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Sample records for landscapes exact dynamics

  1. LETTER: Exact solution of a model of time-dependent evolutionary dynamics in a rugged fitness landscape

    NASA Astrophysics Data System (ADS)

    Sire, Clément; Majumdar, Satya N.; Dean, David S.

    2006-07-01

    A simplified form of the time-dependent evolutionary dynamics of a quasispecies model with a rugged fitness landscape is solved via a mapping onto a random flux model whose asymptotic behaviour can be described in terms of a random walk. The statistics of the number of changes of the dominant genotype from a finite set of genotypes are exactly obtained confirming existing conjectures based on numerics.

  2. 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.

  3. 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.

  4. Understanding patchy landscape dynamics: towards a landscape language.

    PubMed

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

    2012-01-01

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

  5. Understanding Patchy Landscape Dynamics: Towards a Landscape Language

    PubMed Central

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

    2012-01-01

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

  6. Dynamic landscape models of coevolutionary games.

    PubMed

    Richter, Hendrik

    2017-02-24

    Players of coevolutionary games may update not only their strategies but also their networks of interaction. Based on interpreting the payoff of players as fitness, dynamic landscape models are proposed. The modeling procedure is carried out for Prisoner's Dilemma (PD) and Snowdrift (SD) games that both use either birth-death (BD) or death-birth (DB) strategy updating. The main focus is on using dynamic fitness landscapes as a mathematical model of coevolutionary game dynamics. Hence, an alternative tool for analyzing coevolutionary games becomes available, and landscape measures such as modality, ruggedness and information content can be computed and analyzed. In addition, fixation properties of the games and quantifiers characterizing the interaction networks are calculated numerically. Relations are established between landscape properties expressed by landscape measures and quantifiers of coevolutionary game dynamics such as fixation probabilities, fixation times and network properties.

  7. 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 ...

  8. 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.

  9. Dynamical dimer-dimer correlation functions from exact diagonalization

    SciTech Connect

    Werner, Ralph

    2001-05-01

    A regularization method is presented to deduce dynamic correlation functions from exact diagonalization calculations. It is applied to dimer-dimer correlation functions in quantum spin chains relevant for the description of spin-Peierls systems. Exact results for the XY model are presented. The analysis draws into doubt that the dimer-dimer correlation functions show the same scale invariance as spin-spin correlation functions. The results are applied to describe the quasielastic scattering in CuGeO{sub 3} and the hardening of the Peierls-active phonons.

  10. Exact solution for a non-Markovian dissipative quantum dynamics.

    PubMed

    Ferialdi, Luca; Bassi, Angelo

    2012-04-27

    We provide the exact analytic solution of the stochastic Schrödinger equation describing a harmonic oscillator interacting with a non-Markovian and dissipative environment. This result represents an arrival point in the study of non-Markovian dynamics via stochastic differential equations. It is also one of the few exactly solvable models for infinite-dimensional systems. We compute the Green's function; in the case of a free particle and with an exponentially correlated noise, we discuss the evolution of Gaussian wave functions.

  11. 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.

  12. 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.

  13. Archetypal energy landscapes: dynamical diagnosis.

    PubMed

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

    2005-01-08

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  15. 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.

  16. Exact Dynamic Stiffness Matrix for Composite Timoshenko Beams with Applications

    NASA Astrophysics Data System (ADS)

    Bannerjee, J. R.; Williams, F. W.

    1996-07-01

    In this paper, an exact dynamic stiffness matrix is presented for a composite beam. It includes the effects of shear deformation and rotatory inertia: i.e., it is for a composite Timoshenko beam. The theory accounts for the (material) coupling between the bending and torsional deformations which usually occurs for such beams due to the anisotropic nature of fibrous composites. An explicit analytical expression for each of the elements of the dynamic stiffness matrix is derived by rigorous use of the symbolic computing package REDUCE. It is proved that the use of such expressions leads to substantial savings in computer time when compared with the matrix inversion method. The use of this dynamic stiffness matrix to investigate the free vibration characteristics of composite beams (with or without the effects of shear deformation and/or rotatory inertia included) is demonstrated by applying the Wittrick-Williams algorithm. Numerical results for which comparative results are available in the literature are discussed.

  17. Exact Closed Master Equation for Gaussian Non-Markovian Dynamics.

    PubMed

    Ferialdi, L

    2016-03-25

    Non-Markovian master equations describe general open quantum systems when no approximation is made. We provide the exact closed master equation for the class of Gaussian, completely positive, trace preserving, non-Markovian dynamics. This very general result allows us to investigate a vast variety of physical systems. We show that the master equation for non-Markovian quantum Brownian motion is a particular case of our general result. Furthermore, we derive the master equation unraveled by a non-Markovian, dissipative stochastic Schrödinger equation, paving the way for the analysis of dissipative non-Markovian collapse models.

  18. Remote Sensing of Arctic Landscape Dynamics

    NASA Astrophysics Data System (ADS)

    Jones, Benjamin M.

    Amplified warming in the Arctic has likely increased the rate of landscape change and disturbances in northern high latitude regions. Remote sensing provides a valuable tool for assessing the spatial and temporal patterns associated with arctic landscape dynamics over annual, decadal, and centennial time scales. In this dissertation, I focused on remote sensing studies associated with four primary components of arctic landscape change and disturbance: (1) permafrost coastline erosion, (2) thermokarst lake dynamics, (3) tundra fires, and (4) using repeat airborne LiDAR for the measurement of vertical deformation in an arctic coastal lowland landscape. By combining observations from several high resolution satellite images for a 9 km segment of the Beaufort Sea Coast between 2008 and 2012, I demonstrated that the report of heightened erosion at the beginning of the 2000s was equaled or exceeded in every year except 2010 and that the mean annual erosion rate was tightly coupled to the number of open water days and the number of storms. By combining historical aerial photographs from the 1950s and 1980s with recent high-resolution satellite imagery from the mid-2000s, I assessed the expansion and drainage of thermokarst lakes on the northern Seward Peninsula. I found that more than half of the lakes in the study area were expanding as a result of permafrost degradation along their margins but that the rate of expansion was fairly consistent (0.35 and 0.39 m/yr) between the 1950s and 1980s and 1980s and mid-2000s, respectively. However, it appeared that in a number of instances that expansion of lakes led to the lateral drainage and that over the 55-year study period the total lake area decreased by 24%. While these studies highlight the utility of quantifying disturbance during the remotely sensed image archive period (~1950s to present) they are inherently limited temporally. Thus, I also demonstrated techniques in which field studies and remote sensing data could be

  19. 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.

  20. Exact solutions for kinetic models of macromolecular dynamics.

    PubMed

    Chemla, Yann R; Moffitt, Jeffrey R; Bustamante, Carlos

    2008-05-15

    Dynamic biological processes such as enzyme catalysis, molecular motor translocation, and protein and nucleic acid conformational dynamics are inherently stochastic processes. However, when such processes are studied on a nonsynchronized ensemble, the inherent fluctuations are lost, and only the average rate of the process can be measured. With the recent development of methods of single-molecule manipulation and detection, it is now possible to follow the progress of an individual molecule, measuring not just the average rate but the fluctuations in this rate as well. These fluctuations can provide a great deal of detail about the underlying kinetic cycle that governs the dynamical behavior of the system. However, extracting this information from experiments requires the ability to calculate the general properties of arbitrarily complex theoretical kinetic schemes. We present here a general technique that determines the exact analytical solution for the mean velocity and for measures of the fluctuations. We adopt a formalism based on the master equation and show how the probability density for the position of a molecular motor at a given time can be solved exactly in Fourier-Laplace space. With this analytic solution, we can then calculate the mean velocity and fluctuation-related parameters, such as the randomness parameter (a dimensionless ratio of the diffusion constant and the velocity) and the dwell time distributions, which fully characterize the fluctuations of the system, both commonly used kinetic parameters in single-molecule measurements. Furthermore, we show that this formalism allows calculation of these parameters for a much wider class of general kinetic models than demonstrated with previous methods.

  1. 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,...

  2. The dynamical landscape of marine phytoplankton diversity

    PubMed Central

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

    2015-01-01

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

  3. The dynamical landscape of marine phytoplankton diversity.

    PubMed

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

    2015-10-06

    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.

  4. Badlands: A parallel basin and landscape dynamics model

    NASA Astrophysics Data System (ADS)

    Salles, T.

    Over more than three decades, a number of numerical landscape evolution models (LEMs) have been developed to study the combined effects of climate, sea-level, tectonics and sediments on Earth surface dynamics. Most of them are written in efficient programming languages, but often cannot be used on parallel architectures. Here, I present a LEM which ports a common core of accepted physical principles governing landscape evolution 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 topography development at various space and time scales.

  5. 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.

  6. 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.

  7. 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).

  8. 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

  9. 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.

  10. LanDPro: Landscape Dynamics Program

    DTIC Science & Technology

    2012-09-18

    making. These same types of sites were rarely found on landscapes formed on deposits derived from coarse-grained igneous rock sources, such as granite...grained igneous rocks . Our premise is that if our conceptual model were applied at the U.S. Army Yuma Proving Ground (YPG) it would indicate a dominance...of sites on the most stable landscape units developed on deposits derived from fine-grained igneous rocks . At YPG, these landscape units would be

  11. 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...

  12. Bacterial predator–prey dynamics in microscale patchy landscapes

    PubMed Central

    Rotem, Or; Jurkevitch, Edouard; Dekker, Cees

    2016-01-01

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

  13. Universality in exact quantum state population dynamics and control

    SciTech Connect

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

    2010-09-15

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

  14. From Water Dynamics to Rainfed Landscapes with GRASS GIS

    NASA Astrophysics Data System (ADS)

    Chemin, Yann; van Brakel, Martin; Johnston, Robyn; Curnow, Jayne

    2014-05-01

    Variability in water availability is a key determinant of risk and constraint to productivity in rainfed agricultural systems. Understanding the dynamics of water availability across both spatial and temporal scales is essential to managing water and optimize production. This research proposes to look at both the physical measurement of water availability and water user perceptions of landscapes and water availability. Evapotranspiration makes up about three quarters of the transiting water in a landscape, it is composed of evaporation (water bodies, soil) and transpiration, the vegetation biomass growing quantity. This work will develop a methodology for defining landscapes based on water dynamics to be used at the interface of WLE research. The GRASS GIS Imagery, Landscape and Temporal toolkits form the basis of the methodological development, from evapotranspiration modeling and landscape analysis to spatio-temporal analysis.

  15. New exact dynamic field solutions of Einstein's equation

    NASA Astrophysics Data System (ADS)

    Felber, Franklin

    2009-05-01

    An exact metric first derived, but not analyzed, by Hartle, Thorne, and Price [1] is used to calculate the exact time-dependent gravitational field of a spherical mass moving with arbitrarily high constant velocity. The exact field solutions [2] confirm that even the weak field of a spherical mass moving faster than 3-1/2c is repulsive in the forward and backward directions [3]. The exact threshold conditions required for gravitational repulsion of particles at rest are determined as a function of source speed and field strength and particle position with respect to the relativistic source. The results are consistent with the repulsion of relativistic particles by a weak static Schwarzschild field, discovered 85 years ago by Hilbert [4]. [4pt] [1] J. B. Hartle, K. S. Thorne, and R. H. Price in Black Holes: The Membrane Paradigm, edited by K. S. Thorne, R. H. Price, D. A. Macdonald (Yale U. Press, New Haven, Conn., 1986), Ch. V.[0pt] [2] F. S. Felber, arXiv:0803.2864v4 [physics.gen-ph] 2008.[0pt] [3] F. S. Felber, arXiv:gr-qc/0505098v2, 2005.[0pt] [4] D. Hilbert, Math. Ann. 92, 1 (1924).

  16. 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.

  17. Soil erosion dynamics response to landscape pattern.

    PubMed

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

    2010-02-15

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

  18. Biophysical Fitness Landscapes and Evolutionary Dynamics of Proteins

    NASA Astrophysics Data System (ADS)

    Manhart, Michael; Morozov, Alexandre

    2014-03-01

    The molecular biophysics of proteins fundamentally shapes their fitness landscapes and evolutionary dynamics. For example, the evolution of new function in a protein is constrained by the need to maintain folding stability. We investigate the role of molecular biophysics in protein evolution by developing a class of fitness landscapes based on protein folding and binding energetics. We characterize the properties of these landscapes, such as their epistasis, accessibility, and number of local maxima. We also use a recently-developed path-based approach to random walks on networks to analyze the dynamics of populations evolving on these landscapes, focusing especially on the distribution and diversity of adaptive trajectories. These models make qualitative predictions relevant to both natural evolution as well as directed evolution experiments.

  19. Exact Classical and Quantum Dynamics in Background Electromagnetic Fields

    NASA Astrophysics Data System (ADS)

    Heinzl, Tom; Ilderton, Anton

    2017-03-01

    Analytic results for (Q)ED processes in external fields are limited to a few special cases, such as plane waves. However, the strong focusing of intense laser fields implies a need to go beyond the plane wave model. By exploiting Poincaré symmetry and superintegrability we show how to construct, and solve without approximation, new models of laser-matter interactions. We illustrate the method with a model of a radially polarized (TM) laser beam, for which we exactly determine the classical orbits and quantum wave functions. Including in this way the effects of transverse field structure should improve predictions and analyses for experiments at intense laser facilities.

  20. 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.

  1. Dynamically Encircling Exceptional Points: Exact Evolution and Polarization State Conversion

    NASA Astrophysics Data System (ADS)

    Hassan, Absar U.; Zhen, Bo; Soljačić, Marin; Khajavikhan, Mercedeh; Christodoulides, Demetrios N.

    2017-03-01

    We show that a two-level non-Hermitian Hamiltonian with constant off-diagonal exchange elements can be analyzed exactly when the underlying exceptional point is perfectly encircled in the complex plane. The state evolution of this system is explicitly obtained in terms of an ensuing transfer matrix, even for large encirclements, regardless of adiabatic conditions. Our results clearly explain the direction-dependent nature of this process and why in the adiabatic limit its outcome is dominated by a specific eigenstate—irrespective of initial conditions. Moreover, numerical simulations suggest that this mechanism can still persist in the presence of nonlinear effects. We further show that this robust process can be harnessed to realize an optical omnipolarizer: a configuration that generates a desired polarization output regardless of the input polarization state, while from the opposite direction it always produces the counterpart eigenstate.

  2. Dynamically Encircling Exceptional Points: Exact Evolution and Polarization State Conversion.

    PubMed

    Hassan, Absar U; Zhen, Bo; Soljačić, Marin; Khajavikhan, Mercedeh; Christodoulides, Demetrios N

    2017-03-03

    We show that a two-level non-Hermitian Hamiltonian with constant off-diagonal exchange elements can be analyzed exactly when the underlying exceptional point is perfectly encircled in the complex plane. The state evolution of this system is explicitly obtained in terms of an ensuing transfer matrix, even for large encirclements, regardless of adiabatic conditions. Our results clearly explain the direction-dependent nature of this process and why in the adiabatic limit its outcome is dominated by a specific eigenstate-irrespective of initial conditions. Moreover, numerical simulations suggest that this mechanism can still persist in the presence of nonlinear effects. We further show that this robust process can be harnessed to realize an optical omnipolarizer: a configuration that generates a desired polarization output regardless of the input polarization state, while from the opposite direction it always produces the counterpart eigenstate.

  3. 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.

  4. Exploring the control landscape for nonlinear quantum dynamics

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

  5. Landscape matrix mediates occupancy dynamics of Neotropical avian insectivores.

    PubMed

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

    2011-07-01

    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 insectivorous birds in 99 forest patches embedded in four matrix types (agriculture, suburban development, 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.

  6. 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.

  7. Criticality in conserved dynamical systems: experimental observation vs. exact properties.

    PubMed

    Marković, Dimitrije; Gros, Claudius; Schuelein, André

    2013-03-01

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

  8. 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…

  9. Dynamic modes of quasispherical vesicles: exact analytical solutions.

    PubMed

    Guedda, M; Abaidi, M; Benlahsen, M; Misbah, C

    2012-11-01

    In this paper we introduce a simple mathematical analysis to reexamine vesicle dynamics in the quasispherical limit (small deformation) under a shear flow. In this context, a recent paper [Misbah, Phys. Rev. Lett. 96, 028104 (2006)] revealed a dynamic referred to as the vacillating-breathing (VB) mode where the vesicle main axis oscillates about the flow direction and the shape undergoes a breathinglike motion, as well as the tank-treading and tumbling (TB) regimes. Our goal here is to identify these three modes by obtaining explicit analytical expressions of the vesicle inclination angle and the shape deformation. In particular, the VB regime is put in evidence and the transition dynamics is discussed. Not surprisingly, our finding confirms the Keller-Skalak solutions (for rigid particles) and shows that the VB and TB modes coexist, and whether one prevails over the other depends on the initial conditions. An interesting additional element in the discussion is the prediction of the TB and VB modes as functions of a control parameter Γ, which can be identified as a TB-VB parameter.

  10. 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.

  11. [Dynamics of land use landscape pattern in Hangzhou City during its rapid urbanization].

    PubMed

    Deng, Jin-Song; Li, Jun; Yu, Liang; Wang, Ke

    2008-09-01

    Based on the multi-temporal SPOT images of Hangzhou City in 1996, 2000, 2003, and 2006, a method combining Principal Component Analysis (PCA) and hybrid classifier was adopted to accurately extract the land use change information. Meantime, the dynamics and characteristics of landscape pattern change were analyzed by using landscape indexes. The results showed that from 1996 to 2006, the rapid urbanization in Hangzhou induced a tremendous conversion of landscape pattern. Owing to the anthropogenic disturbance, the agricultural landscape was gradually replaced by man-made landscape, and the dynamics of the landscape pattern in Hangzhou exhibited complexity and diversity. Cropland landscape was impacted most seriously, being encroached at large scale; orchard landscape suffered from slight impact due to its small occupation in the landscape; forest landscape was insensitive to the impact due to its aggregated distribution; while water landscape was impacted greatly but exhibited slight fragmentation. Urban land landscape was the one undergone the biggest and quickest change.

  12. Inchworm Monte Carlo for exact non-adiabatic dynamics. II. Benchmarks and comparison with established methods

    NASA Astrophysics Data System (ADS)

    Chen, Hsing-Ta; Cohen, Guy; Reichman, David R.

    2017-02-01

    In this second paper of a two part series, we present extensive benchmark results for two different inchworm Monte Carlo expansions for the spin-boson model. Our results are compared to previously developed numerically exact approaches for this problem. A detailed discussion of convergence and error propagation is presented. Our results and analysis allow for an understanding of the benefits and drawbacks of inchworm Monte Carlo compared to other approaches for exact real-time non-adiabatic quantum dynamics.

  13. 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.

  14. Exact Potential Driving the Electron Dynamics in Enhanced Ionization of H(2)(+).

    PubMed

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

    2015-12-31

    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 H(2)(+) 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.

  15. General Properties of Landscapes: Vacuum Structure, Dynamics and Statistics

    NASA Astrophysics Data System (ADS)

    Zukowski, Claire Elizabeth

    Even the simplest extra-dimensional theory, when compactified, can lead to a vast and complex landscape. To make progress, it is useful to focus on generic features of landscapes and compactifications. In this work we will explore universal features and consequences of (i) vacuum structure, (ii) dynamics resulting from symmetry breaking, and (iii) statistical predictions for low-energy parameters and observations. First, we focus on deriving general properties of the vacuum structure of a theory independent of the details of the geometry. We refine the procedure for performing compactifications by proposing a general gauge-invariant method to obtain the full set of Kaluza-Klein towers of fields for any internal geometry. Next, we study dynamics in a toy model for flux compactifications. We show that the model exhibits symmetry-breaking instabilities for the geometry to develop lumps, and suggest that similar dynamical effects may occur generically in other landscapes. The questions of the observed arrow of time as well as the observed value of the neutrino mass lead us to consider statistics within a landscape, and we verify that our observations are in fact typical given the correct vacuum structure and (in the case of the arrow of time) initial conditions. Finally, we address the question of subregion duality in AdS/CFT, arguing for a criterion for a bulk region to be reconstructable from a given boundary subregion by local operators. While of less direct relevance to cosmological space-times, this work provides an improved understanding of the UV/IR correspondence, a principle that underlies the construction of many holographically-inspired measures used to make statistical predictions in landscapes.

  16. The dynamic landscape of the cell nucleus.

    PubMed

    Austin, Christopher M; Bellini, Michel

    2010-01-01

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

  17. 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.

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

    SciTech Connect

    Caprio, M. A.

    2011-06-15

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

  19. Dynamical behaviours and exact travelling wave solutions of modified generalized Vakhnenko equation

    NASA Astrophysics Data System (ADS)

    Xiao, Junjun; Feng, Dahe; Meng, Xia; Cheng, Yuanquan

    2017-01-01

    By using the bifurcation theory of planar dynamical systems and the qualitative theory of differential equations, we studied the dynamical behaviours and exact travelling wave solutions of the modified generalized Vakhnenko equation (mGVE). As a result, we obtained all possible bifurcation parametric sets and many explicit formulas of smooth and non-smooth travelling waves such as cusped solitons, loop solitons, periodic cusp waves, pseudopeakon solitons, smooth periodic waves and smooth solitons. Moreover, we provided some numerical simulations of these solutions.

  20. 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.

  1. 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.

  2. BarMap: RNA folding on dynamic energy landscapes

    PubMed Central

    Hofacker, Ivo L.; Flamm, Christoph; Heine, Christian; Wolfinger, Michael T.; Scheuermann, Gerik; Stadler, Peter F.

    2010-01-01

    Dynamical changes of RNA secondary structures play an important role in the function of many regulatory RNAs. Such kinetic effects, especially in time-variable and externally triggered systems, are usually investigated by means of extensive and expensive simulations of large sets of individual folding trajectories. Here we describe the theoretical foundations of a generic approach that not only allows the direct computation of approximate population densities but also reduces the efforts required to analyze the folding energy landscapes to a one-time preprocessing step. The basic idea is to consider the kinetics on individual landscapes and to model external triggers and environmental changes as small but discrete changes in the landscapes. A “barmap” links macrostates of temporally adjacent landscapes and defines the transfer of population densities from one “snapshot” to the next. Implemented in the BarMap software, this approach makes it feasible to study folding processes at the level of basins, saddle points, and barriers for many nonstationary scenarios, including temperature changes, cotranscriptional folding, refolding in consequence to degradation, and mechanically constrained kinetics, as in the case of the translocation of a polymer through a pore. PMID:20504954

  3. Dynamics of glassy systems using new algorithms for exact sampling on multiple scales

    NASA Astrophysics Data System (ADS)

    Middleton, A. Alan

    2010-03-01

    The complex aging and memory effects seen in glassy materials result from relaxation times that are much longer than microscopic times: direct numerical simulations that seek to reproduce these effects of course suffer from the need to run simulations for very long times. It is therefore of interest to find algorithms that will simulate nonequilbrium dynamics on very long time scales. I will present methods for rapid simulation of memory and aging effects in spin glasses and results from those simulations. The methods are based on (1) an algorithm that allows for exact sampling of equilibrium states and (2) simple coarse graining approaches to the dynamics based on exact sampling and ground state calculations. The exact sampling algorithms extend classical Pfaffian techniques to directly generate spin configurations in two-dimensional Ising spin glasses according to their Boltzmann weights, thereby avoiding the long run times needed for Markov chain Monte Carlo simulations. Equilibration can then be imposed at a chosen length scale by repeated selection of subconfigurations (patches) at that scale chosen from a larger sample. At T=0, memory effects can be replicated using this patchwork dynamics. Correlation functions at any temperature can also be exactly calculated. Results on thermodynamic quantities and nonequilibrium effects will be presented for samples of size at least 512^2. This work was carried out in collaboration with Creighton K. Thomas.

  4. A Model with Darwinian Dynamics on a Rugged Landscape

    NASA Astrophysics Data System (ADS)

    Brotto, Tommaso; Bunin, Guy; Kurchan, Jorge

    2017-02-01

    We discuss the population dynamics with selection and random diffusion, keeping the total population constant, in a fitness landscape associated with Constraint Satisfaction, a paradigm for difficult optimization problems. We obtain a phase diagram in terms of the size of the population and the diffusion rate, with a glass phase inside which the dynamics keeps searching for better configurations, and outside which deleterious `mutations' spoil the performance. The phase diagram is analogous to that of dense active matter in terms of temperature and drive.

  5. 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

  6. Death and landscape dynamics: The effect of tree throw on sediment transport and landscape evolution

    NASA Astrophysics Data System (ADS)

    Hancock, G. R.; Evans, K.; McDonnell, J. J.; Hopp, L.; Reaney, S.

    2010-12-01

    In many regions of the world tree throw occurs as a result of storms. The fall of a tree usually produces a pit where the tree roots and surrounding soil are removed and a mound of dumped soil placed adjacent to the pit. This pit-mound topography has the potential to increase sediment transport and also be a point of incision for the commencement of gullies. Little work has been done to evaluate how tree throw affects hillslope and catchment evolution over decadal to centennial time scales. Here we examine this issue for a small study catchment in Arnhem Land, Northern Territory, Australia. In 2006 a Category 5 cyclone (Cyclone Monica) passed over the region with wind speeds greater than 100 m/s. Data on tree throw including number and size of trees, species, as well as size and depth of the pit-mound topography was measured. The pit-mound topography was input into a 1m DEM of a small 20 ha catchment and the effect of the cyclone induced tree throw was evaluated using a computer based Landscape Evolution Model (LEM) at both the annual and decadal time scales. Results show that a single tree throw event has little effect on sediment transport and landscape evolution over geological time scales. However, multiple tree-throw events at characteristic Category 5 hurricane recurrence intervals have quantifiable effects on erosion and landscape evolution. The results demonstrate changes in sediment transport as well as subtle changes in hillslope form. The modelling results are now being compared with available catchment-scale field erosion rates from both pre- and post-cyclone to calibrate the model and to use it as a learning tool for linking life to these dynamic landscape processes.

  7. Statistical characteristics of topographic surfaces and dynamic smoothing of landscapes

    NASA Astrophysics Data System (ADS)

    Bartlett, M. S.; Laio, F.; Ridolfi, L.; Vico, G.; Porporato, A. M.

    2011-12-01

    We analyze the local statistics of topographic surfaces, including slope and aspect, as a function of scale, and explore their relations with landscape features, such as age, vegetation, and geology. These results build upon the previous work of Vico and Porporato (JGR 114, F01011, 2009), which characterized slope using generalized t-Student distributions. We find that the number of degrees of freedom of such distributions, which determines the heaviness of their tails, is linked to the age of the topographic relief of the considered regions, tending to normal distributions for very old mountain ranges. Based on these findings, and inspired by models of critical phenomena, we develop physically-based, space-time stochastic differential equations that reproduce this dynamic smoothing of rough landscapes.

  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. Inchworm Monte Carlo for exact non-adiabatic dynamics. I. Theory and algorithms

    NASA Astrophysics Data System (ADS)

    Chen, Hsing-Ta; Cohen, Guy; Reichman, David R.

    2017-02-01

    In this paper, we provide a detailed description of the inchworm Monte Carlo formalism for the exact study of real-time non-adiabatic dynamics. This method optimally recycles Monte Carlo information from earlier times to greatly suppress the dynamical sign problem. Using the example of the spin-boson model, we formulate the inchworm expansion in two distinct ways: The first with respect to an expansion in the system-bath coupling and the second as an expansion in the diabatic coupling. The latter approach motivates the development of a cumulant version of the inchworm Monte Carlo method, which has the benefit of improved scaling. This paper deals completely with methodology, while Paper II provides a comprehensive comparison of the performance of the inchworm Monte Carlo algorithms to other exact methodologies as well as a discussion of the relative advantages and disadvantages of each.

  10. Exact formula of the distribution of Schmidt eigenvalues for dynamical formation of entanglement in quantum chaos.

    PubMed

    Kubotani, Hiroto; Adachi, Satoshi; Toda, Mikito

    2008-06-20

    The exact formula of the one-level distribution of the Schmidt eigenvalues is obtained for dynamical formation of entanglement in quantum chaos. The formula is based on the random matrix theory of the fixed-trace ensemble, and is derived using the theory of the holonomic system of differential equations. We confirm that the formula describes the universality of the distribution of the Schmidt eigenvalues in quantum chaos.

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

    PubMed

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

    2013-10-07

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

  12. Exact dynamics of dissipative electronic systems and quantum transport: Hierarchical equations of motion approach.

    PubMed

    Jin, Jinshuang; Zheng, Xiao; Yan, YiJing

    2008-06-21

    A generalized quantum master equation theory that governs the exact, nonperturbative quantum dissipation and quantum transport is formulated in terms of hierarchically coupled equations of motion for an arbitrary electronic system in contact with electrodes under either a stationary or a nonstationary electrochemical potential bias. The theoretical construction starts with the influence functional in path integral, in which the electron creation and annihilation operators are Grassmann variables. Time derivatives on the influence functionals are then performed in a hierarchical manner. Both the multiple-frequency dispersion and the non-Markovian reservoir parametrization schemes are considered for the desired hierarchy construction. The resulting hierarchical equations of motion formalism is in principle exact and applicable to arbitrary electronic systems, including Coulomb interactions, under the influence of arbitrary time-dependent applied bias voltage and external fields. Both the conventional quantum master equation and the real-time diagrammatic formalism of Schon and co-workers can be readily obtained at well defined limits of the present theory. We also show that for a noninteracting electron system, the present hierarchical equations of motion formalism terminates at the second tier exactly, and the Landuer-Buttiker transport current expression is recovered. The present theory renders an exact and numerically tractable tool to evaluate various transient and stationary quantum transport properties of many-electron systems, together with the involving nonperturbative dissipative dynamics.

  13. Exact dynamics of dissipative electronic systems and quantum transport: Hierarchical equations of motion approach

    NASA Astrophysics Data System (ADS)

    Jin, Jinshuang; Zheng, Xiao; Yan, Yijing

    2008-06-01

    A generalized quantum master equation theory that governs the exact, nonperturbative quantum dissipation and quantum transport is formulated in terms of hierarchically coupled equations of motion for an arbitrary electronic system in contact with electrodes under either a stationary or a nonstationary electrochemical potential bias. The theoretical construction starts with the influence functional in path integral, in which the electron creation and annihilation operators are Grassmann variables. Time derivatives on the influence functionals are then performed in a hierarchical manner. Both the multiple-frequency dispersion and the non-Markovian reservoir parametrization schemes are considered for the desired hierarchy construction. The resulting hierarchical equations of motion formalism is in principle exact and applicable to arbitrary electronic systems, including Coulomb interactions, under the influence of arbitrary time-dependent applied bias voltage and external fields. Both the conventional quantum master equation and the real-time diagrammatic formalism of Schön and co-workers can be readily obtained at well defined limits of the present theory. We also show that for a noninteracting electron system, the present hierarchical equations of motion formalism terminates at the second tier exactly, and the Landuer-Büttiker transport current expression is recovered. The present theory renders an exact and numerically tractable tool to evaluate various transient and stationary quantum transport properties of many-electron systems, together with the involving nonperturbative dissipative dynamics.

  14. Exact results for spin dynamics and fractionalization in the Kitaev Model.

    PubMed

    Baskaran, G; Mandal, Saptarshi; Shankar, R

    2007-06-15

    We present certain exact analytical results for dynamical spin correlation functions in the Kitaev Model. It is the first result of its kind in nontrivial quantum spin models. The result is also novel: in spite of the presence of gapless propagating Majorana fermion excitations, dynamical two spin correlation functions are identically zero beyond nearest neighbor separation. This shows existence of a gapless but short range spin liquid. An unusual, all energy scale fractionalization of a spin-flip quanta, into two infinitely massive pi fluxes and a dynamical Majorana fermion, is shown to occur. As the Kitaev Model exemplifies topological quantum computation, our result presents new insights into qubit dynamics and generation of topological excitations.

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

    NASA Astrophysics Data System (ADS)

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

    2012-05-01

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

  16. 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

  17. Stroboscopic phenomena in superconductors with dynamic pinning landscape.

    PubMed

    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.

  18. 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.

  19. 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.

  20. Efficient and exact maximum likelihood quantisation of genomic features using dynamic programming.

    PubMed

    Song, Mingzhou; Haralick, Robert M; Boissinot, Stéphane

    2010-01-01

    An efficient and exact dynamic programming algorithm is introduced to quantise a continuous random variable into a discrete random variable that maximises the likelihood of the quantised probability distribution for the original continuous random variable. Quantisation is often useful before statistical analysis and modelling of large discrete network models from observations of multiple continuous random variables. The quantisation algorithm is applied to genomic features including the recombination rate distribution across the chromosomes and the non-coding transposable element LINE-1 in the human genome. The association pattern is studied between the recombination rate, obtained by quantisation at genomic locations around LINE-1 elements, and the length groups of LINE-1 elements, also obtained by quantisation on LINE-1 length. The exact and density-preserving quantisation approach provides an alternative superior to the inexact and distance-based univariate iterative k-means clustering algorithm for discretisation.

  1. 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.

  2. Exact results for the Barabási model of human dynamics.

    PubMed

    Vázquez, Alexei

    2005-12-09

    Human activity patterns display a bursty dynamics with interevent times following a heavy tailed distribution. This behavior has been recently shown to be rooted in the fact that humans assign their active tasks different priorities, a process that can be modeled as a priority queueing system [A.-L. Barabási, Nature (London) 435, 207 (2005)]. In this Letter we obtain exact results for the Barabási model with two tasks, calculating the priority and waiting time distribution of active tasks. We demonstrate that the model has a singular behavior in the extremal dynamics limit, when the highest priority task is selected first. We find that independently of the selection protocol, the average waiting time is smaller or equal to the number of active tasks, and discuss the asymptotic behavior of the waiting time distribution. These results have important implications for understanding complex systems with extremal dynamics.

  3. Exact and approximate many-body dynamics with stochastic one-body density matrix evolution

    SciTech Connect

    Lacroix, Denis

    2005-06-01

    We show that the dynamics of interacting fermions can be exactly replaced by a quantum jump theory in the many-body density matrix space. In this theory, jumps occur between densities formed of pairs of Slater determinants, D{sub ab}= vertical bar {phi}{sub a}><{phi}{sub b} vertical bar, where each state evolves according to the stochastic Schroedinger equation given by O. Juillet and Ph. Chomaz [Phys. Rev. Lett. 88, 142503 (2002)]. A stochastic Liouville-von Neumann equation is derived as well as the associated. Bogolyubov-Born-Green-Kirwood-Yvon hierarchy. Due to the specific form of the many-body density along the path, the presented theory is equivalent to a stochastic theory in one-body density matrix space, in which each density matrix evolves according to its own mean-field augmented by a one-body noise. Guided by the exact reformulation, a stochastic mean-field dynamics valid in the weak coupling approximation is proposed. This theory leads to an approximate treatment of two-body effects similar to the extended time-dependent Hartree-Fock scheme. In this stochastic mean-field dynamics, statistical mixing can be directly considered and jumps occur on a coarse-grained time scale. Accordingly, numerical effort is expected to be significantly reduced for applications.

  4. 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

  5. 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.

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

    PubMed

    Kundu, Anjan; Mukherjee, Abhik; Naskar, Tapan

    2014-04-08

    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.

  7. 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

  8. 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

  9. Evolutionary dynamics of the most populated genotype on rugged fitness landscapes

    NASA Astrophysics Data System (ADS)

    Jain, Kavita

    2007-09-01

    We consider an asexual population evolving on rugged fitness landscapes which are defined on the multidimensional genotypic space and have many local optima. We track the most populated genotype as it changes when the population jumps from a fitness peak to a better one during the process of adaptation. This is done using the dynamics of the shell model which is a simplified version of the quasispecies model for infinite populations and standard Wright-Fisher dynamics for large finite populations. We show that the population fraction of a genotype obtained within the quasispecies model and the shell model match for fit genotypes and at short times, but the dynamics of the two models are identical for questions related to the most populated genotype. We calculate exactly several properties of the jumps in infinite populations, some of which were obtained numerically in previous works. We also present our preliminary simulation results for finite populations. In particular, we measure the jump distribution in time and find that it decays as t-2 as in the quasispecies problem.

  10. 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

  11. 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

  12. Exact real-time dynamics of electron transport in mesoscopic systems

    NASA Astrophysics Data System (ADS)

    Zheng, Xiao; Jin, Jinshuang; Yan, Yijing

    2009-03-01

    We present a formally exact and numerically tractable quantum dissipation theory for time-dependent quantum transport in mesoscopic systems. It is formulated in terms of hierarchically coupled equations of motion, which govern the non-Markovian dynamics of an arbitrary fermionic system interacting with grand canonical electron reservoirs, in the presence of arbitrary time-dependent applied voltages [1-2]. We also present numerical results on the real-time dynamics of open quantum dot systems. The linear response admittance is mapped to classical equivalent circuits; while the nonlinear response dynamics is associated with dot-state transitions, such as the dynamic Coulomb blockade effect involved in interacting quantum dots [3-4]. Real-time Kondo phenomena are also demonstrated, with the cotunneling induced Kondo transition distinguished in the transient response current. This work highlights the significance and versatility of quantum dissipation theory for transient dynamics calculations. [1] J. S. Jin, S. Welack, J. Y. Luo, X. Q. Li, P. Cui, R. X. Xu, and Y. J. Yan, J. Chem. Phys. 126, 134113 (2007). [2] J. S. Jin, X. Zheng, and Y. J. Yan, J. Chem. Phys. 128, 234703 (2008). [3] X. Zheng, J. S. Jin, and Y. J. Yan, J. Chem. Phys. 129, 184112 (2008). [4] X. Zheng, J. S. Jin, and Y. J. Yan, New J. Phys. 10, 093016 (2008).

  13. 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.

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

    PubMed

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

    2016-02-01

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

  15. Dynamical Green's function and an exact optical potential for electron-molecule scattering including nuclear dynamics

    NASA Astrophysics Data System (ADS)

    Brand, Joachim; Cederbaum, Lorenz S.; Meyer, Hans-Dieter

    1999-10-01

    We derive a rigorous optical potential for electron-molecule scattering including the effects of nuclear dynamics by extending the common many-body Green's function approach to optical potentials beyond the fixed-nuclei limit for molecular targets. Our formalism treats the projectile electron and the nuclear motion of the target molecule on the same footing whereby the dynamical optical potential rigorously accounts for the complex many-body nature of the scattering target. One central result of the present work is that the common fixed-nuclei optical potential is a valid adiabatic approximation to the dynamical optical potential even when projectile and nuclear motion are (nonadiabatically) coupled as long as the scattering energy is well below the electronic excitation thresholds of the target. For extremely low projectile velocities, however, when the cross sections are most sensitive to the scattering potential, we expect the influences of the nuclear dynamics on the optical potential to become relevant. For these cases, a systematic way to improve the adiabatic approximation to the dynamical optical potential is presented that yields nonlocal operators with respect to the nuclear coordinates.

  16. 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.

  17. 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.

  18. Temporal coherence of turbulent dynamics in minimal channel flow and its connection to exact coherent states

    NASA Astrophysics Data System (ADS)

    Park, Jae Sung; Graham, Michael

    2016-11-01

    The dynamics of the turbulent near-wall region is known to be dominated by coherent structures. These near-wall coherent structures are observed to burst in an intermittent way, exporting turbulent kinetic energy to the rest of the flow. In addition, they are closely related to invariant solutions known as exact coherent states (ECS), some of which display nonlinear critical layer dynamics. In this study, temporal coherence in minimal channel flow relevant to burst and critical layer dynamics is investigated. The turbulence displays frequencies very close to the critical layer frequency displayed by an ECS family recently identified in the channel flow geometry. The bursting frequency is predominant near the wall, while the critical layer frequency becomes predominant over the bursting frequency as we move away from the wall. In particular, the critical layer frequency becomes more prominent near the channel center and at higher Reynolds number. Finally, turbulent bursts are classified into strong and relatively weak classes with respect to an intermittent approach to a lower branch ECS. The relationship between the strong burst class and the instability of the lower branch ECS 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).

  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. 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...

  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. 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.

  3. 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.

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

    PubMed

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

    2011-01-01

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

  5. 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.

  6. Dynamically dominant exact coherent structures in turbulent Taylor-Couette flow

    NASA Astrophysics Data System (ADS)

    Krygier, Michael; Grigoriev, Roman

    2016-11-01

    Unstable Exact Coherent Structures (ECS), which are solutions to the Navier-Stokes equation, provide a connection between turbulence and dynamical systems and offer a method for exploiting the low dimensionality of weakly turbulent flows. We investigate ECS in an intermittent Taylor-Couette flow (TCF) found in a small-aspect-ratio geometry with counter-rotating cylinders (η = 0 . 5 , Γ = 1 , Rei = - 1200 , Reo = 1200). The presence of end-caps breaks the axial translational symmetry of TCF, but continuous rotational symmetry remains, which suggest that typical ECS should be the relative versions of equilibria and time-periodic orbits. Indeed, previous studies (Meseguer et al., 2009 and Deguchi, Meseguer & Mellibovsky, 2014) found several unstable traveling wave solutions (relative equilibria). We have shown that the dynamically dominant ECS for weakly turbulent TCF in the small-aspect-ratio geometry are relative periodic orbits (not relative equilibria), as evidenced by the frequent visits of their neighborhoods by the turbulent flow. This work is supported by a Grant from the Army Research Office (Contract # W911NF-15-1-0471).

  7. Temperature and bath size in exact diagonalization dynamical mean field theory.

    PubMed

    Liebsch, Ansgar; Ishida, Hiroshi

    2012-02-08

    Dynamical mean field theory (DMFT), combined with finite-temperature exact diagonalization, is one of the methods used to describe electronic properties of strongly correlated materials. Because of the rapid growth of the Hilbert space, the size of the finite bath used to represent the infinite lattice is severely limited. In view of the increasing interest in the effect of multi-orbital and multi-site Coulomb correlations in transition metal oxides, high-T(c) cuprates, iron-based pnictides, organic crystals, etc, it is appropriate to explore the range of temperatures and bath sizes in which exact diagonalization provides accurate results for various system properties. On the one hand, the bath must be large enough to achieve a sufficiently dense level spacing, so that useful spectral information can be derived, especially close to the Fermi level. On the other hand, for an adequate projection of the lattice Green's function onto a finite bath, the choice of the temperature is crucial. The role of these two key ingredients in exact diagonalization DMFT is discussed for a wide variety of systems in order to establish the domain of applicability of this approach. Three criteria are used to illustrate the accuracy of the results: (i) the convergence of the self-energy with the bath size, (ii) the quality of the discretization of the bath Green's function, and (iii) comparisons with complementary results obtained via continuous-time quantum Monte Carlo DMFT. The materials comprise a variety of three-orbital and five-orbital systems, as well as single-band Hubbard models for two-dimensional triangular, square and honeycomb lattices, where non-local Coulomb correlations are important. The main conclusion from these examples is that a larger number of correlated orbitals or sites requires a smaller number of bath levels. Down to temperatures of 5-10 meV (for typical bandwidths W ≈ 2 eV) two bath levels per correlated impurity orbital or site are usually adequate.

  8. Experimental beetle metapopulations respond positively to dynamic landscapes and reduced connectivity.

    PubMed

    Govindan, Byju N; Swihart, Robert K

    2012-01-01

    Interactive effects of multiple environmental factors on metapopulation dynamics have received scant attention. We designed a laboratory study to test hypotheses regarding interactive effects of factors affecting the metapopulation dynamics of red flour beetle, Tribolium castaneum. Within a four-patch landscape we modified resource level (constant and diminishing), patch connectivity (high and low) and patch configuration (static and dynamic) to conduct a 2(3) factorial experiment, consisting of 8 metapopulations, each with 3 replicates. For comparison, two control populations consisting of isolated and static subpopulations were provided with resources at constant or diminishing levels. Longitudinal data from 22 tri-weekly counts of beetle abundance were analyzed using bayesian Poisson generalized linear mixed models to estimate additive and interactive effects of factors affecting abundance. Constant resource levels, low connectivity and dynamic patches yielded greater levels of adult beetle abundance. For a given resource level, frequency of colonization exceeded extinction in landscapes with dynamic patches when connectivity was low, thereby promoting greater patch occupancy. Negative density dependence of pupae on adults occurred and was stronger in landscapes with low connectivity and constant resources; these metapopulations also demonstrated greatest stability. Metapopulations in control landscapes went extinct quickly, denoting lower persistence than comparable landscapes with low connectivity. When landscape carrying capacity was constant, habitat destruction coupled with low connectivity created asynchronous local dynamics and refugia within which cannibalism of pupae was reduced. Increasing connectivity may be counter-productive and habitat destruction/recreation may be beneficial to species in some contexts.

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

    PubMed

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

    2015-06-07

    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.

  10. 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

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

    PubMed Central

    Hemrová, Lucie; Červenková, Zita; Münzbergová, Zuzana

    2012-01-01

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

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

    PubMed

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

    2012-04-01

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

  13. 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

  14. 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

  15. Exact quantum and time-dependent Hartree studies of the HBr/LiF(001) photodissociation dynamics

    NASA Astrophysics Data System (ADS)

    Fang, Jian-Yun; Guo, Hua

    1994-07-01

    Photodissociation dynamics of HBr adsorbed on a LiF(001) surface are investigated using both exact and time-dependent Hartree (TDH) methods on realistic potential energy surfaces. The dissociation dynamics are restricted in two dimensions and two coupled dissociative states of the adsorbate are included. The wave packets are propagated on numerical grids, and fast Fourier transform (FFT) and discrete variable representation (DVR) are used to calculate the action of the Hamiltonian. In the TDH treatment, each excited electronic state is represented by a single nuclear configuration. Final radial, angular, and momentum distributions of the H fragment are calculated. Comparisons between the exact and TDH results reveal that the agreement between the two is generally reasonable and is better for highly averaged quantities. Results also show that nonadiabatic transition dynamics are correctly reproduced by the TDH approximation. Finally, the calculated results are found consistent with the experimental observations.

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

    PubMed

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

    2011-08-21

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

  17. Exact Mesonic Eightfold Way From Dynamics and Confinement in Strongly Coupled Lattice QCD

    NASA Astrophysics Data System (ADS)

    Neto, A. Francisco; O'Carroll, M.; Faria da Veiga, P. A.

    2009-01-01

    We review our results on the exact determination of the mesonic eightfold way from first principles, directly from the quark-gluon dynamics. For this, we consider an imaginary-time functional integral formulation of 3 + 1 dimensional lattice QCD with Wilson action, three flavors, SU(3) f flavor symmetry and SU(3) c local gauge symmetry. We work in the strong coupling regime: a small hopping parameter κ>0 and a much smaller plaquette coupling β>0. By establishing a Feynman-Kac formula and a spectral representation to the two-meson correlation, we provide a rigorous connection between this correlation and the one-meson energy-momentum spectrum. The particle states can be labeled by the usual SU(3) f quantum numbers of total isospin I and its third-component I3, the quadratic Casimir C2 and, by a partial restoration of the continuous rotational symmetry on the lattice, as well as by the total spin J and its z-component Jz. We show that, up to near the two-meson energy threshold of ≈-4lnκ, the spectrum in the meson sector is given only by isolated dispersion curves of the eightfold way mesons. The mesons have all asymptotic mass of -2lnκ and, by deriving convergent expansions for the masses both in κ and β, we also show a κ mass splitting between the J=0,1 states. The splitting persists for β≠0. Our approach employs the decoupling of hyperplane method to uncover the basic excitations, complex analysis to determine the dispersion curves and a correlation subtraction method to show the curves are isolated. Using the latter and recalling our similar results for baryons, we also show confinement up to near the two-meson threshold.

  18. 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)

  19. Importance of ecotone type to landscape dynamics at biome transition zones

    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. Landsc...

  20. 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...

  1. 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.

  2. 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

  3. Solving the spin-2 Gross-Pitaevskii equation using exact nonlinear dynamics and symplectic composition

    NASA Astrophysics Data System (ADS)

    Symes, L. M.; Blakie, P. B.

    2017-01-01

    We develop numerical methods for solving the spin-2 Gross-Pitaevskii equation. The basis of our work is a two-way splitting of this evolution equation that leads to two exactly solvable subsystems. Utilizing second-order and fourth-order composition schemes we realize two fully symplectic integration algorithms, the first such algorithms for evolving spin-2 condensates. We demonstrate the accuracy of these algorithms against other methods on application to an exact continuous wave solution that we derive.

  4. Solving the spin-2 Gross-Pitaevskii equation using exact nonlinear dynamics and symplectic composition.

    PubMed

    Symes, L M; Blakie, P B

    2017-01-01

    We develop numerical methods for solving the spin-2 Gross-Pitaevskii equation. The basis of our work is a two-way splitting of this evolution equation that leads to two exactly solvable subsystems. Utilizing second-order and fourth-order composition schemes we realize two fully symplectic integration algorithms, the first such algorithms for evolving spin-2 condensates. We demonstrate the accuracy of these algorithms against other methods on application to an exact continuous wave solution that we derive.

  5. 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

  6. 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

  7. [Dynamic changes of landscape pattern during desertification in Duolun County of Inner Mongolia].

    PubMed

    Aruhan; Yang, Chi

    2007-11-01

    By using landscape analyzing software Fragstats 3.3 and the interpretation results of remote-sensing images of 1960, 1975, 1987, 1995, 2000 and 2005, this paper analyzed the dynamic changes of landscape pattern during the desertification in Duolun County of Inner Mongolia in 1960-2005. The results showed that in 1960-1995, the desertification area appeared a tendency of increasing first and decreasing then, with a total increase of 212.7 km2. The numbers of desertification landscape patches decreased after an initial increase, landscape diversity and evenness increased, and the shapes of light-, moderate-, and heavy desertification patches tended to be simplex. From 1995 to 2005, the numbers of desertification patches increased greatly, landscape diversity and evenness decreased, and the shapes of light-, moderate-, and heavy desertification patches tended to be complex. Since 1960, the shapes of severe desertification patches had been inclined to complication. In the study period, the whole desertification landscape showed a trend of integrity-broken-integrity-broken, and the broken degree of the patch types of desertification landscape was gradually from light down to severe.

  8. Surface-water dynamics and land use influence landscape connectivity across a major dryland region.

    PubMed

    Bishop-Taylor, Robbi; Tulbure, Mirela G; Broich, Mark

    2017-01-24

    Landscape connectivity is important for the long-term persistence of species inhabiting dryland freshwater ecosystems, with spatiotemporal surface-water dynamics (e.g., flooding) maintaining connectivity by both creating temporary habitats and providing transient opportunities for dispersal. Improving our understanding of how landscape connectivity varies with respect to surface-water dynamics and land use is an important step to maintaining biodiversity in dynamic dryland environments. Using a newly available validated Landsat TM and ETM+ surface-water time series, we modelled landscape connectivity between dynamic surface-water habitats within Australia's 1 million km2 semi-arid Murray Darling Basin across a 25-year period (1987 to 2011). We identified key habitats that serve as well-connected 'hubs', or 'stepping-stones' that allow long-distance movements through surface-water habitat networks. We compared distributions of these habitats for short- and long-distance dispersal species during dry, average and wet seasons, and across land-use types. The distribution of stepping-stones and hubs varied both spatially and temporally, with temporal changes driven by drought and flooding dynamics. Conservation areas and natural environments contained higher than expected proportions of both stepping-stones and hubs throughout the time series; however, highly modified agricultural landscapes increased in importance during wet seasons. Irrigated landscapes contained particularly high proportions of well-connected hubs for long-distance dispersers, but remained relatively disconnected for less vagile organisms. The habitats identified by our study may serve as ideal high-priority targets for land-use specific management aimed at maintaining or improving dispersal between surface-water habitats, potentially providing benefits to biodiversity beyond the immediate site scale. Our results also highlight the importance of accounting for the influence of spatial and temporal

  9. 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

  10. Energy landscape analysis of the subcortical brain network unravels system properties beneath resting state dynamics.

    PubMed

    Kang, Jiyoung; Pae, Chongwon; Park, Hae-Jeong

    2017-04-01

    The configuration of the human brain system at rest, which is in a transitory phase among multistable states, remains unknown. To investigate the dynamic systems properties of the human brain at rest, we constructed an energy landscape for the state dynamics of the subcortical brain network, a critical center that modulates whole brain states, using resting state fMRI. We evaluated alterations in energy landscapes following perturbation in network parameters, which revealed characteristics of the state dynamics in the subcortical brain system, such as maximal number of attractors, unequal temporal occupations, and readiness for reconfiguration of the system. Perturbation in the network parameters, even those as small as the ones in individual nodes or edges, caused a significant shift in the energy landscape of brain systems. The effect of the perturbation on the energy landscape depended on the network properties of the perturbed nodes and edges, with greater effects on hub nodes and hubs-connecting edges in the subcortical brain system. Two simultaneously perturbed nodes produced perturbation effects showing low sensitivity in the interhemispheric homologous nodes and strong dependency on the more primary node among the two. This study demonstrated that energy landscape analysis could be an important tool to investigate alterations in brain networks that may underlie certain brain diseases, or diverse brain functions that may emerge due to the reconfiguration of the default brain network at rest.

  11. 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.

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

    PubMed

    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.

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

    EPA Science Inventory

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

  16. Hopping on the Bethe lattice: Exact results for densities of states and dynamical mean-field theory

    NASA Astrophysics Data System (ADS)

    Eckstein, Martin; Kollar, Marcus; Byczuk, Krzysztof; Vollhardt, Dieter

    2005-06-01

    We derive an operator identity which relates tight-binding Hamiltonians with arbitrary hopping on the Bethe lattice to the Hamiltonian with nearest-neighbor hopping. This provides an exact expression for the density of states (DOS) of a noninteracting quantum-mechanical particle for any hopping. We present analytic results for the DOS corresponding to hopping between nearest and next-nearest neighbors, and also for exponentially decreasing hopping amplitudes. Conversely it is possible to construct a hopping Hamiltonian on the Bethe lattice for any given DOS. These methods are based only on the so-called distance regularity of the infinite Bethe lattice, and not on the absence of loops. Results are also obtained for the triangular Husimi cactus, a recursive lattice with loops. Furthermore we derive the exact self-consistency equations arising in the context of dynamical mean-field theory, which serve as a starting point for studies of Hubbard-type models with frustration.

  17. Ferrofluid patterns in a radial magnetic field: linear stability, nonlinear dynamics, and exact solutions.

    PubMed

    Oliveira, Rafael M; Miranda, José A; Leandro, Eduardo S G

    2008-01-01

    The response of a ferrofluid droplet to a radial magnetic field is investigated, when the droplet is confined in a Hele-Shaw cell. We study how the stability properties of the interface and the shape of the emerging patterns react to the action of the magnetic field. At early linear stages, it is found that the radial field is destabilizing and determines the growth of fingering structures at the interface. In the weakly nonlinear regime, we have verified that the magnetic field favors the formation of peaked patterned structures that tend to become sharper and sharper as the magnitude of the magnetic effects is increased. A more detailed account of the pattern morphology is provided by the determination of nontrivial exact stationary solutions for the problem with finite surface tension. These solutions are obtained analytically and reveal the development of interesting polygon-shaped and starfishlike patterns. For sufficiently large applied fields or magnetic susceptibilities, pinch-off phenomena are detected, tending to occur near the fingertips. We have found that the morphological features obtained from the exact solutions are consistent with our linear and weakly nonlinear predictions. By contrasting the exact solutions for ferrofluids under radial field with those obtained for rotating Hele-Shaw flows with ordinary nonmagnetic fluids, we deduce that they coincide in the limit of very small susceptibilities.

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

    PubMed

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

    2014-01-01

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

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

    PubMed

    Thibodeau, Paul H; Boroditsky, Lera

    2015-01-01

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

  20. 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

  1. Vegetation composition, nutrient, and sediment dynamics along a floodplain landscape

    USGS Publications Warehouse

    Rybicki, Nancy B.; Noe, Gregory; Hupp, Cliff R.; Robinson, Myles

    2015-01-01

    Forested floodplains are important landscape features for retaining river nutrients and sediment loads but there is uncertainty in how vegetation influences nutrient and sediment retention. In order to understand the role of vegetation in nutrient and sediment trapping, we quantified species composition and the uptake of nutrients in plant material relative to landscape position and ecosystem attributes in an urban, Piedmont watershed in Virginia, USA. We investigated in situ interactions among vegetative composition, abundance, carbon (C), nitrogen (N) and phosphorus (P) fluxes and ecosystem attributes such as water level, shading, soil nutrient mineralization, and sediment deposition. This study revealed strong associations between vegetation and nutrient and sediment cycling processes at the plot scale and in the longitudinal dimension, but there were few strong patterns between these aspects at the scale of geomorphic features (levee, backswamp, and toe-slope). Patterns reflected the nature of the valley setting rather than a simple downstream continuum. Plant nutrient uptake and sediment trapping were greatest at downstream sites with the widest floodplain and lowest gradient where the hydrologic connection between the floodplain and stream is greater. Sediment trapping increased in association with higher herbaceous plant coverage and lower tree canopy density that, in turn, was associated with a more water tolerant tree community found in the lower watershed but not at the most downstream site in the watershed. Despite urbanization effects on the hydrology, this floodplain functioned as an efficient nutrient trap. N and P flux rates of herbaceous biomass and total litterfall more than accounted for the N and P mineralization flux rate, indicating that vegetation incorporated nearly all mineralized nutrients into biomass.

  2. 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

  3. 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.

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

    DOE PAGES

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

    2014-10-30

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

  5. 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.

  6. [Dynamic changes of land desertification landscape pattern in agriculture and pasturage interlaced zone of northern Shaanxi].

    PubMed

    Jia, Ke-Li; Chang, Qing-Rui

    2007-09-01

    By using the 1986, 1993 and 2003 Landsat TM images and with the help of GIS, the dynamic changes of land desertification landscape pattern in agriculture and pasturage interlaced zone of northern Shaanxi in 1986-2003 were analyzed. The results showed that in the past 17 years, the desertification area in the zone decreased by 206,655.2 hm2, with the patches in landscape structure reduced and fragmentation abated. Fortunately, the desertification degree decreased obviously, and moderate and light desertification took the leading position. From 1986 to 2003, the spatial centroid of desertification landscape patches expanded southwestward and northeastward, giving serious threat to the ecological safety of the southeast and northeast loess gully and hilly areas.

  7. Mean occupancy time: linking mechanistic movement models, population dynamics and landscape ecology to population persistence.

    PubMed

    Cobbold, Christina A; Lutscher, Frithjof

    2014-02-01

    Reaction-diffusion models for the dynamics of a biological population in a fragmented landscape can incorporate detailed descriptions of movement and behavior, but are difficult to analyze and hard to parameterize. Patch models, on the other hand, are fairly easy to analyze and can be parameterized reasonably well, but miss many details of the movement process within and between patches. We develop a framework to scale up from a reaction-diffusion process to a patch model and, in particular, to determine movement rates between patches based on behavioral rules for individuals. Our approach is based on the mean occupancy time, the mean time that an individuals spends in a certain area of the landscape before it exits that area or dies. We illustrate our approach using several different landscape configurations. We demonstrate that the resulting patch model most closely captures persistence conditions and steady state densities as compared with the reaction-diffusion model.

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

    PubMed

    Hadley, Adam S; Betts, Matthew G

    2012-08-01

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

  9. 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.

  10. 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.

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

    USGS Publications Warehouse

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

    2013-01-01

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

  12. 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.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2003-11-01

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

  15. 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

    2015-07-01

    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.

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

    NASA Astrophysics Data System (ADS)

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

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

  17. Organization and scaling of carbon dynamics in complex landscapes: Implications of water, life, and landform feedbacks for terrestrial carbon cycling

    NASA Astrophysics Data System (ADS)

    McGlynn, B. L.; Riveros-Iregui, D.; Emanuel, R. E.; Epstein, H. E.

    2011-12-01

    Complex topography, topology, vegetation, and environmental gradients in mountainous terrain impart fundamental controls on the distribution and redistribution of water, energy, and nutrients across the landscape. Many of these variables exhibit spatial patterns influenced by landscape structure and hydrologically and biologically mediated redistribution processes. Landforms therefore can lead to emergent organization of ecosystem dynamics. Diel, seasonal and interannual fluctuations in hydrometeorology also manifest differently across complex landscapes due to strong biophysical gradients and redistribution processes less influential in simpler terrain. Here, we examine the complex interactions among physical and biological variables at the landscape-scale, and the interconnectedness of nutrients, water, energy, vegetation, and microbial dynamics at the local scale and how they manifest in system level observations via focus on the components of net ecosystem exchange of carbon. We suggest landscape complexity imparts organization on observed heterogeneity that can be used to gain new understanding of fundamental controls on ecosystem processes across scales.

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

    PubMed

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

    2013-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  20. 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.

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

    PubMed Central

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

    2015-01-01

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

  2. Correlations between the dynamics of parallel tempering and the free-energy landscape in spin glasses

    NASA Astrophysics Data System (ADS)

    Yucesoy, Burcu; Machta, Jonathan; Katzgraber, Helmut G.

    2013-01-01

    We present the results of a large-scale numerical study of the equilibrium three-dimensional Edwards-Anderson Ising spin glass with Gaussian disorder. Using parallel tempering (replica exchange) Monte Carlo we measure various static, as well as dynamical quantities, such as the autocorrelation times and round-trip times for the parallel tempering Monte Carlo method. The correlation between static and dynamic observables for 5000 disorder realizations and up to 1000 spins down to temperatures at 20% of the critical temperature is examined. Our results show that autocorrelation times are directly correlated with the roughness of the free-energy landscape.

  3. Thermostat with a local heat-bath coupling for exact energy conservation in dissipative particle dynamics.

    PubMed

    Pastewka, Lars; Kauzlarić, David; Greiner, Andreas; Korvink, Jan G

    2006-03-01

    We present a Markov process which models particle hydrodynamics with conservation of the first three momenta. This is achieved by extending the [Peters, Europhys. Lett. 66, 311 (2004)] and [Lowe, Europhys. Lett. 47, 145 (1999)] method to incorporate energy conservation. The equivalence of the energy conserving Peters method and dissipative particle dynamics with energy conservation (DPDE) in the limit of a vanishing time step is shown. Simple numerical experiments clearly demonstrate the applicability of the methods. This overcomes current limitations of DPDE in the study of complex fluids in the (N,V,E) ensemble.

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

    PubMed

    Goicochea, Armando Gama; Alarcón, Francisco

    2011-01-07

    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.

  5. 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.

  6. 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.

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

    PubMed

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

    2006-05-22

    Movements of wide-ranging top predators can now be studied effectively using satellite and archival telemetry. However, the motivations underlying movements remain difficult to determine because trajectories are seldom related to key biological gradients, such as changing prey distributions. Here, we use a dynamic prey landscape of zooplankton biomass in the north-east Atlantic Ocean to examine active habitat selection in the plankton-feeding basking shark Cetorhinus maximus. The relative success of shark searches across this landscape was examined by comparing prey biomass encountered by sharks with encounters by random-walk simulations of 'model' sharks. Movements of transmitter-tagged sharks monitored for 964 days (16754 km estimated minimum distance) were concentrated on the European continental shelf in areas characterized by high seasonal productivity and complex prey distributions. We show movements by adult and sub-adult sharks yielded consistently higher prey encounter rates than 90% of random-walk simulations. Behavioural patterns were consistent with basking sharks using search tactics structured across multiple scales to exploit the richest prey areas available in preferred habitats. Simple behavioural rules based on learned responses to previously encountered prey distributions may explain the high performances. This study highlights how dynamic prey landscapes enable active habitat selection in large predators to be investigated from a trophic perspective, an approach that may inform conservation by identifying critical habitat of vulnerable species.

  8. Forest dynamics in Oregon landscapes: evaluation and application of an individual-based model.

    PubMed

    Busing, Richard T; Solomon, Allen M; McKane, Robert B; Burdick, Connie A

    2007-10-01

    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.

  9. [Dynamic evaluation on landscape connectivity of ecological land: a case study of Shenzhen, Guangdong Province of South China].

    PubMed

    Wu, Jian-Sheng; Liu, Hong-Meng; Huang, Xiu-Lan; Feng, Zhe

    2012-09-01

    Ecological land is the most crucial and sensitive land use type in rapidly urbanizing areas. Landscape connectivity can help us to better understand the interactions between landscape structure and landscape function. By using the land use data of Shenzhen from 1996 to 2008 and the graph theory- based integral index of connectivity (IIC), probability index of connectivity (PC), and importance value of patches (dPC), a dynamic evaluation on the landscape connectivity of ecological land in the City was conducted, and a spatial assessment was made to identify the most important patches for maintaining overall landscape connectivity. In combining with the basic ecological controlling line in Shenzhen, the variations of the landscape connectivity of the ecological land inside and outside the basic ecological controlling line were evaluated. From 1996 to 2008, the overall landscape connectivity of the ecological land in Shenzhen displayed a downward trend, the importance and the spatial distribution of the important patches for maintaining the overall landscape connectivity changed, and the basic ecological controlling line played definite roles in maintaining the landscape connectivity of ecological land inside the line.

  10. Characterization of the dynamics of glass-forming liquids from the properties of the potential energy landscape.

    PubMed

    Banerjee, Sumilan; Dasgupta, Chandan

    2012-02-01

    We develop a framework for understanding the difference between strong and fragile behavior in the dynamics of glass-forming liquids from the properties of the potential energy landscape. Our approach is based on a master equation description of the activated jump dynamics among the local minima of the potential energy (the so-called inherent structures) that characterize the potential energy landscape of the system. We study the dynamics of a small atomic cluster using this description as well as molecular dynamics simulations and demonstrate the usefulness of our approach for this system. Many of the remarkable features of the complex dynamics of glassy systems emerge from the activated dynamics in the potential energy landscape of the atomic cluster. The dynamics of the system exhibits typical characteristics of a strong supercooled liquid when the system is allowed to explore the full configuration space. This behavior arises because the dynamics is dominated by a few lowest-lying minima of the potential energy and the potential energy barriers between these minima. When the system is constrained to explore only a limited region of the potential energy landscape that excludes the basins of attraction of a few lowest-lying minima, the dynamics is found to exhibit the characteristics of a fragile liquid.

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. Dynamical Interactions Between Human Populations and Landscapes in Barrier Island Environments

    NASA Astrophysics Data System (ADS)

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

    2003-12-01

    Although much research has focused on how humans affect landscapes or how landform processes affect humans, little attention has been paid to dynamical interactions between the two. Based on the hypothesis that landscape and human dynamics both self-organize into a temporal hierarchy of scale-separated behaviors, we model the evolution of a coupled human population and barrier island system. Barrier islands are represented as a series of alongshore nodes, with each node specifying the width, height, cross-shore position, and profile of the island and the beach width, dune position and dune height. These characteristics evolve according to rules governing sediment transport during acretionary phases, erosion from storms, dune growth and migration, tidal delta formation, overwash, inlet formation, alongshore sediment transport, and dune and backbarrier vegetation growth. At each of these nodes, human populations and their cultural accoutrements are represented by mean property value, fraction of land used for tourist accommodations and tourist population. The dynamics of these variables is determined by simulating the competition for economic resources amongst the local population and the desire of the tourist population for adequate recreational beaches. The human and barrier subsystems are coupled through beach replenishment and a dependence of tourist population on beach width. Model results fall into three general categories of dynamical behavior, as classified by the (linearized) time scale of recovery from perturbations for the uncoupled systems. When the time scale for barrier islands is much less than that of the human population, the long-time-scale evolution of the barrier island follows human dynamics. In the reverse case, the long-time-scale evolution of the human population follows barrier dynamics. When the time scales are similar, new long-time-scale, spatially varying behavior of the coupled system emerges. Implications for prediction and optimization

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

    NASA Astrophysics Data System (ADS)

    Reinhardt, Liam; Ellis, Michael A.

    2015-07-01

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

  17. Politics and Graduate Medical Education in Internal Medicine: A Dynamic Landscape.

    PubMed

    Wardrop, Richard M; Berkowitz, Lee R

    2017-02-01

    The promotion of change and growth within medical education is oftentimes the result of a complex mix of societal, cultural and economic forces. Graduate medical education in internal medicine is not immune to these forces. Several entities and organizations can be identified as having a major influence on internal medicine training and graduate medical education as a whole. We have reviewed how this is effectively accomplished through these entities and organizations. The result is a constantly changing and dynamic landscape for internal medicine training.

  18. 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

  19. 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

  20. 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

  1. 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.

  2. 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

  3. The Influence of Ecohydrologic Dynamics on Landscape Evolution: a Stochastic Approach

    NASA Astrophysics Data System (ADS)

    Deal, E.; Favre Pugin, A. C.; Botter, G.; Braun, J.

    2015-12-01

    The stream power incision model (SPIM) has a long history of use in modeling landscape evolution. Despite simplifications made in its formulation, it has emerged over the last 30 years as a powerful tool to interpret the histories of tectonically active landscapes and to understand how they evolve over millions of years. However, intense interest in the relationship between climate and erosion has revealed that the standard SPIM has some significant shortcomings. First, it fails to account for the role of erosion thresholds, which have been shown to be important and require an approach that addresses the variable or stochastic nature of erosion processes and drivers. Second, the standard SPIM does not address the influence of catchment hydrology, which modulates the incoming precipitation to produce discharge that in turn drives fluvial erosion. Hydrological processes alter in particular the frequency and magnitude of extreme events which are highly relevant for landscape erosion. To address these weaknesses we introduce a new analytical stochastic-threshold formulation of the stream power incision model that is driven by probabilistic hydrology. The hydrological model incorporates a stochastic description of soil moisture which takes into account the random nature of the rainfall forcing and the dynamics of the soil layer. The soil layer dynamics include infiltration and evapotranspiration which are both modelled as being dependent on the time varying soil moisture level (state dependent). The stochastic approach allows us to integrate these effects over long periods of time to understand their influence on the longterm average erosion rate without the need to explicitly model processes on the short timescales where they are relevant. Our model can therefore represent the role of soil properties (thickness, porosity) and vegetation (through evapotranspiration rates) in the longterm catchment-wide water balance, and in turn the longterm erosion rate. We identify

  4. Local epiphyte establishment and future metapopulation dynamics in landscapes with different spatiotemporal properties.

    PubMed

    Belinchón, Rocío; Harrison, Philip J; Mair, Louise; Várkonyi, Gergely; Snäll, Tord

    2017-03-01

    Understanding the relative importance of different ecological processes on the metapopulation dynamics of species is the basis for accurately forecasting metapopulation size in fragmented landscapes. Successful local colonization depends on both species dispersal range and how local habitat conditions affect establishment success. Moreover, there is limited understanding of the effects of different spatiotemporal landscape properties on future metapopulation size. We investigate which factors drive the future metapopulation size of the epiphytic model lichen species Lobaria pulmonaria in a managed forest landscape. First, we test the importance of dispersal and local conditions on the colonization-extinction dynamics of the species using Bayesian state-space modelling of a large-scale data set collected over a 10-yr period. Second, we test the importance of dispersal and establishment limitation in explaining establishment probability and subsequent local population growth, based on a 10-yr propagule sowing experiment. Third, we test how future metapopulation size is affected by different metapopulation and spatiotemporal landscape dynamics, using simulations with the metapopulation models fitted to the empirical data. The colonization probability increased with tree inclination and connectivity, with a mean dispersal distance of 97 m (95% credible intervals, 5-530 m). Local extinctions were mainly deterministic set by tree mortality, but also by tree cutting by forestry. No experimental establishments took place on clearcuts, and in closed forest the establishment probability was higher on trees growing on moist than on dry-mesic soils. The subsequent local population growth rate increased with increasing bark roughness. The simulations showed that the restricted dispersal range estimated (compared to non-restricted dispersal range), and short tree rotation length (65 yr instead of 120) had approximately the same negative effects on future metapopulation size

  5. 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.

  6. 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.

  7. 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.

  8. Spatiotemporal dynamics of landscape pattern and hydrologic process in watershed systems

    NASA Astrophysics Data System (ADS)

    Randhir, Timothy O.; Tsvetkova, Olga

    2011-06-01

    SummaryLand use change is influenced by spatial and temporal factors that interact with watershed resources. Modeling these changes is critical to evaluate emerging land use patterns and to predict variation in water quantity and quality. The objective of this study is to model the nature and emergence of spatial patterns in land use and water resource impacts using a spatially explicit and dynamic landscape simulation. Temporal changes are predicted using a probabilistic Markovian process and spatial interaction through cellular automation. The MCMC (Monte Carlo Markov Chain) analysis with cellular automation is linked to hydrologic equations to simulate landscape patterns and processes. The spatiotemporal watershed dynamics (SWD) model is applied to a subwatershed in the Blackstone River watershed of Massachusetts to predict potential land use changes and expected runoff and sediment loading. Changes in watershed land use and water resources are evaluated over 100 years at a yearly time step. Results show high potential for rapid urbanization that could result in lowering of groundwater recharge and increased storm water peaks. The watershed faces potential decreases in agricultural and forest area that affect open space and pervious cover of the watershed system. Water quality deteriorated due to increased runoff which can also impact stream morphology. While overland erosion decreased, instream erosion increased from increased runoff from urban areas. Use of urban best management practices (BMPs) in sensitive locations, preventive strategies, and long-term conservation planning will be useful in sustaining the watershed system.

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

    PubMed

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

    2008-12-09

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

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

    NASA Astrophysics Data System (ADS)

    Strand, Eva K.

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

  11. [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.

  12. 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

  13. [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.

  14. 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.

  15. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. A Dynamic Protein Interaction Landscape of the Human Centrosome-Cilium Interface.

    PubMed

    Gupta, Gagan D; Coyaud, Étienne; Gonçalves, João; Mojarad, Bahareh A; Liu, Yi; Wu, Qianzhu; Gheiratmand, Ladan; Comartin, David; Tkach, Johnny M; Cheung, Sally W T; Bashkurov, Mikhail; Hasegan, Monica; Knight, James D; Lin, Zhen-Yuan; Schueler, Markus; Hildebrandt, Friedhelm; Moffat, Jason; Gingras, Anne-Claude; Raught, Brian; Pelletier, Laurence

    2015-12-03

    The centrosome is the primary microtubule organizing center of the cells and templates the formation of cilia, thereby operating at a nexus of critical cellular functions. Here, we use proximity-dependent biotinylation (BioID) to map the centrosome-cilium interface; with 58 bait proteins we generate a protein topology network comprising >7,000 interactions. Analysis of interaction profiles coupled with high resolution phenotypic profiling implicates a number of protein modules in centriole duplication, ciliogenesis, and centriolar satellite biogenesis and highlights extensive interplay between these processes. By monitoring dynamic changes in the centrosome-cilium protein interaction landscape during ciliogenesis, we also identify satellite proteins that support cilia formation. Systematic profiling of proximity interactions combined with functional analysis thus provides a rich resource for better understanding human centrosome and cilia biology. Similar strategies may be applied to other complex biological structures or pathways.

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

    USGS Publications Warehouse

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

    2007-01-01

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

  4. Linking Inundation Patterns and Dynamics in a Permafrost Landscape to Hydrologic, Thermal, Biogeochemical and Ecosystem Processes

    NASA Astrophysics Data System (ADS)

    Wilson, C. J.; Hinzman, L. D.; Iwahana, G.; Lara, M. J.; Liljedahl, A.; Painter, S. L.; Romanovsky, V. E.; Wullschleger, S. D.

    2014-12-01

    The Arctic coastal plain is characterized by multi-scale geomorphic features including thaw lakes, drained thaw lake basins, and clusters of ice wedge polygons composed of troughs, centers, and rims. The topographic and subsurface properties of these features control the lateral and vertical drainage pathways of snow melt and precipitation as well as the spatial and temporal dynamics of standing water in the landscape. The Next Generation Ecosystem Experiment, NGEE-Arctic, project combines multi-scale in-situ and remote surface and subsurface observations that quantify the interactions between landscape structure, hydrology, the carbon cycle and energy balance of Arctic permafrost environments, with the aim of improving representation of Arctic ecosystem processes in global climate models. Data and models from the project show distinct relationships exist between the hydro-geomorphic features mapped on the ground and observed in remote sensing imagery, and the measured in-situ thermal, biogeochemical and ecosystem responses coincident with those features. The relationships between micro-topographic setting, snow distribution, inundation, subsurface temperature and thaw depth observed at the NGEE Barrow field sites are now well reproduced in process resolving models such as Pflotran and the Arctic Terrestrial Simulator. Current modeling efforts are investigating how topographically controlled thermal-hydrologic dynamics impact the carbon cycle. The next challenge is to scale these relationships for application in a global climate model grid cell to enable pan-Arctic predictions of future change, including the change in topography and inundation resulting from thawing permafrost and melting ground ice. NGEE-Arctic is funded by the DOE Office of Science, Biological and Environmental Research program.

  5. 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...

  6. 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

  7. 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.

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

    USGS Publications Warehouse

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

    2015-01-01

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

  9. 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.

  10. 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

  11. 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.

  12. 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

  13. Measurement of two-state energy landscapes on amorphous hafnium diboride surface by direct observation of dynamics

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

    Direct visualization of free energy landscape for individual Cooperatively Rearranging Regions (CRRs) is important in glassy dynamics, both for the bulk and the surface. We used scanning tunneling microscopy to track individual CRRs on amorphous hafnium diboride surface, temporally from microseconds to hours with sub-nanometer spatial resolution. CRRs have a diameter of ~5 atoms and mostly relax in a two-state fashion. From single cluster tunneling current traces, we can reconstruct local free energy landscapes, complete with energy difference, barrier height, a numerically defined reaction corrdinate and shape of the free energy minima.

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

    PubMed

    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.

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. Relationship of Integrated Landscape Dynamics to Water Quality in Lake Maumelle, Arkansas

    NASA Astrophysics Data System (ADS)

    Robinson, A. C.; McMillan, M. E.; Johnson, D.; Stites, C.

    2009-12-01

    Lake Maumelle is an east-west trending drinking water reservoir created in 1957 by impoundment of the Big Maumelle River and associated tributaries. The reservoir serves as a natural receptacle that integrates Critical Zone Processes occurring across a diverse landscape. Creeks in the northern part of the watershed flow through regions with different geologic formations, thus providing different aqueous geochemical constituents than the creeks flowing into the lake from the south. Specifically soils from the north side of the lake are Ultisols derived from weathering of quartz sandstones, whereas the southern part of the lake contains soils formed on both shales and sandstones. To evaluate the significance of landscape dynamics in the context of this geologic framework, we used a combination of organic and inorganic geochemical parameters to track inputs to creeks and coves along the northern and southern boundaries of the lake. Some parameters were consistent between coves suggesting perhaps the creek inputs may undergo internal reservoir mixing, thus masking the signal from the adjacent watershed. However, we sampled creeks to see if there were distinct signatures associated with each tributary. The creeks had higher fractions of organic matter derived from vascular plants compared to the coves, suggesting that some of the organic matter that arrives at the lake margin gets remineralized, buried or reworked. Our results have shown elevated sediment flux and increased vascular plant derived dissolved organic carbon in streams draining areas that have undergone clear cutting in the recent past. Differences in the frequency of land surface disturbance, between clear-cut areas versus stable forested regions, indentify the temporal control on these geochemical parameters. Transfers from different soils systems get integrated along the stream reaches, with dissolved and particulate phase constituents likely following separate trajectories once reaching the lake margin

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

    PubMed

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

    2015-10-01

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

  2. 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.

  3. Flood dynamics in urbanised landscapes: 100 years of climate and humans’ interaction

    NASA Astrophysics Data System (ADS)

    Sofia, G.; Roder, G.; Dalla Fontana, G.; Tarolli, P.

    2017-01-01

    Raising interest in the interaction between humans and climate drivers to understand the past and current development of floods in urbanised landscapes is of great importance. This study presents a regional screening of land-use, rainfall regime and flood dynamics in north-eastern Italy, covering the timeframe 1900–2010. This analysis suggests that, statistically, both climate and land-use have been contributing to a significant increase of the contribution of short duration floods to the increase in the number of flooded locations. The analysis also suggests that interaction arises, determining land-use dynamics to couple with climatic changes influencing the flood aggressiveness simultaneously. Given that it is not possible to control the climatic trend, an effective disaster management clearly needs an integrated approach to land planning and supervision. This research shows that land management and planning should include the investigation of the location of the past and future social and economic drivers for development, as well as past and current climatic trends.

  4. Free-energy landscape of intrinsically disordered proteins investigated by all-atom multicanonical molecular dynamics.

    PubMed

    Higo, Junichi; Umezawa, Koji

    2014-01-01

    We introduce computational studies on intrinsically disordered proteins (IDPs). Especially, we present our multicanonical molecular dynamics (McMD) simulations of two IDP-partner systems: NRSF-mSin3 and pKID-KIX. McMD is one of enhanced conformational sampling methods useful for conformational sampling of biomolecular systems. IDP adopts a specific tertiary structure upon binding to its partner molecule, although it is unstructured in the unbound state (i.e. the free state). This IDP-specific property is called "coupled folding and binding". The McMD simulation treats the biomolecules with an all-atom model immersed in an explicit solvent. In the initial configuration of simulation, IDP and its partner molecules are set to be distant from each other, and the IDP conformation is disordered. The computationally obtained free-energy landscape for coupled folding and binding has shown that native- and non-native-complex clusters distribute complicatedly in the conformational space. The all-atom simulation suggests that both of induced-folding and population-selection are coupled complicatedly in the coupled folding and binding. Further analyses have exemplified that the conformational fluctuations (dynamical flexibility) in the bound and unbound states are essentially important to characterize IDP functioning.

  5. Flood dynamics in urbanised landscapes: 100 years of climate and humans’ interaction

    PubMed Central

    Sofia, G.; Roder, G.; Dalla Fontana, G.; Tarolli, P.

    2017-01-01

    Raising interest in the interaction between humans and climate drivers to understand the past and current development of floods in urbanised landscapes is of great importance. This study presents a regional screening of land-use, rainfall regime and flood dynamics in north-eastern Italy, covering the timeframe 1900–2010. This analysis suggests that, statistically, both climate and land-use have been contributing to a significant increase of the contribution of short duration floods to the increase in the number of flooded locations. The analysis also suggests that interaction arises, determining land-use dynamics to couple with climatic changes influencing the flood aggressiveness simultaneously. Given that it is not possible to control the climatic trend, an effective disaster management clearly needs an integrated approach to land planning and supervision. This research shows that land management and planning should include the investigation of the location of the past and future social and economic drivers for development, as well as past and current climatic trends. PMID:28079147

  6. 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

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

    NASA Astrophysics Data System (ADS)

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

    2006-12-01

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

  8. 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

  9. 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.

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

    PubMed

    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.

  11. 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

  12. 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.

  13. Exact exponent for the number of persistent spins in the zero-temperature dynamics of the one-dimensional Potts model

    NASA Astrophysics Data System (ADS)

    Derrida, Bernard; Hakim, Vincent; Pasquier, Vincent

    1996-12-01

    For the zero-temperature Glauber dynamics of the q-state Potts model, the fraction r(q, t) of spins which never flip up to time t decays like a power law r(q, t)˜t -θ(q) when the initial condition is random. By mapping the problem onto an exactly soluble one-species coagulation model ( A+A→A) or alternatively by transforming the problem into a free-fermion model, we obtain the exact expression of θ( q) for all values of q. The exponent π( q) is in general irrational, θ(3)=0.53795082..., θ(4)=0.63151575..., ..., with the exception of q=2 and q=∞, for which θ(2)=3/8 and θ(∞)=1.

  14. 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.

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

    PubMed

    Wu, Wei; Wang, Jin

    2013-09-28

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

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

    PubMed

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

    2016-03-18

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

  18. 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.

  19. Dynamics of warped compactifications and the shape of the warped landscape

    SciTech Connect

    Giddings, Steven B.; Maharana, Anshuman

    2006-06-15

    The dynamics of warped/flux compactifications is studied, including warping effects, providing a firmer footing for investigation of the 'landscape'. We present a general formula for the four-dimensional potential of warped compactifications in terms of ten-dimensional quantities. This allows a systematic investigation of moduli-fixing effects and potentials for mobile branes. We provide a necessary criterion, 'slope dominance', for evading 'no-go' results for de Sitter vacua. We outline the ten-dimensional derivation of the nonperturbative effects that should accomplish this in examples of Kachru, Kallosh, Linde and Trivedi and outline a systematic discussion of their corrections. We show that potentials for mobile branes receive generic contributions inhibiting slow-roll inflation. We give a linearized analysis of general scalar perturbations of warped IIB compactifications, revealing new features for both time-independent and dependent moduli, and new aspects of the kinetic part of the four-dimensional effective action. The universal Kahler modulus is found not to be a simple scaling of the internal metric, and a prescription is given for defining holomorphic Kahler moduli, including warping effects. In the presence of mobile branes, this prescription elucidates couplings between bulk and brane fields. Our results are thus relevant to investigations of the existence of de Sitter vacua in string theory, and of their phenomenology, cosmology, and statistics.

  20. 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.

  1. 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.

  2. 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.

  3. Characterizing the landscape dynamics of an invasive plant and risk of invasion using remote sensing.

    PubMed

    Bradley, Bethany A; Mustard, John F

    2006-06-01

    Improved understanding of the spatial dynamics of invasive plant species may lead to more effective land management and reduced future invasion. Here, we identified the spatial extents of nonnative cheatgrass (Bromus tectorum) in the north central Great Basin using remotely sensed data from Landsat MSS, TM, and ETM+. We compared cheatgrass extents in 1973 and 2001 to six spatially explicit landscape variables: elevation, aspect, hydrographic channels, cultivation, roads, and power lines. In 2001, Cheatgrass was 10% more likely to be found in elevation ranges from 1400 to 1700 m (although the data suggest a preferential invasion into lower elevations by 2001), 6% more likely on west and northwest facing slopes, and 3% more likely within hydrographic channels. Over this time period, cheatgrass expansion was also closely linked to proximity to land use. In 2001, cheatgrass was 20% more likely to be found within 3 km of cultivation, 13% more likely to be found within 700 m of a road, and 15% more likely to be found within 1 km of a power line. Finally, in 2001 cheatgrass was 26% more likely to be present within 150 m of areas occupied by cheatgrass in 1973. Using these relationships, we created a risk map of future cheatgrass invasion that may aid land management. These results highlight the importance of including land use variables and the extents of current plant invasion in predictions of future risk.

  4. Probing the energy landscape of alanine dipeptide and decalanine using temperature as a tunable parameter in molecular dynamics

    NASA Astrophysics Data System (ADS)

    Chatterjee, A.; Bhattacharya, S.

    2016-10-01

    We perform several molecular dynamics (MD) calculations of solvated alanine dipeptide and decalanine in vacuum with temperature as a tunable parameter and in the process, generate Markov state models (MSMs) at each temperature. An interesting observation that the kinetic rates appear to obey the Arrhenius rate law allows us to predict the dynamics of alanine dipeptide at 300 K at the microsecond timescales using the nanoseconds long high temperature calculations without actually performing MD simulations at 300 K. We conclude that the energy landscape of alanine dipeptide contains superbasins deeper than kBT and determine the energy barriers associated with the moves from the Arrhenius rate expression. Similar insights regarding the energy landscape associated with folding/unfolding pathways of a deca-alanine molecule are obtained using kinetic rates calculated at different temperatures.

  5. Secondary succession dynamics in estuarine marshes across landscape-scale salinity gradients.

    PubMed

    Crain, Caitlin Mullan; Albertson, Lindsey K; Bertness, Mark D

    2008-10-01

    Secondary succession plays a critical role in driving community structure in natural communities, yet how succession dynamics vary with environmental context is generally unknown. We examined the importance of seedling and vegetative recruitment in the secondary succession of coastal marsh vegetation across a landscape-scale environmental stress gradient. Replicate bare patches were initiated in salt, brackish, and oligohaline marshes in Narragansett Bay, Rhode Island, USA, and allowed to recover unmanipulated or with colonizing seedlings or vegetative runners removed for three years. Seed dispersal and seed bank studies were conducted at the same sites. We found that rates of recovery were 3-10 times faster in brackish and oligohaline marshes than in salt marshes. The fast pace of recovery in oligohaline marshes was driven by seedling colonization, while recovery was dominated by vegetative runners in brackish marshes and by both seedlings and runners in salt marshes. Seed and seedling availability was much greater in oligohaline marshes with up to 24 times the seed bank density compared with salt marshes. In contrast to the facilitated succession generally found in salt marshes, oligohaline marshes follow the tolerance model of succession where numerous species colonize from seed and are slowly displaced by clonal grasses whose recovery is slowed by preemptive competition from seedlings, contributing to the higher species diversity of oligohaline marshes. These findings reveal fundamental differences in the dynamics and assembly of marsh plant communities along estuarine salinity gradients that are important for conceptually understanding wetlands and for guiding the management and restoration of various types of coastal marshes.

  6. 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.

  7. Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics.

    PubMed

    Preto, Jordane; Clementi, Cecilia

    2014-09-28

    The reaction pathways characterizing macromolecular systems of biological interest are associated with high free energy barriers. Resorting to the standard all-atom molecular dynamics (MD) to explore such critical regions may be inappropriate as the time needed to observe the relevant transitions can be remarkably long. In this paper, we present a new method called Extended Diffusion-Map-directed Molecular Dynamics (extended DM-d-MD) used to enhance the sampling of MD trajectories in such a way as to rapidly cover all important regions of the free energy landscape including deep metastable states and critical transition paths. Moreover, extended DM-d-MD was combined with a reweighting scheme enabling to save on-the-fly information about the Boltzmann distribution. Our algorithm was successfully applied to two systems, alanine dipeptide and alanine-12. Due to the enhanced sampling, the Boltzmann distribution is recovered much faster than in plain MD simulations. For alanine dipeptide, we report a speedup of one order of magnitude with respect to plain MD simulations. For alanine-12, our algorithm allows us to highlight all important unfolded basins in several days of computation when one single misfolded event is barely observable within the same amount of computational time by plain MD simulations. Our method is reaction coordinate free, shows little dependence on the a priori knowledge of the system, and can be implemented in such a way that the biased steps are not computationally expensive with respect to MD simulations thus making our approach well adapted for larger complex systems from which little information is known.

  8. 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

  9. 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

  10. Exactly solvable spin dynamics of an electron coupled to a large number of nuclei; the electron-nuclear spin echo in a quantum dot

    SciTech Connect

    Kozlov, G. G.

    2007-10-15

    The model used to describe the spin dynamics in quantum dots after optical excitation is considered. Problems of the electron-spin polarization decay and the dependence of the steady-state polarization on magnetic field are solved on the basis of exact diagonalization of the model Hamiltonian. An important role of the nuclear state is shown and methods of its calculation for different regimes of optical excitation are proposed. The effect of spin echo generation after application of a {pi} pulse of a magnetic field is predicted for the system under consideration.

  11. 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.

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

    USGS Publications Warehouse

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

    2005-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  14. Modeling the influence of dynamic zoning of forest harvesting on ecological succession in a northern hardwoods landscape.

    PubMed

    Zollner, Patrick A; Gustafson, Eric J; He, Hong S; Radeloff, Volker C; Mladenoff, David J

    2005-04-01

    Dynamic zoning (systematic alteration in the spatial and temporal allocation of even-aged forest management practices) has been proposed as a means to change the spatial pattern of timber harvest across a landscape to maximize forest interior habitat while holding timber harvest levels constant. Simulation studies have established that dynamic zoning strategies produce larger tracts of interior, closed canopy forest, thus increasing the value of these landscapes for interior-dependent wildlife. We used the simulation model LANDIS to examine how the implementation of a dynamic zoning strategy would change trajectories of ecological succession in the Great Divide Ranger District of the Chequamegon-Nicolet National Forest in northern Wisconsin over 500 years. The components of dynamic zoning strategies (number of zones in a scenario and the length of the hiatus between successive entries into zones) and their interaction had highly significant impacts on patterns of forest succession. Dynamic zoning scenarios with more zones and shorter hiatus lengths increased the average amount of the forest dominated by early successional aspen (Populus sp.). Dynamic zoning scenarios with two zones produced more late successional mature northern hardwoods than scenarios with four zones. Dynamic zoning scenarios with very short (30 years) or very long (120 years) hiatus lengths resulted in more late successional mature northern hardwoods than scenarios with intermediate hiatus lengths (60 and 90 years). However, none of the dynamic scenarios produced as much late successional mature northern hardwoods as the static alternative. Furthermore, the amounts of all habitat types in all dynamic zoning scenarios fluctuated greatly in time and space relative to static alternatives, which could negatively impact wildlife species that require a stable amount of habitat above some minimum critical threshold. Indeed, implementing dynamic zoning scenarios of different designs would have both

  15. Dynamics of Gas Exchange through the Fractal Architecture of the Human Lung, Modeled as an Exactly Solvable Hierarchical Tree

    NASA Astrophysics Data System (ADS)

    Mayo, Michael; Pfeifer, Peter; Gheorghiu, Stefan

    2008-03-01

    The acinar airways lie at the periphery of the human lung and are responsible for the transfer of oxygen from air to the blood during respiration. This transfer occurs by the diffusion-reaction of oxygen over the irregular surface of the alveolar membranes lining the acinar airways. We present an exactly solvable diffusion-reaction model on a hierarchically branched tree, allowing a quantitative prediction of the oxygen current over the entire system of acinar airways responsible for the gas exchange. We discuss the effect of diffusional screening, which is strongly coupled to oxygen transport in the human lung. We show that the oxygen current is insensitive to a loss of permeability of the alveolar membranes over a wide range of permeabilities, similar to a ``constant-current source'' in an electric network. Such fault tolerance has been observed in other treatments of the gas exchange in the lung and is obtained here as a fully analytical result.

  16. 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

  17. Potentially amyloidogenic conformational intermediates populate the unfolding landscape of transthyretin: Insights from molecular dynamics simulations

    PubMed Central

    Rodrigues, J Rui; Simões, Carlos J V; Silva, Cândida G; Brito, Rui M M

    2010-01-01

    Protein aggregation into insoluble fibrillar structures known as amyloid characterizes several neurodegenerative diseases, including Alzheimer's, Huntington's and Creutzfeldt-Jakob. Transthyretin (TTR), a homotetrameric plasma protein, is known to be the causative agent of amyloid pathologies such as FAP (familial amyloid polyneuropathy), FAC (familial amyloid cardiomiopathy) and SSA (senile systemic amyloidosis). It is generally accepted that TTR tetramer dissociation and monomer partial unfolding precedes amyloid fibril formation. To explore the TTR unfolding landscape and to identify potential intermediate conformations with high tendency for amyloid formation, we have performed molecular dynamics unfolding simulations of WT-TTR and L55P-TTR, a highly amyloidogenic TTR variant. Our simulations in explicit water allow the identification of events that clearly discriminate the unfolding behavior of WT and L55P-TTR. Analysis of the simulation trajectories show that (i) the L55P monomers unfold earlier and to a larger extent than the WT; (ii) the single α-helix in the TTR monomer completely unfolds in most of the L55P simulations while remain folded in WT simulations; (iii) L55P forms, early in the simulations, aggregation-prone conformations characterized by full displacement of strands C and D from the main β-sandwich core of the monomer; (iv) L55P shows, late in the simulations, severe loss of the H-bond network and consequent destabilization of the CBEF β-sheet of the β-sandwich; (v) WT forms aggregation-compatible conformations only late in the simulations and upon extensive unfolding of the monomer. These results clearly show that, in comparison with WT, L55P-TTR does present a much higher probability of forming transient conformations compatible with aggregation and amyloid formation. PMID:19937650

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

    PubMed

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

    2013-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  1. 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.

  2. Assessing the role of landscape connectivity on Opisthorchis viverrini transmission dynamics.

    PubMed

    Wang, Yi-Chen; Yuen, Roy; Feng, Chen-Chieh; Sithithaworn, Paiboon; Kim, Ick-Hoi

    2016-06-02

    Opisthorchis viverrini (Ov) is one of the most important human parasitic diseases in Southeast Asia. Although the concept of connectivity is widely used to comprehend disease dispersal, knowledge of the influences of landscape connectivity on Ov transmission is still rudimentary. This study aimed to investigate the role of landscape connectivity in Ov transmission between the human and the first intermediate snail hosts. Fieldwork was conducted in three villages respectively in Kamalasai District, Kalasin Province, Phu Wiang District, Khon Kaen Province, and Nong Saeng District, Udon Thani Province. Bithynia snails were collected to examine parasitic infections, water samples were analyzed for fecal contamination, and locations of septic tanks and connections between habitat patches with observable water movement were surveyed. Euclidean distance, topological link and distance, and graph measures were employed to quantify the connectivity between human and snail habitats. The findings showed that snail patches with higher fecal contents were generally located nearer to septic tanks. The statistically significant results for the topological link and distance measures highlighted the importance of water in functionally facilitating Ov transmission. Graph measures revealed differences in landscape connectivity across the sites. The site with the largest landscape component size and the most mutually connected snail patches coincided with the presence of Ov parasite, reinforcing its higher risk for human to snail transmission. The site with the dissected landscape structure potentially limited the transmission. This study underscored the potential effect of landscape connectivity on Ov transmission, contributing to the understanding of the spatial variation of Ov infection risk.

  3. 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.

  4. Stable isotope paleoaltimetry of high relief terrain: An atmospheric dynamics and landscape evolution perspective

    NASA Astrophysics Data System (ADS)

    Galewsky, J.

    2009-04-01

    Stable isotope ratios in rain and snow from mountainous regions show a strong correlation with altitude. To the extent that these isotopic ratios are preserved in the geological record, they may provide a powerful constraint on the surface uplift history of mountain belts. Existing interpretive frameworks for paleoaltimetry are based on linear regressions of modern precipitation isotope transects or on a Rayleigh distillation model of air parcel ascent along a moist adiabatic temperature lapse rate. Neither of these frameworks accounts for the fully nonlinear dynamics of airflow over high-relief terrain, which predicts substantial deviations from the moist-adiabatic ascent model under common atmospheric conditions. The Weather Research and Forecast model (WRF), a numerical weather prediction model, has been modified to include a simplified isotope physics parameterization and has been used to explore the links between topography, atmospheric state, and precipitation isotopes. The controlling nondimensional parameter for atmospheric flow over terrain is Nh/U, where N is the Brunt-Vaisala frequency, a measure of atmospheric stability, h is the orogen- scale relief, and U is the horizontal wind speed. When Nh/U<1, winds can flow directly over topography and WRF precipitation isotopes match those predicted by the moist-adiabatic Rayleigh model. When Nh/U>1, the winds are blocked by the topography and are deflected around it. In these cases, the maximum elevation of condensation is much lower than the range crest, and precipitation isotopes are consequently substantially less depleted than predicted by the moist adiabatic Rayleigh model. Furthermore, the along-strike length of an orogen and the presence of valleys are shown to exert a strong influence on precipitation isotopes in blocked flow regimes because of the dynamical link between terrain length and atmospheric flow blocking. Terrain- blocked atmospheric conditions are common, especially in regions of high relief

  5. 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

  6. 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.

  7. Quantification of motor network dynamics in Parkinson’s disease by means of landscape and flux theory

    PubMed Central

    Yan, Han; Wang, Jin

    2017-01-01

    The basal ganglia neural circuit plays an important role in motor control. Despite the significant efforts, the understanding of the principles and underlying mechanisms of this modulatory circuit and the emergence of abnormal synchronized oscillations in movement disorders is still challenging. Dopamine loss has been proved to be responsible for Parkinson’s disease. We quantitatively described the dynamics of the basal ganglia-thalamo-cortical circuit in Parkinson’s disease in terms of the emergence of both abnormal firing rates and firing patterns in the circuit. We developed a potential landscape and flux framework for exploring the modulatory circuit. The driving force of the circuit can be decomposed into a gradient of the potential, which is associated with the steady-state probability distributions, and the curl probability flux term. We uncovered the underlying potential landscape as a Mexican hat-shape closed ring valley where abnormal oscillations emerge due to dopamine depletion. We quantified the global stability of the network through the topography of the landscape in terms of the barrier height, which is defined as the potential difference between the maximum potential inside the ring and the minimum potential along the ring. Both a higher barrier and a larger flux originated from detailed balance breaking result in more stable oscillations. Meanwhile, more energy is consumed to support the increasing flux. Global sensitivity analysis on the landscape topography and flux indicates how changes in underlying neural network regulatory wirings and external inputs influence the dynamics of the system. We validated two of the main hypotheses(direct inhibition hypothesis and output activation hypothesis) on the therapeutic mechanism of deep brain stimulation (DBS). We found GPe appears to be another effective stimulated target for DBS besides GPi and STN. Our approach provides a general way to quantitatively explore neural networks and may help for

  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. Reaction dynamics under confinement: an exact path integral treatment of a two-stage model of stochastic gene expression

    NASA Astrophysics Data System (ADS)

    Sharma, Rati; Cherayil, Binny J.

    2013-10-01

    Gene expression in living systems is inherently stochastic, and tends to produce varying numbers of proteins over repeated cycles of transcription and translation. In this paper, an expression is derived for the steady-state protein number distribution starting from a two-stage kinetic model of the gene expression process involving p proteins and r mRNAs. The derivation is based on an exact path integral evaluation of the joint distribution, P(p,r,t), of p and r at time t, which can be expressed in terms of the coupled Langevin equations for p and r that represent the two-stage model in continuum form. The steady-state distribution of p alone, P(p), is obtained from P(p,r,t) (a bivariate Gaussian) by integrating out the r degrees of freedom and taking the limit t → ∞. P(p) is found to be proportional to the product of a Gaussian and a complementary error function. It provides a generally satisfactory fit to simulation data on the same two-stage process when the translational efficiency (a measure of intrinsic noise levels in the system) is relatively low; it is less successful as a model of the data when the translational efficiency (and noise levels) are high.

  10. Rotation operator approach for the dynamics of non-dissipative multi-state Landau-Zener problems: Exact solutions

    NASA Astrophysics Data System (ADS)

    Ateuafack, M. E.; Diffo, J. T.; Fai, L. C.; Jipdi, M. N.

    2017-01-01

    The paper investigates exact time-dependent analytical solutions of the Landau-Zener (LZ) transitions for spin one-half subjected to classical noise field using rotation operator approach introduced by Zhou and co-authors. The particular case of the LZ model subjected to colored noise field is studied and extended to arbitrary spin magnitude. Transition probabilities are derived regardless of the initial configuration of the system and are found to be functions of the sort for Stokes constant. It is observed that the latter may be completely evaluated provided we have knowledge of the phase difference between noise in x - and y - directions. Transition probabilities are found to depend not only on the LZ parameter and noise frequency, but also on the states involved in the study. In particular, the coherence of the system is sustained for an exceedingly long time when many levels are considered in an atom and if in addition, the LZ parameter tends to unity and the noise' frequency is low.

  11. 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

  12. 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

  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. 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.

  15. An integrative analysis of the dynamics of landscape- and local-scale colonization of Mediterranean woodlands by Pinus halepensis.

    PubMed

    Sheffer, Efrat; Canham, Charles D; Kigel, Jaime; Perevolotsky, Avi

    2014-01-01

    Afforestation efforts have resulted in extensive plantations of either native or non-native conifers, which in many regions has led to the spread of those conifers into surrounding natural vegetation. This process of species colonization can trigger profound changes in both community dynamics and ecosystem processes. Our study disentangled the complexity of a process of colonization in a heterogeneous landscape into a simple set of rules. We analyzed the factors that control the colonization of natural woodland ecosystems by Pinus halepensis dispersing from plantations in the Mediterranean region of Israel. We developed maximum-likelihood models to explain the densities of P. halepensis colonizing natural woodlands. Our models unravel how P. halepensis colonization is controlled by factors that determine colonization pressure by dispersing seeds and by factors that control resistance to colonization of the natural ecosystems. Our models show that the combination of different seed arrival processes from local, landscape, and regional scales determine pine establishment potential, but the relative importance of each component varied according to seed source distribution. Habitat resistance, determined by abiotic and biotic conditions, was as important as propagule input in determining the density of pine colonization. Thus, despite the fact that pine propagules disperse throughout the landscape, habitat heterogeneity within the natural ecosystems generates significant variation in the actual densities of colonized pine. Our approach provides quantitative measures of how processes at different spatial scales affect the distribution and densities of colonizing species, and a basis for projection of expected distributions. Variation in colonization rates, due to landscape-scale heterogeneity in both colonization pressure and resistance to colonization, can be expected to produce a diversity of new ecosystems. This work provides a template for understanding species

  16. An Integrative Analysis of the Dynamics of Landscape- and Local-Scale Colonization of Mediterranean Woodlands by Pinus halepensis

    PubMed Central

    Sheffer, Efrat; Canham, Charles D.; Kigel, Jaime; Perevolotsky, Avi

    2014-01-01

    Afforestation efforts have resulted in extensive plantations of either native or non-native conifers, which in many regions has led to the spread of those conifers into surrounding natural vegetation. This process of species colonization can trigger profound changes in both community dynamics and ecosystem processes. Our study disentangled the complexity of a process of colonization in a heterogeneous landscape into a simple set of rules. We analyzed the factors that control the colonization of natural woodland ecosystems by Pinus halepensis dispersing from plantations in the Mediterranean region of Israel. We developed maximum-likelihood models to explain the densities of P. halepensis colonizing natural woodlands. Our models unravel how P. halepensis colonization is controlled by factors that determine colonization pressure by dispersing seeds and by factors that control resistance to colonization of the natural ecosystems. Our models show that the combination of different seed arrival processes from local, landscape, and regional scales determine pine establishment potential, but the relative importance of each component varied according to seed source distribution. Habitat resistance, determined by abiotic and biotic conditions, was as important as propagule input in determining the density of pine colonization. Thus, despite the fact that pine propagules disperse throughout the landscape, habitat heterogeneity within the natural ecosystems generates significant variation in the actual densities of colonized pine. Our approach provides quantitative measures of how processes at different spatial scales affect the distribution and densities of colonizing species, and a basis for projection of expected distributions. Variation in colonization rates, due to landscape-scale heterogeneity in both colonization pressure and resistance to colonization, can be expected to produce a diversity of new ecosystems. This work provides a template for understanding species

  17. An exact analytical solution of the unsteady magnetohydrodynamics nonlinear dynamics of laminar boundary layer due to an impulsively linear stretching sheet

    NASA Astrophysics Data System (ADS)

    Mahabaleshwar, U. S.; Nagaraju, K. R.; Vinay Kumar, P. N.; Baleanu, Dumitru; Lorenzini, Giulio

    2017-03-01

    In this paper, we investigate the theoretical analysis for the unsteady magnetohydrodynamic laminar boundary layer flow due to impulsively stretching sheet. The third-order highly nonlinear partial differential equation modeling the unsteady boundary layer flow brought on by an impulsively stretching flat sheet was solved by applying Adomian decomposition method and Pade approximants. The exact analytical solution so obtained is in terms of rapidly converging power series and each of the variants are easily computable. Variations in parameters such as mass transfer (suction/injection) and Chandrasekhar number on the velocity are observed by plotting the graphs. This particular problem is technically sound and has got applications in expulsion process and related process in fluid dynamics problems.

  18. An exact analytical solution of the unsteady magnetohydrodynamics nonlinear dynamics of laminar boundary layer due to an impulsively linear stretching sheet

    NASA Astrophysics Data System (ADS)

    Mahabaleshwar, U. S.; Nagaraju, K. R.; Vinay Kumar, P. N.; Baleanu, Dumitru; Lorenzini, Giulio

    2016-12-01

    In this paper, we investigate the theoretical analysis for the unsteady magnetohydrodynamic laminar boundary layer flow due to impulsively stretching sheet. The third-order highly nonlinear partial differential equation modeling the unsteady boundary layer flow brought on by an impulsively stretching flat sheet was solved by applying Adomian decomposition method and Pade approximants. The exact analytical solution so obtained is in terms of rapidly converging power series and each of the variants are easily computable. Variations in parameters such as mass transfer (suction/injection) and Chandrasekhar number on the velocity are observed by plotting the graphs. This particular problem is technically sound and has got applications in expulsion process and related process in fluid dynamics problems.

  19. 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

  20. Long-term experimental loss of foundation species: consequences for dynamics at ecotones across heterogeneous landscapes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Long-term (> 13 years) patterns in dominance and community composition were examined following the experimental removal of one of three foundation species at an arid - semiarid biome transition zone. Objectives were to identify key processes influencing these patterns, and to predict future landscap...

  1. 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...

  2. 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 ...

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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

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

    PubMed Central

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

    2012-01-01

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

  9. Soil water retention dynamics in Luvisols at contrasting slope positions in lysimeter monoliths from an eroded soil landscape

    NASA Astrophysics Data System (ADS)

    Herbrich, Marcus; Gerke, Horst H.; Sommer, Michael

    2015-04-01

    Modeling water flow and solute transport in variably saturated soils requires the proper description of the soil water retention curve. The problem is that under field conditions, water retention may be hysteretic or otherwise changing in time due to changing soil properties. In arable soil landscapes, these changes may depend on the erosion history which created spatial patterns of soil properties such as texture and organic matter content and differences in crop development. The objective of this study was to analyze the dynamics in field-measured water retention data for Luvisols in 10 cm, 30 cm and 50 cm soil depth (Ap, E, and Bt horizons) at two contrasting at slope positions characterized by different degrees of soil erosion under intensive agricultural cultivation. Drying and wetting water retention was obtained from tensiometer/MPS and TDR data in depths representing same soil horizons. For comparison, we used drying retention data obtained from soil cores using the evaporation method (Hyprop). Drying data were fitted to the unconstrained water retention function proposed by van Genuchten (1980) and the bimodal model of Durner (1994). For wetting data, hydraulic model parameters were determined by using the Pedroso-Williams model (2010). The water contents of wetting and drying branches were dynamically changing. These changes in water retention were different for several horizons of the more eroded Luvisol as compared to the less eroded one. Differences in water retention dynamics could be related to soil tillage and the erosion history at the different slope positions. The water differences in retention could be explained by hysteresis and temporal changes in soil water repellency. Field and lab retention data differed as reported earlier. The results suggest that estimation of soil water retention curves without resorting to time-consuming field measurements remains challenging. The results suggest that for erosion-affected arable soils of the hummocky

  10. 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.

  11. Shock compression of organic polymers and proteins: Ultrafast structural relaxation dynamics and energy landscapes

    SciTech Connect

    Kim, H.; Hambir, S.A.; Dlott, D.D.

    2000-05-04

    The response of organic polymers and proteins including poly(methyl methacrylate) and the protein bovine serum albumin (BSA) to a short duration 4.5 GPa shock pulse, termed a nanoshock, is studied using ultrafast coherent Raman spectroscopy (CARS) to monitor density-dependent vibrational frequency shifts of a dye molecule probe. In conventional shock compression experiments, a two-part response of PMMA to fast compression is usually explained with a phenomenological viscoelastic model. The molecular basis for this two-part response is discussed here using an energy landscape model to describe large-amplitude structural relaxation of shocked supercooled liquids. The polymers and the protein show an instantaneous response to the steeply rising shock front, viewed as a vertical transition to a new region of the energy landscape with radically different topography. A slower {approximately}300 ps response is also observed, attributed to large-amplitude structural relaxation along the rugged shocked energy landscape. A viscoelastic model is used to determine an effective shock viscosity {eta} {approx} 3 Pa{center_dot}s for the solid samples. This extremely small value (compared to {eta} > 10{sup 12} Pa{center_dot}s expected for supercooled liquids) is explained as a result of the very large strain rate and the extensive plastic deformation, which causes even seemingly rigid solids to flow. After the short duration ({approximately}2 ns) nanoshock unloads and the samples become frozen, for at least tens of nanoseconds, in a state where the dye vibrational shift indicates a negative pressure of about {minus}1 GPa. The negative pressure means the local density near the dye has decreased, the sample has become more permeable, and the sample is unstable to spontaneous expansion of the polymer chains. The energy landscape model provides a framework for understanding the fast cycle of compression and expansion and how to optimize the generation and detection of large

  12. Dynamic evolution study of wetland landscape pattern in urban Wuhan based on TM images

    NASA Astrophysics Data System (ADS)

    Kong, Chunfang; Xu, Kai; Wu, Chonglong; Deng, Hongbin; Zhang, Yi

    2007-11-01

    Based on analysis of the terrain maps, remote sensing images, statistic data of wetland of Wuhan urban from 1985 to 2005, and with the technology of Remote Sensing (abbr. RS) and Geographic Information System (abbr. GIS), the wetland landscape spatial database and attribute database of Wuhan urban are set up using ARCGIS software of the year of 1985, 1995 and 2005. At the same time, according to fractal geometry and landscape ecological methodology and the theories, we can quantitatively analyze the form characters, evolution rules, and change factors of the wetland landscape pattern of Wuhan urban by calculating its diversity index, dominance index, equality index, fragmentation index, isolation index and fractal dimension, and so on. As a result, the wetland's form characters and evolution process of Wuhan urban are compared and analyzed; its time-spatial evolution character during the past 20 years is demonstrated. In the end, some advice will be given that human beings should adjust land-use structure in lake districts, reasonably develop, recover and reconstruct positive eco-environment, and promote its sustainable development in Wuhan urban according to its ecological environment characteristics.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. Exact Adjustment of Dynamic Forces in Presence of Non-Linear Feedback and SINGULARITY—THEORY and Algorithm

    NASA Astrophysics Data System (ADS)

    Bucher, I.

    1998-11-01

    This paper describes the theory and algorithm allowing one to tune a multi-exciter system in order to obtain specified temporal and spatial structural response properties. Considerable effort is being put upon the desire to overcome practical difficulties and limitations as found in real-world systems. The main application that was envisaged for this algorithm is the creation of travelling vibration waves in structures. Such waves may be useful in testing and diagnostic applications or in ultrasonic motors for generating motion. The proposed method adaptively modifies a set of perturbations applied to the model so that an increasing amount of information is extracted from the system. The algorithm strives to overcome the following difficulties: (a) singular model inversion, (b) poor signal to noise ratio, (c) feedback, and (d) certain types of non-linear behaviour. High response levels, exciter-structure coupling and the inherent feedback existing in electro-mechanical systems are demonstrated to cause singularity, poor signal to noise levels and, to some extent, non linear behaviour. These phenomena pose some difficulties under operating conditions commonly encountered during dynamic testing of structures. The tuning of the multi-shaker system is approached in this work, as a non-linear optimisation problem where insight into the physical behaviour is emphasised in choosing the algorithmic strategy. The system's unknown model is inverted in an implicit manner using an automatic orthogonal and adaptive search direction. This adaptation uses the measured responses and forces at each step in order to determine the direction of progression during the tuning process. The non-linear behaviour of the exciters is compensated, in this work, by identification of the high-order (Volterra-like) transfer functions. This high-order model is than inverted allowing one to create a signal that cancels the unwanted harmonics. The proposed approach is analytically shown to converge

  18. Seagrass landscape-scale changes in response to disturbance created by the dynamics of barrier-islands: A case study from Ria Formosa (Southern Portugal)

    NASA Astrophysics Data System (ADS)

    Cunha, A. H.; Santos, R. P.; Gaspar, A. P.; Bairros, M. F.

    2005-09-01

    This study documents long-term changes of a Zostera noltii landscape induced by a natural cyclic event in a coastal lagoon. The barrier-islands forming this system are very dynamic with drifting movements controlling ecological patterns and processes occurring in this area. Changes in the areal extent of the Z. noltii meadows were assessed using historical aerial photographs from 1940, 1980, 1989, 1996 and 1998. Landscape indices such as total patch area (TA), mean patch size (MPS), number of patches (NP), mean shape coefficient of variation (CV) and landscape fractal dimension (D) were calculated for each year and related to an index of disturbance intensity. The spatial distribution of the Z. noltii meadows varied greatly during the studied period and changes observed were related to the disturbance created by the barrier-islands' spatial dynamics. After an artificial inlet relocation the Z. noltii area, number of patches, patch mean size and coefficient of variation decreased. The fractal dimension of the Z. noltii landscape increased by 50% showing that besides a decrease in total area, number of patches, and patch mean area, patch fragmentation was an important consequence of this anthropogenic disturbance. Seagrass natural distribution patterns changed in response to natural and human-induced activities. This study emphasizes the importance of the landscape approach and the historical perspective when studying seagrass changes and the importance of taking into consideration long-term changes in seagrass landscapes to avoid confusion between man-induced effects with natural cyclic events.

  19. 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

  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 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

  1. 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

  2. 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.

  3. 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

  4. Population dynamics of a generalist rodent in relation to variability in pulsed food resources in a fragmented landscape.

    PubMed

    Marcello, Gregg J; Wilder, Shawn M; Meikle, Douglas B

    2008-01-01

    1. Pulsed food resources are often considered equivalent in their potential impact on the reproduction and population dynamics of consumers, but differences in the attributes of food pulses and their distribution in the landscape may cause differences in their effects. 2. We tested whether a perishable pulsed resource (periodical cicadas, Magicicada spp.) had similar effects on the population dynamics of a generalist forest rodent, Peromyscus leucopus, as have been reported for a cacheable pulsed resource (acorn mast). 3. Because the availability of periodical cicadas may vary between edge and interior habitat, we also tested whether habitat type (edge vs. interior) and fragment size affected the abundance of cicadas and P. leucopus. 4. Nearly 90% of the variation in the relative population densities of P. leucopus was explained by the variation in the relative densities of periodical cicadas, and fragments with more cicadas tended to have more reproductive female mice and litters. 5. We found more cicadas and more P. leucopus in edge than interior habitat, but no differences in the relative densities of either in relation to fragment size. 6. Data from a non-emergence year revealed no differences other than the presence of periodical cicadas that could explain the 50% higher relative densities of P. leucopus in the emergence year. 7. At the beginning of the emergence of periodical cicadas, the three fragments with the highest numbers of emergence holes had three times more mice than the fragments with the lowest numbers of emergence holes, suggesting that P. leucopus is able to anticipate the emergence of periodical cicadas and increase reproduction prior to the pulse. 8. Hence, despite differences in perishability, seasonal timing and nutritional quality of pulsed food resources in a fragmented landscape, they appear to have similar positive effects on the population dynamics of the generalist rodent, P. leucopus and, in fact, P. leucopus may be able to

  5. 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.

  6. A dynamic early East Antarctic Ice Sheet suggested by ice-covered fjord landscapes.

    PubMed

    Young, Duncan A; Wright, Andrew P; Roberts, Jason L; Warner, Roland C; Young, Neal W; Greenbaum, Jamin S; Schroeder, Dustin M; Holt, John W; Sugden, David E; Blankenship, Donald D; van Ommen, Tas D; Siegert, Martin J

    2011-06-02

    The first Cenozoic ice sheets initiated in Antarctica from the Gamburtsev Subglacial Mountains and other highlands as a result of rapid global cooling ∼34 million years ago. In the subsequent 20 million years, at a time of declining atmospheric carbon dioxide concentrations and an evolving Antarctic circumpolar current, sedimentary sequence interpretation and numerical modelling suggest that cyclical periods of ice-sheet expansion to the continental margin, followed by retreat to the subglacial highlands, occurred up to thirty times. These fluctuations were paced by orbital changes and were a major influence on global sea levels. Ice-sheet models show that the nature of such oscillations is critically dependent on the pattern and extent of Antarctic topographic lowlands. Here we show that the basal topography of the Aurora Subglacial Basin of East Antarctica, at present overlain by 2-4.5 km of ice, is characterized by a series of well-defined topographic channels within a mountain block landscape. The identification of this fjord landscape, based on new data from ice-penetrating radar, provides an improved understanding of the topography of the Aurora Subglacial Basin and its surroundings, and reveals a complex surface sculpted by a succession of ice-sheet configurations substantially different from today's. At different stages during its fluctuations, the edge of the East Antarctic Ice Sheet lay pinned along the margins of the Aurora Subglacial Basin, the upland boundaries of which are currently above sea level and the deepest parts of which are more than 1 km below sea level. Although the timing of the channel incision remains uncertain, our results suggest that the fjord landscape was carved by at least two iceflow regimes of different scales and directions, each of which would have over-deepened existing topographic depressions, reversing valley floor slopes.

  7. 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

  8. 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

  9. Spatial dynamics of the invasive defoliator amber-marked birch leafminer across the Anchorage landscape.

    PubMed

    Lundquist, J E; Reich, R M; Tuffly, M

    2012-10-01

    The amber-marked birch leafminer (Profenusa thomsoni [Konow]) (Hymenoptera: Tenthredinidae) has caused severe infestations of birch species in Anchorage, AK, since 2002. Its spatial distribution has been monitored since 2006 and summarized using interpolated surfaces based on simple kriging. Results indicate that this insect pest is unevenly distributed, occurring in multineighborhood sized patches that migrate from year to year. Patches showing heavy infestation one year are followed by light infestations the following year. In this study, we developed methods of assessing and describing spatial distributions of P. thomsoni as they vary from year to year, and speculate on potential causes of these trends in landscape patterns.

  10. Ancient landforms in dynamic landscapes: Inheritance, transience and congruence in Earth-surface systems

    NASA Astrophysics Data System (ADS)

    Gunnell, Yanni

    2015-03-01

    This special issue of Geomorphology offers a range of research papers presented at the International Association of Geomorphologists' 8th International Conference, held at the Cité des Sciences et de l'Industrie, in Paris (France), from August 27th to August 31st, 2013. All of the research published here was presented in Session S08 on "Geomorphic processes and long-term landscape evolution". The volume contains contributions by 34 authors from 9 different countries, covering study areas on four continents.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. Navigating membrane protein structure, dynamics, and energy landscapes using spin labeling and EPR spectroscopy

    PubMed Central

    Claxton, Derek P; Kazmier, Kelli; Mishra, Smriti; Mchaourab, Hassane S

    2017-01-01

    A detailed understanding of the functional mechanism of a protein entails the characterization of its energy landscape. Achieving this ambitious goal requires the integration of multiple approaches including determination of high resolution crystal structures, uncovering conformational sampling under distinct biochemical conditions, characterizing the kinetics and thermodynamics of transitions between functional intermediates using spectroscopic techniques, and interpreting and harmonizing the data into novel computational models. With increasing sophistication in solution-based and ensemble-oriented biophysical approaches such as electron paramagnetic resonance (EPR) spectroscopy, atomic resolution structural information can be directly linked to conformational sampling in solution. Here, we detail how recent methodological and technological advances in EPR spectroscopy have contributed to the elucidation of membrane protein mechanisms. Furthermore, we aim to assist investigators interested in pursuing EPR studies by providing an introduction to the technique, a primer on experimental design, and a description of the practical considerations of the method towards generating high quality data. PMID:26477257

  17. 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.

  18. 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 ...

  19. 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...

  20. 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

  1. Energy landscapes of dynamic ensembles of rolling triplet repeat bulge loops: implications for DNA expansion associated with disease states.

    PubMed

    Völker, Jens; Gindikin, Vera; Klump, Horst H; Plum, G Eric; Breslauer, Kenneth J

    2012-04-04

    DNA repeat domains can form ensembles of canonical and noncanonical states, including stable and metastable DNA secondary structures. Such sequence-induced structural diversity creates complex conformational landscapes for DNA processing pathways, including those triplet expansion events that accompany replication, recombination, and/or repair. Here we demonstrate further levels of conformational complexity within repeat domains. Specifically, we show that bulge loop structures within an extended repeat domain can form dynamic ensembles containing a distribution of loop positions, thereby yielding families of positional loop isomers, which we designate as "rollamers". Our fluorescence, absorbance, and calorimetric data are consistent with loop migration/translocation between sites within the repeat domain ("rollamerization"). We demonstrate that such "rollameric" migration of bulge loops within repeat sequences can invade and disrupt previously formed base-paired domains via an isoenthalpic, entropy-driven process. We further demonstrate that destabilizing abasic lesions alter the loop distributions so as to favor "rollamers" with the lesion positioned at the duplex/loop junction, sites where the flexibility of the abasic "universal hinge" relaxes unfavorable interactions and/or facilitates topological accommodation. Another strategic siting of an abasic site induces directed loop migration toward denaturing domains, a phenomenon that merges destabilizing domains. In the aggregate, our data reveal that dynamic ensembles within repeat domains profoundly impact the overall energetics of such DNA constructs as well as the distribution of states by which they denature/renature. These static and dynamic influences within triplet repeat domains expand the conformational space available for selection and targeting by the DNA processing machinery. We propose that such dynamic ensembles and their associated impact on DNA properties influence pathways that lead to DNA

  2. 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

  3. 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

  4. 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.

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

    PubMed Central

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

    2016-01-01

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

  6. Laser probes of the potential energy landscapes and conformational isomerization dynamics of flexible biomolecules

    NASA Astrophysics Data System (ADS)

    Dian, Brian; Clarkson, Jasper; Zwier, Timothy

    2003-03-01

    Using a combination of 2-color resonant two-photon ionization (R2PI), laser-induced fluorescence excitation (LIF), resonant ion-dip infrared spectroscopy (RIDIRS), fluorescence-dip infrared spectroscopy (FDIRS), and UV-UV hole-burning spectroscopy, the conformational preferences of a series of flexible biomolecules, including melatonin, N-acetyl-tryptophan methyl amide (NATMA), and their close analogs, have been determined in a molecular beam. These molecules are sufficiently complex to have hundreds of conformational minima, yet small enough that their potential energy landscapes can be explored in some detail. Once the conformational preferences of the molecules are established, these molecules are then studied using infrared-ultraviolet hole-filling and IR-induced population transfer spectroscopy. These methods utilize selective infrared excitation of single conformations of the molecule in the early portions of a gas-phase expansion, followed by collisional re-cooling of the excited population into its conformational minima for subsequent conformation-specific detection. Efficient isomerization is induced by the infrared excitation that redistributes population between the same conformations that have population in the absence of infrared excitation. Examples will be given in which the quantum yields for transfer of the population into the various conformational minima depend both on which conformation is excited and on which hydride stretch vibration is excited within a given conformation; that is, they are both conformation-selective and mode-selective.

  7. 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.

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

    PubMed

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

    2016-05-03

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

    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.

  10. Interplay between dynamic topography and flexure along the U.S. Atlantic passive margin: Insights from landscape evolution modeling

    NASA Astrophysics Data System (ADS)

    Moucha, Robert; Ruetenik, Gregory A.

    2017-02-01

    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 (Moucha et al., 2008; Spasojević et al., 2008; Rowley et al., 2013; Rovere et al., 2015). However, reconciling these geodynamic models with the observed offshore sedimentary record directly is complex because the sedimentary record integrates changes in climate, sea level, lithology, and tectonics. To circumvent this, we instead focus on modeling the observed deformation of the Orangeburg scarp, a well-documented 3.5 million year old mid-Pliocene shoreline (e.g. Rovere et al., 2015). Herein, we present results from a new landscape evolution model and demonstrate that flexural effects along this margin are comparable to changes in dynamic topography (Rowley et al., 2013) and are required to fully explain deformation of the Orangeburg scarp. Moreover, using the Orangeburg scarp as a datum subject to glacial isostatic adjustment, we demonstrate that a 15 m mid-Pliocene sea level above present-day is most consistent with interspersed coastal plain sediment and surface deformation derived from mantle convection and flexural-isostasy.

  11. 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.

  12. 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.

  13. The chromatin landscape of the moss Physcomitrella patens and its dynamics during development and drought stress.

    PubMed

    Widiez, Thomas; Symeonidi, Aikaterini; Luo, Chongyuan; Lam, Eric; Lawton, Michael; Rensing, Stefan A

    2014-07-01

    The moss Physcomitrella patens is an important model organism for evo-devo studies. Here, we determined the genome-wide chromatin landscape of five important histone three (H3) modifications (H3K4me3, H3K27me3, H3K27Ac, H3K9Ac and H3K9me2) and describe the changes to these histone marks in two contrasted situations, developmental transition and abiotic (drought) stress. Integrative analysis of these histone H3 modifications revealed their preferential association into 15 chromatin states (CS) in genic regions of the P. patens genome. Synergistic relationships that influence expression levels were revealed for the three activating marks H3K4me3, H3K27Ac and H3K9Ac, while an antagonistic relationship was found between CS containing the H3K27me3 and H3K27Ac marks, suggesting that H3K27 is a key indexing residue regarding transcriptional output. Concerning the alteration of histone marks in response to developmental transition (juvenile to adult) and drought stress, the three activating marks H3K4me3, H3K27Ac and H3K9Ac show significant changes in both situations. However, changes to H3K27me3 are central only for genes differentially expressed during development. Interestingly, genes induced during drought stress show significant histone mark toggling during developmental transition. This situation suggests that drought induced adult (gametophore expressed) genes are primed to respond to this stress during the juvenile to adult transition.

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

    PubMed

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

    2014-08-28

    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.

  15. 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

  16. Exploring water cycle dynamics by sampling multiple stable water isotope pools in a developed landscape in Germany

    NASA Astrophysics Data System (ADS)

    Orlowski, Natalie; Kraft, Philipp; Pferdmenges, Jakob; Breuer, Lutz

    2016-09-01

    A dual stable water isotope (δ2H and δ18O) study was conducted in the developed (managed) landscape of the Schwingbach catchment (Germany). The 2-year weekly to biweekly measurements of precipitation, stream, and groundwater isotopes revealed that surface and groundwater are isotopically disconnected from the annual precipitation cycle but showed bidirectional interactions between each other. Apparently, snowmelt played a fundamental role for groundwater recharge explaining the observed differences to precipitation δ values. A spatially distributed snapshot sampling of soil water isotopes at two soil depths at 52 sampling points across different land uses (arable land, forest, and grassland) revealed that topsoil isotopic signatures were similar to the precipitation input signal. Preferential water flow paths occurred under forested soils, explaining the isotopic similarities between top- and subsoil isotopic signatures. Due to human-impacted agricultural land use (tilling and compression) of arable and grassland soils, water delivery to the deeper soil layers was reduced, resulting in significant different isotopic signatures. However, the land use influence became less pronounced with depth and soil water approached groundwater δ values. Seasonally tracing stable water isotopes through soil profiles showed that the influence of new percolating soil water decreased with depth as no remarkable seasonality in soil isotopic signatures was obvious at depths > 0.9 m and constant values were observed through space and time. Since classic isotope evaluation methods such as transfer-function-based mean transit time calculations did not provide a good fit between the observed and calculated data, we established a hydrological model to estimate spatially distributed groundwater ages and flow directions within the Vollnkirchener Bach subcatchment. Our model revealed that complex age dynamics exist within the subcatchment and that much of the runoff must has been stored

  17. 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

  18. 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

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

    DOE PAGES

    Keedy, Daniel A.; Kenner, Lillian R.; Warkentin, Matthew; ...

    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

  20. 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

  1. 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.

  2. Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis.

    PubMed

    Nepal, Chirag; Hadzhiev, Yavor; Previti, Christopher; Haberle, Vanja; Li, Nan; Takahashi, Hazuki; Suzuki, Ana Maria M; Sheng, Ying; Abdelhamid, Rehab F; Anand, Santosh; Gehrig, Jochen; Akalin, Altuna; Kockx, Christel E M; van der Sloot, Antoine A J; van Ijcken, Wilfred F J; Armant, Olivier; Rastegar, Sepand; Watson, Craig; Strähle, Uwe; Stupka, Elia; Carninci, Piero; Lenhard, Boris; Müller, Ferenc

    2013-11-01

    Spatiotemporal control of gene expression is central to animal development. Core promoters represent a previously unanticipated regulatory level by interacting with cis-regulatory elements and transcription initiation in different physiological and developmental contexts. Here, we provide a first and comprehensive description of the core promoter repertoire and its dynamic use during the development of a vertebrate embryo. By using cap analysis of gene expression (CAGE), we mapped transcription initiation events at single nucleotide resolution across 12 stages of zebrafish development. These CAGE-based transcriptome maps reveal genome-wide rules of core promoter usage, structure, and dynamics, key to understanding the control of gene regulation during vertebrate ontogeny. They revealed the existence of multiple classes of pervasive intra- and intergenic post-transcriptionally processed RNA products and their developmental dynamics. Among these RNAs, we report splice donor site-associated intronic RNA (sRNA) to be specific to genes of the splicing machinery. For the identification of conserved features, we compared the zebrafish data sets to the first CAGE promoter map of Tetraodon and the existing human CAGE data. We show that a number of features, such as promoter type, newly discovered promoter properties such as a specialized purine-rich initiator motif, as well as sRNAs and the genes in which they are detected, are conserved in mammalian and Tetraodon CAGE-defined promoter maps. The zebrafish developmental promoterome represents a powerful resource for studying developmental gene regulation and revealing promoter features shared across vertebrates.

  3. ExactPack Documentation

    SciTech Connect

    Singleton, Jr., Robert; Israel, Daniel M.; Doebling, Scott William; Woods, Charles Nathan; Kaul, Ann; Walter, Jr., John William; Rogers, Michael Lloyd

    2016-05-09

    For code verification, one compares the code output against known exact solutions. There are many standard test problems used in this capacity, such as the Noh and Sedov problems. ExactPack is a utility that integrates many of these exact solution codes into a common API (application program interface), and can be used as a stand-alone code or as a python package. ExactPack consists of python driver scripts that access a library of exact solutions written in Fortran or Python. The spatial profiles of the relevant physical quantities, such as the density, fluid velocity, sound speed, or internal energy, are returned at a time specified by the user. The solution profiles can be viewed and examined by a command line interface or a graphical user interface, and a number of analysis tools and unit tests are also provided. We have documented the physics of each problem in the solution library, and provided complete documentation on how to extend the library to include additional exact solutions. ExactPack’s code architecture makes it easy to extend the solution-code library to include additional exact solutions in a robust, reliable, and maintainable manner.

  4. Governance and management dynamics of landscape restoration at multiple scales: Learning from successful environmental managers in Sweden.

    PubMed

    Dawson, Lucas; Elbakidze, Marine; Angelstam, Per; Gordon, Johanna

    2017-03-14

    Due to a long history of intensive land and water use, habitat networks for biodiversity conservation are generally degraded in Sweden. Landscape restoration (LR) is an important strategy for achieving representative and functional green infrastructures. However, outcomes of LR efforts are poorly studied, particularly the dynamics of LR governance and management. We apply systems thinking methods to a series of LR case studies to analyse the causal structures underlying LR governance and management in Sweden. We show that these structures appear to comprise of an interlinked system of at least three sets of drivers and four core processes. This system exhibits many characteristics of a transformative change towards an integrated, adaptive approach to governance and management. Key challenges for Swedish LR projects relate to institutional and regulatory flexibility, the timely availability of sufficient funds, and the management of learning and knowledge production processes. In response, successful project leaders develop several key strategies to manage complexity and risk, and enhance perceptions of the attractiveness of LR projects.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Inferring changes in water cycle dynamics of intensively managed landscapes via the theory of time-variant travel time distributions

    NASA Astrophysics Data System (ADS)

    Danesh-Yazdi, Mohammad; Foufoula-Georgiou, Efi; Karwan, Diana L.; Botter, Gianluca

    2016-10-01

    Climatic trends and anthropogenic changes in land cover and land use are impacting the hydrology and water quality of streams at the field, watershed, and regional scales in complex ways. In poorly drained agricultural landscapes, subsurface drainage systems have been successful in increasing crop productivity by removing excess soil moisture. However, their hydroecological consequences are still debated in view of the observed increased concentrations of nitrate, phosphorus, and pesticides in many streams, as well as altered runoff volumes and timing. In this study, we employ the recently developed theory of time-variant travel time distributions within the StorAge Selection function framework to quantify changes in water cycle dynamics resulting from the combined climate and land use changes. Our results from analysis of a subbasin in the Minnesota River Basin indicate a significant decrease in the mean travel time of water in the shallow subsurface layer during the growing season under current conditions compared to the pre-1970s conditions. We also find highly damped year-to-year fluctuations in the mean travel time, which we attribute to the "homogenization" of the hydrologic response due to artificial drainage. The dependence of the mean travel time on the spatial heterogeneity of some soil characteristics as well as on the basin scale is further explored via numerical experiments. Simulations indicate that the mean travel time is independent of scale for spatial scales larger than approximately 200 km2, suggesting that hydrologic data from larger basins may be used to infer the average of smaller-scale-driven changes in water cycle dynamics.

  13. 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.

  14. 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.

  15. 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.

  16. The Roles of Groundwater Flowpaths and Stream Network Expansion in Landscape Connectivity and Resulting Runoff and Solute Dynamics in an Ephemeral Piedmont Catchment

    NASA Astrophysics Data System (ADS)

    Zimmer, M. A.; McGlynn, B. L.

    2014-12-01

    Much catchment hydrology has been conducted in steep, perennial stream watersheds with shallow soil. In contrast, we investigated an ephemeral stream watershed with deep, highly weathered soils, gentle relief, and the dynamic hydro-climatology of the Piedmont region of the United States. We seek to gain new understanding about increasingly recognized challenges in the hydrological sciences, including influences of shallow and deep flowpath connectivity and the role of ephemeral streams in hydrologically connecting distal portions of landscapes. We investigated how overland, shallow soil, and deep subsurface flow across landscape positions and antecedent conditions manifest in observed baseflow and stormflow generation and the dynamics of dissolved organic carbon, electrical conductivity, and a suite of cations and anions. Extensive channel expansion and contraction coupled with spatially and temporally variable shallow and deep groundwater flowpaths led to both clockwise and counter-clockwise hysteresis in the relationship between runoff and solute concentrations as a function of antecedent moisture conditions. This suggests that vertical and horizontal hillslope connectivity to the aquatic system is variable across seasons and storms and influences biogeochemical expression at the watershed scale. Our research in Duke Forest, North Carolina has begun to elucidate the interrelationships between the space-time dynamics of runoff generation processes and observed biogeochemical behavior in this deeply weathered, low relief landscape, to provide new insight into processes widely active but less easily identified and quantified elsewhere.

  17. Linking the terrestrial and aquatic system across scales: The role of connectivity, landscape organization and catchment size for the dynamics of DOC

    NASA Astrophysics Data System (ADS)

    Laudon, Hjalmar

    2014-05-01

    While the production and export of DOC - dissolved organic carbon - from the terrestrial landscape has been extensively studied during the past decades, mechanistic understanding of processes that control stream water quality at the soil/water interface, across different spatial scales, are still at its infancy. To improve the process description of DOC regulation, I use data and understanding from three decades of research that has been conducted within the interdisciplinary, multi-scale Krycklan Catchment Study (KCS) in northern Sweden (www.slu.se/Krycklan). KCS consists of 17 intensively long-term monitored catchments ranging over three orders of magnitude in size, from 3 ha to over 6780 ha, to elucidate the dominate hydrobiogeophysical processes regulating the concentration and export of nutrients, metals and organic pollutants. By combining the use of detailed catchment information with natural isotopes and the dynamics of stream biogeochemistry we can directly link variability in hydrological flow pathways, catchment characteristics and scale with the spatial and temporal dynamics of DOC. Our results suggest that the contrasting spatial variability in the flow pathways among the different landscape types has a first order control on the DOC. As a result, large variations in the dynamics of DOC and its quality are observed that varies with changes in hydrological connectivity, landscape organization and catchment size.

  18. Quasispecies on Fitness Landscapes.

    PubMed

    Schuster, Peter

    2016-01-01

    Selection-mutation dynamics is studied as adaptation and neutral drift on abstract fitness landscapes. Various models of fitness landscapes are introduced and analyzed with respect to the stationary mutant distributions adopted by populations upon them. The concept of quasispecies is introduced, and the error threshold phenomenon is analyzed. Complex fitness landscapes with large scatter of fitness values are shown to sustain error thresholds. The phenomenological theory of the quasispecies introduced in 1971 by Eigen is compared to approximation-free numerical computations. The concept of strong quasispecies understood as mutant distributions, which are especially stable against changes in mutations rates, is presented. The role of fitness neutral genotypes in quasispecies is discussed.

  19. Population dynamics of hispid cotton rats (Sigmodon hispidus) across a nitrogen-amended landscape

    USGS Publications Warehouse

    Clark, J.E.; Hellgren, E.C.; Jorgensen, E.E.; Tunnell, S.J.; Engle, David M.; Leslie, David M.

    2003-01-01

    We conducted a mark-recapture experiment to examine the population dynamics of hispid cotton rats (Sigmodon hispidus) in response to low-level nitrogen amendments (16.4 kg nitrogen/ha per year) and exclosure fencing in an old-field grassland. The experimental design consisted of sixteen 0.16-ha plots with 4 replicates of each treatment combination. We predicted that densities, reproductive success, movement probabilities, and survival rates of cotton rats would be greater on nitrogen-amended plots because of greater aboveground biomass and canopy cover. Population densities of cotton rats tended to be highest on fenced nitrogen plots, but densities on unfenced nitrogen plots were similar to those on control and fenced plots. We observed no distinct patterns in survival rates, reproductive success, or movement probabilities with regard to nitrogen treatments. However, survival rates and reproductive success tended to be higher for cotton rats on fenced plots than for those on unfenced plots and this was likely attributable to decreased predation on fenced plots. As low-level nitrogen amendments continue to be applied, we predict that survival, reproduction, and population-growth rates of cotton rats on control plots, especially fenced plots with no nitrogen amendment, will eventually exceed those on nitrogen-amended plots as a result of higher plant-species diversity, greater food availability, and better quality cover.

  20. 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.

  1. 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

  2. Effect of environment and fallow period on Cosmopolites sordidus population dynamics at the landscape scale.

    PubMed

    Duyck, P-F; Dortel, E; Vinatier, F; Gaujoux, E; Carval, D; Tixier, P

    2012-10-01

    Understanding how the population dynamics of insect pests are affected by environmental factors and agricultural practices is important for pest management. To investigate how the abundance of the banana weevil, Cosmopolites sordidus (Coleoptera: Curculionidae), is related to environmental factors and the length of the fallow period in Martinique, we developed an extensive data set (18,130 observations of weevil abundance obtained with pheromone traps plus associated environmental data) and analysed it with generalized mixed-effects models. At the island scale, C. sordidus abundance was positively related to mean temperature and negatively related to mean rainfall but was not related to soil type. The number of insects trapped was highest during the driest months of the year. Abundance of C. sordidus decreased as the duration of the preceding fallow period increased. The latter finding is inconsistent with the view that fallow-generated decomposing banana tissue is an important resource for larvae that leads to an increase in the pest population. The results are consistent with the view that fallows, in association with pheromone traps, are effective for the control of the banana weevil.

  3. Dispersal and life history strategies in epiphyte metacommunities: alternative solutions to survival in patchy, dynamic landscapes.

    PubMed

    Löbel, Swantje; Rydin, Håkan

    2009-09-01

    Host trees for obligate epiphytes are dynamic patches that emerge, grow and fall, and metacommunity diversity critically depends on efficient dispersal. Even though species that disperse by large asexual diaspores are strongly dispersal limited, asexual dispersal is common. The stronger dispersal limitation of asexually reproducing species compared to species reproducing sexually via small spores may be compensated by higher growth rates, lower sensitivity to habitat conditions, higher competitive ability or younger reproductive age. We compared growth and reproduction of different groups of epiphytic bryophytes with contrasting dispersal (asexual vs. sexual) and life history strategies (colonists, short- and long-lived shuttle species, perennial stayers) in an old-growth forest stand in the boreo-nemoral region in eastern Sweden. No differences were seen in relative growth rates between asexual and sexual species. Long-lived shuttles had lower growth rates than colonists and perennial stayers. Most groups grew best at intermediate bark pH. Interactions with other epiphytes had a small, often positive effect on growth. Neither differences in sensitivity of growth to habitat conditions nor differences in competitive abilities among species groups were found. Habitat conditions, however, influenced the production of sporophytes, but not of asexual diaspores. Presence of sporophytes negatively affected growth, whereas presence of asexual diaspores did not. Sexual species had to reach a certain colony size before starting to reproduce, whereas no such threshold existed for asexual reproduction. The results indicate that the epiphyte metacommunity is structured by two main trade-offs: dispersal distance vs. reproductive age, and dispersal distance vs. sensitivity to habitat quality. There seems to be a trade-off between growth and sexual reproduction, but not asexual. Trade-offs in species traits may be shaped by conflicting selection pressures imposed by habitat

  4. Urban expansion dynamics and natural habitat loss in China: a multiscale landscape perspective.

    PubMed

    He, Chunyang; Liu, Zhifeng; Tian, Jie; Ma, Qun

    2014-09-01

    China's extensive urbanization has resulted in a massive loss of natural habitat, which is threatening the nation's biodiversity and socioeconomic sustainability. A timely and accurate understanding of natural habitat loss caused by urban expansion will allow more informed and effective measures to be taken for the conservation of biodiversity. However, the impact of urban expansion on natural habitats is not well-understood, primarily due to the lack of accurate spatial information regarding urban expansion across China. In this study, we proposed an approach that can be used to accurately summarize the dynamics of urban expansion in China over two recent decades (1992-2012), by integrating data on nighttime light levels, a vegetation index, and land surface temperature. The natural habitat loss during the time period was evaluated at the national, ecoregional, and local scales. The results revealed that China had experienced extremely rapid urban growth from 1992 to 2012 with an average annual growth rate of 8.74%, in contrast with the global average of 3.20%. The massive urban expansion has resulted in significant natural habitat loss in some areas in China. Special attention needs to be paid to the Pearl River Delta, where 25.79% or 1518 km(2) of the natural habitat and 41.99% or 760 km(2) of the local wetlands were lost during 1992-2012. This raises serious concerns about species viability and biodiversity. Effective policies and regulations must be implemented and enforced to sustain regional and national development in the context of rapid urbanization.

  5. 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

  6. 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.

  7. 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

  8. 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.

  9. Adaptation dynamics of the quasispecies model

    NASA Astrophysics Data System (ADS)

    Jain, Kavita

    2009-02-01

    We study the adaptation dynamics of an initially maladapted population evolving via the elementary processes of mutation and selection. The evolution occurs on rugged fitness landscapes which are defined on the multi-dimensional genotypic space and have many local peaks separated by low fitness valleys. We mainly focus on the Eigen's model that describes the deterministic dynamics of an infinite number of self-replicating molecules. In the stationary state, for small mutation rates such a population forms a {\\it quasispecies} which consists of the fittest genotype and its closely related mutants. The quasispecies dynamics on rugged fitness landscape follow a punctuated (or step-like) pattern in which a population jumps from a low fitness peak to a higher one, stays there for a considerable time before shifting the peak again and eventually reaches the global maximum of the fitness landscape. We calculate exactly several properties of this dynamical process within a simplified version of the quasispecies model.

  10. Vegetation and landscape dynamics under natural and anthropogenic forcing on the Azores Islands: A 700-year pollen record from the São Miguel Island

    NASA Astrophysics Data System (ADS)

    Rull, Valentí; Lara, Arantza; Rubio-Inglés, María Jesús; Giralt, Santiago; Gonçalves, Vítor; Raposeiro, Pedro; Hernández, Armand; Sánchez-López, Guiomar; Vázquez-Loureiro, David; Bao, Roberto; Masqué, Pere; Sáez, Alberto

    2017-03-01

    The Azores archipelago has provided significant clues to the ecological, biogeographic and evolutionary knowledge of oceanic islands. Palaeoecological records are comparatively scarce, but they can provide relevant information on these subjects. We report the palynological reconstruction of the vegetation and landscape dynamics of the São Miguel Island before and after human settlement using the sediments of Lake Azul. The landscape was dominated by dense laurisilvas of Juniperus brevifolia and Morella faya from ca. 1280 CE to the official European establishment (1449 CE). After this date, the original forests were replaced by a complex of Erica azorica/Myrsine africana forests/shrublands and grassy meadows, which remained until ca. 1800 CE. Extractive forestry, cereal cultivation (rye, maize, wheat) and animal husbandry progressed until another extensive deforestation (ca. 1774 CE), followed by the large-scale introduction (1845 CE) of the exotic forest species Cryptomeria japonica and Pinus pinaster, which shaped the present-day landscape. Fire was a significant driver in these vegetation changes. The lake levels experienced a progressive rise during the time interval studied, reaching a maximum by ca. 1778-1852 CE, followed by a hydrological decline likely due to a combination of climatic and anthropogenic drivers. Our pollen record suggests that São Miguel were already settled by humans by ca. 1287 CE, approximately one century and a half prior to the official historically documented occupation of the archipelago. The results of this study are compared with the few palynological records available from other Azores islands (Pico and Flores).

  11. 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.

  12. 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

  13. Bioregionalism in the Heartland: Exploring Broad-Scale, Bioregional Dynamics of Place and Landscapes in the Western Great Lakes

    ERIC Educational Resources Information Center

    Eanes, Francis R.

    2016-01-01

    How can researchers and practitioners meaningfully engage the public in matters of environmental stewardship and landscape conservation? Traditional approaches to answering this question have erroneously relied upon the assumption that the simple combination of knowledge and awareness of environmental challenges will motivate desirable behavior…

  14. LanDPro: Landscape Dynamics Program in Support of Natural and Cultural Resources Management and Range Maintenance

    DTIC Science & Technology

    2008-12-01

    Mediterranean Division, California Coastal Chaparral Province 322 – Tropical-Subtropical Desert Division, American Semi-Desert Province 341 – Temperate...areas: natural resources, cultural resources, and range management. 1. INTRODUCTION Successful military training to meet readiness and...Recent DRI research in the southern California coastal region has identified discrete landscape responses to apparent climate change events

  15. 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. ...

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

    NASA Astrophysics Data System (ADS)

    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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Landscape dynamics assessment of dry climatic zones on the Baikal-Gobi transect from NDVI time series and field investigations data

    NASA Astrophysics Data System (ADS)

    Sayapina, D. O.; Zharnikova, M. A.; Tsydypov, B. Z.; Sodnomov, B. V.; Garmaev, E. Zh

    2016-11-01

    Starting in the eighties of the 20th century, the scientists of the Baikal Institute of Nature Management (BINM SB RAS) have been conducting field observations of the Transbaikalia geosystems transformation due to the change of climate and nature management. An utmost importance is placed on the study of a negative response of the land geosystems. This is shown through their deterioration, degradation, and desertification in particular. Through the years of research (1985-2015) in dry areas of the north of Central Asia, the scientists of the BINM SB RAS established a network of key sites for contact monitoring of the status and dynamics of the geosystems and the negative natural-anthropogenic processes along the Baikal-Gobi meridional transect (51-44° N, 105-107° E). The monitoring of the status and dynamics of the vegetation cover of some key sites is conducted by processing and analysis of multitemporal and multispectral Landsat and MODIS Terra imagery. An automatic analysis of the time variation of NDVI and a comparison with the progress of the index in the previous seasons are performed. The landscape indication of the key sites is made on the basis of satellite imagery and complete geobotanical descriptions. Landscape profiles and facies maps with natural boundaries are created.

  2. 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.

  3. Relaxation dynamics of Sierpinski hexagon fractal polymer: Exact analytical results in the Rouse-type approach and numerical results in the Zimm-type approach

    NASA Astrophysics Data System (ADS)

    Jurjiu, Aurel; Galiceanu, Mircea; Farcasanu, Alexandru; Chiriac, Liviu; Turcu, Flaviu

    2016-12-01

    In this paper, we focus on the relaxation dynamics of Sierpinski hexagon fractal polymer. The relaxation dynamics of this fractal polymer is investigated in the framework of the generalized Gaussian structure model using both Rouse and Zimm approaches. In the Rouse-type approach, by performing real-space renormalization transformations, we determine analytically the complete eigenvalue spectrum of the connectivity matrix. Based on the eigenvalues obtained through iterative algebraic relations we calculate the averaged monomer displacement and the mechanical relaxation moduli (storage modulus and loss modulus). The evaluation of the dynamical properties in the Rouse-type approach reveals that they obey scaling in the intermediate time/frequency domain. In the Zimm-type approach, which includes the hydrodynamic interactions, the relaxation quantities do not show scaling. The theoretical findings with respect to scaling in the intermediate domain of the relaxation quantities are well supported by experimental results.

  4. 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

  5. Labyrinthine granular landscapes.

    PubMed

    Caps, H; Vandewalle, N

    2001-11-01

    We have numerically studied a model of granular landscape eroded by wind. We show the appearance of labyrinthic patterns when the wind orientation turns by 90 degrees. The occurrence of such structures is discussed. Moreover, we introduce the density n(k) of "defects" as the dynamic parameter governing the landscape evolution. A power-law behavior of n(k) is found as a function of time. In the case of wind variations, the exponent (drastically) shifts from two to one. The presence of two asymptotic values of n(k) implies the irreversibility of the labyrinthic formation process.

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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...

  12. Evolutionary trajectories in rugged fitness landscapes

    NASA Astrophysics Data System (ADS)

    Jain, Kavita; Krug, Joachim

    2005-04-01

    We consider the evolutionary trajectories traced out by an infinite population undergoing mutation-selection dynamics in static, uncorrelated random fitness landscapes. Starting from the population that consists of a single genotype, the most populated genotype jumps from one local fitness maximum to another and eventually reaches the global maximum. We use a strong selection limit, which reduces the dynamics beyond the first time step to the competition between independent mutant subpopulations, to study the dynamics of this model and of a simpler one-dimensional model which ignores the geometry of the sequence space. We find that the fit genotypes that appear along a trajectory are a subset of suitably defined fitness records, and exploit several results from the record theory for non-identically distributed random variables. The genotypes that contribute to the trajectory are those records that are not bypassed by superior records arising further away from the initial population. Several conjectures concerning the statistics of bypassing are extracted from numerical simulations. In particular, for the one-dimensional model, we propose a simple relation between the bypassing probability and the dynamic exponent which describes the scaling of the typical evolution time with genome size. The latter can be determined exactly in terms of the extremal properties of the fitness distribution.

  13. Exact solution of the robust knapsack problem☆

    PubMed Central

    Monaci, Michele; Pferschy, Ulrich; Serafini, Paolo

    2013-01-01

    We consider an uncertain variant of the knapsack problem in which the weight of the items is not exactly known in advance, but belongs to a given interval, and an upper bound is imposed on the number of items whose weight differs from the expected one. For this problem, we provide a dynamic programming algorithm and present techniques aimed at reducing its space and time complexities. Finally, we computationally compare the performances of the proposed algorithm with those of different exact algorithms presented so far in the literature for robust optimization problems. PMID:24187428

  14. 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…

  15. [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.

  16. 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.

  17. 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

  18. 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.

  19. Exact coherent structures for the turbulent cascade

    NASA Astrophysics Data System (ADS)

    Eckhardt, Bruno; Zammert, Stefan

    2016-11-01

    The exact coherent structures that are connected with the transition to turbulence in interior flows usually extend across the full height of the domain. Using exact coherent states that are localized in the shear direction together with scaling ideas for the Navier-Stokes equation that combine length and Reynolds number, we show how such large scale structures can be morphed into smaller scale coherent structures. As the Reynolds number increases, more of these states with ever smaller scales appear, all the way down to the Kolmogorov scale. We present the structure and dynamical properties of several families of exact coherent solution in plane Couette flow, with different degrees of spatial localization: Some of them remain localized in the center and help to built the turbulence cascade, others are localized near the walls and contribute to shaping the boundary layer profile.

  20. 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.

  1. 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.

  2. Informational landscapes in art, science, and evolution.

    PubMed

    Cohen, Irun R

    2006-07-01

    An informational landscape refers to an array of information related to a particular theme or function. The Internet is an example of an informational landscape designed by humans for purposes of communication. Once it exists, however, any informational landscape may be exploited to serve a new purpose. Listening Post is the name of a dynamic multimedia work of art that exploits the informational landscape of the Internet to produce a visual and auditory environment. Here, I use Listening Post as a prototypic example for considering the creative role of informational landscapes in the processes that beget evolution and science.

  3. Hiking Over Quantum Control Landscapes

    NASA Astrophysics Data System (ADS)

    Rabitz, Herschel

    2008-03-01

    Seeking the best control over a posed quantum dynamic objective entails climbing over the associated control landscape, which is defined as the quantum mechanical observable as a function of the controls. The topology and general structure of quantum control landscapes as input output maps dictate the final attainable yield, the efficiency of the search for an effective control, the possible existence of multiple dynamically equivalent controls, and the robustness of any viable control solution. Normal optimization problems in virtually any area of engineering and science typically have landscape topologies that remain a mystery. Quantum mechanics appears out to be quite special in that the topology of quantum control landscapes can be established generically based on minimal physical assumptions. Various features of these landscapes will be discussed and illustrated for circumstances where the controls are either an external field or the time independent portions of the Hamiltonian; the latter circumstance corresponds to subjecting the material or molecules to systematic variation and hence viewed in the context of being controls. Both theoretical and experimental findings on control landscapes and their consequences will be discussed, including issues of robustness to noise, search algorithm efficiency, existence of multiple control solutions, prospects for identifying reduced sets of control variables, simultaneous control of multiple quantum systems (optimal dynamic discrimination (ODD)), and mechanism analysis.

  4. Exact law of live nature

    NASA Astrophysics Data System (ADS)

    Azbel, Mark Ya.

    2005-07-01

    Exact law of mortality dynamics in changing populations and environment is derived. It includes no explicit characteristics of animal- environment interactions (metabolism etc) which are a must for life; it is universal for all animals, from single cell yeast to humans, with their drastically different biology, evolutionary history, and complexity; it is rapidly (within few percent of life span) reversible. Such law is unique for live systems with their homeostatic self-adjustment to environment (cf. thermodynamics of liquids and glasses). The law which is valid for all live, and only live, systems is their specific natural law. Mortality is an instrument of natural selection and biological diversity. Its law, which is preserved in evolution of all species, is a conservation law of mortality, selection, evolution, biology. The law implies new kind of intrinsic mortality and adaptation which dominate in evolutionary unprecedented protected populations and, in contrast to species specific natural selection, proceed via universal stepwise rungs and reduce to universal cellular mechanism. The law demonstrates that intrinsic mortality and at least certain aspects of aging are disposable evolutionary byproducts, and directed genetic and/or biological changes may yield healthy and vital Methuselah lifespan. This is consistent with experiments. Universality implies that single cell yeast may provide a master key to the cellular mechanism of universal mortality, aging, selection, evolution, and its regulation in all animals. One may look for its manifestations in animal cells also, e.g., in their replicative senescence and cancer. Evolutionary origin and genetic nature of universality are suggested.

  5. 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.

  6. 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

  7. 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

  8. 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

  9. Structures and free energy landscapes of the wild-type and A30P mutant-type α-synuclein proteins with dynamics.

    PubMed

    Wise-Scira, Olivia; Aloglu, Ahmet Kemal; Dunn, Aquila; Sakallioglu, Isin Tuna; Coskuner, Orkid

    2013-03-20

    The genetic missense A30P mutation of the wild-type α-synuclein protein results in the replacement of the 30th amino acid residue from alanine (Ala) to proline (Pro) and was initially found in the members of a German family who developed Parkinson's disease. Even though the structures of these proteins have been measured before, detailed understanding about the structures and their relationships with free energy landscapes is lacking, which is of interest to provide insights into the pathogenic mechanism of Parkinson's disease. We report the secondary and tertiary structures and conformational free energy landscapes of the wild-type and A30P mutant-type α-synuclein proteins in an aqueous solution environment via extensive parallel tempering molecular dynamics simulations along with thermodynamic calculations. In addition, we present the residual secondary structure component transition stabilities at the atomic level with dynamics in terms of free energy change calculations using a new strategy that we reported most recently. Our studies yield new interesting results; for instance, we find that the A30P mutation has local as well as long-range effects on the structural properties of the wild-type α-synuclein protein. The helical content at Ala18-Gly31 is less prominent in comparison to the wild-type α-synuclein protein. The β-sheet structure abundance decreases in the N-terminal region upon A30P mutation of the wild-type α-synuclein, whereas the NAC and C-terminal regions possess larger tendencies for β-sheet structure formation. Long-range intramolecular protein interactions are less abundant upon A30P mutation, especially between the NAC and C-terminal regions, which is linked to the less compact and less stable structures of the A30P mutant-type rather than the wild-type α-synuclein protein. Results including the usage of our new strategy for secondary structure transition stabilities show that the A30P mutant-type α-synuclein tendency toward

  10. 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

  11. 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

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

    DOE PAGES

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

    2014-09-17

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

  13. Organic Carbon Dynamics beyond the Perspective of Monitoring: Impact of Historical Landscape Utilization on the Past Lake-Water Carbon Trajectory in Central Boreal Sweden

    NASA Astrophysics Data System (ADS)

    Meyer-Jacob, C.; Tolu, J.; Bigler, C.; Bindler, R.

    2014-12-01

    To date, the key drivers behind the recent observed increase in organic carbon (OC) concentrations in surface waters are still controversial. The lack of long-term monitoring data - over centuries and millennia - leaves us with an ambiguous understanding of the past trajectory of OC concentrations in surface waters, and inhibits a better mechanistic understanding of past and a reliable prediction of future changes in OC levels.By using a paleolimnological approach, we reconstructed past lake-water total organic carbon (TOC) concentrations in lakes across the boreal landscape of central Sweden. Reconstructions are based on a transfer function between visible near-infrared spectra of surface sediments and the corresponding TOC concentration in the water column. Potential drivers behind changes in TOC were determined by a multi-proxy analysis of one of the studied lake sediment records including organic and inorganic geochemistry as well as biological proxies (pollen, diatoms).Our results show a significant decrease in lake-water TOC beginning already ~550 years ago. This decline continued until the mid-20th century when TOC concentrations started to increase again. These dynamics in TOC coincide with changes in proxies indicating catchment disturbance by human activities. The chronology of these changes corresponds to the expansion and decline of a landscape-wide system of summer forest grazing and farming in central Sweden from the 15th century to the turn of the 20th century. Frequent grazing and exploitation of forests and mires reduce aboveground vegetation and physically disturb soils. This further affects the carbon cycling by enhancing carbon turnover, reducing the thickness of organic soils and consequently altering the transport of OC from the catchment to lakes.Our findings suggest that recent changes in lake-water TOC in Sweden are strongly associated with historical patterns in land use and not only on-going changes in climate or sulfur deposition.

  14. 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.

  15. 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.

  16. What exactly do numbers mean?

    PubMed Central

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

    2014-01-01

    Number words are generally used to refer to the exact cardinal value of a set, but cognitive scientists disagree about their meanings. Although most psychological analyses presuppose that numbers have exact semantics (two means EXACTLY TWO), many linguistic accounts propose that numbers have lower-bounded semantics (AT LEAST TWO), and that speakers restrict their reference through a pragmatic inference (scalar implicature). We address this debate through studies of children who are in the process of acquiring the meanings of numbers. Adults and 2- and 3-year-olds were tested in a novel paradigm that teases apart semantic and pragmatic aspects of interpretation (the covered box task). Our findings establish that when scalar implicatures are cancelled in the critical trials of this task, both adults and children consistently give exact interpretations for number words. These results, in concert with recent work on real-time processing, provide the first unambiguous evidence that number words have exact semantics. PMID:25285053

  17. 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.

  18. 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 ...

  19. Exact Pressure Evolution Equation for Incompressible Fluids

    NASA Astrophysics Data System (ADS)

    Tessarotto, M.; Ellero, M.; Aslan, N.; Mond, M.; Nicolini, P.

    2008-12-01

    An important aspect of computational fluid dynamics is related to the determination of the fluid pressure in isothermal incompressible fluids. In particular this concerns the construction of an exact evolution equation for the fluid pressure which replaces the Poisson equation and yields an algorithm which is a Poisson solver, i.e., it permits to time-advance exactly the same fluid pressure without solving the Poisson equation. In fact, the incompressible Navier-Stokes equations represent a mixture of hyperbolic and elliptic pde's, which are extremely hard to study both analytically and numerically. This amounts to transform an elliptic type fluid equation into a suitable hyperbolic equation, a result which usually is reached only by means of an asymptotic formulation. Besides being a still unsolved mathematical problem, the issue is relevant for at least two reasons: a) the proliferation of numerical algorithms in computational fluid dynamics which reproduce the behavior of incompressible fluids only in an asymptotic sense (see below); b) the possible verification of conjectures involving the validity of appropriate equations of state for the fluid pressure. Another possible motivation is, of course, the ongoing quest for efficient numerical solution methods to be applied for the construction of the fluid fields {ρ,V,p}, solutions of the initial and boundary-value problem associated to the incompressible N-S equations (INSE). In this paper we intend to show that an exact solution to this problem can be achieved adopting the approach based on inverse kinetic theory (IKT) recently developed for incompressible fluids by Tessarotto et al. [7, 6, 7, 8, 9]. In particular we intend to prove that the evolution of the fluid fields can be achieved by means of a suitable dynamical system, to be identified with the so-called Navier-Stokes (N-S) dynamical system. As a consequence it is found that the fluid pressure obeys a well-defined evolution equation. The result appears

  20. Density-based clustering: A ‘landscape view’ of multi-channel neural data for inference and dynamic complexity analysis

    PubMed Central

    Gigante, Guido; Del Giudice, Paolo

    2017-01-01

    Two, partially interwoven, hot topics in the analysis and statistical modeling of neural data, are the development of efficient and informative representations of the time series derived from multiple neural recordings, and the extraction of information about the connectivity structure of the underlying neural network from the recorded neural activities. In the present paper we show that state-space clustering can provide an easy and effective option for reducing the dimensionality of multiple neural time series, that it can improve inference of synaptic couplings from neural activities, and that it can also allow the construction of a compact representation of the multi-dimensional dynamics, that easily lends itself to complexity measures. We apply a variant of the ‘mean-shift’ algorithm to perform state-space clustering, and validate it on an Hopfield network in the glassy phase, in which metastable states are largely uncorrelated from memories embedded in the synaptic matrix. In this context, we show that the neural states identified as clusters’ centroids offer a parsimonious parametrization of the synaptic matrix, which allows a significant improvement in inferring the synaptic couplings from the neural activities. Moving to the more realistic case of a multi-modular spiking network, with spike-frequency adaptation inducing history-dependent effects, we propose a procedure inspired by Boltzmann learning, but extending its domain of application, to learn inter-module synaptic couplings so that the spiking network reproduces a prescribed pattern of spatial correlations; we then illustrate, in the spiking network, how clustering is effective in extracting relevant features of the network’s state-space landscape. Finally, we show that the knowledge of the cluster structure allows casting the multi-dimensional neural dynamics in the form of a symbolic dynamics of transitions between clusters; as an illustration of the potential of such reduction, we define

  1. Exact law of live nature

    NASA Astrophysics Data System (ADS)

    Azbel‧, Mark Ya.

    2005-08-01

    The exact law of mortality dynamics in changing populations and environment is derived. It includes no explicit characteristics of animal-environment interactions (metabolism, etc.) which are a must for life; it is universal for all animals, from single-cell yeast to humans, with their drastically different biology, evolutionary history, and complexity; it is rapidly (within few percent of life span) reversible. Such a law is unique for live systems with their homeostatic self-adjustment to environment (cf. thermodynamics of liquids and glasses). The law which is valid for all live, and only live, systems is their specific natural law. Mortality is an instrument of natural selection and biological diversity. Its law, which is preserved in evolution of all species, is a conservation law of mortality, selection, evolution, biology. The law implies new kinds of intrinsic mortality and adaptation which dominate in evolutionary unprecedented protected populations and, in contrast to species-specific natural selection, proceed via universal stepwise rungs and reduce to universal cellular mechanism. The law demonstrates that intrinsic mortality and at least certain aspects of aging are disposable evolutionary byproducts, and directed genetic and/or biological changes may yield healthy and vital Methuselah lifespan. This is consistent with experiments. Universality implies that single-cell yeast may provide a master key to the cellular mechanism of universal mortality, aging, selection, evolution, and its regulation in all animals. One may look for its manifestations in animal cells also, e.g., in their replicative senescence and cancer. Evolutionary origin and genetic nature of universality are suggested.

  2. Dynamical Mueller's Ratchet: Population Size Dependence of Evolutionary Paths in Bacteria

    NASA Astrophysics Data System (ADS)

    Lorenz, Dirk; Park, Jeong-Man; Deem, Michael; Michael Deem Team

    2011-03-01

    Experimental evolution has recently enabled the complete quantitative description of small-dimensional fitness landscapes. Quasispecies theory allows the mathematical modeling of evolution on such a landscape. Typically, analytic solutions for these models are only exactly solvable for the case of an infinite population. Here we use a functional integral representation of population dynamics and solve it using the Schwinger Boson method. This allows us to compute the first-order correction to the average fitness for finite populations. We will use these results to explain the experimental observations of dynamics of evolution in finite populations.

  3. 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

  4. 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.

  5. Linking catchment structure to hydrologic function: Implications of catchment topography for patterns of landscape hydrologic connectivity and stream flow dynamics

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

    The relationship between catchment structure (topography and topology), stream network hydrologic connectivity, and runoff response remains poorly understood. Hillslope-riparian-stream (HRS) water table connectivity serves as the hydrologic linkage between a catchment’s uplands and the channel network and facilitates the transmission of water and solutes to streams. While there has been tremendous interest in the concept of hydrological connectivity to characterize catchments, there are relatively few studies that have quantified hydrologic connectivity at the stream network and catchment scales. Here, we examine how catchment topography influenced patterns of stream network HRS connectivity and resultant runoff dynamics across 11 nested headwater catchments in the Tenderfoot Creek Experimental Forest (TCEF), MT. This study extends the empirical findings of Jencso et al. (2009) who found a strong linear relationship (r2 = 0.92) between the upslope accumulated area (UAA) and annual duration of shallow ground water table connectivity observed across 24 HRS transects (146 groundwater recording wells) within the TCEF. We applied this relationship to the entire stream network to quantify the frequency distribution of stream network connectivity through time (as a function of UAA) and ascertain its relationship to catchment-scale runoff dynamics. Each catchment’s estimated connectivity duration curve (CDC) was highly related to its flow duration curve (FDC); albeit the rate of change of runoff with respect to stream network connectedness varied significantly across catchments. To ascertain potential reasons for these differences we compared the slope of each catchment’s CDC-FDC relationship (annual, peak, transition and baseflow periods) in multiple linear models against median values of common terrain indices and land cover-vegetation characteristics. Significant predictors (p<0.05) included the flow path distance to the creek (DFC), the flow path gradient to the

  6. "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.

  7. 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.

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

    PubMed

    Bello-Rivas, Juan M; Elber, Ron

    2016-03-05

    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.

  9. PESP Landscaping Initiative

    EPA Pesticide Factsheets

    Landscaping practices can positively or negatively affect local environments and human health. The Landscaping Initiative seeks to enhance benefits of landscaping while reducing need for pesticides, fertilizers, etc., by working with partners.

  10. 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

  11. 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

  12. 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.

  13. Landscape dynamics in Mediterranean oak forests under global change: understanding the role of anthropogenic and environmental drivers across forest types.

    PubMed

    Acácio, Vanda; Dias, Filipe S; Catry, Filipe X; Rocha, Marta; Moreira, Francisco

    2017-03-01

    The Mediterranean region is projected to be extremely vulnerable to global change, which will affect the distribution of typical forest types such as native oak forests. However, our understanding of Mediterranean oak forest responses to future conditions is still very limited by the lack of knowledge on oak forest dynamics and species-specific responses to multiple drivers. We compared the long-term (1966-2006) forest persistence and land cover change among evergreen (cork oak and holm oak) and deciduous oak forests and evaluated the importance of anthropogenic and environmental drivers on observed changes for Portugal. We used National Forest Inventories to quantify the changes in oak forests and explored the drivers of change using multinomial logistic regression analysis and an information theoretical approach. We found distinct trends among oak forest types, reflecting the differences in oak economic value, protection status and management schemes: cork oak forests were the most persistent (62%), changing mostly to pines and eucalypt; holm oak forests were less persistent (53.2%), changing mostly to agriculture; and deciduous oak forests were the least persistent (45.7%), changing mostly to shrublands. Drivers of change had distinct importance across oak forest types, but drivers from anthropogenic origin (wildfires, population density, and land accessibility) were always among the most important. Climatic extremes were also important predictors of oak forest changes, namely extreme temperatures for evergreen oak forests and deficit of precipitation for deciduous oak forests. Our results indicate that under increasing human pressure and forecasted climate change, evergreen oak forests will continue declining and deciduous oak forests will be replaced by forests dominated by more xeric species. In the long run, multiple disturbances may change competitive dominance from oak forests to pyrophytic shrublands. A better understanding of forest dynamics and the

  14. Metapopulation capacity of evolving fluvial landscapes

    NASA Astrophysics Data System (ADS)

    Bertuzzo, Enrico; Rodriguez-Iturbe, Ignacio; Rinaldo, Andrea

    2015-04-01

    The form of fluvial landscapes is known to attain stationary network configurations that settle in dynamically accessible minima of total energy dissipation by landscape-forming discharges. Recent studies have highlighted the role of the dendritic structure of river networks in controlling population dynamics of the species they host and large-scale biodiversity patterns. Here, we systematically investigate the relation between energy dissipation, the physical driver for the evolution of river networks, and the ecological dynamics of their embedded biota. To that end, we use the concept of metapopulation capacity, a measure to link landscape structures with the population dynamics they host. Technically, metapopulation capacity is the leading eigenvalue λM of an appropriate "landscape" matrix subsuming whether a given species is predicted to persist in the long run. λM can conveniently be used to rank different landscapes in terms of their capacity to support viable metapopulations. We study how λM changes in response to the evolving network configurations of spanning trees. Such sequence of configurations is theoretically known to relate network selection to general landscape evolution equations through imperfect searches for dynamically accessible states frustrated by the vagaries of Nature. Results show that the process shaping the metric and the topological properties of river networks, prescribed by physical constraints, leads to a progressive increase in the corresponding metapopulation capacity and therefore on the landscape capacity to support metapopulations—with implications on biodiversity in fluvial ecosystems.

  15. Applying landscape genetics to the microbial world.

    PubMed

    Dudaniec, Rachael Y; Tesson, Sylvie V M

    2016-07-01

    Landscape genetics, which explicitly quantifies landscape effects on gene flow and adaptation, has largely focused on macroorganisms, with little attention given to microorganisms. This is despite overwhelming evidence that microorganisms exhibit spatial genetic structuring in relation to environmental variables. The increasing accessibility of genomic data has opened up the opportunity for landscape genetics to embrace the world of microorganisms, which may be thought of as 'the invisible regulators' of the macroecological world. Recent developments in bioinformatics and increased data accessibility have accelerated our ability to identify microbial taxa and characterize their genetic diversity. However, the influence of the landscape matrix and dynamic environmental factors on microorganism genetic dispersal and adaptation has been little explored. Also, because many microorganisms coinhabit or codisperse with macroorganisms, landscape genomic approaches may improve insights into how micro- and macroorganisms reciprocally interact to create spatial genetic structure. Conducting landscape genetic analyses on microorganisms requires that we accommodate shifts in spatial and temporal scales, presenting new conceptual and methodological challenges not yet explored in 'macro'-landscape genetics. We argue that there is much value to be gained for microbial ecologists from embracing landscape genetic approaches. We provide a case for integrating landscape genetic methods into microecological studies and discuss specific considerations associated with the novel challenges this brings. We anticipate that microorganism landscape genetic studies will provide new insights into both micro- and macroecological processes and expand our knowledge of species' distributions, adaptive mechanisms and species' interactions in changing environments.

  16. Molecular dynamics and energy landscape of decanethiolates in self-assembled monolayers on Au(111) studied by scanning tunneling microscopy.

    PubMed

    Sotthewes, Kai; Wu, Hairong; Kumar, Avijit; Vancso, G Julius; Schön, Peter M; Zandvliet, Harold J W

    2013-03-19

    The energetics and dynamics of the various phases of decanethiolate self-assembled monolayers on Au(111) surfaces were studied with scanning tunneling microscopy. We have observed five different phases of the decanethiolate monolayer on Au(111): four ordered phases (β, δ, χ*, and φ) and one disordered phase (ε). We have determined the boundary free energies between the disordered and order phases by analyzing the thermally induced meandering of the domain boundaries. On the basis of these results, we are able to accurately predict the two-dimensional phase diagram of the decanethiolate/Au(111) system. The order-disorder phase transition of the χ* phase occurs at 295 K, followed by the order-disorder phase transition of the β phase at 325 K. Above temperatures of 325 K, only the densely packed φ and disordered ε phases remain. Our findings are in good agreement with the phase diagram of the decanethiolate/Au(111) system that was put forward by Poirier et al. [Langmuir 2001, 17 (4), 1176-1183].

  17. Landscape refuges delay resistance of the European corn borer to Bt-maize: a demo-genetic dynamic model.

    PubMed

    Tyutyunov, Yuri; Zhadanovskaya, Ekaterina; Bourguet, Denis; Arditi, Roger

    2008-08-01

    We constructed a reaction-diffusion model of the development of resistance to transgenic insecticidal Bt crops in pest populations. Kostitzin's demo-genetic model describes local interactions between three competing pest genotypes with alleles conferring resistance or susceptibility to transgenic plants, the spatial spread of insects being modelled by diffusion. This new approach makes it possible to combine a spatial demographic model of population dynamics with classical genetic theory. We used this model to examine the effects of pest dispersal and of the size and shape of the refuge on the efficiency of the "high-dose/refuge" strategy, which was designed to prevent the development of resistance in populations of insect pests, such as the European corn borer, Ostrinia nubilalis Hübner (Lepidoptera, Crambidae). We found that, with realistic combinations of refuge size and pest dispersal, the development of resistance could be considerably delayed. With a small to medium-sized farming area, contiguous refuge plots are more efficient than a larger number of smaller refuge patches. We also show that the formal coupling of classical Fisher-Haldane-Wright population genetics equations with diffusion terms inaccurately describes the development of resistance in a spatially heterogeneous pest population, notably overestimating the speed with which Bt resistance is selected in populations of pests targeted by Bt crops.

  18. Exact probability distribution functions for Parrondo's games

    NASA Astrophysics Data System (ADS)

    Zadourian, Rubina; Saakian, David B.; Klümper, Andreas

    2016-12-01

    We study the discrete time dynamics of Brownian ratchet models and Parrondo's games. Using the Fourier transform, we calculate the exact probability distribution functions for both the capital dependent and history dependent Parrondo's games. In certain cases we find strong oscillations near the maximum of the probability distribution with two limiting distributions for odd and even number of rounds of the game. Indications of such oscillations first appeared in the analysis of real financial data, but now we have found this phenomenon in model systems and a theoretical understanding of the phenomenon. The method of our work can be applied to Brownian ratchets, molecular motors, and portfolio optimization.

  19. 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).

  20. 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

  1. Landscape predictions from cosmological vacuum selection

    SciTech Connect

    Bousso, Raphael; Bousso, Raphael; Yang, Sheng

    2007-04-23

    In Bousso-Polchinski models with hundreds of fluxes, we compute the effects of cosmological dynamics on the probability distribution of landscape vacua. Starting from generic initial conditions, we find that most fluxes are dynamically driven into a different and much narrower range of values than expected from landscape statistics alone. Hence, cosmological evolution will access only a tiny fraction of the vacua with small cosmological constant. This leads to a host of sharp predictions. Unlike other approaches to eternal inflation, the holographic measure employed here does not lead to staggering, an excessive spread of probabilities that would doom the string landscape as a solution to the cosmological constant problem.

  2. Intermediate disturbance in experimental landscapes improves persistence of beetle metapopulations.

    PubMed

    Govindan, Byju N; Feng, Zhilan; DeWoody, Yssa D; Swihart, Robert K

    2015-03-01

    Human-dominated landscapes often feature patches that fluctuate in suitability through space and time, but there is little experimental evidence relating the consequences of dynamic patches for species persistence. We used a spatially and temporally dynamic metapopulation model to assess and compare metapopulation capacity and persistence for red flour beetles (Tribolium castaneum) in experimental landscapes differentiated by resource structure, patch dynamics (destruction and restoration), and connectivity. High connectivity increased the colonization rate of beetles, but this effect was less pronounced in heterogeneous relative to homogeneous landscapes. Higher connectivity and faster patch dynamics increased extinction rates in landscapes. Lower connectivity promoted density-dependent emigration. Heterogeneous landscapes containing patches of different carrying capacity enhanced landscape-level occupancy probability. The highest metapopulation capacity and persistence was observed in landscapes with heterogeneous patches, low connectivity, and slow patch dynamics. Control landscapes with no patch dynamics exhibited rapid declines in abundance and approached extinction due to increased adult mortality in the matrix, higher pupal cannibalism by adults, and extremely low rates of exchange between remaining habitable patches. Our results highlight the role of intermediate patch dynamics, intermediate connectivity, and the nature of density dependence of emigration for persistence of species in heterogeneous landscapes. Our results also demonstrate the importance of incorporating local dynamics into the estimation of metapopulation capacity for conservation planning.

  3. Wildlife Population Dynamics in Human-Dominated Landscapes under Community-Based Conservation: The Example of Nakuru Wildlife Conservancy, Kenya.

    PubMed

    Ogutu, Joseph O; Kuloba, Bernard; Piepho, Hans-Peter; Kanga, Erustus

    2017-01-01

    Wildlife conservation is facing numerous and mounting challenges on private and communal lands in Africa, including in Kenya. We analyze the population dynamics of 44 common wildlife species in relation to rainfall variation in the Nakuru Wildlife Conservancy (NWC), located in the Nakuru-Naivasha region of Kenya, based on ground total counts carried out twice each year from March 1996 to May 2015. Rainfall in the region was quasi-periodic with cycle periods dependent on the rainfall component and varying from 2.8 years for the dry season to 10.9 years for the wet season. These oscillations are associated with frequent severe droughts and food scarcity for herbivores. The trends for the 44 wildlife species showed five general patterns during 1996-2015. 1) Steinbuck, bushbuck, hartebeest and greater kudu numbers declined persistently and significantly throughout 1996-2015 and thus merit the greatest conservation attention. 2) Klipspringer, mongoose, oribi, porcupine, cheetah, leopard, ostrich and Sykes monkey numbers also decreased noticeably but not significantly between 1996 and 2015. 3) Dik dik, eland, African hare, Jackal, duiker, hippo and Thomson's gazelle numbers first increased and then declined between 1996 and 2015 but only significantly for duiker and hippo. 4) Aardvark, serval cat, colobus monkey, bat-eared fox, reedbuck, hyena and baboon numbers first declined and then increased but only the increases in reedbuck and baboon numbers were significant. 5) Grant's gazelle, Grevy's zebra, lion, spring hare, Burchell's zebra, bushpig, white rhino, rock hyrax, topi, oryx, vervet monkey, guinea fowl, giraffe, and wildebeest numbers increased consistently between 1996 and 2015. The increase was significant only for rock hyrax, topi, vervet monkey, guinea fowl, giraffe and wildebeest. 6) Impala, buffalo, warthog, and waterbuck, numbers increased significantly and then seemed to level off between 1996 and 2015. The aggregate biomass of primates and carnivores

  4. Wildlife Population Dynamics in Human-Dominated Landscapes under Community-Based Conservation: The Example of Nakuru Wildlife Conservancy, Kenya

    PubMed Central

    Ogutu, Joseph O.; Kuloba, Bernard; Piepho, Hans-Peter; Kanga, Erustus

    2017-01-01

    Wildlife conservation is facing numerous and mounting challenges on private and communal lands in Africa, including in Kenya. We analyze the population dynamics of 44 common wildlife species in relation to rainfall variation in the Nakuru Wildlife Conservancy (NWC), located in the Nakuru-Naivasha region of Kenya, based on ground total counts carried out twice each year from March 1996 to May 2015. Rainfall in the region was quasi-periodic with cycle periods dependent on the rainfall component and varying from 2.8 years for the dry season to 10.9 years for the wet season. These oscillations are associated with frequent severe droughts and food scarcity for herbivores. The trends for the 44 wildlife species showed five general patterns during 1996–2015. 1) Steinbuck, bushbuck, hartebeest and greater kudu numbers declined persistently and significantly throughout 1996–2015 and thus merit the greatest conservation attention. 2) Klipspringer, mongoose, oribi, porcupine, cheetah, leopard, ostrich and Sykes monkey numbers also decreased noticeably but not significantly between 1996 and 2015. 3) Dik dik, eland, African hare, Jackal, duiker, hippo and Thomson’s gazelle numbers first increased and then declined between 1996 and 2015 but only significantly for duiker and hippo. 4) Aardvark, serval cat, colobus monkey, bat-eared fox, reedbuck, hyena and baboon numbers first declined and then increased but only the increases in reedbuck and baboon numbers were significant. 5) Grant’s gazelle, Grevy’s zebra, lion, spring hare, Burchell’s zebra, bushpig, white rhino, rock hyrax, topi, oryx, vervet monkey, guinea fowl, giraffe, and wildebeest numbers increased consistently between 1996 and 2015. The increase was significant only for rock hyrax, topi, vervet monkey, guinea fowl, giraffe and wildebeest. 6) Impala, buffalo, warthog, and waterbuck, numbers increased significantly and then seemed to level off between 1996 and 2015. The aggregate biomass of primates and

  5. [Applications of 2D and 3D landscape pattern indices in landscape pattern analysis of mountainous area at county level].

    PubMed

    Lu, Chao; Qi, Wei; Li, Le; Sun, Yao; Qin, Tian-Tian; Wang, Na-Na

    2012-05-01

    Landscape pattern indices are the commonly used tools for the quantitative analysis of landscape pattern. However, the traditional 2D landscape pattern indices neglect the effects of terrain on landscape, existing definite limitations in quantitatively describing the landscape patterns in mountains areas. Taking the Qixia City, a typical mountainous and hilly region in Shandong Province of East China, as a case, this paper compared the differences between 2D and 3D landscape pattern indices in quantitatively describing the landscape patterns and their dynamic changes in mountainous areas. On the basis of terrain structure analysis, a set of landscape pattern indices were selected, including area and density (class area and mean patch size), edge and shape (edge density, landscape shape index, and fractal dimension of mean patch), diversity (Shannon's diversity index and evenness index) , and gathering and spread (contagion index). There existed obvious differences between the 3D class area, mean patch area, and edge density and the corresponding 2D indices, but no significant differences between the 3D landscape shape index, fractal dimension of mean patch, and Shannon' s diversity index and evenness index and the corresponding 2D indices. The 3D contagion index and 2D contagion index had no difference. Because the 3D landscape pattern indices were calculated by using patch surface area and surface perimeter whereas the 2D landscape pattern indices were calculated by adopting patch projective area and projective perimeter, the 3D landscape pattern indices could be relative accurate and efficient in describing the landscape area, density and borderline, in mountainous areas. However, there were no distinct differences in describing landscape shape, diversity, and gathering and spread between the 3D and 2D landscape pattern indices. Generally, by introducing 3D landscape pattern indices to topographic pattern, the description of landscape pattern and its dynamic

  6. Landscaping for energy efficiency

    SciTech Connect

    1995-04-01

    This publication by the National Renewable Energy Laboratory addresses the use of landscaping for energy efficiency. The topics of the publication include minimizing energy expenses; landscaping for a cleaner environment; climate, site, and design considerations; planning landscape; and selecting and planting trees and shrubs. A source list for more information on landscaping for energy efficiency and a reading list are included.

  7. Analysis of the Free Energy Landscapes for the Opening-Closing Dynamics of the Maltose Transporter ATPase MalK2 Using Enhanced-Sampling Molecular Dynamics Simulation.

    PubMed

    Hsu, Wei-Lin; Furuta, Tadaomi; Sakurai, Minoru

    2015-07-30

    Protein dynamics are considered significant for many physiological processes, such as metabolism, biomolecular recognition, and the regulation of several vital cellular processes. Due to their flexibility, proteins may stay in different substates with or without the existence of the cognate substrates. To describe these phenomena, two models have been proposed: the "induced fit" and the "conformational selection" mechanisms. In this study, we used MalK2, the subunits that mainly include the nucleotide-binding domains (NBDs) of the maltose transporter from Escherichia coli, as a target to understand the NBD dimerization mechanism. Accelerated and conventional molecular dynamics have been performed. The results revealed that Mg-ATP binding to MalK2 led to a significant change in the free energy profile and thus stabilized the closed conformation. On the contrary, when Mg-ATP was removed, the open conformation would be favored. The fact that ligand binding induces a drastic free energy change leads to a significant inference: MalK2 dimerization would occur through the induced-fit mechanism rather than the conformational selection mechanism. This study sheds new light on the NBD dimerization mechanism and would be of wide applicability to other ABC transporters.

  8. Interactions of landscape disturbances and climate change dictate ecological pattern and process: spatial modeling of wildfire, insect, and disease dynamics under future climates

    USGS Publications Warehouse

    Loehman, Rachel; Keane, Robert E.; Holsinger, Lisa M.; Wu, Zhiwei

    2016-01-01

    ContextInteractions among disturbances, climate, and vegetation influence landscape patterns and ecosystem processes. Climate changes, exotic invasions, beetle outbreaks, altered fire regimes, and human activities may interact to produce landscapes that appear and function beyond historical analogs.ObjectivesWe used the mechanistic ecosystem-fire process model FireBGCv2 to model interactions of wildland fire, mountain pine beetle (Dendroctonus ponderosae), and white pine blister rust (Cronartium ribicola) under current and future climates, across three diverse study areas.MethodsWe assessed changes in tree basal area as a measure of landscape response over a 300-year simulation period for the Crown of the Continent in north-central Montana, East Fork of the Bitterroot River in western Montana, and Yellowstone Central Plateau in western Wyoming, USA.ResultsInteracting disturbances reduced overall basal area via increased tree mortality of host species. Wildfire decreased basal area more than beetles or rust, and disturbance interactions modeled under future climate significantly altered landscape basal area as compared with no-disturbance and current climate scenarios. Responses varied among landscapes depending on species composition, sensitivity to fire, and pathogen and beetle suitability and susceptibility.ConclusionsUnderstanding disturbance interactions is critical for managing landscapes because forest responses to wildfires, pathogens, and beetle attacks may offset or exacerbate climate influences, with consequences for wildlife, carbon, and biodiversity.

  9. Multi-drug resistance profile of PR20 HIV-1 protease is attributed to distorted conformational and drug binding landscape: molecular dynamics insights.

    PubMed

    Chetty, Sarentha; Bhakat, Soumendranath; Martin, Alberto J M; Soliman, Mahmoud E S

    2016-01-01

    The PR20 HIV-1 protease, a variant with 20 mutations, exhibits high levels of multi-drug resistance; however, to date, there has been no report detailing the impact of these 20 mutations on the conformational and drug binding landscape at a molecular level. In this report, we demonstrate the first account of a comprehensive study designed to elaborate on the impact of these mutations on the dynamic features as well as drug binding and resistance profile, using extensive molecular dynamics analyses. Comparative MD simulations for the wild-type and PR20 HIV proteases, starting from bound and unbound conformations in each case, were performed. Results showed that the apo conformation of the PR20 variant of the HIV protease displayed a tendency to remain in the open conformation for a longer period of time when compared to the wild type. This led to a phenomena in which the inhibitor seated at the active site of PR20 tends to diffuse away from the binding site leading to a significant change in inhibitor-protein association. Calculating the per-residue fluctuation (RMSF) and radius of gyration, further validated these findings. MM/GBSA showed that the occurrence of 20 mutations led to a drop in the calculated binding free energies (ΔGbind) by ~25.17 kcal/mol and ~5 kcal/mol for p2-NC, a natural peptide substrate, and darunavir, respectively, when compared to wild type. Furthermore, the residue interaction network showed a diminished inter-residue hydrogen bond network and changes in inter-residue connections as a result of these mutations. The increased conformational flexibility in PR20 as a result of loss of intra- and inter-molecular hydrogen bond interactions and other prominent binding forces led to a loss of protease grip on ligand. It is interesting to note that the difference in conformational flexibility between PR20 and WT conformations was much higher in the case of substrate-bound conformation as compared to DRV. Thus, developing analogues of DRV by

  10. Vacuum selection on axionic landscapes

    SciTech Connect

    Wang, Gaoyuan; Battefeld, Thorsten E-mail: tbattefe@astro.physik.uni-goettingen.de

    2016-04-01

    We compute the distribution of minima that are reached dynamically on multi-field axionic landscapes, both numerically and analytically. Such landscapes are well suited for inflationary model building due to the presence of shift symmetries and possible alignment effects (the KNP mechanism). The resulting distribution of dynamically reached minima differs considerably from the naive expectation based on counting all vacua. These differences are more pronounced in the presence of many fields due to dynamical selection effects: while low lying minima are preferred as fields roll down the potential, trajectories are also more likely to get trapped by one of the many nearby minima. We show that common analytic arguments based on random matrix theory in the large D-limit to estimate the distribution of minima are insufficient for quantitative arguments pertaining to the dynamically reached ones. This discrepancy is not restricted to axionic potentials. We provide an empirical expression for the expectation value of such dynamically reached minimas' height and argue that the cosmological constant problem is not alleviated in the absence of anthropic arguments. We further comment on the likelihood of inflation on axionic landscapes in the large D-limit.

  11. Landscape moderation of biodiversity patterns and processes - eight hypotheses.

    PubMed

    Tscharntke, Teja; Tylianakis, Jason M; Rand, Tatyana A; Didham, Raphael K; Fahrig, Lenore; Batáry, Péter; Bengtsson, Janne; Clough, Yann; Crist, Thomas O; Dormann, Carsten F; Ewers, Robert M; Fründ, Jochen; Holt, Robert D; Holzschuh, Andrea; Klein, Alexandra M; Kleijn, David; Kremen, Claire; Landis, Doug A; Laurance, William; Lindenmayer, David; Scherber, Christoph; Sodhi, Navjot; Steffan-Dewenter, Ingolf; Thies, Carsten; van der Putten, Wim H; Westphal, Catrin

    2012-08-01

    Understanding how landscape characteristics affect biodiversity patterns and ecological processes at local and landscape scales is critical for mitigating effects of global environmental change. In this review, we use knowledge gained from human-modified landscapes to suggest eight hypotheses, which we hope will encourage more systematic research on the role of landscape composition and configuration in determining the structure of ecological communities, ecosystem functioning and services. We organize the eight hypotheses under four overarching themes. Section A: 'landscape moderation of biodiversity patterns' includes (1) the landscape species pool hypothesis-the size of the landscape-wide species pool moderates local (alpha) biodiversity, and (2) the dominance of beta diversity hypothesis-landscape-moderated dissimilarity of local communities determines landscape-wide biodiversity and overrides negative local effects of habitat fragmentation on biodiversity. Section B: 'landscape moderation of population dynamics' includes (3) the cross-habitat spillover hypothesis-landscape-moderated spillover of energy, resources and organisms across habitats, including between managed and natural ecosystems, influences landscape-wide community structure and associated processes and (4) the landscape-moderated concentration and dilution hypothesis-spatial and temporal changes in landscape composition can cause transient concentration or dilution of populations with functional consequences. Section C: 'landscape moderation of functional trait selection' includes (5) the landscape-moderated functional trait selection hypothesis-landscape moderation of species trait selection shapes the functional role and trajectory of community assembly, and (6) the landscape-moderated insurance hypothesis-landscape complexity provides spatial and temporal insurance, i.e. high resilience and stability of ecological processes in changing environments. Section D: 'landscape constraints on

  12. What can a numerical landscape evolution model tell us about the evolution of a real landscape? Two examples of modeling a real landscape without recreating it

    NASA Astrophysics Data System (ADS)

    Gasparini, N. M.; Whipple, K. X.; Willenbring, J.; Crosby, B. T.; Brocard, G. Y.

    2013-12-01

    Numerical landscape evolution models (LEMs) offer us the unique opportunity to watch a landscape evolve under any set of environmental forcings that we can quantify. The possibilities for using LEMs are infinite, but complications arise when trying to model a real landscape. Specifically, numerical models cannot recreate every aspect of a real landscape because exact initial conditions are unknown, there will always be gaps in the known tectonic and climatic history, and the geomorphic transport laws that govern redistribution of mass due to surface processes will always be a simplified representation of the actual process. Yet, even with these constraints, numerical models remain the only tool that offers us the potential to explore a limitless range of evolutionary scenarios, allowing us to, at the very least, identify possible drivers responsible for the morphology of the current landscape, and just as importantly, rule out others. Here we highlight two examples in which we use a numerical model to explore the signature of different forcings on landscape morphology and erosion patterns. In the first landscape, the Northern Bolivian Andes, the relative imprint of rock uplift and precipitation patterns on landscape morphology is widely contested. We use the CHILD LEM to systematically vary climate and tectonics and quantify their fingerprints on channel profiles across a steep mountain front. We find that rock uplift and precipitation patterns in this landscape and others can be teased out by examining channel profiles of variably sized catchments that drain different parts of the topography. In the second landscape, the South Fork Eel River (SFER), northern California, USA, the tectonic history is relatively well known; a wave of rock uplift swept through the watershed from headwaters to outlet, perturbing the landscape and sending a wave of bedrock incision upstream. Nine millennial-scale erosion rates from along the mainstem of the river illustrate a pattern of

  13. Exact models for isotropic matter

    NASA Astrophysics Data System (ADS)

    Thirukkanesh, S.; Maharaj, S. D.

    2006-04-01

    We study the Einstein-Maxwell system of equations in spherically symmetric gravitational fields for static interior spacetimes. The condition for pressure isotropy is reduced to a recurrence equation with variable, rational coefficients. We demonstrate that this difference equation can be solved in general using mathematical induction. Consequently, we can find an explicit exact solution to the Einstein-Maxwell field equations. The metric functions, energy density, pressure and the electric field intensity can be found explicitly. Our result contains models found previously, including the neutron star model of Durgapal and Bannerji. By placing restrictions on parameters arising in the general series, we show that the series terminate and there exist two linearly independent solutions. Consequently, it is possible to find exact solutions in terms of elementary functions, namely polynomials and algebraic functions.

  14. Exact controllability of complex networks

    PubMed Central

    Yuan, Zhengzhong; Zhao, Chen; Di, Zengru; Wang, Wen-Xu; Lai, Ying-Cheng

    2013-01-01

    Controlling complex networks is of paramount importance in science and engineering. Despite the recent development of structural controllability theory, we continue to lack a framework to control undirected complex networks, especially given link weights. Here we introduce an exact controllability paradigm based on the maximum multiplicity to identify the minimum set of driver nodes required to achieve full control of networks with arbitrary structures and link-weight distributions. The framework reproduces the structural controllability of directed networks characterized by structural matrices. We explore the controllability of a large number of real and model networks, finding that dense networks with identical weights are difficult to be controlled. An efficient and accurate tool is offered to assess the controllability of large sparse and dense networks. The exact controllability framework enables a comprehensive understanding of the impact of network properties on controllability, a fundamental problem towards our ultimate control of complex systems. PMID:24025746

  15. What Exactly is Space Logistics?

    DTIC Science & Technology

    2011-01-01

    information on the space shuttle in the news and have inferred by now that resupply missions to the International Space Sta- tion, Hubble Space ... Telescope repair missions, and satellite deployment missions are space logistics—and you would be technically correct. The science of logistics as applied...What Exactly is Space Logistics? James C. Breidenbach Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the

  16. Multi-scale forest landscape pattern characterization

    NASA Astrophysics Data System (ADS)

    Wang, Jialing

    The purpose of this dissertation is to examine several important issues in landscape pattern analysis, including the identification of important landscape metrics, the impact of the modifiable areal unit problem (MAUP) in landscape pattern analysis, the linkage between pattern and process, and the application of landscape pattern analysis. A theoretical framework of hierarchical patch dynamics paradigm and a technical framework of GIS and remote sensing integration are employed to address these questions. The Red Hills region of southwestern Georgia and northern Florida is chosen as the study area. Land use/cover (LULC) and longleaf pine distribution maps were generated through satellite image classification. Sub-watersheds were used as the main analysis units. Principal component analysis (PCA) was conducted on 43 sub-watersheds at three hierarchical LULC levels to identify important landscape metrics. At both landscape- and class-levels, the measurement of fragmentation was identified as the most important landscape dimension. Other dimensions and important metrics varied with different scales. Hexagons were used as an alternative zoning system to examine the MAUP impact in landscape pattern analysis. The results indicated that landscape pattern analyses at class level and at broader scales were more sensitive to MAUP than at landscape level and at finer scales. Local-scale pattern analysis based on moving window analysis greatly reduced the impact of MAUP at class level, but had little effects at landscape level. An examination of the relationship between landscape pattern variables and biophysical/socio-economic variables was undertaken by using statistical analysis. The biophysical variables of soil drainage and mean slope and the socio-economic variables of road density, population density, distance to Tallahassee, Florida, and plantation amount were found to be closely correlated to the landscape patterns in this region. However, a large amount of variation

  17. The oxidation of landscapes

    NASA Astrophysics Data System (ADS)

    Rempe, D.; Hahm, W. J.; Dietrich, W. E.

    2015-12-01

    At the base of the critical zone, fresh rock is transformed through chemical alteration of minerals and fracturing. The resulting hydrologically dynamic weathered bedrock zone strongly influences how mass is routed throughout a landscape. Studies of weathering in a variety of lithologies and climates have documented the role of oxygen in driving the onset of weathering. Porosity is generated through processes such as the formation of sulfuric acid via oxidative pyrite dissolution and strain via iron oxidation in biotite. The transport of meteoric oxygen is therefore a mechanism that links the topographic surface to weathering processes at depth. Here, we present an alternative to the theory that the advance of an oxidation front is driven by downward advection and diffusion of meteoric fluid. We present field data and theory that suggest that the slow drainage of groundwater within fresh bedrock drives the displacement of unreactive pore fluid from low-porosity fresh bedrock. This drainage, and the subsequent introduction of meteoric fluid to fresh rock, is a hillslope scale process driven by channel incision. The resulting distribution of weathered rock across the landscape is thus controlled by the fresh bedrock porosity and permeability and the rate of channel incision.

  18. Biotic and abiotic processes of eastside ecosystems: The effects of management on plant and community ecology, and on stand and landscape vegetation dynamics. Forest Service general technical report

    SciTech Connect

    Johnson, C.G.; Clausnitzer, R.R.; Mehringer, P.J.; Oilver, C.D.

    1994-02-01

    Paleo-vegetation studies have shown that vegetation has changed in composition and extent in the intermountain Pacific Northwest over the past 20,000 years. Today, both natural and human-induced disturbances have long-term influence on the structure and composition of eastside vegetation. Disturbance may enhance landscape diversity, therefore, the scale of modifying events and activities needs to shift from species and stand to the landscape level. Knowledge of plant succession is the foundation of a sound vegetation management program where the primary goal is to retard, arrest, or accelerate the natural forces of vegetation change.

  19. Oasis dynamics change and its influence on landscape pattern on Jinta oasis in arid China from 1963a to 2010a: Integration of multi-source satellite images

    NASA Astrophysics Data System (ADS)

    Xie, Yuchu; Gong, Jie; Sun, Peng; Gou, Xiaohua

    2014-12-01

    As one of the vital research highlights of global land use and cover change, oasis change and its interaction with landscape pattern have been regarded as an important content of regional environmental change research in arid areas. Jinta oasis, a typical agricultural oasis characterized by its dramatic exploitation and use of water and land resources in Hexi corridor, northwest arid region in China, was selected as a case to study the spatiotemporal oasis change and its effects on oasis landscape pattern. Based on integration of Keyhole satellite photographs, KATE-200 photographs, Landsat MSS, TM and ETM+ images, we evaluated and analyzed the status, trend and spatial pattern change of Jinta oasis and the characteristics of landscape pattern change by a set of mathematical models and combined this information with landscape metrics and community surveys. During the period of 1963a-2010a, Jinta oasis expanded gradually with an area increase of 219.15 km2, and the conversion between oasis and desert was frequent with a state of “imbalance-balance-extreme imbalance conditions”. Moreover, most of the changes took place in the ecotone between oasis and desert and the interior of oasis due to the reclamation of abandoned land, such as Yangjingziwan and Xiba townships. Furthermore, the area, size and spatial distribution of oasis were influenced by human activities and resulted in fundamental changes of oasis landscape pattern. The fractal characteristics, dispersion degree and fragmentation of Jinta oasis decreased and the oasis landscape tended to be simple and uniform. Oasis change trajectories and its landscape pattern were mainly influenced by water resource utilization, policies (especially land policies), demographic factors, technological advancements, as well as regional economic development. We found that time series analysis of multi-source remote sensing images and the application of an oasis change model provided a useful approach to monitor oasis change

  20. Exact analytical solutions for ADAFs

    NASA Astrophysics Data System (ADS)

    Habibi, Asiyeh; Abbassi, Shahram; Shadmehri, Mohsen

    2017-02-01

    We obtain two-dimensional exact analytic solutions for the structure of the hot accretion flows without wind. We assume that the only non-zero component of the stress tensor is Trϕ. Furthermore, we assume that the value of viscosity coefficient α varies with θ. We find radially self-similar solutions and compare them with the numerical and the analytical solutions already studied in the literature. The no-wind solution obtained in this paper may be applied to the nuclei of some cool-core clusters.

  1. Landscape Management: Field Supervisor.

    ERIC Educational Resources Information Center

    Newton, Deborah; Newton, Steve

    This module is the third volume in a series of instructional materials on landscape management. The materials are designed to help teachers train students in the job skills they will need in landscape occupations. The module contains six instructional units that cover the following topics: orientation; basic landscape design principles; irrigation…

  2. Landscape reorganization under changing climatic forcing: Results from an experimental landscape

    NASA Astrophysics Data System (ADS)

    Singh, Arvind; Reinhardt, Liam; Foufoula-Georgiou, Efi

    2015-06-01

    Understanding how landscapes respond to climate dynamics in terms of macroscale (average topographic features) and microscale (landform reorganization) is of interest both for deciphering past climates from today's landscapes and for predicting future landscapes in view of recent climatic trends. Although several studies have addressed macro-scale response, only a few have focused on quantifying smaller-scale basin reorganization. To that goal, a series of controlled laboratory experiments were conducted where a self-organized complete drainage network emerged under constant precipitation and uplift dynamics. Once steady state was achieved, the landscape was subjected to a fivefold increase in precipitation (transient state). Throughout the evolution, high-resolution spatiotemporal topographic data in the form of digital elevation models were collected. The steady state landscape was shown to possess three distinct geomorphic regimes (unchannelized hillslopes, debris-dominated channels, and fluvially dominated channels). During transient state, landscape reorganization was observed to be driven by hillslopes via accelerated erosion, ridge lowering, channel widening, and reduction of basin relief as opposed to channel base-level reduction. Quantitative metrics on which these conclusions were based included slope-area curve, correlation analysis of spatial and temporal elevation increments, and wavelet spectral analysis of the evolving landscapes. Our results highlight that landscape reorganization in response to increased precipitation seems to follow "an arrow of scale": major elevation change initiates at the hillslope scale driving erosional regime change at intermediate scales and further cascading to geomorphic changes at the channel scale as time evolves.

  3. Landscape genetics of high mountain frog metapopulations

    USGS Publications Warehouse

    Murphy, M.A.; Dezzani, R.; Pilliod, D.S.; Storfer, A.

    2010-01-01

    Explaining functional connectivity among occupied habitats is crucial for understanding metapopulation dynamics and species ecology. Landscape genetics has primarily focused on elucidating how ecological features between observations influence gene flow. Functional connectivity, however, may be the result of both these between-site (landscape resistance) landscape characteristics and at-site (patch quality) landscape processes that can be captured using network based models. We test hypotheses of functional connectivity that include both between-site and at-site landscape processes in metapopulations of Columbia spotted frogs (Rana luteiventris) by employing a novel justification of gravity models for landscape genetics (eight microsatellite loci, 37 sites, n = 441). Primarily used in transportation and economic geography, gravity models are a unique approach as flow (e.g. gene flow) is explained as a function of three basic components: distance between sites, production/attraction (e.g. at-site landscape process) and resistance (e.g. between-site landscape process). The study system contains a network of nutrient poor high mountain lakes where we hypothesized a short growing season and complex topography between sites limit R. luteiventris gene flow. In addition, we hypothesized production of offspring is limited by breeding site characteristics such as the introduction of predatory fish and inherent site productivity. We found that R. luteiventris connectivity was negatively correlated with distance between sites, presence of predatory fish (at-site) and topographic complexity (between-site). Conversely, site productivity (as measured by heat load index, at-site) and growing season (as measured by frost-free period between-sites) were positively correlated with gene flow. The negative effect of predation and positive effect of site productivity, in concert with bottleneck tests, support the presence of source-sink dynamics. In conclusion, gravity models provide a

  4. Landscape genetics of high mountain frog metapopulations.

    PubMed

    Murphy, Melanie A; Dezzani, R; Pilliod, D S; Storfer, A

    2010-09-01

    Explaining functional connectivity among occupied habitats is crucial for understanding metapopulation dynamics and species ecology. Landscape genetics has primarily focused on elucidating how ecological features between observations influence gene flow. Functional connectivity, however, may be the result of both these between-site (landscape resistance) landscape characteristics and at-site (patch quality) landscape processes that can be captured using network based models. We test hypotheses of functional connectivity that include both between-site and at-site landscape processes in metapopulations of Columbia spotted frogs (Rana luteiventris) by employing a novel justification of gravity models for landscape genetics (eight microsatellite loci, 37 sites, n = 441). Primarily used in transportation and economic geography, gravity models are a unique approach as flow (e.g. gene flow) is explained as a function of three basic components: distance between sites, production/attraction (e.g. at-site landscape process) and resistance (e.g. between-site landscape process). The study system contains a network of nutrient poor high mountain lakes where we hypothesized a short growing season and complex topography between sites limit R. luteiventris gene flow. In addition, we hypothesized production of offspring is limited by breeding site characteristics such as the introduction of predatory fish and inherent site productivity. We found that R. luteiventris connectivity was negatively correlated with distance between sites, presence of predatory fish (at-site) and topographic complexity (between-site). Conversely, site productivity (as measured by heat load index, at-site) and growing season (as measured by frost-free period between-sites) were positively correlated with gene flow. The negative effect of predation and positive effect of site productivity, in concert with bottleneck tests, support the presence of source-sink dynamics. In conclusion, gravity models provide a

  5. Exact finite elements for conduction and convection

    NASA Technical Reports Server (NTRS)

    Thornton, E. A.; Dechaumphai, P.; Tamma, K. K.

    1981-01-01

    An appproach for developing exact one dimensional conduction-convection finite elements is presented. Exact interpolation functions are derived based on solutions to the governing differential equations by employing a nodeless parameter. Exact interpolation functions are presented for combined heat transfer in several solids of different shapes, and for combined heat transfer in a flow passage. Numerical results demonstrate that exact one dimensional elements offer advantages over elements based on approximate interpolation functions. Previously announced in STAR as N81-31507

  6. Exact finite elements for conduction and convection

    NASA Technical Reports Server (NTRS)

    Thornton, E. A.; Dechaumphai, P.; Tamma, K. K.

    1981-01-01

    An approach for developing exact one dimensional conduction-convection finite elements is presented. Exact interpolation functions are derived based on solutions to the governing differential equations by employing a nodeless parameter. Exact interpolation functions are presented for combined heat transfer in several solids of different shapes, and for combined heat transfer in a flow passage. Numerical results demonstrate that exact one dimensional elements offer advantages over elements based on approximate interpolation functions.

  7. Landscape genetics of plants.

    PubMed

    Holderegger, Rolf; Buehler, Dominique; Gugerli, Felix; Manel, Stéphanie

    2010-12-01

    Landscape genetics is the amalgamation of landscape ecology and population genetics to help with understanding microevolutionary processes such as gene flow and adaptation. In this review, we examine why landscape genetics of plants lags behind that of animals, both in number of studies and consideration of landscape elements. The classical landscape distance/resistance approach to study gene flow is challenging in plants, whereas boundary detection and the assessment of contemporary gene flow are more feasible. By contrast, the new field of landscape genetics of adaptive genetic variation, establishing the relationship between adaptive genomic regions and environmental factors in natural populations, is prominent in plant studies. Landscape genetics is ideally suited to study processes such as migration and adaptation under global change.

  8. Exact Bremsstrahlung and effective couplings

    NASA Astrophysics Data System (ADS)

    Mitev, Vladimir; Pomoni, Elli

    2016-06-01

    We calculate supersymmetric Wilson loops on the ellipsoid for a large class of mathcal{N} = 2 SCFT using the localization formula of Hama and Hosomichi. From them we extract the radiation emitted by an accelerating heavy probe quark as well as the entanglement entropy following the recent works of Lewkowycz-Maldacena and Fiol-Gerchkovitz-Komargodski. Comparing our results with the mathcal{N} = 4 SYM ones, we obtain interpolating functions f ( g 2) such that a given mathcal{N} = 2 SCFT observable is obtained by replacing in the corresponding mathcal{N} = 4 SYM result the coupling constant by f ( g 2). These "exact effective couplings" encode the finite, relative renormalization between the mathcal{N} = 2 and the mathcal{N} = 4 gluon propagator and they interpolate between the weak and the strong coupling. We discuss the range of their applicability.

  9. Exact propagators in harmonic superspace

    NASA Astrophysics Data System (ADS)

    Kuzenko, Sergei M.

    2004-10-01

    Within the background field formulation in harmonic superspace for quantum N = 2 super-Yang-Mills theories, the propagators of the matter, gauge and ghost superfields possess a complicated dependence on the SU(2) harmonic variables via the background vector multiplet. This dependence is shown to simplify drastically in the case of an on-shell vector multiplet. For a covariantly constant background vector multiplet, we exactly compute all the propagators. In conjunction with the covariant multi-loop scheme developed in arxiv:hep-th/0302205, these results provide an efficient (manifestly N = 2 supersymmetric) technical setup for computing multi-loop quantum corrections to effective actions in N = 2 supersymmetric gauge theories, including the N = 4 super-Yang-Mills theory.

  10. High Resolution Thermometry for EXACT

    NASA Technical Reports Server (NTRS)

    Panek, J. S.; Nash, A. E.; Larson, M.; Mulders, N.

    2000-01-01

    High Resolution Thermometers (HRTs) based on SQUID detection of the magnetization of a paramagnetic salt or a metal alloy has been commonly used for sub-nano Kelvin temperature resolution in low temperature physics experiments. The main applications to date have been for temperature ranges near the lambda point of He-4 (2.177 K). These thermometers made use of materials such as Cu(NH4)2Br4 *2H2O, GdCl3, or PdFe. None of these materials are suitable for EXACT, which will explore the region of the He-3/He-4 tricritical point at 0.87 K. The experiment requirements and properties of several candidate paramagnetic materials will be presented, as well as preliminary test results.

  11. Constructing and exploring wells of energy landscapes

    NASA Astrophysics Data System (ADS)

    Aubin, Jean-Pierre; Lesne, Annick

    2005-04-01

    Landscape paradigm is ubiquitous in physics and other natural sciences, but it has to be supplemented with both quantitative and qualitatively meaningful tools for analyzing the topography of a given landscape. We here consider dynamic explorations of the relief and introduce as basic topographic features "wells of duration T and altitude y." We determine an intrinsic exploration mechanism governing the evolutions from an initial state in the well up to its rim in a prescribed time, whose finite-difference approximations on finite grids yield a constructive algorithm for determining the wells. Our main results are thus (i) a quantitative characterization of landscape topography rooted in a dynamic exploration of the landscape, (ii) an alternative to stochastic gradient dynamics for performing such an exploration, (iii) a constructive access to the wells, and (iv) the determination of some bare dynamic features inherent to the landscape. The mathematical tools used here are not familiar in physics: They come from set-valued analysis (differential calculus of set-valued maps and differential inclusions) and viability theory (capture basins of targets under evolutionary systems) that have been developed during the last two decades; we therefore propose a minimal Appendix exposing them at the end of this paper to bridge the possible gap.

  12. Evolution and selection of river networks: Statics, dynamics, and complexity

    PubMed Central

    Rinaldo, Andrea; Rigon, Riccardo; Banavar, Jayanth R.; Maritan, Amos; Rodriguez-Iturbe, Ignacio

    2014-01-01

    Moving from the exact result that drainage network configurations minimizing total energy dissipation are stationary solutions of the general equation describing landscape evolution, we review the static properties and the dynamic origins of the scale-invariant structure of optimal river patterns. Optimal channel networks (OCNs) are feasible optimal configurations of a spanning network mimicking landscape evolution and network selection through imperfect searches for dynamically accessible states. OCNs are spanning loopless configurations, however, only under precise physical requirements that arise under the constraints imposed by river dynamics—every spanning tree is exactly a local minimum of total energy dissipation. It is remarkable that dynamically accessible configurations, the local optima, stabilize into diverse metastable forms that are nevertheless characterized by universal statistical features. Such universal features explain very well the statistics of, and the linkages among, the scaling features measured for fluvial landforms across a broad range of scales regardless of geology, exposed lithology, vegetation, or climate, and differ significantly from those of the ground state, known exactly. Results are provided on the emergence of criticality through adaptative evolution and on the yet-unexplored range of applications of the OCN concept. PMID:24550264

  13. Nonequilibrium landscape theory of neural networks.

    PubMed

    Yan, Han; Zhao, Lei; Hu, Liang; Wang, Xidi; Wang, Erkang; Wang, Jin

    2013-11-05

    The brain map project aims to map out the neuron connections of the human brain. Even with all of the wirings mapped out, the global and physical understandings of the function and behavior are still challenging. Hopfield quantified the learning and memory process of symmetrically connected neural networks globally through equilibrium energy. The energy basins of attractions represent memories, and the memory retrieval dynamics is determined by the energy gradient. However, the realistic neural networks are asymmetrically connected, and oscillations cannot emerge from symmetric neural networks. Here, we developed a nonequilibrium landscape-flux theory for realistic asymmetrically connected neural networks. We uncovered the underlying potential landscape and the associated Lyapunov function for quantifying the global stability and function. We found the dynamics and oscillations in human brains responsible for cognitive processes and physiological rhythm regulations are determined not only by the landscape gradient but also by the flux. We found that the flux is closely related to the degrees of the asymmetric connections in neural networks and is the origin of the neural oscillations. The neural oscillation landscape shows a closed-ring attractor topology. The landscape gradient attracts the network down to the ring. The flux is responsible for coherent oscillations on the ring. We suggest the flux may provide the driving force for associations among memories. We applied our theory to rapid-eye movement sleep cycle. We identified the key regulation factors for function through global sensitivity analysis of landscape topography against wirings, which are in good agreements with experiments.

  14. Pseudoknots in RNA folding landscapes

    PubMed Central

    Kucharík, Marcel; Hofacker, Ivo L.; Stadler, Peter F.; Qin, Jing

    2016-01-01

    Motivation: The function of an RNA molecule is not only linked to its native structure, which is usually taken to be the ground state of its folding landscape, but also in many cases crucially depends on the details of the folding pathways such as stable folding intermediates or the timing of the folding process itself. To model and understand these processes, it is necessary to go beyond ground state structures. The study of rugged RNA folding landscapes holds the key to answer these questions. Efficient coarse-graining methods are required to reduce the intractably vast energy landscapes into condensed representations such as barrier trees or basin hopping graphs (BHG) that convey an approximate but comprehensive picture of the folding kinetics. So far, exact and heuristic coarse-graining methods have been mostly restricted to the pseudoknot-free secondary structures. Pseudoknots, which are common motifs and have been repeatedly hypothesized to play an important role in guiding folding trajectories, were usually excluded. Results: We generalize the BHG framework to include pseudoknotted RNA structures and systematically study the differences in predicted folding behavior depending on whether pseudoknotted structures are allowed to occur as folding intermediates or not. We observe that RNAs with pseudoknotted ground state structures tend to have more pseudoknotted folding intermediates than RNAs with pseudoknot-free ground state structures. The occurrence and influence of pseudoknotted intermediates on the folding pathway, however, appear to depend very strongly on the individual RNAs so that no general rule can be inferred. Availability and implementation: The algorithms described here are implemented in C++ as standalone programs. Its source code and Supplemental material can be freely downloaded from http://www.tbi.univie.ac.at/bhg.html. Contact: qin@bioinf.uni-leipzig.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID

  15. An exact formulation of hyperdynamics simulations.

    PubMed

    Chen, L Y; Horing, N J M

    2007-06-14

    We introduce a new formula for the acceleration weight factor in the hyperdynamics simulation method, the use of which correctly provides an exact simulation of the true dynamics of a system. This new form of hyperdynamics is valid and applicable where the transition state theory (TST) is applicable and also where the TST is not applicable. To illustrate this new formulation, we perform hyperdynamics simulations for four systems ranging from one degree of freedom to 591 degrees of freedom: (1) We first analyze free diffusion having one degree of freedom. This system does not have a transition state. The TST and the original form of hyperdynamics are not applicable. Using the new form of hyperdynamics, we compute mean square displacement for a range of time. The results obtained agree perfectly with the analytical formula. (2) Then we examine the classical Kramers escape rate problem. The rate computed is in perfect agreement with the Kramers formula over a broad range of temperature. (3) We also study another classical problem: Computing the rate of effusion out of a cubic box through a tiny hole. This problem does not involve an energy barrier. Thus, the original form of hyperdynamics excludes the possibility of using a nonzero bias and is inappropriate. However, with the new weight factor formula, our new form of hyperdynamics can be easily implemented and it produces the exact results. (4) To illustrate applicability to systems of many degrees of freedom, we analyze diffusion of an atom adsorbed on the (001) surface of an fcc crystal. The system is modeled by an atom on top of a slab of six atomic layers. Each layer has 49 atoms. With the bottom two layers of atoms fixed, this system has 591 degrees of freedom. With very modest computing effort, we are able to characterize its diffusion pathways in the exchange-with-the-substrate and hop-over-the-bridge mechanisms.

  16. An exact formulation of hyperdynamics simulations

    NASA Astrophysics Data System (ADS)

    Chen, L. Y.; Horing, N. J. M.

    2007-06-01

    We introduce a new formula for the acceleration weight factor in the hyperdynamics simulation method, the use of which correctly provides an exact simulation of the true dynamics of a system. This new form of hyperdynamics is valid and applicable where