Science.gov

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. Landscape Construction in Dynamical Systems

    NASA Astrophysics Data System (ADS)

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

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

  3. Dynamic landscape management.

    Treesearch

    Valerie. Rapp

    2003-01-01

    Pacific Northwest forests and all their species evolved with fires, floods, windstorms, landslides, and other disturbances. The dynamics of disturbance were basic to how forests changed and renewed. Disturbance regimes, as scientists call the long-term patterns of these events—what kind of event, how often, how large, and how severe—created the landscape patterns seen...

  4. Dynamic landscape management

    Treesearch

    Valerie . Rapp

    2002-01-01

    Pacific Northwest forests and all their species evolved with fires, floods, windstorms, landslides, and other disturbances. The dynamics of disturbance were basic to how forests changed and renewed. Disturbance regimes, as scientists call the long-term patterns of these events—what kind of event, how often, how large, and how severe—created the landscape patterns seen...

  5. 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.

  6. Reserves, resilience and dynamic landscapes.

    PubMed

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

    2003-09-01

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

  7. 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.

  8. 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

  9. Landscape dynamics of mountain pine beetles

    Treesearch

    John E. Lundquist; Robin M. Reich

    2014-01-01

    The magnitude and urgency of current mountain pine beetle outbreaks in the western United States and Canada have resulted in numerous studies of the dynamics and impacts of these insects in forested ecosystems. This paper reviews some of the aspects of the spatial dynamics and landscape ecology of this bark beetle. Landscape heterogeneity influences dispersal patterns...

  10. 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.

  11. Exact dynamic theories on a given background in gravitation

    SciTech Connect

    Popova, A.D. ); Petrov, A.N. )

    1988-01-01

    In any field theory the variables can always be decomposed into a sum of background and dynamic parts. The authors analyse exact dynamic theories in which the dynamic field is not small;an arbitrary theory of gravity is meant. In the initial theory the choice of variables is inessential. Dynamic theories constructed for different choices of initial variables which are then decomposed, turn out to be in a certain sense inequivalent. They show that the dynamic stress-energy tensors differ in terms that do not vanish on the solutions both background and dynamic equations of motion. This property is exact, i.e., it is valid irrespective of any approximations. They consider gauge invariance of dynamic theories under gauge transformations induced by finite-displacements of the 4-space. They discuss peculiarities of dynamic theories in the Einstein theory with material fields as sources.

  12. 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 ...

  13. 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 ...

  14. Exact dynamic properties of molecular motors.

    PubMed

    Boon, N J; Hoyle, R B

    2012-08-28

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

  15. Exact dynamic properties of molecular motors

    NASA Astrophysics Data System (ADS)

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

    2012-08-01

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

  16. Messy world: managing dynamic landscape.

    Treesearch

    Sally. Duncan

    1999-01-01

    What lessons does historical disturbance hold for the management of future landscapes? Fred Swanson, a researcher at the Pacific Northwest Research Station and John Cissel, research liaison for the Willamette NF, are members of a team of scientists and land managers who are examining the way we think about and manage landscapes.The team found that past...

  17. Simulating historical landscape dynamics using the landscape fire succession model LANDSUM version 4.0

    Treesearch

    Robert E. Keane; Lisa M. Holsinger; Sarah D. Pratt

    2006-01-01

    The range and variation of historical landscape dynamics could provide a useful reference for designing fuel treatments on today's landscapes. Simulation modeling is a vehicle that can be used to estimate the range of conditions experienced on historical landscapes. A landscape fire succession model called LANDSUMv4 (LANDscape SUccession Model version 4.0) is...

  18. 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.

  19. 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.

  20. 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.

  1. Exact computation of probability landscape of stochastic networks of Single Input and Coupled Toggle Switch Modules.

    PubMed

    Terebus, Anna; Cao, Youfang; Liang, Jie

    2014-01-01

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

  2. 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.

  3. Optimal enumeration of state space of finitely buffered stochastic molecular networks and exact computation of steady state landscape probability.

    PubMed

    Cao, Youfang; Liang, Jie

    2008-03-29

    Stochasticity plays important roles in many molecular networks when molecular concentrations are in the range of 0.1 muM to 10nM (about 100 to 10 copies in a cell). The chemical master equation provides a fundamental framework for studying these networks, and the time-varying landscape probability distribution over the full microstates, i.e., the combination of copy numbers of molecular species, provide a full characterization of the network dynamics. A complete characterization of the space of the microstates is a prerequisite for obtaining the full landscape probability distribution of a network. However, there are neither closed-form solutions nor algorithms fully describing all microstates for a given molecular network. We have developed an algorithm that can exhaustively enumerate the microstates of a molecular network of small copy numbers under the condition that the net gain in newly synthesized molecules is smaller than a predefined limit. We also describe a simple method for computing the exact mean or steady state landscape probability distribution over microstates. We show how the full landscape probability for the gene networks of the self-regulating gene and the toggle-switch in the steady state can be fully characterized. We also give an example using the MAPK cascade network. Data and server will be available at URL: http://scsb.sjtu.edu.cn/statespace. Our algorithm works for networks of small copy numbers buffered with a finite copy number of net molecules that can be synthesized, regardless of the reaction stoichiometry, and is optimal in both storage and time complexity. The algorithm can also be used to calculate the rates of all transitions between microstates from given reactions and reaction rates. The buffer size is limited by the available memory or disk storage. Our algorithm is applicable to a class of biological networks when the copy numbers of molecules are small and the network is closed, or the network is open but the net gain in

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. Global structure of exact scalar hairy dynamical black holes

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  14. 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,...

  15. 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,...

  16. 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

  17. 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.

  18. Metapopulation dynamics in a complex ecological landscape.

    PubMed

    Colombo, E H; Anteneodo, C

    2015-08-01

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

  19. 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).

  20. Spacetime dynamics of spinning particles: Exact electromagnetic analogies

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Exact milestoning

    PubMed Central

    Bello-Rivas, Juan M.; Elber, Ron

    2015-01-01

    A new theory and an exact computer algorithm for calculating kinetics and thermodynamic properties of a particle system are described. The algorithm avoids trapping in metastable states, which are typical challenges for Molecular Dynamics (MD) simulations on rough energy landscapes. It is based on the division of the full space into Voronoi cells. Prior knowledge or coarse sampling of space points provides the centers of the Voronoi cells. Short time trajectories are computed between the boundaries of the cells that we call milestones and are used to determine fluxes at the milestones. The flux function, an essential component of the new theory, provides a complete description of the statistical mechanics of the system at the resolution of the milestones. We illustrate the accuracy and efficiency of the exact Milestoning approach by comparing numerical results obtained on a model system using exact Milestoning with the results of long trajectories and with a solution of the corresponding Fokker-Planck equation. The theory uses an equation that resembles the approximate Milestoning method that was introduced in 2004 [A. K. Faradjian and R. Elber, J. Chem. Phys. 120(23), 10880-10889 (2004)]. However, the current formulation is exact and is still significantly more efficient than straightforward MD simulations on the system studied. PMID:25747056

  6. 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.

  7. Dynamic-landscape metapopulation models predict complex response of wildlife populations to climate and landscape change

    Treesearch

    Thomas W. Bonnot; Frank R. Thompson; Joshua J. Millspaugh

    2017-01-01

    The increasing need to predict how climate change will impact wildlife species has exposed limitations in how well current approaches model important biological processes at scales at which those processes interact with climate. We used a comprehensive approach that combined recent advances in landscape and population modeling into dynamic-landscape metapopulation...

  8. Landscape Disturbance History and Belowground Carbon Dynamics.

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  9. 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}.

  10. An indicator of forest dynamics using a shifting landscape mosaic

    Treesearch

    Kurt H. Riitters; James D. Wickham; Timothy G. Wade

    2009-01-01

    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 360,000 km2 study area in the southern United States. The indicator...

  11. Biodiversity and ecosystem functioning in dynamic landscapes.

    PubMed

    Brose, Ulrich; Hillebrand, Helmut

    2016-05-19

    in dynamic communities of real-world landscapes. © 2016 The Author(s).

  12. 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

  13. 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).

  14. 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

  15. 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...

  16. 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...

  17. 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

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

    PubMed

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

    2016-02-10

    Soil is a microenvironment with a fragmented (patchy) spatial structure in which many bacterial species interact. Here, we explore the interaction between the predatory bacterium Bdellovibrio bacteriovorus and its prey Escherichia coli in microfabricated landscapes. We ask how fragmentation influences the prey dynamics at the microscale and compare two landscape geometries: a patchy landscape and a continuous landscape. By following the dynamics of prey populations with high spatial and temporal resolution for many generations, we found that the variation in predation rates was twice as large in the patchy landscape and the dynamics was correlated over shorter length scales. We also found that while the prey population in the continuous landscape was almost entirely driven to extinction, a significant part of the prey population in the fragmented landscape persisted over time. We observed significant surface-associated growth, especially in the fragmented landscape and we surmise that this sub-population is more resistant to predation. Our results thus show that microscale fragmentation can significantly influence bacterial interactions. © 2016 The Author(s).

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  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. 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…

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

    SciTech Connect

    Dominy, Jason; Rabitz, Herschel

    2012-08-15

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

  11. Landscape dynamics of aspen and conifer forests

    Treesearch

    Dale L. Bartos

    2001-01-01

    Quaking aspen (Populus tremuloides Michx.) is widely dispersed across the landscape of North America. Seventy-five percent of the aspen in the western United States occurs in the states of Colorado (50%) and Utah (25%). Reproduction in aspen is primarily by asexual means, e.g., root sprouts that are generally referred to as suckers. An aspen clone consists of numerous...

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. [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.

  20. 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.

  1. Synchrony in small mammal community dynamics across a forested landscape

    Treesearch

    Ryan B. Stephens; Daniel J. Hocking; Mariko Yamasaki; Rebecca J. Rowe

    2016-01-01

    Long- term studies at local scales indicate that fluctuations in abundance among trophically similar species are often temporally synchronized. Complementary studies on synchrony across larger spatial extents are less common, as are studies that investigate the subsequent impacts on community dynamics across the landscape. We investigate the impact of species...

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

    PubMed

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

    2015-05-21

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

  3. Field dynamics and tunneling in a flux landscape

    SciTech Connect

    Johnson, Matthew C.; Larfors, Magdalena

    2008-10-15

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

  4. Dynamic lipid landscape of picornavirus replication organelles.

    PubMed

    Belov, George A

    2016-08-01

    Picornavirus infection induces rapid reorganization of the cellular membrane architecture and appearance of novel membranous structures associated with the viral RNA replication and virion assembly-replication organelles. Recent studies significantly advanced our understanding of their lipid composition and cellular mechanisms involved in their development. Picornaviruses activate synthesis of both structural and signaling lipids and reroute cellular cholesterol trafficking pathways to create unique membranous domains favoring viral replication. Rapidly replicating picornaviruses rely on posttranslational activation and/or specific recruitment of cellular proteins rather than on modulation of expression of cellular genes to create favorable membrane microenvironment. At the same time picornaviruses demonstrate remarkable adaptability to changes in the lipid landscape which should be taken into account when developing novel antiviral strategies. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. 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.

  6. 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.

  7. Microscopic derivation of particle-based coarse-grained dynamics: Exact expression for memory function

    NASA Astrophysics Data System (ADS)

    Izvekov, Sergei

    2017-03-01

    We consider the generalized Langevin equations of motion describing exactly the particle-based coarse-grained dynamics in the classical microscopic ensemble that were derived recently within the Mori-Zwanzig formalism based on new projection operators [S. Izvekov, J. Chem. Phys. 138(13), 134106 (2013)]. The fundamental difference between the new family of projection operators and the standard Zwanzig projection operator used in the past to derive the coarse-grained equations of motion is that the new operators average out the explicit irrelevant trajectories leading to the possibility of solving the projected dynamics exactly. We clarify the definition of the projection operators and revisit the formalism to compute the projected dynamics exactly for the microscopic system in equilibrium. The resulting expression for the projected force is in the form of a "generalized additive fluctuating force" describing the departure of the generalized microscopic force associated with the coarse-grained coordinate from its projection. Starting with this key expression, we formulate a new exact formula for the memory function in terms of microscopic and coarse-grained conservative forces. We conclude by studying two independent limiting cases of practical importance: the Markov limit (vanishing correlations of projected force) and the limit of weak dependence of the memory function on the particle momenta. We present computationally affordable expressions which can be efficiently evaluated from standard molecular dynamics simulations.

  8. 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.

  9. 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.

  10. Tardis: a visual exploration environment for landscape dynamics

    NASA Astrophysics Data System (ADS)

    Carpendale, M. Sheelagh T.; Cowperthwaite, D. J.; Tigges, M.; Fall, A. J.; Fracchia, F. D.

    1999-03-01

    This paper presents the creation of a visual environment for exploring landscape patterns and changes to such patterns over time. Dynamic landscape patterns can involve both spatial and temporal complexity. Exploration of spatio-temporal landscape patterns should provide the ability to view information at different scales to permit navigation of a vast amount of information in a manner that facilitates comprehension rather than confusion. One way of achieving this goal is to support selection, navigation and comparison of progressively refined segments of time and space. We have entitled this system Tardis after the time machine of Dr. Who, to emphasize the exploration of time dependent data and because our use of elastic presentation has the effect of providing more internal space than the external volume suggests. Of special concern in this research is the extent of the data and its inter- relationships that need to be understood over multiple scales, and the challenge inherent in implementing viewing methods to facilitate understanding.

  11. Bound electron dynamics: Exact solution for a one-dimensional oscillator-string model

    NASA Astrophysics Data System (ADS)

    Dekker, H.

    1984-11-01

    The dynamical problem of a harmonically bound electron with standard dipole model coupling to the electromagnetic field in a finite one-dimensional space is solved exactly in a simple manner. It is easily shown that in this model the coupling between the electron and the field is “rigid”, in the sense of and in complete analogy with a recent treatment of a purely mechanical particle on a string. As a consequence the electron's quantum mechanical momentum fluctuations exhibit a logarithmic ultraviolet divergence. In the limit of infinite spatial extension of the field, and apart from quantal noise, the electron behaves exactly as a simple linearly damped harmonic oscillator.

  12. 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.

  13. 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.

  14. 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.

  15. Long-term stable time integration scheme for dynamic analysis of planar geometrically exact Timoshenko beams

    NASA Astrophysics Data System (ADS)

    Nguyen, Tien Long; Sansour, Carlo; Hjiaj, Mohammed

    2017-05-01

    In this paper, an energy-momentum method for geometrically exact Timoshenko-type beam is proposed. The classical time integration schemes in dynamics are known to exhibit instability in the non-linear regime. The so-called Timoshenko-type beam with the use of rotational degree of freedom leads to simpler strain relations and simpler expressions of the inertial terms as compared to the well known Bernoulli-type model. The treatment of the Bernoulli-model has been recently addressed by the authors. In this present work, we extend our approach of using the strain rates to define the strain fields to in-plane geometrically exact Timoshenko-type beams. The large rotational degrees of freedom are exactly computed. The well-known enhanced strain method is used to avoid locking phenomena. Conservation of energy, momentum and angular momentum is proved formally and numerically. The excellent performance of the formulation will be demonstrated through a range of examples.

  16. The dynamic landscape of exceptional language development.

    PubMed

    Peltzer-Karpf, Annemarie

    2012-06-01

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

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. Exact results for the probability and stochastic dynamics of fixation in the Wright-Fisher model.

    PubMed

    Shafiey, Hassan; Waxman, David

    2017-10-07

    In this work we consider fixation of an allele in a population. Fixation is key to understanding the way long-term evolutionary change occurs at the gene and molecular levels. Two basic aspects of fixation are: (i) the chance it occurs and (ii) the way the gene frequency progresses to fixation. We present exact results for both aspects of fixation for the Wright-Fisher model. We give the exact fixation probability for some different schemes of frequency-dependent selection. We also give the corresponding exact stochastic difference equation that generates frequency trajectories which ultimately fix. Exactness of the results means selection need not be weak. There are possible applications of this work to data analysis, modelling, and tests of approximations. The methodology employed illustrates that knowledge of the fixation probability, for all initial frequencies, fully characterises the dynamics of the Wright-Fisher model. The stochastic equations for fixing trajectories allow insight into the way fixation occurs. They provide the alternative picture that fixation is driven by the injection of one carrier of the fixing allele into the population each generation. The stochastic equations allow explicit calculation of some properties of fixing trajectories and their efficient simulation. The results are illustrated and tested with simulations. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Delving Into Dissipative Quantum Dynamics: From Approximate to Numerically Exact Approaches

    NASA Astrophysics Data System (ADS)

    Chen, Hsing-Ta

    In this thesis, I explore dissipative quantum dynamics of several prototypical model systems via various approaches, ranging from approximate to numerically exact schemes. In particular, in the realm of the approximate I explore the accuracy of Pade-resummed master equations and the fewest switches surface hopping (FSSH) algorithm for the spin-boson model, and non-crossing approximations (NCA) for the Anderson-Holstein model. Next, I develop new and exact Monte Carlo approaches and test them on the spin-boson model. I propose well-defined criteria for assessing the accuracy of Pade-resummed quantum master equations, which correctly demarcate the regions of parameter space where the Pade approximation is reliable. I continue the investigation of spin-boson dynamics by benchmark comparisons of the semiclassical FSSH algorithm to exact dynamics over a wide range of parameters. Despite small deviations from golden-rule scaling in the Marcus regime, standard surface hopping algorithm is found to be accurate over a large portion of parameter space. The inclusion of decoherence corrections via the augmented FSSH algorithm improves the accuracy of dynamical behavior compared to exact simulations, but the effects are generally not dramatic for the cases I consider. Next, I introduce new methods for numerically exact real-time simulation based on real-time diagrammatic Quantum Monte Carlo (dQMC) and the inchworm algorithm. These methods optimally recycle Monte Carlo information from earlier times to greatly suppress the dynamical sign problem. In the context of the spin-boson model, I 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. In addition, a cumulant version of the inchworm Monte Carlo method is motivated by the latter expansion, which allows for further suppression of the growth of the sign error. I provide a comprehensive comparison of the

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Combining pressure and temperature control in dynamics on energy landscapes

    NASA Astrophysics Data System (ADS)

    Hoffmann, Karl Heinz; Christian Schön, J.

    2017-05-01

    Complex systems from science, technology or mathematics usually appear to be very different in their specific dynamical evolution. However, the concept of an energy landscape with its basins corresponding to locally ergodic regions separated by energy barriers provides a unifying approach to the description of complex systems dynamics. In such systems one is often confronted with the task to control the dynamics such that a certain basin is reached with the highest possible probability. Typically one aims for the global minimum, e.g. when dealing with global optimization problems, but frequently other local minima such as the metastable compounds in materials science are of primary interest. Here we show how this task can be solved by applying control theory using magnesium fluoride as an example system, where different modifications of MgF2 are considered as targets. In particular, we generalize previous work restricted to temperature controls only and present controls which simultaneously adjust temperature and pressure in an optimal fashion.

  16. Smooth landscape solvent dynamics in electron transfer reactions

    NASA Astrophysics Data System (ADS)

    Leite, Vitor B. P.

    1999-05-01

    Solvent effects play a major role in controlling electron-transfer reactions. The solvent dynamics happens on a very high-dimensional surface, and this complex landscape is populated by a large number of minima. A critical problem is to understand the conditions under which the solvent dynamics can be represented by a single collective reaction coordinate. When this unidimensional representation is valid, one recovers the successful Marcus theory. In this study the approach used in a previous work [V. B. P. Leite and J. N. Onuchic; J. Phys. Chem. 100, 7680 (1996)] is extended to treat a more realistic solvent model, which includes energy correlation. The dynamics takes place in a smooth and well behaved landscape. The single shell of solvent molecules around a cavity is described by a two-dimensional system with periodic boundary conditions with nearest neighbor interaction. It is shown how the polarization-dependent effects can be inferred. The existence of phase transitions depends on a factor γ proportional to the contribution from the two parameters of the model. For the present model, γ suggests the existence of "weak kinetic phase transitions," which are used in the analysis of solvent effects in charge-transfer reactions.

  17. Effects of landscape evolution on soil organic carbon dynamics in intensively managed agricultural landscapes

    NASA Astrophysics Data System (ADS)

    Yan, Q.; Kumar, P.

    2016-12-01

    Soil organic matter (SOM) plays a critical role in nutrient dynamics and carbon sequestration. Significant research has been done to predict changes of organic carbon and nitrogen in the soil by studying the interaction between soil, climate, and vegetation. However, an important factor in this system, the landscape evolution (LE), which interacts extensively with the soil, climate, and vegetation over a longer time scale, is usually not represented in such studies. Natural and anthropogenic drivers change the surface topography. Agricultural practices, such as fertilizer application and tillage episodically disturb the system. Here we simulate this system by coupling chemically based C-N model with physically based hydro-geomorphologic model at hillslope scale to understand 1) how LE impacts C-N dynamics; 2) how SOM affects LE; 3) how farming activities modify the interaction between LE and SOM dynamics. Our results show that LE plays a dominant role in SOC both above- and below-ground. Contrary to an assumption used in many models that a vertical profile of SOC concentration decreases exponentially, we find that in many situations SOC concentration below-ground could be higher than the one at the surface in both deposition and erosion sites. Tillage mixes the SOC in top 5cm-30cm of the soil. On one hand, tillage enhances the SOC storage by increasing below ground SOC concentration; On the other hand, tillage could accelerate soil erosion, which increase SOC loss. In general, tillage causes the soil vertical profile to become more uniform. Our model also shows that tillage can change the C-N oscillation cycle and then increase the time to reach a dynamic equilibrium. The SOC measured in the field site of Intensively Managed Landscapes Critical Zone Observatory (IMLCZO) is consistent with our model results. This study not only helps us understand the natural carbon-nitrogen cycle, but also serve as an instrument to develop practical means for reducing soil erosion

  18. 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.

  19. The dynamic energy landscape of dihydrofolate reductase catalysis.

    PubMed

    Boehr, David D; McElheny, Dan; Dyson, H Jane; Wright, Peter E

    2006-09-15

    We used nuclear magnetic resonance relaxation dispersion to characterize higher energy conformational substates of Escherichia coli dihydrofolate reductase. Each intermediate in the catalytic cycle samples low-lying excited states whose conformations resemble the ground-state structures of preceding and following intermediates. Substrate and cofactor exchange occurs through these excited substates. The maximum hydride transfer and steady-state turnover rates are governed by the dynamics of transitions between ground and excited states of the intermediates. Thus, the modulation of the energy landscape by the bound ligands funnels the enzyme through its reaction cycle along a preferred kinetic path.

  20. 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.

  1. How fuel treatment types, locations, and amounts impact landscape-scale fire behavior and carbon dynamics

    Treesearch

    Christopher A. Dicus; Kevin J. Osborne

    2015-01-01

    When managing for fire across a large landscape, the types of fuel treatments, the locations of treatments, and the percentage of the landscape being treated should all interact to impact not only potential fire size, but also carbon dynamics across that landscape. To investigate these interactions, we utilized a forest growth model (FVS-FFE) and fire simulation...

  2. 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.

  3. Exciton-phonon dynamics on complex networks: Comparison between a perturbative approach and exact calculations

    NASA Astrophysics Data System (ADS)

    Yalouz, Saad; Pouthier, Vincent; Falvo, Cyril

    2017-08-01

    A method combining perturbation theory with a simplifying ansatz is used to describe the exciton-phonon dynamics in complex networks. This method, called PT*, is compared to exact calculations based on the numerical diagonalization of the exciton-phonon Hamiltonian for eight small-sized networks. It is shown that the accuracy of PT* depends on the nature of the network, and three different situations were identified. For most graphs, PT* yields a very accurate description of the dynamics. By contrast, for the Wheel graph and the Apollonian network, PT* reproduces the dynamics only when the exciton occupies a specific initial state. Finally, for the complete graph, PT* breaks down. These different behaviors originate in the interplay between the degenerate nature of the excitonic energy spectrum and the strength of the exciton-phonon interaction so that a criterion is established to determine whether or not PT* is relevant. When it succeeds, our study shows the undeniable advantage of PT* in that it allows us to perform very fast simulations when compared to exact calculations that are restricted to small-sized networks.

  4. 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.

  5. 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

  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. Exact diagonalization as an impurity solver in dynamical mean field theory

    NASA Astrophysics Data System (ADS)

    Lu, Yi; Haverkort, Maurits W.

    2017-07-01

    The dynamical mean-field theory (DMFT) maps a correlated lattice problem onto an impurity problem of a single correlated site coupled to an uncorrelated bath. Most implementations solve the DMFT equations using quantum Monte-Carlo sampling on the imaginary time and frequency (Matsubara) axis. We will here review alternative methods using exact diagonalization, i.e., representing the many-body ground state of the impurity as a sum over Slater determinants and calculating Green's functions using iterative Lanczos procedures. The advantage being that these methods have no sign problem, can handle involved multi-orbital Hamiltonians (low crystal symmetry, spin-orbit coupling) and - when working completely on the real axis - do not need a mathematically ill-posed analytical continuation. The disadvantage of traditional implementations of exact diagonalization has been the exponential scaling of the calculation problem as a function of number of bath discretization points. In the last part we will review how recent advances in exact diagonalization can evade the exponential barrier thereby increasing the number of bath discretization points to reach the thermodynamic limit.

  8. Stroboscopic phenomena in superconductors with dynamic pinning landscape

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

  9. 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.

  10. 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

  11. 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.

  12. Landscape dynamics in the Otterbach catchment (Bavarian Forest, Southern Germany)

    NASA Astrophysics Data System (ADS)

    Schwindt, Daniel; Scheck, Sebastian; Scholz, Emanuel; Waltl, Peter; Völkel, Jörg

    2017-04-01

    As part of the TUM-CZO (TU-Munich Critical Zone Observatory), the Otterbach Valley has been focus of numerous research approaches, focusing on soil carbon dynamics, hydrological processes as well as landscape dynamics. Aim of this contribution is the reconstruction of the landscape evolution of the Otterbach catchment in context with anthropogenic land use and natural process dynamics. Therefore, studies focus on alluvial and colluvial sediments which are usually regarded as correlated with anthropogenically induced erosion. Located in the western Bavarian Forest the Otterbach is a creek of 2nd stream order and runs directly into the Danube River. Geologically, most parts of the catchment are composed of granitic rocks, mylonites and saprolites. While agricultural land use is dominant in the upper and lower reaches of the Otterbach, the steep middle reaches are forested, floodplains are used as grasslands. Settlement history points out that the forest of the so-called "Thiergarten", covering large parts of the catchment, has been used invariably for forestry, makes this study site valuable for the reconstruction of anthropogenic impact on landscape evolution. Characterization of the shallow subsurface is based on the analysis of soil pits (up to 2 m depth), core samples (up to 18 m depth) and geophysical measurements (electrical resistivity tomography, seismic refraction tomography). Temporal contextualization of sediments is achieved using radiocarbon dating. As a result of illuvial processes, clay curtains are observed almost continuously up to 18 m depth within the slope sediments, suggesting a genesis during Pleistocene warm stages. Radiocarbon dating in the alluvial floodplain point to pronounced sedimentary relocation processes between around 2.400 and 1.000 BP. This emphasizes the importance of naturally caused process dynamics as population density in the surroundings of the Otterbach catchment was low during this period and the area was mostly forested

  13. Measuring urban tree loss dynamics across residential landscapes.

    PubMed

    Ossola, Alessandro; Hopton, Matthew E

    2017-09-05

    The spatial arrangement of urban vegetation depends on urban morphology and socio-economic settings. Urban vegetation changes over time because of human management. Urban trees are removed due to hazard prevention or aesthetic preferences. Previous research attributed tree loss to decreases in canopy cover. However, this provides little information about location and structural characteristics of trees lost, as well as environmental and social factors affecting tree loss dynamics. This is particularly relevant in residential landscapes where access to residential parcels for field surveys is limited. We tested whether multi-temporal airborne LiDAR and multi-spectral imagery collected at a 5-year interval can be used to investigate urban tree loss dynamics across residential landscapes in Denver, CO and Milwaukee, WI, covering 400,705 residential parcels in 444 census tracts. Position and stem height of trees lost were extracted from canopy height models calculated as the difference between final (year 5) and initial (year 0) vegetation height derived from LiDAR. Multivariate regression models were used to predict number and height of tree stems lost in residential parcels in each census tract based on urban morphological and socio-economic variables. A total of 28,427 stems were lost from residential parcels in Denver and Milwaukee over 5years. Overall, 7% of residential parcels lost one stem, averaging 90.87 stems per km(2). Average stem height was 10.16m, though trees lost in Denver were taller compared to Milwaukee. The number of stems lost was higher in neighborhoods with higher canopy cover and developed before the 1970s. However, socio-economic characteristics had little effect on tree loss dynamics. The study provides a simple method for measuring urban tree loss dynamics within and across entire cities, and represents a further step toward high resolution assessments of the three-dimensional change of urban vegetation at large spatial scales. Published by

  14. Exact non-Markovian dynamics of qubits coupled to two interacting environments

    NASA Astrophysics Data System (ADS)

    Shen, H. Z.; Li, D. X.; Su, Shi-Lei; Zhou, Y. H.; Yi, X. X.

    2017-09-01

    As the memory effect may be helpful in quantum information processing, non-Markovian dynamics plays an important role in the description of many-body open systems. Among these topics, the system consisting of independent qubits interacting with several coupled environments is of particular interest. In this paper, we study the exact non-Markovian dynamics of two independent qubits. Each of the qubits interacts individually with its environment, and these two environments coupled with each other. We investigate the non-Markovianity measure of the system for the whole parameter regime without the rotating-wave approximation (RWA) and compare the results with that under the RWA. We find that the non-Markovianity measure for two qubits manifests a transition from a non-Markovian to Markovian regime regardless of the coupling strength between the environments. The physical origin of this transition is revealed, and a possible observation of the prediction in superconducting quantum interference devices is discussed.

  15. Exact nonequilibrium dynamics of finite-temperature Tonks-Girardeau gases

    NASA Astrophysics Data System (ADS)

    Atas, Y. Y.; Gangardt, D. M.; Bouchoule, I.; Kheruntsyan, K. V.

    2017-04-01

    Describing finite-temperature nonequilibrium dynamics of interacting many-particle systems is a notoriously challenging problem in quantum many-body physics. Here we provide an exact solution to this problem for a system of strongly interacting bosons in one dimension in the Tonks-Girardeau regime of infinitely strong repulsive interactions. Using the Fredholm determinant approach and the Bose-Fermi mapping, we show how the problem can be reduced to a single-particle basis, wherein the finite-temperature effects enter the solution via an effective "dressing" of the single-particle wave functions by the Fermi-Dirac occupation factors. We demonstrate the utility of our approach and its computational efficiency in two nontrivial out-of-equilibrium scenarios: collective breathing-mode oscillations in a harmonic trap and collisional dynamics in the Newton's cradle setting involving real-time evolution in a periodic Bragg potential.

  16. 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).

  17. Exploring the role of fire, succession, climate, and weather on landscape dynamics using comparative modeling

    Treesearch

    Robert E. Keane; Geoffrey J. Cary; Mike D. Flannigan; Russell A. Parsons; Ian D. Davies; Karen J. King; Chao Li; Ross A. Bradstock; Malcolm Gill

    2013-01-01

    An assessment of the relative importance of vegetation change and disturbance as agents of landscape change under current and future climates would (1) provide insight into the controls of landscape dynamics, (2) help inform the design and development of coarse scale spatially explicit ecosystem models such as Dynamic Global Vegetation Models (DGVMs), and (3) guide...

  18. 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

  19. 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/. Copyright © 2016 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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).

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

    PubMed

    Hiebeler, David E; Hill, Jack L

    2016-10-21

    We examine a spatially explicit population model on a dynamic landscape with suitable and unsuitable habitat driven by voter or contagion dynamics. We consider four cases, consisting of all combinations of local and global interactions for both population dispersal and habitat dynamics. For both local and global population dispersal, using local habitat dynamics always increases population density relative to the case with global habitat dynamics, due to the resulting segregation of habitat turnover, decrease in effective habitat turnover rate, and presence of stable habitat corridors. With global habitat dynamics, a population using local dispersal exhibits lower density than one with global dispersal due to local crowding as well as frequent disturbance due to habitat transitions. On the other hand, with local habitat dynamics, a population using local dispersal can exploit suitable habitat patches and use dynamic corridors to colonize new regions. The latter effect is not seen with static landscapes, where clustered habitat can lead to the isolation of suitable patches due to surrounding unsuitable habitat. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. 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.

  9. The Role of Landscape Gradients on Dynamics of Stream Carbon

    NASA Astrophysics Data System (ADS)

    Lee, Seung-Cheol; Lee, Eun-Ju; Cha, Ji-Yeon; Go, Minjung; Oh, Neung-Hwan

    2017-04-01

    Understanding the quantities and qualities of stream carbon species provides crucial information for managing water resources and predicting the changes of regional carbon cycle. We investigated the dynamics of stream carbon species across two different landscape gradients; a forest-urban gradient and a forest-cropland gradient under the temperate monsoon climates. We measured [DIC], [DOC], [POC], [PIC], pCO2, and carbon dioxide efflux at 8 points within streams along the forest-urban gradient, and 7 points along the forest-cropland gradient. The [DIC] of the urban stream increased along the reaches downstream in general, varying from 8 to 103 mg/L, whereas [DIC] of the cropland stream decreased downstream varying from 11 to 30 mg/L. The [DOC] increased downstream for both landscape gradients, but for the forest-urban gradient, the [DOC] varied from 0.8 to 4.5 mg/L, whereas for the forest-cropland gradient, the [DOC] varied from 0.1 to 1.2 mg/L. The [POC] was higher in the urban stream than in the cropland stream. The pCO2 of the cropland stream was under 700 ppmv, but the pCO2 of the urban stream varied from 70 to 12,000 ppmv with a tendency to increase downstream. The amount of protein-like components of DOC detected by fluorescence spectroscopy relative to other components was higher in the urban stream than in the cropland stream. The results suggest that the inputs from a metropolitan city compared to cropland can significantly increase riverine CO2 efflux although the source of urban stream CO2 further needs to be identified.

  10. The dynamic landscape of gene regulation during Bombyx mori oogenesis.

    PubMed

    Zhang, Qiang; Sun, Wei; Sun, Bang-Yong; Xiao, Yang; Zhang, Ze

    2017-09-11

    Oogenesis in the domestic silkworm (Bombyx mori) is a complex process involving previtellogenesis, vitellogenesis and choriogenesis. During this process, follicles show drastic morphological and physiological changes. However, the genome-wide regulatory profiles of gene expression during oogenesis remain to be determined. In this study, we obtained time-series transcriptome data and used these data to reveal the dynamic landscape of gene regulation during oogenesis. A total of 1932 genes were identified to be differentially expressed among different stages, most of which occurred during the transition from late vitellogenesis to early choriogenesis. Using weighted gene co-expression network analysis, we identified six stage-specific gene modules that correspond to multiple regulatory pathways. Strikingly, the biosynthesis pathway of the molting hormone 20-hydroxyecdysone (20E) was enriched in one of the modules. Further analysis showed that the ecdysteroid 20-hydroxylase gene (CYP314A1) of steroidgenesis genes was mainly expressed in previtellogenesis and early vitellogenesis. However, the 20E-inactivated genes, particularly the ecdysteroid 26-hydroxylase encoding gene (Cyp18a1), were highly expressed in late vitellogenesis. These distinct expression patterns between 20E synthesis and catabolism-related genes might ensure the rapid decline of the hormone titer at the transition point from vitellogenesis to choriogenesis. In addition, we compared landscapes of gene regulation between silkworm (Lepidoptera) and fruit fly (Diptera) oogeneses. Our results show that there is some consensus in the modules of gene co-expression during oogenesis in these insects. The data presented in this study provide new insights into the regulatory mechanisms underlying oogenesis in insects with polytrophic meroistic ovaries. The results also provide clues for further investigating the roles of epigenetic reconfiguration and circadian rhythm in insect oogenesis.

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

    NASA Astrophysics Data System (ADS)

    McKetterick, Thomas John; Giuggioli, Luca

    2014-10-01

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

  12. Exact solution for the quench dynamics of a nested integrable system

    NASA Astrophysics Data System (ADS)

    Mestyán, Márton; Bertini, Bruno; Piroli, Lorenzo; Calabrese, Pasquale

    2017-08-01

    Integrable models provide an exact description for a wide variety of physical phenomena. For example nested integrable systems contain different species of interacting particles with a rich phenomenology in their collective behavior, which is the origin of the unconventional phenomenon of spin-charge separation. So far, however, most of the theoretical work in the study of non-equilibrium dynamics of integrable systems has focussed on models with an elementary (i.e. not nested) Bethe ansatz. In this work we explicitly investigate quantum quenches in nested integrable systems, by generalizing the application of the quench action approach. Specifically, we consider the spin-1 Lai-Sutherland model, described, in the thermodynamic limit, by the theory of two different species of Bethe-ansatz particles, each one forming an infinite number of bound states. We focus on the situation where the quench dynamics starts from a simple matrix product state for which the overlaps with the eigenstates of the Hamiltonian are known. We fully characterize the post-quench steady state and perform several consistency checks for the validity of our results. Finally, we provide predictions for the propagation of entanglement and mutual information after the quench, which can be used as signature of the quasi-particle content of the model.

  13. 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.

  14. 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).

  15. Modeling of excitation dynamics in photosynthetic light-harvesting complexes: exact versus perturbative approaches

    NASA Astrophysics Data System (ADS)

    Novoderezhkin, Vladimir I.; van Grondelle, Rienk

    2017-06-01

    We compare various theoretical approaches that are frequently used for modeling the excitation dynamics in photosynthetic light-harvesting complexes. As an example, we calculate the dynamics in the major light-harvesting complex from higher plants using the standard Redfield theory, the coherent modified Redfield theory combined with the generalized Förster theory, and the scaled hierarchical equation of motion (HEOM). The modified Redfield and coherent modified Redfield theories predict unrealistically fast transfers between weakly coupled and isoenergetic sites due to the secular character of these approaches. This shortcoming can be excluded by the artificial breaking of exciton mixing between these sites and invoking a generalized Förster theory to calculate the transfers between them. A critical cutoff indicating which exciton couplings should be broken is dependent on the energy gap between the corresponding sites (and therefore can be different for different parts of the complex). An adequate determination of the strongly coupled compartments of the whole complex allows us to obtain a quantitatively correct description with the combined Redfield-Förster approach, resulting in kinetics not much different from the exact HEOM solution.

  16. 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.

  17. Exact results for a fully asymmetric exclusion process with sequential dynamics and open boundaries

    NASA Astrophysics Data System (ADS)

    Brankov, Jordan; Pesheva, Nina; Valkov, Nikola

    2000-03-01

    An exact and rigorous calculation of the current and density profile in the steady state of the one-dimensional fully asymmetric simple-exclusion process with open boundaries and forward-ordered sequential dynamics is presented. The method is based on a matrix product representation of the steady-state probability distribution. The main idea is to choose a suitable representation in which the scalar products describing the current and local density profile for a chain of arbitrary finite size depend only on the elements in a finite number of rows and columns. This makes possible the use of a truncated finite-dimensional representation of the matrices and vectors involved. After performing the calculations, we lift the truncation by letting its dimensionality go to infinity. In this limit the results become exact for any size of the chain. By rescaling one of the infinite-dimensional matrix representations found in the work of Derrida et al. [J. Phys. A 26, 1493 (1993)] for their algebra, we obtain a symmetric ``propagator'' matrix. Its truncated version is diagonalized by orthogonal transformation for easy calculation of the relevant scalar products. An interpretation of the phase transitions between the different phases is given in terms of eigenvalue splitting from a bounded quasicontinuous spectrum. A precise description of the local density profiles is given for all values of the parameters. It is shown that the leading-order asymptotic form of the position-dependent terms in the local density changes within the low- and high-density phases, signaling the presence of a higher-order transition.

  18. 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.

  19. 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...

  20. Spatially explicit modeling of mixed-severity fire regimes and landscape dynamics

    Treesearch

    Michael C. Wimberly; Rebecca S.H. Kennedy

    2008-01-01

    Simulation models of disturbance and succession are being increasingly applied to characterize landscape composition and dynamics under natural fire regimes, and to evaluate alternative management strategies for ecological restoration and fire hazard reduction. However, we have a limited understanding of how landscapes respond to changes in fire frequency, and about...

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

    USDA-ARS?s Scientific Manuscript database

    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...

  2. 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...

  3. 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.

  4. 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.

  5. Nonequilibrium dynamics of random field Ising spin chains: exact results via real space renormalization group.

    PubMed

    Fisher, D S; Le Doussal, P; Monthus, C

    2001-12-01

    The nonequilibrium dynamics of classical random Ising spin chains with nonconserved magnetization are studied using an asymptotically exact real space renormalization group (RSRG). We focus on random field Ising model (RFIM) spin chains with and without a uniform applied field, as well as on Ising spin glass chains in an applied field. For the RFIM we consider a universal regime where the random field and the temperature are both much smaller than the exchange coupling. In this regime, the Imry-Ma length that sets the scale of the equilibrium correlations is large and the coarsening of domains from random initial conditions (e.g., a quench from high temperature) occurs over a wide range of length scales. The two types of domain walls that occur diffuse in opposite random potentials, of the form studied by Sinai, and domain walls annihilate when they meet. Using the RSRG we compute many universal asymptotic properties of both the nonequilibrium dynamics and the equilibrium limit. We find that the configurations of the domain walls converge rapidly toward a set of system-specific time-dependent positions that are independent of the initial conditions. Thus the behavior of this nonequilibrium system is pseudodeterministic at long times because of the broad distributions of barriers that occur on the long length scales involved. Specifically, we obtain the time dependence of the energy, the magnetization, and the distribution of domain sizes (found to be statistically independent). The equilibrium limits agree with known exact results. We obtain the exact scaling form of the two-point equal time correlation function and the two-time autocorrelations . We also compute the persistence properties of a single spin, of local magnetization, and of domains. The analogous quantities for the +/-J Ising spin glass in an applied field are obtained from the RFIM via a gauge transformation. In addition to these we compute the two-point two

  6. Dynamically incorporating late-successional forest in sustainable landscapes

    Treesearch

    Ann E. Camp; Paul F. Hessburg; Richard L. Everett

    1996-01-01

    Ecosystems and landscapes change over time as a function of vegetation characteristics and disturbance regimes, including fire. Interactions between disturbance events and forest development (succession) create patterns of vegetation across landscapes. These patterns result from, and change with respect to, species compositions and structures that arise from...

  7. Eddy current and coupled landscapes for nonadiabatic and nonequilibrium complex system dynamics

    PubMed Central

    Zhang, Kun; Sasai, Masaki; Wang, Jin

    2013-01-01

    Physical and biological systems are often involved with coupled processes of different time scales. In the system with electronic and atomic motions, for example, the interplay between the atomic motion along the same energy landscape and the electronic hopping between different landscapes is critical: the system behavior largely depends on whether the intralandscape motion is slower (adiabatic) or faster (nonadiabatic) than the interlandscape hopping. For general nonequilibrium dynamics where Hamiltonian or energy function is unknown a priori, the challenge is how to extend the concepts of the intra- and interlandscape dynamics. In this paper we establish a theoretical framework for describing global nonequilibrium and nonadiabatic complex system dynamics by transforming the coupled landscapes into a single landscape but with additional dimensions. On this single landscape, dynamics is driven by gradient of the potential landscape, which is closely related to the steady-state probability distribution of the enlarged dimensions, and the probability flux, which has a curl nature. Through an example of a self-regulating gene circuit, we show that the curl flux has dramatic effects on gene regulatory dynamics. The curl flux and landscape framework developed here are easy to visualize and can be used to guide further investigation of physical and biological nonequilibrium systems. PMID:23980160

  8. 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. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. [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.

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

    SciTech Connect

    Shahinpoor, M.; Hawke, R.S.

    1987-08-01

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

  11. 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.

  12. Landscape dynamics in the wildland-urban interface

    Treesearch

    Wayne C. Zipperer

    2012-01-01

    The wildland–urban interface represents landscape change—changes brought about by urbanization, by shifts in forest management, and altered disturbance regimes, each having ecological, social, and economic ramifications. In this chapter, I will focus on some of the ecological ramifications associated with landscape change, primarily forest fragmentation and...

  13. 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.

  14. 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. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  15. 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

  16. 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.

  17. 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.

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

    SciTech Connect

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

    1993-09-01

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

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

    PubMed

    Hemrová, Lucie; Cervenková, Zita; Münzbergová, Zuzana

    2012-11-01

    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. 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). 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. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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

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

    PubMed

    Kannan, Lavanya; Wheeler, Ward C

    2014-04-01

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

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

    PubMed Central

    Wheeler, Ward C.

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    USDA-ARS?s Scientific Manuscript database

    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...

  11. 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)

  12. Temporal dynamics of shrub proliferation: Linking patches to landscapes

    USDA-ARS?s Scientific Manuscript database

    Shifts in vegetation composition and cover are generally characterized by processes acting at different levels such as landscapes, hill slopes, or plant interspaces. Object-oriented analytical approaches are based upon the inherently hierarchical nature of complex systems and are well-suited to res...

  13. Estimating density of a territorial species in a dynamic landscape

    Treesearch

    Elizabeth M. Glenn; Damon B. Lesmeister; Raymond J. Davis; Bruce Hollen; Anne Poopatanapong

    2017-01-01

    Context Conservation planning for at-risk species requires understanding of where species are likely to occur, how many individuals are likely to be supported on a given landscape, and the ability to monitor those changes through time. Objectives We developed a distribution model for northern spotted owls that...

  14. 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)

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

    NASA Astrophysics Data System (ADS)

    Ashwin, S. S.; Sasai, Masaki

    2015-11-01

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

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

    PubMed Central

    Ashwin, S. S.; Sasai, Masaki

    2015-01-01

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

  17. Geomorphic transport laws for predicting landscape form and dynamics

    NASA Astrophysics Data System (ADS)

    Dietrich, William E.; Bellugi, Dino G.; Sklar, Leonard S.; Stock, Jonathan D.; Heimsath, Arjun M.; Roering, Joshua J.

    A geomorphic transport law is a mathematical statement derived from a physical principle or mechanism, which expresses the mass flux or erosion caused by one or more processes in a manner that: 1) can be parameterized from field measurements, 2) can be tested in physical models, and 3) can be applied over geomorphically significant spatial and temporal scales. Such laws are a compromise between physics-based theory that requires extensive information about materials and their interactions, which may be hard to quantify across real landscapes, and rules-based approaches, which cannot be tested directly but only can be used in models to see if the model outcomes match some expected or observed state. We propose that landscape evolution modeling can be broadly categorized into detailed, apparent, statistical and essential realism models and it is the latter, concerned with explaining mechanistically the essential morphodynamic features of a landscape, in which geomorphic transport laws are most effectively applied. A limited number of studies have provided verification and parameterization of geomorphic transport laws for: linear slope-dependent transport, non-linear transport due to dilational disturbance of soil, soil production from bedrock, and river incision into bedrock. Field parameterized geomorphic transport laws, however, are lacking for many processes including landslides, debris flows, surface wash, and glacial scour. We propose the use of high-resolution topography, as initial conditions, in landscape evolution models and explore the applicability of locally parameterized geomorphic transport laws in explaining hillslope morphology in the Oregon Coast Range. This modeling reveals unexpected morphodynamics, suggesting that the use of real landscapes with geomorphic transport laws may provide new insights about the linkages between process and form.

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Iqbal, J.; Garcia, C. V.

    2009-04-01

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

  20. [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.

  1. Analysis of dynamic changes in land use based on landscape metrics in Nagasaki, Japan

    NASA Astrophysics Data System (ADS)

    Wang, Jianhua; Ogawa, Susumu

    2017-01-01

    Land use changes are a reflection of the effects of human activity on Earth's ecosystems. Land use in Nagasaki has changed significantly in recent years with built-up land area increasing from 34 to 62 km2 during the study period (1976 to 2009). Landscape metrics are quantitative indexes that can streamline landscape pattern information and reflect its characteristic structural composition and spatial configuration. Using patches as landscape elements, 12 landscape metrics at two levels (class and landscape levels) were selected to analyze the dynamic changes in land use. At the class level, the following observations were made: (1) merger development of most land use types; (2) a trend toward merging and extension of built-up land and forest; and (3) land use types dominated by nature showed higher shape complexity and lower uniformity in patch area distribution than land use types dominated by human activities. At the landscape level, the results showed an increasing degree of fragmentation and decreasing degree of patch shape complexity in the study period. The study is the first analysis to be done on this scale in Nagasaki that showed the change characteristics in land use by landscape metrics.

  2. 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

  3. Influence of dynamic topography on landscape evolution and passive continental margin stratigraphy

    NASA Astrophysics Data System (ADS)

    Ding, Xuesong; Salles, Tristan; Flament, Nicolas; Rey, Patrice

    2017-04-01

    Quantifying the interaction between surface processes and tectonics/deep Earth processes is one important aspect of landscape evolution modelling. Both observations and results from numerical modelling indicate that dynamic topography - a surface expression of time-varying mantle convection - plays a significant role in shaping landscape through geological time. Recent research suggests that dynamic topography also has non-negligible effects on stratigraphic architecture by modifying accommodation space available for sedimentation. In addition, dynamic topography influences the sediment supply to continental margins. We use Badlands to investigate the evolution of a continental-scale landscape in response to transient dynamic uplift or subsidence, and to model the stratigraphic development on passive continental margins in response to sea-level change, thermal subsidence and dynamic topography. We consider a circularly symmetric landscape consisting of a plateau surrounded by a gently sloping continental plain and a continental margin, and a linear wave of dynamic topography. We analyze the evolution of river catchments, of longitudinal river profiles and of the χ values to evaluate the dynamic response of drainage systems to dynamic topography. We calculate the amount of cumulative erosion and deposition, and sediment flux at shoreline position, as a function of precipitation rate and erodibility coefficient. We compute the stratal stacking pattern and Wheeler diagram on vertical cross-sections at the continental margin. Our results indicate that dynamic topography 1) has a considerable influence on drainage reorganization; 2) contributes to shoreline migration and the distribution of depositional packages by modifying the accommodation space; 3) affects sediment supply to the continental margin. Transient dynamic topography contributes to the migration of drainage divides and to the migration of the mainstream in a drainage basin. The dynamic uplift

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

    NASA Astrophysics Data System (ADS)

    Walker, David John

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

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

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

  12. 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.

  13. Reduced and exact quantum dynamics of the vibrational relaxation of a molecular system interacting with a finite-dimensional bath.

    PubMed

    Bouakline, Foudhil; Lüder, Franziska; Martinazzo, Rocco; Saalfrank, Peter

    2012-11-26

    We investigate the vibrational relaxation of a Morse oscillator, nonlinearly coupled to a finite-dimensional bath of harmonic oscillators at zero temperature, using two different approaches: Reduced dynamics with the help of the Lindblad formalism of reduced density matrix theory in combination with Fermi's Golden Rule, and exact dynamics (within the chosen model) with the multiconfiguration time-dependent Hartree (MCTDH) method. Two different models have been constructed, the situation where the bath spectrum is exactly resonant with the anharmonic oscillator transition frequencies, and the case for which the subsystem is slightly off-resonant with the environment. At short times, reduced dynamics calculations describe the relaxation process qualitatively well but fail to reproduce recurrences observed with MCTDH for longer times. Lifetimes of all the vibrational levels of the Morse oscillator have been calculated, and both Lindblad and MCTDH results show the same dependence of the lifetimes on the initial vibrational state quantum number. A prediction, which should be generic for adsorbate systems is a striking, sharp increase of lifetimes of the subsystem vibrational levels close to the dissociation limit. This is contradictory with harmonic/linear extrapolation laws, which predict a monotonic decrease of the lifetime with initial vibrational quantum number.

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

    Treesearch

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

    2016-01-01

    The challenges posed by observing host-pathogen-environment interactions across large geographic extents and over meaningful time scales limit our ability to understand and manage wildland epidemics. We conducted a landscape-scale, longitudinal study designed to analyze the dynamics of sudden oak death (an emerging forest disease caused by Phytophthora...

  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. 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...

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

    USDA-ARS?s Scientific Manuscript database

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

  18. 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...

  19. 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.

  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. Developmental dynamics of Ambystoma tigrinum in a changing landscape

    PubMed Central

    2010-01-01

    Background Loss of pond habitat is catastrophic to aquatic larval amphibians, but even reduction in the amount of time a breeding site holds water (hydroperiod) can influence amphibian development and limit reproductive success. Using the landscape variation of a glacial valley in the Greater Yellowstone Ecosystem as the context for a natural experiment, we examined variation in growth pattern and life history of the salamander Ambystoma tigrinum melanostictum and determined how these developmental characteristics varied with hydroperiod over several summers. Results In ponds that dried early in the season, maximum larval size was reduced relative to the sizes achieved in permanent ponds. Ephemeral ponds were associated with early metamorphosis at small body sizes, while permanent ponds facilitated longer larval periods and later metamorphosis. Paedomorphosis resulted from indefinite metamorphic postponement, and was identified only in the most permanent environments. Patterns of growth and allometry were similar between ponds with different hydroperiods, but considerable life history variation was derived from modulating the timing of and size at metamorphosis. Considering maximum rates of growth and inferring the minimum size at metamorphosis across 25 ponds over the course of three years, we calculated that hydroperiods longer than three months are necessary to support these populations through metamorphosis and/or reproductive maturity. Conclusions Landscape heterogeneity fosters life history variation in this natural population. Modulation of the complex ambystomatid life cycle allows this species to survive in unpredictable environments, but current trends towards rapid pond drying will promote metamorphosis at smaller sizes and could eliminate the paedomorphic phenotype from this region. Metamorphosis at small size is has been linked to altered fitness traits, including reduced survival and fecundity. Thus, widespread environmental truncation of larval

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

    NASA Astrophysics Data System (ADS)

    Beylich, A. A.; Molau, U.

    2012-04-01

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

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

    PubMed

    Ross, J V

    2006-02-01

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

  5. 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

  6. Exact dynamics following an interaction quench in a one-dimensional anyonic gas

    NASA Astrophysics Data System (ADS)

    Piroli, Lorenzo; Calabrese, Pasquale

    2017-08-01

    We study the nonequilibrium quench dynamics of a one-dimensional anyonic gas. We focus on the integrable anyonic Lieb-Liniger model and consider the quench from noninteracting to hard-core anyons. We study the dynamics of the local properties of the system. By means of integrability-based methods, we compute analytically the one-body density matrix and the density-density correlation function at all times after the quench and in particular at infinite time. Our results show that the system evolves from an initial state where the local momentum distribution function is nonsymmetric to a steady state where it becomes symmetric. Furthermore, while the initial momentum distribution functions (and the equilibrium ones) explicitly depend on the anyonic parameter, the final ones do not. This is reminiscent of the dynamical fermionization observed in the context of free expansions after release from a confining trap.

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

    PubMed

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

    2016-06-22

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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. [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.

  13. 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.

  14. 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.

  15. 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

  16. 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

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

    PubMed Central

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

    2016-01-01

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

  18. Path integral centroid variables and the formulation of their exact real time dynamics

    NASA Astrophysics Data System (ADS)

    Jang, Seogjoo; Voth, Gregory A.

    1999-08-01

    A formalism is presented in this paper which, for the first time, establishes the theoretical basis for the quantum time evolution of path integral centroid variables and also provides clear motivation for using these variables to study condensed phase quantum dynamics. The equilibrium centroid distribution is first shown to be a well-defined distribution function which is specific to the canonical density operator. A quantum mechanical quasi-density operator (QDO) is associated with each value of the distribution so that, upon application of the standard quantum mechanical formalism, the QDO can be used to provide a rigorous definition of both static and dynamical centroid variables. Various properties of the dynamical centroid variables are derived, including the perspective that the centroid constraint on the imaginary time paths introduces a nonstationarity in the equilibrium ensemble which, in turn, can be shown to yield information on the correlations of spontaneous fluctuations. The analytic solution for the harmonic oscillator and a numerical solution for a double well system are provided which illustrate the various aspects of the theory. The theory contained herein provides the basis for a derivation of Centroid Molecular Dynamics, as well as the systematic improvements of that theory.

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

    NASA Astrophysics Data System (ADS)

    Beylich, Achim A.

    2015-04-01

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

  20. 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.

  1. Population Dynamics of Southern Pine Beetle in Forest Landscapes

    Treesearch

    Andrew Birt

    2011-01-01

    Southern pine beetle (SPB) is an important pest of Southeastern United States pine forests. Periodic regional outbreaks are characterized by localized areas of tree mortality (infestations) surrounded by areas with little or no damage. Ultimately, this spatiotemporal pattern of tree mortality is driven by the dynamics of SPB populations—more specifically, by rates of...

  2. Computationally exact methods for stochastic periodic dynamics: Spatiotemporal dispersal and temporally forced transmission.

    PubMed

    Ross, J V

    2010-01-07

    The dynamics of many diseases and populations possess distinct recurring phases. For example, many species breed only during a subset of the year and the infection dynamics of many pathogens have transmission rates that vary with season. Here I investigate computational methods for studying transient and long-term behaviour of stochastic models which have periodic phases-several different potential techniques for studying long-term behaviour will be contrasted. I illustrate the results with two studies: The first is of a spatially realistic metapopulation model of malleefowl (Leipoa ocellata), a species which disperses only during a quarter of the year; this model is used to highlight the advantages and disadvantages of the particular methods presented. The second study is of a model for disease dynamics which incorporates seasonality in both the rate of within-population transmission and also in the rate of transmission effected via aerosol importation. This model has applications to studying disease invasion and persistence in captive-breeding populations. We demonstrate, via comparison to appropriately matched models with constant transmission rates and also no aerosol transmission, that seasonality and aerosol importation may alter control choices, with possibly an increase in the threshold population size for local control surveillance, transfer of importance to limiting aerosol transmission, and the use of temporally targetted surveillance. The methodology presented is the gold-standard for dealing with many phased processes in ecology and epidemiology, but its application is limited to systems of small size.

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

    SciTech Connect

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

    2000-12-15

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

  4. 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.

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  7. 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.

  8. 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.

  9. 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.

  10. A phase transition induces chaos in a predator-prey ecosystem with a dynamic fitness landscape.

    PubMed

    Gilpin, William; Feldman, Marcus W

    2017-07-01

    In many ecosystems, natural selection can occur quickly enough to influence the population dynamics and thus future selection. This suggests the importance of extending classical population dynamics models to include such eco-evolutionary processes. Here, we describe a predator-prey model in which the prey population growth depends on a prey density-dependent fitness landscape. We show that this two-species ecosystem is capable of exhibiting chaos even in the absence of external environmental variation or noise, and that the onset of chaotic dynamics is the result of the fitness landscape reversibly alternating between epochs of stabilizing and disruptive selection. We draw an analogy between the fitness function and the free energy in statistical mechanics, allowing us to use the physical theory of first-order phase transitions to understand the onset of rapid cycling in the chaotic predator-prey dynamics. We use quantitative techniques to study the relevance of our model to observational studies of complex ecosystems, finding that the evolution-driven chaotic dynamics confer community stability at the "edge of chaos" while creating a wide distribution of opportunities for speciation during epochs of disruptive selection-a potential observable signature of chaotic eco-evolutionary dynamics in experimental studies.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  18. Interactive controls of herbivory and fluvial dynamics on landscape vegetation patterns on the Tanana River floodplain, interior Alaska.

    Treesearch

    Lem G. Butler; Knut Kielland; T. Scott Rupp; Thomas A. Hanley

    2007-01-01

    We examined the interactive effects of mammalian herbivory and fluvial dynamics on vegetation dynamics and composition along the Tanana River in interior Alaska between Fairbanks and Manley Hot Springs. We used a spatially explicit model of landscape dynamics (ALFRESCO) to simulate vegetation changes on a 1-year time-step. The model was run for 250 years and was...

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

    PubMed

    Wright, Justin P

    2009-12-01

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

  20. Processes on the emergent landscapes of biochemical reaction networks and heterogeneous cell population dynamics: differentiation in living matters

    PubMed Central

    Li, Fangting

    2017-01-01

    The notion of an attractor has been widely employed in thinking about the nonlinear dynamics of organisms and biological phenomena as systems and as processes. The notion of a landscape with valleys and mountains encoding multiple attractors, however, has a rigorous foundation only for closed, thermodynamically non-driven, chemical systems, such as a protein. Recent advances in the theory of nonlinear stochastic dynamical systems and its applications to mesoscopic reaction networks, one reaction at a time, have provided a new basis for a landscape of open, driven biochemical reaction systems under sustained chemostat. The theory is equally applicable not only to intracellular dynamics of biochemical regulatory networks within an individual cell but also to tissue dynamics of heterogeneous interacting cell populations. The landscape for an individual cell, applicable to a population of isogenic non-interacting cells under the same environmental conditions, is defined on the counting space of intracellular chemical compositions x = (x1,x2, … ,xN) in a cell, where xℓ is the concentration of the ℓth biochemical species. Equivalently, for heterogeneous cell population dynamics xℓ is the number density of cells of the ℓth cell type. One of the insights derived from the landscape perspective is that the life history of an individual organism, which occurs on the hillsides of a landscape, is nearly deterministic and ‘programmed’, while population-wise an asynchronous non-equilibrium steady state resides mostly in the lowlands of the landscape. We argue that a dynamic ‘blue-sky’ bifurcation, as a representation of Waddington's landscape, is a more robust mechanism for a cell fate decision and subsequent differentiation than the widely pictured pitch-fork bifurcation. We revisit, in terms of the chemostatic driving forces upon active, living matter, the notions of near-equilibrium thermodynamic branches versus far-from-equilibrium states. The emergent

  1. 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.

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

    PubMed Central

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

    2006-01-01

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

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

    PubMed

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

    2015-11-01

    Assessing the impact of climate change on urban landscape dynamics (ULD) is the foundation for adapting to climate change and maintaining urban landscape sustainability. This paper demonstrates an alternative future analysis by coupling a system dynamics (SD) and a cellular automata (CA) model. The potential impact of different climate change scenarios on ULD from 2009 to 2030 was simulated and evaluated in the Beijing-Tianjin-Tangshan megalopolis cluster area (BTT-MCA). The results suggested that the integrated model, which combines the advantages of the SD and CA model, has the strengths of spatial quantification and flexibility. Meanwhile, the results showed that the influence of climate change would become more severe over time. In 2030, the potential urban area affected by climate change will be 343.60-1260.66 km(2) (5.55 -20.37 % of the total urban area, projected by the no-climate-change-effect scenario). Therefore, the effects of climate change should not be neglected when designing and managing urban landscape. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. 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.

  5. 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.

  6. [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.

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

    PubMed Central

    2012-01-01

    Abstract Recent progress in stem cell biology, notably cell fate conversion, calls for novel theoretical understanding for cell differentiation. The existing qualitative concept of Waddington’s “epigenetic landscape” has attracted particular attention because it captures subsequent fate decision points, thus manifesting the hierarchical (“tree-like”) nature of cell fate diversification. Here, we generalized a recent work and explored such a developmental landscape for a two-gene fate decision circuit by integrating the underlying probability landscapes with different parameters (corresponding to distinct developmental stages). The change of entropy production rate along the parameter changes indicates which parameter changes can represent a normal developmental process while other parameters’ change can not. The transdifferentiation paths over the landscape under certain conditions reveal the possibility of a direct and reversible phenotypic conversion. As the intensity of noise increases, we found that the landscape becomes flatter and the dominant paths more straight, implying the importance of biological noise processing mechanism in development and reprogramming. We further extended the landscape of the one-step fate decision to that for two-step decisions in central nervous system (CNS) differentiation. A minimal network and dynamic model for CNS differentiation was firstly constructed where two three-gene motifs are coupled. We then implemented the SDEs (Stochastic Differentiation Equations) simulation for the validity of the network and model. By integrating the two landscapes for the two switch gene pairs, we constructed the two-step development landscape for CNS differentiation. Our work provides new insights into cellular differentiation and important clues for better reprogramming strategies. PMID:23300518

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    PubMed

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

    2016-10-01

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

  10. The Exact Nuclear Overhauser Enhancement: Recent Advances.

    PubMed

    Nichols, Parker J; Born, Alexandra; Henen, Morkos A; Strotz, Dean; Orts, Julien; Olsson, Simon; Güntert, Peter; Chi, Celestine N; Vögeli, Beat

    2017-07-14

    Although often depicted as rigid structures, proteins are highly dynamic systems, whose motions are essential to their functions. Despite this, it is difficult to investigate protein dynamics due to the rapid timescale at which they sample their conformational space, leading most NMR-determined structures to represent only an averaged snapshot of the dynamic picture. While NMR relaxation measurements can help to determine local dynamics, it is difficult to detect translational or concerted motion, and only recently have significant advances been made to make it possible to acquire a more holistic representation of the dynamics and structural landscapes of proteins. Here, we briefly revisit our most recent progress in the theory and use of exact nuclear Overhauser enhancements (eNOEs) for the calculation of structural ensembles that describe their conformational space. New developments are primarily targeted at increasing the number and improving the quality of extracted eNOE distance restraints, such that the multi-state structure calculation can be applied to proteins of higher molecular weights. We then review the implications of the exact NOE to the protein dynamics and function of cyclophilin A and the WW domain of Pin1, and finally discuss our current research and future directions.

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

    NASA Astrophysics Data System (ADS)

    Plowes, Robert Merrick

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

  12. Exact wave packet dynamics of singlet fission in unsubstituted and substituted polyene chains within long-range interacting models

    NASA Astrophysics Data System (ADS)

    Prodhan, Suryoday; Ramasesha, S.

    2017-08-01

    Singlet fission (SF) is a potential pathway for significant enhancement of efficiency in organic solar cells (OSC). In this paper, we study singlet fission in a pair of polyene molecules in two different stacking arrangements employing exact many-body wave packet dynamics. In the noninteracting model, the SF yield is absent. The individual molecules are treated within Hubbard and Pariser-Parr-Pople (PPP) models and the interaction between them involves transfer terms, intersite electron repulsions, and site-charge-bond-charge repulsion terms. Initial wave packet is constructed from excited singlet state of one molecule and ground state of the other. Time development of this wave packet under the influence of intermolecular interactions is followed within the Schrödinger picture by an efficient predictor-corrector scheme. In unsubstituted Hubbard and PPP chains, 2 1A excited singlet state leads to significant SF yield while the 1 1B state gives negligible fission yield. On substitution by donor-acceptor groups of moderate strength, the lowest excited state will have sufficient 2 1A character and hence results in significant SF yield. Because of rapid internal conversion, the nature of the lowest excited singlet will determine the SF contribution to OSC efficiency. Furthermore, we find the fission yield depends considerably on the stacking arrangement of the polyene molecules.

  13. 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. © 2012 American Physical Society

  14. 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

  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. 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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2016-09-09

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

  20. 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.

  1. Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations.

    PubMed

    Lei, Hongxing; Wu, Chun; Liu, Haiguang; Duan, Yong

    2007-03-20

    High-accuracy ab initio folding has remained an elusive objective despite decades of effort. To explore the folding landscape of villin headpiece subdomain HP35, we conducted two sets of replica exchange molecular dynamics for 200 ns each and three sets of conventional microsecond-long molecular dynamics simulations, using AMBER FF03 force field and a generalized-Born solvation model. The protein folded consistently to the native state; the lowest C(alpha)-rmsd from the x-ray structure was 0.46 A, and the C(alpha)- rmsd of the center of the most populated cluster was 1.78 A at 300 K. ab initio simulations have previously not reached this level. The folding landscape of HP35 can be partitioned into the native, denatured, and two intermediate-state regions. The native state is separated from the major folding intermediate state by a small barrier, whereas a large barrier exists between the major folding intermediate and the denatured states. The melting temperature T(m) = 339 K extracted from the heat-capacity profile was in close agreement with the experimentally derived T(m) = 342 K. A comprehensive picture of the kinetics and thermodynamics of HP35 folding emerges when the results from replica exchange and conventional molecular dynamics simulations are combined.

  2. 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.

  3. 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.

  4. 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

  5. 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

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

    PubMed

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

    2012-01-01

    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. 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. 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.

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

    PubMed

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

    2015-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  10. Modeling the Influence of Dynamic Zoning of Forest Harvesting on Ecological Succession in a Northern Hardwoods Landscape

    Treesearch

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

    2005-01-01

    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...

  11. Influence of dynamic topography on the evolution of the Australian landscape since the Late Jurassic

    NASA Astrophysics Data System (ADS)

    Flament, N. E.; Salles, T.; Müller, D.

    2016-12-01

    Australia is an outstanding natural laboratory to study the influence of dynamic topography on landscape evolution, having been largely unaffected by tectonic deformation since the Jurassic. For instance, the sedimentary deposits of the Eromanga inland sea that covered a third of Australia between 130 and 100 Myr ago were laid down because of flow deep within the Earth. We coupled CitcomS (a finite element code for thermochemical mantle convection) to Badlands (a finite volume code for geomorphological and stratigraphic evolution) to quantify the feedbacks between mantle flow, landscape dynamics and sediment transport at continental scale. Here we apply the approach to the evolution of the Australian landscape over the last 150 Myr. The mantle flow model predicts that Australia was dynamically tilted down to the east 150 Myr ago due to long-lived subduction along the eastern border of the continent. Subduction ceased 100 Myr ago and the eastward migration of eastern Australia over sinking ancient Gondwanaland slabs caused it to rebound from being drawn down. Following a period of absolute plate motion stagnation, renewed uplift of the eastern highlands occurred during the Cenozoic, as the Australian plate migrated over the Pacific Superswell. We forced Badlands models with this predicted evolution of dynamic topography in addition to a history of varying climate and long-term sea-level. The Badlands models quantify the time dependence of erosion and deposition, as well as the evolution of catchment dynamics, drainage capture and drainage network reorganisation. They show that the motion of the Australian plate resulted in significant changes in river drainage, intercontinental erosion and sedimentation. The predicted cumulative denudation and sedimentation is compatible with thermochronology data in the eastern highlands and with the sediment thickness in the Ceduna Basin. The present-day eastern Australian river profiles and drainage are in agreement with

  12. 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.

  13. 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

  14. 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

  15. 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

  16. 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.

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

    USGS Publications Warehouse

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

    2007-01-01

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

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

    DOE PAGES

    Damschen, Ellen I.; Brudvig, Lars A.; Haddad, Nick M.; ...

    2008-12-05

    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 togenerate 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-dispersedmore » 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.« less

  19. 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.

  20. 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.

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

    SciTech Connect

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

    2008-12-05

    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 togenerate 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.

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

    SciTech Connect

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

    2007-10-01

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

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

    PubMed Central

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

    2007-01-01

    Microscopic statistical pressure fluctuations can, in principle, lead to corresponding fluctuations in the shape of a protein energy landscape. To examine this, nanosecond molecular dynamics simulations of lysozyme are performed covering a range of temperatures and pressures. The well known dynamical transition with temperature is found to be pressure-independent, indicating that the effective energy barriers separating conformational substates are not significantly influenced by pressure. In contrast, vibrations within substates stiffen with pressure, due to increased curvature of the local harmonic potential in which the atoms vibrate. The application of pressure is also shown to selectively increase the damping of the anharmonic, low-frequency collective modes in the protein, leaving the more local modes relatively unaffected. The critical damping frequency, i.e., the frequency at which energy is most efficiently dissipated, increases linearly with pressure. The results suggest that an invariant description of protein energy landscapes should be subsumed by a fluctuating picture and that this may have repercussions in, for example, mechanisms of energy dissipation accompanying functional, structural, and chemical relaxation. PMID:17956984

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

    PubMed

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

    2007-10-30

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

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

    SciTech Connect

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

    2007-08-01

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

  6. 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.

  7. 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

  8. [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.

  9. 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

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

    PubMed

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

    2010-12-01

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

  11. 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.

  12. Characterizing permafrost active layer dynamics and sensitivity to landscape spatial heterogeneity: A case study in Alaska

    NASA Astrophysics Data System (ADS)

    Yi, Y.; Kimball, J. S.; Moghaddam, M.; Reichle, R. H.

    2016-12-01

    An important feature of the Arctic is the large spatial heterogeneity in permafrost and active layer conditions, which are generally poorly represented in global climate and carbon models and can lead to large uncertainties in predicting regional ecosystem responses and feedbacks to climate change. In this study, we developed a spatially integrated analysis and modeling framework to investigate the sensitivity of permafrost active layer processes to sub-grid heterogeneity in vegetation, terrain and disturbance factors. The model framework combines detailed field measurements of vegetation, microclimate and active layer properties with local scale ( 100m resolution) soil active layer retrievals from airborne radar remote sensing, and landscape level (≥1-km resolution) environmental observations from satellite microwave and optical-infrared sensors. Satellite observations, including land surface temperature, snow cover extent and soil moisture from the MODIS and SMAP sensors, are used as primary model drivers for estimating snow/soil thermal conductivity and soil temperature profiles. The model estimates regional patterns and recent changes (2001-present) in permafrost extent (PE) and ALT across Alaska at landscape scale ( 1-km resolution). Local scale maps of active layer conditions and additional land parameters include soil moisture and surface organic layer thickness from combined low frequency (L+P-band) airborne radar backscatter from the NASA UAVSAR and AirMOSS sensors will be used to inform the coarser landscape model simulations and quantify the effects of surface organic layer and soil moisture spatial heterogeneity on the estimated soil active layer dynamics. These results are used to clarify regional patterns and recent changes in permafrost active layer conditions, and underlying environmental controls across Alaska.

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. 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.

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

    PubMed

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

    2016-05-01

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

  19. Structure and energy landscape of a photoswitchable peptide: a replica exchange molecular dynamics study.

    PubMed

    Nguyen, Phuong H; Mu, Yuguang; Stock, Gerhard

    2005-08-15

    A replica exchange molecular dynamics (REMD) simulation of a bicyclic azobenzene peptide in explicit dimethyl sulfoxide solution is presented in order to characterize the conformational structures and energy landscape of a photoswitchable peptide. It is shown that an enhanced-sampling technique such as the REMD method is essential to obtain a converged conformational sampling of the peptide at room temperature. This is because conventional MD simulations of less than approximately 100-ns length are either trapped in local minima (at 295 K) or-if run at high temperature-do not resemble the room-temperature REMD results. Calculating various nuclear Overhauser effects (NOEs) and (3)J-couplings, a good overall agreement between the REMD simulations and the NMR experiments of Renner et al. (Biopolymers 2000;54:501-514) is found. In particular, the REMD study confirms the general picture drawn by Renner et al. that the trans-isomer of the azobenzene peptide exhibits a well-defined structure, while the cis-isomer is a conformational heterogeneous system; that is, the trans-isomer occurs in 2 well-defined conformers, while the cis-isomer represents an energetically frustrated system that leads to an ensemble of conformational structures. Employing a principal component analysis of the REMD data, the free energy landscape of the systems is studied at various temperatures. The implications for the folding and unfolding pathways of the system are discussed. (c) 2005 Wiley-Liss, Inc.

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

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

    Natural forest structures vary at multiple spatial scales. This variation reflects the occurrence of driving factors, such as disturbances and variation in soil or topography. To explore and understand the linkages of forest structural characteristics and factors driving their variation, we need to recognize how the structural characteristics vary in relation to spatial scale. This can be achieved by identifying scale-dependent features in forest structure within unmanaged forest landscapes. By identifying these features and examining their relationship with potential driving factors, we can better understand the dynamics of forest structural development. Here, we examine the spatial variation in forest structures at multiple spatial scales, utilizing data from old-growth boreal forests in two regions with contrasting disturbance regimes: northern Finland and north-eastern Québec, Canada ( 67° 45'N, 29° 36'E, 49° 39'N, 67° 55'W, respectively). The three landscapes (4 km2 each) in Finland are dominated by Pinus sylvestris and Picea abies, whereas the two landscapes in Québec are dominated by Abies balsamea and Picea mariana. Québec's forests are a subject to cyclic outbreaks of the eastern spruce budworm, causing extensive mortality especially in A. balsamea-dominated stands. In the Finnish landscapes, gap- to patch-scale disturbances due to tree senescence, fungi and wind, as well as infrequent surface fires in areas dominated by P. sylvestris, prevail. Owing to the differences in the species compositions and the disturbance regimes, we expect differing scales of variation between the landscapes. To quantify patterns of variation, we visually interpret stereopairs of recent aerial photographs. From the photographs, we collect information on forest canopy coverage, species composition and dead wood. For the interpretation, each 4 km2 plot is divided into 0.1ha square cells (4096 per plot). Interpretations are validated against field observations and compiled

  3. 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. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. 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.

  5. 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.

  6. 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...

  7. 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...

  8. Dynamics of ecosystem service values in response to landscape pattern changes from 1995 to 2005 in Guangzhou, Southern China

    Treesearch

    Yanqiong Ye; Jia' en Zhang; Lili Chen; Ying Ouyang; Prem Parajuli

    2015-01-01

    This study analyzed the landscape pattern changes, the dynamics of the ecosystem service values (ESVs) and the spatial distribution of ESVs from 1995 to 2005 in Guangzhou, which is the capital of Guangdong Province and a regional central city in South China. Remote sensing data and geographic information system techniques, in conjunction with spatial metrics, were used...

  9. Landscape context and long-term tree influences shape the dynamics of forest-meadow ecotones in mountain ecosystems

    Treesearch

    R.E. Haugo; C.B. Halpern; J.D. Bakker

    2011-01-01

    Forest-meadow ecotones are prominent and dynamic features of mountain ecosystems. Understanding how vegetation changes are shaped by long-term interactions with trees and are mediated by the physical environment is critical to predicting future trends in biological diversity across these landscapes. We examined 26 yr of vegetation change (1983-2009) across 20 forest-...

  10. 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.

  11. 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.

  12. 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.

  13. Construction of the Free Energy Landscape of Peptide Aggregation from Molecular Dynamics Simulations.

    PubMed

    Riccardi, Laura; Nguyen, Phuong H; Stock, Gerhard

    2012-04-10

    To describe the structure and dynamics of oligomers during peptide aggregation, a method is proposed that considers both the intramolecular and intermolecular structures of the multimolecule system and correctly accounts for its degeneracy. The approach is based on the "by-parts" strategy, which partitions a complex molecular system into parts, determines the metastable conformational states of each part, and describes the overall conformational state of the system in terms of a product basis of the states of the parts. Starting from a molecular dynamics simulation of n molecules, the method consists of three steps: (i) characterization of the intramolecular structure, that is, of the conformational states of a single molecule in the presence of the other molecules (e.g., β-strand or random coil); (ii) characterization of the intermolecular structure through the identification of all occurring aggregate states of the peptides (dimers, trimers, etc.); and (iii) construction of the overall conformational states of the system in terms of a product basis of the n "single-molecule" states and the aggregate states. Considering the Alzheimer β-amyloid peptide fragment Aβ16-22 as a first application, about 700 overall conformational states of the trimer (Aβ16-22)3 were constructed from all-atom molecular dynamics simulation in explicit water. Based on these states, a transition network reflecting the free energy landscape of the aggregation process can be constructed that facilitates the identification of the aggregation pathways.

  14. 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

  15. The energy landscape underpinning module dynamics in the human brain connectome.

    PubMed

    Ashourvan, Arian; Gu, Shi; Mattar, Marcelo G; Vettel, Jean M; Bassett, Danielle S

    2017-06-07

    Human brain dynamics can be viewed through the lens of statistical mechanics, where neurophysiological activity evolves around and between local attractors representing mental states. Many physically-inspired models of these dynamics define brain states based on instantaneous measurements of regional activity. Yet, recent work in network neuroscience has provided evidence that the brain might also be well-characterized by time-varying states composed of locally coherent activity or functional modules. We study this network-based notion of brain state to understand how functional modules dynamically interact with one another to perform cognitive functions. We estimate the functional relationships between regions of interest (ROIs) by fitting a pair-wise maximum entropy model to each ROI's pattern of allegiance to functional modules. This process uses an information theoretic notion of energy (as opposed to a metabolic one) to produce an energy landscape in which local minima represent attractor states characterized by specific patterns of modular structure. The clustering of local minima highlights three classes of ROIs with similar patterns of allegiance to community states. Visual, attention, sensorimotor, and subcortical ROIs are well-characterized by a single functional community. The remaining ROIs affiliate with a putative executive control community or a putative default mode and salience community. We simulate the brain's dynamic transitions between these community states using a random walk process. We observe that simulated transition probabilities between basins are statistically consistent with empirically observed transitions in resting state fMRI data. These results offer a view of the brain as a dynamical system that transitions between basins of attraction characterized by coherent activity in groups of brain regions, and that the strength of these attractors depends on the ongoing cognitive computations. Copyright © 2017 The Authors. Published by

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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

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

    PubMed

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

    2014-01-01

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

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. Metapopulation persistence in a dynamic landscape: more habitat or better stewardship?

    PubMed

    Ross, Joshua V; Sirl, David J; Pollett, Philip K; Possingham, Hugh P

    2008-04-01

    Habitat loss and fragmentation has created metapopulations where there were once continuous populations. Ecologists and conservation biologists have become interested in the optimal way to manage and conserve such metapopulations. Several authors have considered the effect of patch disturbance and recovery on metapopulation persistence, but almost all such studies assume that every patch is equally susceptible to disturbance. We investigated the influence of protecting patches from disturbance on metapopulation persistence, and used a stochastic metapopulation model to answer the question: How can we optimally trade off returns from protection of patches vs. creation of patches? We considered the problem of finding, under budgetary constraints, the optimal combination of increasing the number of patches in the metapopulation network vs. increasing the number of protected patches in the network. We discovered that the optimal trade-off is dependent upon all of the properties of the system: the species dynamics, the dynamics of the landscape, and the relative costs of each action. A stochastic model and accompanying methodology are provided allowing a manager to determine the optimal policy for small metapopulations. We also provide two approximations, including a rule of thumb, for determining the optimal policy for larger metapopulations. The method is illustrated with an example inspired by information for the greater bilby, Macrotis lagotis, inhabiting southwestern Queensland, Australia. We found that given realistic costs for each action, protection of patches should be prioritized over patch creation for improving the persistence of the greater bilby during the next 20 years.

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

    NASA Astrophysics Data System (ADS)

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

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

  15. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

  17. 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

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

    USGS Publications Warehouse

    Mueller, Thomas; Olson, K.A.; Dressler, G.; Leimgruber, Peter; Fuller, Todd K.; Nicholson, Craig; Novaro, A.J.; Bolgeri, M.J.; Wattles, D.; Destefano, Stephen; Calabrese, J.M.; Fagan, William 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

  19. 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

  20. The DYNAFLUX / DYNACOLD (Dynamics, Fluxes, Stability, Succession and Landscape Formation in Cold Environments) Network (2004-2017)

    NASA Astrophysics Data System (ADS)

    Beylich, Achim A.

    2017-04-01

    There is a wide range of high-latitude and high-altitude cold climate landscapes within 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 unique opportunity to study the interactions between geo-, bio-, social and socio-economic systems at the land surface. The DYNAFLUX / DYNACOLD Network (2004-2017) bridges across the geo-, bio-, social and socio-economic sciences in order to analyze the complex dynamics of adjustment, stabilization, succession and landscape formation during and after ice retreat and under ongoing anthropogenic influences. The network provides a multidisciplinary forum where researchers come together and discuss. In addition, this network is linking a number of other scientific networks, working groups and programs and creates an umbrella network and a forum for sharing knowledge and experience. The scientific focus of DYNAFLUX / DYNACOLD is also relevant for a number of end users, including risk and vulnerability assessment, sustainable land use, land management and conservation. In addition, present key questions related to environmental change like, e.g., hazards, permafrost degradation and loss of biodiversity are addressed and discussed. Further information is found under http://www.ngu.no/sediflux.

  1. 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.

  2. 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.

  3. 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

  4. Spatiotemporal dynamics of climate and agricultural landscape patterns in Xinjiang, China (2000-2015)

    NASA Astrophysics Data System (ADS)

    Huang, T.; Du, Q. Y.; Zou, J. Q.

    2017-07-01

    This study integrated remote sensing, geographic information system, landscape ecology, and spatial analysis, and is based on meteorological data and four remote sensing images (2000-2015). The aim of this study was to analyse climate trends and spatiotemporal changes in agricultural landscape patterns, and calculate agricultural ecosystem service value (AESV) in Xinjiang, China. In addition, correlation analysis further enabled the quantification of agricultural landscape pattern changes in response to climate change. Results showed that temperature and precipitation registered a fluctuating ascending trend in most areas of Xinjiang. Landscape diversity and fragmentation increased during the same period. AESV showed a trend of gradual increase, the waste disposal and the water retention are the most important ecological functions. Besides, agricultural landscape pattern significantly correlated to climate and the effect of precipitation on agricultural landscape patterns has been greater than the effect of temperature during 2000-2015.

  5. 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

  6. Historical and projected trends in landscape drivers affecting carbon dynamics in Alaska.

    PubMed

    Pastick, Neal J; Duffy, Paul; Genet, Hélène; Rupp, T Scott; Wylie, Bruce K; Johnson, Kristofer D; Jorgenson, M Torre; Bliss, Norman; McGuire, A David; Jafarov, Elchin E; Knight, Joseph F

    2017-07-01

    Modern climate change in Alaska has resulted in widespread thawing of permafrost, increased fire activity, and extensive changes in vegetation characteristics that have significant consequences for socioecological systems. Despite observations of the heightened sensitivity of these systems to change, there has not been a comprehensive assessment of factors that drive ecosystem changes throughout Alaska. Here we present research that improves our understanding of the main drivers of the spatiotemporal patterns of carbon dynamics using in situ observations, remote sensing data, and an array of modeling techniques. In the last 60 yr, Alaska has seen a large increase in mean annual air temperature (1.7°C), with the greatest warming occurring over winter and spring. Warming trends are projected to continue throughout the 21st century and will likely result in landscape-level changes to ecosystem structure and function. Wetlands, mainly bogs and fens, which are currently estimated to cover 12.5% of the landscape, strongly influence exchange of methane between Alaska's ecosystems and the atmosphere and are expected to be affected by thawing permafrost and shifts in hydrology. Simulations suggest the current proportion of near-surface (within 1 m) and deep (within 5 m) permafrost extent will be reduced by 9-74% and 33-55% by the end of the 21st century, respectively. Since 2000, an average of 678 595 ha/yr was burned, more than twice the annual average during 1950-1999. The largest increase in fire activity is projected for the boreal forest, which could result in a reduction in late-successional spruce forest (8-44%) and an increase in early-successional deciduous forest (25-113%) that would mediate future fire activity and weaken permafrost stability in the region. Climate warming will also affect vegetation communities across arctic regions, where the coverage of deciduous forest could increase (223-620%), shrub tundra may increase (4-21%), and graminoid tundra

  7. Historical and Projected Trends in Landscape Drivers Affecting Carbon Dynamics in Alaska

    NASA Astrophysics Data System (ADS)

    Pastick, N. J.; Duffy, P.; Genet, H.; Rupp, S. T.; Wylie, B. K.; Johnson, K. D.; Jorgenson, T.; McGuire, A. D.; Jafarov, E. E.; Knight, J. F.

    2016-12-01

    Modern climate change in Alaska has resulted in widespread thawing of permafrost, increased fire activity, and extensive changes in vegetation characteristics that have significant consequences for socio-ecological systems. Despite observations of the heightened sensitivity of these systems to change, there has not been a comprehensive assessment of factors that drive ecosystem changes throughout Alaska. Here we present research that improves understanding of the main drivers of the spatiotemporal patterns of carbon dynamics using in situ observations, remote sensing data, and an array of modeling and statistical techniques. In the last 60 years, Alaska has seen a large increase in mean annual air temperature ( 1.7 °C) and growing season length (50-75%), with the greatest warming occurring over winter and spring. Warming trends are projected to continue throughout the 21st Century and will likely result in landscape-level changes to ecosystem structure and function. Wetlands, mainly bogs and fens, which are currently estimated to cover 12.5% of the landscape, strongly influence exchange of CH4 between Alaska's ecosystems and the atmosphere and are expected to be affected by thawing permafrost and shifts in hydrology. Simulations suggest the current proportion of near-surface (within 1 m) and deep (within 5 m) permafrost extent will be reduced by 9-74% and 33-55% by the end of the 21st Century, respectively. Since 2000, an average of 678,595 ha/yr was burned, more than twice the annual average during 1950-1999. The largest increase in fire activity is projected for the boreal forest, which could result in a reduction in late-successional spruce forest (8-44%) and an increase in early-successional deciduous forest (25-113%) that would mediate future fire activity and weaken permafrost stability in the region. Climate warming will also affect vegetation communities across arctic regions, where the coverage of deciduous forest could increase (223-620%), shrub tundra

  8. Historical and Projected Trends in Landscape Drivers Affecting Carbon Dynamics in Alaska

    DOE PAGES

    Pastick, Neal J.; Duffy, Paul; Genet, Hélène; ...

    2017-04-08

    Modern climate change in Alaska has resulted in widespread thawing of permafrost, increased fire activity, and extensive changes in vegetation characteristics that have significant consequences for socio-ecological systems. Despite observations of the heightened sensitivity of these systems to change, there has not been a comprehensive assessment of factors that drive ecosystem changes throughout Alaska. In this paper, we present research that improves our understanding of the main drivers of the spatiotemporal patterns of carbon dynamics using in situ observations, remote sensing data, and an array of modeling techniques. In the last 60 years, Alaska has seen a large increase inmore » mean annual air temperature (1.7 °C), with the greatest warming occurring over winter and spring. Warming trends are projected to continue throughout the 21st century and will likely result in landscape-level changes to ecosystem structure and function. Wetlands, mainly bogs and fens, which are currently estimated to cover 12.5% of the landscape, strongly influence exchange of methane between Alaska's ecosystems and the atmosphere and are expected to be affected by thawing permafrost and shifts in hydrology. Simulations suggest the current proportion of near-surface (within 1 m) and deep (within 5 m) permafrost extent will be reduced by 9–74% and 33–55% by the end of the 21st century, respectively. Since 2000, an average of 678,595 ha/yr was burned, more than twice the annual average during 1950–1999. The largest increase in fire activity is projected for the boreal forest, which could result in a reduction in late-successional spruce forest (8–44%) and an increase in early-succession deciduous forest (25–113%) that would mediate future fire activity and weaken permafrost stability in the region. Climate warming will also affect vegetation communities across arctic regions, where the coverage of deciduous forest could increase (223–620%), shrub tundra may increase (4

  9. Historical and projected trends in landscape drivers affecting carbon dynamics in Alaska

    USGS Publications Warehouse

    Pastick, Neal J.; Duffy, Paul A; Genet, Hélène; Rupp, T. Scott; Wylie, Bruce K.; Johnson, Kristofer; Jorgenson, M. Torre; Bliss, Norman B.; McGuire, Anthony David; Jafarov, Elchin; Knight, Joseph F.

    2017-01-01

    Modern climate change in Alaska has resulted in widespread thawing of permafrost, increased fire activity, and extensive changes in vegetation characteristics that have significant consequences for socioecological systems. Despite observations of the heightened sensitivity of these systems to change, there has not been a comprehensive assessment of factors that drive ecosystem changes throughout Alaska. Here we present research that improves our understanding of the main drivers of the spatiotemporal patterns of carbon dynamics using in situ observations, remote sensing data, and an array of modeling techniques. In the last 60 yr, Alaska has seen a large increase in mean annual air temperature (1.7°C), with the greatest warming occurring over winter and spring. Warming trends are projected to continue throughout the 21st century and will likely result in landscape-level changes to ecosystem structure and function. Wetlands, mainly bogs and fens, which are currently estimated to cover 12.5% of the landscape, strongly influence exchange of methane between Alaska's ecosystems and the atmosphere and are expected to be affected by thawing permafrost and shifts in hydrology. Simulations suggest the current proportion of near-surface (within 1 m) and deep (within 5 m) permafrost extent will be reduced by 9–74% and 33–55% by the end of the 21st century, respectively. Since 2000, an average of 678 595 ha/yr was burned, more than twice the annual average during 1950–1999. The largest increase in fire activity is projected for the boreal forest, which could result in a reduction in late-successional spruce forest (8–44%) and an increase in early-successional deciduous forest (25–113%) that would mediate future fire activity and weaken permafrost stability in the region. Climate warming will also affect vegetation communities across arctic regions, where the coverage of deciduous forest could increase (223–620%), shrub tundra may increase (4–21%), and

  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. 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.

  13. 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

  14. 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

  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. 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.

  17. 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.

  18. 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.

  19. 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.

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

    PubMed Central

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

    2011-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  6. Dynamic regulation on energy landscape evolution of single-molecule protein by conformational fluctuation.

    PubMed

    Lin, Chien Y; Huang, Jung Y; Lo, Leu-Wei

    2012-08-01

    We formalize a theory to help explore the effect of conformational fluctuation on the energy landscape evolution of single-molecule protein. Using this formalization, we investigate the photon emission from single photoactivated fluorescent protein. A bimodal regulation on the energy landscape evolution was discovered, and its origin was attributed to slow conformational fluctuations of the protein matrix.

  7. Adaptation approaches for conserving ecosystems services and biodiversity in dynamic landscapes caused by climate change

    Treesearch

    Oswald J. Schmitz; Anne M. Trainor

    2014-01-01

    Climate change stands to cause animal species to shift their geographic ranges. This will cause ecosystems to become reorganized across landscapes as species migrate into and out of specific locations with attendant impacts on values and services that ecosystems provide to humans. Conservation in an era of climate change needs to ensure that landscapes are resilient by...

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

    Treesearch

    T.A. Spies; W.J. Ripple; G.A. Bradshaw

    1994-01-01

    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-km2 managed forest landscape in western Oregon was classified into two forest types, closed-canopy conifer forest (CF) (typically, > 60% conifer cover) and...

  9. Range and variation in landscape patch dynamics: Implications for ecosystem management

    Treesearch

    Robert E. Keane; Janice L. Garner; Casey Teske; Cathy Stewart; Paul Hessburg

    2001-01-01

    Northern Rocky Mountain landscape patterns are shaped primarily by fire and succession, and conversely, these vegetation patterns influence burning patterns and plant colonization processes. Historical range and variability (HRV) of landscape pattern can be quantified from three sources: (1) historical chronosequences, (2) spatial series, and (3) simulated...

  10. Simulating fire and forest dynamics for a coordinated landscape fuel treatment project in the Sierra Nevada

    Treesearch

    Brandon M. Collins; Scott L. Stephens; Gary B. Roller; John Battles

    2011-01-01

    We evaluate an actual landscape fuel treatment project that was designed by local U. S. Forest Service managers in the northern Sierra Nevada. We model the effects of this project at reducing landscape-level fire behavior at multiple time steps, up to nearly 30 yr beyond treatment implementation. Additionally, we modeled planned treatments under multiple diameter-...

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function

    PubMed Central

    Quarta, Giulio; Sin, Ken; Schlick, Tamar

    2012-01-01

    Riboswitches are RNAs that modulate gene expression by ligand-induced conformational changes. However, the way in which sequence dictates alternative folding pathways of gene regulation remains unclear. In this study, we compute energy landscapes, which describe the accessible secondary structures for a range of sequence lengths, to analyze the transcriptional process as a given sequence elongates to full length. In line with experimental evidence, we find that most riboswitch landscapes can be characterized by three broad classes as a function of sequence length in terms of the distribution and barrier type of the conformational clusters: low-barrier landscape with an ensemble of different conformations in equilibrium before encountering a substrate; barrier-free landscape in which a direct, dominant “downhill” pathway to the minimum free energy structure is apparent; and a barrier-dominated landscape with two isolated conformational states, each associated with a different biological function. Sharing concepts with the “new view” of protein folding energy landscapes, we term the three sequence ranges above as the sensing, downhill folding, and functional windows, respectively. We find that these energy landscape patterns are conserved in various riboswitch classes, though the order of the windows may vary. In fact, the order of the three windows suggests either kinetic or thermodynamic control of ligand binding. These findings help understand riboswitch structure/function relationships and open new avenues to riboswitch design. PMID:22359488

  3. Influence of dynamic topography on the evolution of the eastern Australian landscape since the Upper Jurassic Epoch

    NASA Astrophysics Data System (ADS)

    Salles, Tristan; Flament, Nicolas; Müller, Dietmar

    2017-04-01

    Australia is an outstanding natural laboratory to study the influence of dynamic topography on landscape evolution, having been largely unaffected by tectonic deformation since the Jurassic. Recent studies of the past eastern Australian landscape from present-day longitudinal river profiles and from mantle flow models suggest that the interaction of plate motion with mantle convection accounts for the two phases of large-scale uplift of the region since 120 Ma. We coupled the dynamic topography predicted by one of these mantle flow models (using the finite element code for thermochemical mantle convection CitcomS) to a surface process model (using the finite volume code for geomorphological and stratigraphic evolution Badlands) to quantify the feedbacks between mantle flow, landscape dynamics and sediment transport at continental scale. Here we apply the approach to the evolution of the Australian landscape over the last 150 Myr. The mantle flow model predicts that Australia was dynamically tilted down to the east 150 Myr ago due to long-lived subduction along the eastern border of the continent. Subduction rolled back 100 Myr ago and the eastward migration of eastern Australia over sinking ancient Gondwanaland slabs caused it to rebound from being drawn down. Following a period of absolute plate motion stagnation, renewed uplift of the eastern highlands occurred during the Cenozoic, as the Australian plate migrated over the Pacific Superswell. We forced Badlands models with this predicted evolution of dynamic topography, varying rainfall regime, erodibility, long-term sea level variations, dynamic topography magnitude and elastic thickness across a series of experiments. The Badlands models quantify the time dependence of erosion and deposition, as well as the evolution of catchment dynamics, drainage capture and drainage network reorganisation. The predicted temporal and spatial changes in longitudinal river profiles as well as erosion and deposition maps show

  4. 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.

  5. 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

  6. 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

  7. 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

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

    PubMed

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

    2013-01-01

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

  9. Simulation of the Vortex Dynamics in a Real Pinning Landscape of YBa2Cu3O7-δ Coated Conductors

    DOE PAGES

    Sadovskyy, I. A.; Koshelev, A. E.; Glatz, A.; ...

    2016-01-01

    The ability of high-temperature superconductors (HTSs) to carry very large currents with almost no dissipation makes them irreplaceable for high-power applications. The development and further improvement of HTS-based cables require an in-depth understanding of the superconducting vortex dynamics in the presence of complex pinning landscapes. We present a critical current analysis of a real HTS sample in a magnetic field by combining state-of-the-art large-scale Ginzburg-Landau simulations with reconstructive three-dimensional scanning-transmission-electron-microscopy tomography of the pinning landscape in Dy-doped YBa2Cu3O7-δ. This methodology provides a unique look at the vortex dynamics in the presence of a complex pinning landscape responsible for the high-current-carrying-capacitymore » characteristic of commercial HTS wires. Finally, our method demonstrates very good functional and quantitative agreement of the critical current between simulation and experiment, providing a new predictive tool for HTS wire designs.« less

  10. The Approach Towards Equilibrium in a Reversible Ising Dynamics Model: An Information-Theoretic Analysis Based on an Exact Solution

    NASA Astrophysics Data System (ADS)

    Lindgren, Kristian; Olbrich, Eckehard

    2017-08-01

    We study the approach towards equilibrium in a dynamic Ising model, the Q2R cellular automaton, with microscopic reversibility and conserved energy for an infinite one-dimensional system. Starting from a low-entropy state with positive magnetisation, we investigate how the system approaches equilibrium characteristics given by statistical mechanics. We show that the magnetisation converges to zero exponentially. The reversibility of the dynamics implies that the entropy density of the microstates is conserved in the time evolution. Still, it appears as if equilibrium, with a higher entropy density is approached. In order to understand this process, we solve the dynamics by formally proving how the information-theoretic characteristics of the microstates develop over time. With this approach we can show that an estimate of the entropy density based on finite length statistics within microstates converges to the equilibrium entropy density. The process behind this apparent entropy increase is a dissipation of correlation information over increasing distances. It is shown that the average information-theoretic correlation length increases linearly in time, being equivalent to a corresponding increase in excess entropy.

  11. The Approach Towards Equilibrium in a Reversible Ising Dynamics Model: An Information-Theoretic Analysis Based on an Exact Solution

    NASA Astrophysics Data System (ADS)

    Lindgren, Kristian; Olbrich, Eckehard

    2017-06-01

    We study the approach towards equilibrium in a dynamic Ising model, the Q2R cellular automaton, with microscopic reversibility and conserved energy for an infinite one-dimensional system. Starting from a low-entropy state with positive magnetisation, we investigate how the system approaches equilibrium characteristics given by statistical mechanics. We show that the magnetisation converges to zero exponentially. The reversibility of the dynamics implies that the entropy density of the microstates is conserved in the time evolution. Still, it appears as if equilibrium, with a higher entropy density is approached. In order to understand this process, we solve the dynamics by formally proving how the information-theoretic characteristics of the microstates develop over time. With this approach we can show that an estimate of the entropy density based on finite length statistics within microstates converges to the equilibrium entropy density. The process behind this apparent entropy increase is a dissipation of correlation information over increasing distances. It is shown that the average information-theoretic correlation length increases linearly in time, being equivalent to a corresponding increase in excess entropy.

  12. 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.

  13. [Dynamic changes of land use and landscape patterns in middle reaches of Shule River, Northwest China].

    PubMed

    Pan, Jing-Hu; Su, You-Cai; Huang, Yong-Sheng; Liu, Xiao

    2012-04-01

    By using the MSS images in 1976, TM images in 1989 and 2010, and ETM+ images in 2000, in combining with GIS and landscape ecological methods, this paper analyzed the changes of land use/cover and landscape patterns in Yumen County at the middle reaches of Shule River from 1976 to 2010. In the study period, the major patterns of land use change in the County were the conversions from grassland and Gobi to farmland, from farmland to construction land, and from grassland to Gobi. Such a land use change underwent a process of 'slow - tremendous - obvious', during which, the landscape density increased, the largest path index decreased after an initial increase, the weighted area index increased, and the landscape shape became irregular. In the meantime, the nearest distances between patches and the separation among different patches decreased, the patches became more complex, and the landscape diversity and evenness increased after an initial decrease. The increased landscape diversity and fragmentation also showed that the land uses became more complex. The growth of agricultural population and the development of economy were the most direct driving forces of the land use/cover change in Yumen City, whereas the climatic and policy factors also had important effects on the land use change in the study area.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. Joint Effects of Habitat Heterogeneity and Species’ Life-History Traits on Population Dynamics in Spatially Structured Landscapes

    PubMed Central

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

    2014-01-01

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

  19. The control of grain-scale mechanics on channel form, landscape dynamics, and climatic perturbations in gravel-bedded rivers

    NASA Astrophysics Data System (ADS)

    Phillips, Colin B.

    Landscapes evolve over millions of years, through the complex interplay of climate and tectonics. Mountains in particular represent a staggering range of spatial and temporal scales, challenging our ability to understand how the landscape is sculpted. Mountains do not simply disappear by bulk denudation. The key process of river incision results from the entrainment, displacement, and collision of coarse particles with the bed; a phenomenon known as bed load transport. This dissertation seeks to elucidate how bed load transport in natural rivers is driven by floods, to provide a mechanistic connection between climate and landscape evolution. Field surveys of coarse particle displacement and channel geometry are combined with hydrological time series, to study the interaction between floods and bed load dynamics, and their implications for channel form. Results from tagged cobbles demonstrate that mean particle displacement is proportional to applied fluid momentum in excess of the threshold of motion, while dispersion of tracers is superdiffusive due to the burial and excavation of cobbles. These field surveys reveal that particle motion remains in a state of partial transport for a diverse population of flows, and that particle sorting and transport distances closely match theory developed from small-scale laboratory experiments. Analysis of hydrological time series shows that the threshold of particle motion truncates the distribution of applied stress, resulting in thin-tailed distributions of forcing for flows above the threshold of motion. This analysis further shows that, because a coarse-grained river adjusts its geometry so that the flow at the banks is at the threshold of motion, the probability of experiencing larger stresses diminishes exponentially. Field surveys of channel geometry and particle size reveal that the geomorphological impacts of urbanization are reduced for coarse-grained channels adjusted to frequent sediment transport events. Taken

  20. 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

  1. 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

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

    PubMed

    Roques, Lionel; Bonnefon, Olivier

    2016-01-01

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

  3. 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.

  4. 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.

  5. 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.

  6. 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

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

    NASA Astrophysics Data System (ADS)

    Bunting, Erin L.

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

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

    PubMed

    Ryabov, Artem; Berestneva, Ekaterina; Holubec, Viktor

    2015-09-21

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

  9. 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

  10. 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

  11. A 'dynamic' landscape of fear: prey responses to spatiotemporal variations in predation risk across the lunar cycle.

    PubMed

    Palmer, M S; Fieberg, J; Swanson, A; Kosmala, M; Packer, C

    2017-09-12

    Ambiguous empirical support for 'landscapes of fear' in natural systems may stem from failure to consider dynamic temporal changes in predation risk. The lunar cycle dramatically alters night-time visibility, with low luminosity increasing hunting success of African lions. We used camera-trap data from Serengeti National Park to examine nocturnal anti-predator behaviours of four herbivore species. Interactions between predictable fluctuations in night-time luminosity and the underlying risk-resource landscape shaped herbivore distribution, herding propensity and the incidence of 'relaxed' behaviours. Buffalo responded least to temporal risk cues and minimised risk primarily through spatial redistribution. Gazelle and zebra made decisions based on current light levels and lunar phase, and wildebeest responded to lunar phase alone. These three species avoided areas where likelihood of encountering lions was high and changed their behaviours in risky areas to minimise predation threat. These patterns support the hypothesis that fear landscapes vary heterogeneously in both space and time. © 2017 John Wiley & Sons Ltd/CNRS.

  12. Free energy landscape and folding mechanism of a beta-hairpin in explicit water: a replica exchange molecular dynamics study.

    PubMed

    Nguyen, Phuong H; Stock, Gerhard; Mittag, Emil; Hu, Chin-Kun; Li, Mai Suan

    2005-12-01

    The free energy landscape and the folding mechanism of the C-terminal beta-hairpin of protein G is studied by extensive replica exchange molecular dynamics simulations (40 replicas and 340 ns total simulation time), using the GROMOS96 force field and the SPC explicit water solvent. The study reveals that the system preferentially adopts a beta-hairpin structure at biologically important temperatures, and that the helix content is low at all temperatures studied. Representing the free energy landscape as a function of several types of reaction coordinates, four local minima corresponding to the folded, partially folded, molten globule, and unfolded states are identified. The findings suggest that the folding of the beta-hairpin occurs as the sequence: collapse of hydrophobic core --> formation of H-bond --> formation of the turn. Identifying the folded and molten globule states as the main conformations, the free energy landscape of the beta-hairpin is consistent with a two-state behavior with a broad transition state. The temperature dependence of the folding-unfolding transition is investigated in some detail. The enthalpy and entropy jumps at the folding transition temperature are found to be about three times lower than the experimental estimates, indicating that the folding-unfolding transition in silico is less cooperative than its in vitro counterpart. Proteins 2005. 2005 Wiley-Liss, Inc.

  13. Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis.

    PubMed

    Pass, Daniel Antony; Sornay, Emily; Marchbank, Angela; Crawford, Margaret R; Paszkiewicz, Konrad; Kent, Nicholas A; Murray, James A H

    2017-09-01

    All eukaryotic genomes are packaged as chromatin, with DNA interlaced with both regularly patterned nucleosomes and sub-nucleosomal-sized protein structures such as mobile and labile transcription factors (TF) and initiation complexes, together forming a dynamic chromatin landscape. Whilst details of nucleosome position in Arabidopsis have been previously analysed, there is less understanding of their relationship to more dynamic sub-nucleosomal particles (subNSPs) defined as protected regions shorter than the ~150bp typical of nucleosomes. The genome-wide profile of these subNSPs has not been previously analysed in plants and this study investigates the relationship of dynamic bound particles with transcriptional control. Here we combine differential micrococcal nuclease (MNase) digestion and a modified paired-end sequencing protocol to reveal the chromatin structure landscape of Arabidopsis cells across a wide particle size range. Linking this data to RNAseq expression analysis provides detailed insight into the relationship of identified DNA-bound particles with transcriptional activity. The use of differential digestion reveals sensitive positions, including a labile -1 nucleosome positioned upstream of the transcription start site (TSS) of active genes. We investigated the response of the chromatin landscape to changes in environmental conditions using light and dark growth, given the large transcriptional changes resulting from this simple alteration. The resulting shifts in the suites of expressed and repressed genes show little correspondence to changes in nucleosome positioning, but led to significant alterations in the profile of subNSPs upstream of TSS both globally and locally. We examined previously mapped positions for the TFs PIF3, PIF4 and CCA1, which regulate light responses, and found that changes in subNSPs co-localized with these binding sites. This small particle structure is detected only under low levels of MNase digestion and is lost on more

  14. 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

  15. 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

  16. 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.

  17. 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

  18. Time series evaluation of landscape dynamics using annual Landsat imagery and spatial statistical modeling: Evidence from the Phoenix metropolitan region

    NASA Astrophysics Data System (ADS)

    Fan, Chao; Myint, Soe W.; Rey, Sergio J.; Li, Wenwen

    2017-06-01

    Urbanization is a natural and social process involving simultaneous changes to the Earth's land systems, energy flow, demographics, and the economy. Understanding the spatiotemporal pattern of urbanization is increasingly important for policy formulation, decision making, and natural resource management. A combination of satellite remote sensing and patch-based models has been widely adopted to characterize landscape changes at various spatial and temporal scales. Nevertheless, the validity of this type of framework in identifying long-term changes, especially subtle or gradual land modifications is seriously challenged. In this paper, we integrate annual image time series, continuous spatial indices, and non-parametric trend analysis into a spatiotemporal study of landscape dynamics over the Phoenix metropolitan area from 1991 to 2010. We harness local indicators of spatial dependence and modified Mann-Kendall test to describe the monotonic trends in the quantity and spatial arrangement of two important land use land cover types: vegetation and built-up areas. Results suggest that declines in vegetation and increases in built-up areas are the two prevalent types of changes across the region. Vegetation increases mostly occur at the outskirts where new residential areas are developed from natural desert. A sizable proportion of vegetation declines and built-up increases are seen in the central and southeast part. Extensive land conversion from agricultural fields into urban land use is one important driver of vegetation declines. The xeriscaping practice also contributes to part of vegetation loss and an increasingly heterogeneous landscape. The quantitative framework proposed in this study provides a pathway to effective landscape mapping and change monitoring from a spatial statistical perspective.

  19. 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.

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

    NASA Astrophysics Data System (ADS)

    Farvacque, Manon; Valla, Pierre

    2016-04-01

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

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

    USDA-ARS?s Scientific Manuscript database

    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 ...

  2. Can Landscape-scale management influence insect outbreak dynamics? A natural experiment for eastern spruce budworm

    Treesearch

    Brian R. Sturtevant; V. Quinn; L.E. Robert; D. Kneeshaw; P. James; M.-J. Fortin; P. Wolter; P. Townsend; B. Cooke; D. Anderson

    2010-01-01

    The balance of evidence suggests forest insect outbreaks today are more damaging than ever because of changes in forest composition and structure induced by fire suppression and post-harvest proliferation of tree species intolerant to herbivory. We hypothesized that landscape connectivity of acceptable host trees increases defoliator population connectivity, altering...

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    USDA-ARS?s Scientific Manuscript database

    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...

  5. Integrating remote sensing, GIS and dynamic models for landscape-level simulation of forest insect disturbance

    USDA-ARS?s Scientific Manuscript database

    Cellular automata (CA) is a powerful tool in modeling the evolution of macroscopic scale phenomena as it couples time, space, and variable together while remaining in a simplified form. However, such application has remained challenging in landscape-level chronic forest insect epidemics due to the h...

  6. Predicting landscape vegetation dynamics using state-and-transition simulation models

    Treesearch

    Colin J. Daniel; Leonardo. Frid

    2012-01-01

    This paper outlines how state-and-transition simulation models (STSMs) can be used to project changes in vegetation over time across a landscape. STSMs are stochastic, empirical simulation models that use an adapted Markov chain approach to predict how vegetation will transition between states over time, typically in response to interactions between succession,...

  7. Analysing spatio-temporal dynamics of processes and parameters in a hydrological model to understand catchment similarities among different landscapes

    NASA Astrophysics Data System (ADS)

    Guse, Björn; Pfannerstill, Matthias; Kiesel, Jens; Strauch, Michael; Volk, Martin; Fohrer, Nicola

    2017-04-01

    The hydrological behaviour of catchments differs due to varying relevance of processes in space and time. These differences are related to landscape and climate conditions but also to seasonal variations of driving factors such as precipitation or temperature. Due to that, catchments are characterised by typical temporal patterns of dominant processes. Universally applicable hydrological models aim to represent these typical characteristics of contrasting catchments making use of site-specific model parameter values as well as emphasising the hydrological processes that are of major relevance. With respect to hydrological modelling, patterns of temporal dynamics in dominant modelled processes and their corresponding parameters are a fingerprint of how a model represents the hydrological system. In this study, it is demonstrated how fingerprints from catchment data and model results can be jointly used to understand the reasons for hydrological similarity and dissimilarity among different catchments. At first, catchment metrics are used to characterise contrasting catchments representing different landscape conditions (lowland, upland and alpine) in a data-based approach. Simulations are carried out by applying a complex hydrological model to calculate the temporal variability of dominant processes and parameters using a temporally resolved sensitivity analysis (TEDPAS). Temporal dynamics of dominant processes and model parameters are related to catchment metrics to analyse how catchment metrics explain temporal variations in process dominance in the model. In each catchment, three to four typical phases during the year are identified that show strong differences in the dominant processes. These phases can be related to selected catchment metrics and explain the similarity between the catchments. All catchments show a typical hierarchical process appearance following the concept of the vertical water redistribution. Following a landscape gradient, high flow phases

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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

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

    PubMed

    Aguilar-Arnal, Lorena; Sassone-Corsi, Paolo

    2015-06-02

    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.

  15. 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

  16. 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.

  17. 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

  18. Probing Single-Molecule Protein Conformational Folding-Unfolding Dynamics: The multiple-State and Multiple-Channel Energy Landscape

    NASA Astrophysics Data System (ADS)

    Lu, H. Peter; Wang, Zhijiang; He, Yufan

    2013-03-01

    The folding-unfolding dynamics of protein provides an important understanding of the protein conformational dynamics and functions. We have used single-molecule fluorescence resonance energy transfer combined with statistical data analysis to characterize enzyme and signaling protein fundamental conformational dynamics of Calmodulin (CaM) and kinase (6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK). The concentration dependence of FRET efficiency of GdmCl indicates the unfolding conformational transition of the proteins. At 2M of denaturant solvent, the majority of the HPPK and CaM protein molecules are under fluctuating folding-unfolding conformational changes, spending about half time in their native state and half time in their unfolded state. We obtained the fluctuation rates from the autocorrelation function analyses of the protein conformational fluctuation trajectories, and we have identified multiple intermediate states involving in bunched time dynamics and the related energy landscape. We had also analyzed the protein folding-unfolding pathways using detailed balance theoretical model analysis in order to understand the complex multiple-state and multiple-channel protein dynamics.

  19. 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.

  20. 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.

  1. 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.

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

    PubMed

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

    2011-09-01

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

  3. 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.

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

    PubMed

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

    2014-01-01

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

  5. 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.

  6. Closed-form exact solution to H-infinity optimization of dynamic vibration absorber: II. Development of an algebraic approach and its application to a standard problem

    NASA Astrophysics Data System (ADS)

    Nishihara, Osamu; Asami, Toshihiko

    2000-04-01

    The fixed-points method for the dynamic vibration absorber (DVA) is widely accepted and the results are prevalent for practical applications. However, they usually have to fall back to a heuristic approach from the point of view of its optimization criterion. A typical design problem to minimize the maximum amplitude magnification factor of the primary system, for which the fixed-points method was originally developed, is an example of such common cases. In the present paper, a new algebraic formulation is developed to this classic problem and closed-form exact solutions to both the optimum tuning ratio and the optimum damping parameters are derived, on the assumption of undamped primary system. This algebraic approach is based on an observation of trade-off between two resonance amplitude magnification factors. Thus, the problem reduces to a solution of an algebraic equation, which is derived as a discriminant of quartic algebraic equation. In undamped case, it was proven that the optimum parameters, the minimum amplitude magnification factor, the resonance and antiresonance frequencies, and sensitivities of the amplitude magnification factors are totally algebraic. A numerical extension enables efficient solutions for the damped primary system and has more direct applicability.

  7. 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

  8. 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

  9. 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

  10. From Particles and Point Clouds to Voxel Models: High Resolution Modeling of Dynamic Landscapes in Open Source GIS

    NASA Astrophysics Data System (ADS)

    Mitasova, H.; Hardin, E. J.; Kratochvilova, A.; Landa, M.

    2012-12-01

    Multitemporal data acquired by modern mapping technologies provide unique insights into processes driving land surface dynamics. These high resolution data also offer an opportunity to improve the theoretical foundations and accuracy of process-based simulations of evolving landforms. We discuss development of new generation of visualization and analytics tools for GRASS GIS designed for 3D multitemporal data from repeated lidar surveys and from landscape process simulations. We focus on data and simulation methods that are based on point sampling of continuous fields and lead to representation of evolving surfaces as series of raster map layers or voxel models. For multitemporal lidar data we present workflows that combine open source point cloud processing tools with GRASS GIS and custom python scripts to model and analyze dynamics of coastal topography (Figure 1) and we outline development of coastal analysis toolbox. The simulations focus on particle sampling method for solving continuity equations and its application for geospatial modeling of landscape processes. In addition to water and sediment transport models, already implemented in GIS, the new capabilities under development combine OpenFOAM for wind shear stress simulation with a new module for aeolian sand transport and dune evolution simulations. Comparison of observed dynamics with the results of simulations is supported by a new, integrated 2D and 3D visualization interface that provides highly interactive and intuitive access to the redesigned and enhanced visualization tools. Several case studies will be used to illustrate the presented methods and tools and demonstrate the power of workflows built with FOSS and highlight their interoperability.Figure 1. Isosurfaces representing evolution of shoreline and a z=4.5m contour between the years 1997-2011at Cape Hatteras, NC extracted from a voxel model derived from series of lidar-based DEMs.

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