were used to minimize errors from water absorption and heterogeneity. In combination with our pollen, spores, macrofossil, organic/inorganic content profiles, and radiometric dating (C-14, Cs-137, and Pb-210) at Piermont (Pederson et al., 2005) and Iona (Peteet et al., 2006), we found many emerging XRF proxies for droughts, landscape changes, inorganic matter content, sedimentation rate, pollution history, and human impacts. Both cores captured human disturbances after the European Settlement, when there are pronounced changes in plants composition, invasive species expansion, organic/inorganic content, and sediment dynamics. At the longer time scale, where Pederson et al.(2005) identify Medieval Warming mega-droughts at Piermont, we found zinc, titanium, and potassium to be useful. The results suggest, 1) Many metal pollutants, such as lead, copper, and zinc, can be quantified quickly with these methods, 2) The profiles of these pollutants agree with the Ambrosia rise and radiometric dating, so the peaks can be rapidly identified and used as an additional time marker, 3) Zinc concentrations prior to the Industrial Revolution vary to a greater degree than the anthropogenic signal. The trend is closely related to the trend of charcoal and moisture-sensitive vegetation, which is linked

  4. Exact methods for self interacting neutrinos

    SciTech Connect

    Pehlivan, Y.; Balantekin, A. B.; Kajino, Toshitaka

    2014-06-24

    The effective many-body Hamiltonian which describes vacuum oscillations and self interactions of neutrinos in a two flavor mixing scheme under the single angle approximation has the same dynamical symmetries as the well known BCS pairing Hamiltonian. These dynamical symmetries manifest themselves in terms of a set of constants of motion and can be useful in formulating the collective oscillation modes in an intuitive way. In particular, we show that a neutrino spectral split can be simply viewed as an avoided level crossing between the eigenstates of a mean field Hamiltonian which includes a Lagrange multiplier in order to fix the value of an exact many-body constant of motion. We show that the same dynamical symmetries also exist in the three neutrino mixing scheme by explicitly writing down the corresponding constants of motion.

  5. Matrix inflation and the landscape of its potential

    SciTech Connect

    Ashoorioon, Amjad; Firouzjahi, Hassan; Sheikh-Jabbari, Mohammmad Mahdi E-mail: firouz@ipm.ir

    2010-05-01

    Recently we introduced an inflationary setup in which the inflaton fields are matrix valued scalar fields with a generic quartic potential, M-flation. In this work we study the landscape of various inflationary models arising from M-flation. The landscape of the inflationary potential arises from the dynamics of concentric multiple branes in appropriate flux compactifications of string theory. After discussing the classical landscape of the theory we study the possibility of transition among various inflationary models appearing at different points on the landscape, mapping the quantum landscape of M-flation. As specific examples, we study some two-field inflationary models arising from this theory in the landscape.

  6. Compensatory role of double mutation N348I/M184V on nevirapine binding landscape: insight from molecular dynamics simulation.

    PubMed

    Karubiu, Wilson; Bhakat, Soumendranath; Soliman, Mahmoud E S

    2014-10-01

    Non-nucleoside reverse transcriptase inhibitors (NNRTI) have emerged as gold standards in current anti-AIDS drug discovery and development by allosterically inhibiting HIV reverse transcriptase (HIV-RT). Connection sub-domain mutation, N348I and the M184V active site mutation decreases HIV-1 RT susceptibility to NNRTI, nevirapine (NVP), whereas concurrence of both mutations improves enzyme susceptibility to NVP. Molecular dynamics simulation and enhanced post-dynamics analyses were applied to gain molecular insight into occurrence of N348I, M184V and N348I/M184V double mutations and their effect on NVP binding landscape. Results showed that the presence of the double mutation (N348I/M184V) ameliorates the drastic effects of connection sub-domain mutation, N348I alone on NVP binding, which correlates with experimental findings. We showed that the binding of NVP to the NNRTI binding pocket (NNIBP) is drastically distorted in the presence of connection sub-domain mutation, N348I and may further explain the impaired motions of mutant RTs compared to the wild type. The residue based fluctuation further suggested that the occurrence of N348I decreased the overall flexibility of NVP-HIV-RT complex whereas concurrence of N348I/M184V double mutation restored the conformational flexibility as compared to single mutant. This phenomenon was further validated by the trends of binding free energy as well as the per-residue footprints which showed an increased ∆Gbind in case of N348I/M184V double mutant as compared to N348I variant. Further, for the first time residue interaction network highlighted the structural changes due to occurrence of M184V and N348I mutations which gives a conclusive evidence of these mutations. This work provides the most comprehensive analysis of NVP resistance and the impact of double (N348I/M184V) mutation to date from a dynamics perspective and provides information that should prove useful for understanding the drug resistance mechanism against

  7. Exact discretization by Fourier transforms

    NASA Astrophysics Data System (ADS)

    Tarasov, Vasily E.

    2016-08-01

    A discretization of differential and integral operators of integer and non-integer orders is suggested. New type of differences, which are represented by infinite series, is proposed. A characteristic feature of the suggested differences is an implementation of the same algebraic properties that have the operator of differentiation (property of algebraic correspondence). Therefore the suggested differences are considered as an exact discretization of derivatives. These differences have a property of universality, which means that these operators do not depend on the form of differential equations and the parameters of these equations. The suggested differences operators allows us to have difference equations whose solutions are equal to the solutions of corresponding differential equations. The exact discretization of the derivatives of integer orders is given by the suggested differences of the same integer orders. Similarly, the exact discretization of the Riesz derivatives and integrals of integer and non-integer order is given by the proposed fractional differences of the same order.

  8. Dynamics and Reversibility of the DNA Methylation Landscape of Grapevine Plants (Vitis vinifera) Stressed by In Vitro Cultivation and Thermotherapy.

    PubMed

    Baránek, Miroslav; Čechová, Jana; Raddová, Jana; Holleinová, Věra; Ondrušíková, Eva; Pidra, Miroslav

    2015-01-01

    There is relatively little information concerning long-term alterations in DNA methylation following exposure of plants to environmental stress. As little is known about the ratio of non-heritable changes in DNA methylation and mitotically-inherited methylation changes, dynamics and reversibility of the DNA methylation states were investigated in grapevine plants (Vitis vinifera) stressed by in vitro cultivation. It was observed that significant part of induced epigenetic changes could be repeatedly established by exposure to particular planting and stress conditions. However, once stress conditions were discontinued, many methylation changes gradually reverted and plants returned to epigenetic states similar to those of maternal plants. In fact, in the period of one to three years after in vitro cultivation it was difficult to distinguish the epigenetic states of somaclones and maternal plants. Forty percent of the observed epigenetic changes disappeared within a year subsequent to termination of stress conditions ending and these probably reflect changes caused by transient and reversible stress-responsive acclimation mechanisms. However, sixty percent of DNA methylation diversity remained after 1 year and probably represents mitotically-inherited epimutations. Sequencing of regions remaining variable between maternal and regenerant plants revealed that 29.3% of sequences corresponded to non-coding regions of grapevine genome. Eight sequences (19.5%) corresponded to previously identified genes and the remaining ones (51.2%) were annotated as "hypothetical proteins" based on their similarity to genes described in other species, including genes likely to undergo methylation changes following exposure to stress (V. vinifera gypsy-type retrotransposon Gret1, auxin-responsive transcription factor 6-like, SAM-dependent carboxyl methyltransferase). PMID:25973746

  9. Dynamics and Reversibility of the DNA Methylation Landscape of Grapevine Plants (Vitis vinifera) Stressed by In Vitro Cultivation and Thermotherapy

    PubMed Central

    Baránek, Miroslav; Čechová, Jana; Raddová, Jana; Holleinová, Věra; Ondrušíková, Eva

    2015-01-01

    There is relatively little information concerning long-term alterations in DNA methylation following exposure of plants to environmental stress. As little is known about the ratio of non-heritable changes in DNA methylation and mitotically-inherited methylation changes, dynamics and reversibility of the DNA methylation states were investigated in grapevine plants (Vitis vinifera) stressed by in vitro cultivation. It was observed that significant part of induced epigenetic changes could be repeatedly established by exposure to particular planting and stress conditions. However, once stress conditions were discontinued, many methylation changes gradually reverted and plants returned to epigenetic states similar to those of maternal plants. In fact, in the period of one to three years after in vitro cultivation it was difficult to distinguish the epigenetic states of somaclones and maternal plants. Forty percent of the observed epigenetic changes disappeared within a year subsequent to termination of stress conditions ending and these probably reflect changes caused by transient and reversible stress-responsive acclimation mechanisms. However, sixty percent of DNA methylation diversity remained after 1 year and probably represents mitotically-inherited epimutations. Sequencing of regions remaining variable between maternal and regenerant plants revealed that 29.3% of sequences corresponded to non-coding regions of grapevine genome. Eight sequences (19.5%) corresponded to previously identified genes and the remaining ones (51.2%) were annotated as “hypothetical proteins” based on their similarity to genes described in other species, including genes likely to undergo methylation changes following exposure to stress (V. vinifera gypsy-type retrotransposon Gret1, auxin-responsive transcription factor 6-like, SAM-dependent carboxyl methyltransferase). PMID:25973746

  10. Surface water and groundwater nitrogen dynamics in a well drained riparian forest within a poorly drained agricultural landscape.

    PubMed

    Davis, Jennifer H; Griffith, Stephen M; Wigington, Parker J

    2011-01-01

    The effectiveness of riparian zones in mitigating nutrient in ground and surface water depends on the climate, management, and hydrogeomorphology of a site. The purpose of this study was to determine the efficacy of a well drained, mixed-deciduous riparian forest to buffer a river from N originating from a poorly drained grass seed cropping system. The study site was adjacent to the Calapooia River in the Willamette Valley, Oregon. Water was found to move from the rapid drainage of swale surface water. During winter hydrological events, the riparian forest also received river water. Low nitrate (NO3-) concentrations (0.2-0.4 mg NO3- -NL(-1)) in the shallow groundwater of the cropping system were associated with low rates of mineralization and nitrification (33 kg N ha(-1) yr(-1)) and high grass seed crop uptake of N (155 kg N ha(-1) yr(-1)). The riparian forest soil had higher rates of mineralization (117 kg N ha(-1) yr(-1)) that produced quantities of soil N that were within the range of literature values for plant uptake, leading to relatively